Incidental Observations of Birds in the Vicinity of Hell Gate Polynya, Nunavut: Species, Timing, and Diversity

Our knowledge of the distribution of Arctic birds and how their ranges may be responding to environmental changes in the Canadian Arctic is limited. We gathered five years of species observation data from three sites in the Hell Gate – Cardigan Strait Polynya (Cape Vera, St. Helena Island, and Devil Island) to create an inventory of avian species observed in the polynya, and we compared it to previous observations made at our sites and other sites throughout the Arctic. We examined species diversity measurements over time to suggest possible effects of the polynya on the timing of spring arrival of breeding and migrant species. Of the 39 species observed during our study, 12 were local breeders. Our records provide the northernmost observations for eight species. Species diversity index values at St. Helena Island peaked quickly in mid-June and stabilized by late June, reflecting the arrival and dispersal of migrating species relatively early in the season. These data highlight the importance of the open-water feeding habitat of the polynya not only for breeding birds, but also for migrants.Nos connaissances de la distribution des oiseaux de l’Arctique et de la façon dont leurs parcours sont adaptés en fonction des changements environnementaux de l’Arctique canadien sont restreintes. Nous avons rassemblé les données d’observation d’espèces diverses échelonnées sur cinq ans à partir de trois emplacements de la polynie de Hell Gate – Cardigan Strait (cap Vera, île St. Helena et île Devil) dans le but de dresser l’inventaire des espèces aviaires observées dans la polynie, puis nous les avons comparées aux observations faites antérieurement à nos emplacements de même qu’à d’autres emplacements de l’Arctique. Nous avons examiné les mesures de la diversité des espèces au fil du temps afin de pouvoir suggérer les effets possibles de la polynie sur le moment de l’arrivée du printemps des espèces nicheuses et des espèces migrantes. Au nombre des 39 espèces ayant fait l’objet de notre étude, 12 étaient des oiseaux nicheurs de la région. Nos données constituent les observations prélevées les plus au nord pour huit des espèces. Les valeurs de l’indice de la diversité des espèces à l’île St. Helena ont atteint leur sommet à la mi-juin, puis se sont stabilisées vers la fin juin, ce qui était le reflet de l’arrivée et de la dispersion d’espèces migrantes relativement tôt dans la saison. Ces données font ressortir l’importance de l’habitat alimentaire en eaux libres de la polynie, non seulement pour les oiseaux nicheurs mais également pour les oiseaux migrants

Long-term Declines in the Size of Northern Fulmar (Fulmarus glacialis) Colonies on Eastern Baffin Island, Canada

We censused three colonies of Northern Fulmars (Fulmarus glacialis) along eastern Baffin Island, Canada, that were estimated to support 155 000 breeding pairs in 1973, but had not been adequately counted since then. The colonies were surveyed in July and August 2018 using photographs taken from a helicopter or a drone. The combined estimated colony sizes were 36 500 pairs, much smaller than historical estimates. Although the 1973 estimates were coarse, this difference represents an apparent 3+% annual decline in numbers at each colony over approximately four decades or more than 87% over three generations (66 years). Several factors may be contributing to these declines, including changes in winter food supplies and the susceptibility of fulmars to fisheries bycatch. We recommend efforts to survey the remaining major fulmar colonies in Arctic Canada to assess the overall population size and trends, and allow for further analyses of potential population drivers.Nous avons recensé trois colonies de fulmars boréaux (Fulmarus glacialis) sur la côte est de l’île de Baffin, au Canada. Selon des estimations réalisées en 1973, 155 000 couples reproducteurs y nichaient, mais aucun dénombrement adéquat n’avait été effectué depuis. Les colonies ont été recensées en juillet et en août 2018 au moyen de photographies prises à partir d’un hélicoptère ou d’un drone. La taille combinée des colonies a été estimée à 36500 couples, soit un nombre beaucoup moins élevé que les estimations précédentes. Bien que les estimations de 1973 étaient des estimations grossières, cette différence représente une baisse annuelle apparente de plus de 3 % à chacune des colonies sur environ quatre décennies, soit plus de 87 % sur trois générations (66 ans). Ces diminutions peuvent être attribuables à plusieurs facteurs, dont les changements caractérisant les approvisionnements en nourriture pendant l’hiver et la susceptibilité des fulmars à faire l’objet de captures accessoires. Nous recommandons que des efforts soient faits pour recenser les grandes colonies de fulmars qui restent dans l’Arctique canadien afin d’évaluer la taille globale de la population et les tendances la caractérisant, ainsi que pour pousser plus loin l’analyse des facteurs susceptibles d’avoir un effet sur leurs populations

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Predicting Seabird Foraging Habitat for Conservation Planning in Atlantic Canada: Integrating Telemetry and Survey Data Across Thousands of Colonies

Conservation of mobile organisms is difficult in the absence of detailed information about movement and habitat use. While the miniaturization of tracking devices has eased the collection of such information, it remains logistically and financially difficult to track a wide range of species across a large geographic scale. Predictive distribution models can be used to fill this gap by integrating both telemetry and census data to construct distribution maps and inform conservation goals and planning. We used tracking data from 520 individuals of 14 seabird species in Atlantic Canada to first compare foraging range and distance to shorelines among species across colonies, and then developed tree-based machine-learning models to predict foraging distributions for more than 5000 breeding sites distributed along more than 5000 km of shoreline. Despite large variability in foraging ranges among species, tracking data revealed clusters of species using similar foraging habitats (e.g., nearshore vs. offshore foragers), and within species, foraging range was highly colony-specific. Even with this variability, distance from the nesting colony was an important predictor of distribution for nearly all species, while distance from coastlines and bathymetry (slope and ruggedness) were additional important predictors for some species. Overall, we demonstrated the utility of tree-based machine-learning approach when modeling tracking data to predict distributions at un-sampled colonies. Although tracking and colony data have some shortcomings (e.g., fewer data for some species), where results need to be interpreted with care in some cases, applying methods for modeling breeding season distributions of seabirds allows for broader-scale conservation assessment. The modeled distributions can be used in decisions about planning for offshore recreation and commercial activities and to inform conservation planning at regional scales

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastomaclose

Genomic Classification of Cutaneous Melanoma

We describe the landscape of genomic alterations in cutaneous melanomas through DNA, RNA, and protein-based analysis of 333 primary and/or metastatic melanomas from 331 patients. We establish a framework for genomic classification into one of four sub-types based on the pattern of the most prevalent significantly mutated genes: mutant BRAF, mutant RAS, mutant NF1, and Triple-WT (wild-type). Integrative analysis reveals enrichment of KIT mutations and focal amplifications and complex structural rearrangements as a feature of the Triple-WT subtype. We found no significant outcome correlation with genomic classification, but samples assigned a transcriptomic subclass enriched for immune gene expression associated with lymphocyte infiltrate on pathology review and high LCK protein expression, a T cell marker, were associated with improved patient survival. This clinicopathological and multidimensional analysis suggests that the prognosis of melanoma patients with regional metastases is influenced by tumor stroma immunobiology, offering insights to further personalize therapeutic decision-makingclose3