Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs.

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), also known as Long-COVID, encompasses a variety of complex and varied outcomes following COVID-19 infection that are still poorly understood. We clustered over 600 million condition diagnoses from 14 million patients available through the National COVID Cohort Collaborative (N3C), generating hundreds of highly detailed clinical phenotypes. Assessing patient clinical trajectories using these clusters allowed us to identify individual conditions and phenotypes strongly increased after acute infection.

Harnessing Consumer Wearable Digital Biomarkers for Individualized Recognition of Postpartum Depression Using the All of Us Research Program Data Set: Cross-Sectional Study.

Background: Postpartum depression (PPD) poses a significant maternal health challenge. The current approach to detecting PPD relies on in-person postpartum visits, which contributes to underdiagnosis. Furthermore, recognizing PPD symptoms can be challenging.

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research.

Harnessing consumer wearable digital biomarkers for individualized recognition of postpartum depression using the Research Program dataset.

Postpartum depression (PPD), afflicting one in seven women, poses a major challenge in maternal health. Existing approaches to detect PPD heavily depend on in-person postpartum visits, leading to cases of the condition being overlooked and untreated. We explored the potential of consumer wearable-derived digital biomarkers for PPD recognition to address this gap.

A Bayesian multi-stage modelling framework to evaluate impacts of energy development on wildlife populations: an application to greater sage-grouse ().

Increased demand for domestic production of renewable energy has led to expansion of energy infrastructure across western North America. Much of the western U.S.

Post-recovery COVID-19 and incident heart failure in the National COVID Cohort Collaborative (N3C) study.

Cardiac involvement has been noted in COVID-19 infection. However, the relationship between post-recovery COVID-19 and development of de novo heart failure has not been investigated in a large, nationally representative population. We examined post-recovery outcomes of 587,330 patients hospitalized in the United States (257,075 with COVID-19 and 330,255 without), using data from the National COVID Cohort Collaborative study.

Targeting Sagebrush (Artemisia Spp.) Restoration Following Wildfire with Greater Sage-Grouse (Centrocercus Urophasianus) Nest Selection and Survival Models.

Unprecedented conservation efforts for sagebrush (Artemisia spp.) ecosystems across the western United States have been catalyzed by risks from escalated wildfire activity that reduces habitat for sagebrush-obligate species such as Greater Sage-Grouse (Centrocercus urophasianus). However, post-fire restoration is challenged by spatial variation in ecosystem processes influencing resilience to disturbance and resistance to non-native invasive species, and spatial and temporal lags between slower sagebrush recovery processes and faster demographic responses of sage-grouse to loss of important habitat.

Nesting, brood rearing, and summer habitat selection by translocated greater sage-grouse in North Dakota, USA.

Human enterprise has led to large-scale changes in landscapes and altered wildlife population distribution and abundance, necessitating efficient and effective conservation strategies for impacted species. Greater sage-grouse (; hereafter sage-grouse) are a widespread sagebrush ( spp.) obligate species that has experienced population declines since the mid-1900s resulting from habitat loss and expansion of anthropogenic features into sagebrush ecosystems.

Wildfire and the ecological niche: Diminishing habitat suitability for an indicator species within semi-arid ecosystems.

Globally accelerating frequency and extent of wildfire threatens the persistence of specialist wildlife species through direct loss of habitat and indirect facilitation of exotic invasive species. Habitat specialists may be especially prone to rapidly changing environmental conditions because their ability to adapt lags behind the rate of habitat alteration. As a result, these populations may become increasingly susceptible to ecological traps by returning to suboptimal breeding habitats that were dramatically altered by disturbance.

Territoriality drives preemptive habitat selection in recovering wolves: Implications for carnivore conservation.

According to the ideal-free distribution (IFD), individuals within a population are free to select habitats that maximize their chances of success. Assuming knowledge of habitat quality, the IFD predicts that average fitness will be approximately equal among individuals and between habitats, while density varies, implying that habitat selection will be density dependent. Populations are often assumed to follow an IFD, although this assumption is rarely tested with empirical data, and may be incorrect when territoriality indicates habitat selection tactics that deviate from the IFD (e.

Territorial landscapes: incorporating density-dependence into wolf habitat selection studies.

Habitat selection is a process that spans space, time and individual life histories. Ecological analyses of animal distributions and preferences are most accurate when they account for inherent dynamics of the habitat selection process. Strong territoriality can constrain perception of habitat availability by individual animals or groups attempting to colonize or establish new territory.

Spatially varying density dependence drives a shifting mosaic of survival in a recovering apex predator ().

Understanding landscape patterns in mortality risk is crucial for promoting recovery of threatened and endangered species. Humans affect mortality risk in large carnivores such as wolves (), but spatiotemporally varying density dependence can significantly influence the landscape of survival. This potentially occurs when density varies spatially and risk is unevenly distributed.

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient.

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and nonecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations.

Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment.

Understanding the genetic basis of pathogen susceptibility in various crop plants is crucial to increasing the stability of food, feed, and fuel production. Varietal differences in defence responses provide insights into the mechanisms of resistance and are a key resource for plant breeders. To explore the role of salicylic acid in the regulation of defence in cacao, we demonstrated that SA treatment decreased susceptibility to a pod rot pathogen, Phytophthora tropicalis in two genotypes, Scavina 6 and Imperial College Selection 1, which differ in their resistance to several agriculturally important pathogens.

Habitat capacity for cougar recolonization in the Upper Great Lakes region.

Background: Recent findings indicate that cougars (Puma concolor) are expanding their range into the midwestern United States. Confirmed reports of cougar in Michigan, Minnesota, and Wisconsin have increased dramatically in frequency during the last five years, leading to speculation that cougars may re-establish in the Upper Great Lakes (UGL) region, USA. Recent work showed favorable cougar habitat in northeastern Minnesota, suggesting that the northern forested regions of Michigan and Wisconsin may have similar potential.

A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.

Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv.

Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

Local adaptation of populations could preclude or slow range expansions in response to changing climate, particularly when dispersal is limited. To investigate the differential responses of populations to changing climatic conditions, we exposed poleward peripheral and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared their whole-transcriptome expression. We found evidence of simple population differentiation in both species, and in the species with previously identified population structure and phenotypic local adaptation, we found several hundred genes that responded in a synchronized and localized fashion.

Assessing De Novo transcriptome assembly metrics for consistency and utility.

Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality.

Results: We simulated sequencing transcripts of Drosophila melanogaster.

Haplotype and minimum-chimerism consensus determination using short sequence data.

Background: Assembling haplotypes given sequence data derived from a single individual is a well studied problem, but only recently has haplotype assembly been considered for population-sampled data. We discuss a software tool called Hapler, which is designed specifically for low-diversity, low-coverage data such as ecological samples derived from natural populations. Because such data may contain error as well as ambiguous haplotype information, we developed methods that increase confidence in these assemblies.

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon.

Background: Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis.