Biocor

The study aims to explore the active molecules of traditional Chinese medicine that specifically bind to interleukin-15 receptor α (IL-15Rα) using molecular docking and surface plasmon resonance (SPR) technology. AutoDock molecular docking software was used to perform simulated docking of more than 3 000 compounds from 48 traditional Chinese medicines at IL-15Rα and screen the specific binding compounds. Then Biocore T200 biomolecular interaction analysis system of SPR was used to confirm the binding specificity of the selected target compounds...

As an essential component of the sarcomere, actin thin filament stems from the Z-disk extend toward the middle of the sarcomere and overlaps with myosin thick filaments. Elongation of the cardiac thin filament is essential for normal sarcomere maturation and heart function. This process is regulated by the actin-binding proteins Leiomodins (LMODs), among which LMOD2 has recently been identified as a key regulator of thin filament elongation to reach a mature length. Few reports have implicated homozygous loss of function variants of LMOD2 in neonatal dilated cardiomyopathy (DCM) associated with thin filament shortening...

Excessive osteoclast activation, which depends on dramatic changes in actin dynamics, causes osteoporosis (OP). The molecular mechanism of osteoclast activation in OP related to type 1 diabetes (T1D) remains unclear. Glia maturation factor beta (GMFB) is considered a growth and differentiation factor for both glia and neurons. Here, we demonstrated that Gmfb deficiency effectively ameliorated the phenotype of T1D-OP in rats by inhibiting osteoclast hyperactivity. In vitro assays showed that GMFB participated in osteoclast activation rather than proliferation...

One of the main issues of the peculiarities of the immune reactions of the gastrointestinal tract is the mechanisms of ensuring tolerance to food antigens. Concentrations of antibodies to food antigens actually reflect the state of the intestinal mucosa barrier function, and the degree of penetration of antigens into the blood determines the level of immune response to them. The aim of the study was to determine the risk criteria for violation of tolerance to food antigens. Material and methods . The study included the results of a survey and examination of 1334 adults living in the north of the European part of the Russian Federation, including 1100 born in the North, of which 970 were women and 364 were men...

Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web of Life (WoL) reference database hosting 10,575 reference genomes and growing, the percentage of ambiguous reads will only increase. The resulting artifacts create both the illusion of co-occurrence and a long tail end of extraneous reference hits that confound interpretation. We introduce genome cover, the fraction of reference genome overlapped by reads, to distinguish these artifacts...

OBJECTIVES: Assess the validity and feasibility of current instrumented mouthguards (iMGs) and associated systems. METHODS: Phase I; four iMG systems (Biocore-Football Research Inc (FRI), HitIQ, ORB, Prevent) were compared against dummy headform laboratory criterion standards (25, 50, 75, 100 g ). Phase II; four iMG systems were evaluated for on-field validity of iMG-triggered events against video-verification to determine true-positives, false-positives and false-negatives (20±9 player matches per iMG)...

OBJECTIVES: This study was conducted to evaluate the outcome of the transcatheter valve-in-valve implantation for degenerated tricuspid bioprosthetic valves with transcatheter aortic valves. METHODS: This retrospective study enrolled all consecutive patients who were considered high risk for reoperations by the heart team and who underwent transcatheter valve-in-valve implantation for degenerated tricuspid bioprosthetic valves in Tehran Heart Center, Tehran, Iran...

Science, technology, engineering, and mathematics (STEM) career barriers persist for individuals from marginalized communities due to financial and educational inequality, unconscious bias, and other disadvantaging factors. To evaluate differences in plans and interests between historically underrepresented (UR) and well-represented (WR) groups, we surveyed more than 3000 undergraduates enrolled in chemistry courses. Survey responses showed all groups arrived on campus with similar interests in learning more about science research...

Microbiome data are sparse and high dimensional, so effective visualization of these data requires dimensionality reduction. To date, the most commonly used method for dimensionality reduction in the microbiome is calculation of between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold Approximation and Projection (UMAP) is an alternative method that can reduce the dimensionality of beta diversity distance matrices. Here, we demonstrate the benefits and limitations of using UMAP for dimensionality reduction on microbiome data...

BACKGROUND: Aortic Stentless Bioprosthetic Valve (SLBPV), either porcine or pericardial, minimizes transvalvular gradient and favour regression of left ventricular hypertrophy. The drawback consists of longer time for suturing. While structural valve deterioration (SVD) in stented porcine and pericardial BPVs has been extensively investigated, less information is available on SLBPVs. MATERIAL AND METHODS: We studied 82 SLBPVs explants, either porcine [Toronto SPV,(St...

Operating in a neglected niche in research equipment sharing, a new program has shown to reduce individual laboratory expenses (i.e., cost avoidance on research equipment purchases) and is enabling researchers to conduct experiments that may otherwise be beyond their reach due to lack of equipment. While core facilities offer access to specialized instrumentation and services, the BioCore at the University of Colorado Boulder centralizes management of small- to mid-scale shared equipment in three biology departments to a single point of contact and a single manager...

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Chamber-specific and temporally regulated perinatal cardiac growth and maturation is critical for functional adaptation of the heart and may be altered significantly in response to perinatal stress, such as systemic hypoxia (hypoxemia), leading to significant pathology, even mortality. Understanding transcriptome regulation of neonatal heart chambers in response to hypoxemia is necessary to develop chamber-specific therapies for infants with cyanotic congenital heart defects (CHDs). We sought to determine chamber-specific transcriptome programming during hypoxemic perinatal circulatory transition...

The Vision and Change report called for the biology community to mobilize around teaching the core concepts of biology. This essay describes a collection of resources developed by several different groups that can be used to respond to the report's call to transform undergraduate education at both the individual course and departmental levels. First, we present two frameworks that help articulate the Vision and Change core concepts, the BioCore Guide and the Conceptual Elements (CE) Framework, which can be used in mapping the core concepts onto existing curricula and designing new curricula that teach the biology core concepts...

Granules of calcium/phosphate biomaterials are used to fill small bone defects in oral and maxilla-facial surgery. Granules of natural (e.g., trabecular bone, coral) or synthetic biomaterials are provided by industry. Small granules can also form of putty. The 3D geometry of granules creates a macroporosity allowing invasion of vascular and bone cells when pores are larger than 300 μm. We analyzed the 3D-porosity of 11 different stacks of biomaterials: Osteopure®, CopiOs®, Bio-Oss®, TCP Dental HP®, KeraOs®, TCH®, Biocoral®, EthOss® and Nanostim®...

The phenotypic spectrum of congenital heart defects (CHDs) is contributed by both genetic and environmental factors. Their interactions are profoundly heterogeneous but may operate on common pathways as in the case of hypoxia signaling during postnatal heart development in the context of CHDs. Tetralogy of Fallot (TOF) is the most common cyanotic (hypoxemic) CHD. However, how the hypoxic environment contributes to TOF pathogenesis after birth is poorly understood. We performed Genome-wide transcriptome analysis on right ventricle outflow tract (RVOT) specimens from cyanotic and noncyanotic TOF...

Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github.com/biocore/mmvec) to estimate the conditional probability that each molecule is present given the presence of a specific microorganism. We show with known environmental (desert soil biocrust wetting) and clinical (cystic fibrosis lung) examples, our ability to recover microbe-metabolite relationships, and demonstrate how the method can discover relationships between microbially produced metabolites and inflammatory bowel disease...

SUMMARY: Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single threaded on binary set operations, PyRanges is in median 2.3-9.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster...

SUMMARY: Data from chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) generally contain either narrow peaks or broad and diffusely enriched domains. The SICER ChIP-seq caller has proven adept at finding diffuse domains in ChIP-seq data, but it is slow, requires much memory, needs manual installation steps and is hard to use. epic2 is a complete rewrite of SICER that is focused on speed, low memory overhead and ease-of-use. AVAILABILITY AND IMPLEMENTATION: The MIT-licensed code is available at https://github...

The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics...