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Systematic review and meta-analysis of the literature describing the effect of preoperative fasting on aspiration

Background To drive translational medicine, modern day biobanks need to integrate with other sources of data (clinical, genomics) to support novel data-intensive research. Currently, vast amounts of research and clinical data remain in silos, held and managed by individual researchers, operating under different standards and governance structures; a framework that impedes sharing and effective use of data. In this article, we describe the journey of British Columbia���s Gynecological Cancer Research Program (OVCARE) in moving a traditional tumour biobank, outcomes unit, and a collection of data silos, into an integrated data commons to support data standardization and resource sharing under collaborative governance, as a means of providing the gynecologic cancer research community in British Columbia access to tissue samples and associated clinical and molecular data from thousands of patients. Results Through several engagements with stakeholders from various research institutions within our research community, we identified priorities and assessed infrastructure needs required to optimize and support data collections, storage and sharing, under three main research domains: (1) biospecimen collections, (2) molecular and genomics data, and (3) clinical data. We further built a governance model and a resource portal to implement protocols and standard operating procedures for seamless collections, management and governance of interoperable data, making genomic, and clinical data available to the broader research community. Conclusions Proper infrastructures for data collection, sharing and governance is a translational research imperative. We have consolidated our data holdings into a data commons, along with standardized operating procedures to meet research and ethics requirements of the gynecologic cancer community in British Columbia. The developed infrastructure brings together, diverse data, computing frameworks, as well as tools and applications for managing, analyzing, and sharing data. Our data commons bridges data access gaps and barriers to precision medicine and approaches for diagnostics, treatment and prevention of gynecological cancers, by providing access to large datasets required for data-intensive science.

Several neurodegenerative diseases involve the accumulation of cellular DNA damage. Comet assays are a popular way of estimating the extent of DNA damage. Current literature on the use of deep learning to quantify DNA damage presents an empirical approach to hyper-parameter optimization and does not include uncertainty estimates. Deep ensemble averaging is a standard approach to estimating uncertainty but it requires several iterations of network training, which makes it time-consuming. Here we present an approach to quantify the extent of DNA damage that combines deep learning with a rigorous and comprehensive method to optimize the hyper-parameters with the help of statistical tests. We also use an architecture that allows for a faster computation of deep ensemble averaging and performs statistical tests applicable to networks using transfer learning. We applied our approach to a comet assay dataset with more than 1300 images and achieved an $R^2$ of 0.84, where the output included the confidence interval for each prediction. The proposed architecture is an improvement over the current approaches since it speeds up the uncertainty estimation by 30X while being statistically more rigorous.

Gauze is an excellent material for infant apparel which can made in various forms and by a variety of methods, and thus have attracted great attention in baby care market. This study aims to identify the wicking property of the gauze fabric in baby care products, and to analyse the relationships between the wicking ability and fabric structure of baby soft gauze products. The experimental results revealed that a significant difference occurred for the gauze in the wicking ability. The cotton gauzes were found to show higher wicking rate than bamboo counterparts because of the higher hydrophilic property of cotton material. The fiber content and structure of fabric were the major parameters that affects the wicking ability.

Additional file 1. Evaluation of identified biobanking library information management systems.

