Genetic Polymorphism of 16 X-STR Loci in Xinjiang Uygur Population.

OBJECTIVES: To study the genetic polymorphism and population genetic parameters of 16 X-STR loci in Xinjiang Uygur population. METHODS: The Goldeneye® DNA identification system 17X was used to amplify 16 X-STR loci in 502 unrelated individuals (251 females and 251 males). The amplified products were detected by 3130xl genetic analyzer. Allele frequencies and population genetic parameters were analyzed statistically. The genetic distances between Uygur and other 8 populations were calculated. Multidimensional scaling and phylogenetic tree were constructed based on genetic distance. RESULTS: In the 16 X-STR loci, a total of 67 alleles were detected in 502 Xinjiang Uygur unrelated individuals. The allele frequencies ranged from 0.001 3 to 0.572 4. PIC ranged from 0.568 8 to 0.855 3. The cumulative discrimination power in females and males were 0.999 999 999 999 999 and 0.999 999 999 743 071, respectively. The cumulative mean paternity exclusion chance in trios and in duos were 0.999 999 997 791 859 and 0.999 998 989 000 730, respectively. The genetic distance between Uygur population and Kazakh population was closer, and the genetic distance between Uygur and Han population was farther. CONCLUSIONS: The 16 X-STR loci are highly polymorphic and suitable for identification in Uygur population, which can provide a powerful supplement for the study of individual identification, paternity identification and population genetics.

Application of SifaInDel 45plex System in the Han and Mongolian Populations.

OBJECTIVES: To investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine. METHODS: SifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels (A-InDels). The phylogenetic trees and multidimensional scaling (MDS) analysis diagrams were constructed accordingly. RESULTS: Among two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPEtrio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMECtrio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations. CONCLUSIONS: The InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.

FW-PSO Algorithm to Enhance the Invulnerability of Industrial Wireless Sensor Networks Topology.

When an industrial wireless sensor network (WSN) is seriously disturbed and intentionally attacked, sometimes it fails easily, even leading to the paralysis of the entire industrial wireless network. In order to improve the invulnerability of networks, in this paper, the scale-free network in complex networks is taken as the research object, and the industrial WSN with scale-free characteristics is modeled. Based on the advantages of the fireworks algorithm, such as strong searching ability and diversity of population, a so-called fireworks and particle swarm optimization (FW-PSO) algorithm is proposed, which can improve the global search ability and convergence speed effectively. The proposed FW-PSO algorithm is used to optimize the network topology and form a network with the largest natural connectivity, which can effectively promote the ability of network to resist the cascade failure problem. The dynamic invulnerability of the optimized network under highest-degree (HD) attack and lowest-degree (LD) attack strategies, as well as the static invulnerability under random attack, were evaluated respectively. Simulation experiments show that the industrial WSN optimized by FW-PSO can significantly improve the performance of the dynamic and static invulnerabilities compared with the initial network and the networks optimized by the other two existing algorithms.

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.

MOTIVATION: The importance of testing associations allowing for interactions has been demonstrated by Marchini et al. (2005). A fast method detecting associations allowing for interactions has been proposed by Wan et al. (2010a). The method is based on likelihood ratio test with the assumption that the statistic follows the χ(2) distribution. Many single nucleotide polymorphism (SNP) pairs with significant associations allowing for interactions have been detected using their method. However, the assumption of χ(2) test requires the expected values in each cell of the contingency table to be at least five. This assumption is violated in some identified SNP pairs. In this case, likelihood ratio test may not be applicable any more. Permutation test is an ideal approach to checking the P-values calculated in likelihood ratio test because of its non-parametric nature. The P-values of SNP pairs having significant associations with disease are always extremely small. Thus, we need a huge number of permutations to achieve correspondingly high resolution for the P-values. In order to investigate whether the P-values from likelihood ratio tests are reliable, a fast permutation tool to accomplish large number of permutations is desirable. RESULTS: We developed a permutation tool named PBOOST. It is based on GPU with highly reliable P-value estimation. By using simulation data, we found that the P-values from likelihood ratio tests will have relative error of >100% when 50% cells in the contingency table have expected count less than five or when there is zero expected count in any of the contingency table cells. In terms of speed, PBOOST completed 10(7) permutations for a single SNP pair from the Wellcome Trust Case Control Consortium (WTCCC) genome data (Wellcome Trust Case Control Consortium, 2007) within 1 min on a single Nvidia Tesla M2090 device, while it took 60 min in a single CPU Intel Xeon E5-2650 to finish the same task. More importantly, when simultaneously testing 256 SNP pairs for 10(7) permutations, our tool took only 5 min, while the CPU program took 10 h. By permuting on a GPU cluster consisting of 40 nodes, we completed 10(12) permutations for all 280 SNP pairs reported with P-values smaller than 1.6 × 10⁻¹² in the WTCCC datasets in 1 week. AVAILABILITY AND IMPLEMENTATION: The source code and sample data are available at http://bioinformatics.ust.hk/PBOOST.zip. CONTACT: gyang@ust.hk; eeyu@ust.hk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effect of fluvoxamine on the pharmacokinetics and pharmacodynamics of clopidogrel in rats.

1. Fluvoxamine, a selective serotonin reuptake inhibitor (SSRI), is often coprescribed with clopidogrel for the treatment of ischemic vascular diseases. The aim of this study was to explore the effect of fluvoxamine on the pharmacokinetics and pharmacodynamics of clopidogrel. 2. Twelve male rats were employed to investigate the effect of fluvoxamine on the pharmacokinetics of clopidogrel in vivo. Clopidogrel carboxylic acid was used for the pharmacokinetic study of clopidogrel. 3. After pretreatment with high dose of fluvoxamine (27 mg/kg), there were significant increases in the AUC0-t (from 9850±4060 to 27,300±6910 µg/l h; p<0.05), AUC0-∞ (from 9850±4060 to 27,600±6800 µg/l h; p<0.05) and t1/2 (from 2.07±0.0942 to 7.49±1.22 h; p<0.05) of clopidogrel carboxylic acid. The pharmacokinetic data for clopidogrel carboxylic acid showed significant decreases in VLz/F (from 0.765±0.299 to 0.256±0.0594 l/kg; p<0.05) after pretreatment with high dose of fluvoxamine. Pharmacodynamic studies that measure platelet aggregation percentage (from 21.63±6.05% to 45.98±5.11%; p<0.01) show that high doses of fluvoxamine significantly inhibit the effect of clopidogrel. 4. In conclusion, the pharmacokinetics and pharmacodynamics of clopidogrel were significantly affected by high doses of fluvoxamine. This study indicated that potential drug-drug interaction between fluvoxamine and clopidogrel should be taken into consideration in clinical use.

Mitochondrial Protease Oct1p Regulates Mitochondrial Homeostasis and Influences Pathogenicity through Affecting Hyphal Growth and Biofilm Formation Activities in Candida albicans.

Mitochondria, as the core metabolic organelles, play a crucial role in aerobic respiration/biosynthesis in fungi. Numerous studies have demonstrated a close relationship between mitochondria and Candida albicans virulence and drug resistance. Here, we report an octapeptide-aminopeptidase located in the mitochondrial matrix named Oct1p. Its homolog in the model fungus Saccharomyces cerevisiae is one of the key proteins in maintaining mitochondrial respiration and protein stability. In this study, we utilized evolutionary tree analysis, gene knockout experiments, mitochondrial function detection, and other methods to demonstrate the impact of Oct1p on the mitochondrial function of C. albicans. Furthermore, through transcriptome analysis, real-time quantitative PCR, and morphological observation, we discovered that the absence of Oct1p results in functional abnormalities in C. albicans, affecting hyphal growth, cell adhesion, and biofilm formation. Finally, the in vivo results of the infection of Galleria mellonella larvae and vulvovaginal candidiasis in mice indicate that the loss of Oct1p led to the decreased virulence of C. albicans. In conclusion, this study provides a solid theoretical foundation for treating Candida diseases, developing new targeted drugs, and serves as a valuable reference for investigating the connection between mitochondria and virulence in other pathogenic fungi.

MAE-TransRNet: An improved transformer-ConvNet architecture with masked autoencoder for cardiac MRI registration.

The heart is a relatively complex non-rigid motion organ in the human body. Quantitative motion analysis of the heart takes on a critical significance to help doctors with accurate diagnosis and treatment. Moreover, cardiovascular magnetic resonance imaging (CMRI) can be used to perform a more detailed quantitative analysis evaluation for cardiac diagnosis. Deformable image registration (DIR) has become a vital task in biomedical image analysis since tissue structures have variability in medical images. Recently, the model based on masked autoencoder (MAE) has recently been shown to be effective in computer vision tasks. Vision Transformer has the context aggregation ability to restore the semantic information in the original image regions by using a low proportion of visible image patches to predict the masked image patches. A novel Transformer-ConvNet architecture is proposed in this study based on MAE for medical image registration. The core of the Transformer is designed as a masked autoencoder (MAE) and a lightweight decoder structure, and feature extraction before the downstream registration task is transformed into the self-supervised learning task. This study also rethinks the calculation method of the multi-head self-attention mechanism in the Transformer encoder. We improve the query-key-value-based dot product attention by introducing both depthwise separable convolution (DWSC) and squeeze and excitation (SE) modules into the self-attention module to reduce the amount of parameter computation to highlight image details and maintain high spatial resolution image features. In addition, concurrent spatial and channel squeeze and excitation (scSE) module is embedded into the CNN structure, which also proves to be effective for extracting robust feature representations. The proposed method, called MAE-TransRNet, has better generalization. The proposed model is evaluated on the cardiac short-axis public dataset (with images and labels) at the 2017 Automated Cardiac Diagnosis Challenge (ACDC). The relevant qualitative and quantitative results (e.g., dice performance and Hausdorff distance) suggest that the proposed model can achieve superior results over those achieved by the state-of-the-art methods, thus proving that MAE and improved self-attention are more effective and promising for medical image registration tasks. Codes and models are available at https://github.com/XinXiao101/MAE-TransRNet.

Pressure Drop Performance of Porous Composites Based on Cotton Cellulose Nanofiber and Aramid Nanofiber for Cigarette Filter Rod.

Porous composites have been widely used in the adsorption and catalysis field due to their special structure, abundant sites, and light weight. In this work, an environmentally friendly porous composite was successfully prepared via a facile freeze-drying method, in which cotton cellulose nanofiber (CCNF) was adopted as the main framework to construct the connected flue structure, and aramid nanofiber (ANF) was used as a reinforcer to enhance its thermal property. As-prepared porous materials retained a regulated inter-connected hole structure and controllable porosity after ice template evolution and possessed improved resistance to thermal collapse with the introduction of a small amount of aramid nanofiber, as evaluated and verified by FTIR, SEM, and TGA measurements. With the increased addition of cotton cellulose nanofiber and aramid nanofiber, the porous composites exhibited decreased porosity and increased pressure drop performance. For the CCNF/ANF-5 sample, the pressure drop was 1867 Pa with a porosity of 7.46 cm3/g, which best met the required pressure drop value of 1870 Pa. As-prepared porous composite with adjustable interior structure and enhanced thermal property could be a promising candidate in the tobacco field.

Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations.

Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications.

Ubiquitination of ASCL1 mediates CD47 transcriptional activation of the AKT signaling pathway, and glycolysis promotes osteogenic differentiation of hBMSCs.

