50 Works

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Data from: Neural correlates of domain-specific cognitive decline: the ARIC-NCS study

Andrea Lauren Christman Schneider, Matthew L Senjem, Aozhou Wu, Alden Gross, David S. Knopman, Jeffrey L Gunter, Christopher G Schwarz, Tom H. Mosley, Rebecca F. Gottesman, A. Richey Sharrett & Clifford R. Jack
Objective: To evaluate the association of cognitive declines in the domains of memory, language, and executive function with brain gray matter (GM) volume in old age. Methods: Prospective study of 1,846 participants in the Atherosclerosis Risk in Communities (ARIC) study who underwent 3T brain MRI scans in 2011-2013. Participants were categorized by cognitive domain performance trajectory over the prior 20 years (cut-point to define decline: 20th percentile). Associations between GM volume and cognitive declines were...

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

Neural network learning of the Russian genitive of negation: optionality and structure sensitivity

Natalia Talmina & Tal Linzen

Data from: Competition and constraint drove Cope's rule in the evolution of giant flying reptiles

Roger B. J. Benson, Rachel A. Frigot, Anjali Goswami, Brian Andres & Richard J. Butler
The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope’s rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope’s rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain....

Extending adaptor grammars to learn phonological alternations

Canaan Breiss & Colin Wilson

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Michael Benatar, Lanyu Zhang, Lily Wang, Volkan Granit, Jeffrey Statland, Richard Barohn, Andrea Swenson, John Ravitz, Carlayne Jackson, Ted Burns, Jaya Trivedi, Erik Pioro, James Caress, Jonathan Katz, Jacob McCauley, Rosa Rademakers, Andrea Malaspina, Lyle Ostrow & Joanne Wuu
Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results....

Data from: A prospective study of serum metabolites and risk of ischemic stroke

Daokun Sun, Steffen Tiedt, Bing Yu, Xueqiu Jian, Rebecca F. Gottesman, Tom H. Mosley, Eric Boerwinkle, Martin Dichgans & Myriam Fornage
Objective: To identify promising blood-based biomarkers and novel etiological pathways of disease risk, we applied an untargeted serum metabolomics profiling in a community-based prospective study of ischemic stroke (IS). Methods: In 3,904 men and women from the Atherosclerosis Risk In Communities (ARIC) study, Cox proportional hazard models were used to estimate the association of incident IS with the standardized level of 245 fasting serum metabolites individually, adjusting for age, sex, race, field center, batch, diabetes,...

Data from: Lower carotid revascularization rates after stroke in ethnic minority-serving US hospitals

Roland Faigle, Lisa A. Cooper & Rebecca F. Gottesman
Objective: We sought to determine whether the use of carotid revascularization procedures after stroke due to carotid stenosis differs between minority-serving hospitals and hospitals serving predominantly white patients. Methods: We identified ischemic stroke cases due to carotid disease, identified by ICD9-CM codes, from 2007-2011 in the Nationwide Inpatient Sample. The use of carotid endarterectomy (CEA) and carotid artery stenting (CAS) was recorded. Hospitals with ≥40% ethnic minority patients (minority-serving hospitals) were compared to hospitals with...

Data from: Ethanol abolishes vigilance-dependent astroglia network activation in mice by inhibiting norepinephrine release

Martin Paukert, Liang Ye, Murat Orynbayev, Xiangyu Zhu, Eunice Lim, Ram Dereddi, Amit Agarwal, Dwight Bergles & Manzoor Bhat
This collection of data sets was obtained during a study of the effect of acute ethanol intoxication on vigilance-dependent astroglia network activation in mice. The main findings have been that ethanol inhibits astroglia activation by inhibiting vigilance-dependent norepinephrine release. This leads to a failure of activation of alpha1A-adrenergic receptors on astroglia. Further, this study has revealed that ethanol inhibition of cerebellar Bergmann glia Ca2+ activation does not account for ataxic motor behavior, but may rather...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Substance P signalling in primary motor cortex facilitates motor learning in rats

