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Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological insights on the gene set level. However, platforms exploring cancer multi-omics data using GSA methods are lacking. In this study, we upgraded our GSCALite to GSCA (gene set cancer analysis, http://bioinfo.life.hust.edu.cn/GSCA) for cancer GSA at genomic, pharmacogenomic and immunogenomic levels. In this improved GSCA, we integrated expression, mutation, drug sensitivity and clinical data from four public data sources for 33 cancer types. We introduced useful features to GSCA, including associations between immune infiltration with gene expression and genomic variations, and associations between gene set expression/mutation and clinical outcomes. GSCA has four main functional modules for cancer GSA to explore, analyze and visualize expression, genomic variations, tumor immune infiltration, drug sensitivity and their associations with clinical outcomes. We used case studies of three gene sets: (i) seven cell cycle genes, (ii) tumor suppressor genes of PI3K pathway and (iii) oncogenes of PI3K pathway to prove the advantage of GSCA over single gene analysis. We found novel associations of gene set expression and mutation with clinical outcomes in different cancer types on gene set level, while on single gene analysis level, they are not significant associations. In conclusion, GSCA is a user-friendly web server and a useful resource for conducting hypothesis tests by using GSA methods at genomic, pharmacogenomic and immunogenomic levels.

Platelets are reprogrammed by cancer via a process called education, which favors cancer development. The transcriptional profile of tumor-educated platelets (TEPs) is skewed and therefore practicable for cancer detection. This intercontinental, hospital-based, diagnostic study included 761 treatment-naïve inpatients with histologically confirmed adnexal masses and 167 healthy controls from nine medical centers (China, n = 3; Netherlands, n = 5; Poland, n = 1) between September 2016 and May 2019. The main outcomes were the performance of TEPs and their combination with CA125 in two Chinese (VC1 and VC2) and the European (VC3) validation cohorts collectively and independently. Exploratory outcome was the value of TEPs in public pan-cancer platelet transcriptome datasets. The AUCs for TEPs in the combined validation cohort, VC1, VC2, and VC3 were 0.918 (95% CI 0.889–0.948), 0.923 (0.855–0.990), 0.918 (0.872–0.963), and 0.887 (0.813–0.960), respectively. Combination of TEPs and CA125 demonstrated an AUC of 0.922 (0.889–0.955) in the combined validation cohort; 0.955 (0.912–0.997) in VC1; 0.939 (0.901–0.977) in VC2; 0.917 (0.824–1.000) in VC3. For subgroup analysis, TEPs exhibited an AUC of 0.858, 0.859, and 0.920 to detect early-stage, borderline, non-epithelial diseases and 0.899 to discriminate ovarian cancer from endometriosis. TEPs had robustness, compatibility, and universality for preoperative diagnosis of ovarian cancer since it withstood validations in populations of different ethnicities, heterogeneous histological subtypes, and early-stage ovarian cancer. However, these observations warrant prospective validations in a larger population before clinical utilities.

Pilomatricoma, a benign skin appendage tumor, also known as calcifying epithelioma, consists of islands of epithelial cells histologically that contain anucleated cells in the center surrounded by basophilic cells and partial calcification. Sporadic pilomatricomas commonly have somatic mutations in the gene CTNNB1, but causative genes from germline and the underlying pathophysiology are unclear. In this study, we identified a germline missense variant of PLCD1 encoding PLCδ1, c.1186G>A (p.Glu396Lys), in a large Chinese family with autosomal dominant multiple pilomatricomas. Phospholipase C, a key enzyme playing critical roles in intracellular signal transduction, is essential for epidermal barrier integrity. The p.Glu396Lys variant increased the enzymatic activity of PLCδ1, leading to protein kinase C/protein kinase D/extracellular signal–regulated kinase1/2 pathway activation and TPRV6 channel closure, which not only resulted in excessive proliferation of keratinocytes in vitro and in vivo but also induced local accumulation of calcium in the pilomatricoma-like tumor that developed spontaneously in the skin of Plcd1E396K/E396K mice. Our results implicate this p.Glu396Lys variant of PLCD1 from germline leading to gain-of-function of PLCδ1 as a causative genetic defect in familial multiple pilomatricomas.

The aim of this experiment was to investigate the effect of soy lecithin on serum-related indicators and liver health in laying hens under the influence of high-fat diets. 180 peak laying hens at 40 weeks of age were randomly assigned to one of the four diets using a 2 × 2 factorial and fed for 5 weeks. The results showed that compared to the low-fat group, the high-fat group had lower egg production (p < 0.05) and higher average daily feed intake and feed-to-egg ratio (p < 0.05). At the 21st day, the serum levels of triglyceride (TC) and superoxide dismutase (SOD) were higher (p < 0.05), high-density lipoproteins cholesterol (HDL-C) levels were lower (p < 0.01), catalase (CAT) activity was lower (p < 0.05), TC and malondialdehyde (MDA) levels in liver were higher (p < 0.01) and SOD activity in liver was lower (p < 0.05) in layers supplemented with soy lecithin. CAT activity in serum was increased (p < 0.01) and total antioxidant capacity (T-AOC) activity in the liver was decreased (p < 0.05) after increasing the dietary fat concentration. The addition of soy lecithin and the increase in dietary fat concentration had a highly significant interaction on serum CAT activity and liver TC content in layers (p < 0.01). At the 35th day, the serum alanine aminotransferase (ALT) activity was higher (p < 0.01), serum glutathione peroxidase (GSH-Px) and CAT activity were higher (p < 0.05), and serum triglyceride (TG) content and total T-AOC capacity activity were lower (p < 0.05) in layers supplemented with soy lecithin. Increasing dietary fat concentration decreased alanine aminotransferase (ALT), aspartate aminotransferase (AST) and GSH-Px activity in serum (p < 0.05). However, it increased TG and MDA content in liver (p < 0.05), and highly decreased SOD content in liver (p < 0.01) in layers. The addition of soy lecithin and increasing dietary fat concentration had a highly significant reciprocal effect on serum ALT viability and CAT viability (p < 0.01) and liver TG and MDA content and SOD viability (p < 0.05) in layers. In conclusion, feeding high-fat diets will adversely affect the laying performance of laying hens, while long-term addition of lecithin can improve the blood lipids and liver lipids of laying hens, enhance the antioxidant capacity of the liver, and maintain liver health.

