SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data.

Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework.

Inhibitory effect of silymarin on CCl-induced liver fibrosis by reducing Ly6C monocytes infiltration.

It has been well established that silymarin has hepatoprotective and anti-fibrotic effects. But the mechanisms are poorly understood. In recent years, the role of Ly6C monocytes in liver fibrosis has been well demonstrated.

Risk factors associated with fatality of severe fever with thrombocytopenia syndrome: a meta-analysis.

Severe fever with thrombocytopenia syndrome is an emerging life-threatening infectious disease identified in 2009. Given high case-fatality rate among patients with severe fever with thrombocytopenia syndrome, identification of the risk factors at acute phase associated with fatality is crucial for treatment. Therefore, we aimed to meta-analytically evaluate risk factors of fatal clinical outcome of severe fever with thrombocytopenia syndrome.

Gypsophila elegans isoorientin-2″-O-α-l-arabinopyranosyl ameliorates porcine serum-induced immune liver fibrosis by inhibiting NF-κB signaling pathway and suppressing HSC activation.

The present study was to investigate the inhibitory effect of Gypsophila elegans isoorientin-2″-O-α-l-arabinopyranosyl (GEI) on hepatic stellate cells (HSCs), to reveal the underlying mechanism of GEI against hepatic fibrosis. Our study showed that GEI significantly alleviated liver injury induced by porcine serum (PS) in rats; it notably alleviated collagen accumulation as evidenced by a significant decrease in the levels of collagen biomarkers including hyaluronic acid, laminin, hydroxyproline and procollagen III N-terminal peptide. Moreover, GEI treatment markedly decreased the secretion of inflammatory cytokines by inhibiting the NF-κB pathway and significantly inhibited the generation of excessive extracellular matrix (ECM) components by restoring the balance between matrix metalloproteinases (MMPs) and tissue inhibitor of matrix metalloproteinases (TIMPs).

TFCP2 Is Required for YAP-Dependent Transcription to Stimulate Liver Malignancy.

Although YAP-dependent transcription is closely associated with liver tumorigenesis, the mechanism by which YAP maintains its function is poorly understood. Here, we show that TFCP2 is required for YAP-dependent transcription and liver malignancy. Mechanistically, YAP function is stimulated by TFCP2 via a WW-PSY interaction.

High expression of brain-derived neurotrophic factor in intrahepatic cholangiocarcinoma is associated with intraneural invasion and unfavorable prognosis.

Aim: Brain-derived neurotrophic factor (BDNF) could promote the survival and differentiation of neural cells in peripheral and central nervous systems during development. Emerging evidences identified BDNF as an oncoprotein which could promotes progression and prognosis of tumors such as giloma, lung cancer and gastric cancer. We performed experiments to investigate the expression and clinical significance of BDNF in intrahepatic cholangiocarcinoma (IHCC).

A novel predictive model using routinely clinical parameters to predict liver fibrosis in patients with chronic hepatitis B.

Objectives: Noninvasive models have been established for the assessment of liver fibrosis in patients with chronic hepatitis B(CHB). However, the predictive performance of these established models remains inconclusive. We aimed to develop a novel predictive model for liver fibrosis in CHB based on routinely clinical parameters.

A scoring model for predicting prognosis of patients with severe fever with thrombocytopenia syndrome.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging epidemic infectious disease caused by the SFTS bunyavirus (SFTSV) with an estimated high case-fatality rate of 12.7% to 32.6%.

Screening of primary gp120 immunogens to formulate the next generation polyvalent DNA prime-protein boost HIV-1 vaccines.

Our previous preclinical studies and a Phase I clinical trial DP6-001 have indicated that a polyvalent Env formulation was able to elicit broadly reactive antibody responses including low titer neutralizing antibody responses against viral isolates of subtypes A, B, C and AE. In the current report, a panel of 62 gp120 immunogens were screened in a rabbit model to identify gp120 immunogens that can elicit improved binding and neutralizing antibody responses and some of them can be included in the next polyvalent formulation. Only about 19% of gp120 immunogens in this panel were able to elicit neutralizing antibodies against greater than 50% of the viruses included in a high throughput PhenoSense neutralization assay when these immuongens were tested as a DNA prime followed by a fixed 5-valent gp120 protein vaccine boost.

Biomarkers of disease can be detected in mice as early as 4 weeks after initiation of exposure to third-hand smoke levels equivalent to those found in homes of smokers.

Third-hand smoke (THS) is a newly discovered environmental health hazard that results from accumulation and aging of second-hand smoke (SHS) toxins on surfaces where smoking has occurred. Our objective was to determine whether there is a time-dependent effect of THS exposure on health. Using an exposure mouse system that mimics exposure of humans to THS, we investigated its effects on biomarkers found in serum, and in liver and brain tissues.

Redundant and incoherent regulations of multiple phenotypes suggest microRNAs' role in stability control.

Each microRNA (miRNA) represses a web of target genes and, through them, controls multiple phenotypes. The difficulties inherent in such controls cast doubt on how effective miRNAs are in driving phenotypic changes. A "simple regulation" model posits "one target-one phenotype" control under which most targeting is nonfunctional.

Ailanthone induces G2/M cell cycle arrest and apoptosis of SGC‑7901 human gastric cancer cells.

