131 Works

Additional file 1 of PrEP-related stigma and PrEP use among gay, bisexual and other men who have sex with men in Ontario and British Columbia, Canada

Oscar Javier Pico-Espinosa, Mark Hull, Paul MacPherson, Daniel Grace, Mark Gaspar, Nathan Lachowsky, Saira Mohammed, James Demers, Marshall Kilduff, Robinson Truong & Darrell H. S. Tan
Supplementary Figures and Tables.

PrEP-related stigma and PrEP use among gay, bisexual and other men who have sex with men in Ontario and British Columbia, Canada

Oscar Javier Pico-Espinosa, Mark Hull, Paul MacPherson, Daniel Grace, Mark Gaspar, Nathan Lachowsky, Saira Mohammed, James Demers, Marshall Kilduff, Robinson Truong & Darrell H. S. Tan
Abstract Background We aimed to explore the association between PrEP-related stereotypes and perceived disapproval (hereafter PrEP-related stigma), and PrEP use. Methods We used data from a cross-sectional online survey among adult gay, bisexual, other men who have sex with men in Ontario and British Columbia, Canada. Participants were recruited 2019–2020 in-person from sexual health clinics and outreach programs, and online through dating mobile applications and websites. We used logistic regression models to explore the relationship...

Additional file 1 of The Revised Identification of Seniors At Risk screening tool predicts readmission in older hospitalized patients: a cohort study

Jane McCusker, Rebecca N. Warburton, Sylvie D. Lambert, Eric Belzile & Manon de Raad
Additional file 1. ISAR tool: Original and revised versions

Inhibition of histone binding by supramolecular hosts

Hillary F. Allen, Kevin D. Daze, Takashi Shimbo, Anne Lai, Catherine A. Musselman, Jennifer K. Sims, Paul A. Wade, Fraser Hof & Tatiana G. Kutateladze
We report a new set of calixarene-based host compounds and show their applicability in characterizing functions of methyllysine-recognizing epigenetic readers. Calixarenes disrupt the association of the PHD finger of CHD4 with a trimethylated, but not an unmodified, histone tail.

Data from: Infectious adaptation: potential host range of a defensive endosymbiont in Drosophila

Tamara S. Haselkorn, Sarah N. Cockburn, Phineas T. Hamilton, Steve. J Perlman & John Jaenike
Maternally transmitted symbionts persist over macroevolutionary time scales by undergoing occasional lateral transfer to new host species. To invade a new species, a symbiont must survive and reproduce in the new host, undergo maternal transmission, and confer a selective benefit sufficient to overcome losses due to imperfect maternal transmission. Drosophila neotestacea is naturally infected with a strain of Spiroplasma that restores fertility to nematode-parasitized females, which are otherwise sterilized by parasitism. We experimentally transferred Spiroplasma...

Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

Armando Geraldes, Steve P. DiFazio, Gancho T. Slavov, Priya Ranjan, Wellington Muchero, Jan Hannemann, Lee E. Gunter, Ann M. Wymore, Christopher J. Grassa, Nima Farzaneh, Ilga Porth, Athena D. Mckown, Oleksandr Skyba, Eryang Li, Miki Fujita, Jaroslav Klápště, Joel Martin, Wendy Schackwitz, Christa Pennacchio, Daniel Rokhsar, Michael C. Friedmann, Geoffrey O. Wasteneys, Robert D. Guy, Yousry A. El-Kassaby, Shawn D. Mansfield … & Gerald A. Tuskan
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a...

Data from: A year in hypoxia: epibenthic community responses to severe oxygen deficit at a subsea observatory in a coastal inlet

Marjolaine Matabos, Verena Tunnicliffe, S. Kim Juniper & Courtney Dean
Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of...

Data from: Testing a “genes-to-ecosystems” approach to understanding aquatic-terrestrial linkages

Gregory Crutsinger, Seth Rudman, Mariano Rodriguez-Cabal, Athena Mckown, Takuya Sato, Andrew M. MacDonald, Julian Heavyside, Armando Geraldes, Edmund Hart, Carri LeRoy, Rana El-Sabaawi, Athena D. McKown, Gregory M. Crutsinger, Seth M. Rudman, Mariano A. Rodriguez-Cabal, Edmund M. Hart, Carri J. LeRoy & Rana W. El-Sabaawi
A ‘genes-to-ecosystems’ approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with the underlying genetic architecture of a species in order to shed light on the relationships among hierarchies of ecological organization (genes [RIGHTWARDS ARROW] individuals [RIGHTWARDS ARROW] communities [RIGHTWARDS ARROW] ecosystems). However, attempts to identify genes with major effect on the structure of communities and/or ecosystem processes have been limited and a comprehensive test of this approach...

