Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the Genus Betacoronavirus and Its Different Subgenera

The genus Betacoronavirus, consisting of four main subgenera (Embecovirus, Merbecovirus, Nobecovirus, and Sarbecovirus), encompasses all clinically significant coronaviruses (CoVs), including SARS, MERS, and the SARS-CoV-2 virus responsible for current COVID-19 pandemic. Very few molecular characteristics are known that are specific for the genus Betacoronavirus or its different subgenera. In this study, our analyses of the sequences of four essential proteins of CoVs, viz., spike, nucleocapsid, envelope, and RNA-dependent RNA polymerase (RdRp), identified ten novel molecular signatures consisting of conserved signature indels (CSIs) in these proteins which are specific for the genus Betacoronavirus or its subgenera. Of these CSIs, two 14-aa-conserved deletions found within the heptad repeat motifs 1 and 2 of the spike protein are specific for all betacoronaviruses, except for their shared presence in the highly infectious avian coronavirus. Six additional CSIs present in the nucleocapsid protein and one CSI in the RdRp protein are distinctive characteristics of either the Merbecovirus, Nobecovirus, or Sarbecovirus subgenera. In addition, a 4-aa insert is present in the spike protein, which is uniquely shared by all viruses from the subgenera Merbecovirus, Nobecovirus, and Sarbecovirus, but absent in Embecovirus and all other genera of CoVs. This molecular signature provides evidence that viruses from the three subgenera sharing this CSI are more closely related to each other, and they evolved after the divergence of embecoviruses and other CoVs. As all CSIs specific for different groups of CoVs are flanked by conserved regions, their sequences provide novel means for identifying the above groups of CoVs and for developing novel diagnostic tests. Furthermore, our analyses of the structures of the spike and nucleocapsid proteins show that all identified CSIs are localized in the surface-exposed loops of these protein. It is postulated that these surface loops, through their interactions with other cellular proteins/ligands, play important roles in the biology/pathology of these viruses

Impaired Proteostasis in Obese Skeletal Muscle Relates to Altered Immunoproteasome Activity

Obesity-associated inflammation and/or oxidative stress can damage intramuscular proteins and jeopardize muscle integrity. The immunoproteasome (iProt) is vital to remove oxidatively modified proteins, but this function may be compromised with obesity. We sought to elucidate whether diet-induced obesity (DIO) alters intramuscular iProt content and activity in mice to identify a possible mechanism for impaired muscle proteostasis in the obese state. Total proteasome content and activity and estimates of muscle oxidative damage, inflammation, muscle mass and strength were also assessed. Twenty-three male, 5-week-old C57BL/6J mice were fed a high-fat, high-sucrose (HFS, 45% kcal fat, 17% sucrose, n = 12) or low-fat, low-sucrose (LFS, 10% kcal fat, 0% sucrose, n = 11) diet for 12 weeks. Strength was assessed via a weightlifting test. Despite no change in pro-inflammatory cytokines (P > 0.05), oxidative protein damage was elevated within the gastrocnemius (P = 0.036) and tibialis anterior (P = 0.033) muscles of HFS-fed mice. Intramuscular protein damage coincided with reduced iProt and total proteasome activity (PThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Impact of the COVID-19 Pandemic on Non-COVID-19 Clinical Trials

Randomized controlled trials (RCT) were impacted by the COVID-19 pandemic, but no systematic analysis has evaluated the overall impact of COVID-19 on non-COVID-19-related RCTs. The ClinicalTrials.gov database was queried in February 2020. Eligible studies included all randomized trials with a start date after 1 January 2010 and were active during the period from 1 January 2015 to 31 December 2020. The effect of the pandemic period on non-COVID-19 trials was determined by piece-wise regression models using 11 March 2020 as the start of the pandemic and by time series analysis (models fitted using 2015–2018 data and forecasted for 2019–2020). The study endpoints were early trial stoppage, normal trial completion, and trial activation. There were 161,377 non-COVID-19 trials analyzed. The number of active trials increased annually through 2019 but decreased in 2020. According to the piece-wise regression models, trial completion was not affected by the pandemic (p = 0.56) whereas trial stoppage increased (p = 0.001). There was a pronounced decrease in trial activation early during the pandemic (p < 0.001) which then recovered. The findings from the time series models were consistent comparing forecasted and observed results (trial completion p = 0.22; trial stoppage p < 0.01; trial activation, p = 0.01). During the pandemic, there was an increase in non-COVID-19 RCTs stoppage without changes in RCT completion. There was a sharp decline in new RCTs at the beginning of the pandemic, which later recovered

Investigating frontline service provider burnout : working with youth victims and perpetrators of inappropriate sexual behaviours

