60 Works

Data from: Distributed acoustic cues for caller identity in macaque vocalization

Makoto Fukushima, Alexandra M. Doyle, Matthew P. Mullarkey, Mortimer Mishkin, Bruno B. Averbeck & Alex M. Doyle
Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured ‘coo’ call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a...

Data from: Genome sequencing highlights the dynamic early history of dogs

Adam H. Freedman, Ilan Gronau, Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Holly Beale, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins … & John Novembre
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow....

Data from: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner

Candida Bhagwandin, Erin L. Ashbeck, Michael Whalen, Joanna Bandola-Simon, Paul A. Roche, Adam Szajman, Sarah Mai Truong, Betsy C. Wertheim, Yann C. Klimentidis, Satoshi Ishido, Benjamin J. Renquist & Lonnie Lybarger
Type 2 diabetes is typified by insulin-resistance in adipose tissue, skeletal muscle, and liver, leading to chronic hyperglycemia. Additionally, obesity and type 2 diabetes are characterized by chronic low-grade inflammation. Membrane-associated RING-CH-1 (MARCH1) is an E3 ubiquitin ligase best known for suppression of antigen presentation by dendritic and B cells. MARCH1 was recently found to negatively regulate the cell surface levels of the insulin receptor via ubiquitination. This, in turn, impaired insulin sensitivity in mouse...

Data from: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith & Andrew Rambaut
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata,...

Data from: Imperfect vaccination can enhance the transmission of highly virulent pathogens

Andrew F. Read, Susan J. Baigent, Claire Powers, Lydia B. Kgosana, Luke Blackwell, Lorraine P. Smith, David A. Kennedy, Stephen W. Walkden-Brown & Venugopal K. Nair
Could some vaccines drive the evolution of more virulent pathogens? Conventional wisdom is that natural selection will remove highly lethal pathogens if host death greatly reduces transmission. Vaccines that keep hosts alive but still allow transmission could thus allow very virulent strains to circulate in a population. Here we show experimentally that immunization of chickens against Marek's disease virus enhances the fitness of more virulent strains, making it possible for hyperpathogenic strains to transmit. Immunity...

Neurofilament light as a biomarker in traumatic brain injury

Pashtun Shahim, Adam Politis, Andre Van Der Merwe, Brian Moore, Yi-Yu Chou, Dzung Pham, John Butman, Ramon Diaz-Arrastia, Jessica Gill, David Brody, Henrik Zetterberg, Kaj Blennow & Leighton Chan
Objective: To determine whether serum neurofilament light (NfL) correlates with CSF NfL, traumatic brain injury (TBI) diagnosis, injury severity, brain volume, and diffusion tensor imaging (DTI) estimates of traumatic axonal injury (TAI). Methods: Participants were prospectively enrolled in Sweden and the United States between 2011 and 2019. The Swedish cohort included 45 hockey players with acute concussion sampled at 6 days, 31 with repetitive concussion with persistent postconcussive symptoms (PCS) assessed with paired CSF and...

Harnessing clinical annotations to improve deep learning performance in prostate segmentation

Karthik V. Sarma, Alex G. Raman, Nikhil J. Dhinagar, Alan M. Priester, Stephanie Harmon, Thomas Sanford, Sherif Mehralivand, Baris Turkbey, Leonard S. Marks, Steven S. Raman, William Speier & Corey W. Arnold
Purpose Developing large-scale datasets with research-quality annotations is challenging due to the high cost of refining clinically generated markup into high precision annotations. We evaluated the direct use of a large dataset with only clinically generated annotations in development of high-performance segmentation models for small research-quality challenge datasets. Materials and methods We used a large retrospective dataset from our institution comprised of 1,620 clinically generated segmentations, and two challenge datasets (PROMISE12: 50 patients, ProstateX-2: 99...

Data from: The evolutionary consequences of blood-stage vaccination on the rodent malaria Plasmodium chabaudi

Victoria C. Barclay, Derek Sim, Brian H. K. Chan, Lucas A. Nell, Maia A. Rabaa, Andrew S. Bell, Robin F. Anders & Andrew F. Read
Malaria vaccine developers are concerned that antigenic escape will erode vaccine efficacy. Evolutionary theorists have raised the possibility that some types of vaccine could also create conditions favoring the evolution of more virulent pathogens. Such evolution would put unvaccinated people at greater risk of severe disease. Here we test the impact of vaccination with a single highly purified antigen on the malaria parasite Plasmodium chabaudi evolving in laboratory mice. The antigen we used, AMA-1, is...

