Integrated Database Research Articles

EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.

Eye diseases are remarkably common and encompass a large and diverse range of morbidities that affect different components of the visual system and visual function. With advances in omics technology of eye disorders, genome-scale datasets have been rapidly accumulated in genetics and epigenetics field. However, the efficient collection and comprehensive analysis of different kinds of omics data are lacking. Herein, we developed EyeDiseases (https://eyediseases.bio-data.cn/), the first database for multi-omics data integration and interpretation of human eyes diseases. It contains 1344 disease-associated genes with genetic variation, 1774 transcription files of bulk cell expression and single-cell RNA-seq, 105 epigenomics data across 185 kinds of human eye diseases. Using EyeDiseases, we investigated SARS-CoV-2 potential tropism in eye infection and found that the SARS-CoV-2 entry factors, ACE2 and TMPRSS2 are highly correlated with cornea and keratoconus, suggest that ocular surface cells are susceptible to infection by SARS-CoV-2. Additionally, integrating analysis of Age-related macular degeneration (AMD) GWAS loci and co-expression data revealed 9 associated genes involved in HIF-1 signaling pathway and voltage-gate potassium channel complex. The EyeDiseases provides a valuable resource for accelerating the discovery and validation of candidate loci and genes contributed to the molecular diagnosis and therapeutic vulnerabilities with various eyes diseases.

Information workflow proposal for integrating cost estimating, scheduling, and monitoring with BIM in SMEs

Abstract Although many studies have emphasized the benefits of the integration of Building Information Modeling (BIM), there is no consensus on the information workflow among main processes used in construction, particularly in small- and medium-size enterprises (SMEs). Therefore, this work proposes an information workflow that integrates 3D BIM modeling, cost estimating, scheduling, and monitoring processes in SMEs (ICSM Information Workflow). This research adopts the design science research approach, which includes (a) a literature review and a study of the information workflow among the processes, (b) a proposal of an information workflow based on certain assumptions for integration, (c) a participatory process for testing and adapting the proposed workflow, and (d) an evaluation of the proposed information workflow. The results indicate the participatory and cyclical processes that were proposed to define the work packages using a standard WBS and a database for information integration were the key for integrating people, technologies, and processes. The main contributions of this study are the proposal of an information workflow that integrates cost estimating, scheduling, and monitoring with BIM in SMEs, and the lessons learned based on the pilot test and evaluation of the ICSM Information Workflow in one of the two projects studied.

Different Training Durations and Frequencies of Tai Chi for Bone Mineral Density Improvement: A Systematic Review and Meta-Analysis.

Objective Tai Chi shows potential as a safe and cost-effective intervention to improve bone mineral density (BMD). However, the various effects caused by different training durations and frequencies have not been evaluated. This updated systematic review aims to explore the effectiveness of Tai Chi in attenuating bone mineral density loss based on different training durations and frequencies. Methods We conducted an extensive database search in Cochrane Central Register of Controlled Trials, PubMed, EMBASE, Web of Science, Chinese Biomedical Literature Database, China Knowledge Resource Integrated Database, Wanfang Data, and China Science and Technology Journal Database on randomized controlled trials that examined Tai Chi for BMD improvement. Two reviewers independently performed data screening and extraction. Study quality was evaluated using the Cochrane Handbook for Systematic Reviews of Interventions. Results A total of 23 randomized controlled trials involving 1582 patients were identified. The aggregated results have shown significant benefits in favor of Tai Chi on BMD improvement in the lumbar spine (SMD = 0.36, 95% [0.13, 0.59], P=0.002), femoral neck (SMD = 0.40, 95% [0.16, 0.63], P=0.0009), femoral trochanter (SMD = 0.43, 95% CI [0.20, 0.66], P=0.0002), and Ward's triangle (SMD = 0.31, 95% [0.15, 0.48], P=0.002). Such favorable benefits in Tai Chi can only be seen when compared with the nonexercise group, and Tai Chi showed no significant improvement in BMD change when compared with other exercises group. Subgroup analyses showed various effects of BMD improvement based on different training durations and frequencies of Tai Chi. Tai Chi is effective in attenuating BMD loss with an intervention frequency of >4 days/week in the lumbar spine, with an intervention frequency of >4 days/week or an intervention duration of >10 months in the femoral neck, and with an intervention duration of >10 months or a frequency of ≤4 days/week in Ward's triangle. Conclusions The results demonstrated that Tai Chi may have benefits in attenuating BMD loss. Different training durations and frequencies may result in variable effectiveness. Researchers should focus more on the training durations and frequencies of Tai Chi so that a more definitive claim can be made regarding the beneficial effects for BMD improvement.

