Recent publications
Why animals migrate is a fundamental question in biology. While the adaptive significance of some animal migrations is well understood (e.g., to find food, to pursue more‐favorable habitats, to spawn, or to give birth), others remain unknown. The adaptive significance of whale migration, for example, is unresolved and multiple hypotheses have been proposed to explain it. One recently proposed hypothesis that challenges the long‐standing “feeding‐breeding” whale migration model is a “feeding‐molting” model, where whales undertake latitudinal migrations to warmer waters to molt skin. In July 2019, we attached satellite‐tracking tags to northern bottlenose whales (Hyperoodon ampullatus) in the Canadian Arctic. One of these tagged whales completed a round‐trip movement between the Arctic and the temperate western North Atlantic, traveling 7281 km in 67 days (and spanning 27° of latitude). The whale was tagged in sea‐surface temperatures of ~4°C, but migrated south, reaching ~23°C surface waters, where it remained for 7 days before returning to the Arctic. The whale's occupancy of warm water was accompanied by a distinct shift in dive behavior, remaining near the ocean's surface. Four other tagged whales initiated similar long‐distance movements. We conclude that feeding or breeding were unlikely reasons for this movement and that northern bottlenose whales migrate to warmer latitudes to molt skin.
Aspartate (Asp) metabolism‐mediated antioxidant functions have important implications for neonatal growth and intestinal health; however, the antioxidant mechanisms through which Asp regulates the gut microbiota and influences RIP activation remain elusive. This study reports that chronic oxidative stress disrupts gut microbiota and metabolite balance and that such imbalance is intricately tied to the perturbation of Asp metabolism. Under normal conditions, in vivo and in vitro studies reveal that exogenous Asp improves intestinal health by regulating epithelial cell proliferation, nutrient uptake, and apoptosis. During oxidative stress, Asp reduces Megasphaera abundance while increasing Ruminococcaceae. This reversal effect depends on the enhanced production of the antioxidant eicosapentaenoic acid mediated through Asp metabolism and microbiota. Mechanistically, the application of exogenous Asp orchestrates the antioxidant responses in enterocytes via the modulation of the RIP3‐MLKL and RIP1‐Nrf2‐NF‐κB pathways to eliminate excessive reactive oxygen species and maintain mitochondrial functionality and cellular survival. These results demonstrate that Asp signaling alleviates oxidative stress by dynamically modulating the gut microbiota and RIP‐dependent mitochondrial function, providing a potential therapeutic strategy for oxidative stress disease treatment.
The St. Lawrence Estuary (SLE) beluga (Delphinapterus leucas) population in Canada is Endangered, and endocrine disrupting contaminants, such as polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and other halogenated flame retardants, have been identified as a threat to the recovery of this population. Here, potential impacts of these contaminants on SLE beluga were evaluated by comparing skin transcriptome profiles and biological pathways between this population and a population less exposed to contaminants (Eastern Beaufort Sea) used as a reference. Differential gene expression analysis indicated potential seasonal or geography-related (Arctic vs temperate regions) effects on the skin transcriptome. Among the gene transcripts that were associated with Σ31PCB (123 genes), Σ29PBDE (198genes), HBB (347 genes), and PBEB (126 genes) blubber concentrations, several were related to immune response pathways. In addition, 18 toxicology-related gene transcripts selected from the literature were correlated with organohalogen concentrations and were used to derive new threshold values in beluga skin for potential biological effects of ΣPCB (1,500 ng/glw), ΣPBDE (52 ng/g lw), and two other flame retardants, i.e., HBB (1.2 ng/g lw) and PBEB (0.04 ng/g lw). Results suggest that exposure to these organohalogens pose a risk to the immune system of SLE beluga.
Ceres, the largest object in the asteroid belt, is the only potential ocean world in the inner Solar System. Previous studies identified deposits of aliphatic organics in and around the Ernutet crater, and at small locations at Inamahari and Urvara craters. The origin of organics, either endogenic or exogenic, in these fresh exposures is still under debate. This study addresses the origin of the organics by analyzing their global distribution and geologic context. Our first step involved a global search for organic‐rich sites that might have escaped previous detections. We achieved this by using a deep neural network, utilizing spectral redness in the Dawn's Framing Camera multispectral data to identify potential organic‐rich sites. The identified sites were further studied by using IR spectrometer data to infer the compositions of materials showing spectral redness. Of the newly identified red‐sloped sites, only two can be considered certain to be organic‐rich. We also identified sites with spectral redness, but without any signature of organics in their infrared spectra. These sites could be attributed to the aqueous alteration of magnetite into ferric‐iron bearing phases. At Ernutet, Inamahari, and Urvara, the organic‐rich material is confined to the near surface only. Additionally, the absence of tectonic/volcanic features at these sites makes an endogenic origin questionable. The global rarity of detectable organics also supports this assessment. Consequently, we suggest that organics at these sites were originally delivered by low‐velocity, organic‐rich impactor(s) from the main belt and subsequently excavated, rather than originating from endogenous processes.
