355 Works

Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence

Frederick E. Dewey, Rong Chen, Sergio P. Cordero, Kelly E. Ormond, Colleen Caleshu, Konrad J. Karczewski, Michelle Whirl-Carrillo, Matthew T. Wheeler, Joel T. Dudley, Jake T. Byrnes, Omar E. Cornejo, Joshua W. Knowles, Mark Woon, Katrin Sangkuhl, Li Gong, Caroline F. Thorn, Joan M. Hebert, Emidio Capriotti, Sean P. David, Aleksandra Pavlovic, Anne West, Joseph V. Thakuria, Madeline P. Ball, Alexander W. Zaranek, Heidi L. Rehm … & Jake K. Byrnes
Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date...

Data from: Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials

Leonard H Van Den Berg, Eric Sorenson, Gary Gronseth, Eric A. Macklin, Jinsy Andrews, Robert H. Baloh, Michael Benatar, James D. Berry, Adriano Chio, Philippe Corcia, Angela Genge, Amelie K. Gubitz, Catherine Lomen-Hoerth, Christopher J. McDermott, Erik P. Pioro, Jeffrey Rosenfeld, Vincenzo Silani, Martin R. Turner, Markus Weber, Benjamin Rix Brooks, Robert G. Miller & Hiroshi Mitsumoto
Objective: To revise the 1999 Airlie House consensus guidelines for the design and implementation of preclinical therapeutic studies and clinical trials in amyotrophic lateral sclerosis (ALS). Methods: A consensus committee comprising 140 key members of the international ALS community (ALS researchers, clinicians, patient representatives, research funding representatives, industry and regulatory agencies) addressed nine areas of need within ALS research: 1. Pre-clinical studies; 2. Biological and phenotypic heterogeneity; 3. Outcome measures; 4. Disease-modifying and symptomatic interventions;...

Data from: Vision fine-tunes preparation for landing in the cane toad, Rhinella marina

Laura J. Ekstrom, Christopher Panzini, Gary B. Gillis & Chris Panzini
In toad hopping, the hindlimbs generate the propulsive force for takeoff while the forelimbs resist the impact forces associated with landing. Preparing to perform a safe landing, in which impact forces are managed appropriately, likely involves the integration of multiple types of sensory feedback. In toads, vestibular and/or proprioceptive feedback are critical for coordinated landing, however, the role of vision remains unclear. To clarify this role, this study compares pre-landing forelimb muscle activation patterns in...

Data from: Association between aspirin dose and subarachnoid hemorrhage from saccular aneurysms: a case-control study

Anil Can, Robert F. Rudy, Victor M. Castro, Sheng Yu, Dmitriy Dligach, Sean Finan, Vivian Gainer, Nancy A. Shadick, Guergana Savova, Shawn Murphy, Tianxi Cai, Scott T. Weiss & Rose Du
Objective: We aimed to determine the association between ruptured saccular aneurysms and aspirin use/aspirin dose. Methods: 4,701 patients who were diagnosed at the Massachusetts General Hospital and Brigham and Women’s Hospital between 1990 and 2016 with 6,411 unruptured and ruptured saccular intracranial aneurysms were evaluated. Univariable and multivariable logistic regression analyses were performed to determine the association between aSAH and aspirin use, including aspirin dose. Inverse probability weighting using propensity scores was used to adjust...

Data from: Developmental loss of neurofibromin across distributed neuronal circuits drives excessive grooming in Drosophila

Seth Tomchik, Lanikea King, Tamara Boto, Valentina Botero, Ari Aviles, Breanna Jomsky, Chevara Joseph & James Walker
Neurofibromatosis type 1 is a monogenetic disorder that predisposes individuals to tumor formation and cognitive and behavioral symptoms. The neuronal circuitry and developmental events underlying these neurological symptoms are unknown. To better understand how mutations of the underlying gene (NF1) drive behavioral alterations, we have examined grooming in the Drosophila neurofibromatosis 1 model. Mutations of the fly NF1 ortholog drive excessive grooming, and increased grooming was observed in adults when Nf1 was knocked down during...

Association of caffeine and related analytes with resistance to Parkinson’s disease among LRRK2 mutation carriers: a metabolomic study

Grace F Crotty, Romeo Maciuca, Eric A Macklin, Junhua Wang, Manuel Montalban, Sonnet S. Davis, Jamal I Alkabsh, Rachit Bakshi, Xiqun Chen, Alberto Ascherio, Giuseppe Astarita, Sarah Huntwork-Rodriguez & Michael A Schwarzschild
Objective: To identify markers of resistance to developing Parkinson’s disease (PD) among LRRK2 mutation (LRRK2+) carriers, we carried out metabolomic profiling in individuals with PD and unaffected controls (UC), with and without the LRRK2 mutation. Methods: Plasma from 368 PD and UC subjects in the LRRK2 Cohort Consortium (LCC), comprising 118 LRRK2+/PD+, 115 LRRK2+/UC, 70 LRRK2-/PD+ and 65 LRRK2-/UC, and CSF available from 68 of them were analyzed by liquid chromatography with mass spectrometry. For...

