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1. A new 3D full-Stokes calving algorithm within Elmer/Ice (v9.0)

Author: I. Wheel, D. I. Benn, A. J. Crawford, J. Todd, and T. Zwinger
Subjects: Geology, QE1-996.5
Abstract: A new calving algorithm is developed in the glacier model Elmer/Ice that allows unrestricted calving and terminus advance in 3D. The algorithm uses the meshing software Mmg to implement anisotropic remeshing and allow mesh adaptation at each time step. The development of the algorithm, along with the implementation of the crevasse depth law, produces a new full-Stokes calving model capable of simulating calving and terminus advance across an array of complex geometries. Using a synthetic tidewater glacier geometry, the model is tested to highlight the numerical model parameters that can alter calving when using the crevasse depth law. For a system with no clear attractor at a pinning point, the model time step and mesh resolution are shown to alter the simulated calving. In particular, the vertical mesh resolution has a large impact, increasing calving, as the frontal bending stresses are better resolved. However, when the system has a strong attractor, provided by basal pinning points, numerical model parameters have a limited effect on the terminus evolution. Conversely, transient systems with no clear attractors are highly influenced by the choice of numerical model parameters. The new algorithm is capable of implementing unlimited terminus advance and retreat, as well as unrestricted calving geometries, applying any vertically varying melt distribution to the front for use in conjunction with any calving law or potentially advecting variables downstream. In overcoming previous technical hurdles, the algorithm opens up the opportunity to improve both our understanding of the physical processes and our ability to predict calving.
Published: 2024
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2. Gas exchange and time to reach maximum rate of photosynthetic rateand their relationship with whole-plant traits in sugarcane in water abundant Louisiana, USA

Author: P.Z. ELLSWORTH, P.M. WHITE JR., and J. TODD
Subjects: gas exchange, phenotyping, photosynthesis, stomatal conductance, stomatal propensity to remain open, sugarcane, Botany, QK1-989
Abstract: Variety development of sugarcane (Saccharum spp. hybrids) is necessary to continue improving sugar yields and selecting photosynthetic traits can improve sugar production through increased carbon inputs. In this study, gas exchange and whole-plant measurements were made on 55 sugarcane genotypes in Louisiana. Variation in the relationship between photosynthetic rate and stomatal conductance suggests that sugarcane exhibits variation in both photosynthetic capacity and CO2 substrate availability. Genotypes that reached maximum photosynthetic rate (TRMPR) in the gas-exchange cuvette more quickly had greater CO2 assimilation during transitory periods. Temporary shading and fluctuating light are common transitory conditions in the field, so increasing TRMPR can improve photosynthesis in water-abundant regions. Canopy leaf area was positively correlated with stalk mass, but gas-exchange traits were not correlated with whole-plant traits. A better understanding of the relationship between leaf and whole-plant traits is necessary to identify physiological traits that lead to increased genetic gain.
Published: 2024
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3. Specialized pro-resolution mediators in the bladder: effects of resolvin E1 on diabetic bladder dysfunction in the type 1 diabetic male Akita mouse model

Author: Anissa Cervantes, Francis M. Hughes, Huixia Jin, and J. Todd Purves
Subjects: Diabetes, Diabetic bladder, Pro-resolution, Resolvin, Inflammation, Cystitis, Diseases of the genitourinary system. Urology, RC870-923
Abstract: Abstract Background One of the most common, but least studied, diabetic complication is diabetic bladder dysfunction. Current therapies include glucose control and symptom-based interventions. However, efficacy of these therapies is mixed and often have undesirable side effects. Diabetes is now known to be a chronic inflammatory disease. Specialized pro-resolving mediators are a class of compounds that promote the resolution of inflammation and have been shown to be effective in treating chronic inflammatory conditions. In this study we examine the ability of resolvin E1 to improve signs of diabetic bladder dysfunction. Methods Male Akita mice (Type 1 diabetic) develop hyperglycemia at 4 weeks and signs of bladder underactivity by 15 weeks. Starting at 15 weeks, mice were given one or two weeks of daily resolvin E1 and compared to age-matched wild type and untreated Akita mice. Results Resolvin E1 did not affect diabetic blood glucose after one week, although there was a slight decrease after two weeks. Diabetes decreased body weight and increased bladder weights and this was not affected by resolvin E1. Evan’s blue dye extravasation (an indirect index of inflammation) was dramatically suppressed after one week of resolvin E1 treatment, but, surprisingly, had returned to diabetic levels after two weeks of treatment. Using cystometry, untreated Akita mice showed signs of underactivity (increased void volumes and intercontraction intervals). One week of resolvin E1treatment restored these cystometric findings back to control levels. After two weeks of treatment, cystometric changes were changed from controls but still significantly different from untreated levels, indicating a durable treatment effect even in the presence of increased inflammation at 2 weeks. Conclusions Resolvin E1 has a beneficial effect on diabetic bladder dysfunction in the type 1 diabetic male Akita mouse model.
Published: 2024
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4. A framework for time-dependent ice sheet uncertainty quantification, applied to three West Antarctic ice streams

Author: B. Recinos, D. Goldberg, J. R. Maddison, and J. Todd
Subjects: Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract: Ice sheet models are the main tool to generate forecasts of ice sheet mass loss, a significant contributor to sea level rise; thus, knowing the likelihood of such projections is of critical societal importance. However, to capture the complete range of possible projections of mass loss, ice sheet models need efficient methods to quantify the forecast uncertainty. Uncertainties originate from the model structure, from the climate and ocean forcing used to run the model, and from model calibration. Here we quantify the latter, applying an error propagation framework to a realistic setting in West Antarctica. As in many other ice sheet modelling studies we use a control method to calibrate grid-scale flow parameters (parameters describing the basal drag and ice stiffness) with remotely sensed observations. Yet our framework augments the control method with a Hessian-based Bayesian approach that estimates the posterior covariance of the inverted parameters. This enables us to quantify the impact of the calibration uncertainty on forecasts of sea level rise contribution or volume above flotation (VAF) due to the choice of different regularization strengths (prior strengths), sliding laws, and velocity inputs. We find that by choosing different satellite ice velocity products our model leads to different estimates of VAF after 40 years. We use this difference in model output to quantify the variance that projections of VAF are expected to have after 40 years and identify prior strengths that can reproduce that variability. We demonstrate that if we use prior strengths suggested by L-curve analysis, as is typically done in ice sheet calibration studies, our uncertainty quantification is not able to reproduce that same variability. The regularization suggested by the L curves is too strong, and thus propagating the observational error through to VAF uncertainties under this choice of prior leads to errors that are smaller than those suggested by our two-member “sample” of observed velocity fields.
Published: 2023
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5. Cytokine expression in subjects with Mycobacterium avium ssp. paratuberculosis positive blood cultures and a meta-analysis of cytokine expression in Crohn’s disease

Author: J. Todd Kuenstner, Qiang Xu, Tim J. Bull, Antonio C. G. Foddai, Irene R. Grant, Saleh A. Naser, Raghava Potula, Peilin Zhang, Ira Shafran, Serhat Emre Akhanli, Svetlana Khaiboullina, and Russell Kruzelock
Subjects: MAP, Crohn’s disease, bacteremia, inflammatory bowel disease (IBD), autoimmune disease, Microbiology, QR1-502
Abstract: Objectives1) Culture Mycobacterium avium ssp. paratuberculosis (MAP)from blood, 2) assess infection persistence, 3) determine Crohn’s disease (CD) cytokine expression, 4) compare CD cytokine expression to tuberculosis, and 5) perform a meta-analysis of cytokine expression in CD.MethodsThe Temple University/Abilene Christian University (TU/ACU) study had a prospective case control design with 201 subjects including 61 CD patients and 140 non-CD controls. The culture methods included MGIT, TiKa and Pozzato broths, and were deemed MAP positive, if IS900 PCR positive. A phage amplification assay was also performed to detect MAP. Cytokine analysis of the TU/ACU samples was performed using Simple Plex cytokine reagents on the Ella ELISA system. Statistical analyses were done after log transformation using the R software package. The meta-analysis combined three studies.ResultsMost subjects had MAP positive blood cultures by one or more methods in 3 laboratories. In our cytokine study comparing CD to non-CD controls, IL-17, IFNγ and TNFα were significantly increased in CD, but IL-2, IL-5, IL-10 and GM-CSF were not increased. In the meta-analysis, IL-6, IL-8 and IL-12 were significantly increased in the CD patients.ConclusionMost subjects in our sample had MAP infection and 8 of 9 subjects remained MAP positive one year later indicating persistent infection. While not identical, cytokine expression patterns in MAP culture positive CD patients in the TU/ACU study showed similarities (increased IL-17, IFNγ and TNFα) to patterns of patients with Tuberculosis in other studies, indicating the possibilities of similar mechanisms of pathogen infection and potential strategies for treatment.
Published: 2024
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6. Female Type 1 Diabetic Akita Mice Demonstrate Increased Bladder Contractility via FP Receptor Activation due to NLRP3-Mediated Inflammation

Author: Michael R. Odom, Francis M. Hughes Jr., NiQuava Pope, Huixia Jin, and J. Todd Purves
Subjects: nlrp3, diabetic bladder dysfunction, akita, type 1 diabetes, prostaglandin, fp receptor, inflammation, myograph, Biochemistry, QD415-436, Biology (General), QH301-705.5
Abstract: Background: Diabetic bladder dysfunction (DBD) is driven in part by inflammation which dysregulates prostaglandin release in the bladder. Precise inflammatory mechanisms responsible for such dysregulation have been elusive. Since prostaglandins impact bladder contractility, elucidating these mechanisms may yield potential therapeutic targets for DBD. In female Type 1 diabetic Akita mice, inflammation mediated by the nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) inflammasome is responsible for DBD. Here, we utilized female Akita mice crossbred with NLRP3 knock-out mice to determine how NLRP3-driven inflammation impacts prostaglandin release within the bladder and prostaglandin-mediated bladder contractions. Methods: Akita mice were crossbred with NLRP3-⁣/- mice to yield four groups of non-diabetics and diabetics with and without the NLRP3 gene. Females were aged to 30 weeks when Akitas typically exhibit DBD. Urothelia and detrusors were stretched ex vivo to release prostaglandins. Prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) were quantified using enzyme linked immunosorbent assays (ELISA). In separate samples, ex vivo contractile force to PGE2 and PGF2α +/– the prostaglandin F (FP) receptor antagonist, AL8810, was measured. FP receptor protein expression was determined via western blotting. Results: Stretch-induced PGE2 release increases in urothelia but decreases in detrusors of diabetics. However, PGE2-mediated bladder contractions are not impacted. Conversely, diabetics show no changes in PGF2α release, but PGF2α-mediated contractions increase significantly. This is likely due to signaling through the FP receptors as FP receptor antagonism prevents this increase and diabetics demonstrate a four-fold increase in FP receptor proteins. Without NLRP3-mediated inflammation, changes in prostaglandin release, contractility, and receptor expression do not occur. Conclusion: NLRP3-dependent inflammation dysregulates prostaglandin release and prostaglandin-mediated bladder contractions in diabetic female Akita mice via FP receptor upregulation.
Published: 2024
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7. Myocardial contrast echocardiography assessment of perfusion abnormalities in hypertrophic cardiomyopathy

Author: Paola Roldan, Sriram Ravi, James Hodovan, J. Todd Belcik, Stephen B. Heitner, Ahmad Masri, and Jonathan R. Lindner
Subjects: Hypertrophic cardiomyopathy, Ischemia, Myocardial contrast echocardiography, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract: Abstract Background Perfusion defects during stress can occur in hypertrophic cardiomyopathy (HCM) from either structural or functional abnormalities of the coronary microcirculation. In this study, vasodilator stress myocardial contrast echocardiography (MCE) was used to quantify and spatially characterize hyperemic myocardial blood flow (MBF) deficits in HCM. Methods Regadenoson stress MCE was performed in patients with septal-variant HCM (n = 17) and healthy control subjects (n = 15). The presence and spatial distribution (transmural diffuse, patchy, subendocardial) of perfusion defects was determined by semiquantitative analysis. Kinetic analysis of time-intensity data was used to quantify MBF, microvascular flux rate (β), and microvascular blood volume. In patients undergoing septal myectomy (n = 3), MCE was repeated > 1 years after surgery. Results In HCM subjects, perfusion defects during stress occurred in the septum in 80%, and in non-hypertrophied regions in 40%. The majority of septal defects (83%) were patchy or subendocardial, while 67% of non-hypertrophied defects were transmural and diffuse. On quantitative analysis, hyperemic MBF was approximately 50% lower (p
Published: 2022
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8. The Relationship between Kinetic and Magnetic Helicity in Solar Active Regions

Author: Yang Liu, Rudolf Komm, Nicholas H. Brummell, J. Todd Hoeksema, Bhishek Manek, and Gherardo Valori
Subjects: Solar interior, Solar photosphere, Solar active region magnetic fields, Solar dynamo, Astrophysics, QB460-466
Abstract: Using Helioseismic and Magnetic Imager/Solar Dynamics Observatory data, we search for a relationship between kinetic helicity and magnetic helicity in solar active regions (ARs) using a sample of 62 ARs from 2010 May to 2015 May. The sample includes 32 mature ARs and 30 emerging ARs. We calculate kinetic helicity in the interior in the depth range from 0.6 to 11.6 Mm, magnetic helicity in the corona, helicity flux across the photosphere, and the magnetic twist and magnetic writhe of the ARs at the photosphere. From these data, relationships are found between magnetic helicity, helicity flux, and magnetic twist. However, magnetic writhe appears not to be related to the other magnetic quantities. No relationship is found between the kinetic helicity and any magnetic quantity. In particular, no relationship is found between the kinetic helicity and any of the following: magnetic helicity, magnetic helicity flux, magnetic twist, or magnetic writhe. These results suggest that (1) the magnetic helicity in the corona above ARs is mainly derived from the magnetic twist, and (2) the flow dynamics in the region from 0.6 to 11.6 Mm below the photosphere is not the primary source for the generation of magnetic helicity in ARs.
Published: 2024
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9. SuperSynthIA: Physics-ready Full-disk Vector Magnetograms from HMI, Hinode, and Machine Learning

Author: Ruoyu Wang, David F. Fouhey, Richard E. L. Higgins, Spiro K. Antiochos, Graham Barnes, J. Todd Hoeksema, K. D. Leka, Yang Liu, Peter W. Schuck, and Tamas I. Gombosi
Subjects: Solar magnetic fields, Convolutional neural networks, Computational methods, Astrophysics, QB460-466
Abstract: Vector magnetograms of the Sun’s photosphere are cornerstones for much of solar physics research. These data are often produced by data-analysis pipelines combining per-pixel Stokes polarization vector inversion with a disambiguation that resolves an intrinsic 180° ambiguity. We introduce a learning-based method, SuperSynthIA, that produces full-disk vector magnetograms from Stokes vector observations. As input, SuperSynthIA uses Stokes polarization images from Solar Dynamics Observatory (SDO)/Helioseismic and Magnetic Imager (HMI). As output, SuperSynthIA simultaneously emulates the inversion and disambiguation outputs from the Hinode/Solar Optical Telescope-Spectro-Polarimeter (SOT-SP) pipeline. Our method extends our previous approach SynthIA with heliographic outputs as well as using an improved data set and inference method. SuperSynthIA provides a new tool for improved magnetic fields from full-disk SDO/HMI observations using information derived from the enhanced capabilities of Hinode/SOT-SP. Compared to our previous SynthIA, SuperSynthIA provides physics-ready vector magnetograms and mitigates unphysical angle preferences and banding artifacts in SynthIA. SuperSynthIA data are substantially more temporally consistent than those from the SDO/HMI pipeline, most notably seen in, e.g., evolving active regions. SuperSynthIA substantially reduces noise in low-signal areas, resulting in less center-to-limb bias outside of strong-signal areas. We show that outputs from SuperSynthIA track the SDO/HMI-recorded evolution of the magnetic field. We discuss the limitations of SuperSynthIA that the user must understand, and we demonstrate a broad set of evaluations to test SuperSynthIA and discuss remaining known artifacts. Our tests provide both methodology and evidence that SuperSynthIA outputs are ready for use by the community, and that learning-based approaches are suitable for physics-ready magnetograms.
Published: 2024
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10. Music to My Ears: Neural modularity and flexibility differ in response to real-world music stimuli

Author: Melia E. Bonomo, Anthony K. Brandt, J. Todd Frazier, and Christof Karmonik
Subjects: Brain network, Modularity, Flexibility, Music, Culture, FMRI, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Music listening involves many simultaneous neural operations, including auditory processing, working memory, temporal sequencing, pitch tracking, anticipation, reward, and emotion, and thus, a full investigation of music cognition would benefit from whole-brain analyses. Here, we quantify whole-brain activity while participants listen to a variety of music and speech auditory pieces using two network measures that are grounded in complex systems theory: modularity, which measures the degree to which brain regions are interacting in communities, and flexibility, which measures the rate that brain regions switch the communities to which they belong. In a music and brain connectivity study that is part of a larger clinical investigation into music listening and stroke recovery at Houston Methodist Hospital’s Center for Performing Arts Medicine, functional magnetic resonance imaging (fMRI) was performed on healthy participants while they listened to self-selected music to which they felt a positive emotional attachment, as well as culturally familiar music (J.S. Bach), culturally unfamiliar music (Gagaku court music of medieval Japan), and several excerpts of speech. There was a marked contrast among the whole-brain networks during the different types of auditory pieces, in particular for the unfamiliar music. During the self-selected and Bach tracks, participants’ whole-brain networks exhibited modular organization that was significantly coordinated with the network flexibility. Meanwhile, when the Gagaku music was played, this relationship between brain network modularity and flexibility largely disappeared. In addition, while the auditory cortex’s flexibility during the self-selected piece was equivalent to that during Bach, it was more flexible during Gagaku. The results suggest that the modularity and flexibility measures of whole-brain activity have the potential to lead to new insights into the complex neural function that occurs during music perception of real-world songs.
Published: 2022
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11. Editorial: Connecting solar flows and fields to understand surface magnetism

Author: Kiran Jain, Mausumi Dikpati, and J. Todd Hoeksema
Subjects: sun, solar interior, solar atmosphere, solar active regions, solar magnetic fields, solar meridional circulation, Astronomy, QB1-991, Geophysics. Cosmic physics, QC801-809
Published: 2023
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12. Thermal Characterization and Interaction of the Subunits from the Multimeric Bacteriophage Endolysin PlyC

Author: J. Todd Hoopes, Ryan D. Heselpoth, Frederick P. Schwarz, and Daniel C. Nelson
Subjects: PlyC, endolysin, antimicrobial, thermal stability, thermodynamic characterization, differential scanning calorimetry, Biology (General), QH301-705.5
Abstract: Bacteriophage endolysins degrade the bacterial peptidoglycan and are considered enzymatic alternatives to small-molecule antibiotics. In particular, the multimeric streptococcal endolysin PlyC has appealing antibacterial properties. However, a comprehensive thermal analysis of PlyC is lacking, which is necessary for evaluating its long-term stability and downstream therapeutic potential. Biochemical and kinetic-based methods were used in combination with differential scanning calorimetry to investigate the structural, kinetic, and thermodynamic stability of PlyC and its various subunits and domains. The PlyC holoenzyme structure is irreversibly compromised due to partial unfolding and aggregation at 46 °C. Unfolding of the catalytic subunit, PlyCA, instigates this event, resulting in the kinetic inactivation of the endolysin. In contrast to PlyCA, the PlyCB octamer (the cell wall-binding domain) is thermostable, denaturing at ~75 °C. The isolation of PlyCA or PlyCB alone altered their thermal properties. Contrary to the holoenzyme, PlyCA alone unfolds uncooperatively and is thermodynamically destabilized, whereas the PlyCB octamer reversibly dissociates into monomers and forms an intermediate state at 74 °C in phosphate-buffered saline with each subunit subsequently denaturing at 92 °C. Adding folded PlyCA to an intermediate state PlyCB, followed by cooling, allowed for in vitro reconstitution of the active holoenzyme.
Published: 2023
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13. Telemedicine-delivered cognitive-behavioral therapy for insomnia in alcohol use disorder (AUD): study protocol for a randomized controlled trial

Author: J. Todd Arnedt, M. Elizabeth Cardoni, Deirdre A. Conroy, Mandilyn Graham, Sajni Amin, Kipling M. Bohnert, Andrew D. Krystal, and Mark A. Ilgen
Subjects: Alcohol use disorder, Insomnia, Non-medication treatment, Relapse, Medicine (General), R5-920
Abstract: Abstract Background Alcohol use disorder (AUD) is a leading preventable cause of morbidity and mortality, but relapse rates are high even with available treatments. Insomnia is a robust predictor of relapse and pilot studies have shown that CBT for insomnia improves insomnia and daytime functioning in adults with AUD and insomnia. The impact of CBT for insomnia on relapse, however, is unclear. This trial will compare telemedicine-delivered CBT for insomnia (CBT-TM) with sleep hygiene education (SHE-TM) on improving insomnia/sleep, daytime symptom, and drinking outcomes in treatment-seeking AUD adults with insomnia. The study will also determine the effects of treatment on sleep mechanisms and their association with clinical outcomes. Methods This is a single-site randomized controlled trial with planned enrollment of 150 adults meeting criteria for both AUD and chronic insomnia. Eligible participants will be randomized 1:1 to 6 sessions of telemedicine-delivered Cognitive Behavioral Therapy for Insomnia (CBT-TM) or Sleep Hygiene Education (SHE-TM) with clinical assessments conducted at pre-treatment, post- treatment, and at 3, 6, and 12 months post-treatment. Overnight polysomnography will be conducted before and after treatment. Primary clinical outcomes will include post-treatment scores on the Insomnia Severity Index and the General Fatigue subscale of the Multidisciplinary Fatigue Inventory, and the percent of days abstinent (PDA) on the interview-administered Time Line Follow Back. EEG delta activity, derived from overnight polysomnography, will be the primary endpoint to assess the sleep homeostasis mechanism. Discussion This adequately powered randomized controlled trial will provide clinically relevant information about whether targeting insomnia is effective for improving treatment outcomes among treatment-seeking adults with AUD. Additionally, the study will offer new scientific insights on the impact of an evidence-based non-medication treatment for insomnia on a candidate mechanism of sleep dysfunction in this population - sleep homeostasis. Trial registration CClinicalTrials.gov NCT # 04457674 . Registered on 07 July 2020.
Published: 2022
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14. Learning to Learn: A pilot study on explicit strategy instruction to incoming college students

