SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.

The incorporation of sequencing technologies in frontline and public health healthcare settings was vital in developing virus surveillance programs during the Coronavirus Disease 2019 (COVID-19) pandemic caused by transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, increased data acquisition poses challenges for both rapid and accurate analyses. To overcome these hurdles, we developed the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) for quick bulk analyses of Illumina short-read sequencing data.

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial TFs-DNA interactions remains an intricate challenge. A deeper understanding of DNA secondary structures could greatly enhance our knowledge of how TFs recognize and interact with DNA, thereby elucidating their biological function.

Comparison of nociceptor properties using electrophysiology in preclinical models of osteoarthritis.

Osteoarthritis (OA) pain originates in the joint by sensitization of articular nociceptors. While behavioural assessments provide valuable information regarding pain symptoms, the techniques are subjective and open to interpretation by the experimenter. This study used in vivo electrophysiological approaches to measure objectively joint nociceptor properties in three rodent models of OA.

Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression.

Temporal RNA-sequencing (RNA-seq) studies of bulk samples provide an opportunity for improved understanding of gene regulation during dynamic phenomena such as development, tumor progression or response to an incremental dose of a pharmacotherapeutic. Moreover, single-cell RNA-seq (scRNA-seq) data implicitly exhibit temporal characteristics because gene expression values recapitulate dynamic processes such as cellular transitions. Unfortunately, temporal RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are often difficult to interpret.

Resection of colorectal carcinoma liver metastases: A population-based study in outcomes and factors associated with recurrent disease.

Objective: To assess the hepatic disease-free survival (HDFS) and overall survival (OS) of patients who underwent resection of colorectal cancer liver metastases (CRCLM) in our population, and evaluate what factors are associated with these outcomes.

Methods: Patients with resected non-mucinous CRCLM between January 2013-February 2020 were retrospectively identified. Dates of diagnosis, surgery, and, if applicable, death were recorded.

Ketotifen directly modifies the fibrotic response of human skin fibroblasts.

Fibrosis is a destructive, end-stage disease process. In the skin, it is associated with systemic sclerosis and scarring with considerable health burden. Ketotifen is a clinical antihistamine and mast cell stabilizer.

Trends in socioeconomic inequalities in breast cancer mortality in Canada: 1992-2019.

Purpose: Breast cancer is the second leading cause of death from cancer among Canadian females. This study aimed to quantify and assess trends in education and income inequalities in the mortality rate of breast cancer in Canada from 1992 to 2019.

Methods: We constructed a census division-level dataset pooled from the Canadian Vital Death Statistics Database (CVSD), the Canadian Census of the Population (CCP), and the National Household Survey (NHS) to examine trends in education and income inequalities in the mortality rate of breast cancer in Canada over the study period.

Early change in fatigue, insomnia, and cognitive impairment and symptom severity 3 years post-treatment in breast cancer survivors.

Purpose: Breast cancer is the most common form of cancer among Canadian women. Survivorship challenges include fatigue, sleep disturbance, and cognitive impairment. This study examined (1) symptom trajectory from diagnosis to 3 years; (2) whether symptom change in the first 4 months was associated with prolonged difficulties after 3 years; and (3) which factors were associated with deterioration in symptoms during the first 4 months.

Food environment research in Canada: a rapid review of methodologies and measures deployed between 2010 and 2021.

Numerous research methodologies have been used to examine food environments. Existing reviews synthesizing food environment measures have examined a limited number of domains or settings and none have specifically targeted Canada. This rapid review aimed to 1) map research methodologies and measures that have been used to assess food environments; 2) examine what food environment dimensions and equity related-factors have been assessed; and 3) identify research gaps and priorities to guide future research.

Analgesic potential of voltage gated sodium channel modulators for the management of pain.

Neuronal electrochemical signals involve the flux of sodium ions through voltage-gated sodium channels (Na) located in the neurolemma. Of the nine sodium channel subtypes, Na-1.7, 1.

Methylation analysis by targeted bisulfite sequencing in large for gestational age (LGA) newborns: the LARGAN cohort.

Background: In 1990, David Barker proposed that prenatal nutrition is directly linked to adult cardiovascular disease. Since then, the relationship between adult cardiovascular risk, metabolic syndrome and birth weight has been widely documented. Here, we used the TruSeq Methyl Capture EPIC platform to compare the methylation patterns in cord blood from large for gestational age (LGA) vs adequate for gestational age (AGA) newborns from the LARGAN cohort.

Examining gender differences in adolescent exposure to food and beverage marketing through go-along interviews.

This study explores how adolescents engage with unhealthy food and beverage marketing in online settings, from a gender perspective. Employing an online ethnography approach and using go-along interviews, we explored the experiences of adolescent boys and girls aged 13-17 as they navigated their online experiences with digital food and beverage marketing. Notable themes emerged, including the identification of predatory actions by food companies, the role of protective factors such as family, and the influence of social media influencers in shaping adolescent dietary preferences.

Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities.

We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp.

Assessing the potential for healthier consumer food substitutions in Canada: population-level differences in dietary intakes of whole grains, refined grains, red meats, and legumes.

The potential for healthier consumer food substitutions is an important factor in the study of food environments, dietary choices, and population nutrition promotion. The burden of diet-related non-communicable diseases is unevenly distributed across Canada and variation in the food environment sub-nationally may be an important explanation. We used population-based 24 h dietary recall data from the 2015 Canadian Community Health Survey-Nutrition for Canadian adults ( = 13 919) to examine dietary intakes of two food group pairings (whole grains/refined grains and legumes/red meats) where consumer substitutions have been recognized to be of importance in promoting healthy and sustainable population diet.

Intravitreal injection of FGF and TGF-β inhibitors disrupts cranial cartilage development.

Cartilage development is a tightly regulated process that requires the interaction of epithelial and mesenchymal tissues layers to initiate the aggregation of mesenchyme in a condensation. Several signaling molecules have been implicated in cartilage formation including FGFs, WNTs, and members of the TGF-β super family. However, little is known about the earliest signals involved in these initial phases of development.

Effect of a relative pricing intervention and active merchandising on snack purchases: interrupted time series analysis of a hospital retailer-led strategy.

Background: Pricing policies have been shown to be an effective lever for promoting healthier dietary choices in consumer food environments. It is not yet well understood how pricing can be used to encourage healthier substitute purchases. The aim of the study was to assess the effect of a retailer-led relative pricing intervention on weekly purchases of targeted snack foods and beverages.

Parallel Dysregulated Immune Response in Severe Forms of COVID-19 and Bacterial Sepsis via Single-Cell Transcriptome Sequencing.

Critically ill COVID-19 patients start developing single respiratory organ failure that often evolves into multiorgan failure. Understanding the immune mechanisms in severe forms of an infectious disease (either critical COVID-19 or bacterial septic shock) would help to achieve a better understanding of the patient's clinical trajectories and the success of potential therapies. We hypothesized that a dysregulated immune response manifested by the abnormal activation of innate and adaptive immunity might be present depending on the severity of the clinical presentation in both COVID-19 and bacterial sepsis.

Sex-based analysis of treatment responses in animal models of sepsis: a preclinical systematic review protocol.

Background: The importance of investigating sex- and gender-dependent differences has been recently emphasized by major funding agencies. Notably, the influence of biological sex on clinical outcomes in sepsis is unclear, and observational studies suffer from the effect of confounding factors. The controlled experimental environment afforded by preclinical studies allows for clarification and mechanistic evaluation of sex-dependent differences.

Observational study of population level disparities in food costs in 2021 in Canada: A digital national nutritious food basket (dNNFB).

The aim of this work was to assess the feasibility and effect of applying a nationally representative and highly disaggregated food costing measure across Canada, through the novel application of web-scraping technology to the methods of the National Nutritious Food Basket (NNFB). Further, this study tested the hypothesis that a product-matched digital NNFB (dNNFB) correlates with existing market basket measures and quantified any differences in costs. This was an observational cross-sectional study using web scraped food price data collected in November 2021.

A secondary mixed methods analysis examining midwives' responses regarding patient sexual orientation and gender identity (SOGI) disclosure.

Objective: Recent research suggests that midwives generally have positive attitudes towards sexual and gender minority (SGM) clients; however, little research has examined whether and how these attitudes translate into specific clinical practices. In this study, we performed a secondary mixed methods analysis to examine midwives' beliefs and practices regarding the importance of asking and knowing their patients' sexual orientation and gender identity (SOGI).

Methods: A confidential, anonymous paper survey was mailed to all midwifery practice groups (n = 131) in Ontario, Canada.

Implementation of a food retail intervention to reduce purchase of unhealthy food and beverages in remote Australia: mixed-method evaluation using the consolidated framework for implementation research.

Background: Adoption of health-enabling food retail interventions in food retail will require effective implementation strategies. To inform this, we applied an implementation framework to a novel real-world food retail intervention, the Healthy Stores 2020 strategy, to identify factors salient to intervention implementation from the perspective of the food retailer.

Methods: A convergent mixed-method design was used and data were interpreted using the Consolidated Framework for Implementation Research (CFIR).

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution.

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of and one strain of ) and generated chromosome-scale assemblies for all strains of the emerging model system .

Reactivity and mechanism in chemical and synthetic biology.

Physical organic chemistry and mechanistic thinking provide a strong intellectual framework for understanding the chemical logic of evolvable informational macromolecules and metabolic transformations in living organisms. These concepts have also led to numerous successes in designing and applying tools to delineate biological function in health and disease, chemical ecology and possible alternative chemistries employed by extraterrestrial life. A symposium at the 2020 Pacifichem meeting was scheduled in December 2020 to discuss designing and exploiting expanded genetic alphabets, methods to understand the biosynthesis of natural products and re-engineering primary metabolism in bacteria.