Data from: Aggressive chemotherapy and the selection of drug resistant pathogens

Silvie Huijben, Andrew S. Bell, Derek G. Sim, Danielle Tomasello, Nicole Mideo, Troy Day & Andrew F. Read
Drug resistant pathogens are one of the key public health challenges of the 21st century. There is a widespread belief that resistance is best managed by using drugs to rapidly eliminate target pathogens from patients so as to minimize the probability that pathogens acquire resistance de novo. Yet strong drug pressure imposes intense selection in favor of resistance through alleviation of competition with wild-type populations. Aggressive chemotherapy thus generates opposing evolutionary forces which together determine...

Data from: Sexually coercive male chimpanzees sire more offspring

Joseph T. Feldblum, Emily E. Wroblewski, Rebecca S. Rudicell, Beatrice H. Hahn, Thais Paiva, Mine Cetinkaya-Rundel, Anne E. Pusey & Ian C. Gilby
In sexually reproducing animals, male and female reproductive strategies often conflict. In some species, males use aggression to overcome female choice, but debate persists over the extent to which this strategy is successful. Previous studies of male aggression toward females among wild chimpanzees have yielded contradictory results about the relationship between aggression and mating behavior. Critically, however, copulation frequency in primates is not always predictive of reproductive success. We analyzed a 17-year sample of behavioral...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: isolating independent associations with diet/energy balance and body weight

Isaac J. Perron, Brendan T. Keenan, Karthikeyani Chellappa, Nicholas F. Lahens, Nicole Y. Yohn, Keith R. Shockley, Allan I. Pack & Sigrid C. Veasey
Background and Aims: Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities. Here, we use dietary challenges to parse apart the relative influence of diet and/or energy balance from body weight on various metabolic and behavioral outcomes. Materials and Methods: Seventy male mice (mus musculus) were subjected...

Data from: Emergence and evolution of novel reassortant influenza A viruses in canines in southern China

Ying Chen, Nídia S. Trovão, Guojun Wang, Weifeng Zhao, Ping He, Huabo Zhou, Yanning Mo, Zuzhang Wei, Kang Ouyang, Weijiang Huang, Adolfo García-Sastre, Martha I. Nelson & Weijian Huang
The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to...

Data from: Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring

Laura C. Pollitt, Derek Sim, Rahel Salathé & Andrew F. Read
Artemisinin-based drugs are the front-line weapon in the treatment of human malaria cases, but there is concern that recent reports of slow clearing infections may signal developing resistance to treatment. In the absence of molecular markers for resistance, current efforts to monitor drug efficacy are based on the rate at which parasites are cleared from infections. However, some knowledge of the standing variation in parasite susceptibility is needed to identify a meaningful increase in infection...

Data from: From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells

Julián Candia, Ryan Maunu, Meghan Driscoll, Angélique Biancotto, Pradeep Dagur, , H. Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B. Nussenblatt, Jayanth R. Banavar, Wolfgang Losert & J. Philip McCoy
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of “supercell statistics”, a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number...

Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Benjamin Roche, John M. Drake, Justin Brown, David E. Stallknecht, Trevor Bedford & Pejman Rohani
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker...

Data from: Global distribution maps of the Leishmaniases

David M. Pigott, Samir Bhatt, Nick Golding, Kirsten A. Duda, Katherine E. Battle, Oliver J. Brady, Jane P. Messina, Yves Balard, Patrick Bastien, Francine Pratlong, John S. Brownstein, Clark C Freifeld, Sumiko R. Mekaru, Peter W. Gething, Dylan B. George, Monica F. Myers, Richard Reithinger & Simon I. Hay
The leishmaniases are vector-borne diseases that have a broad global distribution throughout much of the Americas, Africa and Asia. Despite representing a significant public health burden, our understanding of the global distribution of the leishmaniases remains vague, reliant upon expert opinion and limited to poor spatial resolution. A global assessment of the consensus of evidence for leishmaniasis was performed at a sub-national level by aggregating information from a variety of sources. A database of records...