Socioeconomy as a prognostic factor for location of death in Swedish palliative cancer patients

BackgroundAn important aspect of end-of-life care is the place of death. A majority of cancer patients prefer home death to hospital death. At the same time, the actual location of death is often against patient’s last-known wish. The aim of this study was to analyze whether socioeconomic factors influence if Swedish palliative cancer patients die at home or at a hospital. There is no previous study on location of death encompassing several years in Swedish cancer patients.MethodsData was collected from the Swedish Register of Palliative Care for patients diagnosed with brain tumor, lung, colorectal, prostate or breast cancer recorded between 2011 and 2014. The data was linked to the Swedish Cancer Register, the Cause of Death Register and the Longitudinal Integration Database for health-insurance and labor-market studies. A total of 8990 patients were included.ResultsWe found that marital status was the factor that seemed to affect the place of death. Lack of a partner, compared to being married, was associated with a higher likelihood of dying at a hospital.ConclusionOur findings are in line with similar earlier studies encompassing only 1 year and based on patients in other countries. Whether inequalities at least partly explain the differences remains to be investigated. Patients dying of cancer in Sweden, who do not have a life partner, may not have the option of dying at home due to lack of informal support. Perhaps the need of extensive community support services to enable home death have to improve, and further studies are warranted to answer this question.

Analysis of the potential and mechanism of Ginkgo biloba in the treatment of Alzheimer's disease based on network pharmacology.

Study the principle and possible mechanism of Ginkgo biloba in the treatment of Alzheimer's disease (AD) which is based on network pharmacology. The potential targets of active ingredients of Ginkgo biloba were collected by Traditional Chinese Medicine Integrated Database platform (TCMSP). TCMSP is a pharmacological system for drug discovery from Chinese herbal medicine. The disease targets of AD were searched and collected by the database of gene-disease associations (DisGeNET) and literature. The obtained targets were standardized by the UniProt database. STING network platform and Cytoscape were used to construct protein-protein interaction network (PPI) of the key targets. According to Materscape, we clarify the possible mechanism of action including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analysis. The compound-target network contains 27 active ingredients, 191 related targets, 18 key targets, including PLAU, HMOX1, TNF, INSR, MPO, MAOB, IGF2, IL1B, ESR1, BCL2, ACHE, BAX, GSK3B, PPARG, SLC2A4, NOS3, CASP3, VEGFA. GO enrichment analysis has got a total of 640 GO items, including 609 biological process (BP) items (95.1%), 16 molecular function (MF) items (2.5%) and 15 cellular component (CC) items (2.4%). After KEGG enrichment, 44 pathways were obtained. Through the construction of "component-target-pathway", GO biological function and KEGG pathway enrichment analysis were performed on core targets, and the possibility of Ginkgo biloba for the treatment of AD was explored from multiple targets and pathways, which provided a new approach for multi-target treatment.

Deciphering potential pharmacological mechanism of Sha-Shen-Mai-Dong decoction on primary Sjogren\u2019s syndrome

BackgroundSha-Shen-Mai-Dong decoction (SSMD) is a classical prescription widely used in primary Sjogren’s Syndrome (pSS) therapy. This study aims to explore the potential pharmacological mechanism of SSMD on pSS.MethodsActive components of SSMD were obtained from Traditional Chinese Medicine Integrative Database and Traditional Chinese Medicine Systems Pharmacology databases and targets of SSMD were predicted by Pharmmapper and STITCH database. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out to explore the function characteristics of SSMD. The expression matrix of microarray of pSS was obtained from Gene Expression Omnibus and we obtained 162 differentially expressed genes (DEGs). Protein-protein interaction (PPI) networks were constructed to identify the hub targets. Principal component analysis (PCA) and molecular docking were conducted to further elucidate the possibility of SSMD for pSS.ResultsSSMD contained a total of 1056 active components, corresponding to 88 targets, among which peripheral myelin protein 2(PMP2), androgen receptor (AR) and glutamic acid decarboxylase 1(GAD1) are associated with multiple active components in SSMD and may be the core targets. Moreover, these targets were closely related to tissue pathological injury in SS, such as lacrimal gland, salivary gland and nervous system injury. GO and KEGG analysis showed that 88 targets enriched in REDOX process, transcriptional regulation and negative regulation of apoptosis process. Besides, SSMD may influence the cell proliferation, gene transcription through regulating Ras and cAMP-related signaling pathways. In addition, SSMD may show effects on immune regulation, such as macrophage differentiation, Toll-like receptor 4 signaling pathway and T-helper 1 in SS. Moreover, PPI network suggested that FN1, MMP-9 may be the hub targets in SSMD. Result of PCA and molecular docking analysis further determined the feasibility of SSMD in treating pSS.ConclusionSSMD can regulate multiple biological processes by virtue of its multiple active components, thus showing prominent advantage in the treatment of pSS. The discovery of active ingredients and targets in SSMD provides valuable resources for drug research and development for pSS.