Competitive fitness is a fundamental concept in evolutionary biology that captures the ability of organisms to survive, reproduce, and compete for resources in their environment. Competitive fitness is typically assessed in the lab by growing two or more competitors together and measuring the frequency of each at multiple time points. Traditional microbial competitive fitness assays are labor intensive and involve plating on solid medium and counting colonies. Here, we describe a method to quantitatively measure competitive fitness using fluorescence microscopic imaging and machine‐learning‐enabled image analysis to directly count the number of cells from each competitor in the mixed population. This high‐throughput, primarily automated, and efficient process gives accurate and reproducible results for competitive fitness. Here, we describe the entire process, from sample preparation through microscopy to quantification, and provide instructions and scripts for the image analysis, fitness calculations, and sample data visualizations. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.
Basic Protocol 1 : Sample preparation
Basic Protocol 2 : Photographing fluorescing and non‐fluorescing cells using an EVOS microscope
Basic Protocol 3 : Counting fluorescing and non‐fluorescing cells with Orbit Image Analysis
Basic Protocol 4 : Getting the average cell counts per well and changing the file names
Basic Protocol 5 : Calculating competitive fitness using R
Before the end of the Spanish-Dutch war in 1648 and the loss of Dutch Brazil in 1654, Dutch-Indigenous relations in the South Atlantic were shaped by the West India Company’s desire to establish anti-Iberian alliances with Native peoples. This chapter examines Dutch policies toward Indigenous peoples in the Caribbean and the Guianas after the end of the Dutch war with Spain and the loss of Dutch Brazil. In developing Indigenous policies, Dutch officials in Curaçao, Tobago, and Suriname imitated and adapted practices that they had earlier learned and observed from Iberian colonizers in the Caribbean and Brazil. At the same time, the Indigenous peoples of the Caribbean and Suriname reshaped the Dutch Empire in the Atlantic. In Suriname, the Caribs forced the Dutch to end the enslavement of their people. On Curaçao the Caquetios used the growth of Dutch-Spanish trade to attract Catholic missionaries to the Dutch island-colony.
The introduction of invasive species is known to cause changes in the structure and composition of native communities. These changes are not only restricted to the aboveground vegetation, but may be equally expressed in corresponding soil seed banks, which are legacy effects of the vegetation. This study assessed the impact of the invasive plant, Alternanthera brasiliana, on the vegetation community and its soil seed bank in Ile-Ife, Nigeria. Sample plots were established in invaded plant communities, with high density of Alternanthera brasiliana, and uninvaded plant communities with low density or no presence of Alternanthera brasiliana. Subplots were placed in each large sample plot and in each subplot all rooted plant species were identified and counted. Samples from the post-dispersal soil seed bank were collected to estimate the soil seed bank density and floristics. The species composition of soil seed bank was compared with that of the above-ground vegetation to assess the invader’s impact on the vegetation and soil seed bank. The results showed that the presence of Alternanthera brasiliana significantly impacted on the species diversity (t = 5.27; df = 18; p = 0.0003) and species evenness (t = 4.50; df = 18; p = 0.00005) in the aboveground vegetation, and the species diversity (t = 5.37; df = 18; p = 0.00004) and species evenness (t = 6.19; df = 18; p < 0.0001) in the soil seed bank. This study showed that Alternanthera brasiliana has caused ecological alterations in the aboveground vegetation as well as in the soil seed bank. It is likely that with increasing resident time, the impacts on native species will increase as Alternanthera brasiliana spreads.
We show how to obtain, via a unified framework provided by logic and automata theory, many classical results of Brillhart and Morton on Rudin-Shapiro sums. The techniques also facilitate easy proofs for new results.
Background
Comprehensively mapping the hierarchical structure of breast cancer protein communities and identifying potential biomarkers from them is a promising way for breast cancer research. Existing approaches are subjective and fail to take information from protein sequences into consideration. Deep learning can automatically learn features from protein sequences and protein–protein interactions for hierarchical clustering.
