482 Works

WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction

Meredith Lee, Jesse Raffa, Marzyeh Ghassemi, Tom Pollard, Sharada Kalanidhi, Omar Badawi, Karen Matthys & Leo Anthony Celi
WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction focuses on patient health through data from MIT’s GOSSIS (Global Open Source Severity of Illness Score) initiative. Brought to you by the Global WiDS team, the West Big Data Innovation Hub, and the WiDS Datathon Committee, this year’s datathon is launching on Kaggle: bit.ly/WiDSdatathon2020kaggle.

Data from: Ecological specialization in populations adapted to constant versus heterogeneous environments

Ao Wang, Amardeep Singh, Yuheng Huang & Aneil F. Agrawal
Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (i) a salt-enriched environment, (ii) a cadmium-enriched environment, (iii) a temporally varying environment, and (iv) a spatially varying environment. Juvenile viability...

Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient

James Santangelo, Ken Thompson, Beata Cohan, Jibran Syed, Rob Ness & Marc Johnson
Cities are emerging as models for addressing the fundamental question of whether populations evolve in parallel to similar environments. Here, we examine the environmental factors that drive the evolution of parallel urban-rural clines in a Mendelian trait—the cyanogenic antiherbivore defense of white clover (Trifolium repens). Previous work suggested urban-rural gradients in frost and snow depth could drive the evolution of reduced hydrogen cyanide (HCN) frequencies in urban populations. Here, we sampled over 700 urban and...

Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation

Brechann McGoey, Kathryn Hodgins & John Stinchcombe
As introduced species expand their ranges, they often encounter differences in climate which are often correlated with geography. For introduced species, encountering a geographically variable climate sometimes leads to the re-establishment of clines seen in the native range. However, clines can also be caused by neutral processes, and so it is important to gather additional evidence that population differentiation is the result of selection as opposed to non-adaptive processes. Here, we examine phenotypic and genetic...

Data from: Invasive dominance and resident diversity: unpacking the impact of plant invasion on biodiversity and ecosystem function

Stuart Livingstone, Marney Isaac & Marc Cadotte
Plant invasions have consistently been shown to cause significant reductions in the diversity of recipient plant communities; an effect that can cascade through ecosystems to impact the stocks and flows of nutrients and energy as well as the diversity of higher trophic levels. However, the manner in which invasive plants alter ecosystem functioning and trophic interactions is highly variable can occur through the direct effects of the invader’s abundance and its indirect effects via changes...

Clinician-researcher’s perspectives on clinical research during the COVID-19 pandemic

Sarah Silverberg, Lisa Puchalski-Ritchie, Nina Gobat, Alistair Nichol & Srinavas Murthy
Objectives: The outcome of well-performed clinical research is essential for evidence-based patient management during pandemics. However, conducting clinical research amidst a pandemic requires researchers to balance clinical and research demands. We seek to understand the values, experiences, and beliefs of physicians working at the onset of the COVID-19 pandemic in order to inform clinical research planning. We aim to understand whether pandemic settings affect physician comfort with research practices, and how physician experiences shape their...

Screening the Sigma LOPAC®1280 library of compounds for protective effects against cisplatin-induced oto- and nephrotoxicity

Jaime Wertman, Nicole Melong, Matthew Stoyek, Olivia Piccolo, Stewart Langley, Benno Orr, Shelby Steele, Babak Razaghi & Jason Berman
Dose-limiting toxicities for cisplatin administration, including ototoxicity and nephrotoxicity, impact the clinical utility of this effective chemotherapy agent and lead to lifelong complications, particularly in pediatric cancer survivors. Using a two-pronged drug screen employing the zebrafish lateral line as an in vivo readout for ototoxicity and kidney cell-based nephrotoxicity assay, we screened 1280 compounds and identified 22 that were both oto- and nephroprotective. Of these, dopamine and L-mimosine, a plant-based amino acid active in the...

