Colorectal cancer (CRC) is the third most common worldwide. Its incidence still increasing, and mortality rate high, for which new therapeutic prognostic strategies are urgently needed. It became increasingly recognized that gut microbiota composition differs significantly between healthy people CRC patients. Thus, identifying difference of patients fundamental to understand microbes' functional roles in development CRC. We analyzed microbial community structure a metagenomic dataset 156...

Abstract Motivation: Local similarity analysis of biological time series data helps elucidate the varying dynamics systems. However, its applications to large scale high-throughput are limited by slow permutation procedures for statistical significance evaluation. Results: We developed a theoretical approach approximate local based on tail distribution maximum partial sum independent identically distributed (i.i.d.) random variables. Simulations show that derived formula approximates...

Periodontitis is an inflammatory disease affecting the tissues supporting teeth (periodontium). Integrative analysis of metagenomic samples from multiple periodontitis studies a powerful way to examine microbiota diversity and interactions within host oral cavity. A total 43 subjects were recruited participate in two previous profiling microbial community human subgingival plaque using shotgun sequencing. We integrated sequence data those studies, including six healthy controls, 14 sites...

Pregnancy is a physiological process with pronounced hormonal fluctuations in females, and relatively little known regarding how pregnancy influences the ecological shifts of supragingival microbiota. In this study, plaques salivary hormones were collected from 11 pregnant women during (P1, ≤14 weeks; P2, 20-25 P3, 33-37 weeks) postpartum period (P4, 6 weeks after childbirth). Seven non-pregnant volunteers sampled at same time intervals. The microbial genetic repertoire was obtained by 16S...

The imbalance of human gut microbiota has been associated with colorectal cancer. In recent years, metagenomics research provided a large amount scientific data enabling us to study the dedicated roles microbes in onset and progression We removed unrelated redundant features during feature selection by mutual information. then trained random forest classifier on dataset cancer patients healthy people assembled from published reports extracted analysed information learned decision trees....

An effective feature extraction method is key to improving the accuracy of a prediction model. From Gene Expression Omnibus (GEO) database, which includes 13,487 genes, we obtained microarray gene expression data for 238 samples from colorectal cancer (CRC) and normal samples. Twelve modules were by weighted co-expression network analysis (WGCNA) on 173 By calculating Pearson correlation coefficient (PCC) between characteristic genes each module cancer, that was highly correlated with CRC....

As the third generation gene editing technology, Crispr/Cas9 has a wide range of applications. The success Crispr depends on target via functional complex sgRNA and Cas9 proteins. Therefore, highly specific high on-target cleavage efficiency can make this process more accurate efficient. Although there are already many sophisticated machine learning or deep models to predict sgRNA, prediction accuracy remains be improved. XGBoost is good at classification as ensemble model could overcome...

As a simple and programmable nuclease-based genome editing tool, the CRISPR/Cas9 system has been widely used in target-gene repair gene-expression regulation. The DNA mutation generated by CRISPR/Cas9-mediated double-strand breaks determines its biological phenotypic effects. Experiments have demonstrated that CRISPR/Cas9-generated cellular-repair outcomes depend on local sequence features. Therefore, after break can be predicted sequences near cleavage sites. However, existing prediction...

Clear cell renal carcinoma (ccRCC), the most common subtype of carcinoma, has high heterogeneity a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have failed to achieve good therapeutic effects. In this article, single-cell transcriptome sequencing (scRNA-seq) data from six patients downloaded GEO database were adopted describe microenvironment (TME) ccRCC, including its T cells, tumor-associated macrophages (TAMs),...

Colon adenocarcinoma is the most common type of colorectal cancer. The prognosis advanced cancer patients who received treatment still very poor. Therefore, identifying new biomarkers for prediction has important significance improving strategies. However, power biomarker analyses was limited by used sample size individual database. In this study, we combined Genotype-Tissue Expression (GTEx) and Cancer Genome Atlas (TCGA) databases to expand number healthy tissue samples. We screened...

Simulating genome sequence data with variant features facilitates the development and benchmarking of structural analysis programs. However, there are only a few simulators that provide variants in silico even fewer different allelic fraction haplotypes. We developed SVEngine, an open-source tool to address this need. SVEngine simulates next-generation sequencing embedded variations. As input, takes template haploid sequences (FASTA) external file, distribution and/or clonal phylogeny tree...

Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics biological systems. However, slow permutation procedures to evaluate the statistical significance local scores have limited its applications high-throughput analysis, e.g., from next generation sequencing technology based studies. By extending theories for tail probability range sum Markovian random variables, we propose formulae approximating scores. Using simulations and real data, show that...

Discovering the key microbial species and environmental factors of community characterizing their relationships with other members are critical to ecosystem studies. The co-occurrence patterns across a variety settings have been extensively characterized. However, previous studies were limited by restriction toward pairwise relationships, while there was ample evidence third-party mediated in communities.

Colorectal cancer is the third most common worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within primary tumor tissues derived from patients. These implicated relative abundance of these as a contributing factor in progression. Infiltrating are believed to be among major drivers tumorigenesis, progression, and metastasis and, hence, promising targets for new treatments. However, measuring their...

The abstract should be a total of about 250 words and structured to contain the following headings: Background/Objectives, Methods, Results, Conclusions. Background/Objectives: Place question addressed in broad context highlight purpose study; Methods: Describe briefly main methods or treatments applied. Include any relevant preregistration numbers, species strains animals used; Results: Summarize article’s findings; Conclusions: Indicate conclusions interpretations. an objective...

The increasing availability of large-scale time series data allows the inference microbial community dynamics by association network analysis. However, correlation-based analyses are noninformative causal, mediating and time-dependent relationships between functional factors. To address this insufficiency, we introduced Granger causality model to analysis a recent marine dataset. We systematically constructed directed acyclic network, representing both internal external causal among...

Objective . This work is aimed at revealing the role and molecular mechanism of connective tissue growth factor 2 (CTGF) in osteoblast differentiation periodontal ligament stem cells (PDLSCs). Methods The osteogenic PDLSCs was induced by induction medium (OM), expression level related proteins ALP, RUNX2, OCN, CTGF estimated using quantitative real‐time polymerase chain reaction (qRT‐PCR) Western blotting analysis. We constructed cell lines with overexpression or knockdown to verify PDLSCs....

The human gut microbiota plays a major role in maintaining health and was recently recognized as promising target for disease prevention treatment. Many diseases are traceable to dysbiosis, implicating altered microbial ecosystems, or, many cases, disrupted enzymes carrying out essential physio-biochemical reactions. Thus, the changes of enzyme levels may predict disorders. With rapid development high-throughput sequencing technologies, metagenomics analysis has emerged an important method...

Dealing with food safety issues in time through online public opinion incidents can reduce the impact of and protect human health effectively. Therefore, by smart technology extracting entity relationship events field, knowledge graph field is constructed to discover between issues. To solve problem multi-entity relationships incident sentences for few-shot learning, this paper adopts pipeline-type extraction method. Entity extracted from Bidirectional Encoder Representation Transformers...

This study examined the relationship between expression of p16, a tumor suppressor gene, and lymph node metastasis, as well patient prognosis, in cases with ovarian cancer. SKOV-3, an cancer cell line, IOSE80, normal human were selected for testing. Western blot analysis was used to detect p16 culture samples. In study, 20 tissue 64 tissue, including 38 metastasis 26 without also Immunohistochemical techniques protein The influence on SKOV-3 invasion ability studied using gene...