Fine particulate matter and neuroanatomic risk for Alzheimer’s disease in older women

Diana Younan, Xinhui Wang, Ramon Casanova, Ryan Barnard, Sarah Gaussoin, Santiago Saldana, Andrew Petkus, Daniel Beavers, Susan Resnick, JoAnn Manson, Marc Serre, William Vizuete, Victor Henderson, Bonnie Sachs, Joel Salinas, Margaret Gatz, Mark Espeland, Helena Chui, Sally Shumaker, Stephen Rapp & Jiu-Chiuan Chen
Objective: To examine whether late-life exposure to PM2.5 (particulate matter with aerodynamic diameters <2.5-µm) contributes to progressive brain atrophy predictive of Alzheimer’s disease (AD) using a community-dwelling cohort of women (aged 71-89) with up to two brain MRI scans (MRI-1: 2005-6; MRI-2: 2010-11). Methods: AD pattern similarity (AD-PS) scores, developed by supervised machine learning and validated with MRI data from the AD Neuroimaging Initiative, was used to capture high-dimensional gray matter atrophy in brain areas...

Data from: 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

Brian L. Edlow, Azma Mareyam, Andreas Horn, Jonathan R. Polimeni, Thomas Witzel, M. Dylan Tisdall, Jean Augustinack, Jason P. Stockmann, Bram R. Diamond, Allison Stevens, Lee S. Tirrell, Rebecca D. Folkerth, Lawrence L. Wald, Bruce Fischl & Andre Van Der Kouwe
We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of...

Data from: Telemedicine in neurology: telemedicine work group of the American Academy of Neurology update

Jaime M. Hatcher-Martin, Jamie Lynn Adams, Eric R Anderson, Riley Bove, Tamika M. Burrus, Mahan Chehrenama, Mary Dolan O'Brien, Dawn S. Eliashiv, Deniz Erten-Lyons, Barbara S. Giesser, Lauren Moo, Pushpa Narayanaswami, Marvin A. Rossi, Madhu Soni, Nauman Tariq, Jack W. Tsao, Bert Vargas, Scott Vota, Scott Wessels, Hannah Planalp & Raghav Govindarajan
ABSTRACT Purpose: While there is strong evidence supporting the importance of telemedicine in stroke, its role in other areas of neurology is not as clear. The goal of this review is to provide an overview of evidence-based data regarding the role of teleneurology in the care of patients with neurologic disorders other than stroke. Recent findings: Studies across multiple specialties report noninferiority of evaluations by telemedicine compared with traditional, in-person evaluations in terms of patient...

Ligand-dependent effects of methionine-8 oxidation in parathyroid hormone peptide analogs

Thomas Gardella, Vsevolod Katritch, Saheem Zaidi, Eileen Daley, Ashok Khatri & Jean-Pierre Vilardaga
LA-PTH is a long-acting parathyroid hormone (PTH) peptide analog in pre-clinical development for hypoparathyroidism (HP). Like native PTH, LA-PTH contains a methionine at position 8 that is predicted to be critical for function. We assessed the impact of methionine oxidation on the functional properties of LA-PTH and control PTH ligands. Oxidation of PTH(1-34) resulted in marked (~20-fold) reductions in binding affinity on the PTH receptor-1 (PTHR1) in cell membranes, similarly diminished potency for cAMP signaling...

Thalamic encoding of lexical status is lateralized during reading aloud

Dengyu Wang, Witold J. Lipski, Alan Bush, Anna Chrabaszcz, Christina Dastolfo-Hromack, Michael W. Dickey, Julie A. Fiez & R. Mark Richardson
To explore whether the thalamus participates in lexical status encoding, local field potentials were recorded in patients undergoing deep brain stimulation lead implantation while they read aloud single-syllable words and nonwords. Bilateral decreases in thalamic beta (12-30Hz) activity were preferentially locked to stimulus presentation, and these decreases were greater when nonwords were read. Increased broadband gamma (70-150Hz) activity also was locked preferentially to speech onset bilaterally, but greater nonword-related increases in this activity were observed...

Continuous glucose monitoring in cystic fibrosis: glycemic relationships, clinical correlations, and implications for CFRD diagnosis

Melissa Putman & Scully Kevin
Context: The clinical utility and implications of continuous glucose monitoring (CGM) in cystic fibrosis (CF) are unclear. Objective: We examined the correlation between CGM measures and clinical outcomes in adults with CF, investigated the relationship between hemoglobin A1c (HbA1c) and CGM-derived average glucose (AG), and explored CGM measures that distinguish cystic fibrosis–related diabetes (CFRD) from normal and abnormal glucose tolerance. Methods: This prospective observational study included 77 adults with CF who had CGM and HbA1c...

Telerobotic neurovascular interventions with magnetic manipulation

Yoonho Kim, Emily Genevriere, Pablo Harker, Jaehun Choe, Marcin Balicki, Robert W. Regenhardt, Justin E. Vranic, Adam A. Dmytriw, Aman B. Patel & Xuanhe Zhao
Advances in robotic technology have been adopted in various subspecialties of both open and minimally invasive surgery, offering benefits such as enhanced surgical precision and accuracy with reduced fatigue of the surgeon. Despite the advantages, robotic applications to endovascular neurosurgery have remained largely unexplored because of technical challenges such as the miniaturization of robotic devices that can reach the complex and tortuous vasculature of the brain. Although some commercial systems enable robotic manipulation of conventional...

