31,549 results on '"Samuel R"'
Search Results
2. A computational signature of self-other mergence in Borderline Personality Disorder
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Giles W. Story, Sam Ereira, Stephanie Valle, Samuel R. Chamberlain, Jon E. Grant, and Raymond J. Dolan
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Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Abstract A tendency to merge mental representations of self and other is thought to underpin the intense and unstable relationships that feature in Borderline Personality Disorder (BPD). However, clinical theories of BPD do not specify, in computational terms, how the perspectives of self and other might become confused. To address this question, we used a probabilistic false belief task (p-FBT) to examine how individuals with BPD (N = 38) and matched controls from the general population (N = 74) selectively assigned beliefs to self or other. The p-FBT requires participants to track a gradually changing quantity, whilst also predicting another person’s belief about that quantity. We found that BPD participants showed less selectivity in belief assignment compared with controls (Cohen’s d = 0.64). Behaviourally, participants with BPD tended to predict that others’ beliefs resembled their own. Modelling analysis revealed that BPD participants were prone to generalise their own learning signals to others. Furthermore, this generalising tendency correlated with BPD symptomatology across participants, even when controlling for demographic factors and affective psychopathology. Our results support a computational account of self-other mergence, based on a generalisation of learning across agents. Self-other generalisation in learning purports to explain key clinical features of BPD, and suggests a potential transdiagnostic marker of mentalising capability.
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- 2024
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3. Development and assessment of a machine learning tool for predicting emergency admission in Scotland
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James Liley, Gergo Bohner, Samuel R. Emerson, Bilal A. Mateen, Katie Borland, David Carr, Scott Heald, Samuel D. Oduro, Jill Ireland, Keith Moffat, Rachel Porteous, Stephen Riddell, Simon Rogers, Ioanna Thoma, Nathan Cunningham, Chris Holmes, Katrina Payne, Sebastian J. Vollmer, Catalina A. Vallejos, and Louis J. M. Aslett
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Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Abstract Emergency admissions (EA), where a patient requires urgent in-hospital care, are a major challenge for healthcare systems. The development of risk prediction models can partly alleviate this problem by supporting primary care interventions and public health planning. Here, we introduce SPARRAv4, a predictive score for EA risk that will be deployed nationwide in Scotland. SPARRAv4 was derived using supervised and unsupervised machine-learning methods applied to routinely collected electronic health records from approximately 4.8M Scottish residents (2013-18). We demonstrate improvements in discrimination and calibration with respect to previous scores deployed in Scotland, as well as stability over a 3-year timeframe. Our analysis also provides insights about the epidemiology of EA risk in Scotland, by studying predictive performance across different population sub-groups and reasons for admission, as well as by quantifying the effect of individual input features. Finally, we discuss broader challenges including reproducibility and how to safely update risk prediction models that are already deployed at population level.
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- 2024
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4. The effect of laser pulse evolution on down-ramp injection in laser wakefield accelerators
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Arohi Jain, Samuel R. Yoffe, Bernhard Ersfeld, George K. Holt, Devki Nandan Gupta, and Dino A. Jaroszynski
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Medicine ,Science - Abstract
Abstract Electron self-injection in laser wakefield accelerators (LWFAs) is an important determinator of electron beam parameters. Controllable and adjustable LWFA beams are essential for applications. Controlled injection by capturing sheath electrons can be achieved using plasma density down-ramps or bumps, which perturb the LWFA bubble phase velocity by varying the plasma frequency and by affecting relativistic self-focussing of the laser. We report on a comprehensive study, using particle-in-cell simulations, of the effect of laser pulse evolution on injection on density perturbations. We show how the LWFA can be optimised to make it suitable for use in a wide range of applications, in particular those requiring short duration, low slice-emittance and low energy spread, and high-charge electron bunches.
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- 2024
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5. Evaluating attitudes on health-seeking behavior among a network of people who inject drugs
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Ayako Shimada, Ashley L. Buchanan, Natallia V. Katenka, Benjamin Skov, Gabrielle Lemire, Stephen Kogut, and Samuel R. Friedman
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Causal inference ,Dissemination ,Health attitudes ,HIV/AIDS ,Injection drug use ,Interference ,Applied mathematics. Quantitative methods ,T57-57.97 - Abstract
Abstract People who inject drugs (PWID) are often members of HIV/AIDS risk networks, where individuals engage in sexual and injection risk behavior. Engagement in HIV care is important for this population. Low socioeconomic status, stigmatization, and lack of access to medical care often complicate successful engagement in the HIV cascade of care for PWID. This study investigates how individual's attitudes about how much control they have over HIV/AIDS risk in their life (i.e., locus of control and self-blame) affect health-seeking behavior in PWID participants and their community members. We applied causal inference methodology to PWID HIV risk networks ascertained from the Social Factors and HIV Risk Study (SFHR) conducted between 1991 and 1993 in Bushwick, Brooklyn, New York. We estimated protective disseminated effects of attitudes toward HIV/AIDS on the health-seeking behaviors of others in the PWID community. In other words, a positive attitude toward controlling HIV/AIDS can improve the health-seeking behavior of other members of the community who report a pessimistic attitude toward HIV/AIDS control. Given this finding, we also discuss potential network interventions to improve health-seeking behavior among both PWID individuals who receive the intervention and others in the PWID network informed by our analysis of disseminated effects.
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- 2024
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6. Testing the form-function paradigm: body shape correlates with kinematics but not energetics in selectively-bred birds
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Samuel R. R. Cross, Andres C. Marmol-Guijarro, Karl T. Bates, John C. Marrin, Peter G. Tickle, Kayleigh A. Rose, and Jonathan R. Codd
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Biology (General) ,QH301-705.5 - Abstract
Abstract A central concept of evolutionary biology, supported by broad scale allometric analyses, asserts that changing morphology should induce downstream changes in locomotor kinematics and energetics, and by inference selective fitness. However, if these mechanistic relationships exist at local intraspecific scales, where they could provide substrate for fundamental microevolutionary processes, is unknown. Here, analyses of selectively-bred duck breeds demonstrate that distinct body shapes incur kinematic shifts during walking, but these do not translate into differences in energetics. A combination of modular relationships between anatomical regions, and a trade-off between limb flexion and trunk pitching, are shown to homogenise potential functional differences between the breeds, accounting for this discrepancy between form and function. This complex interplay between morphology, motion and physiology indicates that understanding evolutionary links between the avian body plan and locomotor diversity requires studying locomotion as an integrated whole and not key anatomical innovations in isolation.
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- 2024
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7. A randomized clinical trial of the impact of melatonin on influenza vaccine: Outcomes from the melatonin and vaccine response immunity and chronobiology study (MAVRICS)
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Rachel U. Lee, Nora L. Watson, Gena L. Glickman, Lindsey White, Sandra D. Isidean, Chad K. Porter, Monique Hollis-Perry, Samuel R. Walther, Santina Maiolatesi, Martha Sedegah, Harini Ganeshan, Jun Huang, David A. Boulifard, Daniel Ewing, Appavu K. Sundaram, Elizabeth M. Harrison, Katherine DeTizio, Maria Belmonte, Arnel Belmonte, Sandra Inoue, Alexandra Easterling, Elizabeth S. Cooper, and Janine Danko
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Vaccine immunogenicity ,influenza vaccine ,melatonin ,vaccine adjuvant ,humoral immunity ,cellular immunity ,Immunologic diseases. Allergy ,RC581-607 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Vaccine immunogenicity is affected by a variety of factors. Melatonin has been reported to affect immune responses to vaccines and infection. This was a randomized open-label trial – in which adults scheduled to receive the influenza vaccine were randomized to 5 mg melatonin or control to evaluate the effect of post-vaccination melatonin on humoral (hemagglutination-inhibition assays, HAI) and cellular (FluoroSpot) vaccine-specific cytokine responses 14–21 days post-vaccination. A total of 108 participants (melatonin treatment group: 53; control group: 55) completed the study. The groups were similar in baseline characteristics, including sleep as measured by the Pittsburgh Sleep Quality Index. Seroconversion rates or geometric mean fold rises (GMFR) in HAI titers did not vary by treatment group. There were also no statistically significant differences between pre- and post-vaccination levels of interferon gamma (IFN-γ) or granzyme B (GzB) by treatment; however, there was a significantly higher fold rise in the double secretor (IFN-γ + GzB) peripheral blood mononuclear cells for influenza vaccine in subjects taking daily melatonin (GMFR 1.7; 95% CI 1.3, 2.3) compared to those who did not (GMFR 0.9; 95% CI 0.7, 1.1) (p
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- 2024
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8. Compulsive buying disorder: Conceptualization based on addictive, impulsive, and obsessive-compulsive features and comorbidity
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Jon E. Grant and Samuel R. Chamberlain
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Impulsivity ,Compulsivity ,Addiction ,Oniomania ,Compulsive buying ,Psychiatry ,RC435-571 - Abstract
Background: This study sought to examine the conceptualization of compulsive buying disorder in a sample of adults drawn from the community and its associated mental health correlates. Methods: An online survey of “Personality, Mental Health, and Well-Being” was distributed to 300 adults aged 18–75 years. The survey measured a range of behaviors, such as buying behavior, alcohol and drug use, impulse control disorders, and dimensional constructs of impulsivity and obsessive-compulsiveness. Results: A total of 294 participants (54.7% female) completed the survey and were included in the analysis. The overall frequency of probable compulsive buying disorder was 5.4% (n = 16). Compared to adults without compulsive buying disorder, those with probable compulsive buying disorder were significantly less likely to identify as heterosexual and were significantly more likely to endorse attention-deficit hyperactivity disorder, drug use problems, symptoms of borderline personality disorder, binge eating disorder, and had higher levels of compulsivity plus impulsivity. Conclusion: Compulsive buying disorder appears to be fairly common in adults and appears to have symptom or diagnostic overlap with obsessive-compulsive problems, addictive disorders, and impulse control disorders. Findings highlight the need for careful clinical screening to identify often overlooked comorbidities and treat them on an individual patient basis, as well as the need to conduct high-quality clinical trials for compulsive buying disorder itself and to explore its presentation longitudinally at large scale.
