HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors.

MOTIVATION: Genomic distance estimation is a critical workload since exact computation for whole-genome similarity metrics such as Average Nucleotide Identity (ANI) incurs prohibitive runtime overhead. Genome sketching is a fast and memory-efficient solution to estimate ANI similarity by distilling representative k-mers from the original sequences. In this work, we present HyperGen that improves accuracy, runtime performance, and memory efficiency for large-scale ANI estimation. Unlike existing genome sketching algorithms that convert large genome files into discrete k-mer hashes, HyperGen leverages the emerging hyperdimensional computing (HDC) to encode genomes into quasi-orthogonal vectors (Hypervector, HV) in high-dimensional space. HV is compact and can preserve more information, allowing for accurate ANI estimation while reducing required sketch sizes. In particular, the HV sketch representation in HyperGen allows efficient ANI estimation using vector multiplication, which naturally benefits from highly optimized general matrix multiply (GEMM) routines. As a result, HyperGen enables the efficient sketching and ANI estimation for massive genome collections. RESULTS: We evaluate HyperGen s sketching and database search performance using several genome datasets at various scales. HyperGen is able to achieve comparable or superior ANI estimation error and linearity compared to other sketch-based counterparts. The measurement results show that HyperGen is one of the fastest tools for both genome sketching and database search. Meanwhile, HyperGen produces memory-efficient sketch files while ensuring high ANI estimation accuracy. AVAILABILITY: A Rust implementation of HyperGen is freely available under the MIT license as an open-source software project at https://github.com/wh-xu/Hyper-Gen. The scripts to reproduce the experimental results can be accessed at https://github.com/wh-xu/experiment-hyper-gen

RENAL ISCHEMIA REPERFUSION CAUSES BRAIN HIPPOCAMPUS OXIDATIVE DAMAGE AND INHIBITION EFFECT

Background: The acute kidney injury (AKI) may do damage to remote organs. Objective of the study is to investigate effect of seaweed extract (SE) on brain oxidative damage in kidney ischemia/reperfusion rats. Material and Methods: Animals were randomly divided into five groups. SE pre-fed to rats. Results: Kidney I/R may cause oxidative injury in kidneys and brains tissue in rats. SE pre-treatment can decrease lipid peroxidation levels and increase antioxidant enzymes activities in kidney and brain hippocampus of kidney I/R rats. Conclusion: Our results indicate that SE is useful for brain nerve function keeping in kidney I/R rats

INHIBITION OF PACLITAXEL AGAINST NEUROGLIOMA CELLS U251 GROWTH AND ITS MECHANISM

Background: Glioma is the most common primary tumor of the central nervous system, and accounted for about 70% of primary tumors. Materials and Methods: In the study, antitumour activity and mechanism of paclitaxel was investigated. Different concentrations of paclitaxel (200, 300, 400 μmol/L) was treated in neuroglioma cellsU251. Results: Paclitaxel significantly inhibited neuroglioma cells growth, and promoted its apoptosis. Paclitaxel can block tumour cells in the G2/M phase. In addition, apoptosis-related genes caspase-3 and bax expressions were increased after paclitaxel treatment. Conclusion: Our work indicated that paclitaxel displayed strong anti-tumour activity

What is valued most by patients with type 2 diabetes mellitus when selecting second-line antihyperglycemic medications in China

Objective: To estimate patient preferences for second-line antihyperglycemic medications in China. Methods: A face to face survey with the best-worst scaling (BWS) choices was administered in patients with diagnosed type 2 diabetes mellitus (T2DM). Study participants were asked to indicate which attribute they valued most and which attribute they valued least in 11 choice sets, each of which consisted of five alternatives out of 11 antihyperglycemic medication-specific attributes (treatment efficacy, weight change, hypoglycemic events, gastrointestinal side effects, cardiovascular health, urinary tract infection and genital infection side effects, edema, mode of administration, bone fracture, dosing frequency and out-of-pocket cost). A counting approach, a conditional logit model, and K-means clustering were used to estimate the relative importance of items and preference heterogeneity. Results: A total of 362 participants were included with a mean age of 63.6 (standard deviation: 11.8) years. There were 56.4% of participants were women, and 56.3% being diagnosed with diabetes for at least 5 years. Efficacy, cardiovascular health and hypoglycemic events were valued most, while dosing frequency, mode of administration and bone fracture were valued least. The K-means clustering further showed preference heterogeneity in out-of-pocket cost across the participants. Conclusion: Our study suggests that treatment efficacy, cardiovascular health and hypoglycemic events are valued most by Chinese patients with T2DM when selecting second-line antihyperglycemic medications. The study improves the understanding of patients’ preferences for second-line antihyperglycemic medications in China