Data from: Transcriptional responses in a Drosophila defensive symbiosis

Phineas T. Hamilton, Jong S. Leong, Ben F. Koop & Steve J. Perlman
Inherited symbionts are ubiquitous in insects and can have important consequences for the fitness of their hosts. Many inherited symbionts defend their hosts against parasites or other natural enemies; however, the means by which most symbionts confer protection is virtually unknown. We examine the mechanisms of defence in a recently discovered case of symbiont-mediated protection, where the bacterial symbiont Spiroplasma defends the fly Drosophila neotestacea from a virulent nematode parasite, Howardula aoronymphium. Using quantitative PCR...

Data from: Species turnover (β diversity) in ectomycorrhizal fungi linked to NH4+ uptake capacity

John M. Kranabetter, Barbara J. Hawkins, Melanie D. Jones, Samantha Robbins, Tyler Dyer & Tao Li
Ectomycorrhizal (EcM) fungal communities may be shaped by both deterministic and stochastic processes, potentially influencing ecosystem development and function. We evaluated community assembly processes for EcM fungi of Pseudotsuga menziesii among 12 sites up to 400 km apart in southwest British Columbia (Canada) by investigating species turnover (β diversity) in relation to soil nitrogen (N) availability and physical distance. We then examined functional traits for an N-related niche by quantifying net fluxes of NH4+, NO3-...

Data from: Vicariance, long-distance dispersal, and regional extinction–recolonization dynamics explain the disjunct circumpolar distribution of the arctic-alpine plant Silene acaulis

Galina Gussarova, Geraldine A. Allen, Yulia Mikhaylova, Laurie J. McCormick, Virginia Mirré, Kendrick L. Marr, Richard J. Hebda & Christian Brochmann
PREMISE OF THE STUDY: Many arctic-alpine species have vast geographic ranges, but these may encompass substantial gaps whose origins are poorly understood. Here we address the phylogeographic history of Silene acaulis, a perennial cushion plant with a circumpolar distribution except for a large gap in Siberia. METHODS: We assessed genetic variation in a range-wide sample of 103 populations using plastid DNA (pDNA) sequences and AFLPs (amplified fragment length polymorphisms). We constructed a haplotype network and...

Data from: Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle

Yves Basset, Lukas Cizek, Philippe Cuénoud, Raphael K. Didham, Vojtech Novotny, Frode Ødegaard, Tomas Roslin, Alexey K. Tishechkin, Jürgen Schmidl, Neville N. Winchester, David W. Roubik, Henri-Pierre Aberlenc, Johannes Bail, Héctor Barrios, Jonathan R. Bridle, Gabriela Castaño-Meneses, Bruno Corbara, Gianfranco Curletti, Wesley Duarte Da Rocha, Domir De Bakker, Jacques H.C. Delabie, Alain Dejean, Laura L. Fagan, Andreas Floren, Roger L. Kitching … & Jacques H. C. Delabie
Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14...

Data from: Ecological legacies of anthropogenic burning in a British Columbia coastal temperate rain forest

Kira M. Hoffman, Ken P. Lertzman & Brian M. Starzomski
Aim Few long-term fire histories have been reconstructed in coastal temperate rain forests, and little is known regarding the spatial and temporal characteristics of lightning and human ignitions. We use a multidisciplinary approach to assess the impact, scale and ecological legacies of historic fires. Location We focus on perhumid temperate rain forests located on the central coast of British Columbia, Canada. Methods We reconstructed 700 years of temporal and spatial aspects of fire activity with...

Data from: Decay patterns of invasive plants and plastic trash in urban streams

Kimberly T. M. Kennedy & Rana W. El-Sabaawi
Urban streams are impacted by invasion of exotic riparian plants and the accumulation of plastic trash, which alter in-stream litter subsidies, and cause changes that cascade up the aquatic food web. The impacts of these factors on urban streams is poorly understood. We compared decay rates and invertebrate colonizers of 5 litter pack types in 4 urban streams in Victoria, British Columbia, Canada: Native Red alder (Alnus rubra) and Sitka willow (Salix sitchensis), invasive English...

Data from: Genetics and genomics of an unusual selfish sex ratio distortion in an insect

Phineas T. Hamilton, Christina N. Hodson, Caitlin I. Curtis & Steve J. Perlman
Diverse selfish genetic elements have evolved the ability to manipulate reproduction to increase their transmission, and this can result in highly distorted sex ratios. Indeed, one of the major explanations for why sex determination systems are so dynamic is because they are shaped by ongoing coevolutionary arms races between sex ratio distorting elements and the rest of the genome. Here, we use genetic crosses and genome analysis to describe an unusual sex ratio distortion with...

Data from: Spatial patterns and rarity of the white-phased ‘Spirit Bear’ allele reveals gaps in habitat protection

Christina Service, Mathieu Bourbonnais, Megan Adams, Lauren Henson, Douglas Neasloss, Chris Picard, Paul Paquet & Chris Darimont
Preserving genetic and phenotypic diversity can help safeguard not only biodiversity but also cultural and economic values. Here, we present data that emerged from Indigenous-led research at the intersection of evolution and ecology to support conservation planning of a culturally salient, economically valuable, and rare phenotypic variant. We addressed three conservation objectives for the white-phased ‘Spirit bear’ polymorphism, a rare and endemic white-coated phenotype of black bear (Ursus americanus) in Kitasoo/Xai’xais and Gitga’at Territories and...

