The Effect of Dietary Nitrate and Anthocyanins on Anaerobic Exercise Performance

Background: Previously, beetroot and tart cherry supplementations have been investigated for their effects on exercise performance and recovery separately. Beetroot containing nitrate has been used to improve blood flow to enhance exercise tolerance. Tart cherry extract containing anthocyanins has been shown to lower inflammation and improve recovery time in exercise performance. Objective: The purpose of this study was to investigate a possible synergistic effect of nitrate and anthocyanins on exercise performance in healthy individuals. Design: This was a double-blind, randomized crossover study with a duration of twenty-nine days. Inclusion criteria included healthy individuals, able to exercise on a stationary bike, and willing to abstain from caffeine, mouthwash, and high antioxidant foods. Exclusion criteria included orthopedic injuries, use of nonsteroidal anti-inflammatory drugs (NSAIDs), known allergy to tart cherry and/or beetroot, and pregnant or breastfeeding. Participants: Healthy men (n=6) and women (n=23), ranging between 19 and 35 years of age. Participants were recruited from Loma Linda University and surrounding cities. Intervention: Participants were randomized into two groups after baseline. Treatment A was supplemented with 5.05g (3.62 mmol) of beetroot powder and placebo. Treatment B was supplemented with 5.05g (3.62 mmol) of beetroot powder and 480 mg tart cherry capsule for seven-days, followed by a seven-day washout period. Treatment was alternated at the end of the 14-day period. Main outcomes: exercise performance (heart rate, speed, and distance) Secondary outcomes: serum lactate and allantoin Statistics: A mixed model analysis was used to measure changes in continuous variables. Mean and standard deviation were calculated for treatment A and treatment B. Results: During the first five seconds of the 30 second sprint, heart rate of treatment A was significantly lower than treatment B. Difference in heart rate ranged from 1.6 to 2.7 BPM. Participants in treatment B pedaled five meters farther, than treatment A. This outcome was not statistically significant. No significant differences were observed between both treatments on rpm, blood pressure, lactate, and allantoin. Conclusion: Supplementation with beetroot powder and tart cherry for seven days may synergistically improve anaerobic exercise performance by maximizing potential heart rate and energy output

MetaSquare: An integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

MOTIVATION: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource. RESULTS: MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods. AVAILABILITY AND IMPLEMENTATION: Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

AbCD: arbitrary coverage design for sequencing-based genetic studies

Summary: Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbitrary coverage (0.5–30×) and sample size (20–10 000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans). In addition, we also present two software tools: ShotGun and DesignPlanner, which were used to generate the estimates behind AbCD. ShotGun is a flexible short-read simulator for arbitrary user-specified read length and average depth, allowing cycle-specific sequencing error rates and realistic read depth distributions. DesignPlanner is a full pipeline that uses ShotGun to generate sequence data and performs initial SNP discovery, uses our previously presented linkage disequilibrium-aware method to call genotypes, and, finally, provides minor allele frequency-specific effective sample sizes. ShotGun plus DesignPlanner can accommodate effective sample size estimate for any combination of high-depth and low-depth data (for example, whole-genome low-depth plus exonic high-depth) or combination of sequence and genotype data [for example, whole-exome sequencing plus genotyping from existing Genomewide Association Study (GWAS)]

Effects of Salvianolic Acid B on Protein Expression in Human Umbilical Vein Endothelial Cells

Salvianolic acid B (Sal B), a pure water-soluble compound extracted from Radix Salviae miltiorrhizae, has been reported to possess potential cardioprotective efficacy. To identify proteins or pathways by which Sal B might exert its protective activities on the cardiovascular system, two-dimensional gel electrophoresis-based comparative proteomics was performed, and proteins altered in their expression level after Sal B treatment were identified by MALDI-TOF MS/MS. Human umbilical vein endothelial cells (HUVECs) were incubated at Sal B concentrations that can be reached in human plasma by pharmacological intervention. Results indicated that caldesmon, an actin-stabilizing protein, was downregulated in Sal B-exposed HUVECs. Proteins that showed increased expression levels upon Sal B treatment were vimentin, T-complex protein 1, protein disulfide isomerase, tropomyosin alpha, heat shock protein beta-1, UBX domain-containing protein 1, alpha enolase, and peroxiredoxin-2. Additionally, Sal B leads to increased phosphorylation of nucleophosmin in a dose-dependent manner and promotes proliferation of HUVECs. We found that Sal B exhibited a coordinated regulation of enzymes and proteins involved in cytoskeletal reorganization, oxidative stress, and cell growth. Our investigation would provide understanding to the endothelium protection information of Sal B

Low Latency Edge Classification GNN for Particle Trajectory Tracking on FPGAs

In-time particle trajectory reconstruction in the Large Hadron Collider is challenging due to the high collision rate and numerous particle hits. Using GNN (Graph Neural Network) on FPGA has enabled superior accuracy with flexible trajectory classification. However, existing GNN architectures have inefficient resource usage and insufficient parallelism for edge classification. This paper introduces a resource-efficient GNN architecture on FPGAs for low latency particle tracking. The modular architecture facilitates design scalability to support large graphs. Leveraging the geometric properties of hit detectors further reduces graph complexity and resource usage. Our results on Xilinx UltraScale+ VU9P demonstrate 1625x and 1574x performance improvement over CPU and GPU respectively