Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.

To improve imputation quality for genome-wide association studies (GWAS) conducted on the Japanese population, we developed and evaluated four Japanese population-specific reference panels. These panels were constructed through the augmentation of the 1000 Genomes Project (1KG) panel using Japanese whole genome sequencing (WGS) data, with sample sizes ranging from 1 K to 7 K individuals enrolled through the Biobank Japan (BBJ) project, and sequencing depths ranging from 3× to 30×. Among these panels, an augmented reference panel comprising 7472 WGS samples of mixed depth (1KG+7K) exhibit the greatest improvement in imputation quality relative to the Trans-Omics for Precision Medicine (TOPMed) reference panel.

Periodic Bonding Behaviors of Actinide Atoms (An = Th-Cm) with Negatively Curved Nanographene.

The nanographene with negative curvature has been extensively studied due to its interesting properties and potential applications. In the present work, we have performed all-electron scalar relativistic density functional theory (DFT) calculations to understand the periodic interaction mechanisms of actinide atoms (An = Th, Cm) with the TB8C nanographene. The encapsulated complexes (An@TB8C) were formed due to the octagonal vacancy in the TB8C nanographene.

Iodine capture of a two-dimensional layered uranyl-organic framework: a combined DFT and AIMD study.

To develop nuclear energy sustainably, it is important to effectively capture radioiodine in nuclear waste. In this study, we used density functional theory (DFT) and molecular dynamics (AIMD) calculations to investigate how well the uranyl-organic framework (UOF) could capture radioiodine. We found that the uranyl center and C-N ring sites in both cluster and periodic UOF models are very attractive to the I molecule.

Transition metal single-atoms supported on hexagonal ZnInS monolayers for the hydrogen evolution reaction.

Herein, we report a series of 5d transition metal (TM) single atoms supported on ZIS as promising catalysts for the hydrogen evolution reaction using first-principles calculations. The binding behaviors of TMs with the ZIS surface in single-atom catalyst formation are analysed using the adsorption energy (), partial density of states (PDOS), charge density difference (CDD), and crystal orbital Hamilton population (COHP). The TM@ZIS (TM = Ta, W, Re, Os, Ir, and Pt) shows excellent hydrogen evolution performance with the Gibbs free energy (Δ) values from -0.

Environmental arsenic pollution induced liver oxidative stress injury by regulating miR-155 through inhibition of AUF1.

Arsenic (As), a common environmental pollutant, has become a hot topic in recent years due to its potentially harmful effects. Liver damage being a central clinical feature of chronic arsenic poisoning. However, the underlying mechanisms remain unclear.

Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.

Large-scale imputation reference panels are currently available and have contributed to efficient genome-wide association studies through genotype imputation. However, whether large-size multi-ancestry or small-size population-specific reference panels are the optimal choices for under-represented populations continues to be debated. We imputed genotypes of East Asian (180k Japanese) subjects using the Trans-Omics for Precision Medicine reference panel and found that the standard imputation quality metric (Rsq) overestimated dosage r2 (squared correlation between imputed dosage and true genotype) particularly in marginal-quality bins.

East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease.

Peptic ulcer disease (PUD) refers to acid-induced injury of the digestive tract, occurring mainly in the stomach (gastric ulcer (GU)) or duodenum (duodenal ulcer (DU)). In the present study, we conducted a large-scale, cross-ancestry meta-analysis of PUD combining genome-wide association studies with Japanese and European studies (52,032 cases and 905,344 controls), and discovered 25 new loci highly concordant across ancestries. An examination of GU and DU genetic architecture demonstrated that GUs shared the same risk loci as DUs, although with smaller genetic effect sizes and higher polygenicity than DUs, indicating higher heterogeneity of GUs.

Adsorption and diffusion of actinyls on the basal gibbsite (001) surface: a theoretical perspective.