Data from: Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

Nelson Buainain, Roberta Canton, Gabriela Zuquim, Hanna Tuomisto, Tomas Hrbek, Hiromitsu Sato & Camila Ribas
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage

Gregory Reeves, Hadel Al Asafen, Sophia Carrell-Noel, Allison Schloop, Jeramey Friedman & Prasad Bandodkar
In multicellular organisms, the timing and placement of gene expression in a developing tissue assigns the fate of each cell in the embryo in order for a uniform field of cells to differentiate into a reproducible pattern of organs and tissues. This positional information is often achieved through the action of spatial gradients of morphogens. Spatial patterns of gene expression are paradoxically robust to variations in morphogen dosage, given that, by definition, gene expression must...

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews & Charles Boone
Whole-genome duplication has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and...

Data from: New Middle Cambrian bivalved arthropod from the Burgess Shale (British Columbia, Canada)

David A. Legg & Jean-Bernard Caron
The morphology of two new bivalved arthropods, Loricicaris spinocaudatus gen. et sp. nov. and Nereocaris briggsi sp. nov. from the middle Cambrian (Series 3, Stage 5) Burgess Shale Formation (Collins Quarry locality on Mount Stephen, Yoho National Park, British Columbia, Canada), is described. The material was originally assigned to the genus Branchiocaris, but exhibits distinctive character combinations meriting its assignment to other taxa. Loricicaris spinocaudatus possesses an elongate and spinose abdomen comparable to the contemporaneous...

Data from: Indirect interactions shape selection in a multi-species foodweb

Denon Start, Arthur E. Weis & Benjamin Gilbert
Species do not live, interact, or evolve in isolation, but are instead members of complex ecological communities. In ecological terms, complex multi-species interactions can be understood by considering indirect effects that are mediated by changes in traits and abundances of intermediate species. Interestingly, traits and abundances are also central to our understanding of phenotypic selection, suggesting that indirect effects may be extended to understand evolution in complex communities. Here, we explore indirect ecological effects and...

Data from: A large new leanchoiliid from the Burgess Shale and the influence of inapplicable states on stem arthropod phylogeny

Cédric Aria, Jean-Bernard Caron & Robert Gaines
Characterized by atypical frontalmost appendages, leanchoiliids are early arthropods whose phylogenetic placement has been much debated. Morphological interpretations have differed, some of which concern critical characters such as the number of eyes and head appendages, but methodological approaches also have diverged. Here, we describe a new leanchoiliid, Yawunik kootenayi gen. et sp. nov., based on 42 specimens from the newly discovered Marble Canyon locality of the Burgess Shale (Kootenay National Park, British Columbia; middle Cambrian)....

Data from: Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii

Susanne A. Kraemer, Katharina B. Böndel, Robert W. Ness, Peter David Keightley & Nick Colegrave
Although all genetic variation ultimately stems from mutations, their properties are difficult to study directly. Here, we used multiple mutation accumulation (MA) lines derived from five genetic backgrounds of the green algae Chlamydomonas reinhardtii that have been previously subjected to whole genome sequencing to investigate the relationship between the number of spontaneous mutations and change in fitness from a non-evolved ancestor. MA lines were on average less fit than their ancestors and we detected a...

Data from: Condition dependence of female choosiness in a field cricket

Kevin A. Judge, Janice J. Ting & Darryl T. Gwynne
Females generally choose mates that produce the loudest, brightest or most elaborate sexual displays, and these costly male displays are predicted to be condition dependent. However, mate choice itself is a costly behaviour also expected to be condition dependent. Male fall field crickets, Gryllus pennsylvanicus, produce a conspicuous long-distance calling song that attracts females and is condition dependent. In this study, we tested the condition dependence of female preferences (preference function and choosiness) for male...