Bones are extremely dynamic organs that continually develop and remodel. This process involves changes in numerous gene expressions. hBMSC cells can promote osteogenic differentiation. The purpose of this study was to elucidate the mechanism by which ASCL1 promotes osteogenic differentiation in hBMSC cells while decreasing glycolysis. hBMSCs were induced to differentiate into osteoblasts. The ASCL1 expression level during hBMSC osteogenic differentiation was measured by RT‒qPCR, Western blotting, and immunofluorescence. The differentiation level of osteoblasts was observed after staining with ALP and alizarin red. ChIP-qPCR were used to determine the relationship between ASCL1 and CD47, and the expression of glycolysis-related proteins was detected. Overexpression of ASCL1 was used to determine its impact on osteogenic differentiation. si-USP8 was used to verify the ubiquitination of ASCL1-mediated CD47/AKT pathway's impact on hBMSC glycolysis and osteogenic differentiation. The results showed that the expression of ASCL1 was upregulated after the induction of osteogenic differentiation in hBMSCs. From a functional perspective, knocking down USP8 can promote the ubiquitination of ASCL1, while the osteogenic differentiation ability of hBMSCs was improved after the overexpression of ASCL1, indicating that ASCL1 can promote the osteogenic differentiation of hBMSCs. In addition, USP8 regulates the ubiquitination level of ASCL1 and mediates CD47 transcriptional regulation of the AKT pathway to increase the glycolysis level of hBMSCs and cell osteogenic differentiation. USP8 ubiquitination regulates the level of ASCL1. In addition, ubiquitination of ASCL1 mediates CD47 transcription to activate the AKT signaling pathway and increase hBMSC glycolysis to promote osteogenic differentiation.

Preparation of One-Dimensional Polyaniline Nanotubes as Anticorrosion Coatings.

Uniform polyaniline (PANI) nanotubes were synthesized by a self-assembly method under relatively dilute hydrochloric acid (HCl) solution. Scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and UV-Vis-NIR spectroscopy were employed to characterize the morphology and molecular structure of the PANI products. SEM images show that the PANI nanotubes have uniform morphology and form compact coating on the substrate surface. For comparison, aggregated PANI was also synthesized by conventional polymerization method. The performance of the PANI products on carbon steel was studied using eletrochemical measurement and immersion corrosion experiment in 3.5 wt% NaCl aqueous solution. The corrosion potentials of carbon steel samples increase by 0.196 V and 0.060 V after coated with PANI nanotubes and aggregated PANI, respectively, and the corrosion currents density decrease by about 76.32% and 36.64%, respectively. The 6-day immersion experiment showed that the carbon steel samples coated by PANI nanotubes showed more excellent anticorrosion performance, because the more compact coating formed by PANI nanotubes may inhibit the corrosion process between the anodic and cathodic.

A multifunctional enzyme portfolio for α-chaconine and α-solanine degradation in the Phthorimaea operculella gut bacterium Glutamicibacter halophytocola S2 encoded in a trisaccharide utilization locus.

Steroidal glycoalkaloids (SGAs) are secondary metabolites commonly found in members of the family Solanaceae, including potatoes, and are toxic to pests and humans. The predominant SGAs in potato are α-chaconine and α-solanine. We previously reported that Glutamicibacter halophytocola S2, a gut bacterium of the pest Phthorimaea operculella (potato tuber moth), can degrade α-chaconine and α-solanine in potatoes, which can improve the fitness of P. operculella to feed on potatoes with a high content of toxic SGAs. Glutamicibacter halophytocola S2 harbored a gene cluster containing three deglycosylase genes-GE000599, GE000600, and GE000601-that were predicted encode α-rhamnosidase (RhaA), ß-glucosidase (GluA), and ß-galactosidase (GalA). However, there is limited information is available on the enzyme activities of the three enzymes expressed by this gene cluster and how they degrade the major toxic α-chaconine and α-solanine. In the current study, each enzyme of this gene cluster was produced by a prokaryotic expression approach and the activity of the recombinant enzymes for their target substrate and α-chaconine and α-solanine were evaluated by EPOCH microplate spectrophotometer and liquid chromatography mass spectrometry (LC-MS). The three enzymes had multifunctional activities, with RhaA and GluA could hydrolyze α-rhamnose, ß-glucose, and ß-galactose, while GalA can hydrolyze ß-glucose and ß-galactose. The degradation of α-chaconine and α-solanine was consistent with the results of the enzyme activity assays. The final product solanidine could be generated by adding RhaA or GluA alone. In conclusion, this study characterized the multifunctional activity and specific degradation pathway of these three enzymes in G. halophytocola S2. The three multifunctional enzymes have high glycosidic hydrolysis activity and clear gene sequence information, which help facilitates understanding the detoxification mechanism of insect gut microbes. The enzymes have a broad application potential and may be valuable in the removal of toxic SGAs from for potato food consumption.