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- 2024
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9. Detailed immune profiling in pediatric Crohn’s disease using methylation cytometry
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Samuel R. Reynolds, Lucas A. Salas, Ji-Qing Chen, and Brock C. Christensen
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Crohn’s disease ,DNA methylation ,deconvolution ,epigenome wide association study ,pediatric ,Genetics ,QH426-470 - Abstract
ABSTRACTDNA methylation has been extensively utilized to study epigenetic patterns across many diseases as well as to deconvolve blood cell type proportions. This study builds upon previous studies examining methylation patterns in paediatric patients with varying stages of Crohn’s disease to extend the immune profiling of these patients using a novel deconvolution approach. Compared with control subjects, we observed significantly decreased levels of CD4 memory and naive, CD8 naive, and natural killer cells and elevated neutrophil levels in Crohn’s disease. In addition, Crohn’s patients had a significantly elevated neutrophil-to-lymphocyte ratio. Using an epigenome-wide association approach and adjusting for potential confounders, including cell type, we observed 397 differentially methylated CpG (DMC) sites associated with Crohn’s disease. The top genetic pathway associated with the DMCs was the regulation of arginine metabolic processes which are involved in the regulation of T cells.
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- 2024
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10. Sequential Deactivation Across the Hippocampus‐Thalamus‐mPFC Pathway During Loss of Consciousness
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Xiaoai Chen, Samuel R. Cramer, Dennis C.Y. Chan, Xu Han, and Nanyin Zhang
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anesthesia‐induced unconsciousness ,electrophysiology ,fMRI ,hippocampus ,medial prefrontal cortex ,rat ,Science - Abstract
Abstract How consciousness is lost in states such as sleep or anesthesia remains a mystery. To gain insight into this phenomenon, concurrent recordings of electrophysiology signals in the anterior cingulate cortex and whole‐brain functional magnetic resonance imaging (fMRI) are conducted in rats exposed to graded propofol, undergoing the transition from consciousness to unconsciousness. The results reveal that upon the loss of consciousness (LOC), there is a sharp increase in low‐frequency power of the electrophysiological signal. Additionally, fMRI signals exhibit a cascade of deactivation across a pathway including the hippocampus, thalamus, and medial prefrontal cortex (mPFC) surrounding the moment of LOC, followed by a broader increase in brain activity across the cortex during sustained unconsciousness. Furthermore, sliding window analysis demonstrates a temporary increase in synchrony of fMRI signals across the hippocampus‐thalamus‐mPFC pathway preceding LOC. These data suggest that LOC may be triggered by sequential activities in the hippocampus, thalamus, and mPFC, while wide‐spread activity increases in other cortical regions commonly observed during anesthesia‐induced unconsciousness may be a consequence, rather than a cause of LOC. Taken together, the study identifies a cascade of neural events unfolding as the brain transitions into unconsciousness, offering insight into the systems‐level neural mechanisms underpinning LOC.
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- 2024
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11. The β2-adrenergic biased agonist nebivolol inhibits the development of Th17 and the response of memory Th17 cells in an NF-κB-dependent manner
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Mehri Hajiaghayi, Fatemeh Gholizadeh, Eric Han, Samuel R. Little, Niloufar Rahbari, Isabella Ardila, Carolina Lopez Naranjo, Kasra Tehranimeh, Steve C. C. Shih, and Peter J. Darlington
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nebivolol ,Th17 cells ,IL-17A ,biased agonist ,beta-adrenergic receptor ,anti-inflammatory response ,Immunologic diseases. Allergy ,RC581-607 - Abstract
IntroductionAdrenergic receptors regulate metabolic, cardiovascular, and immunological functions in response to the sympathetic nervous system. The effect of β2-adrenergic receptor (AR) as a high expression receptor on different subpopulations of T cells is complex and varies depending on the type of ligand and context. While traditional β2-AR agonists generally suppress T cells, they potentially enhance IL-17A production by Th17 cells. The effects of pharmacological drugs that count as biased agonists of AR like nebivolol are not completely understood. We investigated the impact of nebivolol on human memory CD4+ T (Th1, Th2, Th17) cells and polarized naive Th17 cells, highlighting its potential for IL-17A suppression via a non-canonical β2-AR cell signaling pathway.MethodsThe effects of nebivolol were tested on healthy human peripheral blood mononuclear cells, purified memory Th cells, and polarized naive Th17 cells activated with anti-CD3/anti-CD28/anti-CD2 ImmunoCult reagent. IFN-γ, IL-4, and IL-17A, which are primarily derived from Th1, Th2, and Th17 cells, respectively, were quantified by ELISA and flow cytometry. IL-10 was measured by ELISA. Gene expression of RORC, ADRB1, ADRB2, and ADRB3 was evaluated by qPCR. The ADRB2 gene was knocked out in memory Th cells using CRISPR/Cas9. Protein expression of phosphorylated serine133-CREB and phosphorylated NF-κB p65 was assessed by Western blot. Proliferation was assessed by fluorescent dye loading and flow cytometry.ResultsNebivolol treatment decreased IL-17A and IFN-γ secretion by activated memory Th cells and elevated IL-4 levels. Nebivolol reduced the proportion of IL-17A+ Th cells and downregulated RORC expression. Unlike the β2-AR agonist terbutaline, nebivolol inhibited the shift of naive CD4+ T cells toward the Th17 phenotype. IL-10 and the proliferation index remained unchanged. Nebivolol-treated β2-knockout memory Th cells showed significant inhibition of β2-AR-mediated signaling, evidenced by the absence of IL-17A suppression compared to controls. Phosphorylation of the NF-κB p65 subunit was inhibited by nebivolol, but CREB phosphorylation was not changed, suggesting a selective transcriptional control.ConclusionsThe findings demonstrate that nebivolol acts through a β2-AR-mediated signaling pathway, as a distinctive anti-inflammatory agent capable of selectively shifting Th17 cells and suppressing the phosphorylation of NF-κB. This highlights nebivolol’s potential for therapeutic interventions in chronic autoimmune conditions with elevated IL-17A levels.
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- 2024
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12. Validation of an abbreviated Big Five personality inventory at large population scale: Psychometric structure and associations with common psychiatric and neurological disorders
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Weixi Kang, Jeggan Tiego, Peter J. Hellyer, William Trender, Jon E. Grant, Samuel R. Chamberlain, and Adam Hampshire
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Personality ,Big Five ,Validation ,Reliability ,Psychopathology ,neurology ,Psychiatry ,RC435-571 - Abstract
Background: The five-factor model of personality, as quantified using instruments such as the Big Five Inventory, consists of broad personality domains including Extraversion, Agreeableness, Conscientiousness, Neuroticism (emotional instability), and Openness. Such instruments typically include >40 items. However, instruments with many items can be unwieldly and a cause of measurement error in clinical and cohort studies where multiple scales are sequenced. Conversely, established 5- and 10-item versions of the Big Five Inventory have poor reliability. Here, we developed and validated an abbreviated 18-item Big Five Inventory that balances efficiency, reliability and sensitivity. Method: We analysed three datasets (N = 59,797, N = 21,177, and N = 87,983) from individuals who participated in the online Great British Intelligence Test (GBIT) study, a collaborative citizen science project with BBC2 Horizon. We applied factor analyses (FA), predictive normative modelling, and one-sample t-tests to validate the 18-item version of the Big Five and to investigate its associations with psychiatric and neurological conditions. Results: The 18-item version of the Big Five Inventory had higher validity and retest reliability compared to the other previously shortened versions in the literature, with comparable demographic associations to the full Big Five Inventory. It exhibited strong (i.e. large effect size) associations with psychiatric conditions, and moderate (small-medium) associations with neurological conditions. Neuroticism (emotional instability) was substantially higher in all psychiatric conditions, whereas Conscientiousness, Openness and Extraversion showed differential associations across conditions. Conclusion: The newly validated 18-item version of the Big Five provides a convenient means of measuring personality traits that is suitable for deployment in a range of studies. It retains psychometric structure, retest reliability and clinical-group sensitivity, as compared to the full original scale.
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- 2024
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13. Network model of skeletal muscle cell signalling predicts differential responses to endurance and resistance exercise training
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Annabelle Fowler, Katherine R. Knaus, Stephanie Khuu, Ali Khalilimeybodi, Simon Schenk, Samuel R. Ward, Andrew C. Fry, Padmini Rangamani, and Andrew D. McCulloch
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computational model ,endurance exercise ,exercise ,resistance exercise ,signalling network ,skeletal muscle ,Physiology ,QP1-981 - Abstract
Abstract Exercise‐induced muscle adaptations vary based on exercise modality and intensity. We constructed a signalling network model from 87 published studies of human or rodent skeletal muscle cell responses to endurance or resistance exercise in vivo or simulated exercise in vitro. The network comprises 259 signalling interactions between 120 nodes, representing eight membrane receptors and eight canonical signalling pathways regulating 14 transcriptional regulators, 28 target genes and 12 exercise‐induced phenotypes. Using this network, we formulated a logic‐based ordinary differential equation model predicting time‐dependent molecular and phenotypic alterations following acute endurance and resistance exercises. Compared with nine independent studies, the model accurately predicted 18/21 (85%) acute responses to resistance exercise and 12/16 (75%) acute responses to endurance exercise. Detailed sensitivity analysis of differential phenotypic responses to resistance and endurance training showed that, in the model, exercise regulates cell growth and protein synthesis primarily by signalling via mechanistic target of rapamycin, which is activated by Akt and inhibited in endurance exercise by AMP‐activated protein kinase. Endurance exercise preferentially activates inflammation via reactive oxygen species and nuclear factor κB signalling. Furthermore, the expected preferential activation of mitochondrial biogenesis by endurance exercise was counterbalanced in the model by protein kinase C in response to resistance training. This model provides a new tool for investigating cross‐talk between skeletal muscle signalling pathways activated by endurance and resistance exercise, and the mechanisms of interactions such as the interference effects of endurance training on resistance exercise outcomes.