Data from: The Chlamydiales pangenome revisited: structural stability and functional coherence

Fotis E. Psomopoulos, Victoria I. Siarkou, Nikolas Papanikolaou, Ioannis Iliopoulos, Athanasios S. Tsaftaris, Christos A. Ouzounis & Vasilis J. Promponas
The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Virtual endocasts of fossil Sciuroidea: brain size reduction in the evolution of fossoriality

Ornella C. Bertrand, Farrah Amador-Mughal, Madlen M. Lang & Mary T. Silcox
Aplodontia rufa (Mountain Beaver) is the only extant member of Aplodontidae. The fossil record indicates that this family displayed greater taxonomic and ecological diversity in the past, and that the burrowing adaptations of Aplodontia might be derived. We describe the first virtual endocasts of A. rufa and of three fossil aplodontids: Prosciurus relictus and Pros. aff. saskatchewaensis (Early Oligocene), and Mesogaulus paniensis (late Miocene). Our results show that the endocasts of early aplodontid rodents are...

Data from: Integrating morphology and kinematics in the scaling of hummingbird hovering metabolic rate and efficiency

Derrick J.E. Groom, M. Cecilia B. Toledo, Donald R. Powers, Bret W. Tobalske, , Derrick J. E. Groom & Kenneth C. Welch
Wing kinematics and morphology are influential upon the aerodynamics of flight. However, there is a lack of studies linking these variables to metabolic costs, particularly in the context of morphological adaptation to body size. Furthermore, the conversion efficiency from chemical energy into movement by the muscles (mechanochemical efficiency) scales with mass in terrestrial quadrupeds, but this scaling relationship has not been demonstrated within flying vertebrates. Positive scaling of efficiency with body size may reduce the...

Data from: Inter- and intraspecific variation in leaf economics traits in wheat and maize

Adam R. Martin, Christine E. Hale, Bruno E. L. Cerabolini, Johannes H. C. Cornelissen, Joseph Craine, William A. Gough, Jens Kattge & Cairan K. F. Tirona
Leaf economics spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates (Amax), and leaf nitrogen...

Data from: Rapid adaptation to climate facilitates range expansion of an invasive plant

Robert I. Colautti & Spencer C.H. Barrett
Adaptation to climate, evolving over contemporary time scales, could facilitate rapid range expansion across environmental gradients. Here, we examine local adaptation along a climatic gradient in the North American invasive plant Lythrum salicaria. We show that the evolution of earlier flowering is adaptive at the northern invasion front where it increases fitness as much as, or more than, the effects of enemy release and the evolution of increased competitive ability. However, early flowering decreases investment...

Data from: The ‘filtering’ metaphor revisited: competition and environment jointly structure invasibility and coexistence

Rachel M. Germain, Margaret M. Mayfield & Benjamin Gilbert
‘Filtering’, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, controlled by the environment at large scales and competition at small scales. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence...

Data from: Phylogeny matters: revisiting ‘a comparison of bats and rodents as reservoirs of zoonotic viruses’

Cylita Guy, Jeneni Thiagavel, Nicole Mideo & John M. Ratcliffe
Diseases emerging from wildlife have been the source of many major human outbreaks. Predicting key sources of these outbreaks requires an understanding of the factors that explain pathogen diversity in reservoir species. Comparative methods are powerful tools for understanding variation in pathogen diversity and rely on correcting for phylogenetic relatedness among reservoir species. We reanalyzed a previously published dataset, examining the relative effects of species’ traits on patterns of viral diversity in bats and rodents....

Data from: Simulation assisted analysis of the intrinsic stiffness for short DNA molecules imaged with scanning atomic force microscopy

Haowei Wang & Joshua N. Milstein
Studying the mechanical properties of short segments of dsDNA can provide insight into various biophysical phenomena, from DNA looping to the organization of nucleosomes. Scanning atomic force microscopy (AFM) is able to acquire images of single DNA molecules with near-basepair resolution. From many images, one may use equilibrium statistical mechanics to quantify the intrinsic stiffness (or persistence length) of the DNA. However, this approach is highly dependent upon both the correct microscopic polymer model and...

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