Actinides are an important component of nuclear fuel for nuclear power and affect human health, and a key process in the transport of radionuclides in the environment is adsorption on mineral surfaces. In this work, we have used density functional theory (DFT) to investigate the microscopic adsorption and diffusion mechanisms of actinyls, U(V), U(VI), Np(V), Np(VI) Pu(V), and Pu(VI), on the gibbsite (001) surface. Actinyls(VI) are attached to the gibbsite surface through two An-O bonds, which results in a bidentate inner sphere mode, while actinyls(V) favor a monodentate inner sphere adsorption mode with the gibbsite (001) surface.

Role of SESTRIN2/AMPK/ULK1 pathway activation and lysosomes dysfunction in NaAsO-induced liver injury under oxidative stress.

Arsenic, a serious environmental poison to human health, is widely distributed in nature. As the main organ of arsenic metabolism, liver is easily damaged. In the present study, we found that arsenic exposure can cause liver injury in vivo and in vitro, to date the underlying mechanism of which is yet unclear.

Bone collision detection method for robot assisted fracture reduction based on vibration excitation.

Background And Objective: In the process of robotic fracture reduction, there is a risk of unintended collision of broken bones, which is not conducive to ensuring the safety of the reduction system. In order to solve this problem, this paper proposed a vibration-based collision detection method for fracture reduction process.

Methods: Based on the two degree-of-freedom vibration response model, the factors affecting the respond of the vibration, including the excitation voltage, the clamping length at the proximal and distal ends, the mass and tensile force of the soft tissue, were obtained.

Stroke genetics informs drug discovery and risk prediction across ancestries.

Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.

Mechanism underlying the targeted regulation of the SOD1 3'UTR by the AUF1/Dicer1/miR-155/SOD1 pathway in sodium arsenite-induced liver injury.

Arsenic (As) is a natural hepatotoxicity inducer that is ubiquitous in water, soil, coal, and food. Studies have found that arsenite exposure elicits increased mRNA transcription and decreased protein expression of SOD1 in vivo and in vitro; however, the specific mechanisms remain unclear. Here, we established a model of arsenic-induced chronic liver injury by providing rats with drinking water containing different concentrations of sodium arsenite (NaAsO) and found that NaAsO exposure decreased the mRNA and protein levels of AUF1 and the protein level of SOD1 and elevated the mRNA and protein levels of Dicer1 and miR-155 and the mRNA level of SOD1.

LC/MS/MS-Based Liver Metabolomics to Identify Chronic Liver Injury Biomarkers Following Exposure to Arsenic in Rats.

Arsenic is a widespread natural metalloid element. Long-term chronic exposure to arsenic can lead to different degrees of liver injury. Although the etiology of this disease is well known, to date, the underlying mechanism of arsenic-induced liver injury remains unclear, and no specific treatment exists because of the complexity of arsenic.

Development of IL-15/IL-15Rα sushi domain-IgG4 Fc complexes in Pichia pastoris with potent activities and prolonged half-lives.

Background: Interleukin-15 (IL-15) is a critical cytokine for the development, proliferation, and function of natural killer (NK) cells, NKT cells, and CD8 memory T cells and has become one of the most promising protein molecules for the treatment of cancer and viral diseases. However, there are several limitations in applying IL-15 in therapy, such as its low yield in vitro, limited potency, and short half-life in vivo. To date, there are several recombinant IL-15 agonists based on configurational modifications that are being pursued in the treatment of cancer, such as ALT-803, which are mainly produced from mammalian cells.

Multi-modal neuroimaging feature fusion for diagnosis of Alzheimer's disease.

Background: Compared with single-modal neuroimages classification of AD, multi-modal classification can achieve better performance by fusing different information. Exploring synergy among various multi-modal neuroimages is contributed to identifying the pathological process of neurological disorders. However, it is still problematic to effectively exploit multi-modal information since the lack of an effective fusion method.