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- 2024
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14. Assessing Spillover Effects of Medications for Opioid Use Disorder on HIV Risk Behaviors among a Network of People Who Inject Drugs
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Joseph Puleo, Ashley Buchanan, Natallia Katenka, M. Elizabeth Halloran, Samuel R. Friedman, and Georgios Nikolopoulos
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causal inference ,networks ,spillover ,community detection ,Human Immunodeficiency Virus ,People Who Inject Drugs ,Statistics ,HA1-4737 - Abstract
People who inject drugs (PWID) have an increased risk of HIV infection partly due to injection behaviors often related to opioid use. Medications for opioid use disorder (MOUD) have been shown to reduce HIV infection risk, possibly by reducing injection risk behaviors. MOUD may benefit individuals who do not receive it themselves but are connected through social, sexual, or drug use networks with individuals who are treated. This is known as spillover. Valid estimation of spillover in network studies requires considering the network’s community structure. Communities are groups of densely connected individuals with sparse connections to other groups. We analyzed a network of 277 PWID and their contacts from the Transmission Reduction Intervention Project. We assessed the effect of MOUD on reductions in injection risk behaviors and the possible benefit for network contacts of participants treated with MOUD. We identified communities using modularity-based methods and employed inverse probability weighting with community-level propensity scores to adjust for measured confounding. We found that MOUD may have beneficial spillover effects on reducing injection risk behaviors. The magnitudes of estimated effects were sensitive to the community detection method. Careful consideration should be paid to the significance of community structure in network studies evaluating spillover.
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- 2024
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15. SARS-CoV-2 Disease Severity and Cycle Threshold Values in Children Infected during Pre-Delta, Delta, and Omicron Periods, Colorado, USA, 2021–2022
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Laura Bankers, Shannon C. O’Brien, Diana M. Tapay, Erin Ho, Isaac Armistead, Alexis Burakoff, Samuel R. Dominguez, and Shannon R. Matzinger
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COVID-19 ,coronavirus disease ,SARS-CoV-2 ,severe acute respiratory syndrome coronavirus 2 ,viruses ,respiratory infections ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
In adults, viral load and disease severity can differ by SARS-CoV-2 variant, patterns less understood in children. We evaluated symptomatology, cycle threshold (Ct) values, and SARS-CoV-2 variants among 2,299 pediatric SARS-CoV-2 patients (0–21 years of age) in Colorado, USA, to determine whether children infected with Delta or Omicron had different symptom severity or Ct values than during earlier variants. Children infected during the Delta and Omicron periods had lower Ct values than those infected during pre-Delta, and children
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- 2024
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16. Evaluation of the physical characteristics of reinforced concrete subject to corrosion using a poro-elastic acoustic model inversion technique applied to ultrasonic measurements
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Pierre-Philippe Beaujean, Samuel R. Shaffer, Francisco Presuel-Moreno, and Matthew Brogden
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Non-destructive testing ,Biot-Stoll ,Ultrasonics ,Reinforced concrete corrosion ,Poro-elastic modeling ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Abstract The use of reinforced concrete is foundational to modern infrastructure. Acknowledging this, it is imperative that health monitoring techniques be in place to study corrosion within these structures. By using a non-destructive method for detecting the early formation of cracks within reinforced concrete, the method presented in this paper seeks to improve upon traditional techniques of monitoring corrosion, within reinforced concrete structures. In this paper, the authors present a method to evaluate the physical characteristics of reinforced concrete subject to corrosion using a poro-elastic acoustic model inversion technique applied to a set of ultrasonic measurements, which constitutes a novel approach to the problem of observing the impact of corroding rebars and resulting concrete damage. A non-contact ultrasonic transducer is operated at a carrier frequency of 500 [kHz], with a layer of saltwater separating the sensor from the concrete surface. Following this non-contact measurement collection of the surface and rebar echo responses, a poro-elastic model is used to model the sound propagation, through an adapted version of the Biot-Stoll model. At first, a set of default parameters, obtained from the physical characteristics of the reinforced concrete, are used to match experimental and simulated acoustic signature of the sample. Performing statistical averaging along the corroding rebar within three samples over a period of nearly nine months, a small but monotonous increase in the distance between the concrete surface and the top of the rebar, indicating gradual corrosion of the rebar. Next, a non-linear optimization algorithm is used to optimize the match between measured and simulated echoes. Through the implementation of this model parameter optimization, the root mean square error between measured and simulated responses was reduced by 63.7% for the full signal, and 62.6% for the rebar echo.
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- 2024
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17. Biomolecular condensates form spatially inhomogeneous network fluids
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Furqan Dar, Samuel R. Cohen, Diana M. Mitrea, Aaron H. Phillips, Gergely Nagy, Wellington C. Leite, Christopher B. Stanley, Jeong-Mo Choi, Richard W. Kriwacki, and Rohit V. Pappu
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Science - Abstract
Abstract The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.
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- 2024
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18. Precision measurement of rehabilitation interventions—a secondary analysis of motor error in a clinical trial with young children with cerebral palsy
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Julie C. Skorup, Samuel R. Pierce, Athylia C. Paremski, Morgan Alcott, and Laura A. Prosser
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cerebral palsy ,motor function ,motor error ,precision rehabilitation ,intervention ,Pediatrics ,RJ1-570 - Abstract
IntroductionThe delivery of precision medicine in rehabilitation will require not only precise measurement of participant response, but also precise measurement of the “ingredients” of intervention and their dose. As an example, we report the measurement of motor error in two treatment groups from a randomized controlled trial in toddlers (mean age 26.3 months) with cerebral palsy (CP). Our objective was to measure the type and amount of motor error during physical therapy sessions in young children with CP.MethodsParticipants were stratified by motor function and age and randomly allocated to “conventional” physical therapy that generally prevented falls or to an intervention that encouraged error experience by not preventing falls (experimental group). Baseline motor and cognitive function were measured using the Gross Motor Function Measure-66 (GMFM-66) and Bayley 3 cognitive subscale (B3-C) prior to randomization. Randomly selected video recorded therapy sessions were manually coded to identify losses of balance defined as falls (child contacted floor), rescues (therapist prevented fall) or saves (child recovered their balance independently).ResultsAverage number of losses of balance per session were higher in the experimental group than the conventional group due to significantly greater falls. Saves were infrequent in both groups but were also significantly higher in the experimental group. Average number of rescues did not differ between groups. In the experimental group, greater frequency of falls was significantly related to GMFM-66. In both groups, greater frequency of saves was related to GMFM-66. Neither total losses of balance per session nor rescues were related to GMFM-66 in either group. There were no significant relationships between losses of balance and baseline cognition in either group, except greater frequency of saves was related to higher cognitive ability in the experimental group.DiscussionOur observations suggest that motor error experience is lower in toddlers with CP compared to peers with typical development but can be manipulated to higher doses of error during therapy sessions. Future work should investigate the relationship between type and amount of error experience and rehabilitation outcomes, as well as other “ingredients” of rehabilitation therapy. Tools to automate the precise measurement of intervention content are necessary for broad scale implementation.
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- 2024
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19. Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons
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Eliska Zlamalova, Catherine Rodger, Francesca Greco, Samuel R. Cheers, Julia Kleniuk, Aishwarya G. Nadadhur, Zuzana Kadlecova, and Evan Reid
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Atlastin ,Hereditary spastic paraplegia ,Endoplasmic reticulum morphology ,Endosomal traffic ,Endosomal tubulation ,Lysosome ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Mutation of the ATL1 gene is one of the most common causes of hereditary spastic paraplegia (HSP), a group of genetic neurodegenerative conditions characterised by distal axonal degeneration of the corticospinal tract axons. Atlastin-1, the protein encoded by ATL1, is one of three mammalian atlastins, which are homologous dynamin-like GTPases that control endoplasmic reticulum (ER) morphology by fusing tubules to form the three-way junctions that characterise ER networks. However, it is not clear whether atlastin-1 is required for correct ER morphology in human neurons and if so what the functional consequences of lack of atlastin-1 are. Using CRISPR-inhibition we generated human cortical neurons lacking atlastin-1. We demonstrate that ER morphology was altered in these neurons, with a reduced number of three-way junctions. Neurons lacking atlastin-1 had longer endosomal tubules, suggestive of defective tubule fission. This was accompanied by reduced lysosomal proteolytic capacity. As well as demonstrating that atlastin-1 is required for correct ER morphology in human neurons, our results indicate that lack of a classical ER-shaping protein such as atlastin-1 may cause altered endosomal tubulation and lysosomal proteolytic dysfunction. Furthermore, they strengthen the idea that defective lysosome function contributes to the pathogenesis of a broad group of HSPs, including those where the primary localisation of the protein involved is not at the endolysosomal system.
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- 2024
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20. Adaptive robustness through incoherent signaling mechanisms in a regenerative brain
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Samuel R. Bray, Livia S. Wyss, Chew Chai, Maria E. Lozada, and Bo Wang
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CP: Neuroscience ,Biology (General) ,QH301-705.5 - Abstract
Summary: Animal behavior emerges from collective dynamics of neurons, making it vulnerable to damage. Paradoxically, many organisms exhibit a remarkable ability to maintain significant behavior even after large-scale neural injury. Molecular underpinnings of this extreme robustness remain largely unknown. Here, we develop a quantitative pipeline to measure long-lasting latent states in planarian flatworm behaviors during whole-brain regeneration. By combining >20,000 animal trials with neural network modeling, we show that long-range volumetric peptidergic signals allow the planarian to rapidly restore coarse behavior output after large perturbations to the nervous system, while slow restoration of small-molecule neuromodulator functions refines precision. This relies on the different time and length scales of neuropeptide and small-molecule transmission to generate incoherent patterns of neural activity that competitively regulate behavior. Controlling behavior through opposing communication mechanisms creates a more robust system than either alone and may serve as a generalizable approach for constructing robust neural networks.
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- 2024
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21. Disparity in temporal and spatial relationships between resting-state electrophysiological and fMRI signals
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Wenyu Tu, Samuel R Cramer, and Nanyin Zhang
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resting-state fMRI ,electrophysiology ,rat ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Resting-state brain networks (RSNs) have been widely applied in health and disease, but the interpretation of RSNs in terms of the underlying neural activity is unclear. To address this fundamental question, we conducted simultaneous recordings of whole-brain resting-state functional magnetic resonance imaging (rsfMRI) and electrophysiology signals in two separate brain regions of rats. Our data reveal that for both recording sites, spatial maps derived from band-specific local field potential (LFP) power can account for up to 90% of the spatial variability in RSNs derived from rsfMRI signals. Surprisingly, the time series of LFP band power can only explain to a maximum of 35% of the temporal variance of the local rsfMRI time course from the same site. In addition, regressing out time series of LFP power from rsfMRI signals has minimal impact on the spatial patterns of rsfMRI-based RSNs. This disparity in the spatial and temporal relationships between resting-state electrophysiology and rsfMRI signals suggests that electrophysiological activity alone does not fully explain the effects observed in the rsfMRI signal, implying the existence of an rsfMRI component contributed by ‘electrophysiology-invisible’ signals. These findings offer a novel perspective on our understanding of RSN interpretation.
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- 2024
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22. Too Many Deaths, Too Many Left Behind: A People's External Review of the U.S. Centers for Disease Control and Prevention's COVID-19 Pandemic Response
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Lara Z. Jirmanus, MD, MPH, Rita M. Valenti, RN, Eiryn A. Griest Schwartzman, CHES, Sophia A. Simon-Ortiz, MPH, Lauren I. Frey, MPH, Samuel R. Friedman, PhD, and Mindy T. Fullilove, MD
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COVID-19 pandemic ,U.S. Centers for Disease Control and Prevention ,health equity ,ethics ,population health ,nonpharmaceutical interventions ,Public aspects of medicine ,RA1-1270 - Abstract
The U.S. population has suffered worse health consequences owing to COVID-19 than comparable wealthy nations. COVID-19 had caused more than 1.1 million deaths in the U.S. as of May 2023 and contributed to a 3-year decline in life expectancy. A coalition of public health workers and community activists launched an external review of the Centers for Disease Control and Prevention's pandemic management from January 2021 to May 2023. The authors used a modified Delphi process to identify core pandemic management areas, which formed the basis for a survey and literature review. Their analysis yields 3 overarching shortcomings of the Centers for Disease Control and Prevention's pandemic management: (1) Centers for Disease Control and Prevention leadership downplays the serious impacts and aerosol transmission risks of COVID-19, (2) Centers for Disease Control and Prevention leadership has aligned public guidance with commercial and political interests over scientific evidence, and (3) Centers for Disease Control and Prevention guidance focuses on individual choice rather than emphasizing prevention and equity. Instead, the agency must partner with communities most impacted by the pandemic and encourage people to protect one another using layered protections to decrease COVID-19 transmission. Because emerging variants can already evade existing vaccines and treatments and Long COVID can be disabling and lacks definitive treatment, multifaceted, sustainable approaches to the COVID-19 pandemic are essential to protect people, the economy, and future generations.
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- 2024
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23. Unmet patient needs in monocarboxylate transporter 8 (MCT8) deficiency: a review
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Andrew J. Bauer, Bethany Auble, Amy L. Clark, Tina Y. Hu, Amber Isaza, Kyle P. McNerney, Daniel L. Metzger, Lindsey Nicol, Samuel R. Pierce, and Richard Sidlow
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MCT8 deficiency ,MCT8 ,Allan-Herndon-Dudley syndrome ,AHDS ,developmental delay ,T3 ,Pediatrics ,RJ1-570 - Abstract
Monocarboxylate transporter 8 (MCT8) deficiency is a rare, X-linked disorder arising from mutations in the SLC16A2 gene and resulting from dysfunctional thyroid hormone transport. This disorder is characterized by profound neurodevelopmental delay and motor disability due to a lack of thyroid hormone in the brain, and coexisting endocrinological symptoms, due to chronic thyrotoxicosis, resulting from elevated thyroid hormone outside the central nervous system (CNS). In February 2024, we reviewed the published literature to identify relevant articles reporting on the current unmet needs of patients with MCT8 deficiency. There are several main challenges in the diagnosis and treatment of MCT8 deficiency, with decreased awareness and recognition of MCT8 deficiency among healthcare professionals (HCPs) associated with misdiagnosis and delays in diagnosis. Diagnostic delay may also be attributed to other factors, including the complex symptomology of MCT8 deficiency only becoming apparent several months after birth and pathognomonic serum triiodothyronine (T3) testing not being routinely performed. For patients with MCT8 deficiency, multidisciplinary team care is vital to optimize the support provided to patients and their caregivers. Although there are currently no approved treatments specifically for MCT8 deficiency, earlier identification and diagnosis of this disorder enables earlier access to supportive care and developing treatments focused on improving outcomes and quality of life for both patients and caregivers.
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- 2024
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24. Multimodal Surveillance Model for Enterovirus D68 Respiratory Disease and Acute Flaccid Myelitis among Children in Colorado, USA, 2022
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Kevin Messacar, Shannon Matzinger, Kevin Berg, Kirsten Weisbeck, Molly Butler, Nicholas Pysnack, Hai Nguyen-Tran, Emily Spence Davizon, Laura Bankers, Sarah A. Jung, Meghan Birkholz, Allison Wheeler, and Samuel R. Dominguez
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Enterovirus D68 ,EV-D68 ,surveillance ,disease outbreak ,viruses ,Colorado ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Surveillance for emerging pathogens is critical for developing early warning systems to guide preparedness efforts for future outbreaks of associated disease. To better define the epidemiology and burden of associated respiratory disease and acute flaccid myelitis (AFM), as well as to provide actionable data for public health interventions, we developed a multimodal surveillance program in Colorado, USA, for enterovirus D68 (EV-D68). Timely local, state, and national public health outreach was possible because prospective syndromic surveillance for AFM and asthma-like respiratory illness, prospective clinical laboratory surveillance for EV-D68 among children hospitalized with respiratory illness, and retrospective wastewater surveillance led to early detection of the 2022 outbreak of EV-D68 among Colorado children. The lessons learned from developing the individual layers of this multimodal surveillance program and how they complemented and informed the other layers of surveillance for EV-D68 and AFM could be applied to other emerging pathogens and their associated diseases.
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- 2024
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25. Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome
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Brian Walitt, Komudi Singh, Samuel R. LaMunion, Mark Hallett, Steve Jacobson, Kong Chen, Yoshimi Enose-Akahata, Richard Apps, Jennifer J. Barb, Patrick Bedard, Robert J. Brychta, Ashura Williams Buckley, Peter D. Burbelo, Brice Calco, Brianna Cathay, Li Chen, Snigdha Chigurupati, Jinguo Chen, Foo Cheung, Lisa M. K. Chin, Benjamin W. Coleman, Amber B. Courville, Madeleine S. Deming, Bart Drinkard, Li Rebekah Feng, Luigi Ferrucci, Scott A. Gabel, Angelique Gavin, David S. Goldstein, Shahin Hassanzadeh, Sean C. Horan, Silvina G. Horovitz, Kory R. Johnson, Anita Jones Govan, Kristine M. Knutson, Joy D. Kreskow, Mark Levin, Jonathan J. Lyons, Nicholas Madian, Nasir Malik, Andrew L. Mammen, John A. McCulloch, Patrick M. McGurrin, Joshua D. Milner, Ruin Moaddel, Geoffrey A. Mueller, Amrita Mukherjee, Sandra Muñoz-Braceras, Gina Norato, Katherine Pak, Iago Pinal-Fernandez, Traian Popa, Lauren B. Reoma, Michael N. Sack, Farinaz Safavi, Leorey N. Saligan, Brian A. Sellers, Stephen Sinclair, Bryan Smith, Joseph Snow, Stacey Solin, Barbara J. Stussman, Giorgio Trinchieri, Sara A. Turner, C. Stephenie Vetter, Felipe Vial, Carlotta Vizioli, Ashley Williams, Shanna B. Yang, Center for Human Immunology, Autoimmunity, and Inflammation (CHI) Consortium, and Avindra Nath
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Science - Abstract
Abstract Post-infectious myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) is a disabling disorder, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit PI-ME/CFS participants with matched controls to conduct deep phenotyping. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical conditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.