Results
Using a large amount of publicly available proteomics data, we created a hierarchical tree for breast cancer protein communities using a novel hierarchical graph neural network, with the supervision of gene ontology terms and assistance of a pre-trained deep contextual language model. Then, a group-lasso algorithm was applied to identify protein communities that are under both mutation burden and survival burden, undergo significant alterations when targeted by specific drug molecules, and show cancer-dependent perturbations. The resulting hierarchical map of protein communities shows how gene-level mutations and survival information converge on protein communities at different scales. Internal validity of the model was established through the convergence on BRCA2 as a breast cancer hotspot. Further overlaps with breast cancer cell dependencies revealed SUPT6H and RAD21, along with their respective protein systems, HOST:37 and HOST:861, as potential biomarkers. Using gene-level perturbation data of the HOST:37 and HOST:861 gene sets, three FDA-approved drugs with high therapeutic value were selected as potential treatments to be further evaluated. These drugs include mercaptopurine, pioglitazone, and colchicine.
Conclusion
The proposed graph neural network approach to analyzing breast cancer protein communities in a hierarchical structure provides a novel perspective on breast cancer prognosis and treatment. By targeting entire gene sets, we were able to evaluate the prognostic and therapeutic value of genes (or gene sets) at different levels, from gene-level to system-level biology. Cancer-specific gene dependencies provide additional context for pinpointing cancer-related systems and drug-induced alterations can highlight potential therapeutic targets. These identified protein communities, in conjunction with other protein communities under strong mutation and survival burdens, can potentially be used as clinical biomarkers for breast cancer.
The Arctic environment plays a critical role in the global climate system and marine biodiversity. The region's ice‐covered expanses provide essential breeding and feeding grounds for a diverse assemblage of marine species, who have adapted to thrive in these harsh conditions and consequently are under threat from global warming. The bearded seal ( Erignathus barbatus ), including two subspecies ( E. barbatus nauticus — Pacific and E. barbatus barbatus —Atlantic), is an ice‐obligate Arctic species using sea ice for many aspects of its life history, rendering it particularly vulnerable to sea ice loss. It is one of the least studied and hence enigmatic of the Arctic marine mammals, with little knowledge regarding genetic structure, diversity, adaptations, and demographic history, consequently hampering management and conservation efforts. Here, we sequenced 70 whole nuclear genomes from across most of the species' circumpolar range, finding significant genetic structure between the Pacific and the Atlantic subspecies, which diverged during the Penultimate Glacial Period (~200 KYA). Remarkably, we found fine‐scale genetic structure within both subspecies, with at least two distinct populations in the Pacific and three in the Atlantic. We hypothesise sea‐ice dynamics and bathymetry had a prominent role in shaping bearded seal genetic structure and diversity. Our analyses of highly differentiated genomic regions can be used to complement the health, physiological, and behavioural research needed to conserve this species. In addition, we provide recommendations for management units that can be used to more specifically assess climatic and anthropogenic impacts on bearded seal populations.
Biophysical studies in the last two decades have clearly demonstrated that salts affect biomolecules in an ion‐specific manner (i. e., Hofmeister Effects). Studies performed upon such diverse biological processes such as protein folding, protein precipitation, protein coacervation and phase separation, and protein oligomerization, have all shown that this ion specificity is directly related to how individual ions interact with biomolecular surfaces. Interestingly, although ion‐specific effects upon enzyme catalytic processes are well‐known in the literature, a molecular level description of these effects has not yet been made available. For example, it is not clear whether ion‐specific effects observed in enzyme catalysis are directly related to how ions modulate the enzyme's folding free energy, or not. This work attempts to address this need by investigating ion‐specific effects upon the enzymatic activity and folding free energy of a well‐characterized enzyme system, Ribonuclease A (RNase A). To this end we have developed a robust framework to analyze and quantify ion‐specific effects upon the RNase A catalyzed phosphate ring opening reaction of cCMP (Cytidine 2′:3′‐cyclic monophosphate monosodium salt). Our studies show that both the folding thermodynamics and the Michaelis‐Menten kinetic parameters of this enzyme show ion‐specific salt dependence. However, even through salt addition affects the folding free energy and enzyme catalysis of RNase A in an ion‐specific manner, these effects are not necessarily directly related to each other. Ion‐specific effects observed in protein folding reflects mostly how an individual ion interacts with the overall protein surface; while alternatively, ion‐specific effects on enzyme activity indicate how a given ion interacts with the enzyme active site surface or alternatively, how ions interact with the substrate molecule as represented by changes in the substrate thermodynamic activity coefficient.