Improved genetic selection for feed efficiency in beef and dairy cattle may improve the Canadian cattle production industry profitability and environmental sustainability. However, the application of RNA-Sequencing (RNA-Seq) analysis in livestock research is novel and the underlying biology and genetic architecture of feed efficiency in cattle is not well studied. The aim of this thesis was to characterize the functional genetic architecture underlying feed efficiency using transcriptomic and metagenomic tools, including RNA-Sequencing (RNA-Seq), and Amplicon-Sequencing (Amplicon-Seq) technologies, to identify functional genetic markers (SNPs and INDELs), novel transcripts, metabolic processes, and potential host-microbiome genetic interactions that are playing a role in the regulation of feed efficiency in cattle. First, an optimized RNA-Seq pipeline for genetic variant detection was developed, and applied to a Nellore beef cattle population to determine functional genetic variants (SNPs and INDELs) associated with feed efficiency. The optimized RNA-Seq pipeline was then applied to a Holstein and Jersey population to identify functional variants and associated functional information (candidate genes, biological pathways, overlapping QTLs) related with feed efficiency. Then de novo assembly was performed to identify novel mRNA isoforms associated with feed efficiency, using rumen epithelium tissue transcriptome data from two pure (Angus and Charolais) and one composite (Kinsella) beef breed. Using the transcriptomic data from the latter study, and Amplicon-sequencing (Amplicon-Seq) data of rumen contents from the same animals, correlations were determined between the host transcriptome and rumen microbiome (archaea and bacteria profiles) which were different between extreme RFI groups. These studies lead to accurate detection of functional genetic variants and associated functional information which may influence the regulation of feed efficiency. Additionally, potential host-microbiome genetic interactions that may be influencing the regulation of feed efficiency were identified. In conclusion, this thesis provides valuable information on the underlying genetic architecture of feed efficiency in both beef and dairy cattle, which may serve to help select genetic markers to improve the selection for superior feed efficient beef and dairy cattle, leading to improved of the efficiency and profitability of the beef and dairy industry, and may serve as important information for future genomic research on feed efficiency. The author acknowledges financial support from the Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA), Ontario Ministry of Research and Innovation, Agriculture and Agri-Food Canada (AAFC) and Genome Canada. This study (FDE.13.17) was also supported by the Sustainable Beef and Forage Science Cluster funded by the Canadian Beef Cattle Check-Off, Beef Cattle Research Council (BCRC), Alberta Beef Producers, Alberta Cattle Feeders’ Association, Beef Farmers of Ontario, La Fédération des Productuers de bovins du Québec, and Agriculture and Agri-Food Canada’s Canadian Agricultural Partnership. 2020-08-31

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International audience

International audience

Rumen functional and structural parameters and their associations with feed efficiency were evaluated. Forty-eight crossbred feedlot cattle were assessed for feed efficiency using residual feed intake (RFI) adjusted for body ultrasound measurements. Rumen fluid and tissue samples were evaluated for microbial and VFA profiles, papillae histomorphometry, and rumen pH (RpH) and temperature (RT) and compared between efficient and inefficient cattle. Additionally, microbial and VFA profiles were compared on-farm and at slaughter. Efficient cattle have greater bacteria (P=0.04), lower methanogen concentrations (P=0.04), differences in multiple VFA (P

International audience; Fatty acids are surfactants of particular interest since they can be extracted from agricultural resources. We report the formation of foams that are responsive to multiple external stimuli (light and temperature) obtained from solution of 12-hydroxy stearic acid (12-HSA), which is self-organized in micron scale tubes [Fameau, 2011]. We have previously demonstrated that solutions containing 12-HSA tubes produced foams which were outstandingly stable for months at room temperature conditions (Figure 1.a). The tube suspension combines the advantages of both solid large anisotropic particles and low molecular weight surfactants, since this system foams easily but does not age because of an optimal arrangement of monomers and tubes within the foam structure. Upon heating, tubes re-assemble into micelles at a given temperature, which results in rapid foam destabilization. The foam stability can then be reversibly tuned from high to weak by simply changing the polymorphism of the system by temperature (Figure 1.b). In a further step, we combined these thermoresponsive 12-HSA tubes with carbon black particles, which resulted in foams whose stability could easily be tuned by UV irradiation [Fameau, 2013]. Upon exposure to UV illumination, particles absorb light radiation and act as photothermal heat converters resulting in a temperature increase inside the foam liquid channels. This results in the transition of tubes into micelles in the foam, leading to a very fast foam destabilization (Figure 1.c). The above approach was extended to magnetic particles, producing the first foam exhibiting thermo-photo-magneto-tuneable responsiveness. Our approach based on green surfactants mixed with various particles, successfully provides excellent foamability and results in foams which stability can be reversibly switch between ultrastability and instability by light, temperature and magnetic field.