Benjamin Hertler, Jonas Aurel Hosp, Manuel Buitrago Blanco & Andreas Rüdiger Luft
Among the genes that are up-regulated in response to a reaching training in rats, Tachykinin 1 (Tac1) - a gene that encodes the neuropeptide Substance P (Sub P) - shows an especially strong expression. Using Real-Time RT-PCR, a detailed time-course of Tac1 expression could be defined: a significant peak occurs 7 hours after training ended at the first and second training session, whereas no up-regulation could be detected at a later time-point (sixth training session)....

Structure Here, Bias There: Hierarchical Generalization by Jointly Learning Syntactic Transformations

Karl Mulligan, Robert Frank & Tal Linzen

Data from: Cholera outbreaks (2012) in three districts of Nepal reveal clonal transmission of multi-drug resistant Vibrio cholerae O1

Sameer M. Dixit, Fatema-Tuz Johura, Sulochana Manandhar, Abdus Sadique, Rajesh M. Rajbhandari, Shahnewaj B. Mannan, Mahamud-Ur Rashid, Saiful Islam, Dibesh Karmacharya, Haruo Watanabe, R. Bradley Sack, Alejandro Cravioto & Munirul Alam
Background: Although endemic cholera causes significant morbidity and mortality each year in Nepal, lack of information about the causal bacterium often hinders cholera intervention and prevention. In 2012, diarrheal outbreaks affected three districts of Nepal with confirmed cases of mortality. This study was designed to understand the drug response patterns, source, and transmission of Vibrio cholerae associated with 2012 cholera outbreaks in Nepal. Methods: V. cholerae (n = 28) isolated from 2012 diarrhea outbreaks {n...

Tensor Product Decomposition Networks: Uncovering Representations of Structure Learned by Neural Networks

Richard T. McCoy, Tal Linzen, Ewan Dunbar & Paul Smolensky

Data from: Methods to identify and prioritize patient-centered outcomes for use in comparative effectiveness research

Evan Mayo-Wilson, Asieh Golozar, Terrie Cowley, Nicole Fusco, Gillian Gresham, Jennifer Haythornthwaite, Elizabeth Tolbert, Jennifer L. Payne, Lori Rosman, Susan Hutfless, Joseph K. Canner & Kay Dickersin
Background: We used various methods for identifying and prioritizing patient-centered outcomes (PCOs) for comparative effectiveness research (CER). Methods: We considered potential PCOs (“benefits” and “harms”) related to (1) gabapentin for neuropathic pain and (2) quetiapine for bipolar depression. Part 1 (April 2014 to March 2015): we searched for PCO research and core outcome sets (COSs). We conducted electronic searches of bibliographic databases and key websites and examined FDA prescribing information and reports of clinical trials...

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

James Hall, Emmy Smith, Nobumichi Tamura, Sirine Fakra & Tanja Bosak
Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. One taphomorph exhibits mm-scale ridges and a distinct lower boundary, the other is devoid of these diagnostic features but is similar in size and shape. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe,...

Data from: Suppression and facilitation of human neural responses

Michael-Paul Schallmo, Alexander M. Kale, Rachel Millin, Anastasia V. Flevaris, Zoran Brkanac, Richard A.E. Edden, Raphael A. Bernier, Scott Murray, Scott O Murray & Richard AE Edden
Efficient neural processing depends on regulating responses through suppression and facilitation of neural activity. Utilizing a well-known visual motion paradigm that evokes behavioral suppression and facilitation, and combining 5 different methodologies (behavioral psychophysics, computational modeling, functional MRI, pharmacology, and magnetic resonance spectroscopy), we provide evidence that challenges commonly held assumptions about the neural processes underlying suppression and facilitation. We show that: 1) both suppression and facilitation can emerge from a single, computational principle - divisive...

Data from: Measuring couple relationship quality in a rural African population: validation of a couple functionality assessment tool in Malawi

Allison Ruark, Rachel Chase, John Hembling, Valerie Rhoe Davis, Paul Clayton Perrin & Dorothy Brewster-Lee
Available data suggest that individual and family well-being are linked to the quality of women’s and men’s couple relationships, but few tools exist to assess couple relationship functioning in low and middle-income countries. In response to this gap, Catholic Relief Services has developed a Couple Functionality Assessment Tool (CFAT) to capture valid and reliable data on various domains of relationship quality. This tool is designed to be used by interventions which aim to improve couple...

Data from: Collagen network strengthening following cyclic tensile loading

Monica E. Susilo, Jeffrey A. Paten, Edward A. Sander, Thao D. Nguyen & Jeffrey W. Ruberti
The bulk mechanical properties of tissues are highly tuned to the physiological loads they experience and reflect the hierarchical structure and mechanical properties of their constituent parts. A thorough understanding of the processes involved in tissue adaptation is required to develop multi-scale computational models of tissue remodelling. While extracellular matrix (ECM) remodelling is partly due to the changing cellular metabolic activity, there may also be mechanically directed changes in ECM nano/microscale organization which lead to...

Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A. Eller, Merlin L. Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A. Lythgoe, Gertrude Nakigozi, Thomas C. Quinn, Steven J. Reynolds, Maria J. Wawer & Christophe Fraser
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of...

Data from: Testing conceptual models of early plant succession across a disturbance gradient

Cynthia C. Chang, Charles B. Halpern, Joseph A. Antos, Meghan L. Avolio, Abir Biswas, James E. Cook, Roger Del Moral, Dylan G. Fischer, Andrés Holz, Robert J. Pabst, Mark E. Swanson & Donald B. Zobel
1.Studies of succession have a long history in ecology, but rigorous tests of general, unifying principles are rare. One barrier to these tests of theory is the paucity of longitudinal studies that span the broad gradients of disturbance severity that characterize large, infrequent disturbances. The cataclysmic eruption of Mount St. Helens (Washington, USA) in 1980 produced a heterogeneous landscape of disturbance conditions, including primary to secondary successional habitats, affording a unique opportunity to explore how...

Data from: Red and orange flags for secondary headaches in clinical practice: SNNOOP10 list

Thien Phu Do, Angelique Remmers, Henrik Winther Schytz, Christoph Schankin, Sarah E. Nelson, Mark Obermann, Jakob Møller Hansen, Alexandra J. Sinclair, Andreas R. Ganteinbein & Guus G. Schoonman
A minority of headache patients have a secondary headache disorder. The medical literature presents and promotes red flags to increase the likelihood of identifying a secondary etiology. In this review, we aim to discuss the incidence and prevalence of secondary headaches as well as the data on sensitivity, specificity, and predictive value of red flags for secondary headaches. We review the following red flags: (1) systemic symptoms including fever; (2) neoplasm history; (3) neurologic deficit...

Data from: INTREPAD: a randomized trial of naproxen to slow progress of presymptomatic Alzheimer disease

Pierre-Francois Meyer, Jennifer Tremblay-Mercier, Jeannie Leoutsakos, Cecile Madjar, Marie-Elyse Lafaille-Magnan, Melissa Savard, Pedro Rosa-Neto, Judes Poirier, Pierre Etienne & John Breitner
Objective: Evaluate the safety and efficacy of low-dose naproxen for prevention of progression in pre-symptomatic AD among cognitively intact persons at-risk. Methods: INTREPAD, a two-year double-masked pharmaco-prevention trial, enrolled 195 AD family history-positive elderly (mean age 63 years) screened carefully to exclude cognitive disorder. These were randomized 1:1 to naproxen sodium 220mg twice-daily or placebo. Multimodal imaging, neurosensory, cognitive and (in ~50%) CSF biomarker evaluations were performed at Baseline, 3, 12, and 24 months. A...

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