The role of PSMB5 in sodium arsenite-induced oxidative stress in L-02 cells.

Endemic arsenism is widely distributed in the world, which can damage multiple organs, especially in skin and liver. The etiology is clear, but the mechanisms involved remain unknown. Ubiquitin-proteasome pathway (UPP) is the main pathway regulating protein degradation of which proteasome subunit beta type-5(PSMB5) plays a dominant role.

Incorporation of dumbbell-shaped and Y-shaped cross-linkers in adjustable pullulan/polydopamine hydrogels for selective adsorption of cationic dyes.

Hydrogel adsorbents have attracted considerable attention due to their sludge minimization, good water permeability and renewable performance. Here, a promising strategy for the one-step preparation of pullulan/polydopamine hybird hydrogels (PPGels) was presented. Dumbbell-shaped cross-linker neopentyl glycol diglycidyl ether (NGDE, 2 arms) and Y-shaped cross-linker trimethylolpropane triglycidyl ether (TTE, 3 arms) were selected to study the relationship between cross-linker structure and hydrogel performances.

A coumarin-connected carboxylic indolinium sensor for cyanide detection in absolute aqueous medium and its application in biological cell imaging.

Fluorescent sensor has been noticed in detecting system due to its sensitive, selective, operational simplicity and low cost. We designed a coumarin-connected carboxylic indolium sensor molecule that is water-soluble and cytomembrane-permeable. This infrared (IR) emitter is selectively sensitive towards cyanide detection in aqueous media according to CN nucleophilic attack on the indole C=N function.

Naphthalene-benzoindole derived two novel fluorometric pH-Responsive probes for environmental systems and bioimaging.

In this work, we designed a kind of novel fluorescent probes based on naphthalene-benzoindole conjugate derived for sensitively monitoring the pH fluctuation in environment and biological systems. In the spectral method, these two probes both show significant red shift, color change and fluorescence quenching due to the effect of intramolecular charge transfer (ICT) mechanism. Moreover, we found that the probe bearing with carboxyl group displayed a more hydrophilicity than the one bearing with hydrogen atom instead, and the former exhibits a faster response and higher fluorescence intensity.

Pullulan-derived nanocomposite hydrogels for wastewater remediation: Synthesis and characterization.

Polysaccharide is a renewable, biocompatible and biodegradable material that has received considerable attention. In this work, a series of polysaccharide gels were synthesized from the chemical cross-linking of pullulan with diglycerols. The effects of the diglycerol chain length on the performance of the gels were evaluated by XRD, TGA, SEM, rheological testings and swelling measurements.

Elimination of N-glycosylation by site mutation further prolongs the half-life of IFN-α/Fc fusion proteins expressed in Pichia pastoris.

Background: Interferon (IFN)-α has been commonly used as an antiviral drug worldwide; however, its short half-life in circulation due to its low molecular weight and sensitivity to proteases impacts its efficacy and patient compliance.

Results: In this study, we present an IgG1 Fc fusion strategy to improve the circulation half-life of IFN-α. Three different forms of IgG1 Fc fragments, including the wild type, aglycosylated homodimer and aglycosylated single chain, were each fused with IFN-α and designated as IFN-α/Fc-WT, IFN-α/Fc-MD, and IFN-α/Fc-SC, respectively.

Huai Qi Huang ameliorates proteinuria and hematuria in mild IgA nephropathy patients: a prospective randomized controlled study.

Background/purpose: Huai Qi Huang (HQH) is a compound Chinese herbal medicine that contains Trametes robiniophila murr, wolfberry fruit, and Polygonatum. In the present study, we investigated the effects of HQH on patients with mild immunoglobulin A nephropathy (IgAN) through a prospective randomized controlled study.

Methods: Forty-five adults diagnosed with IgAN according to renal pathology, who had hematuria or/and proteinuria (≤ 2 g/day), were randomly assigned to receive HQH or no treatment for 12 weeks.