Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus- Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.published_or_final_versio

Do statins reduce the risk of hepatocellular carcinoma in patients with chronic hepatitis B?

In subjects with chronic hepatitis B (CHB), the lifetime risk of developing hepatocellular carcinoma (HCC) is estimated to be 25-37 times compared to non-infected subjects. The process of hepatocarcinogenesis is complex and involves well-documented host, viral, and environmental risk factors. The most important risks include host factors such as older age, male gender, the presence of cirrhosis, and viral factors such as the viral load, genotype, and the presence of basal core promoter mutations. To date, antiviral therapy is the only intervention demonstrated to significantly reduce the risk of HCC development in CHB patients. Although oxidative stress has been implicated in cancer development, there is no established benefit shown from treatment with antioxidizing agents such as silymarin, green tea, and vitamin E.published_or_final_versio

EZH2-Mediated H3K27me3 Is Involved in Epigenetic Repression of Deleted in Liver Cancer 1 in Human Cancers

Enhancer of zeste homolog 2 (EZH2), the histone methyltransferase of the Polycomb Repressive complex 2 catalyzing histone H3 lysine 27 tri-methylation (H3K27me3), is frequently up-regulated in human cancers. In this study, we identified the tumor suppressor Deleted in liver cancer 1 (DLC1) as a target of repression by EZH2-mediated H3K27me3. DLC1 is a GTPase-activating protein for Rho family proteins. Inactivation of DLC1 results in hyper-activated Rho/ROCK signaling and is implicated in actin cytoskeleton reorganization to promote cancer metastasis. By chromatin immunoprecipitation assay, we demonstrated that H3K27me3 was significantly enriched at the DLC1 promoter region of a DLC1-nonexpressing HCC cell line, MHCC97L. Depletion of EZH2 in MHCC97L by shRNA reduced H3K27me3 level at DLC1 promoter and induced DLC1 gene re-expression. Conversely, transient overexpression of GFP-EZH2 in DLC1-expressing Huh7 cells reduced DLC1 mRNA level with a concomitant enrichment of EZH2 on DLC1 promoter. An inverse relation between EZH2 and DLC1 expression was observed in the liver, lung, breast, prostate, and ovarian cancer tissues. Treating cancer cells with the EZH2 small molecular inhibitor, 3-Deazaneplanocin A (DZNep), restored DLC1 expression in different cancer cell lines, indicating that EZH2-mediated H3K27me3 epigenetic regulation of DLC1 was a common mechanism in human cancers. Importantly, we found that DZNep treatment inhibited HCC cell migration through disrupting actin cytoskeleton network, suggesting the therapeutic potential of DZNep in targeting cancer metastasis. Taken together, our study has shed mechanistic insight into EZH2-H3K27me3 epigenetic repression of DLC1 and advocated the significant pro-metastatic role of EZH2 via repressing tumor and metastasis suppressors.published_or_final_versio

Predicting the state of charge and health of batteries using data-driven machine learning

Machine learning is a specific application of artificial intelligence that allows computers to learn and improve from data and experience via sets of algorithms, without the need for reprogramming. In the field of energy storage, machine learning has recently emerged as a promising modelling approach to determine the state of charge, state of health and remaining useful life of batteries. First, we review the two most studied types of battery models in the literature for battery state prediction: the equivalent circuit and physics-based models. Based on the current limitations of these models, we showcase the promise of various machine learning techniques for fast and accurate battery state prediction. Finally, we highlight the major challenges involved, especially in accurate modelling over length and time, performing in situ calculations and high-throughput data generation. Overall, this work provides insights into real-time, explainable machine learning for battery production, management and optimization in the future

RhoE/ROCK2 regulates chemoresistance through NF-κB/IL-6/ STAT3 signaling in hepatocellular carcinoma

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Influence of Ionophore Supplementation on Growth Performance, Dietary Energetics and Carcass Characteristics in Finishing Cattle during Period of Heat Stress.

