Exploring the Complexities of Long COVID.

Since the emergence of the SARS-CoV-2 virus in 2019, nearly 700 million COVID-19 cases and 7 million deaths have been reported globally. Despite most individuals recovering within four weeks, the Center for Disease Control (CDC) estimates that 7.5% to 41% develop post-acute infection syndrome (PAIS), known as 'Long COVID'.

A large-scale validation study of aircraft noise modeling for airport arrivals.

In the U.S., the Federal Aviation Administration's Aviation Environmental Design Tool (AEDT) is approved to predict the impacts of aircraft noise and emissions.

Temporal change in urban fish biodiversity-Gains, losses, and drivers of change.

Our aim was to examine temporal change in alpha and beta diversity of freshwater fish communities in rivers that have urbanized over the same period to understand the influence of changes in land use and river connectivity on community change. We used biological (2001-2018), land use (2000-2015), and connectivity data (1987-2017) from Toronto, Ontario, Canada. We used linear mixed effects models to determine the strength of upstream land use, connectivity, and their changes over time to explain temporal change in alpha and beta diversity indices.

Can fish species co-occurrence patterns be predicted by their trait dissimilarities?

Trait-based analyses have been successful in determining and predicting species association outcomes in diverse communities. Most studies have limited the scope of this approach to the biotic responses of a small number of species or geographical regions. We focused on determining whether three biologically relevant traits (body size, temperature preference and trophic level) influence the patterns of co-occurrence between multiple species.

Biodiversity patterns diverge along geographic temperature gradients.

Models applying space-for-time substitution, including those projecting ecological responses to climate change, generally assume an elevational and latitudinal equivalence that is rarely tested. However, a mismatch may lead to different capacities for providing climatic refuge to dispersing species. We compiled community data on zooplankton, ectothermic animals that form the consumer basis of most aquatic food webs, from over 1200 mountain lakes and ponds across western North America to assess biodiversity along geographic temperature gradients spanning nearly 3750 m elevation and 30° latitude.

Putting the Mantel test back together again.

The Mantel test has been widely used in ecology and evolution, but over the last two decades it has been frequently critiqued because results were inconsistent with expectations and there were issues with Type I (false-positive) and Type II (false-negative) error rates. Three-matrix extensions of the Mantel test have been challenged for similar reasons. Even the null hypotheses underlying the Mantel test have been questioned.

Abiotic factors influence species co-occurrence patterns of lake fishes.

Abiotic factors are recognized for their strong influence on community structure. Habitat diversity is related to resource availability that influences species richness and abundance. In lakes, surface area and depth have been used as measures of the size and diversity of habitat, and have strong effects on the structure of entire communities.

TMB and Inflammatory Gene Expression Associated with Clinical Outcomes following Immunotherapy in Advanced Melanoma.

Outcomes for patients with melanoma have improved over the past decade as a result of the development and FDA approval of immunotherapies targeting cytotoxic T lymphocyte antigen-4 (CTLA-4), programmed death-1 (PD-1), and programmed death ligand 1 (PD-L1). However, these therapies do not benefit all patients, and an area of intensive research investigation is identifying biomarkers that can predict which patients are most likely to benefit from them. Here, we report exploratory analyses of the associations of tumor mutational burden (TMB), a 4-gene inflammatory gene expression signature, and mutation status with tumor response, progression-free survival, and overall survival in patients with advanced melanoma treated as part of the CheckMate 066 and 067 phase III clinical trials evaluating immuno-oncology therapies.

Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity.

Human-assisted introductions of exotic species are a leading cause of anthropogenic change in biodiversity; however, context dependencies and interactions with co-occurring stressors impede our ability to predict their ecological impacts. The legacy of historical sportfish stocking in mountainous regions of western North America creates a unique, natural quasiexperiment to investigate factors moderating invasion impacts on native communities across broad geographic and environmental gradients. Here we synthesize fish stocking records and zooplankton relative abundance for 685 mountain lakes and ponds in the Cascade and Canadian Rocky Mountain Ranges, to reveal the effects of predatory sportfish introduction on multiple taxonomic, functional and phylogenetic dimensions of prey biodiversity.

Shifting trophic control of fishery-ecosystem dynamics following biological invasions.

Increasing human population size and mobility have accelerated the translocation of nonnative species globally, which has become a major threat to conservation of biodiversity and ecosystem services. Introduced species can disrupt species interactions of the recipient ecosystem, triggering system-wide events, and amplify or dampen effects of existing pressures. We show how two pervasive intercontinental invasive consumers in North American lakes, dreissenids (filter-feeding mussels) and Bythotrephes (carnivorous zooplankton), nonlinearly modify consumer-resource dynamics and undermine management interventions to rebuild cold-water predatory fish biomass.

Fishing down then up the food web of an invaded lake.

Analysis of commercial catches reveals a serial depletion of some oceanic fish stocks over time, resulting in fisheries focusing on increasingly smaller species closer to the base of the food chain. This effect, described as fishing down the marine food web, is observed when the trophic level of the catch declines over time, raising concerns about the ecosystem impacts of fishing. Freshwater systems also experience harvest, yet do not appear to commonly show the same fishing down response perhaps because time series are too short to witness early depletions, fishing is often recreational, or other factors like stocking and invasive species influence patterns.

Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors.

We investigated the role of chemokines in regulating T cell accumulation in solid tumors. CCL5 and CXCL9 overexpression was associated with CD8 T cell infiltration in solid tumors. T cell infiltration required tumor cell-derived CCL5 and was amplified by IFN-γ-inducible, myeloid cell-secreted CXCL9.

MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma.

Combination anti-cytotoxic T lymphocyte antigen 4 (CTLA-4) and anti-programmed cell death protein 1 (PD-1) therapy promotes antitumor immunity and provides superior benefit to patients with advanced-stage melanoma compared with either therapy alone. T cell immunity requires recognition of antigens in the context of major histocompatibility complex (MHC) class I and class II proteins by CD8 and CD4 T cells, respectively. We examined MHC class I and class II protein expression on tumor cells from previously untreated melanoma patients and correlated the results with transcriptional and genomic analyses and with clinical response to anti-CTLA-4, anti-PD-1, or combination therapy.

Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling.

Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult-to-detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management.

Impacts of temperature and selected chemical digestion methods on microplastic particles.

Alkaline and wet peroxide oxidation chemical digestion techniques used to extract microplastics from organic matrices were assessed for recoveries and for impacts on ability to identify polymer types. Methods using wet peroxide oxidation generated enough heat to result in the complete loss of some types of microplastic particles, and boiling tests confirmed that temperatures >70 °C were responsible for the losses. Fourier transform infrared spectroscopy (FT-IR) confirmed minimal alteration of the recovered polymers by the applied methods.

Long-term spatiotemporal trends and health risk assessment of oyster arsenic levels in coastal waters of northern South China Sea.

Long-term spatiotemporal trends and health risk assessment of oyster arsenic levels in the coastal waters of northern South China Sea were investigated in order to help improve the quality and safety control and sustainable aquaculture for mollusks in China. Cultured oysters (Crassostrea rivularis) collected from the waters of 23 bays, harbors, and estuaries along the coast of northern South China Sea from 1989 to 2012 were examined for spatial patterns and long-term temporal trends of oyster arsenic levels. Single-factor index and health risk assessment were used to quantify arsenic exposure to human health through oyster consumption.

The metabolic consequences of repeated anoxic stress in the western painted turtle, Chrysemys picta bellii.

The painted turtle is known for its extreme tolerance to anoxia, but it is unknown whether previous experience with anoxic stress might alter physiological performance during or following a test bout of anoxia. Repeatedly subjecting 25°C-acclimated painted turtles to 2h of anoxic stress every other day for 19days (10 submergence bouts total) caused resting levels of liver glycogen to decrease by 17% and liver citrate synthase (CS) and cytochrome oxidase (COX) activities to increase by 33% and 112%, respectively. When the repeatedly submerged turtles were studied during a subsequent anoxic stress test, liver COX and CS activities decreased during anoxia to the same levels of naïve turtles, which were unchanged, and remained there throughout metabolic recovery.

The vulnerability of species to range expansions by predators can be predicted using historical species associations and body size.

Climate change threatens species directly through environmental changes and indirectly through its effects on species interactions. We need tools to predict which species are most vulnerable to these threats. Pairwise species associations and body size are simple but promising predictors of the relative impact of species introduced outside of their historical ranges.

The abiotic and biotic factors limiting establishment of predatory fishes at their expanding northern range boundaries in Ontario, Canada.

There is a poor understanding of the importance of biotic interactions in determining species distributions with climate change. Theory from invasion biology suggests that the success of species introductions outside of their historical ranges may be either positively (biotic acceptance) or negatively (biotic resistance) related to native biodiversity. Using data on fish community composition from two survey periods separated by approximately 28 years during which climate was warming, we examined the factors influencing the establishment of three predatory centrarchids: Smallmouth Bass (Micropterus dolomieu), Largemouth Bass (M.

Long-term changes in fish mercury levels in the historically impacted English-Wabigoon River system (Canada).

The English-Wabigoon River system in Northwestern Ontario, Canada, was one of the most heavily mercury-contaminated waterways in the world due to historical discharges in the 1960s from a chlor-alkali plant. This study examines long-term (1970-2010) monitoring data to assess temporal trends in mercury contamination in Walleye, Northern Pike and Lake Whitefish, three species important for sport and subsistence fishing in this region, using dynamic linear modeling and piecewise regression. For all lakes and species, there is a significant decline (36-94%) in mercury concentrations through time; however, there is evidence that this decline is either slowing down or levelling off.

Testing of the effect of missing data estimation and distribution in morphometric multivariate data analyses.

Missing data are an unavoidable problem in biological data sets and the performance of missing data deletion and estimation techniques in morphometric data sets is poorly understood. Here, a novel method is used to measure the introduced error of multiple techniques on a representative sample. A large sample of extant crocodilian skulls was measured and analyzed with principal component analysis (PCA).

Exome sequencing reveals comprehensive genomic alterations across eight cancer cell lines.

It is well established that genomic alterations play an essential role in oncogenesis, disease progression, and response of tumors to therapeutic intervention. The advances of next-generation sequencing technologies (NGS) provide unprecedented capabilities to scan genomes for changes such as mutations, deletions, and alterations of chromosomal copy number. However, the cost of full-genome sequencing still prevents the routine application of NGS in many areas.