ASUSD nuclear data sensitivity and uncertainty program package: Validation on fusion and fission benchmark experiments

Nuclear data (ND) sensitivity and uncertainty (S/U) quantification in shielding applications is performed using deterministic and probabilistic approaches. In this paper the validation of the newly developed deterministic program package ASUSD (ADVANTG + SUSD3D) is presented. ASUSD was developed with the aim of automating the process of ND S/U while retaining the computational efficiency of the deterministic approach to ND S/U analysis. The paper includes a detailed description of each of the programs contained within ASUSD, the computational workflow and validation results.ASUSD was validated on two shielding benchmark experiments from the Shielding Integral Benchmark Archive and Database (SINBAD) - the fission relevant ASPIS Iron 88 experiment and the fusion relevant Frascati Neutron Generator (FNG) Helium Cooled Pebble Bed (HCPB) Test Blanket Module (TBM) mock-up experiment. The validation process was performed in two stages. Firstly, the Denovo discrete ordinates transport solver was validated as a standalone solver. Secondly, the ASUSD program package as a whole was validated as a ND S/U analysis tool. Both stages of the validation process yielded excellent results, with a maximum difference of 17% in final uncertainties due to ND between ASUSD and the stochastic ND S/U approach. Based on these results, ASUSD has proven to be a user friendly and computationally efficient tool for deterministic ND S/U analysis of shielding geometries.

Mitochondrial ubiquitin ligase alleviates Alzheimer\u2019s disease pathology via blocking the toxic amyloid-\u03b2 oligomer generation

Mitochondrial pathophysiology is implicated in the development of Alzheimer’s disease (AD). An integrative database of gene dysregulation suggests that the mitochondrial ubiquitin ligase MITOL/MARCH5, a fine-tuner of mitochondrial dynamics and functions, is downregulated in patients with AD. Here, we report that the perturbation of mitochondrial dynamics by MITOL deletion triggers mitochondrial impairments and exacerbates cognitive decline in a mouse model with AD-related Aβ pathology. Notably, MITOL deletion in the brain enhanced the seeding effect of Aβ fibrils, but not the spontaneous formation of Aβ fibrils and plaques, leading to excessive secondary generation of toxic and dispersible Aβ oligomers. Consistent with this, MITOL-deficient mice with Aβ etiology exhibited worsening cognitive decline depending on Aβ oligomers rather than Aβ plaques themselves. Our findings suggest that alteration in mitochondrial morphology might be a key factor in AD due to directing the production of Aβ form, oligomers or plaques, responsible for disease development.

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach.

Vitiligo is a disease of mysterious origins in the context of its occurrence and pathogenesis. The autoinflammatory theory is perhaps the most widely accepted theory that discusses the occurrence of Vitiligo. The theory elaborates the clinical association of vitiligo with autoimmune disorders such as Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis and Diabetes. In the present work, we discuss the comprehensive set of differentially co-expressed genes involved in the crosstalk events between Vitiligo and associated autoimmune disorders (Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis). We progress our previous tool, Vitiligo Information Resource (VIRdb), and incorporate into it a compendium of Vitiligo-related multi-omics datasets and present it as VIRdb 2.0. It is available as a web-resource consisting of statistically sound and manually curated information. VIRdb 2.0 is an integrative database as its datasets are connected to KEGG, STRING, GeneCards, SwissProt, NPASS. Through the present study, we communicate the major updates and expansions in the VIRdb and deliver the new version as VIRdb 2.0. VIRdb 2.0 offers the maximum user interactivity along with ease of navigation. We envision that VIRdb 2.0 will be pertinent for the researchers and clinicians engaged in drug development for vitiligo.

Valproic acid and socioeconomic associations in Swedish women with epilepsy 2010-2015.