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- 2024
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26. Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer
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Samuel R. Reynolds, Ze Zhang, Lucas A. Salas, and Brock C. Christensen
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Prostate cancer ,Tumor microenvironment ,Deconvolution ,Epigenome-wide association study ,DNA methylation ,Differential expression analysis ,Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background Among men, prostate cancer (PCa) is the second most common cancer and the second leading cause of cancer death. Etiologic factors associated with both prostate carcinogenesis and somatic alterations in tumors are incompletely understood. While genetic variants associated with PCa have been identified, epigenetic alterations in PCa are relatively understudied. To date, DNA methylation (DNAm) and gene expression (GE) in PCa have been investigated; however, these studies did not correct for cell-type proportions of the tumor microenvironment (TME), which could confound results. Methods The data (GSE183040) consisted of DNAm and GE data from both tumor and adjacent non-tumor prostate tissue of 56 patients who underwent radical prostatectomies prior to any treatment. This study builds upon previous studies that examined methylation patterns and GE in PCa patients by using a novel tumor deconvolution approach to identify and correct for cell-type proportions of the TME in its epigenome-wide association study (EWAS) and differential expression analysis (DEA). Results The inclusion of cell-type proportions in EWASs and DEAs reduced the scope of significant alterations associated with PCa. We identified 2,093 significantly differentially methylated CpGs (DMC), and 51 genes associated with PCa, including PCA3, SPINK1, and AMACR. Conclusions This work illustrates the importance of correcting for cell types of the TME when performing EWASs and DEAs on PCa samples, and establishes a more confounding-adverse methodology. We identified a more tumor-cell-specific set of altered genes and epigenetic marks that can be further investigated as potential biomarkers of disease or potential therapeutic targets.
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- 2024
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27. Bipolar androgen therapy plus nivolumab for patients with metastatic castration-resistant prostate cancer: the COMBAT phase II trial
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Mark C. Markowski, Mary-Ellen Taplin, Rahul Aggarwal, Laura A. Sena, Hao Wang, Hanfei Qi, Aliya Lalji, Victoria Sinibaldi, Michael A. Carducci, Channing J. Paller, Catherine H. Marshall, Mario A. Eisenberger, David E. Sanin, Srinivasan Yegnasubramanian, Carolina Gomes-Alexandre, Busra Ozbek, Tracy Jones, Angelo M. De Marzo, Samuel R. Denmeade, and Emmanuel S. Antonarakis
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Science - Abstract
Abstract Cyclic high-dose testosterone administration, known as bipolar androgen therapy (BAT), is a treatment strategy for patients with metastatic castration-resistant prostate cancer (mCRPC). Here, we report the results of a multicenter, single arm Phase 2 study (NCT03554317) enrolling 45 patients with heavily pretreated mCRPC who received BAT (testosterone cypionate, 400 mg intramuscularly every 28 days) with the addition of nivolumab (480 mg intravenously every 28 days) following three cycles of BAT monotherapy. The primary endpoint of a confirmed PSA50 response rate was met and estimated at 40% (N = 18/45, 95% CI: 25.7–55.7%, P = 0.02 one-sided against the 25% null hypothesis). Sixteen of the PSA50 responses were achieved before the addition of nivolumab. Secondary endpoints included objective response rate (ORR), median PSA progression-free survival, radiographic progression-free survival (rPFS), overall survival (OS), and safety/tolerability. The ORR was 24% (N = 10/42). Three of the objective responses occurred following the addition of nivolumab. After a median follow-up of 17.9 months, the median rPFS was 5.6 (95% CI: 5.4–6.8) months, and median OS was 24.4 (95% CI: 17.6–31.1) months. BAT/nivolumab was well tolerated, resulting in only five (11%) drug related, grade-3 adverse events. In a predefined exploratory analysis, clinical response rates correlated with increased baseline levels of intratumoral PD-1 + T cells. In paired metastatic tumor biopsies, BAT induced pro-inflammatory gene expression changes that were restricted to patients achieving a clinical response. These data suggest that BAT may augment antitumor immune responses that are further potentiated by immune checkpoint blockade.
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- 2024
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28. Decarbonization in Australia and India: Bilateral Opportunities and Challenges for the Net Zero Transformation
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Marcello B. Solomon, Swapna S. Rabha, Gustavo Fimbres-Weihs, Himanshu Goyal, Firouzeh R. Taghikhah, Jithin J. Varghese, Samuel R. Wenger, Weibin Liang, Eleanor R. Kearns, Jun Huang, Niket S. Kaisare, and Deanna M. D’Alessandro
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Chemical engineering ,TP155-156 - Published
- 2024
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29. Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia
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Candice R. Gurbatri, Georgette A. Radford, Laura Vrbanac, Jongwon Im, Elaine M. Thomas, Courtney Coker, Samuel R. Taylor, YoungUk Jang, Ayelet Sivan, Kyu Rhee, Anas A. Saleh, Tiffany Chien, Fereshteh Zandkarimi, Ioana Lia, Tamsin R. M. Lannagan, Tongtong Wang, Josephine A. Wright, Hiroki Kobayashi, Jia Q. Ng, Matt Lawrence, Tarik Sammour, Michelle Thomas, Mark Lewis, Lito Papanicolas, Joanne Perry, Tracy Fitzsimmons, Patricia Kaazan, Amanda Lim, Alexandra M. Stavropoulos, Dion A. Gouskos, Julie Marker, Cheri Ostroff, Geraint Rogers, Nicholas Arpaia, Daniel L. Worthley, Susan L. Woods, and Tal Danino
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Science - Abstract
Abstract Bioengineered probiotics enable new opportunities to improve colorectal cancer (CRC) screening, prevention and treatment. Here, first, we demonstrate selective colonization of colorectal adenomas after oral delivery of probiotic E. coli Nissle 1917 (EcN) to a genetically-engineered murine model of CRC predisposition and orthotopic models of CRC. We next undertake an interventional, double-blind, dual-centre, prospective clinical trial, in which CRC patients take either placebo or EcN for two weeks prior to resection of neoplastic and adjacent normal colorectal tissue (ACTRN12619000210178). We detect enrichment of EcN in tumor samples over normal tissue from probiotic-treated patients (primary outcome of the trial). Next, we develop early CRC intervention strategies. To detect lesions, we engineer EcN to produce a small molecule, salicylate. Oral delivery of this strain results in increased levels of salicylate in the urine of adenoma-bearing mice, in comparison to healthy controls. To assess therapeutic potential, we engineer EcN to locally release a cytokine, GM-CSF, and blocking nanobodies against PD-L1 and CTLA-4 at the neoplastic site, and demonstrate that oral delivery of this strain reduces adenoma burden by ~50%. Together, these results support the use of EcN as an orally-deliverable platform to detect disease and treat CRC through the production of screening and therapeutic molecules.
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- 2024
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30. Publisher Correction: Development and assessment of a machine learning tool for predicting emergency admission in Scotland
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James Liley, Gergo Bohner, Samuel R. Emerson, Bilal A. Mateen, Katie Borland, David Carr, Scott Heald, Samuel D. Oduro, Jill Ireland, Keith Moffat, Rachel Porteous, Stephen Riddell, Simon Rogers, Ioanna Thoma, Nathan Cunningham, Chris Holmes, Katrina Payne, Sebastian J. Vollmer, Catalina A. Vallejos, and Louis J. M. Aslett
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Computer applications to medicine. Medical informatics ,R858-859.7 - Published
- 2024
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31. Challenges of COVID-19 Case Forecasting in the US, 2020-2021.
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Velma K Lopez, Estee Y Cramer, Robert Pagano, John M Drake, Eamon B O'Dea, Madeline Adee, Turgay Ayer, Jagpreet Chhatwal, Ozden O Dalgic, Mary A Ladd, Benjamin P Linas, Peter P Mueller, Jade Xiao, Johannes Bracher, Alvaro J Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Khoa Le, Anja Mühlemann, Jarad Niemi, Evan L Ray, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W Zorn, Sen Pei, Jeffrey Shaman, Teresa K Yamana, Samuel R Tarasewicz, Daniel J Wilson, Sid Baccam, Heidi Gurung, Steve Stage, Brad Suchoski, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Lily Wang, Yueying Wang, Shan Yu, Lauren Gardner, Sonia Jindal, Maximilian Marshall, Kristen Nixon, Juan Dent, Alison L Hill, Joshua Kaminsky, Elizabeth C Lee, Joseph C Lemaitre, Justin Lessler, Claire P Smith, Shaun Truelove, Matt Kinsey, Luke C Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Dean Karlen, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dave Osthus, Jiang Bian, Wei Cao, Zhifeng Gao, Juan Lavista Ferres, Chaozhuo Li, Tie-Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Matteo Chinazzi, Jessica T Davis, Kunpeng Mu, Ana Pastore Y Piontti, Alessandro Vespignani, Xinyue Xiong, Robert Walraven, Jinghui Chen, Quanquan Gu, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Graham Casey Gibson, Daniel Sheldon, Ajitesh Srivastava, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan Lewis, Madhav Marathe, Akhil Sai Peddireddy, Przemyslaw Porebski, Srinivasan Venkatramanan, Lijing Wang, Pragati V Prasad, Jo W Walker, Alexander E Webber, Rachel B Slayton, Matthew Biggerstaff, Nicholas G Reich, and Michael A Johansson
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Biology (General) ,QH301-705.5 - Abstract
During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.