Author: Elisabeth J. Ploran, Amy A. Overman, J. Todd Lee, Amy M. Masnick, Kristin M. Weingartner, and Kayla D. Finuf
Subjects: Growth mindset, Learning strategies, Metacognition, Intervention, Psychology, BF1-990
Abstract: The current pilot study implemented a “Learning to Learn” (L2L) course designed to teach first-year college students about the science of how learning works, how to take ownership of their own learning, and how to effectively apply learning strategies to achieve their academic goals. A cognitive apprenticeship model was used in which students planned, executed, and evaluated strategy use in vivo during the course. Two sections of the course were taught at each of two different institutions, distributed across four semesters. Quantitative data showed an increased growth mindset among L2L students at the end of the semester compared to the beginning of the semester. In contrast, first-year students surveyed from control groups in the same semester had a decreased growth mindset. Furthermore, compared to students in the control groups, students in the L2L courses maintained more stable levels of effort across the semester and felt more in control of their learning by the end of the semester. Qualitative data collected from focus groups indicated that the L2L students continued to use the strategies they had learned in the course in the subsequent semester, and that the changes in their perceptions about growth mindset continued beyond the duration of the course. Several L2L students noted a desire for the learning strategies to be taught earlier in their education. Next steps involve feasibility studies on appropriate scaling to support more undergraduates each year, and to support students during the critical transition from K-12 schooling to the college environment.
Published: 2023
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15. Understanding Youth Athlete Motivation, Training, and Activity Progression During and After the COVID-19 Sports Interruption

Author: Elliot Greenberg, Eric Greenberg, J. Todd Lawrence, and Theodore Ganley
Subjects: Sports medicine, RC1200-1245
Abstract: # Background COVID-19 restrictions created a period of disrupted sports participation for youth athletes. The physical conditioning, sports training habits, and patterns of sports activity resumption upon returning to normal sports activity are currently unknown. # Purpose/Hypothesis This study aimed to determine the extent to which youth athletes maintained their training levels during the early stages of the COVID-19 pandemic and understand the strategies that enhanced motivation and adherence to a training regimen while in isolation. A secondary aim was to analyze how youth athletes returned to activity and identify injuries associated with prolonged sports interruption. # Study Design Observational / Survey Study # Methods A survey designed to determine activity changes, type of organized instruction, and athlete preferences for training support were distributed by email using snowball sampling methodology to athletes 14-21 years old who were involved in competitive sports when pandemic restrictions were enacted. As sports activities resumed, a follow-up survey was distributed to the same respondents to identify feelings of preparedness, training habits, and injuries. # Results Of the155 subjects (mean age 16.1 ± 2 years, 64.5% female) that completed the initial survey, 98% reported a stoppage of in-person sports participation and 70% decreased their exercise/training volume, with 41% (n=63) reporting \> 50% reduction. Most athletes (86%) received instruction from coaches, with written workouts (70%) being most common; however, most athletes (70%) preferred instructor-led, group training sessions. Of the 43 subjects that completed the follow-up survey (34% response rate), there was an increase in athletic exposures compared to mid-pandemic levels, and 25% reported sustaining a sports-related injury shortly after resuming sports activities. # Conclusions Pandemic-related sports restrictions resulted in a significant reduction in youth athlete training and conditioning. Coaches attempted to maintain training via the use of written workouts; however, athletes preferred instructor-led, group training sessions. There was a rapid resumption of sports activities, which may have contributed to the high rate of injuries in this study. # Level of Evidence 3
Published: 2022
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16. A Corresponding Point Measurement System Provides Reliable Measurement of Displacement for Medial Epicondyle Fractures

Author: Ryan H. Guzek, MD, Kathleen Harwood, David Isaacs, Divya Talwar, PhD, Eric W. Edmonds, MD, Peter D. Fabricant, MD, MPH, V. Elaine Joughin, MD, FRCSC, Kevin H. Latz, MD, Stephanie W. Mayer, MD, Scott McKay, MD, Donna M. Pacicca, MD, Michael Saper, DO, and J. Todd R. Lawrence, MD, PhD
Subjects: Orthopedic surgery, RD701-811
Abstract: Background:. Little consensus exists on the best method for evaluation and management of pediatric medial epicondyle fractures because of an inability to reliably evaluate fracture displacement with standard imaging techniques. This study aimed to determine the performance of various radiographic views in evaluating displaced medial epicondyle fractures when using a standardized measurement methodology. Methods:. Ten fellowship-trained pediatric orthopaedic surgeons assessed fracture displacement in 6 patients with displaced medial epicondyle fractures using radiographic views (anteroposterior, lateral, axial, internal oblique [IO], and external oblique [EO]) and computed tomographic (CT) views (axial, 3-dimensional [3D] horizontal, and 3D vertical). Raters used a corresponding point method for measuring displacement. For each image, raters measured the absolute displacement, categorized the percent of displacement relative to the size of the fragment and fracture bed, and indicated a treatment option. Interobserver reliability was calculated for each view. Bland-Altman plots were constructed to evaluate the bias between each radiograph and the mean of the CT methods. Results:. For absolute displacement, anteroposterior and EO views showed almost perfect interobserver reliability, with an interclass correlation coefficient (ICC) of 0.944 for the anteroposterior view and an ICC of 0.975 for the EO view. The axial view showed substantial reliability (ICC = 0.775). For the displacement category, almost perfect reliability was shown for the anteroposterior view (ICC = 0.821), the axial view (ICC = 0.911), the EO view (ICC = 0.869), and the IO view (ICC = 0.871). Displacement measurements from the anteroposterior, axial, and EO views corresponded to the measurements from the CT views with a mean bias of 5 mm for all views, indicating a substantial discrepancy between radiographic and CT assessments. Treatment recommendations based on CT changed relative to the recommendation made using the anteroposterior view 29% of the time, the EO view 41% of the time, and the axial view 47% of the time. Conclusions:. Using a corresponding point measurement system, surgeons can reliably measure and categorize fracture displacement using anteroposterior, EO, and axial radiographic views. CT-based measurements are also reliable. However, although the mean difference between the radiograph-based measurements and the CT-based measurements was only about 1 mm, the discrepancy between radiographic views and CT-based methods could be as large as 5 to 6 mm. Level of Evidence:. Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
Published: 2022
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17. Ensemble Kalman Filter Data Assimilation Into Surface Flux Transport Model To Infer Surface Flows: An Observing System Simulation Experiment

Author: Dash, Soumyaranjan, DeRosa, Marc L., Dikpati, Mausumi, Sun, Xudong, Mahajan, Sushant S., Liu, Yang, and Hoeksema, J. Todd
Subjects: Astrophysics - Solar and Stellar Astrophysics, Physics - Space Physics
Abstract: Knowledge of the global magnetic field distribution and its evolution on the Sun's surface is crucial for modeling the coronal magnetic field, understanding solar wind dynamics, computing the heliospheric open flux distribution and predicting solar cycle strength. As the far side of the Sun cannot be observed directly and high-latitude observations always suffer from projection effects, we often rely on surface flux transport simulations (SFT) to model long-term global magnetic field distribution. Meridional circulation, the large-scale north-south component of the surface flow profile, is one of the key components of the SFT simulation that requires further constraints near high latitudes. Prediction of the photospheric magnetic field distribution requires knowledge of the flow profile in the future, which demands reconstruction of that same flow at the current time so that it can be estimated at a later time. By performing Observing System Simulation Experiments, we demonstrate how the Ensemble Kalman Filter technique, when used with a SFT model, can be utilized to make ``posterior'' estimates of flow profiles into the future that can be used to drive the model forward to forecast photospheric magnetic field distribution., Comment: Accepted for publication in The Astrophysical Journal
Published: 2024

18. Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment

Author: B. Abi, R. Acciarri, M. A. Acero, G. Adamov, D. Adams, M. Adinolfi, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, C. Alt, J. Anderson, C. Andreopoulos, M. P. Andrews, F. Andrianala, S. Andringa, A. Ankowski, M. Antonova, S. Antusch, A. Aranda-Fernandez, A. Ariga, L. O. Arnold, M. A. Arroyave, J. Asaadi, A. Aurisano, V. Aushev, D. Autiero, F. Azfar, H. Back, J. J. Back, C. Backhouse, P. Baesso, L. Bagby, R. Bajou, S. Balasubramanian, P. Baldi, B. Bambah, F. Barao, G. Barenboim, G. J. Barker, W. Barkhouse, C. Barnes, G. Barr, J. Barranco Monarca, N. Barros, J. L. Barrow, A. Bashyal, V. Basque, F. Bay, J. L. Bazo Alba, J. F. Beacom, E. Bechetoille, B. Behera, L. Bellantoni, G. Bellettini, V. Bellini, O. Beltramello, D. Belver, N. Benekos, F. Bento Neves, J. Berger, S. Berkman, P. Bernardini, R. M. Berner, H. Berns, S. Bertolucci, M. Betancourt, Y. Bezawada, M. Bhattacharjee, B. Bhuyan, S. Biagi, J. Bian, M. Biassoni, K. Biery, B. Bilki, M. Bishai, A. Bitadze, A. Blake, B. Blanco Siffert, F. D. M. Blaszczyk, G. C. Blazey, E. Blucher, J. Boissevain, S. Bolognesi, T. Bolton, M. Bonesini, M. Bongrand, F. Bonini, A. Booth, C. Booth, S. Bordoni, A. Borkum, T. Boschi, N. Bostan, P. Bour, S. B. Boyd, D. Boyden, J. Bracinik, D. Braga, D. Brailsford, A. Brandt, J. Bremer, C. Brew, E. Brianne, S. J. Brice, C. Brizzolari, C. Bromberg, G. Brooijmans, J. Brooke, A. Bross, G. Brunetti, N. Buchanan, H. Budd, D. Caiulo, P. Calafiura, J. Calcutt, M. Calin, S. Calvez, E. Calvo, L. Camilleri, A. Caminata, M. Campanelli, D. Caratelli, G. Carini, B. Carlus, P. Carniti, I. Caro Terrazas, H. Carranza, A. Castillo, C. Castromonte, C. Cattadori, F. Cavalier, F. Cavanna, S. Centro, G. Cerati, A. Cervelli, A. Cervera Villanueva, M. Chalifour, C. Chang, E. Chardonnet, A. Chatterjee, S. Chattopadhyay, J. Chaves, H. Chen, M. Chen, Y. Chen, D. Cherdack, C. Chi, S. Childress, A. Chiriacescu, K. Cho, S. Choubey, A. Christensen, D. Christian, G. Christodoulou, E. Church, P. Clarke, T. E. Coan, A. G. Cocco, J. A. B. Coelho, E. Conley, J. M. Conrad, M. Convery, L. Corwin, P. Cotte, L. Cremaldi, L. Cremonesi, J. I. Crespo-Anadón, E. Cristaldo, R. Cross, C. Cuesta, Y. Cui, D. Cussans, M. Dabrowski, H. da Motta, L. Da Silva Peres, C. David, Q. David, G. S. Davies, S. Davini, J. Dawson, K. De, R. M. De Almeida, P. Debbins, I. De Bonis, M. P. Decowski, A. de Gouvêa, P. C. De Holanda, I. L. De Icaza Astiz, A. Deisting, P. De Jong, A. Delbart, D. Delepine, M. Delgado, A. Dell’Acqua, P. De Lurgio, J. R. T. de Mello Neto, D. M. DeMuth, S. Dennis, C. Densham, G. Deptuch, A. De Roeck, V. De Romeri, J. J. De Vries, R. Dharmapalan, M. Dias, F. Diaz, J. S. Díaz, S. Di Domizio, L. Di Giulio, P. Ding, L. Di Noto, C. Distefano, R. Diurba, M. Diwan, Z. Djurcic, N. Dokania, M. J. Dolinski, L. Domine, D. Douglas, F. Drielsma, D. Duchesneau, K. Duffy, P. Dunne, T. Durkin, H. Duyang, O. Dvornikov, D. A. Dwyer, A. S. Dyshkant, M. Eads, D. Edmunds, J. Eisch, S. Emery, A. Ereditato, C. O. Escobar, L. Escudero Sanchez, J. J. Evans, E. Ewart, A. C. Ezeribe, K. Fahey, A. Falcone, C. Farnese, Y. Farzan, J. Felix, E. Fernandez-Martinez, P. Fernandez Menendez, F. Ferraro, L. Fields, A. Filkins, F. Filthaut, R. S. Fitzpatrick, W. Flanagan, B. Fleming, R. Flight, J. Fowler, W. Fox, J. Franc, K. Francis, D. Franco, J. Freeman, J. Freestone, J. Fried, A. Friedland, S. Fuess, I. Furic, A. P. Furmanski, A. Gago, H. Gallagher, A. Gallego-Ros, N. Gallice, V. Galymov, E. Gamberini, T. Gamble, R. Gandhi, R. Gandrajula, S. Gao, D. Garcia-Gamez, M. Á. García-Peris, S. Gardiner, D. Gastler, G. Ge, B. Gelli, A. Gendotti, S. Gent, Z. Ghorbani-Moghaddam, D. Gibin, I. Gil-Botella, C. Girerd, A. K. Giri, D. Gnani, O. Gogota, M. Gold, S. Gollapinni, K. Gollwitzer, R. A. Gomes, L. V. Gomez Bermeo, L. S. Gomez Fajardo, F. Gonnella, J. A. Gonzalez-Cuevas, M. C. Goodman, O. Goodwin, S. Goswami, C. Gotti, E. Goudzovski, C. Grace, M. Graham, E. Gramellini, R. Gran, E. Granados, A. Grant, C. Grant, D. Gratieri, P. Green, S. Green, L. Greenler, M. Greenwood, J. Greer, W. C. Griffith, M. Groh, J. Grudzinski, K. Grzelak, W. Gu, V. Guarino, R. Guenette, A. Guglielmi, B. Guo, K. K. Guthikonda, R. Gutierrez, P. Guzowski, M. M. Guzzo, S. Gwon, A. Habig, A. Hackenburg, H. Hadavand, R. Haenni, A. Hahn, J. Haigh, J. Haiston, T. Hamernik, P. Hamilton, J. Han, K. Harder, D. A. Harris, J. Hartnell, T. Hasegawa, R. Hatcher, E. Hazen, A. Heavey, K. M. Heeger, J. Heise, K. Hennessy, S. Henry, M. A. Hernandez Morquecho, K. Herner, L. Hertel, A. S. Hesam, J. Hewes, A. Higuera, T. Hill, S. J. Hillier, A. Himmel, J. Hoff, C. Hohl, A. Holin, E. Hoppe, G. A. Horton-Smith, M. Hostert, A. Hourlier, B. Howard, R. Howell, J. Huang, J. Hugon, G. Iles, N. Ilic, A. M. Iliescu, R. Illingworth, A. Ioannisian, R. Itay, A. Izmaylov, E. James, B. Jargowsky, F. Jediny, C. Jesùs-Valls, X. Ji, L. Jiang, S. Jiménez, A. Jipa, A. Joglekar, C. Johnson, R. Johnson, B. Jones, S. Jones, C. K. Jung, T. Junk, Y. Jwa, M. Kabirnezhad, A. Kaboth, I. Kadenko, F. Kamiya, G. Karagiorgi, A. Karcher, M. Karolak, Y. Karyotakis, S. Kasai, S. P. Kasetti, L. Kashur, N. Kazaryan, E. Kearns, P. Keener, K. J. Kelly, E. Kemp, W. Ketchum, S. H. Kettell, M. Khabibullin, A. Khotjantsev, A. Khvedelidze, D. Kim, B. King, B. Kirby, M. Kirby, J. Klein, K. Koehler, L. W. Koerner, S. Kohn, P. P. Koller, M. Kordosky, T. Kosc, U. Kose, V. A. Kostelecký, K. Kothekar, F. Krennrich, I. Kreslo, Y. Kudenko, V. A. Kudryavtsev, S. Kulagin, J. Kumar, R. Kumar, C. Kuruppu, V. Kus, T. Kutter, A. Lambert, K. Lande, C. E. Lane, K. Lang, T. Langford, P. Lasorak, D. Last, C. Lastoria, A. Laundrie, A. Lawrence, I. Lazanu, R. LaZur, T. Le, J. Learned, P. LeBrun, G. Lehmann Miotto, R. Lehnert, M. A. Leigui de Oliveira, M. Leitner, M. Leyton, L. Li, S. Li, S. W. Li, T. Li, Y. Li, H. Liao, C. S. Lin, S. Lin, A. Lister, B. R. Littlejohn, J. Liu, S. Lockwitz, T. Loew, M. Lokajicek, I. Lomidze, K. Long, K. Loo, D. Lorca, T. Lord, J. M. LoSecco, W. C. Louis, K. B. Luk, X. Luo, N. Lurkin, T. Lux, V. P. Luzio, D. MacFarland, A. A. Machado, P. Machado, C. T. Macias, J. R. Macier, A. Maddalena, P. Madigan, S. Magill, K. Mahn, A. Maio, J. A. Maloney, G. Mandrioli, J. Maneira, L. Manenti, S. Manly, A. Mann, K. Manolopoulos, M. Manrique Plata, A. Marchionni, W. Marciano, D. Marfatia, C. Mariani, J. Maricic, F. Marinho, A. D. Marino, M. Marshak, C. Marshall, J. Marshall, J. Marteau, J. Martin-Albo, N. Martinez, D. A. Martinez Caicedo, S. Martynenko, K. Mason, A. Mastbaum, M. Masud, S. Matsuno, J. Matthews, C. Mauger, N. Mauri, K. Mavrokoridis, R. Mazza, A. Mazzacane, E. Mazzucato, E. McCluskey, N. McConkey, K. S. McFarland, C. McGrew, A. McNab, A. Mefodiev, P. Mehta, P. Melas, M. Mellinato, O. Mena, S. Menary, H. Mendez, A. Menegolli, G. Meng, M. D. Messier, W. Metcalf, M. Mewes, H. Meyer, T. Miao, G. Michna, T. Miedema, J. Migenda, R. Milincic, W. Miller, J. Mills, C. Milne, O. Mineev, O. G. Miranda, S. Miryala, C. S. Mishra, S. R. Mishra, A. Mislivec, D. Mladenov, I. Mocioiu, K. Moffat, N. Moggi, R. Mohanta, T. A. Mohayai, N. Mokhov, J. Molina, L. Molina Bueno, A. Montanari, C. Montanari, D. Montanari, L. M. Montano Zetina, J. Moon, M. Mooney, A. Moor, D. Moreno, B. Morgan, C. Morris, C. Mossey, E. Motuk, C. A. Moura, J. Mousseau, W. Mu, L. Mualem, J. Mueller, M. Muether, S. Mufson, F. Muheim, A. Muir, M. Mulhearn, H. Muramatsu, S. Murphy, J. Musser, J. Nachtman, S. Nagu, M. Nalbandyan, R. Nandakumar, D. Naples, S. Narita, D. Navas-Nicolás, N. Nayak, M. Nebot-Guinot, L. Necib, K. Negishi, J. K. Nelson, J. Nesbit, M. Nessi, D. Newbold, M. Newcomer, D. Newhart, R. Nichol, E. Niner, K. Nishimura, A. Norman, A. Norrick, R. Northrop, P. Novella, J. A. Nowak, M. Oberling, A. Olivares Del Campo, A. Olivier, Y. Onel, Y. Onishchuk, J. Ott, L. Pagani, S. Pakvasa, O. Palamara, S. Palestini, J. M. Paley, M. Pallavicini, C. Palomares, E. Pantic, V. Paolone, V. Papadimitriou, R. Papaleo, A. Papanestis, S. Paramesvaran, J. C. Park, S. Parke, Z. Parsa, M. Parvu, S. Pascoli, L. Pasqualini, J. Pasternak, J. Pater, C. Patrick, L. Patrizii, R. B. Patterson, S. J. Patton, T. Patzak, A. Paudel, B. Paulos, L. Paulucci, Z. Pavlovic, G. Pawloski, D. Payne, V. Pec, S. J. M. Peeters, Y. Penichot, E. Pennacchio, A. Penzo, O. L. G. Peres, J. Perry, D. Pershey, G. Pessina, G. Petrillo, C. Petta, R. Petti, F. Piastra, L. Pickering, F. Pietropaolo, J. Pillow, J. Pinzino, R. Plunkett, R. Poling, X. Pons, N. Poonthottathil, S. Pordes, M. Potekhin, R. Potenza, B. V. K. S. Potukuchi, J. Pozimski, M. Pozzato, S. Prakash, T. Prakash, S. Prince, G. Prior, D. Pugnere, K. Qi, X. Qian, J. L. Raaf, R. Raboanary, V. Radeka, J. Rademacker, B. Radics, A. Rafique, E. Raguzin, M. Rai, M. Rajaoalisoa, I. Rakhno, H. T. Rakotondramanana, L. Rakotondravohitra, Y. A. Ramachers, R. Rameika, M. A. Ramirez Delgado, B. Ramson, A. Rappoldi, G. Raselli, P. Ratoff, S. Ravat, H. Razafinime, J. S. Real, B. Rebel, D. Redondo, M. Reggiani-Guzzo, T. Rehak, J. Reichenbacher, S. D. Reitzner, A. Renshaw, S. Rescia, F. Resnati, A. Reynolds, G. Riccobene, L. C. J. Rice, K. Rielage, Y. Rigaut, D. Rivera, L. Rochester, M. Roda, P. Rodrigues, M. J. Rodriguez Alonso, J. Rodriguez Rondon, A. J. Roeth, H. Rogers, S. Rosauro-Alcaraz, M. Rossella, J. Rout, S. Roy, A. Rubbia, C. Rubbia, B. Russell, J. Russell, D. Ruterbories, R. Saakyan, S. Sacerdoti, T. Safford, N. Sahu, P. Sala, N. Samios, M. C. Sanchez, D. A. Sanders, D. Sankey, S. Santana, M. Santos-Maldonado, N. Saoulidou, P. Sapienza, C. Sarasty, I. Sarcevic, G. Savage, V. Savinov, A. Scaramelli, A. Scarff, A. Scarpelli, T. Schaffer, H. Schellman, P. Schlabach, D. Schmitz, K. Scholberg, A. Schukraft, E. Segreto, J. Sensenig, I. Seong, A. Sergi, F. Sergiampietri, D. Sgalaberna, M. H. Shaevitz, S. Shafaq, M. Shamma, H. R. Sharma, R. Sharma, T. Shaw, C. Shepherd-Themistocleous, S. Shin, D. Shooltz, R. Shrock, L. Simard, N. Simos, J. Sinclair, G. Sinev, J. Singh, V. Singh, R. Sipos, F. W. Sippach, G. Sirri, A. Sitraka, K. Siyeon, D. Smargianaki, A. Smith, E. Smith, P. Smith, J. Smolik, M. Smy, P. Snopok, M. Soares Nunes, H. Sobel, M. Soderberg, C. J. Solano Salinas, S. Söldner-Rembold, N. Solomey, V. Solovov, W. E. Sondheim, M. Sorel, J. Soto-Oton, A. Sousa, K. Soustruznik, F. Spagliardi, M. Spanu, J. Spitz, N. J. C. Spooner, K. Spurgeon, R. Staley, M. Stancari, L. Stanco, H. M. Steiner, J. Stewart, B. Stillwell, J. Stock, F. Stocker, D. Stocks, T. Stokes, M. Strait, T. Strauss, S. Striganov, A. Stuart, D. Summers, A. Surdo, V. Susic, L. Suter, C. M. Sutera, R. Svoboda, B. Szczerbinska, A. M. Szelc, R. Talaga, H. A. Tanaka, B. Tapia Oregui, A. Tapper, S. Tariq, E. Tatar, R. Tayloe, A. M. Teklu, M. Tenti, K. Terao, C. A. Ternes, F. Terranova, G. Testera, A. Thea, J. L. Thompson, C. Thorn, S. C. Timm, J. Todd, A. Tonazzo, M. Torti, M. Tortola, F. Tortorici, D. Totani, M. Toups, C. Touramanis, J. Trevor, W. H. Trzaska, Y.-T. Tsai, Z. Tsamalaidze, K. V. Tsang, N. Tsverava, S. Tufanli, C. Tull, E. Tyley, M. Tzanov, M. A. Uchida, J. Urheim, T. Usher, M. R. Vagins, P. Vahle, G. A. Valdiviesso, E. Valencia, Z. Vallari, J. W. F. Valle, S. Vallecorsa, R. Van Berg, R. G. Van de Water, D. Vanegas Forero, F. Varanini, D. Vargas, G. Varner, J. Vasel, G. Vasseur, K. Vaziri, S. Ventura, A. Verdugo, S. Vergani, M. A. Vermeulen, M. Verzocchi, H. Vieira de Souza, C. Vignoli, C. Vilela, B. Viren, T. Vrba, T. Wachala, A. V. Waldron, M. Wallbank, H. Wang, J. Wang, Y. Wang, K. Warburton, D. Warner, M. Wascko, D. Waters, A. Watson, P. Weatherly, A. Weber, M. Weber, H. Wei, A. Weinstein, D. Wenman, M. Wetstein, M. R. While, A. White, L. H. Whitehead, D. Whittington, M. J. Wilking, C. Wilkinson, Z. Williams, F. Wilson, R. J. Wilson, J. Wolcott, T. Wongjirad, K. Wood, L. Wood, E. Worcester, M. Worcester, C. Wret, W. Wu, Y. Xiao, G. Yang, T. Yang, N. Yershov, K. Yonehara, T. Young, B. Yu, J. Yu, R. Zaki, J. Zalesak, L. Zambelli, B. Zamorano, A. Zani, L. Zazueta, G. P. Zeller, J. Zennamo, K. Zeug, C. Zhang, M. Zhao, Y. Zhao, E. Zhivun, G. Zhu, E. D. Zimmerman, M. Zito, S. Zucchelli, J. Zuklin, V. Zutshi, and R. Zwaska
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.
Published: 2021
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19. Prevalence and incidence rate of tuberculosis among HIV-infected patients enrolled in HIV care, treatment, and support program in mainland Tanzania

