2,442 results on '"Logan, C."'
Search Results
2. Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel
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Parsons, Michael T, de la Hoya, Miguel, Richardson, Marcy E, Tudini, Emma, Anderson, Michael, Berkofsky-Fessler, Windy, Caputo, Sandrine M, Chan, Raymond C, Cline, Melissa S, Feng, Bing-Jian, Fortuno, Cristina, Gomez-Garcia, Encarna, Hadler, Johanna, Hiraki, Susan, Holdren, Megan, Houdayer, Claude, Hruska, Kathleen, James, Paul, Karam, Rachid, Leong, Huei San, Martins, Alexandra, Mensenkamp, Arjen R, Monteiro, Alvaro N, Nathan, Vaishnavi, O'Connor, Robert, Pedersen, Inge Sokilde, Pesaran, Tina, Radice, Paolo, Schmidt, Gunnar, Southey, Melissa, Tavtigian, Sean, Thompson, Bryony A, Toland, Amanda E, Turnbull, Clare, Vogel, Maartje J, Weyandt, Jamie, Wiggins, George AR, Zec, Lauren, Couch, Fergus J, Walker, Logan C, Vreeswijk, Maaike PG, Goldgar, David E, and Spurdle, Amanda B
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Biological Sciences ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Genetics ,Women's Health ,Breast Cancer ,Ovarian Cancer ,Cancer ,Rare Diseases ,Good Health and Well Being ,ACMG/AMP variant curation guidelines ,BRCA1 ,BRCA2 ,ClinGen ,ClinVar ,VCEP ,Humans ,BRCA2 Protein ,BRCA1 Protein ,Female ,Genetic Variation ,Breast Neoplasms ,Genomics ,Databases ,Genetic ,Ovarian Neoplasms ,Genetic Predisposition to Disease ,Genetic Testing ,Medical and Health Sciences ,Genetics & Heredity ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
The ENIGMA research consortium develops and applies methods to determine clinical significance of variants in hereditary breast and ovarian cancer genes. An ENIGMA BRCA1/2 classification sub-group, formed in 2015 as a ClinGen external expert panel, evolved into a ClinGen internal Variant Curation Expert Panel (VCEP) to align with Food and Drug Administration recognized processes for ClinVar contributions. The VCEP reviewed American College of Medical Genetics and Genomics/Association of Molecular Pathology (ACMG/AMP) classification criteria for relevance to interpreting BRCA1 and BRCA2 variants. Statistical methods were used to calibrate evidence strength for different data types. Pilot specifications were tested on 40 variants and documentation revised for clarity and ease of use. The original criterion descriptions for 13 evidence codes were considered non-applicable or overlapping with other criteria. Scenario of use was extended or re-purposed for eight codes. Extensive analysis and/or data review informed specification descriptions and weights for all codes. Specifications were applied to pilot variants with pre-existing ClinVar classification as follows: 13 uncertain significance or conflicting, 14 pathogenic and/or likely pathogenic, and 13 benign and/or likely benign. Review resolved classification for 11/13 uncertain significance or conflicting variants and retained or improved confidence in classification for the remaining variants. Alignment of pre-existing ENIGMA research classification processes with ACMG/AMP classification guidelines highlighted several gaps in the research processes and the baseline ACMG/AMP criteria. Calibration of evidence strength was key to justify utility and strength of different data types for gene-specific application. The gene-specific criteria demonstrated value for improving ACMG/AMP-aligned classification of BRCA1 and BRCA2 variants.
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- 2024
3. Accessibility of countable sets in plane embeddings of arc-like continua
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Anušić, Ana and Hoehn, Logan C.
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Mathematics - General Topology ,Mathematics - Dynamical Systems ,Primary 54F15, 54C25, Secondary 54F50, 37B45, 37E30 - Abstract
We consider the problem of finding embeddings of arc-like continua in the plane for which each point in a given subset is accessible. We establish that, under certain conditions on an inverse system of arcs, there exists a plane embedding of the inverse limit for which each point of a given countable set is accessible. As an application, we show that for any Knaster continuum $K$, and any countable collection $\mathcal{C}$ of composants of $K$, there exists a plane embedding of $K$ in which every point in the union of the composants in $\mathcal{C}$ is accessible. We also exhibit new embeddings of the Knaster buckethandle continuum $K$ in the plane which are attractors of plane homeomorphisms, and for which the restriction of the plane homeomorphism to the attractor is conjugate to a power of the standard shift map on $K$., Comment: 25 pages, 6 figures
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- 2024
4. The Nadler-Quinn problem on accessible points of arc-like continua
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Ammerlaan, Andrea, Anušić, Ana, and Hoehn, Logan C.
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Mathematics - General Topology - Abstract
We show that if $X$ is an arc-like continuum, then for every point $x \in X$ there is a plane embedding of $X$ in which $x$ is an accessible point. This answers a question posed by Nadler in 1972, which has become known as the Nadler-Quinn problem in continuum theory. Towards this end, we develop the theories of truncations and contour factorizations of interval maps. As a corollary, we answer a question of Mayer from 1982 about inequivalent plane embeddings of indecomposable arc-like continua., Comment: 32 pages, 8 figures
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- 2024
5. The Nadler-Quinn problem for simplicial inverse systems
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Ammerlaan, Andrea, Anušić, Ana, and Hoehn, Logan C.
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Mathematics - General Topology ,Primary 54F15, 54C25, Secondary 54F50 - Abstract
We show that if $X$ is an arc-like continuum which can be represented as an inverse limit of a simplicial inverse system on arcs, then for every point $x \in X$ there is a plane embedding of $X$ in which $x$ is accessible. This answers a special case of the Nadler-Quinn question from 1972., Comment: 20 pages, 4 figures. arXiv admin note: text overlap with arXiv:2306.15191
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- 2023
6. Radial departures and plane embeddings of arc-like continua
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Ammerlaan, Andrea, Anušić, Ana, and Hoehn, Logan C.
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Mathematics - General Topology ,Primary 54F15, 54C25, Secondary 54F50 - Abstract
We study the problem of Nadler and Quinn from 1972, which asks whether, given an arc-like continuum $X$ and a point $x \in X$, there exists an embedding of $X$ in $\mathbb{R}^2$ for which $x$ is an accessible point. We develop the notion of a radial departure of a map $f \colon [-1,1] \to [-1,1]$, and establish a simple criterion in terms of the bonding maps in an inverse system on intervals to show that there is an embedding of the inverse limit for which a given point is accessible. Using this criterion, we give a partial affirmative answer to the problem of Nadler and Quinn, under some technical assumptions on the bonding maps of the inverse system., Comment: Some typos fixed. Numeration of theorems and lemmas is changed
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- 2023
7. Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
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Mathis, Sarabeth M., Webber, Alexander E., León, Tomás M., Murray, Erin L., Sun, Monica, White, Lauren A., Brooks, Logan C., Green, Alden, Hu, Addison J., Rosenfeld, Roni, Shemetov, Dmitry, Tibshirani, Ryan J., McDonald, Daniel J., Kandula, Sasikiran, Pei, Sen, Yaari, Rami, Yamana, Teresa K., Shaman, Jeffrey, Agarwal, Pulak, Balusu, Srikar, Gururajan, Gautham, Kamarthi, Harshavardhan, Prakash, B. Aditya, Raman, Rishi, Zhao, Zhiyuan, Rodríguez, Alexander, Meiyappan, Akilan, Omar, Shalina, Baccam, Prasith, Gurung, Heidi L., Suchoski, Brad T., Stage, Steve A., Ajelli, Marco, Kummer, Allisandra G., Litvinova, Maria, Ventura, Paulo C., Wadsworth, Spencer, Niemi, Jarad, Carcelen, Erica, Hill, Alison L., Loo, Sara L., McKee, Clifton D., Sato, Koji, Smith, Claire, Truelove, Shaun, Jung, Sung-mok, Lemaitre, Joseph C., Lessler, Justin, McAndrew, Thomas, Ye, Wenxuan, Bosse, Nikos, Hlavacek, William S., Lin, Yen Ting, Mallela, Abhishek, Gibson, Graham C., Chen, Ye, Lamm, Shelby M., Lee, Jaechoul, Posner, Richard G., Perofsky, Amanda C., Viboud, Cécile, Clemente, Leonardo, Lu, Fred, Meyer, Austin G., Santillana, Mauricio, Chinazzi, Matteo, Davis, Jessica T., Mu, Kunpeng, Pastore y Piontti, Ana, Vespignani, Alessandro, Xiong, Xinyue, Ben-Nun, Michal, Riley, Pete, Turtle, James, Hulme-Lowe, Chis, Jessa, Shakeel, Nagraj, V. P., Turner, Stephen D., Williams, Desiree, Basu, Avranil, Drake, John M., Fox, Spencer J., Suez, Ehsan, Cojocaru, Monica G., Thommes, Edward W., Cramer, Estee Y., Gerding, Aaron, Stark, Ariane, Ray, Evan L., Reich, Nicholas G., Shandross, Li, Wattanachit, Nutcha, Wang, Yijin, Zorn, Martha W., Aawar, Majd Al, Srivastava, Ajitesh, Meyers, Lauren A., Adiga, Aniruddha, Hurt, Benjamin, Kaur, Gursharn, Lewis, Bryan L., Marathe, Madhav, Venkatramanan, Srinivasan, Butler, Patrick, Farabow, Andrew, Ramakrishnan, Naren, Muralidhar, Nikhil, Reed, Carrie, Biggerstaff, Matthew, and Borchering, Rebecca K.