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

MicroRNAs (miRNAs) related single-nucleotide variations (SNVs), including single-nucleotide polymorphisms (SNPs) and disease-related variations (DRVs) in miRNAs and miRNA-target binding sites, can affect miRNA functions and/or biogenesis, thus to impact on phenotypes. miRNASNP is a widely used database for miRNA-related SNPs and their effects. Here, we updated it to miRNASNP-v3 (http://bioinfo.life.hust.edu.cn/miRNASNP/) with tremendous number of SNVs and new features, especially the DRVs data. We analyzed the effects of 7 161 741 SNPs and 505 417 DRVs on 1897 pre-miRNAs (2630 mature miRNAs) and 3′UTRs of 18 152 genes. miRNASNP-v3 provides a one-stop resource for miRNA-related SNVs research with the following functions: (i) explore associations between miRNA-related SNPs/DRVs and diseases; (ii) browse the effects of SNPs/DRVs on miRNA-target binding; (iii) functional enrichment analysis of miRNA target gain/loss caused by SNPs/DRVs; (iv) investigate correlations between drug sensitivity and miRNA expression; (v) inquire expression profiles of miRNAs and their targets in cancers; (vi) browse the effects of SNPs/DRVs on pre-miRNA secondary structure changes; and (vii) predict the effects of user-defined variations on miRNA-target binding or pre-miRNA secondary structure. miRNASNP-v3 is a valuable and long-term supported resource in functional variation screening and miRNA function studies.

Coronavirus disease-2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a global pandemic and brought great crises and disasters to mankind The disease is transmitted mainly through respiratory droplets and close contact, but whether it can be transmitted through the digestive tract and by faeces has been a problem of great concern to the medical community and the general public This review discusses and analyzes the problem in terms of clinical manifestations and digestive system symptoms of COVID-19, detection and isolation of virus, expression and distribution of angiotensin-converting enzyme 2 receptor, etc There is a potential risk of infection and transmission of SARS-CoV-2 through the digestive tract It is suggested to carry out further confirmatory research and strengthen effective means of prevention and control © The Author(s) 2020 Published by Baishideng Publishing Group Inc All rights reserved

Objective To ascertain the biomechanical effects of a degenerated L4 -L5 segment on the lower lumbar spine through a comprehensive simulation of disc degeneration. Methods A three-dimensional nonlinear finite element model of a normal L3 -S1 lumbar spine was constructed and validated. This normal model was then modified such that three degenerated models with different degrees of degeneration (mild, moderate, or severe) at the L4 -L5 level were constructed. While experiencing a follower compressive load (500 N), hybrid moment loads were applied to all models to determine range of motion (ROM), intradiscal pressure (IDP), maximum von Mises stress in the annulus, maximum shear stress in the annulus, and facet joint force. Results As the degree of disc degeneration increased, the ROM of the L4 -L5 degenerated segment declined dramatically in all postures (flexion: 5.79°-1.91°; extension: 5.53°-2.62°; right lateral bending: 4.47°-1.46°; left lateral bending: 4.86°-1.61°; right axial rotation: 2.69°-0.74°; left axial rotation: 2.69°-0.74°), while the ROM in adjacent segments increased (1.88°-8.19°). The largest percent decrease in motion of the L4 -L5 segment due to disc degeneration was in right axial rotation (75%), left axial rotation (69%), flexion (67%), right lateral bending (67%), left lateral bending right (67%), and extension (53%). The change in the trend of the IDP was the same as that of the ROM. Specifically, the IDP decreased (flexion: 0.592-0.09 MPa; extension: 0.678-0.334 MPa; right lateral bending: 0.498-0.205 MPa; left lateral bending: 0.523-0.272 MPa; right axial rotation: 0.535-0.246 MPa; left axial rotation: 0.53-0.266 MPa) in the L4 -L5 segment, while the IDP in adjacent segments increased (0.511-0.789 MPa). The maximum von Mises stress and maximum shear stress of the annulus in whole lumbar spine segments increased (L4 -L5 segment: 0.413-2.626 MPa and 0.412-2.783 MPa, respectively; adjacent segment of L4 -L5 : 0.356-1.493 MPa and 0.359-1.718 MPa, respectively) as degeneration of the disc progressively increased. There was no apparent regularity in facet joint force in the degenerated segment as the degree of disc degeneration increased. Nevertheless, facet joint forces in adjacent healthy segments increased as the degree of disc degeneration increased (extension: 49.7-295.3 N; lateral bending: 3.5-171.2 N; axial rotation: 140.2-258.8 N). Conclusion Degenerated discs caused changes in the motion and loading pattern of the degenerated segments and adjacent normal segments. The abnormal load and motion in the degenerated models risked accelerating degeneration in the adjacent normal segments. In addition, accurate simulation of degenerated facet joints is essential for predicting changes in facet joint loads following disc degeneration.

Motivation T-cell receptors (TCRs) function to recognize antigens and play vital roles in T-cell immunology. Surveying TCR repertoires by characterizing complementarity-determining region 3 (CDR3) is a key issue. Due to the high diversity of CDR3 and technological limitation, accurate characterization of CDR3 repertoires remains a great challenge. Results We propose a computational method named CATT for ultra-sensitive and precise TCR CDR3 sequences detection. CATT can be applied on TCR sequencing, RNA-Seq and single-cell TCR(RNA)-Seq data to characterize CDR3 repertoires. CATT integrated de Bruijn graph-based micro-assembly algorithm, data-driven error correction model and Bayesian inference algorithm, to self-adaptively and ultra-sensitively characterize CDR3 repertoires with high performance. Benchmark results of datasets from in silico and experimental data demonstrated that CATT showed superior recall and precision compared with existing tools, especially for data with short read length and small size and single-cell sequencing data. Thus, CATT will be a useful tool for TCR analysis in researches of cancer and immunology. Availability and implementation http://bioinfo.life.hust.edu.cn/CATT or https://github.com/GuoBioinfoLab/CATT. Supplementary information Supplementary data are available at Bioinformatics online.