Objectives
Physical activity (PA) provides protective effects against cardiovascular diseases, including ischaemic heart disease. However, recommending moderate to vigorous PA (MVPA) to patients with recent acute coronary syndrome (ACS) raises concerns owing to potential risk of recurrent ACS or fatal arrhythmias. This study investigated the association between longitudinal PA changes following an ACS diagnosis and subsequent cardiovascular outcomes, including non-fatal coronary events, non-fatal stroke and cardiovascular mortality.
Methods
This longitudinal cohort study used Korean National Health Insurance Service data from 2010 to 2017, comprising 30 840 patients diagnosed with ACS following invasive coronary angiography or bypass surgery. Leisure-time PA was self-reported, with the frequency and intensity measured weekly. The primary endpoint was a composite of nonfatal coronary events, non-fatal stroke and cardiovascular mortality. Multivariable Cox proportional hazards regression models assessed the association between PA changes and cardiovascular outcomes.
Results
Among patients with ACS (mean age: 60±11 years, men: 81.3%), mean PA levels increased from 544±556 metabolic equivalent task (MET)-min/week to 594±567 MET-min/week. Over 6.7 years of median follow-up, 5639 cardiovascular events occurred. Increased PA was associated with lower cardiovascular event risk (HR 0.95, 95% CI 0.92 to 0.98). Consistent MVPA pre-ACS and post-ACS reduced cardiovascular event risk (HR 0.87, 95% CI 0.79 to 0.96) and MVPA initiation showed a modest risk reduction (HR: 0.91, MET-min/95% CI 0.82 to 1.01).
Conclusions
Longitudinal increases in self-reported PA, maintenance of MVPA and possibly MVPA initiation after ACS reduced the risk of cardiovascular events. Initiating or maintaining MVPA could be an important strategy in improving cardiovascular outcomes following ACS.
Phosphorus (P) loss from soils can contribute significantly toward P enrichment in water bodies, impairing water quality. Application of soil amendments is a viable strategy to decrease soluble P in surface soils. Since soluble P is reduced through different mechanisms that are amendment‐specific, blended amendments could be a better approach than single amendment applications; however, very little information is available on blended amendment effects in reducing P loss from soils. We compared the effectiveness of gypsum (CaSO4·2H2O), Epsom salt (MgSO4·7H2O), and alum [Al2(SO4)3·18H2O] applied singly or blended in different ratios in reducing water‐extractable P (WEP) and Mehlich‐3 P of two soils (0‐ to 15‐cm depth) with contrasting P status (Mehlich‐3 P of 7.1 mg kg⁻¹ and 202 mg kg⁻¹) from the Red River Valley region in MB, Canada. Ten treatments used for the laboratory incubation study were unamended control, gypsum or Epsom salt at 2.5 or 5 Mg ha⁻¹, alum at 2.5 Mg ha⁻¹, and four blended treatments of gypsum: alum or Epsom salt: alum at 1:1 or 2:1. Treated soils were saturated and incubated for 2 weeks and analyzed for WEP (an indicator of risk of P loss) and Mehlich‐3 P (plant‐available P) concentrations. All amendments significantly reduced the WEP concentrations compared to control in both soils. The blended amendments, particularly gypsum–alum blends, performed better than unblended amendments in reducing the potential risk of P loss. Mehlich‐3 P concentration was not influenced by amended treatments, suggesting no significant decrease in plant‐available P with amendments in both soils.
Introduction
Modern surgery incorporates many aspects of care, including preoperative workup, surgical management and multidisciplinary collaboration to achieve favourable outcomes and high patient satisfaction. Current literature identifies variability in surgical practice and quality of care. The objective of this study is to fill the gap in the literature by identifying modifiable surgeon behavioural factors influencing the quality of care and to identify interventions and policies that modify these factors.
Methods and analysis
This scoping review will be reported using Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for scoping review guidelines. The protocol was drafted according to JBI Best Practice Guidance and Reporting Items for the Development of Scoping Review Protocols. A comprehensive search encompassing five databases (OVID Medline, OVID EMBASE, Cochrane Library (Central) and SCOPUS) was conducted. Search terms included ‘surgeons’, ‘surgeon characteristics’, ‘quality of care’ and ‘outcomes’ using AND, OR and ADJ2 Boolean operators. Studies describing interventions aimed at modifying behavioural surgeon factors influencing the quality of healthcare will be included. Studies describing institutional or system factors will be excluded. Searches were limited from 1 January 2000 to 1 January 2024 to capture modern surgery practices. Searches were peer reviewed as per Peer Review of Electronic Search Strategies 2015. Two independent reviewers will perform a title and abstract screening using DistillerSR and extract data on the participants, study methods, modifiable surgeon factors and interventions that modify these factors. The data will be qualitatively analysed using the COM-B Framework which describes how capability, motivation and opportunity constitute behaviour. We expect to compile a list of existing interventions aimed at modifying surgeon behaviours, analysing the success of existing interventions to improve patient outcomes and identifying modifiable surgeon factors that do not have interventions.
