Screening for pathogenic variants in obese cohort using whole-exome sequencing

Objective·To screen mutations of key genes in the leptin-melanocyte stimulating hormone (LEP-MSH) pathway by whole-exome sequencing (WES) in the obese cohort.Methods·A total of 119 obese patients aged 17－65 years old with body mass index (BMI)≥34 kg/m2, who underwent laparoscopic sleeve gastrectomy from January 2011 to July 2019 at Shanghai Sixth People′s Hospital, Shanghai Jiao Tong University School of Medicine were collected. The peripheral blood samples of the research subjects were collected, and whole genome DNA was extracted to perform WES. Bioinformatic methods were applied to detect the mutations in 16 genes in the LEP-MSH pathway (ADCY3, AGRP, BDNF, KSR2, LEP, LEPR, MC3R, MC4R, MCHR1, MRAP2, NTRK2, PCSK1, PHIP, POMC, SH2B1, and SIM1). Rare variants with the minor allele frequency in the total population less than 0.02 and in the East Asian population less than 0.01 in the 1000 Genome (1000G), Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD) were selected for subsequent analysis. Six pieces of prediction software were used to evaluate the deleteriousness of the mutations. Finally, based on the clinical information of each patient, the pathogenicity of all variants was determined according to the guidelines of America College of Medical Genetics and Genomics (ACMG), and only the "pathogenic", "likely pathogenic", and "uncertain significance" variants were retained.Results·A total of 26 variants, 22 kinds of variants were detected in 24 patients from 119 subjects, all of which were heterozygous mutations. The detected variants included 7 in SH2B1 gene (accounting for 26.92% of the total variants), 4 in MCHR1 gene (accounting for 15.38%), 3 in PHIP gene (accounting for 11.53%), 2 in ADCY3 and LEPR genes (accounting for 7.69%, respectively), and 1 in LEP, NTRK2, AGRP, KSR2, MC3R, MC4R, BDNF, and PCSK1 genes, respectively (accounting for 3.85%, respectively). There were 3 patients having the same mutation site in SH2B1 gene, and 2 patients having the same mutation sites in LEPR gene and MCHR1 gene, respectively. In addition, among these mutations, there were 12 ones not included in the East Asian population in 3 public databases, which were novel mutations in the East Asian population, located in SH2B1 (p.V209I, p.R67C, and p.L149F), KSR2 (p.P155T), LEP (p.D106N), LEPR (p.W132R), PHIP (p.K1461R), BDNF (p.N84S), PCSK1 (p.R282W), NTRK2 (p.T732M), MC3R (p.S71P), and MC4R (p.W174X).Conclusion·A total of 22 kinds of rare variations possibly associated with obesity in the LEP-MSH pathway are detected, 12 of which are novel in the East Asian population

Dynamics analysis and testing in air-jet weft insertion

189-195On the basis of fluid dynamics, this paper deduces the pull force formula of main nozzle on air-jet loom and introduces a method of experiment to test the airflow velocity in the exit of nozzle. The effect of different structure parameters of main nozzle on the pull force has been studied. It is observed that the inlet of thread tube is a bottleneck of main nozzle and the main development of main nozzle lengthens the thread tube. The theoretical findings are found to be in good agreement with experimental findings and this verifies that the formula for pull force is reasonabl

Semantic Labeling and Refinement of LIDAR Point Clouds using Deep Neural Network in Urban Areas

In this paper, we propose a framework for obtaining semantic labels of LiDAR point clouds and refining the classification results by combining a deep neural network with a graph-structured smoothing technique. In general, the goal of the semantic scene analysis is to assign a semantic label to each point in the point cloud. Although various related researches have been reported, due to the complexity of urban areas, the semantic labeling of point clouds in urban areas is still a challenging task. In this paper, we address the issues of how to effectively extract features from each point and its local surrounding and how to refine the initial soft labels by considering contextual information in the spatial domain. Specifically, we improve the effectiveness of classification of point cloud in two aspects. Firstly, instead of utilizing handcrafted features as input for classification and refinement, the local context of a point is embedded into deep dimensional space and classified via a deep neural network (PointNet++), and simultaneously soft labels are obtained as initial results for next refinement. Secondly, the initial label probability set is improved by taking the context both in the spatial domain into consideration by constructing a graph structure, and the final labels are optimized by a graph cuts algorithm. To evaluate the performance of our proposed framework, experiments are conducted on a mobile laser scanning (MLS) point cloud dataset. We demonstrate that our approach can achieve higher accuracy in comparison to several commonly-used state-of-the-art baselines. The overall accuracy of our proposed method on TUM dataset can reach 85.38% for labeling eight semantic classes

土壤宏蛋白质组学蛋白质提取方法及其应用

Metaproteomics has a bright future for its broad application in understanding the interaction between environment and function, metabolism of the soil microbial community. Due to the specialty of soil sample, the extraction method is one of the main bottlenecks which limit their wide application. This paper summarized research actuality of soil protein extraction on several aspects from sample preparation, extraction methods and influencing factors, pointed out some currently-existing research problems, and put forward new extraction method and thought exploiture from traditional methods. In general, only by proceeding from the experimental purpose, protein types and follow-up study, setting up the corresponding extraction strategy, can the extraction problem of soil protein be effectively solved. According to the source and distribution, the soil protein can be divided into three types, total protein, extracellular protein and intracellular protein, thus the extraction method of three types of protein are different from each other. The direct extraction method is mostly used in the total protein extraction; the extraction method of extracellular protein does not require lysis; the intracellular protein can be extracted by direct or indirect methods and so on. The extract yield can be affected by the methods of lysis, concentration and removal of humus, as well as the type and pH value of the extraction buffer. In addition, the application prospects of the soil metaproteome and future research work were also discussed

Abundance and diversity of nitrogen-fixing bacteria in rhizosphere and bulk paddy soil under different duration of organic management

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) approaches were used to assess respectively the molecular diversity and quantity of the nifH gene sequences in rhizosphere and bulk paddy soil under conventional management and different duration of organic management (2, 3, 5, 9 years). The phylogenetic distribution of clones based on nifH gene sequence showed that taxonomic groups were consisted of Alphaproteobacteria (27.6%), Betaproteobacteria (24.1%) and Gammaproteobacteria (48.3%). Members of the order Rhizobiales and Pseudomonadales were prevalent among the dominant diazotrophs. When the quantity of the nifH gene sequences was determined by qPCR, 2.27 x 10(5) to 1.14 x 10(6) copies/g of soil were detected. Except for 2 years organically managed soil, nifH gene copy numbers in organic soil, both rhizosphere and bulk, were significantly higher than in CM soil. Moreover, nifH gene copy numbers in the organic rhizosphere soil (3, 5, 9 years) were significantly higher than in bulk soil. The abundance and diversity of nitrogen-fixing bacteria tended to increase with duration of organic management but the highest number of nifH gene copies was observed in the rhizosphere and bulk soil of 5 years organic management. In addition, analysis of variance and canonical correspondence analysis (CCA) showed that C/N, C and N were important factors influencing the abundance and community structure of nitrogen-fixing bacterial

High-Contrast and Compact Integrated Wavelength Diplexer Based on Subwavelength Grating Anisotropic Metamaterial for 1550/2000 nm

A high-contrast and compact wavelength diplexer is presented for conventional 1550 nm and emerging 2000 nm based on a subwavelength-grating (SWG) coupler. The SWG silicon waveguide thoroughly blocks the light propagation around 1550 nm but fully supports 2000 nm (extinction ratio: 43.11 dB). This grating type anisotropic metamaterial not only efficiently reduces the coupling length but also expands the operational bandwidth. Simulated by 3D finite-difference time-domain method, the proposed diplexer possesses a remarkably low insertion loss and a high contrast of 25.24 (31.7) dB at 1550 (2000) nm. The operational bandwidth of 200 (108) nm is achieved with contrast over 15 dB and insertion loss below 0.22 dB. The footprint of diplexer is only 5.27 μm × 11.85 μm. Moreover, such design has the scalability by simply tuning the geometrical parameters of SWG

Age as a predictor of significant fibrosis features in HBeAg-negative chronic hepatitis B virus infection with persistently normal alanine aminotransferase.

Although alanine aminotransferase (ALT) levels reflect the degree of liver damage, not all patients with chronic hepatitis B virus (HBV) infection exhibit persistently elevated ALT levels. In the present study, we aimed to comprehensively evaluate the characteristics of histological abnormalities in a large population of Chinese patients with chronic HBV and persistently normal ALT levels.In total, 2303 consecutive patients who underwent liver biopsy were screened. Of these patients, 273 were categorized as having persistently normal ALT levels (PNALT), whereas 618 were categorized as having persistently or intermittently elevated ALT levels (PIALT). All these patients had at least three ALT values recorded in the year prior to the baseline liver biopsy.Significant necroinflammation was observed in 9.7% (11/113) patients with PNALT, 23.3% (42/180) patients with PIALT (ALT 1-2× upper limit of normal [ULN]), and 27.8% (42/151) patients with PIALT (ALT > 2× ULN), whereas significant fibrosis was observed in 8.8% (10/113) patients with PNALT, 27.8% (42/151) patients with PIALT (ALT 1-2× ULN), and 21.2% (32/151) patients with PIALT (ALT > 2× ULN). Multiple logistic regression analysis indicated that age parameters were associated with significant histological abnormalities in patients with PNALT. The area under the curve showed that age was associated with significant fibrosis characteristics in patients with hepatitis B extracellular antigen (HBeAg)-negative PNALT.Significant histological abnormalities are not often observed in Chinese patients with PNALT. Interestingly, age appears to be a predictor of significant fibrosis in patients with HBeAg-negative PNALT

Light affects the chloroplast ultrastructure and post-storage photosynthetic performance of watermelon (Citrullus lanatus) plug seedlings.

Watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] plug seedlings were stored at 15°C in the light at a photosynthetic photon flux density of 15 µmol·m(-2)·s(-1) or in darkness for 6 days, to evaluate their chloroplast ultrastructure, and associated photosynthetic characteristics. Storage in the dark caused swelling, disordered granal arrangement, and starch grain disappearance in the chloroplasts. In contrast, the chloroplasts stored in the light were relatively normal. As a result, the light-stored seedlings had a significantly higher chlorophyll content, Fv/Fm, and Pn than did dark-stored seedlings. Regardless of whether the seedlings were stored in light or darkness, the Gs and Ls of the seedlings significantly decreased, while the Ci obviously increased when the Pn decreased after 6 days of storage. This result suggests that the decreased Pn is not solely a stomatal effect, as the effects on the chloroplasts contributed to this photosynthetic inhibition. Six days after transplanting, seedlings that were stored in the light or darkness for 2 or 4 days showed complete recovery of chloroplast ultrastructure, chlorophyll content, Fv/Fm, Gs and Pn. When the storage period increased to 6 days, the dark-stored seedlings had a significantly lower Fv/Fm and Pn than the light-stored and control seedlings 6 days after transplanting, which was mainly ascribed to incomplete recovery of chloroplast ultrastructure. Furthermore, the light-stored seedlings exhibited a significantly higher shoot dry weight during storage and a higher percentage dry weight increase after transplanting than the dark-stored seedlings. These effects were enhanced by prolonged storage (4 to 6 days). This study demonstrated that dim light during storage is beneficial for maintaining chloroplast ultrastructure as well as photosynthetic efficiency in watermelon seedlings, thus contributing to the rapid recovery of post-storage photosynthetic performance, which ensures the transplant quality of the seedlings after removal from storage