Author: M. Majigo, G. Somi, A. Joachim, J. Manyahi, J. Nondi, V. Sambu, A. Rwebembera, N. Makyao, A. Ramadhani, W. Maokola, J. Todd, and M. I. Matee
Subjects: Tuberculosis, HIV, Incidence of tuberculosis, Antiretroviral therapy, Collaborative TB/HIV, Arctic medicine. Tropical medicine, RC955-962
Abstract: Abstract Background Despite improvements in access to antiretroviral therapy (ART), mortality in people living with human immunodeficiency virus (PLHIV) is still high and primarily attributed to tuberculosis (TB) infection. In Sub-Saharan Africa, approximately 80% of HIV-related mortality cases are associated with TB. Relatively little is known about the incidence of TB among PLHIV in Tanzania and the determinant factors. We report the prevalence and incidence rate of confirmed TB and determine association with selected demographic and program-related factors based on data in the national HIV care and treatment program from 2011 to 2014. Methods We used the Tanzania National AIDS Control Programme database to obtain information on all HIV clients enrolled in the HIV care and treatment program between January 2011 and December 2014. We analyzed retrospective cohort data to assess the prevalence and TB incidence rate per 1000 person-years. A multivariable Cox proportional hazards regression model was used to estimate hazard ratios and 95% confidence intervals for putatively associated factors. Results Over 4 years, there were 22,071 confirmed cases of pulmonary TB in 1,323,600 person-years. The overall TB incidence was around 16.7 (95% CI 16.4–16.9) cases per 1000 person-years. The annual incidence rate decreased by 12.4 % from 17.0 (95% CI 16.5–17.4) in 2011 to 14.9 (95% CI 14.5–15.4) in 2014. The TB incidence rate was higher in persons not using ART and in males than in females. The incidence of TB was higher in patients with advanced HIV disease and decreased with increasing age. The overall prevalence of TB was 2.2%, with a peak prevalence of 2.5% in 2013 and was higher among children
Published: 2020
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20. Coupled modelling of subglacial hydrology and calving-front melting at Store Glacier, West Greenland

Author: S. J. Cook, P. Christoffersen, J. Todd, D. Slater, and N. Chauché
Subjects: Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract: We investigate the subglacial hydrology of Store Glacier in West Greenland, using the open-source, full-Stokes model Elmer/Ice in a novel 3D application that includes a distributed water sheet, as well as discrete channelised drainage, and a 1D model to simulate submarine plumes at the calving front. At first, we produce a baseline winter scenario with no surface meltwater. We then investigate the hydrological system during summer, focussing specifically on 2012 and 2017, which provide examples of high and low surface-meltwater inputs, respectively. We show that the common assumption of zero winter freshwater flux is invalid, and we find channels over 1 m2 in area occurring up to 5 km inland in winter. We also find that the production of water from friction and geothermal heat is sufficiently high to drive year-round plume activity, with ice-front melting averaging 0.15 m d−1. When the model is forced with seasonally averaged surface melt from summer, we show a hydrological system with significant distributed sheet activity extending 65 and 45 km inland in 2012 and 2017, respectively; while channels with a cross-sectional area higher than 1 m2 form as far as 55 and 30 km inland. Using daily values for the surface melt as forcing, we find only a weak relationship between the input of surface meltwater and the intensity of plume melting at the calving front, whereas there is a strong correlation between surface-meltwater peaks and basal water pressures. The former shows that storage of water on multiple timescales within the subglacial drainage system plays an important role in modulating subglacial discharge. The latter shows that high melt inputs can drive high basal water pressures even when the channelised network grows larger. This has implications for the future velocity and mass loss of Store Glacier, and the consequent sea-level rise, in a warming world.
Published: 2020
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21. Why Are Some People with Lower Urinary Tract Symptoms (LUTS) Depressed? New Evidence That Peripheral Inflammation in the Bladder Causes Central Inflammation and Mood Disorders

Author: Francis M. Hughes, Michael R. Odom, Anissa Cervantes, Austin J. Livingston, and J. Todd Purves
Subjects: inflammation, lower urinary tract symptoms, bladder, depression, mood disorders, cystitis, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract: Anecdotal evidence has long suggested that patients with lower urinary tract symptoms (LUTS) develop mood disorders, such as depression and anxiety, at a higher rate than the general population and recent prospective studies have confirmed this link. Breakthroughs in our understanding of the diseases underlying LUTS have shown that many have a substantial inflammatory component and great strides have been made recently in our understanding of how this inflammation is triggered. Meanwhile, studies on mood disorders have found that many are associated with central neuroinflammation, most notably in the hippocampus. Excitingly, work on other diseases characterized by peripheral inflammation has shown that they can trigger central neuroinflammation and mood disorders. In this review, we discuss the current evidence tying LUTS to mood disorders, its possible bidirectionally, and inflammation as a common mechanism. We also review modern theories of inflammation and depression. Finally, we discuss exciting new animal studies that directly tie two bladder conditions characterized by extensive bladder inflammation (cyclophosphamide-induced hemorrhagic cystitis and bladder outlet obstruction) to neuroinflammation and depression. We conclude with a discussion of possible mechanisms by which peripheral inflammation is translated into central neuroinflammation with the resulting psychiatric concerns.
Published: 2023
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22. Large-scale Spatial Cross-calibration of Hinode/SOT-SP and SDO/HMI

Author: David F. Fouhey, Richard E. L. Higgins, Spiro K. Antiochos, Graham Barnes, Marc L. DeRosa, J. Todd Hoeksema, K. D. Leka, Yang Liu, Peter W. Schuck, and Tamas I. Gombosi
Subjects: Solar magnetic fields, Computational methods, Astrophysics, QB460-466
Abstract: We investigate the cross-calibration of the Hinode/Solar Optical Telescope-Spectro-Polarimeter (SOT-SP) and Solar Dynamics Observatory/Helioseismic and Magnetic Imager (SDO/HMI) instrument metadata, specifically the correspondence of the scaling and pointing information. Accurate calibration of these data sets gives the correspondence needed by interinstrument studies and learning-based magnetogram systems, and is required for physically meaningful photospheric magnetic field vectors. We approach the problem by robustly fitting geometric models on correspondences between images from each instrument’s pipeline. This technique is common in computer vision, but several critical details are required when using scanning-slit spectrograph data like Hinode/SOT-SP. We apply this technique to data spanning a decade of the Hinode mission. Our results suggest corrections to the published Level 2 Hinode/SOT-SP data. First, an analysis on approximately 2700 scans suggests that the reported pixel size in Hinode/SOT-SP Level 2 data is incorrect by around 1%. Second, analysis of over 12,000 scans shows that the pointing information is often incorrect by dozens of arcseconds with a strong bias. Regression of these corrections indicates that thermal effects have caused secular and cyclic drift in Hinode/SOT-SP pointing data over its mission. We offer two solutions. First, direct coalignment with SDO/HMI data via our procedure can improve alignments for many Hinode/SOT-SP scans. Second, since the pointing errors are predictable, simple post-hoc corrections can substantially improve the pointing. We conclude by illustrating the impact of this updated calibration on derived physical data products needed for research and interpretation. Among other things, our results suggest that the pointing errors induce a hemispheric bias in estimates of radial current density.
Published: 2023
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23. Impact of warming shelf waters on ice mélange and terminus retreat at a large SE Greenland glacier

Author: S. L. Bevan, A. J. Luckman, D. I. Benn, T. Cowton, and J. Todd
Subjects: Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract: By the end of 2018 Kangerlussuaq Glacier in southeast Greenland had retreated further inland than at any time in the past 80 years and its terminus was approaching a region of retrograde bed slope from where further rapid retreat would have been inevitable. Here we show that the retreat occurred because the glacier failed to advance during the winters of 2016/17 and 2017/18 owing to a weakened proglacial mélange. This mixture of sea ice and icebergs is normally rigid enough to inhibit calving in winter, but for 2 consecutive years it repeatedly collapsed, allowing Kangerlussuaq Glacier to continue to calve all year round. The mélange break-ups followed the establishment of anomalously warm surface water on the continental shelf during 2016, which likely penetrated the fjord. As calving continued uninterrupted from summer 2016 to the end of 2018 the glacier accelerated by 35 % and thinned by 35 m. These observations demonstrate the importance of near-surface ocean temperatures in tidewater glacier stability and show that it is not only deep-ocean warming that can lead to glacier retreat. During winter 2019 a persistent mélange reformed and the glacier readvanced by 3.5 km.
Published: 2019
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24. Whole exome sequencing of patients who resolved Crohn’s disease and complex regional pain syndrome following treatment for paratuberculosis

Author: J. Todd Kuenstner, Maher Kali, and Christine Welch
Subjects: Mycobacterium avium ssp. paratuberculosis, Crohn’s disease, Complex regional pain syndrome, Lymphangiomatosis, Type 1 diabetes mellitus, Genetic susceptibility, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract: Abstract Background A whole exome sequencing study was performed on an extended family including a patient with Crohn’s disease (CD) and a patient with complex regional pain syndrome (CRPS). The patient with CD and the patient with CRPS have experienced resolution of their disease following treatment for paratuberculosis. The study was performed in order to determine if there is an unusual mutation in this extended family that would explain the susceptibility to mycobacterial infection among many of the members. Results We identified sets of rare single nucleotide polymorphisms (SNPs) that were shared among affected family members, including variants in two genes, IL15RA and CASP10, which have established roles in the immune response. In addition, the CD and CRPS patients were found to have heterozygous mutations in MBL2 and DDX58, mutations that have been associated with susceptibility to tuberculosis. Conclusions The IL15RA and CASP10 variants may contribute to the disease symptoms exhibited in this family. The finding of SNPs associated with immune function supports a complementary role of infection and genetics in these diseases.
Published: 2019
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25. Sensitivity of a calving glacier to ice–ocean interactions under climate change: new insights from a 3-D full-Stokes model

Author: J. Todd, P. Christoffersen, T. Zwinger, P. Råback, and D. I. Benn
Subjects: Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract: Iceberg calving accounts for between 30 % and 60 % of net mass loss from the Greenland Ice Sheet, which has intensified and is now the single largest contributor to global sea level rise in the cryosphere. Changes to calving rates and the dynamics of calving glaciers represent a significant uncertainty in projections of future sea level rise. A growing body of observational evidence suggests that calving glaciers respond rapidly to regional environmental change, but predictive capacity is limited by the lack of suitable models capable of simulating calving mechanisms realistically. Here, we use a 3-D full-Stokes calving model to investigate the environmental sensitivity of Store Glacier, a large outlet glacier in West Greenland. We focus on two environmental processes: undercutting by submarine melting and buttressing by ice mélange, and our results indicate that Store Glacier is likely to be able to withstand moderate warming perturbations in which the former is increased by 50 % and the latter reduced by 50 %. However, severe perturbation with a doubling of submarine melt rates or a complete loss of ice mélange destabilises the calving front in our model runs. Furthermore, our analysis reveals that stress and fracture patterns at Store's terminus are complex and varied, primarily due to the influence of basal topography. Calving style and environmental sensitivity vary greatly, with propagation of surface crevasses significantly influencing iceberg production in the northern side, whereas basal crevasses dominate in the south. Any future retreat is likely to be initiated in the southern side by a combination of increased submarine melt rates in summer and reduced mélange strength in winter. The lateral variability, as well as the importance of rotational and bending forces at the terminus, underlines the importance of using the 3-D full-Stokes stress solution when modelling Greenland's calving glaciers.
Published: 2019
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26. Vps54 regulates Drosophila neuromuscular junction development and interacts genetically with Rab7 to control composition of the postsynaptic density

Author: Prajal H. Patel, Emily C. Wilkinson, Emily L. Starke, Malea R. McGimsey, J. Todd Blankenship, and Scott A. Barbee
Subjects: drosophila, garp, rab7, vps54, neurodevelopment, neuromuscular junction, Science, Biology (General), QH301-705.5
Abstract: Vps54 is a subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). In the wobbler mouse, a model for human motor neuron (MN) disease, reduction in the levels of Vps54 causes neurodegeneration. However, it is unclear how disruption of the GARP complex leads to MN dysfunction. To better understand the role of Vps54 in MNs, we have disrupted expression of the Vps54 ortholog in Drosophila and examined the impact on the larval neuromuscular junction (NMJ). Surprisingly, we show that both null mutants and MN-specific knockdown of Vps54 leads to NMJ overgrowth. Reduction of Vps54 partially disrupts localization of the t-SNARE, Syntaxin-16, to the TGN but has no visible impact on endosomal pools. MN-specific knockdown of Vps54 in MNs combined with overexpression of the small GTPases Rab5, Rab7, or Rab11 suppresses the Vps54 NMJ phenotype. Conversely, knockdown of Vps54 combined with overexpression of dominant negative Rab7 causes NMJ and behavioral abnormalities including a decrease in postsynaptic Dlg and GluRIIB levels without any effect on GluRIIA. Taken together, these data suggest that Vps54 controls larval MN axon development and postsynaptic density composition through a mechanism that requires Rab7.
Published: 2020
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27. Which Metrics Are Being Used to Evaluate Children and Adolescents After ACL Reconstruction? A Systematic Review

Author: Peter D. Fabricant, M.D., M.P.H., Christopher M. Brusalis, M.D., Jonathan M. Schachne, B.A., Matthew J. Matava, M.D., Christian N. Anderson, M.D., Michael T. Busch, M.D., Henry G. Chambers, M.D., Melissa A. Christino, M.D., Frank A. Cordasco, M.D., M.S., Eric W. Edmonds, M.D., Theodore J. Ganley, M.D., Daniel W. Green, M.D., M.S., Benton E. Heyworth, M.D., Mininder S. Kocher, M.D., M.P.H., J. Todd R. Lawrence, M.D., Ph.D., Lyle J. Micheli, M.D., Matthew D. Milewski, M.D., Jeffrey J. Nepple, M.D., Shital N. Parikh, M.D., Andrew T. Pennock, M.D., Paul Saluan, M.D., Kevin G. Shea, M.D., Eric J. Wall, M.D., and Samuel C. Willimon, M.D.
Subjects: Sports medicine, RC1200-1245
Abstract: Purpose: To identify a comprehensive list of outcome measures previously used in the literature to evaluate clinical outcomes after reconstruction of the anterior cruciate ligament (ACL) in patients 18 years of age or younger. Methods: A literature search was performed by querying MEDLINE, Embase and Cochrane computerized databases for relevant articles that reported clinical outcomes in pediatric patients undergoing ACL reconstruction. Studies that were nonclinical, that reported on patients older than 19 years, that were not available in English, or that included fewer than 10 patients were excluded. Outcome measures of all eligible studies were recorded. Results: We identified 77 studies published between 1986 and 2018 in 20 peer-reviewed journals. The mean age of the patients was 13.9 years. The ACL rerupture rate was reported in 60% of studies; 32 studies (42%) reported a rate of return to preinjury activity or sports. The use of adult-validated patient-reported outcome measures were reported in 63 (82%) articles. The Lysholm (64%), International Knee Documentation Committee (IKDC) (56%) and Tegner (37%) scores were the most commonly reported. Two patient-reported outcome measures designed for pediatric patients (the Pedi-IKDC and Hospital for Special Surgery Pediatric Functional Activity Brief Scale (Pedi-FABS) were employed in 5 (6%) recent studies. Conclusions: There is variability across studies in the metrics used to assess clinical outcomes following ACL reconstruction in children and adolescents. Validated pediatric-specific instruments were used infrequently. Clinical Relevance: A large body of existing pediatric ACL-reconstruction literature relies on a variable set of outcome measures that have not been developed or validated for children and adolescents. More recently, contemporary studies have begun to employ pediatric- and adolescent-specific validated measures, yet their use remains uncommon.
Published: 2020
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28. Erratum to: Differential branching fraction and angular analysis of Λ b 0 → Λμ + μ − decays

Author: The LHCb collaboration, R. Aaij, B. Adeva, M. Adinolfi, A. Affolder, Z. Ajaltouni, S. Akar, J. Albrecht, F. Alessio, M. Alexander, S. Ali, G. Alkhazov, P. Alvarez Cartelle, A. A. Alves, S. Amato, S. Amerio, Y. Amhis, L. An, L. Anderlini, J. Anderson, M. Andreotti, J. E. Andrews, R. B. Appleby, O. Aquines Gutierrez, F. Archilli, A. Artamonov, M. Artuso, E. Aslanides, G. Auriemma, M. Baalouch, S. Bachmann, J. J. Back, A. Badalov, C. Baesso, W. Baldini, R. J. Barlow, C. Barschel, S. Barsuk, W. Barter, V. Batozskaya, V. Battista, A. Bay, L. Beaucourt, J. Beddow, F. Bedeschi, I. Bediaga, L. J. Bel, I. Belyaev, E. Ben-Haim, G. Bencivenni, S. Benson, J. Benton, A. Berezhnoy, R. Bernet, A. Bertolin, M.-O. Bettler, M. van Beuzekom, A. Bien, S. Bifani, T. Bird, A. Bizzeti, T. Blake, F. Blanc, J. Blouw, S. Blusk, V. Bocci, A. Bondar, N. Bondar, W. Bonivento, S. Borghi, M. Borsato, T. J. V. Bowcock, E. Bowen, C. Bozzi, S. Braun, D. Brett, M. Britsch, T. Britton, J. Brodzicka, N. H. Brook, A. Bursche, J. Buytaert, S. Cadeddu, R. Calabrese, M. Calvi, M. Calvo Gomez, P. Campana, D. Campora Perez, L. Capriotti, A. Carbone, G. Carboni, R. Cardinale, A. Cardini, P. Carniti, L. Carson, K. Carvalho Akiba, R. Casanova Mohr, G. Casse, L. Cassina, L. Castillo Garcia, M. Cattaneo, Ch. Cauet, G. Cavallero, R. Cenci, M. Charles, Ph. Charpentier, M. Chefdeville, S. Chen, S.-F. Cheung, N. Chiapolini, M. Chrzaszcz, X. Cid Vidal, G. Ciezarek, P. E. L. Clarke, M. Clemencic, H. V. Cliff, J. Closier, V. Coco, J. Cogan, E. Cogneras, V. Cogoni, L. Cojocariu, G. Collazuol, P. Collins, A. Comerma-Montells, A. Contu, A. Cook, M. Coombes, S. Coquereau, G. Corti, M. Corvo, I. Counts, B. Couturier, G. A. Cowan, D. C. Craik, A. C. Crocombe, M. Cruz Torres, S. Cunliffe, R. Currie, C. D’Ambrosio, J. Dalseno, P. N. Y. David, A. Davis, K. De Bruyn, S. De Capua, M. De Cian, J. M. De Miranda, L. De Paula, W. De Silva, P. De Simone, C.-T. Dean, D. Decamp, M. Deckenhoff, L. Del Buono, N. Déléage, D. Derkach, O. Deschamps, F. Dettori, B. Dey, A. Di Canto, F. Di Ruscio, H. Dijkstra, S. Donleavy, F. Dordei, M. Dorigo, A. Dosil Suárez, D. Dossett, A. Dovbnya, K. Dreimanis, G. Dujany, F. Dupertuis, P. Durante, R. Dzhelyadin, A. Dziurda, A. Dzyuba, S. Easo, U. Egede, V. Egorychev, S. Eidelman, S. Eisenhardt, U. Eitschberger, R. Ekelhof, L. Eklund, I. El Rifai, Ch. Elsasser, S. Ely, S. Esen, H. M. Evans, T. Evans, A. Falabella, C. Färber, C. Farinelli, N. Farley, S. Farry, R. Fay, D. Ferguson, V. Fernandez Albor, F. Ferrari, F. Ferreira Rodrigues, M. Ferro-Luzzi, S. Filippov, M. Fiore, M. Fiorini, M. Firlej, C. Fitzpatrick, T. Fiutowski, P. Fol, M. Fontana, F. Fontanelli, R. Forty, O. Francisco, M. Frank, C. Frei, M. Frosini, J. Fu, E. Furfaro, A. Gallas Torreira, D. Galli, S. Gallorini, S. Gambetta, M. Gandelman, P. Gandini, Y. Gao, J. García Pardiñas, J. Garofoli, J. Garra Tico, L. Garrido, D. Gascon, C. Gaspar, U. Gastaldi, R. Gauld, L. Gavardi, G. Gazzoni, A. Geraci, D. Gerick, E. Gersabeck, M. Gersabeck, T. Gershon, Ph. Ghez, A. Gianelle, S. Gianì, V. Gibson, L. Giubega, V. V. Gligorov, C. Göbel, D. Golubkov, A. Golutvin, A. Gomes, C. Gotti, M. Grabalosa Gándara, R. Graciani Diaz, L. A. Granado Cardoso, E. Graugés, E. Graverini, G. Graziani, A. Grecu, E. Greening, S. Gregson, P. Griffith, L. Grillo, O. Grünberg, B. Gui, E. Gushchin, Yu. Guz, T. Gys, C. Hadjivasiliou, G. Haefeli, C. Haen, S. C. Haines, S. Hall, B. Hamilton, T. Hampson, X. Han, S. Hansmann-Menzemer, N. Harnew, S. T. Harnew, J. Harrison, J. He, T. Head, V. Heijne, K. Hennessy, P. Henrard, L. Henry, J. A. Hernando Morata, E. van Herwijnen, M. Heß, A. Hicheur, D. Hill, M. Hoballah, C. Hombach, W. Hulsbergen, T. Humair, N. Hussain, D. Hutchcroft, D. Hynds, M. Idzik, P. Ilten, R. Jacobsson, A. Jaeger, J. Jalocha, E. Jans, A. Jawahery, F. Jing, M. John, D. Johnson, C. R. Jones, C. Joram, B. Jost, N. Jurik, S. Kandybei, W. Kanso, M. Karacson, T. M. Karbach, S. Karodia, M. Kelsey, I. R. Kenyon, M. Kenzie, T. Ketel, B. Khanji, C. Khurewathanakul, S. Klaver, K. Klimaszewski, O. Kochebina, M. Kolpin, I. Komarov, R. F. Koopman, P. Koppenburg, M. Korolev, L. Kravchuk, K. Kreplin, M. Kreps, G. Krocker, P. Krokovny, F. Kruse, W. Kucewicz, M. Kucharczyk, V. Kudryavtsev, K. Kurek, T. Kvaratskheliya, V. N. La Thi, D. Lacarrere, G. Lafferty, A. Lai, D. Lambert, R. W. Lambert, G. Lanfranchi, C. Langenbruch, B. Langhans, T. Latham, C. Lazzeroni, R. Le Gac, J. van Leerdam, J.-P. Lees, R. Lefèvre, A. Leflat, J. Lefrançois, O. Leroy, T. Lesiak, B. Leverington, Y. Li, T. Likhomanenko, M. Liles, R. Lindner, C. Linn, F. Lionetto, B. Liu, S. Lohn, I. Longstaff, J. H. Lopes, P. Lowdon, D. Lucchesi, H. Luo, A. Lupato, E. Luppi, O. Lupton, F. Machefert, F. Maciuc, O. Maev, S. Malde, A. Malinin, G. Manca, G. Mancinelli, P. Manning, A. Mapelli, J. Maratas, J. F. Marchand, U. Marconi, C. Marin Benito, P. Marino, R. Märki, J. Marks, G. Martellotti, M. Martinelli, D. Martinez Santos, F. Martinez Vidal, D. Martins Tostes, A. Massafferri, R. Matev, A. Mathad, Z. Mathe, C. Matteuzzi, A. Mauri, B. Maurin, A. Mazurov, M. McCann, J. McCarthy, A. McNab, R. McNulty, B. Meadows, F. Meier, M. Meissner, M. Merk, D. A. Milanes, M.-N. Minard, D. S. Mitzel, J. Molina Rodriguez, S. Monteil, M. Morandin, P. Morawski, A. Mordà, M. J. Morello, J. Moron, A.-B. Morris, R. Mountain, F. Muheim, K. Müller, M. Mussini, B. Muster, P. Naik, T. Nakada, R. Nandakumar, I. Nasteva, M. Needham, N. Neri, S. Neubert, N. Neufeld, M. Neuner, A. D. Nguyen, T. D. Nguyen, C. Nguyen-Mau, V. Niess, R. Niet, N. Nikitin, T. Nikodem, A. Novoselov, D. P. O’Hanlon, A. Oblakowska-Mucha, V. Obraztsov, S. Ogilvy, O. Okhrimenko, R. Oldeman, C. J. G. Onderwater, B. Osorio Rodrigues, J. M. Otalora Goicochea, A. Otto, P. Owen, A. Oyanguren, A. Palano, F. Palombo, M. Palutan, J. Panman, A. Papanestis, M. Pappagallo, L. L. Pappalardo, C. Parkes, G. Passaleva, G. D. Patel, M. Patel, C. Patrignani, A. Pearce, A. Pellegrino, G. Penso, M. Pepe Altarelli, S. Perazzini, P. Perret, L. Pescatore, K. Petridis, A. Petrolini, E. Picatoste Olloqui, B. Pietrzyk, T. Pilař, D. Pinci, A. Pistone, S. Playfer, M. Plo Casasus, T. Poikela, F. Polci, A. Poluektov, I. Polyakov, E. Polycarpo, A. Popov, D. Popov, B. Popovici, C. Potterat, E. Price, J. D. Price, J. Prisciandaro, A. Pritchard, C. Prouve, V. Pugatch, A. Puig Navarro, G. Punzi, W. Qian, R. Quagliani, B. Rachwal, J. H. Rademacker, B. Rakotomiaramanana, M. Rama, M. S. Rangel, I. Raniuk, N. Rauschmayr, G. Raven, F. Redi, S. Reichert, M. M. Reid, A. C. dos Reis, S. Ricciardi, S. Richards, M. Rihl, K. Rinnert, V. Rives Molina, P. Robbe, A. B. Rodrigues, E. Rodrigues, J. A. Rodriguez Lopez, P. Rodriguez Perez, S. Roiser, V. Romanovsky, A. Romero Vidal, M. Rotondo, J. Rouvinet, T. Ruf, H. Ruiz, P. Ruiz Valls, J. J. Saborido Silva, N. Sagidova, P. Sail, B. Saitta, V. Salustino Guimaraes, C. Sanchez Mayordomo, B. Sanmartin Sedes, R. Santacesaria, C. Santamarina Rios, E. Santovetti, A. Sarti, C. Satriano, A. Satta, D. M. Saunders, D. Savrina, M. Schiller, H. Schindler, M. Schlupp, M. Schmelling, B. Schmidt, O. Schneider, A. Schopper, M.-H. Schune, R. Schwemmer, B. Sciascia, A. Sciubba, A. Semennikov, I. Sepp, N. Serra, J. Serrano, L. Sestini, P. Seyfert, M. Shapkin, I. Shapoval, Y. Shcheglov, T. Shears, L. Shekhtman, V. Shevchenko, A. Shires, R. Silva Coutinho, G. Simi, M. Sirendi, N. Skidmore, I. Skillicorn, T. Skwarnicki, N. A. Smith, E. Smith, J. Smith, M. Smith, H. Snoek, M. D. Sokoloff, F. J. P. Soler, F. Soomro, D. Souza, B. Souza De Paula, B. Spaan, P. Spradlin, S. Sridharan, F. Stagni, M. Stahl, S. Stahl, O. Steinkamp, O. Stenyakin, F. Sterpka, S. Stevenson, S. Stoica, S. Stone, B. Storaci, S. Stracka, M. Straticiuc, U. Straumann, R. Stroili, L. Sun, W. Sutcliffe, K. Swientek, S. Swientek, V. Syropoulos, M. Szczekowski, P. Szczypka, T. Szumlak, S. T’Jampens, M. Teklishyn, G. Tellarini, F. Teubert, C. Thomas, E. Thomas, J. van Tilburg, V. Tisserand, M. Tobin, J. Todd, S. Tolk, L. Tomassetti, D. Tonelli, S. Topp-Joergensen, N. Torr, E. Tournefier, S. Tourneur, K. Trabelsi, M. T. Tran, M. Tresch, A. Trisovic, A. Tsaregorodtsev, P. Tsopelas, N. Tuning, A. Ukleja, A. Ustyuzhanin, U. Uwer, C. Vacca, V. Vagnoni, G. Valenti, A. Vallier, R. Vazquez Gomez, P. Vazquez Regueiro, C. Vázquez Sierra, S. Vecchi, J. J. Velthuis, M. Veltri, G. Veneziano, M. Vesterinen, J. V. Viana Barbosa, B. Viaud, D. Vieira, M. Vieites Diaz, X. Vilasis-Cardona, A. Vollhardt, D. Volyanskyy, D. Voong, A. Vorobyev, V. Vorobyev, C. Voß, J. A. de Vries, R. Waldi, C. Wallace, R. Wallace, J. Walsh, S. Wandernoth, J. Wang, D. R. Ward, N. K. Watson, D. Websdale, A. Weiden, M. Whitehead, D. Wiedner, G. Wilkinson, M. Wilkinson, M. Williams, M. P. Williams, F. F. Wilson, J. Wimberley, J. Wishahi, W. Wislicki, M. Witek, G. Wormser, S. A. Wotton, S. Wright, K. Wyllie, Y. Xie, Z. Xu, Z. Yang, X. Yuan, O. Yushchenko, M. Zangoli, M. Zavertyaev, L. Zhang, Y. Zhang, A. Zhelezov, A. Zhokhov, and L. Zhong
Subjects: Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: The angular distribution of the dimuon system of the decays.
Published: 2018
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29. Integrated Molecular Characterization of Testicular Germ Cell Tumors

Author: Hui Shen, Juliann Shih, Daniel P. Hollern, Linghua Wang, Reanne Bowlby, Satish K. Tickoo, Vésteinn Thorsson, Andrew J. Mungall, Yulia Newton, Apurva M. Hegde, Joshua Armenia, Francisco Sánchez-Vega, John Pluta, Louise C. Pyle, Rohit Mehra, Victor E. Reuter, Guilherme Godoy, Jeffrey Jones, Carl S. Shelley, Darren R. Feldman, Daniel O. Vidal, Davor Lessel, Tomislav Kulis, Flavio M. Cárcano, Kristen M. Leraas, Tara M. Lichtenberg, Denise Brooks, Andrew D. Cherniack, Juok Cho, David I. Heiman, Katayoon Kasaian, Minwei Liu, Michael S. Noble, Liu Xi, Hailei Zhang, Wanding Zhou, Jean C. ZenKlusen, Carolyn M. Hutter, Ina Felau, Jiashan Zhang, Nikolaus Schultz, Gad Getz, Matthew Meyerson, Joshua M. Stuart, Rehan Akbani, David A. Wheeler, Peter W. Laird, Katherine L. Nathanson, Victoria K. Cortessis, Katherine A. Hoadley, David Wheeler, Daniel Hughes, Kyle Covington, Joy C. Jayaseelan, Viktoriya Korchina, Lora Lewis, Jianhong Hu, HarshaVardhan Doddapaneni, Donna Muzny, Richard Gibbs, Daniel Hollern, Benjamin G. Vincent, Shengjie Chai, Christof C. Smith, J. Todd Auman, Yan Shi, Shaowu Meng, Tara Skelly, Donghui Tan, Umadevi Veluvolu, Piotr A. Mieczkowski, Corbin D. Jones, Matthew D. Wilkerson, Saianand Balu, Tom Bodenheimer, Alan P. Hoyle, Stuart R. Jefferys, Lisle E. Mose, Janae V. Simons, Matthew G. Soloway, Jeffrey Roach, Joel S. Parker, D. Neil Hayes, Charles M. Perou, Gordon Saksena, Carrie Cibulskis, Steven E. Schumacher, Rameen Beroukhim, Stacey B. Gabriel, Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Dorothy Cheung, Eric Chuah, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Yussanne Ma, Michael Mayo, Richard A. Moore, A. Gordon Robertson, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Tina Wong, Marco A. Marra, Daniel J. Weisenberger, David J. Van Den Berg, Phillip H. Lai, Mario Berrios, Andrea Holbrook, Moiz S. Bootwalla, Dennis T. Maglinte, Debyani Chakravarty, Jianjiong Gao, Zachary Heins, Ritika Kundra, Angelica Ochoa, Chris Sander, Marc Ladanyi, Vesteinn Thorsson, Amie J. Radenbaugh, Nils Gehlenborg, Doug Voet, Pei Lin, Scott Frazer, Jaegil Kim, Michael S. Lawrence, Sam Meier, Timothy Defreitas, Lynda Chin, John N. Weinstein, Wenbin Liu, Gordon B. Mills, Yiling Lu, Leendert Looijenga, Alan H. Bryce, André L. Carvalho, Darren Feldman, Michael Ittmann, Seth Lerner, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Carmen Helsel, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Sandra Cottingham, David Chesla, Charles Saller, Katherine Tarvin, Luiz Fernando Lopes, Cristovam Scapulatempo-Neto, Natália D.A. Aredes, Wolter Oosterhuis, Ad Gillis, Hans Stoop, Wil Eijkenboom, George Sandusky, Sue Ellen Martin, Manju Aron, Siamak Daneshmand, Hooman Djaladat, David Quinn, Tanya Dorff, Jochen K. Lennerz, Leigh B. Thorne, Marija Gamulin, Zeljko Kastelan, Tvrtko Hudolin, Christian Kubisch, Lori Boice, Mei Huang, Amy H. Perou, W. Kimryn Rathmell, Todd Pihl, Yunhu Wan, Qiang Sun, Rashi Naresh, Sudha Chudamani, Jia Liu, Laxmi Lolla, Ye Wu, Martin L. Ferguson, Jean C. Zenklusen, Jiashan (Julia) Zhang, Margi Sheth, John A. Demchok, Liming Yang, Zhining Wang, Roy Tarnuzzer, Heidi J. Sofia, and Tanja M. Davidsen
Subjects: Biology (General), QH301-705.5
Abstract: Summary: We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance—KIT, KRAS, and NRAS—exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KIT mutations, increased immune infiltration, globally demethylated DNA, and decreased KRAS copy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas. : Shen et al. identify molecular characteristics that classify testicular germ cell tumor types, including a separate subset of seminomas defined by KIT mutations. This provides a set of candidate biomarkers for risk stratification and potential therapeutic targeting. Keywords: The Cancer Genome Atlas, testicular germ cell tumors, seminoma, nonseminoma, DNA methylation, exome sequencing, KIT, copy number, miR-375
Published: 2018
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30. Genome-wide protein phylogenies for four African cichlid species

Author: Ajay Ramakrishnan Varadarajan, Rohini Mopuri, J. Todd Streelman, and Patrick T. McGrath
Subjects: Evolution, QH359-425
Abstract: Abstract Background The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species. Results We used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented. Conclusion These phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.
Published: 2018
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31. CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Author: Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, J. Todd Campbell, Josh Udall, and Dorrie Main
Subjects: bioinformatics, crop improvement, big data, whole genome sequence, genotype, analysis, Botany, QK1-989
Abstract: Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
Published: 2021
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32. Plasma Lipidomic Patterns in Patients with Symptomatic Coronary Microvascular Dysfunction

Author: Jonathan R. Lindner, Brian P. Davidson, Zifeng Song, Claudia S. Maier, Jessica Minnier, Jan Frederick Stevens, Maros Ferencik, Sahar Taqui, J. Todd Belcik, Federico Moccetti, Michael Layoun, Paul Spellman, Mitchell S. Turker, Hagai Tavori, Sergio Fazio, Jacob Raber, and Gerd Bobe
Subjects: coronary artery disease, lipidomics, microvascular dysfunction, myocardial contrast echocardiography, myocardial ischemia, Microbiology, QR1-502
Abstract: Coronary microvascular dysfunction (MVD) is a syndrome of abnormal regulation of vascular tone, particularly during increased metabolic demand. While there are several risk factors for MVD, some of which are similar to those for coronary artery disease (CAD), the cause of MVD is not understood. We hypothesized that MVD in symptomatic non-elderly subjects would be characterized by specific lipidomic profiles. Subjects (n = 20) aged 35–60 years and referred for computed tomography coronary angiography (CTA) for chest pain but who lacked obstructive CAD (>50% stenosis), underwent quantitative regadenoson stress-rest myocardial contrast echocardiography (MCE) perfusion imaging for MVD assessment. The presence of MVD defined by kinetic analysis of MCE data was correlated with lipidomic profiles in plasma measured by liquid chromatography and high-resolution mass spectrometry. Nine of twenty subjects had evidence of MVD, defined by reduced hyperemic perfusion versus other subjects (beta-value 1.62 ± 0.44 vs. 2.63 ± 0.99 s−1, p = 0.009). Neither the presence of high-risk but non-obstructive CAD on CTA, nor CAD risk factors were different for those with versus without MVD. Lipidomic analysis revealed that patients with MVD had lower concentrations of long-carbon chain triacylglycerols and diacylglycerols, and higher concentrations of short-chain triacylglycerols. The diacylglycerol containing stearic and linoleic acid classified all participants correctly. We conclude that specific lipidomic plasma profiles occur in MVD involving saturated long-chain fatty acid-containing acylglycerols that are distinctly different from those in non-obstructive CAD. These patterns could be used to better characterize the pathobiology and potential treatments for this condition.
Published: 2021
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33. Deep Underground Neutrino Experiment (DUNE) Near Detector Conceptual Design Report

Author: A. Abed Abud, B. Abi, R. Acciarri, M. A. Acero, G. Adamov, D. Adams, M. Adinolfi, A. Aduszkiewicz, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, M. Alrashed, C. Alt, A. Alton, P. Amedo, J. Anderson, C. Andreopoulos, M. P. Andrews, F. Andrianala, S. Andringa, N. Anfimov, A. Ankowski, M. Antonova, S. Antusch, A. Aranda-Fernandez, A. Ariga, L. O. Arnold, M. A. Arroyave, J. Asaadi, A. Aurisano, V. Aushev, D. Autiero, M. Ayala-Torres, F. Azfar, A. Back, H. Back, J. J. Back, C. Backhouse, P. Baesso, I. Bagaturia, L. Bagby, S. Balasubramanian, P. Baldi, B. Baller, B. Bambah, F. Barao, G. Barenboim, G. J. Barker, W. Barkhouse, C. Barnes, G. Barr, J. Barranco Monarca, N. Barros, J. L. Barrow, A. Basharina-Freshville, A. Bashyal, V. Basque, E. Belchior, J. B. R. Battat, F. Battisti, F. Bay, J. L. Bazo Alba, J. F. Beacom, E. Bechetoille, B. Behera, L. Bellantoni, G. Bellettini, V. Bellini, O. Beltramello, D. Belver, N. Benekos, F. Bento Neves, S. Berkman, P. Bernardini, R. M. Berner, H. Berns, S. Bertolucci, M. Betancourt, A. Betancur Rodríguez, M. Bhattacharjee, S. Bhuller, B. Bhuyan, S. Biagi, J. Bian, M. Biassoni, K. Biery, B. Bilki, M. Bishai, A. Bitadze, A. Blake, F. D. M. Blaszczyk, G. C. Blazey, E. Blucher, J. Boissevain, S. Bolognesi, T. Bolton, L. Bomben, M. Bonesini, M. Bongrand, F. Bonini, A. Booth, C. Booth, S. Bordoni, A. Borkum, T. Boschi, N. Bostan, P. Bour, C. Bourgeois, S. B. Boyd, D. Boyden, J. Bracinik, D. Braga, D. Brailsford, A. Brandt, J. Bremer, C. Brew, E. Brianne, S. J. Brice, C. Brizzolari, C. Bromberg, G. Brooijmans, J. Brooke, A. Bross, G. Brunetti, M. Brunetti, N. Buchanan, H. Budd, I. Cagnoli, D. Caiulo, P. Calafiura, J. Calcutt, M. Calin, S. Calvez, E. Calvo, A. Caminata, M. Campanelli, K. Cankocak, D. Caratelli, G. Carini, B. Carlus, P. Carniti, I. Caro Terrazas, H. Carranza, T. Carroll, J. F. Castaño Forero, A. Castillo, C. Castromonte, E. Catano-Mur, C. Cattadori, F. Cavalier, F. Cavanna, S. Centro, G. Cerati, A. Cervelli, A. Cervera Villanueva, M. Chalifour, A. Chappell, E. Chardonnet, N. Charitonidis, A. Chatterjee, S. Chattopadhyay, H. Chen, M. Chen, Y. Chen, Z. Chen, D. Cherdack, C. Chi, S. Childress, A. Chiriacescu, G. Chisnall, K. Cho, S. Choate, D. Chokheli, S. Choubey, A. Christensen, D. Christian, G. Christodoulou, A. Chukanov, E. Church, V. Cicero, P. Clarke, T. E. Coan, A. G. Cocco, J. A. B. Coelho, E. Conley, R. Conley, J. M. Conrad, M. Convery, S. Copello, L. Corwin, L. Cremaldi, L. Cremonesi, J. I. Crespo-Anadón, E. Cristaldo, R. Cross, A. Cudd, C. Cuesta, Y. Cui, D. Cussans, M. Dabrowski, O. Dalager, H. da Motta, L. Da Silva Peres, C. David, Q. David, G. S. Davies, S. Davini, J. Dawson, K. De, R. M. De Almeida, P. Debbins, I. De Bonis, M. P. Decowski, A. de Gouvêa, P. C. De Holanda, I. L. De Icaza Astiz, A. Deisting, P. De Jong, A. Delbart, D. Delepine, M. Delgado, A. Dell’Acqua, P. De Lurgio, J. R. T. de Mello Neto, D. M. DeMuth, S. Dennis, C. Densham, G. W. Deptuch, A. De Roeck, V. De Romeri, G. De Souza, R. Dharmapalan, F. Diaz, J. S. Díaz, S. Di Domizio, L. Di Giulio, P. Ding, L. Di Noto, C. Distefano, R. Diurba, M. Diwan, Z. Djurcic, N. Dokania, S. Dolan, M. J. Dolinski, L. Domine, D. Douglas, D. Douillet, G. Drake, F. Drielsma, D. Duchesneau, K. Duffy, P. Dunne, T. Durkin, H. Duyang, O. Dvornikov, D. A. Dwyer, A. S. Dyshkant, M. Eads, A. Earle, D. Edmunds, J. Eisch, L. Emberger, S. Emery, A. Ereditato, C. O. Escobar, G. Eurin, J. J. Evans, E. Ewart, A. C. Ezeribe, K. Fahey, A. Falcone, C. Farnese, Y. Farzan, J. Felix, M. Fernandes Carneiro da Silva, E. Fernandez-Martinez, P. Fernandez Menendez, F. Ferraro, L. Fields, F. Filthaut, A. Fiorentini, R. S. Fitzpatrick, W. Flanagan, B. Fleming, R. Flight, D. V. Forero, J. Fowler, W. Fox, J. Franc, K. Francis, D. Franco, J. Freeman, J. Freestone, J. Fried, A. Friedland, S. Fuess, I. Furic, A. P. Furmanski, A. Gabrielli, A. Gago, H. Gallagher, A. Gallas, A. Gallego-Ros, N. Gallice, V. Galymov, E. Gamberini, T. Gamble, R. Gandhi, R. Gandrajula, F. Gao, S. Gao, D. Garcia-Gamez, M. Á. García-Peris, S. Gardiner, D. Gastler, G. Ge, B. Gelli, A. Gendotti, S. Gent, Z. Ghorbani-Moghaddam, D. Gibin, I. Gil-Botella, S. Gilligan, C. Girerd, A. K. Giri, D. Gnani, O. Gogota, M. Gold, S. Gollapinni, K. Gollwitzer, R. A. Gomes, L. V. Gomez Bermeo, L. S. Gomez Fajardo, F. Gonnella, J. A. Gonzalez-Cuevas, D. Gonzalez-Diaz, M. Gonzalez-Lopez, M. C. Goodman, O. Goodwin, S. Goswami, C. Gotti, E. Goudzovski, C. Grace, M. Graham, R. Gran, E. Granados, P. Granger, A. Grant, C. Grant, D. Gratieri, P. Green, L. Greenler, J. Greer, W. C. Griffith, M. Groh, J. Grudzinski, K. Grzelak, W. Gu, V. Guarino, R. Guenette, E. Guerard, M. Guerzoni, A. Guglielmi, B. Guo, K. K. Guthikonda, R. Gutierrez, P. Guzowski, M. M. Guzzo, S. Gwon, A. Habig, H. Hadavand, R. Haenni, A. Hahn, J. Haiston, P. Hamacher-Baumann, T. Hamernik, P. Hamilton, J. Han, D. A. Harris, J. Hartnell, J. Harton, T. Hasegawa, C. Hasnip, R. Hatcher, K. W. Hatfield, A. Hatzikoutelis, C. Hayes, E. Hazen, A. Heavey, K. M. Heeger, J. Heise, K. Hennessy, S. Henry, M. A. Hernandez Morquecho, K. Herner, L. Hertel, J. Hewes, A. Higuera, T. Hill, S. J. Hillier, A. Himmel, J. Hoff, C. Hohl, A. Holin, E. Hoppe, G. A. Horton-Smith, M. Hostert, A. Hourlier, B. Howard, R. Howell, J. Huang, J. Hugon, G. Iles, N. Ilic, A. M. Iliescu, R. Illingworth, G. Ingratta, A. Ioannisian, L. Isenhower, R. Itay, A. Izmaylov, S. Jackson, V. Jain, E. James, B. Jargowsky, F. Jediny, D. Jena, Y. S. Jeong, C. Jesús-Valls, X. Ji, L. Jiang, S. Jiménez, A. Jipa, R. Johnson, N. Johnston, B. Jones, S. B. Jones, M. Judah, C. K. Jung, T. Junk, Y. Jwa, M. Kabirnezhad, A. Kaboth, I. Kadenko, I. Kakorin, F. Kamiya, N. Kaneshige, G. Karagiorgi, G. Karaman, A. Karcher, M. Karolak, Y. Karyotakis, S. Kasai, S. P. Kasetti, L. Kashur, N. Kazaryan, E. Kearns, P. Keener, K. J. Kelly, E. Kemp, O. Kemularia, W. Ketchum, S. H. Kettell, M. Khabibullin, A. Khotjantsev, A. Khvedelidze, D. Kim, B. King, B. Kirby, M. Kirby, J. Klein, K. Koehler, L. W. Koerner, S. Kohn, P. P. Koller, L. Kolupaeva, M. Kordosky, T. Kosc, U. Kose, V. A. Kostelecký, K. Kothekar, F. Krennrich, I. Kreslo, Y. Kudenko, V. A. Kudryavtsev, S. Kulagin, J. Kumar, P. Kumar, R. Kumar, P. Kunze, N. Kurita, C. Kuruppu, V. Kus, T. Kutter, A. Lambert, B. Land, K. Lande, C. E. Lane, K. Lang, T. Langford, J. Larkin, P. Lasorak, D. Last, C. Lastoria, A. Laundrie, G. Laurenti, A. Lawrence, I. Lazanu, R. LaZur, T. Le, S. Leardini, J. Learned, P. LeBrun, T. LeCompte, G. Lehmann Miotto, R. Lehnert, M. A. Leigui de Oliveira, M. Leitner, L. Li, S. W. Li, T. Li, Y. Li, H. Liao, C. S. Lin, Q. Lin, S. Lin, A. Lister, B. R. Littlejohn, J. Liu, S. Lockwitz, T. Loew, M. Lokajicek, I. Lomidze, K. Long, K. Loo, D. Lorca, T. Lord, J. M. LoSecco, W. C. Louis, X. G. Lu, K. B. Luk, X. Luo, N. Lurkin, T. Lux, V. P. Luzio, D. MacFarlane, A. A. Machado, P. Machado, C. T. Macias, J. R. Macier, A. Maddalena, A. Madera, P. Madigan, S. Magill, K. Mahn, A. Maio, A. Major, J. A. Maloney, G. Mandrioli, R. C. Mandujano, J. Maneira, L. Manenti, S. Manly, A. Mann, K. Manolopoulos, M. Manrique Plata, V. N. Manyam, L. Manzanillas, M. Marchan, A. Marchionni, W. Marciano, D. Marfatia, C. Mariani, J. Maricic, R. Marie, F. Marinho, A. D. Marino, D. Marsden, M. Marshak, C. M. Marshall, J. Marshall, J. Marteau, J. Martin-Albo, N. Martinez, D. A. Martinez Caicedo, S. Martynenko, K. Mason, A. Mastbaum, M. Masud, S. Matsuno, J. Matthews, C. Mauger, N. Mauri, K. Mavrokoridis, I. Mawby, R. Mazza, A. Mazzacane, E. Mazzucato, T. McAskill, E. McCluskey, N. McConkey, K. S. McFarland, C. McGrew, A. McNab, A. Mefodiev, P. Mehta, P. Melas, O. Mena, S. Menary, H. Mendez, D. P. Méndez, A. Menegolli, G. Meng, M. D. Messier, W. Metcalf, T. Mettler, M. Mewes, H. Meyer, T. Miao, G. Michna, T. Miedema, J. Migenda, V. Mikola, R. Milincic, W. Miller, J. Mills, C. Milne, O. Mineev, O. G. Miranda, S. Miryala, C. S. Mishra, S. R. Mishra, A. Mislivec, D. Mladenov, I. Mocioiu, K. Moffat, N. Moggi, R. Mohanta, T. A. Mohayai, N. Mokhov, J. Molina, L. Molina Bueno, A. Montanari, C. Montanari, D. Montanari, E. Montagna, L. M. Montano Zetina, J. Moon, M. Mooney, A. F. Moor, D. Moreno, C. Morris, C. Mossey, E. Motuk, C. A. Moura, J. Mousseau, W. Mu, L. Mualem, J. Mueller, M. Muether, S. Mufson, F. Muheim, A. Muir, M. Mulhearn, D. Munford, H. Muramatsu, S. Murphy, J. Musser, J. Nachtman, S. Nagu, M. Nalbandyan, R. Nandakumar, D. Naples, S. Narita, D. Navas-Nicolás, A. Navrer-Agasson, N. Nayak, M. Nebot-Guinot, K. Negishi, J. K. Nelson, J. Nesbit, M. Nessi, D. Newbold, M. Newcomer, D. Newhart, H. Newton, M. Niccolo, R. Nichol, F. Nicolas-Arnaldos, M. Nicoletta, E. Niner, K. Nishimura, A. Norman, A. Norrick, R. Northrop, P. Novella, J. A. Nowak, M. Oberling, J. P. Ochoa-Ricoux, A. Olivares Del Campo, A. Olivier, A. Olshevskiy, Y. Onel, Y. Onishchuk, J. Ott, L. Pagani, S. Pakvasa, G. Palacio, O. Palamara, S. Palestini, J. M. Paley, M. Pallavicini, C. Palomares, J. L. Palomino-Gallo, E. Pantic, V. Paolone, V. Papadimitriou, R. Papaleo, A. Papanestis, S. Paramesvaran, S. Parke, Z. Parsa, M. Parvu, S. Pascoli, L. Pasqualini, J. Pasternak, J. Pater, C. Patrick, L. Patrizii, R. B. Patterson, S. J. Patton, T. Patzak, A. Paudel, B. Paulos, L. Paulucci, Z. Pavlovic, G. Pawloski, D. Payne, V. Pec, S. J. M. Peeters, E. Pennacchio, A. Penzo, O. L. G. Peres, J. Perry, D. Pershey, G. Pessina, G. Petrillo, C. Petta, R. Petti, F. Piastra, L. Pickering, F. Pietropaolo, R. Plunkett, R. Poling, X. Pons, N. Poonthottathil, F. Poppi, S. Pordes, J. Porter, M. Potekhin, R. Potenza, B. V. K. S. Potukuchi, J. Pozimski, M. Pozzato, S. Prakash, T. Prakash, S. Prince, D. Pugnere, X. Qian, M. C. Queiroga Bazetto, J. L. Raaf, V. Radeka, J. Rademacker, B. Radics, A. Rafique, E. Raguzin, M. Rai, M. Rajaoalisoa, I. Rakhno, A. Rakotonandrasana, L. Rakotondravohitra, Y. A. Ramachers, R. Rameika, M. A. Ramirez Delgado, B. Ramson, A. Rappoldi, G. Raselli, P. Ratoff, S. Raut, R. F. Razakamiandra, J. S. Real, B. Rebel, M. Reggiani-Guzzo, T. Rehak, J. Reichenbacher, S. D. Reitzner, H. Rejeb Sfar, A. Renshaw, S. Rescia, F. Resnati, A. Reynolds, C. Riccio, G. Riccobene, L. C. J. Rice, J. Ricol, A. Rigamonti, Y. Rigaut, D. Rivera, L. Rochester, M. Roda, P. Rodrigues, M. J. Rodriguez Alonso, E. Rodriguez Bonilla, J. Rodriguez Rondon, S. Rosauro-Alcaraz, M. Rosenberg, P. Rosier, B. Roskovec, M. Rossella, J. Rout, P. Roy, S. Roy, A. Rubbia, C. Rubbia, F. C. Rubio, B. Russell, D. Ruterbories, R. Saakyan, S. Sacerdoti, T. Safford, R. Sahay, N. Sahu, P. Sala, N. Samios, O. Samoylov, M. C. Sanchez, D. A. Sanders, D. Sankey, S. Santana, M. Santos-Maldonado, N. Saoulidou, P. Sapienza, C. Sarasty, I. Sarcevic, G. Savage, V. Savinov, A. Scaramelli, A. Scarff, A. Scarpelli, T. Schaffer, H. Schellman, P. Schlabach, D. Schmitz, K. Scholberg, A. Schukraft, E. Segreto, J. Sensenig, I. Seong, A. Sergi, D. Sgalaberna, M. H. Shaevitz, S. Shafaq, M. Shamma, R. Sharankova, H. R. Sharma, R. Sharma, T. Shaw, C. Shepherd-Themistocleous, S. Shin, D. Shooltz, R. Shrock, L. Simard, F. Simon, N. Simos, J. Sinclair, G. Sinev, J. Singh, V. Singh, R. Sipos, F. W. Sippach, G. Sirri, A. Sitraka, K. Siyeon, K. Skarpaas VIII, A. Smith, E. Smith, P. Smith, J. Smolik, M. Smy, E. L. Snider, P. Snopok, M. Soares Nunes, H. Sobel, M. Soderberg, C. J. Solano Salinas, S. Söldner-Rembold, S. Soleti, N. Solomey, V. Solovov, W. E. Sondheim, M. Sorel, J. Soto-Oton, A. Sousa, K. Soustruznik, F. Spagliardi, M. Spanu, J. Spitz, N. J. C. Spooner, K. Spurgeon, R. Staley, M. Stancari, L. Stanco, R. Stanley, R. Stein, H. M. Steiner, J. Stewart, B. Stillwell, J. Stock, F. Stocker, T. Stokes, M. Strait, T. Strauss, S. Striganov, A. Stuart, J. G. Suarez, H. Sullivan, D. Summers, A. Surdo, V. Susic, L. Suter, C. M. Sutera, R. Svoboda, B. Szczerbinska, A. M. Szelc, R. Talaga, H. A. Tanaka, B. Tapia Oregui, A. Tapper, S. Tariq, E. Tatar, R. Tayloe, A. M. Teklu, M. Tenti, K. Terao, C. A. Ternes, F. Terranova, G. Testera, A. Thea, J. L. Thompson, C. Thorn, S. C. Timm, J. Todd, A. Tonazzo, D. Torbunov, M. Torti, M. Tortola, F. Tortorici, D. Totani, M. Toups, C. Touramanis, N. Tosi, R. Travaglini, J. Trevor, S. Trilov, W. H. Trzaska, Y. T. Tsai, Z. Tsamalaidze, K. V. Tsang, N. Tsverava, S. Tufanli, C. Tull, E. Tyley, M. Tzanov, M. A. Uchida, J. Urheim, T. Usher, S. Uzunyan, M. R. Vagins, P. Vahle, G. A. Valdiviesso, E. Valencia, P. Valerio, Z. Vallari, J. W. F. Valle, S. Vallecorsa, R. Van Berg, R. G. Van de Water, F. Varanini, D. Vargas, G. Varner, J. Vasel, S. Vasina, G. Vasseur, N. Vaughan, K. Vaziri, S. Ventura, A. Verdugo, S. Vergani, M. A. Vermeulen, M. Verzocchi, M. Vicenzi, H. Vieira de Souza, C. Vignoli, C. Vilela, B. Viren, T. Vrba, T. Wachala, A. V. Waldron, M. Wallbank, H. Wang, J. Wang, L. Wang, M. H. L. S. Wang, Y. Wang, K. Warburton, D. Warner, M. Wascko, D. Waters, A. Watson, P. Weatherly, A. Weber, M. Weber, H. Wei, A. Weinstein, D. Wenman, M. Wetstein, A. White, L. H. Whitehead, D. Whittington, M. J. Wilking, C. Wilkinson, Z. Williams, F. Wilson, R. J. Wilson, J. Wolcott, T. Wongjirad, A. Wood, K. Wood, E. Worcester, M. Worcester, C. Wret, W. Wu, Y. Xiao, E. Yandel, G. Yang, K. Yang, S. Yang, T. Yang, A. Yankelevich, N. Yershov, K. Yonehara, T. Young, B. Yu, H. Yu, J. Yu, W. Yuan, R. Zaki, J. Zalesak, L. Zambelli, B. Zamorano, A. Zani, L. Zazueta, G. Zeit, G. P. Zeller, J. Zennamo, K. Zeug, C. Zhang, M. Zhao, E. Zhivun, G. Zhu, P. Zilberman, E. D. Zimmerman, M. Zito, S. Zucchelli, J. Zuklin, V. Zutshi, R. Zwaska, and On behalf of the DUNE Collaboration
Subjects: neutrino, near detector, neutrino oscillations, Deep Underground Neutrino Experiment, DUNE, Physics, QC1-999, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: The Deep Underground Neutrino Experiment (DUNE) is an international, world-class experiment aimed at exploring fundamental questions about the universe that are at the forefront of astrophysics and particle physics research. DUNE will study questions pertaining to the preponderance of matter over antimatter in the early universe, the dynamics of supernovae, the subtleties of neutrino interaction physics, and a number of beyond the Standard Model topics accessible in a powerful neutrino beam. A critical component of the DUNE physics program involves the study of changes in a powerful beam of neutrinos, i.e., neutrino oscillations, as the neutrinos propagate a long distance. The experiment consists of a near detector, sited close to the source of the beam, and a far detector, sited along the beam at a large distance. This document, the DUNE Near Detector Conceptual Design Report (CDR), describes the design of the DUNE near detector and the science program that drives the design and technology choices. The goals and requirements underlying the design, along with projected performance are given. It serves as a starting point for a more detailed design that will be described in future documents.
Published: 2021
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34. Planar polarized Rab35 functions as an oscillatory ratchet during cell intercalation in the Drosophila epithelium

Author: Cayla E. Jewett, Timothy E. Vanderleest, Hui Miao, Yi Xie, Roopa Madhu, Dinah Loerke, and J. Todd Blankenship
Subjects: Science
Abstract: Various stages of tissue morphogenesis involve the contraction of epithelial surfaces. Here, the authors identify the Rab GTPase Rab35 as an essential component of this contractile process, which functions as a membrane ratchet to ensure unidirectional movement of intercalating cells.
Published: 2017
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35. Erratum to: Measurement of forward J/ψ production cross-sections in pp collisions at s = 13 $$ \sqrt{s}=13 $$ TeV

Author: The LHCb collaboration, R. Aaij, B. Adeva, M. Adinolfi, A. Affolder, Z. Ajaltouni, S. Akar, J. Albrecht, F. Alessio, M. Alexander, S. Ali, G. Alkhazov, P. Alvarez Cartelle, A. A. Alves, S. Amato, S. Amerio, Y. Amhis, L. An, L. Anderlini, J. Anderson, G. Andreassi, M. Andreotti, J. E. Andrews, R. B. Appleby, O. Aquines Gutierrez, F. Archilli, P. d’Argent, A. Artamonov, M. Artuso, E. Aslanides, G. Auriemma, M. Baalouch, S. Bachmann, J. J. Back, A. Badalov, C. Baesso, W. Baldini, R. J. Barlow, C. Barschel, S. Barsuk, W. Barter, V. Batozskaya, V. Battista, A. Bay, L. Beaucourt, J. Beddow, F. Bedeschi, I. Bediaga, L. J. Bel, V. Bellee, N. Belloli, I. Belyaev, E. Ben-Haim, G. Bencivenni, S. Benson, J. Benton, A. Berezhnoy, R. Bernet, A. Bertolin, M.-O. Bettler, M. van Beuzekom, A. Bien, S. Bifani, P. Billoir, T. Bird, A. Birnkraut, A. Bizzeti, T. Blake, F. Blanc, J. Blouw, S. Blusk, V. Bocci, A. Bondar, N. Bondar, W. Bonivento, S. Borghi, M. Borsato, T. J. V. Bowcock, E. Bowen, C. Bozzi, S. Braun, M. Britsch, T. Britton, J. Brodzicka, N. H. Brook, E. Buchanan, A. Bursche, J. Buytaert, S. Cadeddu, R. Calabrese, M. Calvi, M. Calvo Gomez, P. Campana, D. Campora Perez, L. Capriotti, A. Carbone, G. Carboni, R. Cardinale, A. Cardini, P. Carniti, L. Carson, K. Carvalho Akiba, G. Casse, L. Cassina, L. Castillo Garcia, M. Cattaneo, Ch. Cauet, G. Cavallero, R. Cenci, M. Charles, Ph. Charpentier, M. Chefdeville, S. Chen, S.-F. Cheung, N. Chiapolini, M. Chrzaszcz, X. Cid Vidal, G. Ciezarek, P. E. L. Clarke, M. Clemencic, H. V. Cliff, J. Closier, V. Coco, J. Cogan, E. Cogneras, V. Cogoni, L. Cojocariu, G. Collazuol, P. Collins, A. Comerma-Montells, A. Contu, A. Cook, M. Coombes, S. Coquereau, G. Corti, M. Corvo, B. Couturier, G. A. Cowan, D. C. Craik, A. Crocombe, M. Cruz Torres, S. Cunliffe, R. Currie, C. D’Ambrosio, E. Dall’Occo, J. Dalseno, P. N. Y. David, A. Davis, K. De Bruyn, S. De Capua, M. De Cian, J. M. De Miranda, L. De Paula, P. De Simone, C.-T. Dean, D. Decamp, M. Deckenhoff, L. Del Buono, N. Déléage, M. Demmer, D. Derkach, O. Deschamps, F. Dettori, B. Dey, A. Di Canto, F. Di Ruscio, H. Dijkstra, S. Donleavy, F. Dordei, M. Dorigo, A. Dosil Suárez, D. Dossett, A. Dovbnya, K. Dreimanis, L. Dufour, G. Dujany, F. Dupertuis, P. Durante, R. Dzhelyadin, A. Dziurda, A. Dzyuba, S. Easo, U. Egede, V. Egorychev, S. Eidelman, S. Eisenhardt, U. Eitschberger, R. Ekelhof, L. Eklund, I. El Rifai, Ch. Elsasser, S. Ely, S. Esen, H. M. Evans, T. Evans, A. Falabella, C. Färber, N. Farley, S. Farry, R. Fay, D. Ferguson, V. Fernandez Albor, F. Ferrari, F. Ferreira Rodrigues, M. Ferro-Luzzi, S. Filippov, M. Fiore, M. Fiorini, M. Firlej, C. Fitzpatrick, T. Fiutowski, K. Fohl, P. Fol, M. Fontana, F. Fontanelli, R. Forty, O. Francisco, M. Frank, C. Frei, M. Frosini, J. Fu, E. Furfaro, A. Gallas Torreira, D. Galli, S. Gallorini, S. Gambetta, M. Gandelman, P. Gandini, Y. Gao, J. García Pardiñas, J. Garra Tico, L. Garrido, D. Gascon, C. Gaspar, R. Gauld, L. Gavardi, G. Gazzoni, D. Gerick, E. Gersabeck, M. Gersabeck, T. Gershon, Ph. Ghez, S. Gianì, V. Gibson, O. G. Girard, L. Giubega, V. V. Gligorov, C. Göbel, D. Golubkov, A. Golutvin, A. Gomes, C. Gotti, M. Grabalosa Gándara, R. Graciani Diaz, L. A. Granado Cardoso, E. Graugés, E. Graverini, G. Graziani, A. Grecu, E. Greening, S. Gregson, P. Griffith, L. Grillo, O. Grünberg, B. Gui, E. Gushchin, Yu. Guz, T. Gys, T. Hadavizadeh, C. Hadjivasiliou, G. Haefeli, C. Haen, S. C. Haines, S. Hall, B. Hamilton, X. Han, S. Hansmann-Menzemer, N. Harnew, S. T. Harnew, J. Harrison, J. He, T. Head, V. Heijne, K. Hennessy, P. Henrard, L. Henry, E. van Herwijnen, M. Heß, A. Hicheur, D. Hill, M. Hoballah, C. Hombach, W. Hulsbergen, T. Humair, N. Hussain, D. Hutchcroft, D. Hynds, M. Idzik, P. Ilten, R. Jacobsson, A. Jaeger, J. Jalocha, E. Jans, A. Jawahery, F. Jing, M. John, D. Johnson, C. R. Jones, C. Joram, B. Jost, N. Jurik, S. Kandybei, W. Kanso, M. Karacson, T. M. Karbach, S. Karodia, M. Kecke, M. Kelsey, I. R. Kenyon, M. Kenzie, T. Ketel, E. Khairullin, B. Khanji, C. Khurewathanakul, S. Klaver, K. Klimaszewski, O. Kochebina, M. Kolpin, I. Komarov, R. F. Koopman, P. Koppenburg, M. Kozeiha, L. Kravchuk, K. Kreplin, M. Kreps, G. Krocker, P. Krokovny, F. Kruse, W. Krzemien, W. Kucewicz, M. Kucharczyk, V. Kudryavtsev, A. K. Kuonen, K. Kurek, T. Kvaratskheliya, D. Lacarrere, G. Lafferty, A. Lai, D. Lambert, G. Lanfranchi, C. Langenbruch, B. Langhans, T. Latham, C. Lazzeroni, R. Le Gac, J. van Leerdam, J.-P. Lees, R. Lefèvre, A. Leflat, J. Lefrançois, E. Lemos Cid, O. Leroy, T. Lesiak, B. Leverington, Y. Li, T. Likhomanenko, M. Liles, R. Lindner, C. Linn, F. Lionetto, B. Liu, X. Liu, D. Loh, I. Longstaff, J. H. Lopes, D. Lucchesi, M. Lucio Martinez, H. Luo, A. Lupato, E. Luppi, O. Lupton, A. Lusiani, F. Machefert, F. Maciuc, O. Maev, K. Maguire, S. Malde, A. Malinin, G. Manca, G. Mancinelli, P. Manning, A. Mapelli, J. Maratas, J. F. Marchand, U. Marconi, C. Marin Benito, P. Marino, J. Marks, G. Martellotti, M. Martin, M. Martinelli, D. Martinez Santos, F. Martinez Vidal, D. Martins Tostes, A. Massafferri, R. Matev, A. Mathad, Z. Mathe, C. Matteuzzi, A. Mauri, B. Maurin, A. Mazurov, M. McCann, J. McCarthy, A. McNab, R. McNulty, B. Meadows, F. Meier, M. Meissner, D. Melnychuk, M. Merk, E Michielin, D. A. Milanes, M.-N. Minard, D. S. Mitzel, J. Molina Rodriguez, I. A. Monroy, S. Monteil, M. Morandin, P. Morawski, A. Mordà, M. J. Morello, J. Moron, A. B. Morris, R. Mountain, F. Muheim, D. Müller, J. Müller, K. Müller, V. Müller, M. Mussini, B. Muster, P. Naik, T. Nakada, R. Nandakumar, A. Nandi, I. Nasteva, M. Needham, N. Neri, S. Neubert, N. Neufeld, M. Neuner, A. D. Nguyen, T. D. Nguyen, C. Nguyen-Mau, V. Niess, R. Niet, N. Nikitin, T. Nikodem, A. Novoselov, D. P. O’Hanlon, A. Oblakowska-Mucha, V. Obraztsov, S. Ogilvy, O. Okhrimenko, R. Oldeman, C. J. G. Onderwater, B. Osorio Rodrigues, J. M. Otalora Goicochea, A. Otto, P. Owen, A. Oyanguren, A. Palano, F. Palombo, M. Palutan, J. Panman, A. Papanestis, M. Pappagallo, L. L. Pappalardo, C. Pappenheimer, W. Parker, C. Parkes, G. Passaleva, G. D. Patel, M. Patel, C. Patrignani, A. Pearce, A. Pellegrino, G. Penso, M. Pepe Altarelli, S. Perazzini, P. Perret, L. Pescatore, K. Petridis, A. Petrolini, M. Petruzzo, E. Picatoste Olloqui, B. Pietrzyk, T. Pilař, D. Pinci, A. Pistone, A. Piucci, S. Playfer, M. Plo Casasus, T. Poikela, F. Polci, A. Poluektov, I. Polyakov, E. Polycarpo, A. Popov, D. Popov, B. Popovici, C. Potterat, E. Price, J. D. Price, J. Prisciandaro, A. Pritchard, C. Prouve, V. Pugatch, A. Puig Navarro, G. Punzi, W. Qian, R. Quagliani, B. Rachwal, J. H. Rademacker, M. Rama, M. S. Rangel, I. Raniuk, N. Rauschmayr, G. Raven, F. Redi, S. Reichert, M. M. Reid, A. C. dos Reis, S. Ricciardi, S. Richards, M. Rihl, K. Rinnert, V. Rives Molina, P. Robbe, A. B. Rodrigues, E. Rodrigues, J. A. Rodriguez Lopez, P. Rodriguez Perez, S. Roiser, V. Romanovsky, A. Romero Vidal, J. W. Ronayne, M. Rotondo, J. Rouvinet, T. Ruf, P. Ruiz Valls, J. J. Saborido Silva, N. Sagidova, P. Sail, B. Saitta, V. Salustino Guimaraes, C. Sanchez Mayordomo, B. Sanmartin Sedes, R. Santacesaria, C. Santamarina Rios, M. Santimaria, E. Santovetti, A. Sarti, C. Satriano, A. Satta, D. M. Saunders, D. Savrina, M. Schiller, H. Schindler, M. Schlupp, M. Schmelling, T. Schmelzer, B. Schmidt, O. Schneider, A. Schopper, M. Schubiger, M.-H. Schune, R. Schwemmer, B. Sciascia, A. Sciubba, A. Semennikov, N. Serra, J. Serrano, L. Sestini, P. Seyfert, M. Shapkin, I. Shapoval, Y. Shcheglov, T. Shears, L. Shekhtman, V. Shevchenko, A. Shires, B. G. Siddi, R. Silva Coutinho, L. Silva de Oliveira, G. Simi, M. Sirendi, N. Skidmore, T. Skwarnicki, E. Smith, I. T. Smith, J. Smith, M. Smith, H. Snoek, M. D. Sokoloff, F. J. P. Soler, F. Soomro, D. Souza, B. Souza De Paula, B. Spaan, P. Spradlin, S. Sridharan, F. Stagni, M. Stahl, S. Stahl, S. Stefkova, O. Steinkamp, O. Stenyakin, S. Stevenson, S. Stoica, S. Stone, B. Storaci, S. Stracka, M. Straticiuc, U. Straumann, L. Sun, W. Sutcliffe, K. Swientek, S. Swientek, V. Syropoulos, M. Szczekowski, T. Szumlak, S. T’Jampens, A. Tayduganov, T. Tekampe, M. Teklishyn, G. Tellarini, F. Teubert, C. Thomas, E. Thomas, J. van Tilburg, V. Tisserand, M. Tobin, J. Todd, S. Tolk, L. Tomassetti, D. Tonelli, S. Topp-Joergensen, N. Torr, E. Tournefier, S. Tourneur, K. Trabelsi, M. T. Tran, M. Tresch, A. Trisovic, A. Tsaregorodtsev, P. Tsopelas, N. Tuning, A. Ukleja, A. Ustyuzhanin, U. Uwer, C. Vacca, V. Vagnoni, G. Valenti, A. Vallier, R. Vazquez Gomez, P. Vazquez Regueiro, C. Vázquez Sierra, S. Vecchi, J. J. Velthuis, M. Veltri, G. Veneziano, M. Vesterinen, B. Viaud, D. Vieira, M. Vieites Diaz, X. Vilasis-Cardona, V. Volkov, A. Vollhardt, D. Volyanskyy, D. Voong, A. Vorobyev, V. Vorobyev, C. Voß, J. A. de Vries, R. Waldi, C. Wallace, R. Wallace, J. Walsh, S. Wandernoth, J. Wang, D. R. Ward, N. K. Watson, D. Websdale, A. Weiden, M. Whitehead, G. Wilkinson, M. Wilkinson, M. Williams, M. P. Williams, T. Williams, F. F. Wilson, J. Wimberley, J. Wishahi, W. Wislicki, M. Witek, G. Wormser, S. A. Wotton, S. Wright, K. Wyllie, Y. Xie, Z. Xu, Z. Yang, J. Yu, X. Yuan, O. Yushchenko, M. Zangoli, M. Zavertyaev, L. Zhang, Y. Zhang, A. Zhelezov, A. Zhokhov, L. Zhong, and S. Zucchelli
Subjects: Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Published: 2017
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36. Erratum to: Measurements of prompt charm production cross-sections in pp collisions at s = 13 $$ \sqrt{s}=13 $$ TeV

Author: The LHCb collaboration, R. Aaij, C. Abellán Beteta, B. Adeva, M. Adinolfi, A. Affolder, Z. Ajaltouni, S. Akar, J. Albrecht, F. Alessio, M. Alexander, S. Ali, G. Alkhazov, P. Alvarez Cartelle, A. A. Alves, S. Amato, S. Amerio, Y. Amhis, L. An, L. Anderlini, J. Anderson, G. Andreassi, M. Andreotti, J. E. Andrews, R. B. Appleby, O. Aquines Gutierrez, F. Archilli, P. d’Argent, A. Artamonov, M. Artuso, E. Aslanides, G. Auriemma, M. Baalouch, S. Bachmann, J. J. Back, A. Badalov, C. Baesso, W. Baldini, R. J. Barlow, C. Barschel, S. Barsuk, W. Barter, V. Batozskaya, V. Battista, A. Bay, L. Beaucourt, J. Beddow, F. Bedeschi, I. Bediaga, L. J. Bel, V. Bellee, N. Belloli, I. Belyaev, E. Ben-Haim, G. Bencivenni, S. Benson, J. Benton, A. Berezhnoy, R. Bernet, A. Bertolin, M.-O. Bettler, M. van Beuzekom, A. Bien, S. Bifani, P. Billoir, T. Bird, A. Birnkraut, A. Bizzeti, T. Blake, F. Blanc, J. Blouw, S. Blusk, V. Bocci, A. Bondar, N. Bondar, W. Bonivento, S. Borghi, M. Borsato, T. J. V. Bowcock, E. Bowen, C. Bozzi, S. Braun, M. Britsch, T. Britton, J. Brodzicka, N. H. Brook, E. Buchanan, C. Burr, A. Bursche, J. Buytaert, S. Cadeddu, R. Calabrese, M. Calvi, M. Calvo Gomez, P. Campana, D. Campora Perez, L. Capriotti, A. Carbone, G. Carboni, R. Cardinale, A. Cardini, P. Carniti, L. Carson, K. Carvalho Akiba, G. Casse, L. Cassina, L. Castillo Garcia, M. Cattaneo, Ch. Cauet, G. Cavallero, R. Cenci, M. Charles, Ph. Charpentier, M. Chefdeville, S. Chen, S.-F. Cheung, N. Chiapolini, M. Chrzaszcz, X. Cid Vidal, G. Ciezarek, P. E. L. Clarke, M. Clemencic, H. V. Cliff, J. Closier, V. Coco, J. Cogan, E. Cogneras, V. Cogoni, L. Cojocariu, G. Collazuol, P. Collins, A. Comerma-Montells, A. Contu, A. Cook, M. Coombes, S. Coquereau, G. Corti, M. Corvo, B. Couturier, G. A. Cowan, D. C. Craik, A. Crocombe, M. Cruz Torres, S. Cunliffe, R. Currie, C. D’Ambrosio, E. Dall’Occo, J. Dalseno, P. N. Y. David, A. Davis, O. De Aguiar Francisco, K. De Bruyn, S. De Capua, M. De Cian, J. M. De Miranda, L. De Paula, P. De Simone, C.-T. Dean, D. Decamp, M. Deckenhoff, L. Del Buono, N. Déléage, M. Demmer, D. Derkach, O. Deschamps, F. Dettori, B. Dey, A. Di Canto, F. Di Ruscio, H. Dijkstra, S. Donleavy, F. Dordei, M. Dorigo, A. Dosil Suárez, D. Dossett, A. Dovbnya, K. Dreimanis, L. Dufour, G. Dujany, F. Dupertuis, P. Durante, R. Dzhelyadin, A. Dziurda, A. Dzyuba, S. Easo, U. Egede, V. Egorychev, S. Eidelman, S. Eisenhardt, U. Eitschberger, R. Ekelhof, L. Eklund, I. El Rifai, Ch. Elsasser, S. Ely, S. Esen, H. M. Evans, T. Evans, A. Falabella, C. Färber, N. Farley, S. Farry, R. Fay, D. Ferguson, V. Fernandez Albor, F. Ferrari, F. Ferreira Rodrigues, M. Ferro-Luzzi, S. Filippov, M. Fiore, M. Fiorini, M. Firlej, C. Fitzpatrick, T. Fiutowski, K. Fohl, P. Fol, M. Fontana, F. Fontanelli, D. C. Forshaw, R. Forty, M. Frank, C. Frei, M. Frosini, J. Fu, E. Furfaro, A. Gallas Torreira, D. Galli, S. Gallorini, S. Gambetta, M. Gandelman, P. Gandini, Y. Gao, J. García Pardiñas, J. Garra Tico, L. Garrido, D. Gascon, C. Gaspar, R. Gauld, L. Gavardi, G. Gazzoni, D. Gerick, E. Gersabeck, M. Gersabeck, T. Gershon, Ph. Ghez, S. Gianì, V. Gibson, O. G. Girard, L. Giubega, V. V. Gligorov, C. Göbel, D. Golubkov, A. Golutvin, A. Gomes, C. Gotti, M. Grabalosa Gándara, R. Graciani Diaz, L. A. Granado Cardoso, E. Graugés, E. Graverini, G. Graziani, A. Grecu, E. Greening, S. Gregson, P. Griffith, L. Grillo, O. Grünberg, B. Gui, E. Gushchin, Yu. Guz, T. Gys, T. Hadavizadeh, C. Hadjivasiliou, G. Haefeli, C. Haen, S. C. Haines, S. Hall, B. Hamilton, X. Han, S. Hansmann-Menzemer, N. Harnew, S. T. Harnew, J. Harrison, J. He, T. Head, V. Heijne, K. Hennessy, P. Henrard, L. Henry, E. van Herwijnen, M. Heß, A. Hicheur, D. Hill, M. Hoballah, C. Hombach, W. Hulsbergen, T. Humair, N. Hussain, D. Hutchcroft, D. Hynds, M. Idzik, P. Ilten, R. Jacobsson, A. Jaeger, J. Jalocha, E. Jans, A. Jawahery, F. Jing, M. John, D. Johnson, C. R. Jones, C. Joram, B. Jost, N. Jurik, S. Kandybei, W. Kanso, M. Karacson, T. M. Karbach, S. Karodia, M. Kecke, M. Kelsey, I. R. Kenyon, M. Kenzie, T. Ketel, E. Khairullin, B. Khanji, C. Khurewathanakul, S. Klaver, K. Klimaszewski, O. Kochebina, M. Kolpin, I. Komarov, R. F. Koopman, P. Koppenburg, M. Kozeiha, L. Kravchuk, K. Kreplin, M. Kreps, G. Krocker, P. Krokovny, F. Kruse, W. Krzemien, W. Kucewicz, M. Kucharczyk, V. Kudryavtsev, A. K. Kuonen, K. Kurek, T. Kvaratskheliya, D. Lacarrere, G. Lafferty, A. Lai, D. Lambert, G. Lanfranchi, C. Langenbruch, B. Langhans, T. Latham, C. Lazzeroni, R. Le Gac, J. van Leerdam, J.-P. Lees, R. Lefèvre, A. Leflat, J. Lefrançois, E. Lemos Cid, O. Leroy, T. Lesiak, B. Leverington, Y. Li, T. Likhomanenko, M. Liles, R. Lindner, C. Linn, F. Lionetto, B. Liu, X. Liu, D. Loh, I. Longstaff, J. H. Lopes, D. Lucchesi, M. Lucio Martinez, H. Luo, A. Lupato, E. Luppi, O. Lupton, A. Lusiani, F. Machefert, F. Maciuc, O. Maev, K. Maguire, S. Malde, A. Malinin, G. Manca, G. Mancinelli, P. Manning, A. Mapelli, J. Maratas, J. F. Marchand, U. Marconi, C. Marin Benito, P. Marino, J. Marks, G. Martellotti, M. Martin, M. Martinelli, D. Martinez Santos, F. Martinez Vidal, D. Martins Tostes, A. Massafferri, R. Matev, A. Mathad, Z. Mathe, C. Matteuzzi, A. Mauri, B. Maurin, A. Mazurov, M. McCann, J. McCarthy, A. McNab, R. McNulty, B. Meadows, F. Meier, M. Meissner, D. Melnychuk, M. Merk, E Michielin, D. A. Milanes, M.-N. Minard, D. S. Mitzel, J. Molina Rodriguez, I. A. Monroy, S. Monteil, M. Morandin, P. Morawski, A. Mordà, M. J. Morello, J. Moron, A. B. Morris, R. Mountain, F. Muheim, D. Müller, J. Müller, K. Müller, V. Müller, M. Mussini, B. Muster, P. Naik, T. Nakada, R. Nandakumar, A. Nandi, I. Nasteva, M. Needham, N. Neri, S. Neubert, N. Neufeld, M. Neuner, A. D. Nguyen, T. D. Nguyen, C. Nguyen-Mau, V. Niess, R. Niet, N. Nikitin, T. Nikodem, A. Novoselov, D. P. O’Hanlon, A. Oblakowska-Mucha, V. Obraztsov, S. Ogilvy, O. Okhrimenko, R. Oldeman, C. J. G. Onderwater, B. Osorio Rodrigues, J. M. Otalora Goicochea, A. Otto, P. Owen, A. Oyanguren, A. Palano, F. Palombo, M. Palutan, J. Panman, A. Papanestis, M. Pappagallo, L. L. Pappalardo, C. Pappenheimer, W. Parker, C. Parkes, G. Passaleva, G. D. Patel, M. Patel, C. Patrignani, A. Pearce, A. Pellegrino, G. Penso, M. Pepe Altarelli, S. Perazzini, P. Perret, L. Pescatore, K. Petridis, A. Petrolini, M. Petruzzo, E. Picatoste Olloqui, B. Pietrzyk, T. Pilař, D. Pinci, A. Pistone, A. Piucci, S. Playfer, M. Plo Casasus, T. Poikela, F. Polci, A. Poluektov, I. Polyakov, E. Polycarpo, A. Popov, D. Popov, B. Popovici, C. Potterat, E. Price, J. D. Price, J. Prisciandaro, A. Pritchard, C. Prouve, V. Pugatch, A. Puig Navarro, G. Punzi, W. Qian, R. Quagliani, B. Rachwal, J. H. Rademacker, M. Rama, M. S. Rangel, I. Raniuk, N. Rauschmayr, G. Raven, F. Redi, S. Reichert, M. M. Reid, A. C. dos Reis, S. Ricciardi, S. Richards, M. Rihl, K. Rinnert, V. Rives Molina, P. Robbe, A. B. Rodrigues, E. Rodrigues, J. A. Rodriguez Lopez, P. Rodriguez Perez, S. Roiser, V. Romanovsky, A. Romero Vidal, J. W. Ronayne, M. Rotondo, J. Rouvinet, T. Ruf, P. Ruiz Valls, J. J. Saborido Silva, N. Sagidova, P. Sail, B. Saitta, V. Salustino Guimaraes, C. Sanchez Mayordomo, B. Sanmartin Sedes, R. Santacesaria, C. Santamarina Rios, M. Santimaria, E. Santovetti, A. Sarti, C. Satriano, A. Satta, D. M. Saunders, D. Savrina, M. Schiller, H. Schindler, M. Schlupp, M. Schmelling, T. Schmelzer, B. Schmidt, O. Schneider, A. Schopper, M. Schubiger, M.-H. Schune, R. Schwemmer, B. Sciascia, A. Sciubba, A. Semennikov, N. Serra, J. Serrano, L. Sestini, P. Seyfert, M. Shapkin, I. Shapoval, Y. Shcheglov, T. Shears, L. Shekhtman, V. Shevchenko, A. Shires, B. G. Siddi, R. Silva Coutinho, L. Silva de Oliveira, G. Simi, M. Sirendi, N. Skidmore, T. Skwarnicki, E. Smith, I. T. Smith, J. Smith, M. Smith, H. Snoek, M. D. Sokoloff, F. J. P. Soler, F. Soomro, D. Souza, B. Souza De Paula, B. Spaan, P. Spradlin, S. Sridharan, F. Stagni, M. Stahl, S. Stahl, S. Stefkova, O. Steinkamp, O. Stenyakin, S. Stevenson, S. Stoica, S. Stone, B. Storaci, S. Stracka, M. Straticiuc, U. Straumann, L. Sun, W. Sutcliffe, K. Swientek, S. Swientek, V. Syropoulos, M. Szczekowski, T. Szumlak, S. T’Jampens, A. Tayduganov, T. Tekampe, M. Teklishyn, G. Tellarini, F. Teubert, C. Thomas, E. Thomas, J. van Tilburg, V. Tisserand, M. Tobin, J. Todd, S. Tolk, L. Tomassetti, D. Tonelli, S. Topp-Joergensen, N. Torr, E. Tournefier, S. Tourneur, K. Trabelsi, M. T. Tran, M. Tresch, A. Trisovic, A. Tsaregorodtsev, P. Tsopelas, N. Tuning, A. Ukleja, A. Ustyuzhanin, U. Uwer, C. Vacca, V. Vagnoni, G. Valenti, A. Vallier, R. Vazquez Gomez, P. Vazquez Regueiro, C. Vázquez Sierra, S. Vecchi, J. J. Velthuis, M. Veltri, G. Veneziano, M. Vesterinen, B. Viaud, D. Vieira, M. Vieites Diaz, X. Vilasis-Cardona, V. Volkov, A. Vollhardt, D. Volyanskyy, D. Voong, A. Vorobyev, V. Vorobyev, C. Voß, J. A. de Vries, R. Waldi, C. Wallace, R. Wallace, J. Walsh, S. Wandernoth, J. Wang, D. R. Ward, N. K. Watson, D. Websdale, A. Weiden, M. Whitehead, G. Wilkinson, M. Wilkinson, M. Williams, M. P. Williams, T. Williams, F. F. Wilson, J. Wimberley, J. Wishahi, W. Wislicki, M. Witek, G. Wormser, S. A. Wotton, K. Wyllie, Y. Xie, Z. Xu, Z. Yang, J. Yu, X. Yuan, O. Yushchenko, M. Zangoli, M. Zavertyaev, L. Zhang, Y. Zhang, A. Zhelezov, A. Zhokhov, L. Zhong, and S. Zucchelli
Subjects: Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Published: 2017
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37. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author: Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A. Gordon Robertson, Toshinori Hinoue, Katherine A. Hoadley, Ewan A. Gibb, Jason Roszik, Kyle R. Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Julian M. Hess, J. Todd Auman, Suhn K. Rhie, Reanne Bowlby, Mitesh J. Borad, Andrew X. Zhu, Josh M. Stuart, Chris Sander, Rehan Akbani, Andrew D. Cherniack, Vikram Deshpande, Taofic Mounajjed, Wai Chin Foo, Michael S. Torbenson, David E. Kleiner, Peter W. Laird, David A. Wheeler, Autumn J. McRee, Oliver F. Bathe, Jesper B. Andersen, Nabeel Bardeesy, Lewis R. Roberts, and Lawrence N. Kwong
Subjects: TCGA, cholangiocarcinoma, multi-omics, integrative genomics, DNA methylation, RNA sequencing, lncRNAs, IDH, whole exome, ARID1A, Biology (General), QH301-705.5
Abstract: Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
Published: 2017
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38. Immersive Analytics: Theory and Research Agenda

Author: Richard Skarbez, Nicholas F. Polys, J. Todd Ogle, Chris North, and Doug A. Bowman
Subjects: immersive analytics, visual analytics, immersion, virtual reality, visualization, sensemaking, Mechanical engineering and machinery, TJ1-1570, Electronic computers. Computer science, QA75.5-76.95
Abstract: Advances in a variety of computing fields, including “big data,” machine learning, visualization, and augmented/mixed/virtual reality, have combined to give rise to the emerging field of immersive analytics, which investigates how these new technologies support analysis and decision making. Thus far, we feel that immersive analytics research has been somewhat ad hoc, possibly owing to the fact that there is not yet an organizing framework for immersive analytics research. In this paper, we address this lack by proposing a definition for immersive analytics and identifying some general research areas and specific research questions that will be important for the development of this field. We also present three case studies that, while all being examples of what we would consider immersive analytics, present different challenges, and opportunities. These serve to demonstrate the breadth of immersive analytics and illustrate how the framework proposed in this paper applies to practical research.
Published: 2019
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39. A controlled clinical trial of ultraviolet blood irradiation (UVBI) for hepatitis C infection

Author: J. Todd Kuenstner, Shanker Mukherjee, Zachary Schafer, William Kuenstner, and Thomas Petrie
Subjects: ultraviolet blood irradiation, crohn’s disease, tuberculosis, hepatitis c virus, Medicine
Abstract: The FDA Phase I controlled clinical trial results of ultraviolet blood irradiation (UVBI) to treat patients with hepatitis C Virus (HCV) infection are described in this report. This study was conducted prior to the availability of other highly effective therapies, e.g., the combination of ledipasvir and sofosbuvir (Gilead Sciences, Inc.). Five UVBI treatments were administered to 10 patients in 3 weeks. Viral loads and markers of hepatic inflammation were assessed before and after treatment. The patients were treated with a modified Knott Hemo-Irradiator (AVIcure Bioscience, LLC). After five treatments in nine of the patients, the mean percentage change in viral load was −56.0% and the mean change in log viral load was −0.60 (p = 0.017). During the study, seven of 10 patients demonstrated a > 0.49 log reduction in viral load. There were no significant adverse events. UVBI was safe in all patients and effective for the treatment of HCV infection in a majority of patients (IDE #G030242). This device should be studied for the treatment of other infectious diseases for which there are few treatment options.
Published: 2019
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40. Presence of Infection by Mycobacterium avium subsp. paratuberculosis in the Blood of Patients with Crohn’s Disease and Control Subjects Shown by Multiple Laboratory Culture and Antibody Methods

Author: J. Todd Kuenstner, Raghava Potula, Tim J. Bull, Irene R. Grant, Antonio Foddai, Saleh A. Naser, Horacio Bach, Peilin Zhang, Daohai Yu, Xiaoning Lu, and Ira Shafran
Subjects: MAP, Crohn’s Disease, bacteremia, IBD, autoimmune disease, Biology (General), QH301-705.5
Abstract: Mycobacterium avium subspecies paratuberculosis (MAP) has long been suspected to be involved in the etiology of Crohn’s disease (CD). An obligate intracellular pathogen, MAP persists and influences host macrophages. The primary goals of this study were to test new rapid culture methods for MAP in human subjects and to assess the degree of viable culturable MAP bacteremia in CD patients compared to controls. A secondary goal was to compare the efficacy of three culture methods plus a phage assay and four antibody assays performed in separate laboratories, to detect MAP from the parallel samples. Culture and serological MAP testing was performed blind on whole blood samples obtained from 201 subjects including 61 CD patients (two of the patients with CD had concurrent ulcerative colitis (UC)) and 140 non-CD controls (14 patients in this group had UC only). Viable MAP bacteremia was detected in a significant number of study subjects across all groups. This included Pozzato culture (124/201 or 62% of all subjects, 35/61 or 57% of CD patients), Phage assay (113/201 or 56% of all subjects, 28/61 or 46% of CD patients), TiKa culture (64/201 or 32% of all subjects, 22/61 or 36% of CD patients) and MGIT culture (36/201 or 18% of all subjects, 15/61 or 25% of CD patients). A link between MAP detection and CD was observed with MGIT culture and one of the antibody methods (Hsp65) confirming previous studies. Other detection methods showed no association between any of the groups tested. Nine subjects with a positive Phage assay (4/9) or MAP culture (5/9) were again positive with the Phage assay one year later. This study highlights viable MAP bacteremia is widespread in the study population including CD patients, those with other autoimmune conditions and asymptomatic healthy subjects.
Published: 2020
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41. Measurements of long-range near-side angular correlations in sNN=5 TeV proton-lead collisions in the forward region

Author: R. Aaij, C. Abellán Beteta, B. Adeva, M. Adinolfi, A. Affolder, Z. Ajaltouni, S. Akar, J. Albrecht, F. Alessio, M. Alexander, S. Ali, G. Alkhazov, P. Alvarez Cartelle, A.A. Alves, Jr, S. Amato, S. Amerio, Y. Amhis, L. An, L. Anderlini, J. Anderson, G. Andreassi, M. Andreotti, J.E. Andrews, R.B. Appleby, O. Aquines Gutierrez, F. Archilli, P. d'Argent, A. Artamonov, M. Artuso, E. Aslanides, G. Auriemma, M. Baalouch, S. Bachmann, J.J. Back, A. Badalov, C. Baesso, W. Baldini, R.J. Barlow, C. Barschel, S. Barsuk, W. Barter, V. Batozskaya, V. Battista, A. Bay, L. Beaucourt, J. Beddow, F. Bedeschi, I. Bediaga, L.J. Bel, V. Bellee, N. Belloli, I. Belyaev, E. Ben-Haim, G. Bencivenni, S. Benson, J. Benton, A. Berezhnoy, R. Bernet, A. Bertolin, M.-O. Bettler, M. van Beuzekom, A. Bien, S. Bifani, P. Billoir, T. Bird, A. Birnkraut, A. Bizzeti, T. Blake, F. Blanc, J. Blouw, S. Blusk, V. Bocci, A. Bondar, N. Bondar, W. Bonivento, S. Borghi, M. Borsato, T.J.V. Bowcock, E. Bowen, C. Bozzi, S. Braun, M. Britsch, T. Britton, J. Brodzicka, N.H. Brook, E. Buchanan, C. Burr, A. Bursche, J. Buytaert, S. Cadeddu, R. Calabrese, M. Calvi, M. Calvo Gomez, P. Campana, D. Campora Perez, L. Capriotti, A. Carbone, G. Carboni, R. Cardinale, A. Cardini, P. Carniti, L. Carson, K. Carvalho Akiba, G. Casse, L. Cassina, L. Castillo Garcia, M. Cattaneo, Ch. Cauet, G. Cavallero, R. Cenci, M. Charles, Ph. Charpentier, M. Chefdeville, S. Chen, S.-F. Cheung, N. Chiapolini, M. Chrzaszcz, X. Cid Vidal, G. Ciezarek, P.E.L. Clarke, M. Clemencic, H.V. Cliff, J. Closier, V. Coco, J. Cogan, E. Cogneras, V. Cogoni, L. Cojocariu, G. Collazuol, P. Collins, A. Comerma-Montells, A. Contu, A. Cook, M. Coombes, S. Coquereau, G. Corti, M. Corvo, B. Couturier, G.A. Cowan, D.C. Craik, A. Crocombe, M. Cruz Torres, S. Cunliffe, R. Currie, C. D'Ambrosio, E. Dall'Occo, J. Dalseno, P.N.Y. David, A. Davis, O. De Aguiar Francisco, K. De Bruyn, S. De Capua, M. De Cian, J.M. De Miranda, L. De Paula, P. De Simone, C.-T. Dean, D. Decamp, M. Deckenhoff, L. Del Buono, N. Déléage, M. Demmer, D. Derkach, O. Deschamps, F. Dettori, B. Dey, A. Di Canto, F. Di Ruscio, H. Dijkstra, S. Donleavy, F. Dordei, M. Dorigo, A. Dosil Suárez, D. Dossett, A. Dovbnya, K. Dreimanis, L. Dufour, G. Dujany, F. Dupertuis, P. Durante, R. Dzhelyadin, A. Dziurda, A. Dzyuba, S. Easo, U. Egede, V. Egorychev, S. Eidelman, S. Eisenhardt, U. Eitschberger, R. Ekelhof, L. Eklund, I. El Rifai, Ch. Elsasser, S. Ely, S. Esen, H.M. Evans, T. Evans, A. Falabella, C. Färber, N. Farley, S. Farry, R. Fay, D. Ferguson, V. Fernandez Albor, F. Ferrari, F. Ferreira Rodrigues, M. Ferro-Luzzi, S. Filippov, M. Fiore, M. Fiorini, M. Firlej, C. Fitzpatrick, T. Fiutowski, K. Fohl, P. Fol, M. Fontana, F. Fontanelli, D.C. Forshaw, R. Forty, M. Frank, C. Frei, M. Frosini, J. Fu, E. Furfaro, A. Gallas Torreira, D. Galli, S. Gallorini, S. Gambetta, M. Gandelman, P. Gandini, Y. Gao, J. García Pardiñas, J. Garra Tico, L. Garrido, D. Gascon, C. Gaspar, R. Gauld, L. Gavardi, G. Gazzoni, D. Gerick, E. Gersabeck, M. Gersabeck, T. Gershon, Ph. Ghez, S. Gianì, V. Gibson, O.G. Girard, L. Giubega, V.V. Gligorov, C. Göbel, D. Golubkov, A. Golutvin, A. Gomes, C. Gotti, M. Grabalosa Gándara, R. Graciani Diaz, L.A. Granado Cardoso, E. Graugés, E. Graverini, G. Graziani, A. Grecu, E. Greening, S. Gregson, P. Griffith, L. Grillo, O. Grünberg, B. Gui, E. Gushchin, Yu. Guz, T. Gys, T. Hadavizadeh, C. Hadjivasiliou, G. Haefeli, C. Haen, S.C. Haines, S. Hall, B. Hamilton, X. Han, S. Hansmann-Menzemer, N. Harnew, S.T. Harnew, J. Harrison, J. He, T. Head, V. Heijne, A. Heister, K. Hennessy, P. Henrard, L. Henry, J.A. Hernando Morata, E. van Herwijnen, M. Heß, A. Hicheur, D. Hill, M. Hoballah, C. Hombach, W. Hulsbergen, T. Humair, N. Hussain, D. Hutchcroft, D. Hynds, M. Idzik, P. Ilten, R. Jacobsson, A. Jaeger, J. Jalocha, E. Jans, A. Jawahery, F. Jing, M. John, D. Johnson, C.R. Jones, C. Joram, B. Jost, N. Jurik, S. Kandybei, W. Kanso, M. Karacson, T.M. Karbach, S. Karodia, M. Kecke, M. Kelsey, I.R. Kenyon, M. Kenzie, T. Ketel, E. Khairullin, B. Khanji, C. Khurewathanakul, T. Kirn, S. Klaver, K. Klimaszewski, O. Kochebina, M. Kolpin, I. Komarov, R.F. Koopman, P. Koppenburg, M. Kozeiha, L. Kravchuk, K. Kreplin, M. Kreps, G. Krocker, P. Krokovny, F. Kruse, W. Krzemien, W. Kucewicz, M. Kucharczyk, V. Kudryavtsev, A.K. Kuonen, K. Kurek, T. Kvaratskheliya, D. Lacarrere, G. Lafferty, A. Lai, D. Lambert, G. Lanfranchi, C. Langenbruch, B. Langhans, T. Latham, C. Lazzeroni, R. Le Gac, J. van Leerdam, J.-P. Lees, R. Lefèvre, A. Leflat, J. Lefrançois, E. Lemos Cid, O. Leroy, T. Lesiak, B. Leverington, Y. Li, T. Likhomanenko, M. Liles, R. Lindner, C. Linn, F. Lionetto, B. Liu, X. Liu, D. Loh, I. Longstaff, J.H. Lopes, D. Lucchesi, M. Lucio Martinez, H. Luo, A. Lupato, E. Luppi, O. Lupton, A. Lusiani, F. Machefert, F. Maciuc, O. Maev, K. Maguire, S. Malde, A. Malinin, G. Manca, G. Mancinelli, P. Manning, A. Mapelli, J. Maratas, J.F. Marchand, U. Marconi, C. Marin Benito, P. Marino, J. Marks, G. Martellotti, M. Martin, M. Martinelli, D. Martinez Santos, F. Martinez Vidal, D. Martins Tostes, A. Massafferri, R. Matev, A. Mathad, Z. Mathe, C. Matteuzzi, A. Mauri, B. Maurin, A. Mazurov, M. McCann, J. McCarthy, A. McNab, R. McNulty, B. Meadows, F. Meier, M. Meissner, D. Melnychuk, M. Merk, E. Michielin, D.A. Milanes, M.-N. Minard, D.S. Mitzel, J. Molina Rodriguez, I.A. Monroy, S. Monteil, M. Morandin, P. Morawski, A. Mordà, M.J. Morello, J. Moron, A.B. Morris, R. Mountain, F. Muheim, D. Müller, J. Müller, K. Müller, V. Müller, M. Mussini, B. Muster, P. Naik, T. Nakada, R. Nandakumar, A. Nandi, I. Nasteva, M. Needham, N. Neri, S. Neubert, N. Neufeld, M. Neuner, A.D. Nguyen, T.D. Nguyen, C. Nguyen-Mau, V. Niess, R. Niet, N. Nikitin, T. Nikodem, A. Novoselov, D.P. O'Hanlon, A. Oblakowska-Mucha, V. Obraztsov, S. Ogilvy, O. Okhrimenko, R. Oldeman, C.J.G. Onderwater, B. Osorio Rodrigues, J.M. Otalora Goicochea, A. Otto, P. Owen, A. Oyanguren, A. Palano, F. Palombo, M. Palutan, J. Panman, A. Papanestis, M. Pappagallo, L.L. Pappalardo, C. Pappenheimer, W. Parker, C. Parkes, G. Passaleva, G.D. Patel, M. Patel, C. Patrignani, A. Pearce, A. Pellegrino, G. Penso, M. Pepe Altarelli, S. Perazzini, P. Perret, L. Pescatore, K. Petridis, A. Petrolini, M. Petruzzo, E. Picatoste Olloqui, B. Pietrzyk, T. Pilař, D. Pinci, A. Pistone, A. Piucci, S. Playfer, M. Plo Casasus, T. Poikela, F. Polci, A. Poluektov, I. Polyakov, E. Polycarpo, A. Popov, D. Popov, B. Popovici, C. Potterat, E. Price, J.D. Price, J. Prisciandaro, A. Pritchard, C. Prouve, V. Pugatch, A. Puig Navarro, G. Punzi, W. Qian, R. Quagliani, B. Rachwal, J.H. Rademacker, M. Rama, M.S. Rangel, I. Raniuk, N. Rauschmayr, G. Raven, F. Redi, S. Reichert, M.M. Reid, A.C. dos Reis, S. Ricciardi, S. Richards, M. Rihl, K. Rinnert, V. Rives Molina, P. Robbe, A.B. Rodrigues, E. Rodrigues, J.A. Rodriguez Lopez, P. Rodriguez Perez, S. Roiser, V. Romanovsky, A. Romero Vidal, J.W. Ronayne, M. Rotondo, J. Rouvinet, T. Ruf, P. Ruiz Valls, J.J. Saborido Silva, N. Sagidova, P. Sail, B. Saitta, V. Salustino Guimaraes, C. Sanchez Mayordomo, B. Sanmartin Sedes, R. Santacesaria, C. Santamarina Rios, M. Santimaria, E. Santovetti, A. Sarti, C. Satriano, A. Satta, D.M. Saunders, D. Savrina, S. Schael, M. Schiller, H. Schindler, M. Schlupp, M. Schmelling, T. Schmelzer, B. Schmidt, O. Schneider, A. Schopper, M. Schubiger, M.-H. Schune, R. Schwemmer, B. Sciascia, A. Sciubba, A. Semennikov, A. Sergi, N. Serra, J. Serrano, L. Sestini, P. Seyfert, M. Shapkin, I. Shapoval, Y. Shcheglov, T. Shears, L. Shekhtman, V. Shevchenko, A. Shires, B.G. Siddi, R. Silva Coutinho, L. Silva de Oliveira, G. Simi, M. Sirendi, N. Skidmore, T. Skwarnicki, E. Smith, I.T. Smith, J. Smith, M. Smith, H. Snoek, M.D. Sokoloff, F.J.P. Soler, F. Soomro, D. Souza, B. Souza De Paula, B. Spaan, P. Spradlin, S. Sridharan, F. Stagni, M. Stahl, S. Stahl, S. Stefkova, O. Steinkamp, O. Stenyakin, S. Stevenson, S. Stoica, S. Stone, B. Storaci, S. Stracka, M. Straticiuc, U. Straumann, L. Sun, W. Sutcliffe, K. Swientek, S. Swientek, V. Syropoulos, M. Szczekowski, T. Szumlak, S. T'Jampens, A. Tayduganov, T. Tekampe, M. Teklishyn, G. Tellarini, F. Teubert, C. Thomas, E. Thomas, J. van Tilburg, V. Tisserand, M. Tobin, J. Todd, S. Tolk, L. Tomassetti, D. Tonelli, S. Topp-Joergensen, N. Torr, E. Tournefier, S. Tourneur, K. Trabelsi, M.T. Tran, M. Tresch, A. Trisovic, A. Tsaregorodtsev, P. Tsopelas, N. Tuning, A. Ukleja, A. Ustyuzhanin, U. Uwer, C. Vacca, V. Vagnoni, G. Valenti, A. Vallier, R. Vazquez Gomez, P. Vazquez Regueiro, C. Vázquez Sierra, S. Vecchi, M. van Veghel, J.J. Velthuis, M. Veltri, G. Veneziano, M. Vesterinen, B. Viaud, D. Vieira, M. Vieites Diaz, X. Vilasis-Cardona, V. Volkov, A. Vollhardt, D. Volyanskyy, D. Voong, A. Vorobyev, V. Vorobyev, C. Voß, J.A. de Vries, R. Waldi, C. Wallace, R. Wallace, J. Walsh, S. Wandernoth, J. Wang, D.R. Ward, N.K. Watson, D. Websdale, A. Weiden, M. Whitehead, G. Wilkinson, M. Wilkinson, M. Williams, M.P. Williams, T. Williams, F.F. Wilson, J. Wimberley, J. Wishahi, W. Wislicki, M. Witek, G. Wormser, S.A. Wotton, S. Wright, K. Wyllie, Y. Xie, Z. Xu, Z. Yang, J. Yu, X. Yuan, O. Yushchenko, M. Zangoli, M. Zavertyaev, L. Zhang, Y. Zhang, A. Zhelezov, A. Zhokhov, L. Zhong, V. Zhukov, and S. Zucchelli
Subjects: Physics, QC1-999
Abstract: Two-particle angular correlations are studied in proton-lead collisions at a nucleon–nucleon centre-of-mass energy of sNN=5 TeV, collected with the LHCb detector at the LHC. The analysis is based on data recorded in two beam configurations, in which either the direction of the proton or that of the lead ion is analysed. The correlations are measured in the laboratory system as a function of relative pseudorapidity, Δη, and relative azimuthal angle, Δϕ, for events in different classes of event activity and for different bins of particle transverse momentum. In high-activity events a long-range correlation on the near side, Δϕ≈0, is observed in the pseudorapidity range 2.0
Published: 2016
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42. Performance and applicability of a 2.5-D ice-flow model in the vicinity of a dome

Author: O. Passalacqua, O. Gagliardini, F. Parrenin, J. Todd, F. Gillet-Chaulet, and C. Ritz
Subjects: Geology, QE1-996.5
Abstract: Three-dimensional ice flow modelling requires a large number of computing resources and observation data, such that 2-D simulations are often preferable. However, when there is significant lateral divergence, this must be accounted for (2.5-D models), and a flow tube is considered (volume between two horizontal flowlines). In the absence of velocity observations, this flow tube can be derived assuming that the flowlines follow the steepest slope of the surface, under a few flow assumptions. This method typically consists of scanning a digital elevation model (DEM) with a moving window and computing the curvature at the centre of this window. The ability of the 2.5-D models to account properly for a 3-D state of strain and stress has not clearly been established, nor their sensitivity to the size of the scanning window and to the geometry of the ice surface, for example in the cases of sharp ridges. Here, we study the applicability of a 2.5-D ice flow model around a dome, typical of the East Antarctic plateau conditions. A twin experiment is carried out, comparing 3-D and 2.5-D computed velocities, on three dome geometries, for several scanning windows and thermal conditions. The chosen scanning window used to evaluate the ice surface curvature should be comparable to the typical radius of this curvature. For isothermal ice, the error made by the 2.5-D model is in the range 0–10 % for weakly diverging flows, but is 2 or 3 times higher for highly diverging flows and could lead to a non-physical ice surface at the dome. For non-isothermal ice, assuming a linear temperature profile, the presence of a sharp ridge makes the 2.5-D velocity field unrealistic. In such cases, the basal ice is warmer and more easily laterally strained than the upper one, the walls of the flow tube are not vertical, and the assumptions of the 2.5-D model are no longer valid.
Published: 2016
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43. Search for the lepton-flavour violating decay D0→e±μ∓