We investigated the correlation between socioeconomic status and the prescription of Valproic acid (VPA) in women of fertile age in Sweden. This is a registered-based cohort study including all women living in Sweden aged 18-45years in the years 2010-2015, with a diagnosis of epilepsy and no intellectual disability (n=9143). Data were collected from the National Patient Register, the Drug Prescription Register, and the Longitudinal integration database for health insurance and labor market studies (LISA). Women with only 9years of school were more often prescribed VPA than women with a University degree (12.9% compared to 10.7% in 2015 [p=0.015]). Similar differences were seen between the lowest and highest income group (16.6% compared to 12.7% in 2015 [p<0.001]). The odds of having a VPA prescription in 2015 was 1.59 (p<0.001) in women with 9years of school compared to women with a University degree, and 1.60 (p<0.001) in the lowest income group relative to the highest income group after adjusting for age. From 2010 to 2015, the proportion with VPA prescription in the whole cohort diminished with an absolute reduction of -2.2% (p<0.001). The decrease was similar among the different education and income groups (p=0.919 and p=0.280). The results indicate that the increased knowledge on VPA teratogenicity was implemented across socioeconomic strata in the Swedish healthcare system. Women with lower income or education level remained more frequent VPA users. Whether this difference reflects epilepsy type or severity, or socioeconomic disparities, merit further study.

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach

Vitiligo is a disease of mysterious origins in the context of its occurrence and pathogenesis. The autoinflammatory theory is perhaps the most widely accepted theory that discusses the occurrence of Vitiligo. The theory elaborates the clinical association of vitiligo with autoimmune disorders such as Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis and Diabetes. In the present work, we discuss the comprehensive set of differentially co-expressed genes involved in the crosstalk events between Vitiligo and associated autoimmune disorders (Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis). We progress our previous tool, Vitiligo Information Resource (VIRdb), and incorporate into it a compendium of Vitiligo-related multi-omics datasets and present it as VIRdb 2.0. It is available as a web-resource consisting of statistically sound and manually curated information. VIRdb 2.0 is an integrative database as its datasets are connected to KEGG, STRING, GeneCards, SwissProt, NPASS. Through the present study, we communicate the major updates and expansions in the VIRdb and deliver the new version as VIRdb 2.0. VIRdb 2.0 offers the maximum user interactivity along with ease of navigation. We envision that VIRdb 2.0 will be pertinent for the researchers and clinicians engaged in drug development for vitiligo.

Piloting an integrated SARS-CoV-2 testing and data system for outbreak containment among college students: A prospective cohort study.

BackgroundColleges and universities across the country are struggling to develop strategies for effective control of COVID-19 transmission as students return to campus.Methods and findingsWe conducted a prospective cohort study with students living on or near the UC Berkeley campus from June 1st through August 18th, 2020 with the goal of providing guidance for campus reopening in the safest possible manner. In this cohort, we piloted an alternative testing model to provide access to low-barrier, high-touch testing and augment student-driven testing with data-driven adaptive surveillance that targets higher-risk students and triggers testing notifications based on reported symptoms, exposures, or other relevant information. A total of 2,180 students enrolled in the study, 51% of them undergraduates. Overall, 6,247 PCR tests were administered to 2,178 students over the two-month period. Overall test positivity rate was 0.9%; 2.6% of students tested positive. Uptake and acceptability of regular symptom and exposure surveys was high; 98% of students completed at least one survey, and average completion rate was 67% (Median: 74%, IQR: 39%) for daily reporting of symptoms and 68% (Median: 75%, IQR: 40%) for weekly reporting of exposures. Of symptom-triggered tests, 5% were PCR-positive; of exposure-triggered tests, 10% were PCR-positive. The integrated study database augmented traditional contact tracing during an outbreak; 17 potentially exposed students were contacted the following day and sent testing notifications. At study end, 81% of students selected their desire “to contribute to UC Berkeley’s response to COVID-19” as a reason for their participation in the Safe Campus study.ConclusionsOur results illustrate the synergy created by bringing together a student-friendly, harm reduction approach to COVID-19 testing with an integrated data system and analytics. We recommend the use of a confidential, consequence-free, incentive-based daily symptom and exposure reporting system, coupled with low-barrier, easy access, no stigma testing. Testing should be implemented alongside a system that integrates multiple data sources to effectively trigger testing notifications to those at higher risk of infection and encourages students to come in for low-barrier testing when needed.

Prevalence of short stature among children in China: A systematic review.

