28 Works

Data from: Adaptive dynamics of cuticular hydrocarbons in Drosophila

Subhash Rajpurohit, Robert Hanus, Vladimir Vrkoslav, Emily L. Behrman, Alan O. Bergland, Dmitri Petrov, Josef Cvacka & Paul S. Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore,...

Data from: A curated and standardized adverse drug event resource to accelerate drug safety research

Juan M. Banda, Lee Evans, Rami S. Vanguri, Nicholas P. Tatonetti, Patrick B. Ryan & Nigam H. Shah
Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for...

Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Chris E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Christopher E. Ellison
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and...

Data from: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

Clarissa C. Parker, Shyam Gopalakrishnan, Peter Carbonetto, Natalia M. Gonzales, Emily Leung, Yeonhee J. Park, Emmanuel Aryee, Joe Davis, David A. Blizard, Cheryl L. Ackert-Bicknell, Arimantas Lionikas, Jonathan K. Pritchard & Abraham A. Palmer
Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice....

Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task

Krista K. Ingram, Deborah M. Gordon, Daniel A. Friedman, Michael Greene, John Kahler & Swetha Peteru
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure...

Data from: Competition between engrams influences fear memory formation and recall

Asim J. Rashid, Chen Yan, Valentina Mercaldo, Hwa-Lin Hsiang, Sungmo Park, Christina J. Cole, Antoinetta De Cristofaro, Julia Yu, Charu Ramakrishnan, Soo Yeun Lee, Karl Deisseroth, Paul W. Frankland & Sheena A. Josselyn
Collections of cells called engrams are thought to represent memories. Although there has been progress in identifying and manipulating single engrams, little is known about how multiple engrams interact to influence memory. In lateral amygdala (LA), neurons with increased excitability during training outcompete their neighbors for allocation to an engram. We examined whether competition based on neuronal excitability also governs the interaction between engrams. Mice received two distinct fear conditioning events separated by different intervals....

Data from: Characteristics and outcomes of women utilizing emergency medical services for third-trimester pregnancy-related complaints in India: a prospective observational study

Matthew C. Strehlow, Jennifer A. Newberry, Corey B. Bills, Hyeyoun Min, Ann E. Evensen, Lawrence Leeman, Elizabeth A. Pirrotta, G. V. Ramana Rao & S. V. Mahadevan
Objectives: Characterize the demographics, management, and outcomes of obstetric patients transported by emergency medical services (EMS). Design: Prospective observational study. Setting: Five Indian states utilizing a centralized EMS agency that transported 3.1 million pregnant women in 2014. Participants: This study enrolled a convenience sample of 1684 women in third trimester of pregnancy calling with a “pregnancy-related” complaint for free-of-charge ambulance transport. Calls were deemed “pregnancy-related” if categorized by EMS dispatchers as “pregnancy”, “childbirth”, “miscarriage”, or...

Data from: Discrimination of fast click series produced by tagged Risso’s dolphins (Grampus griseus) for echolocation or communication

Patricia Arranz, Stacy L. DeRuiter, Alison K. Stimpert, Silvana Neves, Ari S. Friedlaender, Jeremy A. Goldbogen, Fleur Visser, John Calambokidis, Brandon L. Southall & Peter L. Tyack
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two...

Data from: Coralline algae in a naturally acidified ecosystem persist by maintaining control of skeletal mineralogy and size

Nicholas A. Kamenos, Gabriela Perna, Maria Cristina Gambi, Fiorenza Micheli & Kristy J. Kroeker
To understand the effects of ocean acidification (OA) on marine calcifiers, the trade-offs among different sublethal responses within individual species and the emergent effects of these trade-offs must be determined in an ecosystem setting. Crustose coralline algae (CCA) provide a model to test the ecological consequences of such sublethal effects as they are important in ecosystem functioning, service provision, carbon cycling and use dissolved inorganic carbon to calcify and photosynthesize. Settlement tiles were placed in...

Data from: Genetic basis of priority effects: insights from nectar yeast

Manpreet K. Dhami, Thomas Hartwig & Tadashi Fukami
Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we de novo assembled the genome of the nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds and complete mitochondrion, with gap-free coverage...