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- 2024
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8. Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
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Sarabeth M. Mathis, Alexander E. Webber, Tomás M. León, Erin L. Murray, Monica Sun, Lauren A. White, Logan C. Brooks, Alden Green, Addison J. Hu, Roni Rosenfeld, Dmitry Shemetov, Ryan J. Tibshirani, Daniel J. McDonald, Sasikiran Kandula, Sen Pei, Rami Yaari, Teresa K. Yamana, Jeffrey Shaman, Pulak Agarwal, Srikar Balusu, Gautham Gururajan, Harshavardhan Kamarthi, B. Aditya Prakash, Rishi Raman, Zhiyuan Zhao, Alexander Rodríguez, Akilan Meiyappan, Shalina Omar, Prasith Baccam, Heidi L. Gurung, Brad T. Suchoski, Steve A. Stage, Marco Ajelli, Allisandra G. Kummer, Maria Litvinova, Paulo C. Ventura, Spencer Wadsworth, Jarad Niemi, Erica Carcelen, Alison L. Hill, Sara L. Loo, Clifton D. McKee, Koji Sato, Claire Smith, Shaun Truelove, Sung-mok Jung, Joseph C. Lemaitre, Justin Lessler, Thomas McAndrew, Wenxuan Ye, Nikos Bosse, William S. Hlavacek, Yen Ting Lin, Abhishek Mallela, Graham C. Gibson, Ye Chen, Shelby M. Lamm, Jaechoul Lee, Richard G. Posner, Amanda C. Perofsky, Cécile Viboud, Leonardo Clemente, Fred Lu, Austin G. Meyer, Mauricio Santillana, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana Pastore y Piontti, Alessandro Vespignani, Xinyue Xiong, Michal Ben-Nun, Pete Riley, James Turtle, Chis Hulme-Lowe, Shakeel Jessa, V. P. Nagraj, Stephen D. Turner, Desiree Williams, Avranil Basu, John M. Drake, Spencer J. Fox, Ehsan Suez, Monica G. Cojocaru, Edward W. Thommes, Estee Y. Cramer, Aaron Gerding, Ariane Stark, Evan L. Ray, Nicholas G. Reich, Li Shandross, Nutcha Wattanachit, Yijin Wang, Martha W. Zorn, Majd Al Aawar, Ajitesh Srivastava, Lauren A. Meyers, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan L. Lewis, Madhav Marathe, Srinivasan Venkatramanan, Patrick Butler, Andrew Farabow, Naren Ramakrishnan, Nikhil Muralidhar, Carrie Reed, Matthew Biggerstaff, and Rebecca K. Borchering
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Science - Abstract
Abstract Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperform the baseline model across forecast weeks and locations in 2021–22 and 12 out of 18 models in 2022–23. Averaging across all forecast targets, the FluSight ensemble is the 2nd most accurate model measured by WIS in 2021–22 and the 5th most accurate in the 2022–23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degrade over longer forecast horizons. In this work we demonstrate that while the FluSight ensemble was a robust predictor, even ensembles face challenges during periods of rapid change.
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- 2024
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9. Role of Air Pollution in the Development of Asthma Among Children with a History of Bronchiolitis in Infancy
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Dearborn, Logan C, Hazlehurst, Marnie F, Loftus, Christine T, Szpiro, Adam A, Carroll, Kecia N, Moore, Paul E, Adgent, Margaret A, Barrett, Emily S, Nguyen, Ruby HN, Sathyanarayana, Sheela, LeWinn, Kaja Z, Bush, Nicole R, Kaufman, Joel D, and Karr, Catherine J
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Epidemiology ,Health Sciences ,Pediatric ,Asthma ,Climate-Related Exposures and Conditions ,Lung ,Clinical Research ,2.2 Factors relating to the physical environment ,Aetiology ,Respiratory ,Sustainable Cities and Communities ,Child ,Child ,Preschool ,Humans ,Infant ,Air Pollutants ,Air Pollution ,Bronchiolitis ,Environmental Exposure ,Ozone ,Particulate Matter ,air pollution ,asthma ,wheeze ,Statistics ,Public Health and Health Services ,Public health - Abstract
BackgroundInfants experiencing bronchiolitis are at increased risk for asthma, but few studies have identified modifiable risk factors. We assessed whether early life air pollution influenced child asthma and wheeze at age 4-6 years among children with a history of bronchiolitis in the first postnatal year.MethodsChildren with caregiver-reported physician-diagnosed bronchiolitis were drawn from ECHO-PATHWAYS, a pooled longitudinal cohort from six US cities. We estimated their air pollution exposure from age 1 to 3 years from validated spatiotemporal models of fine particulate matter (PM 2.5 ), nitrogen dioxide (NO 2 ), and ozone (O 3 ). Caregivers reported children's current wheeze and asthma at age 4-6 years. We used modified Poisson regression to estimate relative risks (RR) and 95% confidence intervals (CI), adjusting for child, maternal, and home environmental factors. We assessed effect modification by child sex and maternal history of asthma with interaction models.ResultsA total of 224 children had caregiver-reported bronchiolitis. Median (interquartile range) 2-year pollutant concentrations were 9.3 (7.8-9.9) µg/m 3 PM 2.5 , 8.5 (6.4-9.9) ppb NO 2 , and 26.6 (25.6-27.7) ppb O 3 . RRs (CI) for current wheeze per 2-ppb higher O 3 were 1.3 (1.0-1.7) and 1.4 (1.1-1.8) for asthma. NO 2 was inversely associated with wheeze and asthma whereas associations with PM 2.5 were null. We observed interactions between NO 2 and PM 2.5 and maternal history of asthma, with lower risks observed among children with a maternal history of asthma.ConclusionOur results are consistent with the hypothesis that exposure to modest postnatal O 3 concentrations increases the risk of asthma and wheeze among the vulnerable subpopulation of infants experiencing bronchiolitis.
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- 2023
10. The role of extracorporeal life support and timing of repair in infants with congenital diaphragmatic hernia
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Tim Jancelewicz, Daniel B Gehle, and Logan C Meyer
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Pediatrics ,RJ1-570 ,Surgery ,RD1-811 - Abstract
Extracorporeal life support (ECLS) serves as a rescue therapy for patients with congenital diaphragmatic hernia (CDH) and severe cardiopulmonary failure, and only half of these patients survive to discharge. This costly intervention has a significant complication risk and is reserved for patients with the most severe disease physiology refractory to maximal cardiopulmonary support. Some contraindications to ECLS do exist such as coagulopathy, lethal chromosomal or congenital anomaly, very preterm birth, or very low birth weight, but many of these limits are being evaluated through further research. Consensus guidelines from the past decade vary in recommendations for ECLS use in patients with CDH but this therapy appears to have a survival benefit in the most severe subset of patients. Improved outcomes have been observed for patients treated at high-volume centers. This review details the evolving literature surrounding management paradigms for timing of CDH repair for patients receiving preoperative ECLS. Most recent data support early repair following cannulation to avoid non-repair which is uniformly fatal in this population. Longer ECLS runs are associated with decreased survival, and patient physiology should guide ECLS weaning and eventual decannulation rather than limiting patients to arbitrary run lengths. Standardization of care across centers is a major focus to limit unnecessary costs and improve short-term and long-term outcomes for these complex patients.