ABSTRACTImportanceThe prevalence and characteristics of short stature (SS) among children in China should be assessed to provide guidance for planning and implementation of nationwide public health policies. Thus far, there have been no accurate estimates of the prevalence of SS in China.ObjectiveTo analyze the prevalence of SS among children in China and to explore the influences of sex, area, age, study year, and study site on prevalence rates.MethodsRelevant literature was identified by searching the following databases: PubMed, Embase, The Cochrane Library, Chinese Biomedical Literature, China Knowledge Resource Integrated, WeiPu, and WanFang databases. Meta‐analysis was carried out using STATA 11.2.ResultsThis meta‐analysis included 39 studies with 348 326 Chinese participants; the studies covered 20 provinces, municipalities, and autonomous regions. The pooled prevalence of SS was 3.2% (95% confidence interval [CI], 2.6%–3.7%; I 2 = 99.8%). The prevalence of SS in boys and girls were 3.1% (95% CI, 2.5%–3.7%) and 3.2% (95% CI, 2.6%–3.9%), respectively. The sex difference was not statistically significant (P > 0.05). The prevalence of SS was higher in rural areas than in urban areas (4.7% [95% CI, 3.6%–5.8%] vs. 2.8% [95% CI, 2.2%–3.4%]; P < 0.001). The prevalence of SS was higher in West China (5.2%; 95% CI, 4.4%–6.0%) than in Northeast China (0.6%; 95% CI, 0.3%–0.8%), East China (2.3%; 95% CI, 1.9%–2.8%), or Central China (2.9%; 95% CI, 1.9%–3.9%).InterpretationThe prevalence of SS among children was higher in western and rural areas of China. Close attention to children’s growth and development is needed to prevent the occurrence of SS.

The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis.

Simple SummaryThere is a tremendous amount of gene expression information available for prostate cancer, but very few tools exist to combine the disparate datasets generated across sample types and technical platforms. We present a method of integrating different types of expression data from different study cohorts to increase analytic power, and improve our understanding of the molecular changes underlying the development and progression of prostate cancer from normal to advanced disease. Using this approach, we identified nine additional disease stage-specific candidate genes with prognostic significance, which were not identified in any one study alone. We have developed a free online tool summarizing our results, and making the complete combined dataset available for further translational research.Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.

Cladding Profilometry Analysis of Experimental Breeder Reactor-II Metallic Fuel Pins with HT9, D9, and SS316 Cladding

BISON finite element method fuel performance simulations were conducted using an existing automated process that couples the Fuels Irradiation &amp; Physics Database (FIPD) and the Integral Fast Reactor Materials Information System database by writing input files and comparing the BISON output to post-irradiation fuel pin profilometry measurements contained within the databases. The importance of this work is to demonstrate the ability to benchmark fuel performance metallic fuel models within BISON using Experimental Breeder Reactor-II fuel pin data for a number of similar pins, while building off previous modeling efforts. Changes to the generic BISON input file include implementing pin specific axial power and flux profiles, pin specific fluences, frictional contact, and irradiation-induced volumetric swelling models for cladding. A statistical analysis of irradiation-induced volumetric swelling models for HT9, D9, and SS316 was performed for experiments X421/X421A, X441/X441A, and X486. Between these three experiments, there were 174 post-irradiation examination (PIE) profilometries used for validating the swelling models presented using a standard error of the estimate (SEE) method. Implementation of the volumetric swelling models for D9 and SS316 claddings was found to have a significant impact on the BISON profilometry simulated, where HT9 clad pins had an insignificant change due to low fluence values. BISON profilometry simulated for HT9, D9, and SS316 fuel pins agreed with PIE profilometry measurements, with assembly SEE values being 4.4 × 10−3 for X421A, 2.0 × 10−3 for X441A, and 2.8 × 10−3 for X486. D9 clad pins in X421/X421A had the highest SEE values, which is due to the BISON simulated profilometry being shifted axially. While this work accomplished its purpose to demonstrate the modeling of multiple fuel pins from the databases to help validate models, the results suggest that the continued development of metallic fuel models is necessary for qualifying new metallic fuel systems to better capture some physical performance phenomena, such as the hot pressing of U-Pu-Zr and the fuel cladding chemical interaction.