Data from: Continuum of vasodilator stress from rest to contrast medium to adenosine hyperemia for fractional flow reserve assessment

Nils P. Johnson, Allen Jeremias, Frederik M. Zimmermann, Julien Adjedj, Nils Witt, Barry Hennigan, Bon-Kwon Koo, Akiko Maehara, Mitsuaki Matsumura, Emanuele Barbato, Giovanni Esposito, Bruno Trimarco, Gilles Rioufol, Seung-Jung Park, Hyoung-Mo Yang, Sérgio B. Baptista, George S. Chrysant, Antonio M. Leone, Colin Berry, Bernard De Bruyne, K. Lance Gould, Richard L. Kirkeeide, Keith G. Oldroyd, Nico H. J. Pijls, William F. Fearon … & Nico H.J. Pijls
OBJECTIVES: We compared the diagnostic performance with adenosine-derived fractional flow reserve (FFR) #0.8 of contrast-based FFR (cFFR), resting distal pressure (Pd)/aortic pressure (Pa), and the instantaneous wave-free ratio (iFR). BACKGROUND: FFR objectively identifies lesions that benefit from medical therapy versus revascularization. However, FFR requires maximal vasodilation, usually achieved with adenosine. Radiographic contrast injection causes submaximal coronary hyperemia. Therefore, intracoronary contrast could provide an easy and inexpensive tool for predicting FFR. METHODS: We recruited patients undergoing...

Data from: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching

Felix Horns, Christopher Vollmers, Derek Croote, Sally F. Mackey, Gary E. Swan, Cornelia L. Dekker, Mark M. Davis & Stephen R. Quake
Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every...

Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

Nina Overgaard Therkildsen & Stephen R. Palumbi
Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a...

Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

James L. O'Donnell, Ryan P. Kelly, Jesse A. Port, Natalie C. Lowell & James L. O’Donnell
Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence...

Data from: Historical DNA documents long distance natal homing in marine fish

Sara Bonanomi, Nina Overgaard Therkildsen, Anja Retzel, Rasmus Berg Hedeholm, Martin Wæver Wæver Pedersen, Dorte Meldrup, Christophe Pampoulie, Jakob Hemmer-Hansen, Peter Grønkjær & Einar Nielsen
The occurrence of natal homing in marine fish remains a fundamental question in fish ecology as its unequivocal demonstration requires tracking of individuals from fertilization to reproduction. Here, we provide evidence of long distance natal homing (> 1000 km) over more than sixty years in Atlantic cod (Gadus morhua), through genetic analysis of archived samples from marked and recaptured individuals. Using a high differentiation Single Nucleotide Polymorphism assay we demonstrate that the vast majority of...

Data from: Detection of human adaptation during the past 2000 years

Yair Field, Evan A. Boyle, Natalie Telis, Ziyue Gao, Kyle J. Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I. McCarthy & Jonathan K. Pritchard
Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the Singleton Density Score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2,000-3,000 years. We see strong signals of selection at lactase and the MHC, and in favor of blond hair and...

Data from: Transforming water: social influence moderates psychological, physiological, and functional response to a placebo product

Alia J. Crum, Damon J. Phillips, J. Parker Goyer, Modupe Akinola & E. Tory Higgins
This paper investigates how social influence can alter physiological, psychological, and functional responses to a placebo product and how such responses influence the ultimate endorsement of the product. Participants consumed a product, "AquaCharge Energy Water," falsely-labeled as containing 200 mg of caffeine but which was actually plain spring water, in one of three conditions: a no social influence condition, a disconfirming social influence condition, and a confirming social influence condition. Results demonstrated that the effect...

Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

Tanja Stadler, James H. Degnan & Noah A. Rosenberg
Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because...

Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

Brian Helmuth, Francis Choi, Allison Matzelle, Jessica L. Torossian, Scott L. Morella, K. A. S. Mislan, Lauren Yamane, Denise Strickland, P. Lauren Szathmary, Sarah Gilman, Alyson Tockstein, Thomas J. Hilbish, Michael T. Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher D. G. Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa M. Foley, Angela Johnson, Megan Poole, Mae M. Noble … & Gerardo Zardi
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements...