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- 2024
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11. Prenatal polycyclic aromatic hydrocarbon exposure and asthma at age 8–9 years in a multi-site longitudinal study
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Allison R. Sherris, Christine T. Loftus, Adam A. Szpiro, Logan C. Dearborn, Marnie F. Hazlehurst, Kecia N. Carroll, Paul E. Moore, Margaret A. Adgent, Emily S. Barrett, Nicole R. Bush, Drew B. Day, Kurunthachalam Kannan, Kaja Z. LeWinn, Ruby H. N. Nguyen, Yu Ni, Anne M. Riederer, Morgan Robinson, Sheela Sathyanarayana, Qi Zhao, and Catherine J. Karr
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PAHs ,Asthma ,Children’s health ,Industrial medicine. Industrial hygiene ,RC963-969 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background and aim Studies suggest prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) may influence wheezing or asthma in preschool-aged children. However, the impact of prenatal PAH exposure on asthma and wheeze in middle childhood remain unclear. We investigated these associations in socio-demographically diverse participants from the ECHO PATHWAYS multi-cohort consortium. Methods We included 1,081 birth parent–child dyads across five U.S. cities. Maternal urinary mono-hydroxylated PAH metabolite concentrations (OH-PAH) were measured during mid-pregnancy. Asthma at age 8–9 years and wheezing trajectory across childhood were characterized by caregiver reported asthma diagnosis and asthma/wheeze symptoms. We used logistic and multinomial regression to estimate odds ratios of asthma and childhood wheezing trajectories associated with five individual OH-PAHs, adjusting for urine specific gravity, various maternal and child characteristics, study site, prenatal and postnatal smoke exposure, and birth year and season in single metabolite and mutually adjusted models. We used multiplicative interaction terms to evaluate effect modification by child sex and explored OH-PAH mixture effects through Weighted Quantile Sum regression. Results The prevalence of asthma in the study population was 10%. We found limited evidence of adverse associations between pregnancy OH-PAH concentrations and asthma or wheezing trajectories. We observed adverse associations between 1/9-hydroxyphenanthrene and asthma and persistent wheeze among girls, and evidence of inverse associations with asthma for 1-hydroxynathpthalene, which was stronger among boys, though tests for effect modification by child sex were not statistically significant. Conclusions In a large, multi-site cohort, we did not find strong evidence of an association between prenatal exposure to PAHs and child asthma at age 8–9 years, though some adverse associations were observed among girls.
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- 2024
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12. Smooth fans that are endpoint rigid
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Hernández-Gutiérrez, Rodrigo and Hoehn, Logan C.
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Mathematics - General Topology ,54F50 (Primary) 54F15, 54G20, 54F65 (Secondary) - Abstract
Let $X$ be a smooth fan and denote its set of endpoints by $E(X)$. Let $E$ be one of the following spaces: the natural numbers, the irrational numbers, or the product of the Cantor set with the natural numbers. We prove that there is a smooth fan $X$ such that $E(X)$ is homeomorphic to $E$ and for every homeomorphism $h \colon X \to X$, the restriction of $h$ to $E(X)$ is the identity. On the other hand, we also prove that if $X$ is any smooth fan such that $E(X)$ is homeomorphic to complete Erd\H{o}s space, then $X$ is necessarily homeomorphic to the Lelek fan; this adds to a 1989 result by W{\l}odzimierz Charatonik., Comment: 15 pages, 4 figures
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- 2022
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13. Broad-line Region Clouds orbiting an AGN sample
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Armijos-Abendaño, J., López, E., Llerena, M., and Logan, C. H. A.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present a spectral and temporal analysis of XMM-Newton data from a sample of six galaxies (NGC 3783, Mrk 279, Mrk 766, NGC 3227, NGC 7314, and NGC 3516). Using the hardness-ratio curves, we identify time-intervals in which clouds are eclipsing the central X-ray source in five of the six sources. We detect three occultations in NGC 3227 and one occultation in NGC 3783, NGC 7314, and NGC 3516, together with the well-known occultations in Mrk 766. We estimate the physical properties of the eclipsing clouds. The derived physical size of the X-ray sources ($\sim$(3-28)$\times$10$^{13}$ cm) is less than that of the eclipsing clouds with column densities of $\sim$10$^{22}$-10$^{23}$ cm$^{-2}$, thus a single cloud may block the X-ray source, leading to notorious temporal variability of the X-ray flux. The eclipsing clouds in Mrk 766, NGC 3227, NGC 7314, and NGC 3516 with distances from the X-ray source of $\sim$(0.3-3.6)$\times$10$^4$ $R_g$ are moving at Keplerian velocities $>$1122 km s$^{-1}$, typical parameters of broad-line region clouds, while the eclipsing cloud in NGC 3783 is likely located in the dusty torus. We also find a good anti-correlation with a slope of -187$\pm$62 between the known masses of the supermassive black hole in the center of the galaxies with the equivalent width (EW) of the 6.4 keV Fe line for the five Seyfert 1 galaxies of our sample, while the Seyfert 2 galaxy NGC 7314 shows an average EW value of 100$\pm$11 eV inconsistent with the above anti-correlation., Comment: 13 pages, 15 figures, accepted for publication in MNRAS
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- 2022
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14. Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants
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Logan C. Ott and Melha Mellata
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horizontal gene transfer ,short-chain fatty acids ,plasmid transfer inhibition ,antimicrobial resistance ,bacterial plasmid conjugation ,Microbiology ,QR1-502 - Abstract
The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p
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- 2024
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15. The XXL Survey: XLVIII; X-ray follow-up of distant XXL clusters: Masses, scaling relations and AGN contamination
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Duffy, R. T., Logan, C. H. A., Maughan, B. J., Eckert, D., Clerc, N., Ettori, S., Gastaldello, F., Koulouridis, E., Pierre, M., Ricci, M., Sereno, M., Valtchanov, I., and Willis, J. P.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We use deep follow-up XMM-Newton observations of 6 clusters discovered in the XXL Survey at $z>1$ to gain robust measurements of their X-ray properties and to investigate the extent to which scaling relations at low redshift are valid at $z>1$. This sample is unique as it has been investigated for AGN contamination, which ensures measurements are not undermined by systematic uncertainties, and pushes to lower mass at higher redshift than is usually possible, for example with Sunyaev-Zel'dovich (SZ) selected clusters. We determine the flux contribution of point sources to the XXL cluster flux in order to test for the presence of AGN in other high-redshift cluster candidates, and find 3XLSS J231626.8-533822 to be a point source misclassified as a cluster and 3XLSS J232737.3-541618 to be a genuine cluster. We present the first attempt to measure the hydrostatic masses in a bright subsample of $z>1$ X-ray selected galaxy clusters with a known selection function. Periods of high particle background significantly reduced the effective exposure times of observations (losing >50% in some cases) limiting the power of this study. When combined with complementary SZ selected cluster samples at higher masses, the data appear broadly consistent with the self-similar evolution of the low redshift scaling relations between ICM properties and cluster mass, suggesting that properties such as the X-ray temperature, gas mass and SZ signal remain reliable mass proxies even at high redshift., Comment: 13 pages, 7 figures, published in MNRAS
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- 2022
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16. Comparing trained and untrained probabilistic ensemble forecasts of COVID-19 cases and deaths in the United States
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Ray, Evan L., Brooks, Logan C., Bien, Jacob, Biggerstaff, Matthew, Bosse, Nikos I., Bracher, Johannes, Cramer, Estee Y., Funk, Sebastian, Gerding, Aaron, Johansson, Michael A., Rumack, Aaron, Wang, Yijin, Zorn, Martha, Tibshirani, Ryan J., and Reich, Nicholas G.
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Statistics - Methodology - Abstract
The U.S. COVID-19 Forecast Hub aggregates forecasts of the short-term burden of COVID-19 in the United States from many contributing teams. We study methods for building an ensemble that combines forecasts from these teams. These experiments have informed the ensemble methods used by the Hub. To be most useful to policy makers, ensemble forecasts must have stable performance in the presence of two key characteristics of the component forecasts: (1) occasional misalignment with the reported data, and (2) instability in the relative performance of component forecasters over time. Our results indicate that in the presence of these challenges, an untrained and robust approach to ensembling using an equally weighted median of all component forecasts is a good choice to support public health decision makers. In settings where some contributing forecasters have a stable record of good performance, trained ensembles that give those forecasters higher weight can also be helpful.
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- 2022
17. Tianeptine, an Antidepressant with Opioid Agonist Effects: Pharmacology and Abuse Potential, a Narrative Review
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Edinoff, Amber N., Sall, Saveen, Beckman, Scott P., Koepnick, Andrew D., Gold, Logan C., Jackson, Eric D., Wenger, Danielle M., Cornett, Elyse M., Murnane, Kevin S., Kaye, Adam M., and Kaye, Alan D.
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- 2023
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18. Effect of Gamma Radiation on Selective Laser Sintered Nylon-12
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Getto, Elizabeth, Schoffstall, Logan C., Hall-Smith, Sidney, Baker, Bradford, Slager, Jonathan, Joyce, Peter J., and Durkin, David P.
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- 2023
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19. The Selah Pilot Study of Spiritual, Mindfulness, and Stress Inoculation Practices on Stress-Related Outcomes Among United Methodist Clergy in the United States
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Proeschold-Bell, Rae Jean, Eagle, David E., Tice, Logan C., Yao, Jia, Rash, Joshua A., Choi, Jessica Y., Stringfield, Beth, and Labrecque, Sofia M.
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- 2023
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20. Intrinsic resistance to ROS1 inhibition in a patient with CD74‐ROS1 mediated by AXL overexpression
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Tara L. Peters, Nan Chen, Logan C. Tyler, Anh T. Le, Anastasios Dimou, and Robert C. Doebele
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AXL ,drug resistance ,NSCLC ,ROS1 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background The vast majority of patients with ROS1 positive non‐small cell lung cancer (NSCLC) derive clinical benefit from currently approved ROS1 therapies, including crizotinib and entrectinib. However, a small proportion of patients treated with ROS1 inhibitors fail to derive any clinical benefit and demonstrate rapid disease progression. The biological mechanisms underpinning intrinsic resistance remain poorly understood for oncogene‐driven cancers. Methods We generated a patient‐derived cell line, CUTO33, from a ROS1 therapy naive patient with CD74‐ROS1+ NSCLC, who ultimately did not respond to a ROS1 inhibitor. We evaluated a panel of ROS1+ patient‐derived NSCLC cell lines and used cell‐based assays to determine the mechanism of intrinsic resistance to ROS1 therapy. Results The CUTO33 cell line expressed the CD74‐ROS1 gene fusion at the RNA and protein level. The ROS1 fusion protein was phosphorylated at baseline consistent with the known intrinsic activity of this oncogene. ROS1 phosphorylation could be inhibited using a wide array of ROS1 inhibitors, however these inhibitors did not block cell proliferation, confirming intrinsic resistance in this model and consistent with the patient's lack of response to a ROS1 inhibitor. CUTO33 expressed high levels of AXL, which has been associated with drug resistance. Combination of an AXL inhibitor or AXL knockdown with a ROS1 inhibitor partially reversed resistance. Conclusions In summary, we demonstrate that AXL overexpression is a mechanism of intrinsic resistance to ROS1 inhibitors.
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- 2023
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21. Highly Effective Teachers' Reported Use of Reading Engagement and Motivation Strategies in the Elementary English Language Arts Classroom in Grades Second through Fifth
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Logan C. Elliott
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Highly effective elementary teachers faced challenges to professional development which differed from their urban or suburban peers. With the increasing need for student proficiency in reading, strategies to help grow their engagement and motivation were necessary to investigate and apply to instructional habits. The purpose of this basic interpretive qualitative study was to examine the perceptions of highly effective teachers on the benefits and limitations of reading engagement and motivation strategies in grades 2nd through 5th across four public school districts in the state of Tennessee. Highly effective elementary teachers from fifteen different schools representing three districts within the East Tennessee region of the United States completed a questionnaire about reading engagement and motivation strategies, the benefits and limitations of those strategies, their personal reading habits, and the impact on students. Highly effective elementary teachers reported using various strategies from the district or self-discovered, benefits such as student positive gains and a love for reading, limitations such as time and scripted curriculum, and being readers themselves. Given the need and legislation for reading proficiency in the state of Tennessee, reading engagement and motivation strategies were important to engage students we are asking to read more every year. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]
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- 2023
22. Clinical Results of Carpal Tunnel Release Using Ultrasound Guidance in Over 100 Patients at Two to Six Years
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Cano, Logan C., Leiby, Braeden M., Shum, Laura C., Ward, Meliza G., and Joseph, Anthony E.
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- 2024
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23. Associations of prenatal ambient air pollution exposures with asthma in middle childhood
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Hazlehurst, Marnie F., Carroll, Kecia N., Moore, Paul E., Szpiro, Adam A., Adgent, Margaret A., Dearborn, Logan C., Sherris, Allison R., Loftus, Christine T., Ni, Yu, Zhao, Qi, Barrett, Emily S., Nguyen, Ruby H.N., Swan, Shanna H., Wright, Rosalind J., Bush, Nicole R., Sathyanarayana, Sheela, LeWinn, Kaja Z., and Karr, Catherine J.
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- 2024
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24. A genome-wide search for pleiotropy in more than 100,000 harmonized longitudinal cognitive domain scores
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Kang, Moonil, Ang, Ting Fang Alvin, Devine, Sherral A., Sherva, Richard, Mukherjee, Shubhabrata, Trittschuh, Emily H., Gibbons, Laura E., Scollard, Phoebe, Lee, Michael, Choi, Seo-Eun, Klinedinst, Brandon, Nakano, Connie, Dumitrescu, Logan C., Durant, Alaina, Hohman, Timothy J., Cuccaro, Michael L., Saykin, Andrew J., Kukull, Walter A., Bennett, David A., Wang, Li-San, Mayeux, Richard P., Haines, Jonathan L., Pericak-Vance, Margaret A., Schellenberg, Gerard D., Crane, Paul K., Au, Rhoda, Lunetta, Kathryn L., Mez, Jesse B., and Farrer, Lindsay A.
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- 2023
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25. Identifying who uses first-person singular pronouns and the psychological impacts this language may have
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Holtzman, Nicholas S., primary and Delgado, Logan C., additional
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- 2023
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26. Smooth fans that are endpoint rigid
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Rodrigo Hernández-Gutiérrez and Logan C. Hoehn
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smooth fan ,rigidity ,lelek fan ,erdős space ,almost zero-dimensional ,Mathematics ,QA1-939 ,Analysis ,QA299.6-433 - Abstract
Let X be a smooth fan and denote its set of endpoints by E(X). Let E be one of the following spaces: the natural numbers, the irrational numbers, or the product of the Cantor set with the natural numbers. We prove that there is a smooth fan X such that E(X) is homeomorphic to E and for every homeomorphism h : X → X , the restriction of h to E(X) is the identity. On the other hand, we also prove that if X is any smooth fan such that E(X) is homeomorphic to complete Erdős space, then X is necessarily homeomorphic to the Lelek fan; this adds to a 1989 result by Włodzimierz Charatonik.