Ethics and dissemination
Ethics approval and patient consent are not required. The results will be submitted to a peer-reviewed journal for publication.
Background and Objectives
Ancient grains like einkorn, emmer, and spelt remain underutilized and underexplored, limiting their market potential. This study evaluates the chemical composition, rheology, pasting, and baking properties of spring growth habit einkorn, emmer, and spelt cultivars grown in the Canadian prairies compared to wholemeal and refined hexaploid wheat.
Findings
Einkorn cultivars (CDC Aixe and CDC Marval) had inferior dough mixing properties and the lowest bread loaf volume. CDC Tatra (emmer) bread had a significantly ( p < .05) higher specific volume (3.32 mL/g) than Canada Western Red Spring (CWRS) wholemeal bread.
Conclusions
Results from mixing and baking indicate that emmer and spelt cultivars have the potential to be used in breadmaking applications, while einkorn cultivars with suboptimal properties need ingredient technology and process modifications to improve their functionalities.
Significance and Novelty
The study was able to identify and characterize an emmer cultivar (CDC Tatra) with excellent mixing and baking properties having the potential as a standalone flour for baking applications. This represents a significant advancement, as prior research had not recognized any emmer cultivars for their suitability in baking. Our results highlight that cultivar‐based assessment is essential in evaluating the end‐use quality of ancient grain species, thereby developing products using such underutilized grains.
Aim
To investigate additional factors contributing to the pathophysiology of chemotherapy‐induced oral mucositis and periodontitis beyond the systemic immune suppression caused by the chemotherapeutic agent 5‐Fluorouracil (5‐FU).
Methods
5‐Fluorouracil was topically delivered to the non‐keratinized, rapidly proliferating junctional epithelium (JE) surrounding the dentition, and acts as an immunologic and functional barrier to bacterial ingression. Various techniques, including EdU incorporation, quantitative immunohistochemistry (qIHC), histology, enzymatic activity assays, and micro‐computed tomographic (μCT) imaging, were employed to analyze the JE at multiple time points following topical 5‐FU treatment. Systemic 5‐FU delivery was used for comparison, and all 5‐FU treated tissues were compared to vehicle‐treated controls.
Results
We first showed that systemic 5‐FU blocked mitotic activity that rapidly led to JE atrophy. This atrophy was accompanied by suppression of the immune system. We then demonstrated that topical 5‐FU delivery effectively inhibited cell proliferation in the JE. Quantitative immunohistochemical (qIHC) analyses further demonstrated a progressive breakdown in JE barrier functions following topical 5‐FU. CBC analyses confirmed that topical 5‐FU did not alter the innate immune system but did suppress the local immune response of the JE. The longer‐term consequences of this disruption in JE barrier functions were significant alveolar bone loss and an increase in porosity. Together, these results document the essential requirement for rapid JE cell proliferation to maintain homeostasis of the periodontium.
Conclusions
The reduction of cell division in the JE due to 5‐FU treatment directly compromises both its structural integrity and immune surveillance capabilities, contributing to the destruction of periodontal hard tissues.
Extensive efforts by both government and private sectors to make the use of recycled packaging in food products more prevalent have not always been successful, partly due to a limited understanding of consumers' complex perceptions towards this practice. In this research, we explore whether recycled food product packaging enhances the appeal of food products, as well as the boundary condition and underlying mechanism of this effect. Using three experimental studies, we find that marketing efforts highlighting the use of recycled packaging can be beneficial, but only for utilitarian food products, not for hedonic ones. We also identify the warm‐glow effect as a key mediating mechanism. This study uniquely contributes to the literature by not only examining the differential effects of recycled packaging but also identifying the warm‐glow effect as a key mediating mechanism. Our findings contribute a more nuanced perspective to the literature on sustainable consumption and provide practical implications for enhancing the effectiveness of recycled food product packaging.
Institution pages aggregate content on ResearchGate related to an institution. The members listed on this page have self-identified as being affiliated with this institution. Publications listed on this page were identified by our algorithms as relating to this institution. This page was not created or approved by the institution. If you represent an institution and have questions about these pages or wish to report inaccurate content, you can contact us here.
Information