Although immune checkpoint blockade (ICB) therapies have achieved great progress, the patient response varies among cancers. In this study, we analyzed the potential genomic indicators contributing to ICB therapy response. The results showed that high tumor mutation burden (TMB) failed to predict response in anti-PD1 treated melanoma. SERPINB3 was the most significant response-related gene in melanoma and mutations in either SERPINB3 or PEG3 can serve as an independent risk factor in melanoma. Some recurrent mutations in CSMD3 were only in responders or non-responders, indicating their diverse impacts on patient response. Enrichment scores (ES) of gene mutations in 12 biological pathways were significantly higher in responders or non-responders. Next, the P-TMB calculated from genes in these pathways was significantly related to patient response with prediction AUC 0.74–0.82 in all collected datasets. In conclusion, our work provides new insights into the application of TMB in predicting patient response, which will benefit to immunotherapy research.

Current experiment was designed to check the effect of dietary supplementation of ramie powder on the growth performance, carcass and meat qualities and antioxidative capacity of Linwu ducks. A total of 312 ducks at 21-day-age were equally divided into 4 groups, fed with control diet, control diet supplemented of 3, 6, or 12% ramie powder, respectively. The results showed that dietary supplementation of 6 and 12% ramie powder increased the final weight and daily body weight gain (P < 0.05), and dietary supplementation of 6% ramie improved the cooking loss of the leg meat 45-mins-postmortem compared with the control group (P < 0.05). Moreover, dietary supplementation of 6% ramie powder promoted the antioxidative capacity of the ducks by increasing the serum activities of superoxide dismutase and glutathione (P < 0.05), as well as the mRNA expressions of glutathione peroxidase 1 in the breast meat and superoxide dismutase 1 in the leg meat (P < 0.05). This experiment demonstrated that dietary supplementation of ramie powder showed beneficial efficacy on the growth performance of Linwu ducks. It corroborated the potential of dietary ramie being used as poultry feed ingredient and suggested that 6% was the proper supplementation rate of ramie powder in Linwu ducks’ feed.

Cortical visualization is essential to understand the dynamic changes in brain microenvironment under physiopathological conditions. However, the turbid scalp and skull severely limit the imaging depth and resolution. Existing cranial windows require invasive scalp excision and various subsequent skull treatments. Non-invasive in vivo imaging of skull bone marrow, meninges, and cortex through scalp and skull with high resolution yet remains a challenge. In this work, a non-invasive trans-scalp/skull optical clearing imaging window is proposed for cortical and calvarial imaging, which is achieved by applying a novel skin optical clearing reagent. The imaging depth and resolution are greatly enhanced in near infrared imaging and optical coherence tomography imaging. Combining this imaging window with adaptive optics, we achieve the visualization and manipulation of the calvarial and cortical microenvironment through the scalp and skull using two-photon imaging for the first time. Our method provides a well-performed imaging window and paves the way for intravital brain studies with the advantages of easy-operation, convenience and non-invasiveness.

Current experiment was designed to check the effect of dietary supplementation of ramie powder on the growth performance, carcass and meat qualities and antioxidative capacity of

Objective To determine the effect of spiral nucleus implant parameters on the biomechanical behavior of the lumbar intervertebral disc after nucleus replacement under compressive loading. Methods A finite element (FE) model of nucleus replacement in the L4-5 intervertebral disc was constructed. The effects of a spiral implant parameters, such as elasticity, size, and friction property, on the biomechanical behavior of the disc under a compressive load were determined. The effect of an implant with a sharp edge on disc biomechanics was also examined. The stress distribution and contact pressure on the endplate and AF, axial stiffness of disc, and annular bulge of the nucleus replacement models were investigated. Results Axial stiffness, annular bulge, and contact pressure were all insensitive to friction properties. Insertion of the spiral implant reversed the changes in the AF and endplates due to the removal of the nucleus. There was a positive correlation between axial stiffness and elasticity with implant size. Annular bulge was positively correlated with size but negatively correlated with elasticity. Compared with the base model, the implant with a sharp edge caused a decrease in disc axial stiffness but an increase in contact pressure on the AF in an annular bulge in the sagittal and coronal axis, respectively. Conclusions A spiral implant may provide similar biomechanical behavior as a normal disc during compressive loading, with an optimal modulus of approximately 7 MPa. The spiral implant should fully conform to the nucleus cavity during replacement for the best biomechanical results.

Aims: Cleft lip with or without cleft palate (CL/P) is a common birth defect with an average prevalence of 1/700 to 1/1000. Almost 70% of CL/P cases are nonsyndromic CL/P (NSCL/P). The aim of this study was to identify the underlying cause of a four-generation Chinese family with autosomal dominant NSCL/P. Methods: Genomic DNA was extracted from peripheral blood leukocytes, and whole-exome sequencing was carried out to identify the underlying genetic cause of the disorder. The mutation was confirmed by Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism methods. Western blotting and coimmunoprecipitation were used to analyze the protein expression level and adhesive dimerization of the CDH1 mutants. Slow aggregation assays were conducted to investigate the cell-cell adhesion ability. Results: A novel missense mutation (c.468G>C/p.Trp156Cys) of CDH1 was identified in the proband and the mutation was shown to cosegregate with the phenotype in the family. Furthermore, we found that the p.Trp156Cys mutation led to decreased E-cadherin dimerization and cell-cell adhesion ability. Conclusions: Our findings identified a novel CDH1 variant (c.468G>C/p.Trp156Cys) responsible for NSCL/P in a Chinese family, which expanded the mutational spectrum of the CDH1 gene and may contribute to understanding the molecular basis of NSCL/P.

Extracellular vesicles (EVs) packing various molecules play vital roles in intercellular communication. Non-coding RNAs (ncRNAs) are important functional molecules and biomarkers in EVs. A comprehensive investigation of ncRNAs expression in EVs under different conditions is a fundamental step for functional discovery and application of EVs. Here, we curated 2030 small RNA-seq datasets for human EVs (1506 sEV and 524 lEV) in 24 conditions and over 40 diseases. We performed a unified reads dynamic assignment algorithm (RDAA) considering mismatch and multi-mapping reads to quantify the expression profiles of seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA). We constructed EVAtlas (http://bioinfo.life.hust.edu.cn/EVAtlas), a comprehensive database for ncRNA expression in EVs with four functional modules: (i) browse and compare the distribution of ncRNAs in EVs from 24 conditions and eight sources (plasma, serum, saliva, urine, sperm, breast milk, primary cell and cell line); (ii) prioritize candidate ncRNAs in condition related tissues based on their expression; (iii) explore the specifically expressed ncRNAs in EVs from 24 conditions; (iv) investigate ncRNA functions, related drugs, target genes and EVs isolation methods. EVAtlas contains the most comprehensive ncRNA expression in EVs and will be a key resource in this field.

Background: Morpho-physiological alternations of platelets provided a rationale to harness RNA sequencing of tumor-educated platelets (TEPs) for preoperative diagnosis of cancer. Timely, accurate, and non-invasive detection of ovarian cancer in women with adnexal masses presents a significant clinical challenge. Patients and Methods: This intercontinental, hospital-based, diagnostic study included 761 treatment-naïve inpatients with histologically confirmed adnexal masses and 167 healthy controls from nine medical centers (China, n=3; Netherlands, n=5; Poland, n=1) between September 2016 and May 2019. The main outcomes were the performance of TEPs and their combination with CA125 in two Chinese (VC1 and VC2) and the European (VC3) validation cohorts collectively and independently. Exploratory outcome was the value of TEPs in public pan-cancer platelet transcriptome datasets. Results: The AUCs for TEPs in the combined validation cohort, VC1, VC2, and VC3 were 0.918 (95% CI 0.889-0.948), 0.923 (0.855-0.990), 0.918 (0.872-0.963), and 0.887 (0.813-0.960), respectively. Combination of TEPs and CA125 demonstrated an AUC of 0.922 (0.889-0.955) in the combined validation cohort; 0.955 (0.912-0.997) in VC1; 0.939 (0.901-0.977) in VC2; 0.917 (0.824-1.000) in VC3. For subgroup analysis, TEPs exhibited an AUC of 0.858, 0.859, and 0.920 to detect early-stage, borderline, non-epithelial diseases and 0.899 to discriminate ovarian cancer from endometriosis. Analysis of public datasets suggested that TEPs had potential to detect multiple malignancies (Table 1). Conclusions: TEPs had robustness, compatibility, and universality for preoperative diagnosis of ovarian cancer since it withstood validations in populations of different ethnicities, heterogeneous histological subtypes, early-stage ovarian cancer as well as other malignancies. However, these observations warrant prospective validations in a larger population before clinical utilities. Table 1. Performance for TEPs in public pan-cancer datasets. Disease n Healthy Control AUC, area under the curve (95% CI) Women NSCLC (non-small-cell lung cancer) 126 77 0.758 (0.691-0.825) Breast cancer 38 77 0.817 (0.726-0.909) Colorectal cancer 18 77 0.973 (0.945-1.000) Pancreatic cancer 16 77 0.993 (0.981-1.000) Glioblastoma 10 77 0.923 (0.831-1.000) Men NSCLC 119 82 0.746 (0.677-0.815) Colorectal cancer 25 82 0.933 (0.884-0.982) Pancreatic cancer 22 82 0.993 (0.984-1.000) Glioblastoma 19 82 0.981 (0.959-1.000) All NSCLC 245 159 0.774 (0.728-0.820) Colorectal cancer 40 159 0.978 (0.961-0.996) Breast cancer 38 159 0.821 (0.736-0.906) Pancreatic cancer 35 159 0.987 (0.974-0.999) Glioblastoma 35 159 0.931 (0.890-0.972) Hepatobiliary carcinomas 14 159 0.991 (0.978-1.000) Citation Format: Yue Gao, Chun-Jie Liu, Hua-Yi Li, Xiao-Ming Xiong, Sjors G.j.g. In ‘t Veld, Gui-Ling Li, Jia-Hao Liu, Guang-Yao Cai, Gui-Yan Xie, Shao-Qing Zeng, Yuan Wu, Jian-Hua Chi, Qiong Zhang, Xiao-Fei Jiao, Lin-Li Shi, Wan-Rong Lu, Wei-Guo Lv, Xing-Sheng Yang, Jurgen M.j. Piek, Cornelis D de Kroon, C.a.r. Lok, Anna Supernat, Sylwia Łapińska-Szumczyk, Anna Łojkowska, Anna J. Żaczek, Jacek Jassem, Bakhos A. Tannous, Nik Sol, Edward Post, Myron G. Best, Bei-Hua Kong, Xing Xie, Ding Ma, Thomas Wurdinger, An-Yuan Guo, Qing-Lei Gao. Platelet RNA signature enables early and accurate detection of ovarian cancer: An intercontinental, biomarker identification study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB168.

Transcription factors (TFs) act as key regulators in biological processes through controlling gene expression. Here, we conducted a systematic study for all human TFs on the expression, regulation, interaction, mutation, phenotype and cancer survival. We revealed that the average expression levels of TFs in normal tissues were lower than 50% expression of non-TFs, whereas TF expression was increased in cancers. TFs that are specifically expressed in an individual tissue or cancer may be potential marker genes. For instance, TGIF2LX/Y were preferentially expressed in testis and NEUROG1, PRDM14, SRY, ZNF705A and ZNF716 were specifically highly expressed in germ cell tumors. We found different distributions of target genes and TF co-regulations in different TF families. Some small TF families have huge protein interaction pairs, suggesting their central roles in transcriptional regulation. The bZIP family is a small family involving many signaling pathways. Survival analysis indicated that most TFs significantly affect survival of one or more cancers. Some survival-related TFs were also specifically highly expressed in the corresponding cancer types, which may be potential targets for cancer therapy. Finally, we identified 43 TFs whose mutations were closely correlated to survival, suggesting their cancer-driven roles. The systematic analysis of TFs provides useful clues for further investigation of TF regulatory mechanisms and the role of TFs in diseases.

Background The number of oblique lumbar interbody fusion (OLIF) procedures has continued to rise over recent years. Adjacent segment degeneration (ASD) is a common complication following vertebral body fusion. Although the precise mechanism remains uncertain, ASD has gradually become more common in OLIF. Therefore, the present study analyzed the association between disc degeneration and OLIF to explore whether adjacent degeneration was promoted by OLIF in degenerative disc disease. Methods A three-dimensional nonlinear finite element (FE) model of the L3-S1 lumbar spine was developed and validated. Three lumbar spine degeneration models with different degrees of degeneration (mild, moderate and severe) and a model of OLIF surgery were constructed at the L4-L5 level. When subjected to a follower compressive load (500 N), hybrid moment loading was applied to all models of the lumbar spine and the range of motion (ROM), intradiscal pressure (IDP), facet joint force (FJF), average mises stress in the annulus (AMSA), average tresca stress in the annulus (ATSA) and average endplate stress (AES) were measured. Results Compared with the healthy lumbar spine model, the ROM, IDP, FJF, AMSA, ATSA and AES of the segments adjacent to the degenerated segment increased in each posture as the degree of disc degeneration increased. In different directions of motion, the ROM, IDP, FJF, AMSA, ATSA and AES in the OLIF model in the L3-L4 and L5-S1 segments were higher than those of the healthy model and each degenerated model. Compared with the healthy model, the largest relative increase in biomechanical parameters above (ROM, IDP, FJF, AMSA, ATSA or AES) was observed in the L3-L4 segment in the OLIF model, of 77.13%, 32.63%, 237.19%, 45.36%, 110.92% and 80.28%, respectively. In the L5-S1 segment the corresponding values were 68.88%, 36.12%, 147.24%, 46.00%, 45.88% and 51.29%, respectively. Conclusions Both degenerated discs and OLIF surgery modified the pattern of motion and load distribution of adjacent segments (L3-L4 and L5-S1 segments). The increases in the biomechanical parameters of segments adjacent to the surgical segment in the OLIF model were more apparent than those of the degenerated models. In summary, OLIF risked accelerating the degeneration of segments adjacent to those of a surgical segment.

Immune checkpoint genes (ICGs) play critical roles in circumventing self-reactivity and represent a novel target to develop treatments for cancers. However, a comprehensive analysis for the expression profile of ICGs at a pan-cancer level and their correlation with patient response to immune checkpoint blockade (ICB) based therapy is still lacking. In this study, we defined three expression patterns of ICGs using a comprehensive survey of RNA-seq data of tumor and immune cells from the functional annotation of the mammalian genome (FANTOM5) project. The correlation between the expression patterns of ICGs and patients survival and response to ICB therapy was investigated. The expression patterns of ICGs were robust across cancers, and upregulation of ICGs was positively correlated with high lymphocyte infiltration and good prognosis. Furthermore, we built a model (ICGe) to predict the response of patients to ICB therapy using five features of ICG expression. A validation scenario of six independent datasets containing data of 261 patients with CTLA-4 and PD-1 blockade immunotherapies demonstrated that ICGe achieved area under the curves of 0.64–0.82 and showed a robust performance and outperformed other mRNA-based predictors. In conclusion, this work revealed expression patterns of ICGs and underlying correlations between ICGs and response to ICB, which helps to understand the mechanisms of ICGs in ICB signal pathways and other anticancer treatments.

Skull is a reservoir for supplying immune cells that mediate brain immune surveillance. However, during intravital optical imaging of brain, conventional cranial windows requiring skull thinning or removal disrupt brain immunity integrity. Here, a novel long-term clearing cranial window (LCCW) based on the intact skull, dedicated to chronic skull transparency maintenance, is proposed. It significantly improves optical imaging resolution and depth, by which the cortical and calvarial vascular injury and regeneration processes after ischemic injury are longitudinally monitored in awake mice. Results show that calvarial blood vessels recover earlier than the cortex. And the transcriptome analysis reveals that gene expression patterns and immune cells abundances exist substantial differences between brain and skull after ischemic injury, which may be one of the causes for the time lag between their vascular recovery. These findings bring great enlightenment to vascular regeneration and reconstruction. Moreover, LCCW provides a minimally invasive approach for imaging the brain and skull bone marrow.

Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance and behaviors. However, the SAGs resulting in the vast majority of phenotypic sex differences are still unknown. To provide a useful resource for the functional study of SAGs, we manually curated public RNA-seq datasets with paired female and male biological replicates from the same condition and systematically re-analyzed the datasets using standardized methods. We identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples of 21 species, including human, chimpanzee, macaque, mouse, rat, cow, horse, chicken, zebrafish, seven fly species and five worm species. All these data were cataloged into SAGD, a user-friendly database of SAGs (http://bioinfo.life.hust.edu.cn/SAGD) where users can browse SAGs by gene, species, drug and dataset. In SAGD, the expression, annotation, targeting drugs, homologs, ontology and related RNA-seq datasets of SAGs are provided to help researchers to explore their functions and potential applications in agriculture and human health.

DNA methylation is an important epigenetic mechanism for regulating gene expression. Aberrant DNA methylation has been observed in various human diseases, including cancer. Single-nucleotide polymorphisms can contribute to tumor initiation, progression and prognosis by influencing DNA methylation, and DNA methylation quantitative trait loci (meQTL) have been identified in physiological and pathological contexts. However, no database has been developed to systematically analyze meQTLs across multiple cancer types. Here, we present Pancan-meQTL, a database to comprehensively provide meQTLs across 23 cancer types from The Cancer Genome Atlas by integrating genome-wide genotype and DNA methylation data. In total, we identified 8 028 964 cis-meQTLs and 965 050 trans-meQTLs. Among these, 23 432 meQTLs are associated with patient overall survival times. Furthermore, we identified 2 214 458 meQTLs that overlap with known loci identified through genome-wide association studies. Pancan-meQTL provides a user-friendly web interface (http://bioinfo.life.hust.edu.cn/Pancan-meQTL/) that is convenient for browsing, searching and downloading data of interest. This database is a valuable resource for investigating the roles of genetics and epigenetics in cancer.

A polarisation grating (PG) based on the hybrid photo-aligned double-frequency liquid crystal has been demonstrated and fabricated in this paper. The single-order diffraction efficiency is above 95% for circular polarisation incident light. The PG can be driven by 2.5 V/µm electric field with alternating frequency and has no Freedericksz transition threshold. In response time, the rise time and decay time are 650 and 950 , respectively; the sub-millisecond can be achieved under a low driving voltage.

Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of cancer samples. Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis. We further performed survival analysis and identified 22 212 eQTLs associated with patient overall survival. Furthermore, we linked the eQTLs to genome-wide association studies (GWAS) data and identified 337 131 eQTLs that overlap with existing GWAS loci. We developed PancanQTL, a user-friendly database (http://bioinfo.life.hust.edu.cn/PancanQTL/), to store cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs to enable searching, browsing and downloading. PancanQTL could help the research community understand the effects of inherited variants in tumorigenesis and development.

Zebrafish is an excellent model to study the mechanisms underlying successful central nervous system (CNS) regeneration. Previous study shows that activating transcription factor 3 (ATF3) promotes neurite outgrowth and is involved in optic nerve regeneration in zebrafish. Here, we used zebrafish model to investigate the role of ATF3 in regeneration following spinal cord injury (SCI). Quantitative polymerase chain reaction (qPCR) and in situ hybridization revealed that ATF3 mRNA levels increased at 12 h and 6 d following SCI. Double labeled immunofluorescence showed that ATF3 expressed in motoneurons. Treatment of anti-sense ATF3 morpholino (MO) inhibited locomotor recovery and decreased axon regeneration of spinal cord injured zebrafish. Further, inhibition of ATF3 up-regulated the expression of inflammatory factors tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β). These data suggest that ATF3 could promote locomotor recovery and axon regrowth in zebrafish SCI model possibly by regulating inflammatory response.

Cancer cell lines (CCLs) as important model systems play critical roles in cancer researches. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphisms, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication,http://bioinfo.life.hust.edu.cn/web/CCLA/) to authenticate 1,291 human CCLs of 28 tissues using gene expression profiles. CCLA curated CCL-specific gene signatures and employed machine learning methods to measure overall similarities and distances between the query sample and each reference CCL. CCLA showed an excellent speed advantage and high accuracy with a top 1 accuracy of 96.58% or 92.15% (top 3 accuracy of 100% or 95.11%) for microarray or RNA-Seq validation data (719 samples, 461 CCLs), respectively. To the best of our knowledge, CCLA is the first approach to authenticate CCLs based on gene expression. Users can freely and conveniently authenticate CCLs using gene expression profiles or NCBI GEO accession on CCLA website.

Objective To ascertain the biomechanical effects of a degenerated L4–L5 segment on the lower lumbar spine through a comprehensive simulation of disc degeneration. Methods A three‐dimensional nonlinear finite element model of a normal L3–S1 lumbar spine was constructed and validated. This normal model was then modified such that three degenerated models with different degrees of degeneration (mild, moderate, or severe) at the L4–L5 level were constructed. While experiencing a follower compressive load (500 N), hybrid moment loads were applied to all models to determine range of motion (ROM), intradiscal pressure (IDP), maximum von Mises stress in the annulus, maximum shear stress in the annulus, and facet joint force. Results As the degree of disc degeneration increased, the ROM of the L4–L5 degenerated segment declined dramatically in all postures (flexion: 5.79°–1.91°; extension: 5.53°–2.62°; right lateral bending: 4.47°–1.46°; left lateral bending: 4.86°–1.61°; right axial rotation: 2.69°–0.74°; left axial rotation: 2.69°–0.74°), while the ROM in adjacent segments increased (1.88°–8.19°). The largest percent decrease in motion of the L4–L5 segment due to disc degeneration was in right axial rotation (75%), left axial rotation (69%), flexion (67%), right lateral bending (67%), left lateral bending right (67%), and extension (53%). The change in the trend of the IDP was the same as that of the ROM. Specifically, the IDP decreased (flexion: 0.592–0.09 MPa; extension: 0.678–0.334 MPa; right lateral bending: 0.498–0.205 MPa; left lateral bending: 0.523–0.272 MPa; right axial rotation: 0.535–0.246 MPa; left axial rotation: 0.53–0.266 MPa) in the L4–L5 segment, while the IDP in adjacent segments increased (0.511–0.789 MPa). The maximum von Mises stress and maximum shear stress of the annulus in whole lumbar spine segments increased (L4–L5 segment: 0.413–2.626 MPa and 0.412–2.783 MPa, respectively; adjacent segment of L4–L5: 0.356–1.493 MPa and 0.359–1.718 MPa, respectively) as degeneration of the disc progressively increased. There was no apparent regularity in facet joint force in the degenerated segment as the degree of disc degeneration increased. Nevertheless, facet joint forces in adjacent healthy segments increased as the degree of disc degeneration increased (extension: 49.7–295.3 N; lateral bending: 3.5–171.2 N; axial rotation: 140.2–258.8 N). Conclusion Degenerated discs caused changes in the motion and loading pattern of the degenerated segments and adjacent normal segments. The abnormal load and motion in the degenerated models risked accelerating degeneration in the adjacent normal segments. In addition, accurate simulation of degenerated facet joints is essential for predicting changes in facet joint loads following disc degeneration.

Transfer RNAs (tRNAs) play critical roles in human cancer. Currently, no database provides the expression landscape and clinical relevance of tRNAs across a variety of human cancers. Utilizing miRNA-seq data from The Cancer Genome Atlas, we quantified the relative expression of tRNA genes and merged them into the codon level and amino level across 31 cancer types. The expression of tRNAs is associated with clinical features of patient smoking history and overall survival, and disease stage, subtype, and grade. We further analysed codon frequency and amino acid frequency for each protein coding gene and linked alterations of tRNA expression with protein translational efficiency. We include these data resources in a user-friendly data portal, tRic (tRNA in cancer, https://hanlab.uth.edu/tRic/ or http://bioinfo.life.hust.edu.cn/tRic/), which can be of significant interest to the research community.

T-cell receptors (TCRs) recognizing antigens play vital roles in T-cell immunology. Surveying TCR repertoires by characterizing complementarity-determining region 3 (CDR3) can provide valuable insights into the immune community underlying pathologic conditions, which will benefit neoantigen discovery and cancer immunotherapy. Here we present a novel tool named CATT, which can apply on TCR sequencing (TCR-Seq), RNA-Seq, and single-cell TCR(RNA)-Seq data to characterize CDR3 repertoires. CATT integrated maximum-network-flow based micro-assembly algorithm, data-driven error correction model, and Bayes classification algorithm, to self-adaptively and ultra-sensitively characterize CDR3 repertoires with high accuracy. Benchmark results of datasets from in silico and real conditions demonstrated that CATT showed superior recall and precision compared with other prevalent tools, especially for datasets with short read length and small data size. By applying CATT on a TCR-Seq dataset from aplastic anemia patients, we found the skewing of TCR repertoire was due to the oligoclonal expansion of effector memory T-cells. CATT will be a powerful tool for researchers conducting TCR and immune repertoire studies. CATT is freely available at http://bioinfo.life.hust.edu.cn/CATT.

1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine (MPTP), which induces the pathological characteristics of Parkinson's disease in rodents, also specifically targets dopaminergic neurons in zebrafish embryos and larvae. Loganin, a traditional Chinese drug, was reported to regulate immune function and possess anti-inflammatory and anti-shock effects. Here, we investigate the role of loganin in MPTP-induced Parkinson-like abnormalities in zebrafish. MPTP treatment-induced abnormal development, in larvae, such as pericardium edema, increased yolk color, yolk sac edema, and retarded yolk sac resorption, as well as defects in brain development. Loganin could block MPTP-induced defects, with little toxicity to the eggs. Results of whole mount in situ hybridization showed loganin prevented the loss of both dopaminergic neurons and locomotor activity, exhibited by larvae treated with MPTP. In addition, loganin significantly rescued MPTP-induced neurotoxicity on PC12 cells, possibly through the suppression of PI3K/Akt/mTOR axis and JNK signaling pathways. In conclusion, loganin blocks MPTP-induced neurotoxicity and abnormal development in zebrafish. J. Cell. Biochem. 118: 615-628, 2017. © 2016 Wiley Periodicals, Inc.

Background Tumor necrosis factor receptor-associated factor 1 (TRAF1) is a member of the TRAF family and is dysregulated in diseases, such as atheroma, lymphoma, and solid tumors, but the role of TRAF1 in gastric cancer remains unknown. This study was aimed to investigate the role of TRAF1 in Helicobacter pylori (H. pylori)-related cell apoptosis and gastric carcinogenesis. Materials and methods The mRNA and protein expression levels of TRAF1 were measured in a panel of gastric cancer cell lines and in H. pylori -infected mice by quantitative real-time PCR (qPCR) and Western blotting. The transcription factor that mainly affects transcription of TRAF1 during H. pylori infection was identified. The roles of H. pylori virulence factors that regulate TRAF1 expression were analyzed using isogenic cagA-, vacA-, and cagE-null mutants. The effects of TRAF1 on gastric cell viability and apoptosis during H. pylori infection were detected using the standard MTS (cell viability) assay and flow cytometry, respectively. Results H. pylori infection induced TRAF1 overexpression in both gastric epithelial cells and mice. The expression of TRAF1 in response to H. pylori infection was majorly regulated by the activation of NF-κB and was strongly related to H. pylori virulence factor CagA. The upregulation of TRAF1 inhibited cell apoptosis and increased the viability of infected cells. Conclusions H. pylori infection induces the overexpression of TRAF1 in gastric epithelial cells. The upregulation of TRAF1 plays an antiapoptotic role in H. pylori -infected gastric cells and may contribute to the gastric carcinogenesis.

The protein translational system, including transfer RNAs (tRNAs) and several categories of enzymes, plays a key role in regulating cell proliferation. Translation dysregulation also contributes to cancer development, though relatively little is known about the changes that occur to the translational system in cancer. Here, we present global analyses of tRNAs and three categories of enzymes involved in translational regulation in ~10,000 cancer patients across 31 cancer types from The Cancer Genome Atlas. By analyzing the expression levels of tRNAs at the gene, codon, and amino acid levels, we identified unequal alterations in tRNA expression, likely due to the uneven distribution of tRNAs decoding different codons. We find that overexpression of tRNAs recognizing codons with a low observed-over-expected ratio may overcome the translational bottleneck in tumorigenesis. We further observed overall overexpression and amplification of tRNA modification enzymes, aminoacyl-tRNA synthetases, and translation factors, which may play synergistic roles with overexpression of tRNAs to activate the translational systems across multiple cancer types., Zhao Zhang, Youqiong Ye et al. present an expression analysis of tRNAs and genes encoding enzymes involved in translation regulation across ~10,000 patients from 31 cancer types in The Cancer Genome Atlas (TCGA). They find that cancer cells may overcome translational bottlenecks by overexpressing rarer tRNAs and other translation factors.

To study the distribution and expressions of inflammatory, growth factors, apoptosis factors in the late stage of pressure ulcer chronic wounds.Twenty patients were recruited from the First Affiliated Hospital of Henan University during Oc-tomber 2013 to July 2015. Including twenty patients of stage Ⅲ,Ⅳ pressure ulcer, ten acute injury patients and six normal health persons. The histological changes of different wounds were observed by HE staining, the distribution of Caspase-3 protein in four groups was detected by immunohistochemistry technique. The expressions of mRNAs for interleukin (IL)-1β, interleukin (IL)-6, tumor necrosis factor-a (TNF-a), vascular endothelial growth factor (VEGF), vascular endothelial growth factor receptor 2(KDR), fibroblast growth factors(bFGF) and fibrob-last growth factors receptor1 (FGFR1)were determined by real-time reverse transcription polymerase chain reaction.Large numbers of inflammatory cells were found in the stage of Ⅲ, Ⅳpressure ulcer wound under HE staining. The levels of Caspase-3 were mainly localized in fibroblasts or endothelial cells. Compared with the other two groups, the expression of Caspase-3 in pressure ulcers groups was higher (Overproduction or prolonged expression of in-flammatory factor and apoptosis factor, the expression of VEGF and its receptor KDR and bFGF and its receptor FGFR1 were significantly de-creased in the stage Ⅲ, Ⅳ pressure ulcer wound. These characteristics can be used to comprehensively evaluate etiology and treatment of pressure ulcer chronic wounds.

Several genetic tools have been developed for use in Bacillus anthracis, but there is still a need for a more marker-free gene inactivation protocols. Thus, we report a method to generate unmarked mutations in B. anthracis. This approach was based on the counter-selectable pheS* gene with assistance by the I-SceI homing endonuclease. Using this strategy, the NprR gene, a transcriptional activator of B. anthracis, was deleted at an extremely high efficiency. Our study indicates that mutated pheS is a useful counter-selective marker to design a valuable genetic tool for in-frame and unmarked gene deletions of B. anthracis.

Summary The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor versus normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes. GSCALite is a user-friendly web server for dynamic analysis and visualization of gene set in cancer and drug sensitivity correlation, which will be of broad utilities to cancer researchers. Availability and implementation GSCALite is available on http://bioinfo.life.hust.edu.cn/web/GSCALite/. Supplementary information Supplementary data are available at Bioinformatics online.

Phytochemical investigation of the aerial parts of Chloranthus angustifolius Oliv. (Chloranthaceae) resulted in the isolation and characterization of seven sesquiterpenes (1–7) and six amide derivatives (8–13). All structures were established based on analysis of their spectroscopic data. This is the first report of compounds 2 and 8–13 from the family Chloranthaceae, and the first report of compounds 3–5 from C. angustifolius. Moreover, the chemotaxonomic significance of these compounds was summarized.

Summary: Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes. We further identified 46 clinically relevant snoRNAs and experimentally demonstrated functional roles of SNORD46 in promoting cell proliferation, migration, and invasion. We developed a user-friendly data portal, SNORic, to benefit the research community. Our study highlights the significant roles of snoRNAs in the development and implementation of biomarkers or therapeutic targets for cancer and provides a valuable resource for cancer research. : Gong et al. analyze snoRNA expression landscape in >10,000 samples across 31 cancer types and perform integrative analyses. They prioritize 46 significant clinically relevant snoRNAs and characterize the functional roles of SNORD46. The data portal, SNORic, allows exploration of snoRNA expression. Keywords: snoRNA, small nucleolar RNA, pan-cancer, clinical relevance, data portal

Different tissues and diseases have distinct transcriptional profilings with specifically expressed genes (SEGs). So, the identification of SEGs is an important issue in the studies of gene function, biological development, disease mechanism and biomarker discovery. However, few accurate and easy-to-use tools are available for RNA sequencing (RNA-seq) data to detect SEGs. Here, we presented SEGtool, a tool based on fuzzy c-means, Jaccard index and greedy annealing method for SEG detection automatically and self-adaptively ignoring data distribution. Testing result showed that our SEGtool outperforms the existing tools, which was mainly developed for microarray data. By applying SEGtool to Genotype-Tissue Expression (GTEx) human tissue data set, we detected 3181 SEGs with tissue-related functions. Regulatory networks reveal tissue-specific transcription factors regulating many SEGs, such as ETV2 in testis, HNF4A in liver and NEUROD1 in brain. Applied to a case study of single-cell sequencing (SCS) data from embryo cells, we identified many SEGs in specific stages of human embryogenesis. Notably, SEGtool is suitable for RNA-seq data and even SCS data with high specificity and accuracy. An implementation of SEGtool R package is freely available at http://bioinfo.life.hust.edu.cn/SEGtool/.

Transcription factors (TFs) are key regulators for gene expression. Here we updated the animal TF database AnimalTFDB to version 2.0 (http://bioinfo. life.hust.edu.cn/AnimalTFDB/). Using the improved prediction pipeline, we identified 72 336 TF genes, 21 053 transcription co-factor genes and 6502 chromatin remodeling factor genes from 65 species covering main animal lineages. Besides the abundant annotations (basic information, gene model, protein functional domain, gene ontology, pathway, protein interaction, ortholog and paralog, etc.) in the previous version, we made several new features and functions in the updated version. These new features are: (i) gene expression from RNA-Seq for nine model species, (ii) gene phenotype information, (iii) multiple sequence alignment of TF DNA-binding domains, and the weblogo and phylogenetic tree based on the alignment, (iv) a TF prediction server to identify new TFs from input sequences and (v) a BLAST server to search against TFs in AnimalTFDB. A new nice web interface was designed for AnimalTFDB 2.0 allowing users to browse and search all data in the database. We aim to maintain the AnimalTFDB as a solid resource for TF identification and studies of transcription regulation and comparative genomics.

A new intact resin glycoside (3) and two glycosidic acids (1 and 2), all having a common trisaccharide moiety and (11S)-hydroxytetradecanoic acid or (3S,11S)-dihydroxytetradecanoic acid as the aglycone, were obtained from the roots of Porana duclouxii. Their structures were elucidated by spectroscopic analyses and chemical correlations. These compounds represent the first examples of resin glycosides from the genus Porana.

Although the machine-made sand was widely used for concrete in recent years in China, it was short of studies on the relations among the basic mechanical properties of fly-ash concrete with machine-made sand (MSFAC). However, these relations such as the compressive strength, the tensile strength and the elastic modulus with the cubic compressive strength (i.e. strength grade) are the basis of design for concrete structures. This paper summarizes the test data from the published references, and discusses the relations among these properties by statistical analyses compared with those of ordinary concrete. The results show that only the tensile strength of MSFAC can be safely forecasted by the same formula of ordinary concrete specified in current Chinese design code. When the strength grade is higher than C45, the axial compressive strength of MSFAC is largely forecasted by the formula of ordinary concrete. The elastic modulus of MSFAC is larger than that of ordinary concrete, which should be prospect by the formula in this paper. This work gives out some cautions for the proper use of the MSFAC in concrete structures.

As part of the studies on the durability of concrete with machine-made sand, this paper introduces the test results and the forecast model of time-dependent chloride penetration of this kind of concrete. Three strength grades of concrete C30, C40 and C50, and the contents of stone powder in machine-made sand of 5%, 9% and 13% in mass were considered in the mix proportion of concrete with machine-made sand. The ordinary concrete with natural river sand in the same strength grade was tested at the same time for comparison. The test was conducted for 360 days, the results showed that the effect of the content of stone powder on the chloride penetration of concrete was obvious at early curing time of 7 days, and tended to be lower with the increase of curing time. When the curing time was longer than 90 days, this effect could be neglected, and the resistance to chloride penetration of concrete with machine-made sand was almost equal to or larger than that of ordinary concrete. The decrement of chloride diffusion coefficient varied from sharp to gentle with the curing time, the resistance of concrete to chloride penetration increased with the increase of concrete strength. Meanwhile, to facilitate the calculation in practice, the forecast model of chloride diffusion coefficient of concrete is proposed.