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- 2023
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27. Mechanical control of cell proliferation patterns in growing epithelial monolayers
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Carpenter, Logan C., Pérez-Verdugo, Fernanda, and Banerjee, Shiladitya
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- 2024
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28. Tuning glycerol plasticization of chitosan with boric acid
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Scott, Holli R., Pearson, Connor J., Ealley, Logan C., Boardman, Brycelyn Marie, and Peters, Gretchen Marie
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- 2024
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29. Rare germline copy number variants (CNVs) and breast cancer risk
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Dennis, Joe, Tyrer, Jonathan P, Walker, Logan C, Michailidou, Kyriaki, Dorling, Leila, Bolla, Manjeet K, Wang, Qin, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Freeman, Laura E Beane, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bogdanova, Natalia V, Bojesen, Stig E, Brenner, Hermann, Castelao, Jose E, Chang-Claude, Jenny, Chenevix-Trench, Georgia, Clarke, Christine L, Collée, J Margriet, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Devilee, Peter, Dörk, Thilo, Dossus, Laure, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, Giles, Graham G, González-Neira, Anna, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Hall, Per, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Howell, Anthony, Jager, Agnes, Jakubowska, Anna, John, Esther M, Johnson, Nichola, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M, Ko, Yon-Dschun, Kosma, Veli-Matti, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Lacey, James V, Lambrechts, Diether, Larson, Nicole L, Linet, Martha, Ogrodniczak, Alicja, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L, Muranen, Taru A, Murphy, Rachel A, Nevanlinna, Heli, Olson, Janet E, Olsson, Håkan, Park-Simon, Tjoung-Won, Perou, Charles M, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Pylkäs, Katri, Rennert, Gad, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Shibli, Rana, Smeets, Ann, and Soucy, Penny
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Human Genome ,Breast Cancer ,Genetics ,Clinical Research ,Cancer ,Prevention ,2.1 Biological and endogenous factors ,Aetiology ,Breast Neoplasms ,Case-Control Studies ,DNA Copy Number Variations ,Female ,Genome ,Human ,Genome-Wide Association Study ,Germ Cells ,Humans ,Risk Factors ,NBCS Collaborators ,CTS Consortium ,ABCTB Investigators ,kConFab/AOCS Investigators - Abstract
Germline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 (P = 3.7E-18). Nine other genes were associated with a p-value
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- 2022
30. Scale setting the M\'obius Domain Wall Fermion on gradient-flowed HISQ action using the omega baryon mass and the gradient-flow scales $t_0$ and $w_0$
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Miller, Nolan, Carpenter, Logan C, Berkowitz, Evan, Chang, Chia Cheng, Hörz, Ben, Howarth, Dean, Monge-Camacho, Henry, Rinaldi, Enrico, Brantley, David A., Körber, Christopher, Bouchard, Chris, Clark, M. A., Gambhir, Arjun Singh, Monahan, Christopher J., Nicholson, Amy, Vranas, Pavlos, and Walker-Loud, André
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High Energy Physics - Lattice ,High Energy Physics - Phenomenology ,Nuclear Theory - Abstract
We report on a sub-percent scale determination using the omega baryon mass and gradient-flow methods. The calculations are performed on 22 ensembles of $N_f=2+1+1$ highly improved, rooted staggered sea-quark configurations generated by the MILC and CalLat Collaborations. The valence quark action used is M\"obius Domain-Wall fermions solved on these configurations after a gradient-flow smearing is applied with a flowtime of $t_{\rm gf}=1$ in lattice units. The ensembles span four lattice spacings in the range $0.06 \lesssim a \lesssim 0.15$ fm, six pion masses in the range $130 \lesssim m_\pi \lesssim 400$ MeV and multiple lattice volumes. On each ensemble, the gradient-flow scales $t_0/a^2$ and $w_0/a$ and the omega baryon mass $a m_\Omega$ are computed. The dimensionless product of these quantities is then extrapolated to the continuum and infinite volume limits and interpolated to the physical light, strange and charm quark mass point in the isospin limit, resulting in the determination of $\sqrt{t_0}=0.1422(14)$ fm and $w_0 = 0.1709(11)$ fm with all sources of statistical and systematic uncertainty accounted for. The dominant uncertainty in this result is the stochastic uncertainty, providing a clear path for a few-per-mille uncertainty, as recently obtained by the Budapest-Marseille-Wuppertal Collaboration., Comment: v3: Published version; v2: Added determination of t_0 as well as w_0; v1: 13 pages plus appendices. The correlation function data, mass results and analysis code accompanying this publication can be found at this github repository: https://github.com/callat-qcd/project_scale_setting_mdwf_hisq
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- 2020
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31. Long-term ozone exposure and lung function in middle childhood
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Hazlehurst, Marnie F., Dearborn, Logan C., Sherris, Allison R., Loftus, Christine T., Adgent, Margaret A., Szpiro, Adam A., Ni, Yu, Day, Drew B., Kaufman, Joel D., Thakur, Neeta, Wright, Rosalind J., Sathyanarayana, Sheela, Carroll, Kecia N., Moore, Paul E., and Karr, Catherine J.
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- 2024
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32. Modeling the future of shoulder arthroplasty
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Stadecker, Monica, Kolakowski, Logan C., Pandy, Marcus G., and Frankle, Mark A.
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- 2024
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33. Tianeptine, an Antidepressant with Opioid Agonist Effects: Pharmacology and Abuse Potential, a Narrative Review
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Amber N. Edinoff, Saveen Sall, Scott P. Beckman, Andrew D. Koepnick, Logan C. Gold, Eric D. Jackson, Danielle M. Wenger, Elyse M. Cornett, Kevin S. Murnane, Adam M. Kaye, and Alan D. Kaye
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Tianeptine ,Zaza ,Opioid agonists ,Overdose ,Gas station supplements ,Suicide ,Anesthesiology ,RD78.3-87.3 - Abstract
Abstract Tianeptine is an antidepressant drug approved for the treatment of major depressive disorder in countries other than the US. It is classified as an atypical tricyclic antidepressant and has shown potential benefits in addressing anxiety and irritable bowel disease. However, it is important to note that tianeptine is not approved for any use by the United States Federal Drug Administration (FDA). Despite its lack of approval by the FDA, tianeptine has been distributed online and at small retail locations. The term “gas station drugs” refers to a wide range of substances typically available for purchase from gas stations, corner stores, bodegas, mini marts, smoke shops, and the Internet. These substances may be produced commercially by drug manufacturers or in clandestine laboratories to mimic the effects of more well-known illicit/controlled substances such as marijuana, cocaine, opioids, etc. Tianeptine has made its way to convenience stores and gas station shelves, branded as “Zaza” and “Tianna Red.” It can also be obtained online from independent vendors without a prescription. Misuse of tianeptine can lead to euphoric, opioid-like highs with the potential for chronic users to develop dependence and tolerance. Overdose and use in suicide attempts have also been documented. This manuscript is a narrative review, highlighting the dangers of tianeptine and other gas station drugs and underscoring the urgent need to regulate these substances.
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- 2023
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34. A genome-wide search for pleiotropy in more than 100,000 harmonized longitudinal cognitive domain scores
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Moonil Kang, Ting Fang Alvin Ang, Sherral A. Devine, Richard Sherva, Shubhabrata Mukherjee, Emily H. Trittschuh, Laura E. Gibbons, Phoebe Scollard, Michael Lee, Seo-Eun Choi, Brandon Klinedinst, Connie Nakano, Logan C. Dumitrescu, Alaina Durant, Timothy J. Hohman, Michael L. Cuccaro, Andrew J. Saykin, Walter A. Kukull, David A. Bennett, Li-San Wang, Richard P. Mayeux, Jonathan L. Haines, Margaret A. Pericak-Vance, Gerard D. Schellenberg, Paul K. Crane, Rhoda Au, Kathryn L. Lunetta, Jesse B. Mez, and Lindsay A. Farrer
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Alzheimer’s disease ,Genome-wide association study ,Cognitive domains ,Longitudinal measures ,Pleiotropy ,Pathway analysis ,Neurology. Diseases of the nervous system ,RC346-429 ,Geriatrics ,RC952-954.6 - Abstract
Abstract Background More than 75 common variant loci account for only a portion of the heritability for Alzheimer’s disease (AD). A more complete understanding of the genetic basis of AD can be deduced by exploring associations with AD-related endophenotypes. Methods We conducted genome-wide scans for cognitive domain performance using harmonized and co-calibrated scores derived by confirmatory factor analyses for executive function, language, and memory. We analyzed 103,796 longitudinal observations from 23,066 members of community-based (FHS, ACT, and ROSMAP) and clinic-based (ADRCs and ADNI) cohorts using generalized linear mixed models including terms for SNP, age, SNP × age interaction, sex, education, and five ancestry principal components. Significance was determined based on a joint test of the SNP’s main effect and interaction with age. Results across datasets were combined using inverse-variance meta-analysis. Genome-wide tests of pleiotropy for each domain pair as the outcome were performed using PLACO software. Results Individual domain and pleiotropy analyses revealed genome-wide significant (GWS) associations with five established loci for AD and AD-related disorders (BIN1, CR1, GRN, MS4A6A, and APOE) and eight novel loci. ULK2 was associated with executive function in the community-based cohorts (rs157405, P = 2.19 × 10–9). GWS associations for language were identified with CDK14 in the clinic-based cohorts (rs705353, P = 1.73 × 10–8) and LINC02712 in the total sample (rs145012974, P = 3.66 × 10–8). GRN (rs5848, P = 4.21 × 10–8) and PURG (rs117523305, P = 1.73 × 10–8) were associated with memory in the total and community-based cohorts, respectively. GWS pleiotropy was observed for language and memory with LOC107984373 (rs73005629, P = 3.12 × 10–8) in the clinic-based cohorts, and with NCALD (rs56162098, P = 1.23 × 10–9) and PTPRD (rs145989094, P = 8.34 × 10–9) in the community-based cohorts. GWS pleiotropy was also found for executive function and memory with OSGIN1 (rs12447050, P = 4.09 × 10–8) and PTPRD (rs145989094, P = 3.85 × 10–8) in the community-based cohorts. Functional studies have previously linked AD to ULK2, NCALD, and PTPRD. Conclusion Our results provide some insight into biological pathways underlying processes leading to domain-specific cognitive impairment and AD, as well as a conduit toward a syndrome-specific precision medicine approach to AD. Increasing the number of participants with harmonized cognitive domain scores will enhance the discovery of additional genetic factors of cognitive decline leading to AD and related dementias.
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- 2023
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35. One heck of a fine purchase (decommissioning of the USS Lexington): interview
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Logan, C. Flack, CAPT, Ret
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AIRCRAFT CARRIERS ,NAVY - United States - Equipment ,NAVY - United States - Training ,SHIPS - Decommissioning - Abstract
illus
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- 1991
36. Instability after reverse shoulder arthroplasty with tendon transfer: a case series
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Kolakowski, Logan C., Livesey, Michael G., Hasan, S. Ashfaq, Horneff, John Gabriel, III, Sykes, Joshua B., Gilotra, Mohit N., and Levy, Jonathan C.
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- 2023
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37. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup
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Biesecker, Leslie G., Harrison, Steven M., Tayoun, Ahmad A., Berg, Jonathan S., Brenner, Steven E., Cutting, Garry R., Ellard, Sian, Greenblatt, Marc S., Kang, Peter, Karbassi, Izabela, Karchin, Rachel, Mester, Jessica, O’Donnell-Luria, Anne, Pesaran, Tina, Plon, Sharon E., Rehm, Heidi L., Strande, Natasha T., Tavtigian, Sean V., Topper, Scott, Walker, Logan C., Hoya, Miguel de la, Wiggins, George A.R., Lindy, Amanda, Vincent, Lisa M., Parsons, Michael T., Canson, Daffodil M., Bis-Brewer, Dana, Cass, Ashley, Tchourbanov, Alexander, Zimmermann, Heather, Byrne, Alicia B., Karam, Rachid, and Spurdle, Amanda B.
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- 2023
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38. Comparing trained and untrained probabilistic ensemble forecasts of COVID-19 cases and deaths in the United States
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Ray, Evan L., Brooks, Logan C., Bien, Jacob, Biggerstaff, Matthew, Bosse, Nikos I., Bracher, Johannes, Cramer, Estee Y., Funk, Sebastian, Gerding, Aaron, Johansson, Michael A., Rumack, Aaron, Wang, Yijin, Zorn, Martha, Tibshirani, Ryan J., and Reich, Nicholas G.
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- 2023
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39. Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson’s disease
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Gaeta, Anthony L., Willicott, Karolina, Willicott, Corey W., McKay, Luke E., Keogh, Candice M., Altman, Tyler J., Kimble, Logan C., Yarbrough, Abigail L., Caldwell, Kim A., and Caldwell, Guy A.
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- 2023
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40. Does needle penetration of the shoulder joint prior to arthroscopy increase infection risk? The effect of preoperative magnetic resonance arthrogram or corticosteroid injection
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Livesey, Michael G., Bains, Sandeep S., Weir, Tristan B., Kolakowski, Logan C., Remily, Ethan A., Sax, Oliver C., Gilotra, Mohit N., and Hasan, S. Ashfaq
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- 2023
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41. Correction for Johansson et al., An open challenge to advance probabilistic forecasting for dengue epidemics
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Johansson, Michael A, Apfeldorf, Karyn M, Dobson, Scott, Devita, Jason, Buczak, Anna L, Baugher, Benjamin, Moniz, Linda J, Bagley, Thomas, Babin, Steven M, Guven, Erhan, Yamana, Teresa K, Shaman, Jeffrey, Moschou, Terry, Lothian, Nick, Lane, Aaron, Osborne, Grant, Jiang, Gao, Brooks, Logan C, Farrow, David C, Hyun, Sangwon, Tibshirani, Ryan J, Rosenfeld, Roni, Lessler, Justin, Reich, Nicholas G, Cummings, Derek AT, Lauer, Stephen A, Moore, Sean M, Clapham, Hannah E, Lowe, Rachel, Bailey, Trevor C, Garcia-Diez, Markel, Carvalho, Marilia Sa, Rodo, Xavier, Sardar, Tridip, Paul, Richard, Ray, Evan L, Sakrejda, Krzysztof, Brown, Alexandria C, Meng, Xi, Osoba, Osonde, Vardavas, Raffaele, Manheim, David, Moore, Melinda, Rao, Dhananjai M, Porco, Travis C, Ackley, Sarah, Liu, Fengchen, Worden, Lee, Convertino, Matteo, Liu, Yang, Reddy, Abraham, Ortiz, Eloy, Rivero, Jorge, Brito, Humberto, Juarrero, Alicia, Johnson, Leah R, Gramacy, Robert B, Cohen, Jeremy M, Mordecai, Erin A, Murdock, Courtney C, Rohr, Jason R, Ryan, Sadie J, Stewart-Ibarra, Anna M, Weikel, Daniel P, Jutla, Antarpreet, Khan, Rakibul, Poultney, Marissa, Colwell, Rita R, Rivera-Garcia, Brenda, Barker, Christopher M, Bell, Jesse E, Biggerstaff, Matthew, Swerdlow, David, Mier-Y-Teran-Romero, Luis, Forshey, Brett M, Trtanj, Juli, Asher, Jason, Clay, Matt, Margolis, Harold S, Hebbeler, Andrew M, George, Dylan, and Chretien, Jean-Paul
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Economics ,Biological Sciences ,Applied Economics ,Good Health and Well Being - Abstract
Correction for “An open challenge to advance probabilistic forecasting for dengue epidemics,” by Michael A. Johansson, Karyn M. Apfeldorf, Scott Dobson, Jason Devita, Anna L. Buczak, Benjamin Baugher, Linda J. Moniz, Thomas Bagley, Steven M. Babin, Erhan Guven, Teresa K. Yamana, Jeffrey Shaman, Terry Moschou, Nick Lothian, Aaron Lane, Grant Osborne, Gao Jiang, Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld, Justin Lessler, Nicholas G. Reich, Derek A. T. Cummings, Stephen A. Lauer, Sean M. Moore, Hannah E. Clapham, Rachel Lowe, Trevor C. Bailey, Markel García-Díez, Marilia Sá Carvalho, Xavier Rodó, Tridip Sardar, Richard Paul, Evan L. Ray, Krzysztof Sakrejda, Alexandria C. Brown, Xi Meng, Osonde Osoba, Raffaele Vardavas, David Manheim, Melinda Moore, Dhananjai M. Rao, Travis C. Porco, Sarah Ackley, Fengchen Liu, Lee Worden, Matteo Convertino, Yang Liu, Abraham Reddy, Eloy Ortiz, Jorge Rivero, Humberto Brito, Alicia Juarrero, Leah R. Johnson, Robert B. Gramacy, Jeremy M. Cohen, Erin A. Mordecai, Courtney C. Murdock, Jason R. Rohr, Sadie J. Ryan, Anna M. Stewart-Ibarra, Daniel P. Weikel, Antarpreet Jutla, Rakibul Khan, Marissa Poultney, Rita R. Colwell, Brenda Rivera-García, Christopher M. Barker, Jesse E. Bell, Matthew Biggerstaff, David Swerdlow, Luis Mier-y-Teran-Romero, Brett M. Forshey, Juli Trtanj, Jason Asher, Matt Clay, Harold S. Margolis, Andrew M. Hebbeler, Dylan George, and Jean-Paul Chretien, which was first published November 11, 2019; 10.1073/pnas.1909865116 (Proc. Natl. Acad. Sci. U.S.A. 116, 24268–24274). The authors note that the following statement should be added to the Acknowledgments: “E.A.M. was supported by NIH Grant R35GM133439.