Onset of depression and anxiety among patients with gout after diagnosis: a population-based incident cohort study

Alyssa Howren, Eric C. Sayre, Hyon K. Choi, J. Antonio Avina-Zubieta, Kam Shojania, Jamie Y. Park & Mary A. De Vera
Abstract Background Gout may be associated with an increased incidence of mental health disorders, however, published findings have been limited and inconsistent. Therefore, our objective was to conduct a population-based cohort study to evaluate the incidence of depression and anxiety after gout diagnosis. Methods We used linked population-based administrative health data in British Columbia, Canada that includes information on demographics, outpatient visits, and inpatient visits from the period of January 1, 1990 to March 31,...

Additional file 1 of The impact of medically tailored meals and nutrition therapy on biometric and dietary outcomes among food-insecure patients with congestive heart failure: a matched cohort study

Lauren Belak, Caroline Owens, Margaret Smith, Eric Calloway, Laura Samnadda, Heartley Egwuogu & Stacie Schmidt
Additional file 1: SupplementalTable 1. Demographics for individuals with pre- and post- weight and BMI data.

Additional file 2 of The impact of medically tailored meals and nutrition therapy on biometric and dietary outcomes among food-insecure patients with congestive heart failure: a matched cohort study

Lauren Belak, Caroline Owens, Margaret Smith, Eric Calloway, Laura Samnadda, Heartley Egwuogu & Stacie Schmidt
Additional file 2: SupplementalTable 2. Demographics for individuals with pre- and post- blood pressure data.

Additional file 5 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 5: Supplemental Table 3. Detailed specification for omnibus and per-feature differential abundance testing models.

Additional file 8 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 8: Supplemental Table 6. Per-study and meta-analytically aggregated effect sizes of tests on the interaction between disease/treatment and sample type/disease on per-feature abundances.

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Abstract Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete...

Analysis of shared cognitive tasks in the application of non-invasive ventilation to patients with COPD exacerbation

Ashley M. Hughes, Karen Riska, Mary Jo S. Farmer, Divya Krishnakumar, Christopher M. Shea, Dean R. Hess, Peter K. Lindenauer & Mihaela S. Stefan
Interprofessional teamwork plays a key role in the uptake of evidence-based interventions, such as noninvasive ventilation (NIV) for patients with exacerbated Chronic Obstructive Pulmonary Disease (COPD). We aimed to identify the shared cognitive tasks in interprofessional teams using NIV for patients with COPD exacerbation. We used a cognitive task analysis approach (CTA) to engage nurses, rapid response team members, respiratory therapists, and physicians involved in the use of NIV to treat patients with COPD exacerbation....

Additional file 2 of Association of co-occurring mental health problems with hepatitis C status among young people who inject drugs in rural New Mexico, 2016–2018

Akash Gupta, Fatma M. Shebl, Yao Tong, Katherine Wagner, Ingrid V. Bassett, Kimberly Page & Erin L. Winstanley
Additional file 2: Table S3. Adjusted modified (robust) Poisson regression models for history of HCV infection, PTSD, and any mental health problems

Additional file 1 of Association of co-occurring mental health problems with hepatitis C status among young people who inject drugs in rural New Mexico, 2016–2018

Akash Gupta, Fatma M. Shebl, Yao Tong, Katherine Wagner, Ingrid V. Bassett, Kimberly Page & Erin L. Winstanley
Additional file 1: Table S1. Baseline population characteristics. Table S2. Mental health problems and engagement in care.

Additional file 4 of Association of co-occurring mental health problems with hepatitis C status among young people who inject drugs in rural New Mexico, 2016–2018

Akash Gupta, Fatma M. Shebl, Yao Tong, Katherine Wagner, Ingrid V. Bassett, Kimberly Page & Erin L. Winstanley
Additional file 4: Table S5. Adjusted modified (robust) Poisson regression models for history of HCV infection, PTSD, and any mental health problems.

Additional file 1 of Gender differences in health protective behaviours and its implications for COVID-19 pandemic in Taiwan: a population-based study

Jasmine Tan, Yilin Yoshida, Kevin Sheng-Kai Ma, Franck Mauvais-Jarvis & Chien-Chang Lee
Supplementary Material 1

Efficient Learning of Quadratic Variance Function Directed Acyclic Graphs via Topological Layers

Wei Zhou, Xin He, Wei Zhong & Junhui Wang
Directed acyclic graph (DAG) models are widely used to represent casual relationships among random variables in many application domains. This article studies a special class of non-Gaussian DAG models, where the conditional variance of each node given its parents is a quadratic function of its conditional mean. Such a class of non-Gaussian DAG models are fairly flexible and admit many popular distributions as special cases, including Poisson, Binomial, Geometric, Exponential, and Gamma. To facilitate learning,...

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