This research paper was completed and submitted at Nipissing University, and is made freely accessible through the University of Toronto’s TSpace repositoryFrontline service providers (FSP) working with youth victims and perpetrators of inappropriate sexual behaviours (ISB) are working in high stress positions. Researchers have demonstrated FSP experience burnout symptoms related to their work, including emotional and physical exhaustion, depersonalization, and feelings of reduced personal accomplishment. However, very few researchers have compared the experiences of burnout between those working with youth victims and youth perpetrators of ISB. Therefore, this study aims to fill the gap of the existing literature. The proposed study investigates the experiences of burnout within FSP working with youth who are victims and perpetrators of ISB. This detailed literature review includes both qualitative and quantitative research to describe burnout while differentiating burnout from similar work stress conditions, the experiences of burnout of FSP in various occupations including policing, social work and mental health fields, and the challenges associated with researching burnout. Results show confounding definitions of burnout throughout disciplines confusing the research and results. Burnout symptoms have been reported in both FSP working with adult sex offenders and youth perpetrators and victims of ISB. It is seen that the experience of the FSP, age of FSP, environment in which FSP work, and the sex of the FSP have shown to influence particular FSP populations, though it is unclear if this includes those working with youth engaging in ISB. Further investigations are required to identify possible influences of burnout, as well as an overarching and accurate definition of burnout for future study

The Journal or Daily Register of the Voyage from Amsterdam the First Day of March, 1598

The LEME Corpus Manual has an editorial introduction, indexes of subjects, proper names, and chronology, a primary bibliography of LEME corpus texts, as well as English language texts not included in the Corpus, a description of the XML encoding and of lemmatization and source analysis tools. The appendix includes lists of language abbreviations and of abbreviations for parts of speech.Social Sciences and Humanities Research Council of CanadaCanada Foundation for InnovationUniversity of Toronto LibrariesUniversity of Toronto PressInformation & Instructional Technology, Faculty of Arts and Science, University of Toront

Decreasing Trend in Incidence of Late Onset Culture Positive Bloodstream Infections but Not Late Onset Meningitis in Preterm Infants <33 Weeks Gestation in Canadian Neonatal Intensive Care Unit

Introduction: Recent studies reported decreased incidence of late onset sepsis in the neonatal intensive care unit (NICU), but it is unclear whether this is also true for late onset meningitis. Recent reports that both meningitis and intraventricular hemorrhage (IVH) are associated with systemic inflammation also raise questions about an association between the 2. Methods: All preterm infants <33 weeks gestational age admitted to CNN NICUs from 2010 to 2018 were included. We compared incidence trends of late onset culture positive bloodstream infection (CPBSI) and late onset meningitis, and examined the association of meningitis and IVH (exposure), after adjustment for potential confounders. Results: Of 36,573 infants included, 32,198 had no infection, 3,977 had only late onset CPBSI and 398 had late onset meningitis. There was significant decrease in incidence of late onset CPBSI (14%–10%; adjusted odds ratio (AOR) = 0.93; 95% confidence interval [CI] 0.92, 0.95) but not late onset meningitis (1.6%–1.2%; AOR = 0.98; 95% CI 0.94, 1.01). Compared to infants with no IVH grade 3 or above, infants with IVH grade 3, or above had higher odds of late onset meningitis versus no infection (AOR 4.16; 95% CI 3.17, 5.44), and higher odds of late onset meningitis versus late onset CPBSI (AOR 4.11; 95% CI 3.08, 5.50). Conclusions: There was a decreasing trend of late onset CPBSI but not late onset meningitis. An association between late onset meningitis and IVH grade 3 or above was observed. Late onset CPBSI and meningitis may have different risk factors and require different prevention strategiesOrganizational support for the Canadian Neonatal Network was provided by the Maternal-infant Care Research Center (MiCare) at Mount Sinai Hospital in Toronto, ON, Canada. MiCare is supported by the Canadian Institutes of Health Research (CIHR) (CTP 87518), the Ontario Ministry of Health and Long-Term Care, and the participating hospitals. PSS holds an Applied Research Chair in Reproductive and Child Health Services and Policy Research from the CIHR (APR-126340)

How gender shapes interprofessional teamwork in the operating room: a qualitative secondary analysis

Abstract Background Despite substantial implications for healthcare provider practice and patient outcomes, gender has yet to be systematically explored with regard to interprofessional operating room (OR) teamwork. We aimed to explore and describe how gender and additional social identity factors shape experiences and perceptions of teamwork in the OR. Methods This study was a qualitative secondary analysis of semi-structured interviews with OR team members conducted between November 2018 and July 2019. Participants were recruited across hospitals in Ontario, Canada. We conducted both purposive and snowball sampling until data saturation was reached. Transcripts were analyzed thematically by two independent research team members, moving from open to axial coding. Results Sixty-six interviews of OR healthcare professionals were completed: anesthesia (n=17), nursing (n=19), perfusion (n=2), and surgery (n=26). Traditional gender roles, norms, and stereotypes were perceived and experienced by both women and men, but with different consequences. Both women and men participants described challenges that women face in the OR, such as being perceived negatively for displaying leadership behaviours. Participants also reported that interactions and behaviours vary depending on the team gender composition, and that other social identities, such as age and race, often interact with gender. Nevertheless, participants indicated a belief that the influence of gender in the OR may be modified. Conclusions The highly gendered reality of the OR creates an environment conducive to breakdowns in communuication and patient safety risks in addition to diminishing team morale, psychological safety, and provider well-being. Consequently, until teamwork interventions adequately account for gender, they are unlikely to be optimally effective or sustainable