Study On Radon Concentration Variation During Subway Construction.

The high radon concentration in the underground space of the subway station during construction often endangers the health of workers. Subway station project No. 16 in Beijing, while under construction, was selected as the main measuring point, a year's monitoring data was obtained to analyse the change of radon concentration. It was found that the concentration of radon was basically within the range of 5 ~ 500 Bq/m3 and showing a low level in the morning and a high level at noon, and presents the seasonal rule, compared with other seasons, the summer radiation is stronger. Furthermore, among the different measuring points, the radon concentration of the heading roadway is the highest, and the construction level of the station hall is the lowest. According to the comprehensive analysis, the concentration of radon during the construction of the subway station is mainly affected by the ambient temperature and air mobility.

Poly(ionic liquid)-Modified Metal Organic Framework for Carbon Dioxide Adsorption.

The design and synthesis of solid sorbents for effective carbon dioxide adsorption are essential for practical applications regarding carbon emissions. Herein, we report the synthesis of composite materials consisting of amine-functionalized imidazolium-type poly(ionic liquid) (PIL) and metal organic frameworks (MOFs) through complexation of amino groups and metal ions. The carbon dioxide adsorption behavior of the synthesized composite materials was evaluated using the temperature-programmed desorption (TPD) technique. Benefiting from the large surface area of metal organic frameworks and high carbon dioxide diffusivity in ionic liquid moieties, the carbon dioxide adsorption capacity of the synthesized composite material reached 19.5 cm3·g-1, which is much higher than that of pristine metal organic frameworks (3.1 cm3·g-1) under carbon dioxide partial pressure of 0.2 bar at 25 °C. The results demonstrate that the combination of functionalized poly(ionic liquid) with metal organic frameworks can be a promising solid sorbent for carbon dioxide adsorption.

Status of research on hydrogen sulphide gas in Chinese mines.

In the process of coal mining, the abnormal gushing of hydrogen sulphide in mines poses a major threat to the health of coal miners and the safe production of mines, as these types of accidents have occurred in many coal-producing countries. China is the largest coal producer and consumer in the world and is one of the countries that are substantially affected by hydrogen sulphide in mines. Based on the existing studies, many investigators in China have conducted research on the actual situation in China and obtained some results. This paper summarizes the previous findings and the current status of hydrogen sulphide in Chinese mines, and predicts the direction of future development. In this paper, we discuss the cause, abnormal distribution, abnormal gushing and prevention and control measures for hydrogen sulphide in mines. In addition, this paper also evaluates the impact of the hydrogen sulphide in mines on the environment and health. This paper outlines a systematic research framework regarding hydrogen sulphide in mines and assesses the interrelationship between subtopics within this system framework. Currently, the scientific research on hydrogen sulphide in mines is not sufficient to meet the needs of the affected individuals Therefore, researchers must increase their efforts in this area to jointly address the challenge of analysing hydrogen sulphide in mines. In addition, we hope that this paper will provide some guidance for the study of hydrogen sulphide in mines.

Fabrication and Anti-Oxidation Ability of SiC-SiO2 Coated Carbon Fibers Using Sol-Gel Method.

The paper proposed a method to improve the anti-oxidation performance of carbon fibers (CF) at high temperature environment by coating silicon dioxide (SiO2) and silicon carbide (SiC). The modified sol-gel method had been used to ensure the proper interface between fibers and coating. We used polydimethylsiloxane and ethyl orthosilicate to make stable emulsion to uniformly disperse SiC nanoparticles. The modified SiO2/SiC coating had been coated on CF successfully. Compared with the untreated CF, the coated fibers started to be oxidized around 900 °C and the residual weight was 57% at 1400 °C. The oxidation mechanism had been discussed. The structure of SiC/SiO2 coated CF had been characterized by scanning electron microscope and X-ray diffraction analysis. Thermal gravimetric analysis was used to test the anti-oxidation ability of CF with different coatings.