Forty-eight crossbred heifers (378.1±18 kg) were used in a 56-d feeding trial (four pens per treatment in a randomised complete block design) to evaluate the influence of ionophore supplementation on growth performance, dietary energetics and carcass characteristics in finishing cattle during a period of heat stress. Heifers were fed a diet based on steam-flaked corn (2.22 Mcal NEm/kg) with and without an ionophore. Treatments were: i) control, no ionophore; ii) 30 mg/kg monensin sodium (RUM30); iii) 20 mg/kg lasalocid sodium (BOV20), and iv) 30 mg/kg lasalocid sodium (BOV30). Both dry matter intake (DMI) and climatic variables were measured daily and the temperature humidity index (THI) was estimated. The maximum THI during the study averaged 93, while the minimum was 70 (THI average = 79.2±2.3). Compared to controls, monensin supplementation did not influence average daily gain, the estimated NE value of the diet, or observed-to-expected DMI, but tended (p = 0.07) to increase (4.8%) gain to feed. Compared to controls, the group fed BOV30 increased (p≤0.03) daily gain (11.8%), gain to feed (8.3%), net energy of the diet (5%), and observed-to-expected DMI (5.2%). Daily weight gain was greater (7.6%, p = 0.05) for heifers fed BOV30 than for heifers fed MON30. Otherwise, differences between the two treatments in DMI, gain to feed, and dietary NE were not statistically significant (p>0.11). Plotting weekly intakes versus THI, observed intake of controls was greater (p<0.05) at THI values ≤77 than ionophore groups. When THI values were greater than 79, DMI of control and MON30 were not different (p = 0.42), although less than that of groups fed lasalocid (p = 0.04). Variation in energy intake was lower (p>0.05) in the ionophores group (CV = 1.7%) than in the control group (CV = 4.5%). Inclusion of ionophores in the diet resulted in relatively minor changes in carcass characteristics. It is concluded that ionophore supplementation did not exacerbate the decline of DM intake in heat-stressed cattle fed a high-energy finishing diet; on the contrary, it stabilised feed intake and favoured feed efficiency. Ionophore supplementation reduced estimated maintenance coefficients around 10% in finishing cattle during a period of heat stress. This effect was greatest for heifers supplemented with 30 mg lasalocid/kg of diet

Dishevelled-3 phosphorylation is governed by HIPK2/PP1Cα/ITCH axis and the non-phosphorylated form promotes cancer stemness via LGR5 in hepatocellular carcinoma

Dishevelled-3 (Dvl3) is regarded as a binding hub with many different interacting partners. However, its regulation and mechanism on cancer stemness remain to be explored. In this study, we showed that Dvl3 was significantly overexpressed in human hepatocellular carcinomas (HCCs) and promoted cancer stemness both in vitro and in vivo. We found that the non-phosphorylated (NP)-Dvl3 was more stable than the phosphorylated form, more active in activating β-catenin transcriptional activity, and more potent in enhancing self-renewal ability in HCC cells. Mechanistically, we confirmed that the homeodomain-interacting protein kinase-2 (HIPK2) and E3 ubiquitin ligase ITCH were able to physically bind to Dvl3 protein. Knockdown of HIPK2 and the protein phosphatase regulatory unit C-alpha (PP1Cα) resulted in sustained Dvl3 phosphorylation and hence decrease in the NP form of Dvl3. On the other hand, knockdown of E3 ubiquitin ligase ITCH reduced the phosphorylation-induced degradation and stabilized the phosphorylated Dvl3 protein. Furthermore, the NP-Dvl3 enhanced the LGR5 promoter activity to upregulate LGR5 expression, which was associated with increased cancer stemness in HCC. Our findings established that HIPK2/PP1Cα/ITCH axis sustains the de-phosphorylation of Dvl3. This post-translational modification of Dvl3 in turn maintains LGR5 expression and enhances the cancer stemness properties in HCC.published_or_final_versio

Down-regulation of TIMP2 by HIF-1α/miR-210/HIF-3α regulatory feedback circuit enhances cancer metastasis in hepatocellular carcinoma