Fatty acids are surfactants of particular interest since they can be extracted from agricultural resources [1]. We report the formation of foams that are responsive to multiple external stimuli (light and temperature) obtained from solution of 12-hydroxy stearic acid (12-HSA), which is self-organized in micron scale tubes [2]. We have previously demonstrated that solutions containing 12-HSA tubes produced foams which were outstandingly stable for months at room temperature conditions (Figure 1.a). We used confocal microscopy, small angle neutron scattering and neutron reflectivity in order to understand the key mechanisms behind the stability of these foams. The tube suspension combines the advantages of both solid large anisotropic particles and low molecular weight surfactants, since this system foams easily but does not age because of an optimal arrangement of monomers and tubes within the foam structure [3]. Upon heating, tubes re-assemble into micelles at a given temperature, which results in rapid foam destabilization. The foam stability can then be reversibly tuned from high to weak by simply changing the polymorphism of the system by temperature (Figure 1.b). In a further step, we combined these thermoresponsive 12-HSA tubes with carbon black particles, which resulted in foams whose stability could easily be tuned by UV irradiation [4]. Upon exposure to UV illumination, particles absorb light radiation and act as photothermal heat converters resulting in a temperature increase inside the foam liquid channels. This results in the transition of tubes into micelles in the foam, leading to a very fast foam destabilization (Figure 1.c). The above approach was extended to magnetic particles, producing the first foam exhibiting thermo-photo-magneto-tuneable responsiveness. Thus, our approach based on green surfactants mixed with various particles, successfully provides excellent foamability and results in foams which stability can be reversibly switch between ultrastability and instability by light, temperature and magnetic field.

The cytosol-facing membranes of cellular organelles contain proteins that enable signal transduction, regulation of morphology and trafficking, protein import and export, and other specialized processes. Discovery of these proteins by traditional biochemical fractionation can be plagued with contaminants and loss of key components. Using peroxidase-mediated proximity biotinylation, we captured and identified endogenous proteins on the outer mitochondrial membrane (OMM) and endoplasmic reticulum membrane (ERM) of living human fibroblasts. The proteomes of 137 and 634 proteins, respectively, are highly specific and highlight 94 potentially novel mitochondrial or ER proteins. Dataset intersection identified protein candidates potentially localized to mitochondria-ER contact sites. We found that one candidate, the tail-anchored, PDZ-domain-containing OMM protein SYNJ2BP, dramatically increases mitochondrial contacts with rough ER when overexpressed. Immunoprecipitation-mass spectrometry identified ribosome-binding protein 1 (RRBP1) as SYNJ2BP’s ERM binding partner. Our results highlight the power of proximity biotinylation to yield insights into the molecular composition and function of intracellular membranes., United States. National Institutes of Health (R01 CA186568), United States. National Institutes of Health (R01 GM077465)

Neurexin and neuroligin are transmembrane adhesion proteins that play an important role in organizing the neuronal synaptic cleft. Our lab previously reported a method for imaging the trans-synaptic binding of neurexin and neuroligin called BLINC (Biotin Labeling of INtercellular Contacts). In BLINC, biotin ligase (BirA) is fused to one protein while its 15-amino acid acceptor peptide substrate (AP) is fused to the binding partner. When the two fusion proteins interact across cellular junctions, BirA catalyzes the site-specific biotinylation of AP, which can be read out by staining with streptavidin-fluorophore conjugates. Here, we report that BLINC in neurons cannot be reproduced using the reporter constructs and labeling protocol previously described. We uncover the technical reasons for the lack of reproducibilty and then re-design the BLINC reporters and labeling protocol to achieve neurexin-neuroligin BLINC imaging in neuron cultures. In addition, we introduce a new method, based on lipoic acid ligase instead of biotin ligase, to image trans-cellular neurexin-neuroligin interactions in human embryonic kidney cells and in neuron cultures. This method, called ID-PRIME for Interaction-Dependent PRobe Incorporation Mediated by Enzymes, is more robust than BLINC due to higher surface expression of lipoic acid ligase fusion constructs, gives stronger and more localized labeling, and is more versatile than BLINC in terms of signal readout. ID-PRIME expands the toolkit of methods available to study trans-cellular protein-protein interactions in living systems., National Institutes of Health (U.S.) (DP1 OD003961)