Ailanthone is a major quassinoid extracted from the Chinese medicinal herb Ailanthus altissima, which has been reported to exert antiproliferative effects on various cancer cells. The present study aimed to investigate the antitumor effects of ailanthone on SGC‑7901 cells, and to analyze its underlying molecular mechanisms. Following treatment with ailanthone, Cell Counting kit‑8 was used to detect the cytotoxic effects of ailanthone on SGC‑7901 cells in vitro.

PIM-1 kinase inhibitor SMI-4a exerts antitumor effects in chronic myeloid leukemia cells by enhancing the activity of glycogen synthase kinase 3β.

The development of targeted tyrosine kinase inhibitors (TKIs) has succeeded in altering the course of chronic myeloid leukemia (CML). However, a number of patients have failed to respond or experienced disease relapse following TKI treatment. Proviral integration site for moloney murine leukemia virus‑1 (PIM‑1) is a serine/threonine kinase that participates in regulating apoptosis, cell cycle, signal transduction and transcriptional pathways, which are associated with tumor progression, and poor prognosis.

Application of α-amino acids for the transition-metal-free synthesis of pyrrolo[1,2-a]quinoxalines.

A practical and concise protocol for the efficient synthesis of pyrrolo[1,2-a]quinoxalines from readily available α-amino acids and 2-(1H-pyrrol-1-yl)anilines under transition metal-free conditions has been established. This protocol, which includes the formation of new C-C and C-N bonds, features a wide substrate scope with a broad range of functional group tolerance.

Sirt1 suppresses Wnt/βCatenin signaling in liver cancer cells by targeting βCatenin in a PKAα-dependent manner.

Here, bioinformatics data from Sirt1 knock-out (KO) and knock-in (KI) mice suggest that Sirt1 inhibits Wnt/βCatenin signaling in the liver. However, it is unclear how this relationship occurs and how it contributes to malignant phenotypes in liver cancer cells. We found that Sirt1 expression promotes phosphorylation of βCatenin at Ser675, which may subsequently decrease expression of total-βCatenin.

Secreted frizzled-related protein 1 (SFRP1) gene methylation changes in the human lung adenocarcinoma cells treated with L-securinine.

Lung cancer remains the leading cause of cancer-related death worldwide. It is important to explore the biomarkers of diagnosis and prognosis in lung cancer. To evaluate the cytotoxicity of L-securinine and the expression and methylation of secreted frizzled-related proteins (SFRPs) genes in the human lung adenocarcinoma cells, cell counting kit-8 (CCK-8) assay was used to assess the proliferation of lung adenocarcinoma cells treated with L-securinine.

A New Formulation of Random Genetic Drift and Its Application to the Evolution of Cell Populations.

Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When drift is defined by the WF model, it becomes stronger as the population size, N, decreases.

The essential role of YAP O-GlcNAcylation in high-glucose-stimulated liver tumorigenesis.

O-GlcNAcylation has been implicated in the tumorigenesis of various tissue origins, but its function in liver tumorigenesis is not clear. Here, we demonstrate that O-GlcNAcylation can enhance the expression, stability and function of Yes-associated protein (YAP), the downstream transcriptional regulator of the Hippo pathway and a potent oncogenic factor in liver cancer. O-GlcNAcylation induces transformative phenotypes of liver cancer cells in a YAP-dependent manner.

A mathematical theory of the transcription repression (TR) therapy of cancer - whether and how it may work.

Transcription repression (TR) therapy of cancer has been widely discussed. Here, TR refers to global repression of transcription rather than specific targeting of cancer-causing genes such as MYC. TR drugs inhibit transcription by binding to the transcribed DNA or to RNA polymerase; for example, actinomycin D has been extensively used in research and therapy to shut down transcription globally [1-7].

NRAGE induces β-catenin/Arm O-GlcNAcylation and negatively regulates Wnt signaling.

The Wnt pathway is crucial for animal development, as well as tumor formation. Understanding the regulation of Wnt signaling will help to elucidate the mechanism of the cell cycle, cell differentiation and tumorigenesis. It is generally accepted that in response to Wnt signals, β-catenin accumulates in the cytoplasm and is imported into the nucleus where it recruits LEF/TCF transcription factors to activate the expression of target genes.

Anti-proliferative and pro-apoptotic effects of cinobufagin on human breast cancer MCF-7 cells and its molecular mechanism.

Cinobufagin (CBF) is an active ingredient isolated from Venenum Bufonis extracted and dried from the secretory glands of Bufo gargarizans Cantor. The purpose of the study was to investigate the effects and underlying mechanisms of CBF on human breast cancer MCF-7 cells in vitro. Our results showed that CBF exhibited obvious cytotoxicity on MCF-7 cells in a dose- and time-dependent manner, as indicated by CCK-8 assays.

Is the oral contraceptive or hormone replacement therapy a risk factor for cholelithiasis: A systematic review and meta-analysis.

Background: Association between exogenous estrogen intake and cholelithiasis risk has been reported in several epidemiological studies, including oral contraceptive (OC) and hormone replacement therapy (HRT), while the results were controversial. This study aimed to perform a comprehensive meta-analysis of this issue.

Methods: PUBMED, EMBASE, and Cochrane library database were searched up to October 2016.