Author: R. Aaij, C. Abellán Beteta, B. Adeva, M. Adinolfi, A. Affolder, Z. Ajaltouni, S. Akar, J. Albrecht, F. Alessio, M. Alexander, S. Ali, G. Alkhazov, P. Alvarez Cartelle, A.A. Alves Jr, S. Amato, S. Amerio, Y. Amhis, L. An, L. Anderlini, J. Anderson, G. Andreassi, M. Andreotti, J.E. Andrews, R.B. Appleby, O. Aquines Gutierrez, F. Archilli, P. d'Argent, A. Artamonov, M. Artuso, E. Aslanides, G. Auriemma, M. Baalouch, S. Bachmann, J.J. Back, A. Badalov, C. Baesso, W. Baldini, R.J. Barlow, C. Barschel, S. Barsuk, W. Barter, V. Batozskaya, V. Battista, A. Bay, L. Beaucourt, J. Beddow, F. Bedeschi, I. Bediaga, L.J. Bel, V. Bellee, N. Belloli, I. Belyaev, E. Ben-Haim, G. Bencivenni, S. Benson, J. Benton, A. Berezhnoy, R. Bernet, A. Bertolin, M.-O. Bettler, M. van Beuzekom, S. Bifani, P. Billoir, T. Bird, A. Birnkraut, A. Bizzeti, T. Blake, F. Blanc, J. Blouw, S. Blusk, V. Bocci, A. Bondar, N. Bondar, W. Bonivento, S. Borghi, M. Borisyak, M. Borsato, T.J.V. Bowcock, E. Bowen, C. Bozzi, S. Braun, M. Britsch, T. Britton, J. Brodzicka, N.H. Brook, E. Buchanan, C. Burr, A. Bursche, J. Buytaert, S. Cadeddu, R. Calabrese, M. Calvi, M. Calvo Gomez, P. Campana, D. Campora Perez, L. Capriotti, A. Carbone, G. Carboni, R. Cardinale, A. Cardini, P. Carniti, L. Carson, K. Carvalho Akiba, G. Casse, L. Cassina, L. Castillo Garcia, M. Cattaneo, Ch. Cauet, G. Cavallero, R. Cenci, M. Charles, Ph. Charpentier, M. Chefdeville, S. Chen, S.-F. Cheung, N. Chiapolini, M. Chrzaszcz, X. Cid Vidal, G. Ciezarek, P.E.L. Clarke, M. Clemencic, H.V. Cliff, J. Closier, V. Coco, J. Cogan, E. Cogneras, V. Cogoni, L. Cojocariu, G. Collazuol, P. Collins, A. Comerma-Montells, A. Contu, A. Cook, M. Coombes, S. Coquereau, G. Corti, M. Corvo, B. Couturier, G.A. Cowan, D.C. Craik, A. Crocombe, M. Cruz Torres, S. Cunliffe, R. Currie, C. D'Ambrosio, E. Dall'Occo, J. Dalseno, P.N.Y. David, A. Davis, O. De Aguiar Francisco, K. De Bruyn, S. De Capua, M. De Cian, J.M. De Miranda, L. De Paula, P. De Simone, C.-T. Dean, D. Decamp, M. Deckenhoff, L. Del Buono, N. Déléage, M. Demmer, D. Derkach, O. Deschamps, F. Dettori, B. Dey, A. Di Canto, F. Di Ruscio, H. Dijkstra, S. Donleavy, F. Dordei, M. Dorigo, A. Dosil Suárez, D. Dossett, A. Dovbnya, K. Dreimanis, L. Dufour, G. Dujany, P. Durante, R. Dzhelyadin, A. Dziurda, A. Dzyuba, S. Easo, U. Egede, V. Egorychev, S. Eidelman, S. Eisenhardt, U. Eitschberger, R. Ekelhof, L. Eklund, I. El Rifai, Ch. Elsasser, S. Ely, S. Esen, H.M. Evans, T. Evans, A. Falabella, C. Färber, N. Farley, S. Farry, R. Fay, D. Ferguson, V. Fernandez Albor, F. Ferrari, F. Ferreira Rodrigues, M. Ferro-Luzzi, S. Filippov, M. Fiore, M. Fiorini, M. Firlej, C. Fitzpatrick, T. Fiutowski, F. Fleuret, K. Fohl, P. Fol, M. Fontana, F. Fontanelli, D.C. Forshaw, R. Forty, M. Frank, C. Frei, M. Frosini, J. Fu, E. Furfaro, A. Gallas Torreira, D. Galli, S. Gallorini, S. Gambetta, M. Gandelman, P. Gandini, Y. Gao, J. García Pardiñas, J. Garra Tico, L. Garrido, D. Gascon, C. Gaspar, R. Gauld, L. Gavardi, G. Gazzoni, D. Gerick, E. Gersabeck, M. Gersabeck, T. Gershon, Ph. Ghez, S. Gianì, V. Gibson, O.G. Girard, L. Giubega, V.V. Gligorov, C. Göbel, D. Golubkov, A. Golutvin, A. Gomes, C. Gotti, M. Grabalosa Gándara, R. Graciani Diaz, L.A. Granado Cardoso, E. Graugés, E. Graverini, G. Graziani, A. Grecu, E. Greening, S. Gregson, P. Griffith, L. Grillo, O. Grünberg, B. Gui, E. Gushchin, Yu. Guz, T. Gys, T. Hadavizadeh, C. Hadjivasiliou, G. Haefeli, C. Haen, S.C. Haines, S. Hall, B. Hamilton, X. Han, S. Hansmann-Menzemer, N. Harnew, S.T. Harnew, J. Harrison, J. He, T. Head, V. Heijne, A. Heister, K. Hennessy, P. Henrard, L. Henry, J.A. Hernando Morata, E. van Herwijnen, M. Heß, A. Hicheur, D. Hill, M. Hoballah, C. Hombach, W. Hulsbergen, T. Humair, N. Hussain, D. Hutchcroft, D. Hynds, M. Idzik, P. Ilten, R. Jacobsson, A. Jaeger, J. Jalocha, E. Jans, A. Jawahery, M. John, D. Johnson, C.R. Jones, C. Joram, B. Jost, N. Jurik, S. Kandybei, W. Kanso, M. Karacson, T.M. Karbach, S. Karodia, M. Kecke, M. Kelsey, I.R. Kenyon, M. Kenzie, T. Ketel, E. Khairullin, B. Khanji, C. Khurewathanakul, T. Kirn, S. Klaver, K. Klimaszewski, O. Kochebina, M. Kolpin, I. Komarov, R.F. Koopman, P. Koppenburg, M. Kozeiha, L. Kravchuk, K. Kreplin, M. Kreps, P. Krokovny, F. Kruse, W. Krzemien, W. Kucewicz, M. Kucharczyk, V. Kudryavtsev, A.K. Kuonen, K. Kurek, T. Kvaratskheliya, D. Lacarrere, G. Lafferty, A. Lai, D. Lambert, G. Lanfranchi, C. Langenbruch, B. Langhans, T. Latham, C. Lazzeroni, R. Le Gac, J. van Leerdam, J.-P. Lees, R. Lefèvre, A. Leflat, J. Lefrançois, E. Lemos Cid, O. Leroy, T. Lesiak, B. Leverington, Y. Li, T. Likhomanenko, M. Liles, R. Lindner, C. Linn, F. Lionetto, B. Liu, X. Liu, D. Loh, I. Longstaff, J.H. Lopes, D. Lucchesi, M. Lucio Martinez, H. Luo, A. Lupato, E. Luppi, O. Lupton, A. Lusiani, F. Machefert, F. Maciuc, O. Maev, K. Maguire, S. Malde, A. Malinin, G. Manca, G. Mancinelli, P. Manning, A. Mapelli, J. Maratas, J.F. Marchand, U. Marconi, C. Marin Benito, P. Marino, J. Marks, G. Martellotti, M. Martin, M. Martinelli, D. Martinez Santos, F. Martinez Vidal, D. Martins Tostes, L.M. Massacrier, A. Massafferri, R. Matev, A. Mathad, Z. Mathe, C. Matteuzzi, A. Mauri, B. Maurin, A. Mazurov, M. McCann, J. McCarthy, A. McNab, R. McNulty, B. Meadows, F. Meier, M. Meissner, D. Melnychuk, M. Merk, E. Michielin, D.A. Milanes, M.-N. Minard, D.S. Mitzel, J. Molina Rodriguez, I.A. Monroy, S. Monteil, M. Morandin, P. Morawski, A. Mordà, M.J. Morello, J. Moron, A.B. Morris, R. Mountain, F. Muheim, D. Müller, J. Müller, K. Müller, V. Müller, M. Mussini, B. Muster, P. Naik, T. Nakada, R. Nandakumar, A. Nandi, I. Nasteva, M. Needham, N. Neri, S. Neubert, N. Neufeld, M. Neuner, A.D. Nguyen, T.D. Nguyen, C. Nguyen-Mau, V. Niess, R. Niet, N. Nikitin, T. Nikodem, A. Novoselov, D.P. O'Hanlon, A. Oblakowska-Mucha, V. Obraztsov, S. Ogilvy, O. Okhrimenko, R. Oldeman, C.J.G. Onderwater, B. Osorio Rodrigues, J.M. Otalora Goicochea, A. Otto, P. Owen, A. Oyanguren, A. Palano, F. Palombo, M. Palutan, J. Panman, A. Papanestis, M. Pappagallo, L.L. Pappalardo, C. Pappenheimer, W. Parker, C. Parkes, G. Passaleva, G.D. Patel, M. Patel, C. Patrignani, A. Pearce, A. Pellegrino, G. Penso, M. Pepe Altarelli, S. Perazzini, P. Perret, L. Pescatore, K. Petridis, A. Petrolini, M. Petruzzo, E. Picatoste Olloqui, B. Pietrzyk, T. Pilař, D. Pinci, A. Pistone, A. Piucci, S. Playfer, M. Plo Casasus, T. Poikela, F. Polci, A. Poluektov, I. Polyakov, E. Polycarpo, A. Popov, D. Popov, B. Popovici, C. Potterat, E. Price, J.D. Price, J. Prisciandaro, A. Pritchard, C. Prouve, V. Pugatch, A. Puig Navarro, G. Punzi, W. Qian, R. Quagliani, B. Rachwal, J.H. Rademacker, M. Rama, M. Ramos Pernas, M.S. Rangel, I. Raniuk, N. Rauschmayr, G. Raven, F. Redi, S. Reichert, M.M. Reid, A.C. dos Reis, S. Ricciardi, S. Richards, M. Rihl, K. Rinnert, V. Rives Molina, P. Robbe, A.B. Rodrigues, E. Rodrigues, J.A. Rodriguez Lopez, P. Rodriguez Perez, S. Roiser, V. Romanovsky, A. Romero Vidal, J.W. Ronayne, M. Rotondo, T. Ruf, P. Ruiz Valls, J.J. Saborido Silva, N. Sagidova, P. Sail, B. Saitta, V. Salustino Guimaraes, C. Sanchez Mayordomo, B. Sanmartin Sedes, R. Santacesaria, C. Santamarina Rios, M. Santimaria, E. Santovetti, A. Sarti, C. Satriano, A. Satta, D.M. Saunders, D. Savrina, S. Schael, M. Schiller, H. Schindler, M. Schlupp, M. Schmelling, T. Schmelzer, B. Schmidt, O. Schneider, A. Schopper, M. Schubiger, M.-H. Schune, R. Schwemmer, B. Sciascia, A. Sciubba, A. Semennikov, A. Sergi, N. Serra, J. Serrano, L. Sestini, P. Seyfert, M. Shapkin, I. Shapoval, Y. Shcheglov, T. Shears, L. Shekhtman, V. Shevchenko, A. Shires, B.G. Siddi, R. Silva Coutinho, L. Silva de Oliveira, G. Simi, M. Sirendi, N. Skidmore, T. Skwarnicki, E. Smith, I.T. Smith, J. Smith, M. Smith, H. Snoek, M.D. Sokoloff, F.J.P. Soler, F. Soomro, D. Souza, B. Souza De Paula, B. Spaan, P. Spradlin, S. Sridharan, F. Stagni, M. Stahl, S. Stahl, S. Stefkova, O. Steinkamp, O. Stenyakin, S. Stevenson, S. Stoica, S. Stone, B. Storaci, S. Stracka, M. Straticiuc, U. Straumann, L. Sun, W. Sutcliffe, K. Swientek, S. Swientek, V. Syropoulos, M. Szczekowski, T. Szumlak, S. T'Jampens, A. Tayduganov, T. Tekampe, M. Teklishyn, G. Tellarini, F. Teubert, C. Thomas, E. Thomas, J. van Tilburg, V. Tisserand, M. Tobin, J. Todd, S. Tolk, L. Tomassetti, D. Tonelli, S. Topp-Joergensen, N. Torr, E. Tournefier, S. Tourneur, K. Trabelsi, M.T. Tran, M. Tresch, A. Trisovic, A. Tsaregorodtsev, P. Tsopelas, N. Tuning, A. Ukleja, A. Ustyuzhanin, U. Uwer, C. Vacca, V. Vagnoni, G. Valenti, A. Vallier, R. Vazquez Gomez, P. Vazquez Regueiro, C. Vázquez Sierra, S. Vecchi, M. van Veghel, J.J. Velthuis, M. Veltri, G. Veneziano, M. Vesterinen, B. Viaud, D. Vieira, M. Vieites Diaz, X. Vilasis-Cardona, V. Volkov, A. Vollhardt, D. Volyanskyy, D. Voong, A. Vorobyev, V. Vorobyev, C. Voß, J.A. de Vries, R. Waldi, C. Wallace, R. Wallace, J. Walsh, J. Wang, D.R. Ward, N.K. Watson, D. Websdale, A. Weiden, M. Whitehead, G. Wilkinson, M. Wilkinson, M. Williams, M.P. Williams, T. Williams, F.F. Wilson, J. Wimberley, J. Wishahi, W. Wislicki, M. Witek, G. Wormser, S.A. Wotton, K. Wraight, S. Wright, K. Wyllie, Y. Xie, Z. Xu, Z. Yang, J. Yu, X. Yuan, O. Yushchenko, M. Zangoli, M. Zavertyaev, L. Zhang, Y. Zhang, A. Zhelezov, A. Zhokhov, L. Zhong, V. Zhukov, and S. Zucchelli
Subjects: Physics, QC1-999
Abstract: A search for the lepton-flavour violating decay D0→e±μ∓ is made with a dataset corresponding to an integrated luminosity of 3.0fb−1 of proton–proton collisions at centre-of-mass energies of 7TeV and 8TeV, collected by the LHCb experiment. Candidate D0 mesons are selected using the decay D⁎+→D0π+ and the D0→e±μ∓ branching fraction is measured using the decay mode D0→K−π+ as a normalization channel. No significant excess of D0→e±μ∓ candidates over the expected background is seen, and a limit is set on the branching fraction, B(D0→e±μ∓)
Published: 2016
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44. Feasibility and Acceptability of a Group Music Creativity Intervention for Adults with Varying Cognitive Function

Author: E. Lydia Wu-Chung, Anthony K. Brandt, Melia E. Bonomo, Bryan T. Denny, Christof Karmonik, J. Todd Frazier, Karl Blench, and Christopher P. Fagundes
Abstract: Maintaining healthy cognitive functioning and delaying cognitive decline in cognitively intact and cognitively impaired adults are major research initiatives for addressing dementia disease burden. Music interventions are promising, non-pharmaceutical treatment options for preserving cognitive function and psychological health in older adults with varying levels of cognitive function. While passive, music interventions have attracted considerable attention in the abnormal cognitive aging literature, active, music interventions such as music creativity are less well-studied. Among 58 older adults with different levels of cognitive function (cognitively healthy to mild cognitive impairment), we examined the feasibility and acceptability of "Project CHROMA", a Stage 1 clinical trial developed to assess the effects of a novel, music creativity curriculum on various health outcomes. Music intervention participation (93%), overall study retention (78%), and intervention satisfaction (100%) rates were comparable to other similarly designed clinical trials. Exploratory analyses using mixed-level modeling tested the efficacy of the intervention on cognitive and psychological outcomes. Compared to those in the control condition, participants in the music condition showed some improvements in cognitive functioning and socioemotional well-being. Findings suggest that a 6-week music creativity clinical trial with several multi-modal health assessments can be feasibly implemented within a sample of varying cognitive ability.
Published: 2024
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45. Effect of Collection Month, Visible Light, and Air Movement on the Attraction of Male Agriotes obscurus L. (Coleoptera: Elateridae) Click Beetles to Female Sex Pheromone

Author: Joyce P. S. Leung, Jenny S. Cory, J. Todd Kabaluk, and Alida F. Janmaat
Subjects: chemical ecology, attraction distance, environmental factors, behavior, pest management, Science
Abstract: Elaterid female sex pheromone, while currently used for monitoring the adult life stage (click beetle), has only recently been explored as a potential management tool. Consequently, there is little understanding of how abiotic and biotic conditions influence the response of click beetles to the pheromone. We examined whether the response of male Agriotes obscurus L. (Coleoptera: Elateridae) beetles to a cellulose-based formulation of female sex pheromone (‘pheromone granules’) is influenced by air movement, presence of visible light, and month of beetle collection. In addition, we investigated the distance from which beetles were attracted to the pheromone granules. Click beetle response was determined by measuring movement parameters in free-walking arena experiments. The response to pheromone was not affected by the presence or absence of visible light. We found that beetles collected earlier in the season had increased activity and interaction with pheromone under moving air conditions, compared to beetles collected later. When controlling for storage time, we confirmed that individuals collected in May were less active than beetles collected in March and April. In the field, beetles were recaptured from up to 14 m away from a pheromone granule source, with over 50% being recovered within 4.4 h from a distance of 7 m or less. Understanding how abiotic and biotic factors affect pest response to pheromone can lead to more effective and novel uses of pheromone-based management strategies.
Published: 2020
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46. Flow-Mediated Vulnerability of Source Waters to Elevated TDS in an Appalachian River Basin

Author: Eric R. Merriam, J. Todd Petty, Melissa O’Neal, and Paul F. Ziemkiewicz
Subjects: water quality, vulnerability, total dissolved solids, drinking water, Hydraulic engineering, TC1-978, Water supply for domestic and industrial purposes, TD201-500
Abstract: Widespread salinization—and, in a broader sense, an increase in all total dissolved solids (TDS)—is threatening freshwater ecosystems and the services they provide (e.g., drinking water provision). We used a mixed modeling approach to characterize long-term (2010−2018) spatio-temporal variability in TDS within the Monongahela River basin and used this information to assess the extent and drivers of vulnerability. The West Fork River was predicted to exceed 500 mg/L a total of 133 days. Occurrence and duration (maximum = 28 days) of—and thus vulnerability to—exceedances within the West Fork River were driven by low flows. Projected decreases in mean daily discharge by ≤10 cfs resulted in an additional 34 days exceeding 500 mg/L. Consistently low TDS within the Tygart Valley and Cheat Rivers reduced vulnerability of the receiving Monongahela River to elevated TDS which was neither observed (maximum = 419 mg/L) nor predicted (341 mg/L) to exceed the secondary drinking water standard of 500 mg/L. Potential changes in future land use and/or severity of low-flow conditions could increase vulnerability of the Monongahela River to elevated TDS. Management should include efforts to increase assimilative capacity by identifying and decreasing sources of TDS. Upstream reservoirs could be managed toward low-flow thresholds; however, further study is needed to ensure all authorized reservoir purposes could be maintained.
Published: 2020
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47. Anti-microbial Antibodies, Host Immunity, and Autoimmune Disease

Author: Peilin Zhang, Lawrence M. Minardi, J. Todd Kuenstner, Steven M. Zekan, and Rusty Kruzelock
Subjects: anti-microbial antibody, autoimmune disease, molecular mimicry, host immunity, autoantibody, Medicine (General), R5-920
Abstract: Autoimmune diseases are a spectrum of clinical inflammatory syndromes with circulating autoantibodies. Autoimmune diseases affect millions of patients worldwide with enormous costs to patients and society. The diagnosis of autoimmune diseases relies on the presence of autoantibodies and the treatment strategy is to suppress the immune system using specific or non-specific immunosuppressive agents. The discovery of anti-microbial antibodies in the blood of patients with Crohn's disease and Sjogren's syndrome and cross-reactivity of anti-microbial antibodies to human tissue suggests a new molecular mechanism of pathogenesis, raising the possibility of designing a new therapeutic strategy for these patients. The presence of anti-microbial antibodies indicates the failure of the innate immunity system to clear the microbial agents from the blood and activation of adaptive immunity through B-lymphocytes/plasma cells. More importantly, the specific antibodies against the microbial proteins are directed toward the commensal microbes commonly present on the surface of the human host, and these commensal microbes are important in shaping the development of the immune system and in maintaining the interaction between the human host and the environment. Persistence of these anti-microbial antibodies in patients but not in normal healthy individuals suggests abnormal interaction between the human host and the commensal microbes in the body. Elimination of the organism/organisms that elicits the antibody response would be a new avenue of therapy to investigate in patients with autoimmune diseases.
Published: 2018
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48. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Author: Christopher J. Ricketts, Aguirre A. De Cubas, Huihui Fan, Christof C. Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A. Gibb, Rehan Akbani, Rameen Beroukhim, Donald P. Bottaro, Toni K. Choueiri, Richard A. Gibbs, Andrew K. Godwin, Scott Haake, A. Ari Hakimi, Elizabeth P. Henske, James J. Hsieh, Thai H. Ho, Rupa S. Kanchi, Bhavani Krishnan, David J. Kwaitkowski, Wembin Lui, Maria J. Merino, Gordon B. Mills, Jerome Myers, Michael L. Nickerson, Victor E. Reuter, Laura S. Schmidt, C. Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George Thomas, Benjamin G. Vincent, Cathy D. Vocke, David A. Wheeler, Lixing Yang, William T. Kim, A. Gordon Robertson, Paul T. Spellman, W. Kimryn Rathmell, W. Marston Linehan, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Toshinori Hinoue, Peter W. Laird, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival. : Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtype-specific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes. Keywords: clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma, CDKN2A, DNA hypermethylation, immune signature, chromatin remodeling, TCGA, PanCanAtlas
Published: 2018
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49. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author: Qingsong Gao, Wen-Wei Liang, Steven M. Foltz, Gnanavel Mutharasu, Reyka G. Jayasinghe, Song Cao, Wen-Wei Liao, Sheila M. Reynolds, Matthew A. Wyczalkowski, Lijun Yao, Lihua Yu, Sam Q. Sun, Ken Chen, Alexander J. Lazar, Ryan C. Fields, Michael C. Wendl, Brian A. Van Tine, Ravi Vij, Feng Chen, Matti Nykter, Ilya Shmulevich, Li Ding, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy. : Gao et al. analyze a 9,624 sample TCGA cohort with 33 cancer types to detect gene fusion events. They provide a landscape of fusion events detected, relate fusions to gene expression, focus on kinase fusion structures, examine mutually exclusive mutation and fusion patterns, and highlight fusion druggability. Keywords: fusion, cancer, RNA, translocation, gene fusions
Published: 2018
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50. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Author: Joel Saltz, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, Vu Nguyen, Dimitris Samaras, Kenneth R. Shroyer, Tianhao Zhao, Rebecca Batiste, John Van Arnam, Ilya Shmulevich, Arvind U.K. Rao, Alexander J. Lazar, Ashish Sharma, Vésteinn Thorsson, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment. : Tumor-infiltrating lymphocytes (TILs) were identified from standard pathology cancer images by a deep-learning-derived “computational stain” developed by Saltz et al. They processed 5,202 digital images from 13 cancer types. Resulting TIL maps were correlated with TCGA molecular data, relating TIL content to survival, tumor subtypes, and immune profiles. Keywords: digital pathology, immuno-oncology, machine learning, lymphocytes, tumor microenvironment, deep learning, tumor-infiltrating lymphocytes, artificial intelligence, bioinformatics, computer vision
Published: 2018
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