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- 2024
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32. Examining the unique relationships between problematic use of the internet and impulsive and compulsive tendencies: network approach
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Chang Liu, Kristian Rotaru, Lei Ren, Samuel R. Chamberlain, Erynn Christensen, Mary-Ellen Brierley, Karyn Richardson, Rico S. C. Lee, Rebecca Segrave, Jon E. Grant, Edouard Kayayan, Sam Hughes, Leonardo F. Fontenelle, Amelia Lowe, Chao Suo, René Freichel, Reinout W. Wiers, Murat Yücel, and Lucy Albertella
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Compulsivity ,impulsivity ,network analysis ,problematic use of the internet (PUI) ,Psychiatry ,RC435-571 - Abstract
Background Both impulsivity and compulsivity have been identified as risk factors for problematic use of the internet (PUI). Yet little is known about the relationship between impulsivity, compulsivity and individual PUI symptoms, limiting a more precise understanding of mechanisms underlying PUI. Aims The current study is the first to use network analysis to (a) examine the unique association among impulsivity, compulsivity and PUI symptoms, and (b) identify the most influential drivers in relation to the PUI symptom community. Method We estimated a Gaussian graphical model consisting of five facets of impulsivity, compulsivity and individual PUI symptoms among 370 Australian adults (51.1% female, mean age = 29.8, s.d. = 11.1). Network structure and bridge expected influence were examined to elucidate differential associations among impulsivity, compulsivity and PUI symptoms, as well as identify influential nodes bridging impulsivity, compulsivity and PUI symptoms. Results Results revealed that four facets of impulsivity (i.e. negative urgency, positive urgency, lack of premeditation and lack of perseverance) and compulsivity were related to different PUI symptoms. Further, compulsivity and negative urgency were the most influential nodes in relation to the PUI symptom community due to their highest bridge expected influence. Conclusions The current findings delineate distinct relationships across impulsivity, compulsivity and PUI, which offer insights into potential mechanistic pathways and targets for future interventions in this space. To realise this potential, future studies are needed to replicate the identified network structure in different populations and determine the directionality of the relationships among impulsivity, compulsivity and PUI symptoms.
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- 2024
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33. Recurrent Postoperative Hemorrhage After Mohs Reconstruction in a Patient on Ruxolitinib
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David P. Grande, Samuel R. Auger, Diana Bolotin, and Joseph B. Meleca
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facial reconstruction ,leukemia ,Mohs reconstruction ,postoperative hemorrhage ,ruxolitinib (Jakafi®) ,tranexamic acid ,Otorhinolaryngology ,RF1-547 ,Surgery ,RD1-811 - Published
- 2024
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34. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia
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Vanessa I. Francis, Corin Liddle, Emma Camacho, Madhura Kulkarni, Samuel R. S. Junior, Jamie A. Harvey, Elizabeth R. Ballou, Darren D. Thomson, Gordon D. Brown, J. Marie Hardwick, Arturo Casadevall, Jonathan Witton, and Carolina Coelho
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microglia ,Cryptococcus neoformans ,blood-brain barrier ,Microbiology ,QR1-502 - Abstract
ABSTRACTCryptococcus neoformans causes lethal meningitis and accounts for approximately 10%–15% of AIDS-associated deaths worldwide. There are major gaps in our understanding of how this fungus invades the mammalian brain. To investigate the dynamics of C. neoformans tissue invasion, we mapped fungal localization and host cell interactions in infected brain, lung, and upper airways using mouse models of systemic and airway infection. To enable this, we developed an in situ imaging pipeline capable of measuring large volumes of tissue while preserving anatomical and cellular information by combining thick tissue sections, tissue clarification, and confocal imaging. We confirm high fungal burden in mouse upper airway after nasal inoculation. Yeast in turbinates were frequently titan cells, with faster kinetics than reported in mouse lungs. Importantly, we observed one instance of fungal cells enmeshed in lamina propria of the upper airways, suggesting penetration of airway mucosa as a possible route of tissue invasion and dissemination to the bloodstream. We extend previous literature positing bloodstream dissemination of C. neoformans, by finding viable fungi in the bloodstream of mice a few days after intranasal infection. As early as 24 h post systemic infection, the majority of C. neoformans cells traversed the blood-brain barrier, and were engulfed or in close proximity to microglia. Our work presents a new method for investigating microbial invasion, establishes that C. neoformans can breach multiple tissue barriers within the first days of infection, and demonstrates microglia as the first cells responding to C. neoformans invasion of the brain.IMPORTANCECryptococcal meningitis causes 10%–15% of AIDS-associated deaths globally. Still, brain-specific immunity to cryptococci is a conundrum. By employing innovative imaging, this study reveals what occurs during the first days of infection in brain and in airways. We found that titan cells predominate in upper airways and that cryptococci breach the upper airway mucosa, which implies that, at least in mice, the upper airways are a site for fungal dissemination. This would signify that mucosal immunity of the upper airway needs to be better understood. Importantly, we also show that microglia, the brain-resident macrophages, are the first responders to infection, and microglia clusters are formed surrounding cryptococci. This study opens the field to detailed molecular investigations on airway immune response, how fungus traverses the blood-brain barrier, how microglia respond to infection, and ultimately how microglia monitor the blood-brain barrier to preserve brain function.
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- 2024
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35. Pilot cadaveric study on the feasibility of cricothyroidotomy and the associated complications in 30 cats
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Julia A. Delle Cave, Samuel R. Larcheveque, Edouard Martin, and Elizabeth O’Toole
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cricothyroidotomy ,CICO ,airway obstruction ,difficult airway ,feline ,cricothyrotomy ,Veterinary medicine ,SF600-1100 - Abstract
ObjectivesThe study’s primary goal was to assess the feasibility of the cricothyroidotomy technique (CTT) in cats and evaluate its success rate (i.e., secure airway access). Secondary outcomes were the assessment of the subjective difficulty of airway access based on body score condition and weight. Further secondary outcomes consisted of procedural time and scoring of associated complications. The current study hypothesized that the CTT procedure would provide secure airway access with a reasonable success rate.Materials and methodsA prospective experimental study assessing the performance of CTT and associated complications was conducted on 30 feline cadavers. A procedural datasheet was completed to subjectively grade difficulty of landmark palpation, guide placement and tube placement and expected success of the procedure. A dissection was then performed post-procedure by a blinded observer to evaluate for any associated damages.ResultsCTT was successful in securing an airway in 100% of the cats. The time to completion of the CTT was rapid, with a median time of 49 s (ranging from 31 to 90 s) for securing an airway. Of importance, this procedure was judged to be overall easy (median “ease of procedure score” of 7/10; ranging from 3 to 10) by the experimenters. The post-procedural lesion rate was elevated (76.7%) in this population of cats, though based on the lesion scores, was deemed mild in 73.9% of the cases.Clinical significanceCTT warrants consideration as the primary option for emergency front-of-neck airway access for cats although further studies are necessary.
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- 2024
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36. The immediate effects of private equity acquisition of urology practices on the management of newly diagnosed prostate cancer
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Kassem S. Faraj, Samuel R. Kaufman, Lindsey A. Herrel, Avinash Maganty, Mary Oerline, Megan E. V. Caram, Vahakn B. Shahinian, and Brent K. Hollenbeck
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cancer ,financial incentives ,private equity ,prostate cancer ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Introduction Some worry that physician practices acquired by private equity may increase the use of services to maximize revenue. We assessed the effects of private equity acquisition on spending, use of treatment, and diagnostic testing in men with prostate cancer. Methods We used a 20% sample of national Medicare claims to perform a retrospective cohort study of men with prostate cancer diagnosed from 2014 through 2019. The primary outcome was prostate cancer spending in the first 12 months after diagnosis. Secondary outcomes included the use of treatment and a composite measure of diagnostic testing (e.g., imaging, genomics) in the first 12 months after diagnosis. Multilevel modeling was used to adjust for differences in patient and market characteristics. The effect of practice acquisition on each outcome was assessed using a difference‐in‐differences design. Results There were 409 and 4021 men with prostate cancer managed by urologists in acquired and nonacquired practices, respectively. After acquisition, prostate cancer spending was comparable between acquired and nonacquired practices (difference‐in‐differences estimate $1182, p = 0.36). Acquisition did not affect the use of treatment (difference‐in‐differences estimate 3.7%, p = 0.30) or the use of diagnostic testing in men who were treated (difference‐in‐differences −5.5%, p = 0.12) and those managed conservatively (difference‐in‐differences −2.0%, p = 0.82). Conclusions In the year following acquisition of urology practices, private equity did not increase prostate cancer spending, the use of treatment or diagnostic testing in men with prostate cancer. Future work should evaluate the effects of private equity acquisition on practice patterns and quality over a longer time horizon.
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- 2023
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37. Adrenal cortical adenoma arising in the setting of renal–adrenal fusion: a case report and review of the literature
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Samuel R. Wang, Richard Morris, Suad Taraif, and Amandeep Aneja
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Renal–adrenal ,Fusion ,Adenoma ,Medicine - Abstract
Abstract Background Renal–adrenal fusion is a rare entity resulting from incomplete encapsulation of the adrenal gland and kidney. Only 18 cases have been reported in English literature to date. Case presentation Our patient is a 77-year-old African American female who presented with a systolic blood pressure of 200 mmHg. Computed tomography showed an enhancing 9 × 6 cm mass anterior and medial to the left kidney. The patient underwent a left adrenalectomy with partial nephrectomy. Gross and histologic examinations revealed an adrenal cortical adenoma and renal–adrenal fusion. Conclusion Renal–adrenal fusion may pose a diagnostic challenge, particularly when there is a concurrent adrenal adenoma. It is important to be aware of this uncommon anomaly to avoid misdiagnosis and overtreatment.
