Data Resource Profile: COVerAGE-DB : a global demographic database of COVID-19 cases and deaths

AvR, JS, and MRN received funding from European Research Council Starting Grant #716323. EA received funding from Social Sciences and Humanities Research Council (Canada) - Postdoctoral grant #756-2019-0768. STL received funding from European Research Council - Starting Grant #864616. FU received funding from the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health #P2CHD047879. RS received funding from Fonds de recherche du Quebec – Societe et culture #2019-B2Z-257115. CL received funding from European Research Council - Starting Grant #834103.Publisher PDFPeer reviewe

Mechanism of faster NO scavenging by older stored red blood cells

The blood storage lesion involves morphological and biochemical changes of red blood cells (RBCs) that occur during storage. These include conversion of the biconcave disc morphology to a spherical one, decreased mean corpuscular hemoglobin concentration, varied mean corpuscular volume, reduced integrity of the erythrocyte membrane with formation of microparticles, and increased cell-free hemoglobin. We studied the extent that older stored red blood cells scavenge nitric oxide (NO) faster than fresher stored red blood cells. Using electron paramagnetic resonance spectroscopy and stopped-flow absorption spectroscopy to measure the rate of NO uptake and reaction with hemoglobin in red cells, we found that older stored red blood cells scavenge NO about 1.8 times faster than fresher ones. Based on these experimental data, we simulated NO scavenging by fresher or older stored red blood cells with a biconcave or spherical geometry, respectively, in order to explore the mechanism of NO scavenging related to changes that occur during blood storage. We found that red blood cells with a spherical geometry scavenges NO about 2 times slower than ones with a biconcave geometry, and a smaller RBC hemoglobin concentration or volume increases NO scavenging by red blood cells. Our simulations demonstrate that even the most extreme possible changes in mean corpuscular hemoglobin concentration and mean corpuscular volume that favor increased NO scavenging are insufficient to account for what is observed experimentally. Therefore, RBC membrane permeability must increase during storage and we find that the permeability is likely to increase between 5 and 70 fold. Simulations using a two-dimensional blood vessel show that even a 5-fold increase in membrane permeability to NO can reduce NO bioavailability at the smooth muscle. Background: Transfusion of older stored blood may be harmful. Results: Older stored red blood cells scavenge nitric oxide more than fresher cells. Conclusion: As stored red blood cells age, structural and biochemical changes occur that lead to faster scavenging. Significance: Increased nitric oxide scavenging by red blood cells as a function of storage age contributes to deleterious effects upon transfusion. © 2014 The Authors

Role of mitochondrial uncoupling protein-4 in energy supply during neuronal differentiation

OBJECTIVES: Neuronal differentiation is involved in brain development. Stimulation of all-trans-retinoic acid (RA) in neuroblastoma cells results in growth inhibition, increased neuron-specific enolase (NSE) activity, and promoted axonal growth. Mitochondrial uncoupling protein-4 (UCP4) is ...published_or_final_versionThe 16th Medical Research Conference (MRC), Department of Medicine, the University of Hong Kong, Hong Kong, 22 January 2011. In Hong Kong Medical Journal, 2011, v. 17 suppl. 1, p. 31, abstract no. 4

Quick and sensitive determination of gene expression of fatty acid synthase in vitro by using real-time polymerase chain reaction amplification (PCR)

Obesity results from an imbalance between energy intake and energy expenditure, which leads to a pathological accumulation of adipose tissue, but the underlying mechanism at gene level, is far from being elucidated. The objective of this study was to investigate the correlation between mRNA express from fatty acid synthase (FAS) with a different glucose level in primary adipocytes by real-time polymerase chain reaction amplification (PCR), which can aid in the understanding of the mechanism of obesity in vitro. By using the following formula, this study was able to quantify the mRNA expression of FAS of unknown samples: Y = -3.156X + 41.21 (Y = threshold cycle, X = log starting quantity). The high concentrations of glucose group significantly improved the mRNA expression of FAS (P < 0.01) rather than 0.25 and 0% concentrations of glucose. These results provide significant data that confirm an association between different glucose level and FAS expression in preadipocytes. The glucose concentration of the high group substantially augmented the mRNA expression of FAS.Key words: Expression, fatty acid synthase, lipid deposition, real-time polymerase chain reaction amplification (PCR)