Prognostic Value of PLXND1 and TGF-β1 Coexpression and Its Correlation With Immune Infiltrates in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with no curative treatments. Plexin D1 (PLXND1) is a cellular receptor whose functions have been explored in several human cancers; however, the critical roles of PLXND1 in HCC have rarely been probed. Therefore, the present study attempted to elucidate the expression pattern, prognostic significance, and potential roles of PLXND1 in HCC. We found that PLXND1 expression in HCC tissues was significantly higher compared with normal liver tissue from Gene Expression Profiling Interactive Analysis (GEPIA) and Integrative Molecular Database of Hepatocellular Carcinoma (HCCDB) databases. This result was further validated by immunohistochemistry staining (IHC) using tissue microarrays, which contained 216 HCC cases collected from our hospital. Additionally, PLXND1 expression showed a significant correlation with several clinical characteristics, including tumor grade and tumor hemorrhage (TH). Moreover, TISIDB and GEPIA databases were used to investigate the roles of PLXND1 in tumor-immune system interactions in HCC. As an immunoinhibitor, transforming growth factor-beta (TGF-β1) displayed the greatest correlations with PLXND1 in HCC. Finally, Kaplan-Meier curves and Cox analysis were conducted to further examine the potential clinical value of PLXND1 in HCC. We described a subclassification of HCC based on PLXND1 and TGF-β1 expression, which could be used to predict clinical outcomes and patient prognosis. Taken together, the results of this study indicate that PLXND1 might be a promising prognostic biomarker and potential therapeutic target in HCC.

ICysMod: an integrative database for protein cysteine modifications in eukaryotes.

As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108030 PCM events for 85747 experimentally identified sites on 31483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.

INTEGRAL discovery of a high-energy tail in the microquasar Cygnus X-3

Context. The X-ray spectra of X-ray binaries are dominated by emission of either soft or hard X-rays which defines their soft and hard spectral states. While the generic picture is relatively well understood, little is known about the interplay of the various media at work, or about the reasons why some sources do not follow common behavior. Cygnus X-3 is amongst the list of X-ray binaries that show quite complex behavior, with various distinct spectral states not seen in other sources. These states have been characterized in many studies. Because of its softness and intrinsic low flux above typically 50 keV, very little is known about the hard X/soft gamma-ray (100–1000 keV) emission in Cygnus X-3. Aims. Using the whole INTEGRAL data base, we aim to explore the 3–1000 keV spectra of Cygnus X-3. This allows to probe this region with the highest sensitivity ever, and search for the potential signature of a high-energy non-thermal component as sometimes seen in other sources. Methods. Our work is based on state classification carried out in previous studies with data from the Rossi X-Ray Timing Explorer. We extend this classification to the whole INTEGRAL data set in order to perform a long-term state-resolved spectral analysis. Six stacked spectra were obtained using 16 years of data from JEM-X (3–25 keV), ISGRI (25–300 keV), and SPI (20–400 keV). Results. We extract stacked images in three different energy bands, and detect the source up to 200 keV. In the hardest states, our purely phenomenological approach clearly reveals the presence of an additonnal component &gt; 50 keV in addition to the component usually interpreted as thermal Comptonization. We apply a more physical model of hybrid thermal/nonthermal corona (EQPAIR) to characterize this nonthermal component and compare our results with those of previous studies and analyses. Our modeling indicates a more efficient acceleration of electrons in states where major ejections are observed. We also evaluate and find a dependence of the photon index of the power law as a function of the strong orbital modulation of the source in the Flaring InterMediate state. This dependence could be due to a higher absorption when Cygnus X-3 is behind its companion. However, the uncertainties on the density column prevent us from drawing any firm conclusions.

TeaPGDB: Tea Plant Genome Database

As the most widely consumed beverage in the world, tea has various nutritional, economic, and global cultural values. With the development of the third-generation sequencing technology, several genome sequences of tea plants have been published. These genomic data have pivotal information that is of benefit to tea plant breeders and biologists in advancing tea plant improvement and the final quality of tea products. We hereby present the integrative online database, Tea Plant Genome Database (TeaPGDB; <a a-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" href="http://eplant.njau.edu.cn/tea">http://eplant.njau.edu.cn/tea</a>), which incorporates the published genome sequences of tea plants. The current release of TeaPGDB hosts published tea plant genome data with various online tools, including JBrowse, gene search, SSR search, BLAST. TeaPGDB also contains a download server, which provides access for the download of genome-related data and rich annotation files. TeaPGDB is committed to collecting, integrating, and annotating published tea plant genome data, providing data support for research on tea plant heredity, evolution, breeding for resistance, plant improvement, and facilitating the characterization of important traits or flavor related genes in the community. Compared with other tea plant databases, this database not only contains more complete genome data and gene annotation information, but also has a user-friendly interface for researchers in the field.