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- 2023
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38. Rational design of a JAK1-selective siRNA inhibitor for the modulation of autoimmunity in the skin
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Qi Tang, Hassan H. Fakih, Mohammad Zain UI Abideen, Samuel R. Hildebrand, Khashayar Afshari, Katherine Y. Gross, Jacquelyn Sousa, Allison S. Maebius, Christina Bartholdy, Pia Pernille Søgaard, Malene Jackerott, Vignesh Hariharan, Ashley Summers, Xueli Fan, Ken Okamura, Kathryn R. Monopoli, David A. Cooper, Dimas Echeverria, Brianna Bramato, Nicholas McHugh, Raymond C. Furgal, Karen Dresser, Sarah J. Winter, Annabelle Biscans, Jane Chuprin, Nazgol-Sadat Haddadi, Shany Sherman, Ümmügülsüm Yıldız-Altay, Mehdi Rashighi, Jillian M. Richmond, Claire Bouix-Peter, Carine Blanchard, Adam Clauss, Julia F. Alterman, Anastasia Khvorova, and John E. Harris
- Subjects
Science - Abstract
Abstract Inhibition of Janus kinase (JAK) family enzymes is a popular strategy for treating inflammatory and autoimmune skin diseases. In the clinic, small molecule JAK inhibitors show distinct efficacy and safety profiles, likely reflecting variable selectivity for JAK subtypes. Absolute JAK subtype selectivity has not yet been achieved. Here, we rationally design small interfering RNAs (siRNAs) that offer sequence-specific gene silencing of JAK1, narrowing the spectrum of action on JAK-dependent cytokine signaling to maintain efficacy and improve safety. Our fully chemically modified siRNA supports efficient silencing of JAK1 expression in human skin explant and modulation of JAK1-dependent inflammatory signaling. A single injection into mouse skin enables five weeks of duration of effect. In a mouse model of vitiligo, local administration of the JAK1 siRNA significantly reduces skin infiltration of autoreactive CD8+ T cells and prevents epidermal depigmentation. This work establishes a path toward siRNA treatments as a new class of therapeutic modality for inflammatory and autoimmune skin diseases.
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- 2023
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39. Duration of Enterovirus D68 RNA Shedding in the Upper Respiratory Tract and Transmission among Household Contacts, Colorado, USA
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Hai Nguyen-Tran, Careese Thompson, Molly Butler, Kristen R. Miller, Laura Pyle, Sarah Jung, Shannon Rogers, Terry Fei Fan Ng, Janell Routh, Samuel R. Dominguez, and Kevin Messacar
- Subjects
Enterovirus D68 ,EV-D68 ,acute flaccid myelitis ,viruses ,respiratory infections ,virus shedding ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Enterovirus D68 (EV-D68) causes cyclical outbreaks of respiratory disease and acute flaccid myelitis. EV-D68 is primarily transmitted through the respiratory route, but the duration of shedding in the respiratory tract is unknown. We prospectively enrolled 9 hospitalized children with EV-D68 respiratory infection and 16 household contacts to determine EV-D68 RNA shedding dynamics in the upper respiratory tract through serial midturbinate specimen collections and daily symptom diaries. Five (31.3%) household contacts, including 3 adults, were EV-D68–positive. The median duration of EV-D68 RNA shedding in the upper respiratory tract was 12 (range 7–15) days from symptom onset. The most common symptoms were nasal congestion (100%), cough (92.9%), difficulty breathing (78.6%), and wheezing (57.1%). The median illness duration was 20 (range 11–24) days. Understanding the duration of RNA shedding can inform the expected rate and timing of EV-D68 detection in associated acute flaccid myelitis cases and help guide public health measures.
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- 2023
- Full Text
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40. Clarifying and extending our understanding of problematic pornography use through descriptions of the lived experience
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Campbell Ince, Leonardo F. Fontenelle, Adrian Carter, Lucy Albertella, Jeggan Tiego, Samuel R. Chamberlain, and Kristian Rotaru
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Medicine ,Science - Abstract
Abstract Problematic pornography use (PPU) is a complex and growing area of research. However, knowledge of the PPU lived experience is limited. To address this gap, we conducted an online qualitative study with 67 individuals who self-identified as having problematic pornography use (76% male; M age = 24.70 years, SD = 8.54). Results indicated several dimensions that have not been fully explored in the literature. These included various mental and physical complaints following periods of heavy pornography use, sexual functioning deficits with real partners, and a subjectively altered state of sexual arousal while using pornography. Moreover, we expanded on current knowledge regarding the inner conflict associated with PPU and clarified the ways that users can progress to increasingly intensified patterns of pornography use, such as tolerance/escalation and pornographic binges. Our study highlights the complex and nuanced nature of PPU and provides suggestions for future research and clinical practice.
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- 2023
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41. Prospects and Current Challenges of Extracellular Vesicle-Based Biomarkers in Cancer
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Samuel R. Lawrence and Karan M. Shah
- Subjects
extracellular vesicles ,biomarker ,liquid biopsy ,cancer diagnosis ,Biology (General) ,QH301-705.5 - Abstract
Cancer continues to impose a substantial global health burden, particularly among the elderly, where the ongoing global demographic shift towards an ageing population underscores the growing need for early cancer detection. This is essential for enabling personalised cancer care and optimised treatment throughout the disease course to effectively mitigate the increasing societal impact of cancer. Liquid biopsy has emerged as a promising strategy for cancer diagnosis and treatment monitoring, offering a minimally invasive method for the isolation and molecular profiling of circulating tumour-derived components. The expansion of the liquid biopsy approach to include the detection of tumour-derived extracellular vesicles (tdEVs) holds significant therapeutic opportunity. Evidence suggests that tdEVs carry cargo reflecting the contents of their cell-of-origin and are abundant within the blood, exhibiting superior stability compared to non-encapsulated tumour-derived material, such as circulating tumour nucleic acids and proteins. However, despite theoretical promise, several obstacles hinder the translation of extracellular vesicle-based cancer biomarkers into clinical practice. This critical review assesses the current prospects and challenges facing the adoption of tdEV biomarkers in clinical practice, offering insights into future directions and proposing strategies to overcome translational barriers. By addressing these issues, EV-based liquid biopsy approaches could revolutionise cancer diagnostics and management.
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- 2024
- Full Text
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42. Calibrating the Discrete Boundary Conditions of a Dynamic Simulation: A Combinatorial Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) Approach
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Jah Shamas, Tim Rogers, Anton Krynkin, Jevgenija Prisutova, Paul Gardner, Kirill V. Horoshenkov, Samuel R. Shelley, and Paul Dickenson
- Subjects
Bayesian inference ,Monte Carlo simulation ,structural vibration ,uncertainty quantification ,Chemical technology ,TP1-1185 - Abstract
This paper presents a novel adaptation of the conventional approximate Bayesian computation sequential Monte Carlo (ABC-SMC) sampling algorithm for parameter estimation in the presence of uncertainties, coined combinatorial ABC-SMC. Inference of this type is used in situations where there does not exist a closed form of the associated likelihood function, which is replaced by a simulating model capable of producing artificial data. In the literature, conventional ABC-SMC is utilised to perform inference on continuous parameters. The novel scheme presented here has been developed to perform inference on parameters that are high-dimensional binary, rather than continuous. By altering the form of the proposal distribution from which to sample candidates in subsequent iterations (referred to as waves), high-dimensional binary variables may be targeted and inferred by the scheme. The efficacy of the proposed scheme is demonstrated through application to vibration data obtained in a structural dynamics experiment on a fibre-optic sensor simulated as a finite plate with uncertain boundary conditions at its edges. Results indicate that the method provides sound inference on the plate boundary conditions, which is validated through subsequent application of the method to multiple vibration datasets. Comparisons between appropriate forms of the metric function used in the scheme are also developed to highlight the effect of this element in the schemes convergence.
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- 2024
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43. Microrollers flow uphill as granular media
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Samuel R. Wilson-Whitford, Jinghui Gao, Maria Chiara Roffin, William E. Buckley, and James F. Gilchrist
- Subjects
Science - Abstract
Abstract Pour sand into a container and only the grains near the top surface move. The collective motion associated with the translational and rotational energy of the grains in a thin flowing layer is quickly dissipated as friction through multibody interactions. Alternatively, consider what will happen to a bed of particles if one applies a torque to each individual particle. In this paper, we demonstrate an experimental system where torque is applied at the constituent level through a rotating magnetic field in a dense bed of microrollers. The net result is the grains roll uphill, forming a heap with a negative angle of repose. Two different regimes have been identified related to the degree of mobility or fluidisation of the particles in the bulk. Velocimetry of the near surface flowing layer reveals the collective motion of these responsive particles scales in a similar way to flowing bulk granular flows. A simple granular model that includes cohesion accurately predicts the apparent negative coefficient of friction. In contrast to the response of active or responsive particles that mimic thermodynamic principles, this system results in macroscopic collective behavior that has the kinematics of a purely dissipative granular system.
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- 2023
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44. Will the Russian war in Ukraine unleash larger epidemics of HIV, TB and associated conditions and diseases in Ukraine?
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Samuel R. Friedman, Pavlo Smyrnov, and Tetyana I. Vasylyeva
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Ukraine ,War ,HIV ,TB ,Big Events ,Risk ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract The Russian war in Ukraine poses many risks for the spread of HIV, TB and associated conditions, including possible increases in the numbers of people who inject drugs or engage in sex work in the years ahead. Ukrainian civil society and volunteer efforts have been able to maintain and at times expand services for HIV Key Populations. The extent of mutual-aid and volunteer efforts as well as the continued strength and vitality of harm reduction organizations such as the Alliance for Public Health and the rest of civil society will be crucial resources for postwar efforts to assist Key Populations and prevent the spread of HIV, TB and other diseases. The postwar period will pose great economic and political difficulties for Ukrainians, including large populations of people physically and/or psychically damaged and in pain who might become people who inject drugs. Local and international support for public health and for harm reduction will be needed to prevent potentially large-scale increases in infectious disease and related mortality.