Data from: Habitat size thresholds for predators: why damselflies only occur in large bromeliads

Diane Sheila Srivastava, Sarah Louise Amundrud, Jacqueline T. Ngai, Brian M. Starzomski & Jessica Lee Ware
Predators are often more sensitive to habitat size than their prey, and frequently occur in only the largest habitats. Four explanations have been proposed for this pattern: (1) small habitats do not have enough energy to support higher trophic levels; (2) small habitats are less likely to contain particular prey required by specialist predators; (3) small habitats are risky for predators with slow life histories or large body sizes; (4) small habitats are numerically unlikely...

Are Legal Texts Grey Literature? Toward a definition of Grey Literature that invites the Preservation of Authentic and Complete Originals

Michael Lines
Legal texts, though they exist in a wide variety of forms, are most typically thought of as Law Books. Law books, hardbound volumes in expensive bindings of browns and blacks, are heavy, difficult, and technical. They are a prop to popular conceptions of the law itself, and resemble more closely than most other earthly books the Platonic form of the ‘weighty tome.’ In fact, some law libraries do a regular, if not exactly brisk, trade...

Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)

Sarah J. Salisbury, Gregory R. McCracken, Robert Perry, Donald Keefe, Kara K. S. Layton, Tony Kess, Cameron M. Nugent, Jong S. Leong, Ian R. Bradbury, Ben F. Koop, Moira M. Ferguson & Daniel E. Ruzzante
The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation...

Cross-continental comparison of parasite communities in a wide-ranging carnivore suggests associations with prey diversity and host density

Astrid Stronen, Barbara Molnar, Paolo Ciucci, Chris Darimont, Lorenza Grottoli, Paul Paquet, Tim Sallows, Judit Smits & Heather Bryan
Parasites are integral to ecosystem functioning yet often overlooked. Improved understanding of host-parasite associations is important, particularly for wide-ranging species for which host range shifts and climate change could alter host-parasite interactions and their effects on ecosystem function. Among the most widely distributed mammals with diverse diets, grey wolves (Canis lupus) host parasites that are transmitted among canids and via prey species. Grey wolf-parasite associations may therefore influence the population dynamics and ecological functions of...

Assembled transcriptome from multiple individuals of Leukoma staminea (Pacific littleneck clam) of gill and digestive gland tissues.

Monique R. Raap, Helen J. Gurney-Smith, Sarah E. Dudas, Christopher M. Pearce, Ben J. Sutherland & Ben F. Koop
A transcriptome that was assembled from RNA-seq data using the program Trinity after quality trimming with Trimmomatic. Multiple clams and tissues were used to assemble the transcriptome.

Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs

Tony Kess, J. Brian Dempson, Sarah J. Lehnert, Kara Layton, Anthony Einfeldt, Paul Bentzen, Sarah Salisbury, Amber Messmer, Steven Duffy, Daniel Ruzzante, Cameron Nugent, Moira Ferguson, Jong Leong, Ben Koop, Michael O'Connell, Ian Bradbury, Kara K. S. Layton, Sarah J. Salisbury, Amber M. Messmer, Daniel E. Ruzzante, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Michael F. O’Connell … & Ian R. Bradbury
Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in these environments are rarely known. Post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Here, we compare genomic and morphometric divergence...

Data from: Shoaling in the Trinidadian guppy: Costs, benefits, and plasticity in response to an ambush predator

Anna Li, Jean Richardson & Helen Rodd
Shoaling, the formation of social groupings in fish, can provide benefits including reduced predation risk. However, it can also inflict costs including increased competition for resources, transmission of parasites, and salience to predators. Trinidadian guppies exhibit inter-population variation in shoaling behavior where individuals coexisting with large piscivorous predators (high predation localities) spend most of their time in shoals and those coexisting with an ambush predator, Rivulus hartii (recently, Anablepsoides hartii), that preys primarily on smaller...

Occupancy model for Rattus spp. in high and low human human refuse supplementation conditions

Ishana Shukla
Globally, the genus Rattus is one of the most influential exotic species due to its high rates of competitive exclusion and large dietary breadth. However, the specific foraging strategies of urban and urban-adjacent populations remain largely unknown. We examined Rattus spp. dependency on human food supplementation in a peri-urban population. Through a natural experiment made possible by the COVID-19 shelter in place order in Santa Cruz California, USA, we measured changes in activity between invasive...

Measuring egestion, excretion, fecal leaching, and foregut-hindgut %P in threespine stickleback

Emily May & Rana El-Sabaawi
Most aquatic research on animal waste production evaluates excretion and not egestion, as it is difficult both to collect feces and to accurately analyze its nutrient content. This limits our understanding of how individuals process their dietary nutrients and how animal waste production impacts ecosystems. In this study, we systematically analyzed whether incubation experiments effectively quantify egestion (at high and low temperatures), estimated fecal phosphorus (P) leaching, and evaluated foregut-hindgut analyses as a complementary method....

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