Data from: Biodiversity response to natural gradients of multiple stressors on continental margins

Erik A. Sperling, Christina A. Frieder & Lisa A. Levin
Sharp increases in atmospheric CO2 are resulting in ocean warming, acidification and deoxygenation that threaten marine organisms on continental margins and their ecological functions and resulting ecosystem services. The relative influence of these stressors on biodiversity remains unclear though, as well as the threshold levels for change and when secondary stressors become important. One strategy to interpret adaptation potential and predict future faunal change is to examine ecological shifts along natural gradients in the modern...

Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials

Benjamin Kasenda, Erik Von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto, Alain Amstutz, Theresa Bengough, Joerg J. Meerpohl, Mihaela Stegert, Kelechi K. Olu, Kari A. O. Tikkinen, Ignacio Neumann, Alonso Carrasco-Labra, Markus Faulhaber, Sohail M. Mulla, Dominik Mertz, Elie A. Akl, Dirk Bassler, Jason W. Busse, Ignacio Ferreira-González, Francois Lamontagne, Alain Nordmann, Viktoria Gloy, Heike Raatz … & Matthias Briel
Background: Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications. We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees. Methods and Findings: We used a retrospective cohort of randomized clinical...

Data from: Evaporimeter and bubble-imaging measures of sweat gland secretion rates

Jeeyeon Kim, Miesha Farahmand, Colleen Dunn, Zoe Davies, Eric Frisbee, Carlos Milla & Jeffrey J. Wine
Beta-adrenergically-stimulated sweat rates determined by evaporimetry or by sweat bubble imaging are useful for measuring CFTR function because they provide a near-linear readout across almost the full range of CFTR function. They differentiate cystic fibrosis (CF) subjects from CF carriers and carriers from controls. However, evaporimetry, unlike bubble imaging, appears to be unable to detect improved levels of CFTR function in G551D subjects taking the CFTR modulator ivacaftor. Here, we quantify the sensitivity of evaporimetry...

Data from: High-throughput screening of inorganic compounds for dielectric and optical properties to enable the discovery of novel materials

Ioannis Petousis, David Mrdjenovich, Eric Ballouz, Miao Liu, Wei Chen, Tanja Graf, Thomas D. Schladt, Kristin A. Persson & Fritz B. Prinz
Dielectrics are an important class of materials that are ubiquitous in modern electronic applications. Even though their properties are important for the performance of devices, the number of compounds with known dielectric constant is on the order of a few hundred. Here, we use Density Functional Perturbation Theory as a way to screen for the dielectric constant and refractive index of materials in a fast and computationally efficient way. Our results form the largest database...

Data from: Qualitative study of physicians' varied uses of biomedical research in the USA

Lauren A. Maggio, Laura L. Moorhead & John M. Willinsky
Objective To investigate the nature of physicians' use of research evidence in experimental conditions of open access to inform training and policy. Design This qualitative study was a component of a larger mixed-methods initiative that provided 336 physicians with relatively complete access to research literature via PubMed and UpToDate, for 1 year via an online portal, with their usage recorded in web logs. Using a semistructured interview protocol, a subset of 38 physician participants were...

Data from: Tensor analysis reveals distinct population structure that parallels the different computational roles of areas M1 and V1

Jeffrey S. Seely, Matthew T. Kaufman, Stephen I. Ryu, Krishna V. Shenoy, John P. Cunningham & Mark M. Churchland
Cortical firing rates frequently display elaborate and heterogeneous temporal structure. One often wishes to compute quantitative summaries of such structure—a basic example is the frequency spectrum—and compare with model-based predictions. The advent of large-scale population recordings affords the opportunity to do so in new ways, with the hope of distinguishing between potential explanations for why responses vary with time. We introduce a method that assesses a basic but previously unexplored form of population-level structure: when...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Stanford University
  • University of Washington
  • Columbia University
  • University of Glasgow
  • Oregon State University
  • Stanford University School of Medicine
  • University of California, Santa Cruz
  • University of New Mexico
  • Biology and Genetics of Plant-Pathogen Interactions
  • Howard Hughes Medical Institute