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- 2023
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45. Health care delivery system contributions to management of newly diagnosed prostate cancer
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Noah Krampe, Samuel R. Kaufman, Mary K. Oerline, Dawson Hill, Megan E. V. Caram, Vahakn B. Shahinian, Brent K. Hollenbeck, and Avinash Maganty
- Subjects
delivery system ,prostate cancer ,variation in treatment ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Despite clinical guidelines advocating for use of conservative management in specific clinical scenarios for men with prostate cancer, there continues to be tremendous variation in its uptake. This variation may be amplified among men with competing health risks, for whom treatment decisions are not straightforward. The degree to which characteristics of the health care delivery system explain this variation remains unclear. Methods Using national Medicare data, men with newly diagnosed prostate cancer between 2014 and 2019 were identified. Hierarchical logistic regression models were used to assess the association between use of treatment and health care delivery system determinants operating at the practice level, which included measures of financial incentives (i.e., radiation vault ownership), practice organization (i.e., single specialty vs. multispecialty groups), and the health care market (i.e., competition). Variance was partitioned to estimate the relative influence of patient and practice characteristics on the variation in use of treatment within strata of noncancer mortality risk groups. Results Among 62,507 men with newly diagnosed prostate cancer, the largest variation in the use of treatment between practices was observed for men with high and very high‐risk of noncancer mortality (range of practice‐level rates of treatment for high: 57%–71% and very high: 41%–61%). Addition of health care delivery system determinants measured at the practice level explained 13% and 15% of the variation in use of treatment among men with low and intermediate risk of noncancer mortality in 10 years, respectively. Conversely, these characteristics explained a larger share of the variation in use of treatment among men with high and very high‐risk of noncancer mortality (26% and 40%, respectively). Conclusions Variation among urology practices in use of treatment was highest for men with high and very high‐risk noncancer mortality. Practice characteristics explained a large share of this variation.
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- 2023
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46. The differences in crystal structure and phase of lead-free perovskite solar cell materials
- Author
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Samuel R. Pering
- Subjects
Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
Abstract Hybrid organic–inorganic lead halide perovskite materials have established themselves as a competitive solar cell technology, with high efficiencies and simple processing. However the main drawback of these materials is currently their stability, which is complicated by the potential to release the toxic element lead into the environment. Attempts to replace lead for less-toxic starting materials have generated significant research interest. Any candidate material must have enhanced stability and comparable performance to lead halide perovskites, and an understanding of the structure is key to developing these materials to be competitive. This review provides a brief overview and reference of experimentally determined crystal structures of lead-free perovskite materials. The most promising potential materials are identified as those that maintain a cubic structure, particularly double-perovskite type absorbers.
- Published
- 2023
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47. Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020
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Anna Yakovleva, Ganna Kovalenko, Matthew Redlinger, Pavlo Smyrnov, Olga Tymets, Anna Korobchuk, Lyudmyla Kotlyk, Anna Kolodiazieva, Anna Podolina, Svitlana Cherniavska, Petro Antonenko, Steffanie A. Strathdee, Samuel R. Friedman, Ian Goodfellow, Joel O. Wertheim, Eric Bortz, Luke Meredith, and Tetyana I. Vasylyeva
- Subjects
Hepatitis C virus ,People who inject drugs ,Displacement ,Phylodynamics ,Nanopore sequencing ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Due to practical challenges associated with genetic sequencing in low-resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) in Ukraine. Methods In this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who were displaced to Odesa, Ukraine, before 2020. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore Technology (ONT) MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships. Results Between June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID (PNAS Nexus.2023;2(3):pgad008). Rapid testing (Wondfo® One Step HCV; Wondfo® One Step HIV1/2) identified an anti-HCV seroprevalence of 67.7%, and 31.1% of participants tested positive for both anti-HCV and HIV. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-displacement. Conclusions Locally generated genomic data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can help inform effective public health strategies. For example, evidence of HCV transmission clusters originating soon after displacement highlights the importance of implementing urgent preventive interventions in ongoing situations of forced displacement.
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- 2023
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48. Paraspinal muscles in individuals undergoing surgery for lumbar spine pathology lack a myogenic response to an acute bout of resistance exercise
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Bahar Shahidi, Bradley Anderson, Angel Ordaz, David B. Berry, Severin Ruoss, Vinko Zlomislic, R. Todd Allen, Steven R. Garfin, Mazda Farshad, Simon Schenk, and Samuel R. Ward
- Subjects
degeneration ,injury ,pain ,Orthopedic surgery ,RD701-811 - Abstract
Abstract Background Lumbar spine pathology (LSP) is a common source of low back or leg pain, and paraspinal muscle in these patients demonstrates fatty and fibrotic infiltration, and cellular degeneration that do not reverse with exercise‐based rehabilitation. However, it is unclear of this lack of response is due to insufficient exercise stimulus, or an inability to mount a growth response. The purpose of this study was to compare paraspinal muscle gene expression between individuals with LSP who do and do not undergo an acute bout of resistance exercise. Methods Paraspinal muscle biopsies were obtained from 64 individuals with LSP undergoing spinal surgery. Eight participants performed an acute bout of machine‐based lumbar extension resistance exercise preoperatively. Gene expression for 42 genes associated with adipogenic/metabolic, atrophic, fibrogenic, inflammatory, and myogenic pathways was measured, and differential expression between exercised and non‐exercised groups was evaluated for (a) the full cohort, and (b) an age, gender, acuity, and etiology matched sub‐cohort. Principal components analyses were used to identify gene expression clustering across clinical phenotypes. Results The exercised cohort demonstrated upregulation of inflammatory gene IL1B, inhibition of extracellular matrix components (increased MMP3&9, decreased TIMP1&3, COL1A1) and metabolic/adipogenic genes (FABP4, PPARD, WNT10B), and downregulation of myogenic (MYOD, ANKRD2B) and atrophic (FOXO3) genes compared to the non‐exercised cohort, with similar patterns in the matched sub‐analysis. There were no clinical phenotypes significantly associated with gene expression profiles. Conclusion An acute bout of moderate‐high intensity resistance exercise did not result in upregulation of myogenic genes in individuals with LSP. The response was characterized by mixed metabolic and fibrotic gene expression, upregulation of inflammation, and downregulation of myogenesis.
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- 2024
- Full Text
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49. Co-optimisation of wind and solar energy and intermittency for renewable generator site selection
- Author
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Hao Wu and Samuel R. West
- Subjects
Renewable generation site selection ,Resource assessment ,Multi-objective optimisation ,Solar farm ,Wind farm ,Australia ,Science (General) ,Q1-390 ,Social sciences (General) ,H1-99 - Abstract
Sites for the construction of wind and solar farms have typically been chosen to maximise total energy generation of an individual site, but rarely consider the intermittency of the renewable resource available at each location. As more renewable generation is added to electricity grids around the world, this intermittency is rapidly becoming a major factor constraining the volume of renewable generation that can be added cost-effectively, as additional fast-response storage or dispatchable generation must compensate for periods of low renewable generation. We present a statistical approach to selecting wind and solar generation sites that assesses energy and intermittency of individual wind, solar and co-sited wind plus solar farm locations, allowing energy and intermittency to be given weight when selecting sites for new generation. A new multi-objective pareto-front approach to identifying high-performing renewable generation sites that allows for optimising multi-site selection using the median (energy) and median absolute difference (intermittency) of historical weather resource is proposed. This technique is then applied to a 30-year, hourly, Australian weather reanalysis dataset to show the potential improvement over the fleet of wind and solar farms currently operating in the Australian National Energy Market. Finally, an analysis of potential sites for optimal offshore wind and combined offshore wind and solar is presented. The proposed wind-only and solar-only sites show an average energy increase of 9% (solar, 67 sites), 28% (wind, 50 sites) more energy for the same level of intermittency, as compared to the existing generation sites. Three existing combined wind and solar sites were compared to the best three proposed sites, which showed a 3-16% energy increase for the same intermittency, or a 2-11% intermittency decrease for the same energy generated.
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- 2024
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50. Airborne Observations Constrain Heterogeneous Nitrogen and Halogen Chemistry on Tropospheric and Stratospheric Biomass Burning Aerosol
- Author
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Zachary C. J. Decker, Gordon A. Novak, Kenneth Aikin, Patrick R. Veres, J. Andrew Neuman, Ilann Bourgeois, T. Paul Bui, Pedro Campuzano‐Jost, Matthew M. Coggon, Douglas A. Day, Joshua P. DiGangi, Glenn S. Diskin, Maximilian Dollner, Alessandro Franchin, Carley D. Fredrickson, Karl D. Froyd, Georgios I. Gkatzelis, Hongyu Guo, Samuel R. Hall, Hannah Halliday, Katherine Hayden, Christopher D. Holmes, Jose L. Jimenez, Agnieszka Kupc, Jakob Lindaas, Ann M. Middlebrook, Richard H. Moore, Benjamin A. Nault, John B. Nowak, Demetrios Pagonis, Brett B. Palm, Jeff Peischl, Felix M. Piel, Pamela S. Rickly, Michael A. Robinson, Andrew W. Rollins, Thomas B. Ryerson, Gregory P. Schill, Kanako Sekimoto, Chelsea R. Thompson, Kenneth L. Thornhill, Joel A. Thornton, Kirk Ullmann, Carsten Warneke, Rebecca A. Washenfelder, Bernadett Weinzierl, Elizabeth B. Wiggins, Christina J. Williamson, Edward L. Winstead, Armin Wisthaler, Caroline C. Womack, and Steven S. Brown
- Subjects
biomass burning ,heterogeneous chemistry ,N2O5 ,ClNO2 ,chloride ,UTLS ,Geophysics. Cosmic physics ,QC801-809 - Abstract
Abstract Heterogeneous chemical cycles of pyrogenic nitrogen and halides influence tropospheric ozone and affect the stratosphere during extreme Pyrocumulonimbus (PyroCB) events. We report field‐derived N2O5 uptake coefficients, γ(N2O5), and ClNO2 yields, φ(ClNO2), from two aircraft campaigns observing fresh smoke in the lower and mid troposphere and processed/aged smoke in the upper troposphere and lower stratosphere (UTLS). Derived φ(ClNO2) varied across the full 0–1 range but was typically
- Published
- 2024
- Full Text
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