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- 2020
42. An open challenge to advance probabilistic forecasting for dengue epidemics
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Johansson, Michael A, Apfeldorf, Karyn M, Dobson, Scott, Devita, Jason, Buczak, Anna L, Baugher, Benjamin, Moniz, Linda J, Bagley, Thomas, Babin, Steven M, Guven, Erhan, Yamana, Teresa K, Shaman, Jeffrey, Moschou, Terry, Lothian, Nick, Lane, Aaron, Osborne, Grant, Jiang, Gao, Brooks, Logan C, Farrow, David C, Hyun, Sangwon, Tibshirani, Ryan J, Rosenfeld, Roni, Lessler, Justin, Reich, Nicholas G, Cummings, Derek AT, Lauer, Stephen A, Moore, Sean M, Clapham, Hannah E, Lowe, Rachel, Bailey, Trevor C, García-Díez, Markel, Carvalho, Marilia Sá, Rodó, Xavier, Sardar, Tridip, Paul, Richard, Ray, Evan L, Sakrejda, Krzysztof, Brown, Alexandria C, Meng, Xi, Osoba, Osonde, Vardavas, Raffaele, Manheim, David, Moore, Melinda, Rao, Dhananjai M, Porco, Travis C, Ackley, Sarah, Liu, Fengchen, Worden, Lee, Convertino, Matteo, Liu, Yang, Reddy, Abraham, Ortiz, Eloy, Rivero, Jorge, Brito, Humberto, Juarrero, Alicia, Johnson, Leah R, Gramacy, Robert B, Cohen, Jeremy M, Mordecai, Erin A, Murdock, Courtney C, Rohr, Jason R, Ryan, Sadie J, Stewart-Ibarra, Anna M, Weikel, Daniel P, Jutla, Antarpreet, Khan, Rakibul, Poultney, Marissa, Colwell, Rita R, Rivera-García, Brenda, Barker, Christopher M, Bell, Jesse E, Biggerstaff, Matthew, Swerdlow, David, Mier-y-Teran-Romero, Luis, Forshey, Brett M, Trtanj, Juli, Asher, Jason, Clay, Matt, Margolis, Harold S, Hebbeler, Andrew M, George, Dylan, and Chretien, Jean-Paul
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Emerging Infectious Diseases ,Rare Diseases ,Vaccine Related ,Infectious Diseases ,Vector-Borne Diseases ,Prevention ,Infection ,Good Health and Well Being ,Dengue ,Disease Outbreaks ,Epidemics ,Epidemiologic Methods ,Humans ,Incidence ,Models ,Statistical ,Peru ,Puerto Rico ,forecast ,dengue ,epidemic - Abstract
A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project-integration with public health needs, a common forecasting framework, shared and standardized data, and open participation-can help advance infectious disease forecasting beyond dengue.
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- 2019
43. MET gene amplification is a mechanism of resistance to entrectinib in ROS1+ NSCLC
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Logan C. Tyler, Anh T. Le, Nan Chen, Hala Nijmeh, Liming Bao, Timothy R. Wilson, David Chen, Brian Simmons, Kristen M. Turner, Dean Perusse, Shailaja Kasibhatla, Jason Christiansen, Arkadiusz Z. Dudek, and Robert C. Doebele
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drug resistance ,entrectinib ,MET ,NSCLC ,ROS1 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background ROS1 tyrosine kinase inhibitors (TKIs) have demonstrated significant clinical benefit for ROS1+ NSCLC patients. However, TKI resistance inevitably develops through ROS1 kinase domain (KD) modification or another kinase driving bypass signaling. While multiple TKIs have been designed to target ROS1 KD mutations, less is known about bypass signaling in TKI‐resistant ROS1+ lung cancers. Methods Utilizing a primary, patient‐derived TPM3‐ROS1 cell line (CUTO28), we derived an entrectinib‐resistant line (CUTO28‐ER). We evaluated proliferation and signaling responses to TKIs, and utilized RNA sequencing, whole exome sequencing, and fluorescence in situ hybridization to detect transcriptional, mutational, and copy number alterations, respectively. We substantiated in vitro findings using a CD74‐ROS1 NSCLC patient's tumor samples. Last, we analyzed circulating tumor DNA (ctDNA) from ROS1+ NSCLC patients in the STARTRK‐2 entrectinib trial to determine the prevalence of MET amplification. Results CUTO28‐ER cells did not exhibit ROS1 KD mutations. MET TKIs inhibited proliferation and downstream signaling and MET transcription was elevated in CUTO28‐ER cells. CUTO28‐ER cells displayed extrachromosomal (ecDNA) MET amplification without MET activating mutations, exon 14 skipping, or fusions. The CD74‐ROS1 patient samples illustrated MET amplification while receiving ROS1 TKI. Finally, two of 105 (1.9%) entrectinib‐resistant ROS1+ NSCLC STARTRK‐2 patients with ctDNA analysis at enrollment and disease progression displayed MET amplification. Conclusions Treatment with ROS1‐selective inhibitors may lead to MET‐mediated resistance. The discovery of ecDNA MET amplification is noteworthy, as ecDNA is associated with more aggressive cancers. Following progression on ROS1‐selective inhibitors, MET gene testing and treatments targeting MET should be explored to overcome MET‐driven resistance.
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- 2022
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44. Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers
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Christopher Hakkaart, John F. Pearson, Louise Marquart, Joe Dennis, George A. R. Wiggins, Daniel R. Barnes, Bridget A. Robinson, Peter D. Mace, Kristiina Aittomäki, Irene L. Andrulis, Banu K. Arun, Jacopo Azzollini, Judith Balmaña, Rosa B. Barkardottir, Sami Belhadj, Lieke Berger, Marinus J. Blok, Susanne E. Boonen, Julika Borde, Angela R. Bradbury, Joan Brunet, Saundra S. Buys, Maria A. Caligo, Ian Campbell, Wendy K. Chung, Kathleen B. M. Claes, GEMO Study Collaborators, EMBRACE Collaborators, Marie-Agnès Collonge-Rame, Jackie Cook, Casey Cosgrove, Fergus J. Couch, Mary B. Daly, Sita Dandiker, Rosemarie Davidson, Miguel de la Hoya, Robin de Putter, Capucine Delnatte, Mallika Dhawan, Orland Diez, Yuan Chun Ding, Susan M. Domchek, Alan Donaldson, Jacqueline Eason, Douglas F. Easton, Hans Ehrencrona, Christoph Engel, D. Gareth Evans, Ulrike Faust, Lidia Feliubadaló, Florentia Fostira, Eitan Friedman, Megan Frone, Debra Frost, Judy Garber, Simon A. Gayther, Andrea Gehrig, Paul Gesta, Andrew K. Godwin, David E. Goldgar, Mark H. Greene, Eric Hahnen, Christopher R. Hake, Ute Hamann, Thomas V. O. Hansen, Jan Hauke, Julia Hentschel, Natalie Herold, Ellen Honisch, Peter J. Hulick, Evgeny N. Imyanitov, SWE-BRCA Investigators, kConFab Investigators, HEBON Investigators, Claudine Isaacs, Louise Izatt, Angel Izquierdo, Anna Jakubowska, Paul A. James, Ramunas Janavicius, Esther M. John, Vijai Joseph, Beth Y. Karlan, Zoe Kemp, Judy Kirk, Irene Konstantopoulou, Marco Koudijs, Ava Kwong, Yael Laitman, Fiona Lalloo, Christine Lasset, Charlotte Lautrup, Conxi Lazaro, Clémentine Legrand, Goska Leslie, Fabienne Lesueur, Phuong L. Mai, Siranoush Manoukian, Véronique Mari, John W. M. Martens, Lesley McGuffog, Noura Mebirouk, Alfons Meindl, Austin Miller, Marco Montagna, Lidia Moserle, Emmanuelle Mouret-Fourme, Hannah Musgrave, Sophie Nambot, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Joanne Ngeow Yuen Yie, Tu Nguyen-Dumont, Liene Nikitina-Zake, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Ana Osorio, Claus-Eric Ott, Sue K. Park, Michael T. Parsons, Inge Sokilde Pedersen, Ana Peixoto, Pedro Perez-Segura, Paolo Peterlongo, Timea Pocza, Paolo Radice, Juliane Ramser, Johanna Rantala, Gustavo C. Rodriguez, Karina Rønlund, Efraim H. Rosenberg, Maria Rossing, Rita K. Schmutzler, Payal D. Shah, Saba Sharif, Priyanka Sharma, Lucy E. Side, Jacques Simard, Christian F. Singer, Katie Snape, Doris Steinemann, Dominique Stoppa-Lyonnet, Christian Sutter, Yen Yen Tan, Manuel R. Teixeira, Soo Hwang Teo, Mads Thomassen, Darcy L. Thull, Marc Tischkowitz, Amanda E. Toland, Alison H. Trainer, Vishakha Tripathi, Nadine Tung, Klaartje van Engelen, Elizabeth J. van Rensburg, Ana Vega, Alessandra Viel, Lisa Walker, Jeffrey N. Weitzel, Marike R. Wevers, Georgia Chenevix-Trench, Amanda B. Spurdle, Antonis C. Antoniou, and Logan C. Walker
- Subjects
Biology (General) ,QH301-705.5 - Abstract
The risk of germline copy number variants (CNVs) in BRCA1 and BRCA2 pathogenic variant carriers in breast cancer is assessed, with CNVs overlapping SULT1A1 decreasing breast cancer risk in BRCA1 carriers.