Data from: Predictive Bayesian selection of multistep Markov chains, applied to the detection of the hot hand and other statistical dependencies in free throws

Joshua C. Chang
When extended to data from the 2016--2017 NBA season specifically for LeBron James, a model depending on the previous shot (single-step Markovian) does not clearly beat a model with independent outcomes. An error-correcting variable length model of two parameters, where James shoots a higher percentage after a missed free throw than otherwise, is more predictive than either model.

Data from: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Ignacio Mena, Martha I. Nelson, Francisco Quezada-Monroy, Jayeeta Dutta, Refugio Cortes-Fernández, J. Horacio Lara-Puente, Felipa Castro-Peralta, Luis F. Cunha, Nídia Sequeira-Trovão, Bernardo Lozano-Dubernard, Andrew Rambaut, Harm Van Bakel & Adolfo García-Sastre
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of...

Data from: Extracellular space preservation aids the connectomic analysis of neural circuits

Marta Pallotto, Paul V. Watkins, Boma Fubara, Joshua H. Singer & Kevin L. Briggman
Dense connectomic mapping of neuronal circuits is limited by the time and effort required to analyze 3D electron microscopy (EM) datasets. Algorithms designed to automate image segmentation suffer from substantial error rates and require significant manual error correction. Any improvement in segmentation error rates would therefore directly reduce the time required to analyze 3D EM data. We explored preserving extracellular space (ECS) during chemical tissue fixation to improve the ability to segment neurites and to...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

Computerized analysis of brain MRI parameters dynamics in young patients with Cushing Syndrome – a case-control study

Amit Tirosh, Harish RaviPrakash, Georgios Z Papadakis, Christina Tatsi, Elena Belyavskaya, Lyssikatos Charalampos, Maya B. Lodish, Ulas Bagci & Constantine A Stratakis
Background – Young patients with Cushing Syndrome (CS) may develop cognitive and behavioral alterations during disease course. Methods - To define the implications of CS on the brain, we analyzed consecutive MRI scans of patients with (n=29) vs. without CS (n=8). Multiple brain compartments were processed for total and gray/white matter (GM/WM) volumes and intensities; and cortical volume, thickness and surface-area. Dynamics (last/baseline scans ratio per parameter) were analyzed vs. cortisol levels and CS status...

Atlas of impact-induced, in vivo human brain kinematics

Arnold Gomez, Philip Bayly, John Butman, Dzung Pham, Jerry Prince & Andrew Knutsen
Accelerations cause brain tissue to move, and this data summarizes MRI-based observations of 3D brain movement during an in vivo impact (brain-skull displacement and brain tissue deformation). The data is a group average, or atlas, of indivudial data from two groups of study participants: neck extension (n=10) and neck rotation (n=9).

Data from: Hot spring frogs (Buergeria japonica) prefer cooler water to hot water

Shohei Komaki, Yoichi Sutoh, Kensuke Kobayashi, Shigeru Saito, Claire Saito, Takeshi Igawa & Quintin Lau
“Hot spring frog” is an informal name used for the Japanese stream tree frog (Buergeria japonica), which is widely distributed in Taiwan and the Ryukyu Archipelago in Japan. Some populations of the species are known to inhabit hot springs. However, water temperature can be extremely high around the sources of hot springs. Thus, it is questionable whether B. japonica selectively inhabits such dangerous environments. To address this question, we conducted a series of observations of...

Ripples reflect a spectrum of synchronous spiking activity in human anterior temporal lobe

Ai Phuong Tong, Alex Vaz, John Wittig, Sara Inati & Kareem Zaghloul
Direct brain recordings have provided important insights into how high-frequency activity captured through intracranial EEG (iEEG) supports human memory retrieval. The extent to which such activity is comprised of transient fluctuations that reflect the dynamic coordination of underlying neurons, however, remains unclear. Here, we simultaneously record iEEG, local field potential (LFP), and single unit activity in the human temporal cortex. We demonstrate that fast oscillations within the previously identified 80–120 Hz ripple band contribute to...

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