The Effect of Sealer Application Methods on Voids Volume after Aging of Three Calcium Silicate-Based Sealers: A Micro-Computed Tomography Study

During obturation, air voids are undesirable as they may provide shelter for microorganisms or passage for fluids. This study aimed to compare the occurrence of voids between three calcium silicate-based sealers (CSBSs) (MTA-Fillapex, BioRoot-RCS, Bio-C) and the change in their volume after aging. In addition, we aimed to compare voids when using two sealer application methods: lentulo-spiral (LS) and gutta-percha (GP) cone. Thirty extracted mandibular premolars (n = 30) were endodontically prepared and obturated using single GP cone (SGPC) technique. Each sealer was applied to 10 teeth (n = 10) using LS or GP. Micro-computed tomography (micro-CT) was used to quantify the volume of root filling and voids before and after 8-week storage in a phosphate-rich medium. The percentage of root filling and voids were compared between the groups using a Mann&ndash;Whitney U test and Kruskal&ndash;Wallis test with a Bonferroni correction. Before aging, the percentages of root filling volume after obturation were comparable with no significant differences between sealers (p = 0.325) or application methods (p = 0.950). After aging, the voids&rsquo; volume increased significantly in all sealers (p &le; 0.05). However, no significant differences were found between sealers (p = 0.302). In conclusion, voids in CSBSs may not reduce in size with aging; hence, SGPC should be carefully selected for suitable cases

Advancing Microfluidic Tumour-on-a-chip Technologies by Integrating Multicellular Tumour Spheroids and Angiogenic Vessels

Angiogenesis, the development of new blood vessels from existing vasculature, is a key mechanism in cancer progression. Solid tumours that are depleted of nutrients induce angiogenesis to recruit blood vessels for access to nutrients and a pathway for metastasis. Anti-angiogenic therapies have been developed, but toxicities, resistance, and limited efficacy have been reported and there remains a strong need for development of in vitro platforms that can model tumour-induced angiogenesis to conduct fundamental and clinical research. Traditional in vitro assays include 2D cell cultures that do not recapitulate cellular functions that are unique to a 3D geometry and are therefore unsuitable for investigations of complex phenomena such as tumour angiogenesis. Microfluidic technology has emerged as a popular tool for 3D cell cultures such as tumour-on-a-chip models that recapitulate the physiological complexities of a tumour microenvironment. The development of a microfluidic model for tumour-induced angiogenesis would facilitate fundamental research on the underlying cellular mechanisms, and clinical research to develop new drug candidates. To accomplish this, a deeper understanding of the microfluidic cell culture components is needed, along with a device design that is well suited for analysis of tumour-induced angiogenesis. The objective of this thesis was to examine the elements of a microfluidic model of tumour-endothelial interactions and develop a microfluidic cell culture where tumour-induced angiogenesis can be observed and quantified. We first characterized 3D spheroids, revealing correlations between external, internal, and secretory profile characteristics of 3D tumour spheroids as they relate to angiogenic potential. Next, we sought to understand how best to incorporate fibroblasts for their critical role in achieving 3D sprout morphology. We identified the utility of fibroblast configuration for influencing the extent of endothelial response in microfluidic co-culture. Finally, we introduced a new microfluidic device for spheroid-endothelial co-cultures where spheroid-induced sprouting was demonstrated using multiple spheroid types and quantified using image analysis. Overall, these studies have developed insights on the characteristics of 3D tumour spheroids, fibroblasts, and endothelial sprouts that allow these cell culture features to be wielded as biological tools, and demonstrated the utility of microfluidics for complex cell cultures to study tumour angiogenesis and cancer progression.Ph.D

Least Squares Twin Support Vector Machines to Classify End-Point Phosphorus Content in BOF Steelmaking

End-point phosphorus content in steel in a basic oxygen furnace (BOF) acts as an indicator of the quality of manufactured steel. An undesirable amount of phosphorus is removed from the steel by the process of dephosphorization. The degree of phosphorus removal is captured numerically by the &lsquo;partition ratio&rsquo;, given by the ratio of %wt phosphorus in slag and %wt phosphorus in steel. Due to the presence of multitudes of process variables, often, it is challenging to predict the partition ratio based on operating conditions. Herein, a robust data-driven classification technique of least squares twin support vector machines (LSTSVM) is applied to classify the &lsquo;partition ratio&rsquo; to two categories (&lsquo;High&rsquo; and &lsquo;Low&rsquo;) steels indicating a greater or lesser degree of phosphorus removal, respectively. LSTSVM is a simpler, more robust, and faster alternative to the twin support vector machines (TWSVM) with respect to non-parallel hyperplanes-based binary classifications. The relationship between the &lsquo;partition ratio&rsquo; and the chemical composition of slag and tapping temperatures is studied based on approximately 16,000 heats from two BOF plants. In our case, a relatively higher model accuracy is achieved, and LSTSVM performed 1.5&ndash;167 times faster than other applied algorithms