Cancer metastasis is a multistep process that involves a series of tumor-stromal interaction, including extracellular matrix (ECM) remodeling, which requires a concerted action of multiple proteolytic enzymes and their endogenous inhibitors. This study investigated the role of tissue inhibitor of metalloproteinases (TIMP) 2 in the context of hepatocellular carcinoma (HCC) metastasis. We found that TIMP2 was the most significantly down-regulated member among the TIMP family in human HCCs. Moreover, TIMP2 underexpression was frequent (41.8%; 23 of 55) in human HCCs and was significantly associated with liver invasion and poorer survival outcomes of HCC patients. Furthermore, stable silencing of TIMP2 in HCC cell lines enhanced cell invasive ability and ECM degradation associated with formation of invadopodia-like feature, suggesting that TIMP2 is a negative regulator of HCC metastasis. Using an orthotopic tumor xenograft model, we demonstrated that ectopic expression of TIMP2 open reading frame in the highly metastatic HCC cell line, MHCC-97L, significantly reduced HCC progression as well as pulmonary metastasis. Mechanistically, TIMP2 suppression, in a hypoxic environment, was induced through a regulatory feedback circuit consisting of hypoxia-inducible factor (HIF) 1 alpha, microRNA-210 (miR-210), and HIF-3alpha. CONCLUSION: TIMP2 is frequently down-regulated in human HCCs and its down-regulation is associated with aggressive tumor behavior and poorer patient outcome. Its suppression is under the regulation of a novel feedback circuit consisting of HIF-1alpha/miR-210/HIF-3alpha. TIMP2 is an important regulator of ECM degradation and HCC metastasis. (Hepatology 2016;64:473-487).published_or_final_versio

Phosphorylation of nucleophosmin at threonine 234/237 is associated with HCC metastasis

Hepatocellular carcinoma (HCC) is frequently complicated by the occurrence of intrahepatic and extrahepatic metastases, leading to poor prognosis. To improve the prognosis for HCC patients, there is an urgent need to understand the molecular mechanisms of metastasis in HCC. Since protein Serine/Threonine phosphorylation emerges to be an important posttranslational modification critical in signaling process associated with cell proliferation, survival and metastasis, we employed a pair of primary tumor-derived and corresponding lung-metastatic counterparts (PLC/PRF/5-PT and PLC/PRF/5-LM) and aimed to identify these changes using CelluSpot Serine/Threonine kinase peptide array. Upon analysis, we found phosphorylated level of nucleophosmin (NPM) at Threonine 234/237 (p-NPM-Thr234/237) had remarkably high level in metastatic HCC cells (PLC-LM) than the corresponding primary HCC cell line (PLC-PT). Similar observation was observed in another match primary and their metastatic counterparts (MHCC-97L and MHCC-97H). By immunohistochemical staining, p-NPM-Thr234/237 was consistently found to be preferentially expressed in metastatic HCCs when compared with primary HCC in 28 HCC cases (p < 0.0001). By overexpressing Flag-tagged NPM and its phosphorylation site mutant (Thr234/237A) into low p-NPM-Thr234/237 expressing cells (Hep3B and Huh7) using a lentiviral based approach, we demonstrated that p-NPM-Thr234/237 is critical in invasion and migration of HCC cells, and this effect was mediated by cyclin-dependent kinase 1 (CDK1). Wild-type NPM was found to physically interact with a metastatic gene, ROCK2, and defective in Thr234/237 phosphorylation decreased its binding affinity, resulting in decrease in ROCK2 mediated signaling pathway. Identification of CDK1/p-NPM/ROCK2 signaling pathway provides a novel target for molecular therapy against HCC metastasis.published_or_final_versio

Bond percolation on isoradial graphs: criticality and universality

In an investigation of percolation on isoradial graphs, we prove the criticality of canonical bond percolation on isoradial embeddings of planar graphs, thus extending celebrated earlier results for homogeneous and inhomogeneous square, triangular, and other lattices. This is achieved via the star-triangle transformation, by transporting the box-crossing property across the family of isoradial graphs. As a consequence, we obtain the universality of these models at the critical point, in the sense that the one-arm and 2j-alternating-arm critical exponents (and therefore also the connectivity and volume exponents) are constant across the family of such percolation processes. The isoradial graphs in question are those that satisfy certain weak conditions on their embedding and on their track system. This class of graphs includes, for example, isoradial embeddings of periodic graphs, and graphs derived from rhombic Penrose tilings.Comment: In v2: extended title, and small changes in the tex