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- 2022
- Full Text
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45. Process-Driven Math: An Auditory Method of Mathematics Instruction and Assessment for Students Who Are Blind or Have Low Vision
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Gulley, Ann P., Smith, Luke A., Price, Jordan A., Prickett, Logan C., and Ragland, Matthew F.
- Abstract
Process-Driven Math is a fully audio method of mathematics instruction and assessment that was created at Auburn University at Montgomery, Alabama, to meet the needs of one particular student, Logan. He was blind, mobility impaired, and he could not speak above a whisper. Logan was not able to use traditional low vision tools like braille and Nemeth code because he lacked the sensitivity in his fingers required to read the raised dots. Logan's need for tools that would enable him to perform the rigorous algebraic manipulations that are common in mathematics courses led to the development of Process-Driven Math. With this method, he was able to succeed in both college algebra and pre-calculus with trigonometry. These tools may help other visually impaired students who are not succeeding in mathematics because they lack access to, or knowledge of, the Nemeth code. Within many algebraic problems, there are processes (algorithms) that must be performed to simplify expressions and solve for variables. Process-Driven Math frees up working memory during the delivery of the mathematic content to the student, and during the student's subsequent manipulation of the equation while working toward a solution. As a result, the student who cannot use or access Nemeth code can better focus on the required algorithms because the cognitive load on working memory is greatly reduced. When using this method, a person who functions as the student's reader and scribe systematically reveals the algebraic expression in layers. The process is highly interactive and places control over the flow of information into the hands of the student.
- Published
- 2017
46. Segmented filamentous bacteria-based treatment to elicit protection against Enterobacteriaceae in Layer chickens
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Jared Meinen-Jochum, Logan C. Ott, and Melha Mellata
- Subjects
segmented filamentous bacteria ,Enterobacteriaceae ,antimicrobial peptides ,cytokines ,layer chickens ,Microbiology ,QR1-502 - Abstract
IntroductionGut microbes like segmented filamentous bacteria (SFB) play a key role in gut maturation during early life, as demonstrated in humans and mice. Our previous study demonstrated oral inoculation of ileum-spores containing SFB to chickens after hatch increases early SFB gut colonization, which increases immune maturation and resistance to bacteria, like Salmonella, as tested in vitro; however, more studies are needed for treatment optimization and in vivo testing. The objectives of this study were to (1) test a treatment that includes both spores and filamentous SFB, (2) validate antimicrobial ability of the treatment in layer hens in vivo, and (3) elucidate its molecular mechanism.MethodsOne-day-old specific pathogen-free layers (n = 12 per group) were orally treated with either PBS (CON) or SFB-based treatment (SFB). At 4 days post-inoculation (DPI), both CON and SFB groups were orally challenged with Salmonella Typhimurium. Total Enterobacteriaceae and Salmonella were examined by plating and enumeration in feces at 7,10 and 14 dpi; and in the ileum, cecum, and spleen at 16 dpi in euthanized birds. The presence and levels of SFB were determined from ilea scrapings via microscopy and qPCR, respectively. Relative gene expression of host-derived antimicrobial peptides and cytokines in the distal ileum was determined by RT-qPCR.ResultsAt 10 and 14 dpi, a significant decrease in total Enterobacteriaceae was observed in the feces of the SFB group. At necropsy, the level of SFB was significantly higher in the SFB group than in the CON group, while a significant decrease in total Enterobacteriaceae and Salmonella was observed in the ceca of the SFB group. RT-qPCR revealed increased expression of β-defensin 14, and cytokines IL-10 and IFNγ.DiscussionThe introduction of SFB at hatch as a prophylactic treatment may benefit commercial partners as well as consumers by reducing the incidence of Enterobacteriaceae in food animals. Reduction of these bacteria in animals would, in turn, increase animal health, productivity, and safety for consumers. Studies to optimize the treatment for poultry industry applications are ongoing in our lab.
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- 2023
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47. Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson’s disease
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Anthony L. Gaeta, Karolina Willicott, Corey W. Willicott, Luke E. McKay, Candice M. Keogh, Tyler J. Altman, Logan C. Kimble, Abigail L. Yarbrough, Kim A. Caldwell, and Guy A. Caldwell
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Neuroscience ,Cognitive neuroscience ,Science - Abstract
Summary: Failure of inherently protective cellular processes and misfolded protein-associated stress contribute to the progressive loss of dopamine (DA) neurons characteristic of Parkinson’s disease (PD). A disease-modifying role for the microbiome has recently emerged in PD, representing an impetus to employ the soil-dwelling nematode, Caenorhabditis elegans, as a preclinical model to correlate changes in gene expression with neurodegeneration in transgenic animals grown on distinct bacterial food sources. Even under tightly controlled conditions, hundreds of differentially expressed genes and a robust neuroprotective response were discerned between clonal C. elegans strains overexpressing human alpha-synuclein in the DA neurons fed either one of only two subspecies of Escherichia coli. Moreover, this neuroprotection persisted in a transgenerational manner. Genetic analysis revealed a requirement for the double-stranded RNA (dsRNA)-mediated gene silencing machinery in conferring neuroprotection. In delineating the contribution of individual genes, evidence emerged for endopeptidase activity and heme-associated pathway(s) as mechanistic components for modulating dopaminergic neuroprotection.
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- 2023
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48. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants
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Richardson, Marcy E., primary, Holdren, Megan, additional, Brannan, Terra, additional, de la Hoya, Miguel, additional, Spurdle, Amanda B., additional, Tavtigian, Sean V., additional, Young, Colin C., additional, Zec, Lauren, additional, Hiraki, Susan, additional, Anderson, Michael J., additional, Walker, Logan C, additional, McNulty Gray, Shannon, additional, Turnbull, Clare, additional, Tischkowitz, Marc, additional, Schon, Katherine, additional, Slavin, Thomas, additional, Foulkes, William D., additional, Cline, Melissa, additional, Monteiro, Alvaro N., additional, Pesaran, Tina, additional, and Couch, Fergus J., additional
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- 2024
- Full Text
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49. The Selah trial: A preference-based partially randomized waitlist control study of three stress management interventions
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Proeschold-Bell, Rae Jean, primary, Eagle, David E, additional, Tice, Logan C, additional, Platt, Alyssa, additional, Yao, Jia, additional, Larkins, Jessie S, additional, Kim, Eunsoo Timothy, additional, and Rash, Joshua A, additional
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- 2024
- Full Text
- View/download PDF
50. Low-Dose Aspirin for Optimization of Postpartum Vascular Recovery Following Severe Preeclampsia: A Pilot Study
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Barr, Logan C., primary, Blom, Jessica N., additional, Pudwell, Jessica, additional, and Smith, Graeme N., additional
- Published
- 2024
- Full Text
- View/download PDF
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