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

Gene panel and exome sequencing have revealed a high rate of molecular diagnoses among diseases where the genetic architecture has proven suitable for sequencing approaches, with a large number of distinct and highly penetrant causal variants identified among a growing list of disease genes. The challenge is, given the DNA sequence of a new patient, to distinguish disease-causing from benign variants. Large samples of human standing variation data highlight regional variation in the tolerance to missense variation within the protein-coding sequence of genes. This information is not well captured by existing bioinformatic tools, but is effective in improving variant interpretation. To address this limitation in existing tools, we introduce the missense tolerance ratio (MTR), which summarizes available human standing variation data within genes to encapsulate population level genetic variation. We find that patient-ascertained pathogenic variants preferentially cluster in low MTR regions (P < 0.005) of well-informed genes. By evaluating 20 publicly available predictive tools across genes linked to epilepsy, we also highlight the importance of understanding the empirical null distribution of existing prediction tools, as these vary across genes. Subsequently integrating the MTR with the empirically selected bioinformatic tools in a gene-specific approach demonstrates a clear improvement in the ability to predict pathogenic missense variants from background missense variation in disease genes. Among an independent test sample of case and control missense variants, case variants (0.83 median score) consistently achieve higher pathogenicity prediction probabilities than control variants (0.02 median score; Mann-Whitney U test, P < 1 × 10(-16)). We focus on the application to epilepsy genes; however, the framework is applicable to disease genes beyond epilepsy

Assessment of Cellular Estrogenic Activity Based on Estrogen Receptor-Mediated Reduction of Soluble-Form Catechol-O-Methyltransferase (COMT) Expression in an ELISA-Based System

published_or_final_versio

Mitochondrial neuronal uncoupling proteins: a target for potential disease-modification in Parkinson's disease

This review gives a brief insight into the role of mitochondrial dysfunction and oxidative stress in the converging pathogenic processes involved in Parkinson's disease (PD). Mitochondria provide cellular energy in the form of ATP via oxidative phosphorylation, but as an integral part of this process, superoxides and other reactive oxygen species are also produced. Excessive free radical production contributes to oxidative stress. Cells have evolved to handle such stress via various endogenous anti-oxidant proteins. One such family of proteins is the mitochondrial uncoupling proteins (UCPs), which are anion carriers located in the mitochondrial inner membrane. There are five known homologues (UCP1 to 5), of which UCP4 and 5 are predominantly expressed in neural cells. In a series of previous publications, we have shown how these neuronal UCPs respond to 1-methyl-4-phenylpyridinium (MPP+; toxic metabolite of MPTP) and dopamine-induced toxicity to alleviate neuronal cell death by preserving ATP levels and mitochondrial membrane potential, and reducing oxidative stress. We also showed how their expression can be influenced by nuclear factor kappa-B (NF-kappaB) signaling pathway specifically in UCP4. Furthermore, we previously reported an interesting link between PD and metabolic processes through the protective effects of leptin (hormone produced by adipocytes) acting via UCP2 against MPP+-induced toxicity. There is increasing evidence that these endogenous neuronal UCPs can play a vital role to protect neurons against various pathogenic stresses including those associated with PD. Their expression, which can be induced, may well be a potential therapeutic target for various drugs to alleviate the harmful effects of pathogenic processes in PD and hence modify the progression of this disease.published_or_final_versio

A framework for automatic semantic video annotation

The rapidly increasing quantity of publicly available videos has driven research into developing automatic tools for indexing, rating, searching and retrieval. Textual semantic representations, such as tagging, labelling and annotation, are often important factors in the process of indexing any video, because of their user-friendly way of representing the semantics appropriate for search and retrieval. Ideally, this annotation should be inspired by the human cognitive way of perceiving and of describing videos. The difference between the low-level visual contents and the corresponding human perception is referred to as the ‘semantic gap’. Tackling this gap is even harder in the case of unconstrained videos, mainly due to the lack of any previous information about the analyzed video on the one hand, and the huge amount of generic knowledge required on the other. This paper introduces a framework for the Automatic Semantic Annotation of unconstrained videos. The proposed framework utilizes two non-domain-specific layers: low-level visual similarity matching, and an annotation analysis that employs commonsense knowledgebases. Commonsense ontology is created by incorporating multiple-structured semantic relationships. Experiments and black-box tests are carried out on standard video databases for action recognition and video information retrieval. White-box tests examine the performance of the individual intermediate layers of the framework, and the evaluation of the results and the statistical analysis show that integrating visual similarity matching with commonsense semantic relationships provides an effective approach to automated video annotation

Combined LRRK2 mutation, aging and chronic low dose oral rotenone as a model of Parkinson’s disease

published_or_final_versio