Successful treatment of refractory ascites in a patient with liver cirrhosis combined with hepatic artery-portal vein malformation: A case report.

INTRODUCTION: Hepatic artery-portal vein malformation is rarely encountered in clinical practice. Here, we reported a case of liver cirrhosis combined with hepatic artery-portal vein malformation with refractory ascites as the main symptom. And it was successfully treated by us. The present case demonstrates the role of hepatic artery-portal vein malformation in cirrhotic ascites and the importance of early diagnosis and interventional treatment. This article may provides some experience for the treatment of such patients. PATIENT CONCERNS: The patient was a 72-year-old woman with a 40-year history of Hepatitis B virus surface antigen positivity who sought medical advice with a chief complaint of abdominal distension for 1 week. DIAGNOSES: Enhanced abdominal computed tomography imaging of this patient revealed liver cirrhosis, splenomegaly, esophageal and gastric varices, massive ascites, and a low-density area in the S4 segment of the liver with an ambiguous boundary. Widening of the left branch of the portal vein was evident, and the portal vein was highlighted in the arterial phase and the venous phase. Digital subtraction angiography revealed substantial thickening of the left hepatic artery, and the administered contrast agent drained through the malformed vascular mass to the thickened left portal vein. Liver cirrhosis combined with hepatic artery-portal vein malformation were diagnosed. And we considered that the artery-portal vein malformation in this patient might be caused by cirrhosis. INTERVENTIONS: The patient was applied diuretics, entecavir and transcatheter embolization. OUTCOMES: The patient ascites did not resolve significantly when treated with diuretics alone. After the transcatheter embolization, the patient ascites relieved remarkably. CONCLUSION: The patient underwent transcatheter embolization for hepatic artery-portal vein malformation, after which her ascites resolved with good short-term curative efficacy. So, the patients who suffered from liver cirrhosis combined with hepatic artery-portal vein malformation and refractory ascites, should be active on transcatheter embolization.

Ball divergence for the equality test of crossing survival curves.

It is a very common problem to test survival equality using the right-censored time-to-event data in clinical research. Although the log-rank test is popularly used in various studies, it may become insensitive when the proportional hazards assumption is violated. As follows, there have a variety of statistical methods being proposed to identify the discrepancy between crossing survival curves or hazard functions. The omnibus tests against general alternatives are usually preferred due to their wide applicability to complicated scenarios in real applications. In this paper, we propose two novel statistics to estimate the ball divergence using the right-censored survival data, and then implement them in the equality test on survival time in two independent groups. The simulation analysis demonstrates their efficiency in identifying the survival discrepancy. Compared to the existing methods, our proposed methods present higher power in situations with complex distributions, especially when there is a scale shift between groups. Real examples illustrate its advantage in practical applications.

ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.

MOTIVATION: Several computational and statistical methods have been developed to analyze data generated through the 3C-based methods, especially the Hi-C. Most of the existing methods do not account for dependency in Hi-C data. RESULTS: Here, we present ZipHiC, a novel statistical method to explore Hi-C data focusing on the detection of enriched contacts. ZipHiC implements a Bayesian method based on a hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC) to detect interactions in two-dimensional space based on a Hi-C contact frequency matrix. ZipHiC uses data on the sources of biases related to the contact frequency matrix, allows borrowing information from neighbours using the Potts model and improves computation speed using the ABC model. In addition to outperforming existing tools on both simulated and real data, our model also provides insights into different sources of biases that affects Hi-C data. We show that some datasets display higher biases from DNA accessibility or Transposable Elements content. Furthermore, our analysis in Drosophila melanogaster showed that approximately half of the detected significant interactions connect promoters with other parts of the genome indicating a functional biological role. Finally, we found that the micro-C datasets display higher biases from DNA accessibility compared to a similar Hi-C experiment, but this can be corrected by ZipHiC. AVAILABILITY AND IMPLEMENTATION: The R scripts are available at https://github.com/igosungithub/HMRFHiC.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Efficient empirical likelihood inference for recovery rate of COVID19 under double-censoring.

Doubly censored data are very common in epidemiology studies. Ignoring censorship in the analysis may lead to biased parameter estimation. In this paper, we highlight that the publicly available COVID19 data may involve high percentage of double-censoring and point out the importance of dealing with such missing information in order to achieve better forecasting results. Existing statistical methods for doubly censored data may suffer from the convergence problems of the EM algorithms or may not be good enough for small sample sizes. This paper develops a new empirical likelihood method to analyze the recovery rate of COVID19 based on a doubly censored dataset. The efficient influence function of the parameter of interest is used to define the empirical likelihood (EL) ratio. We prove that - 2 log (EL-ratio) asymptotically follows a standard χ 2 distribution. This new method does not require any scale parameter adjustment for the log-likelihood ratio and thus does not suffer from the convergence problems involved in traditional EM-type algorithms. Finite sample simulation results show that this method provides much less biased estimate than existing methods, when censoring percentage is large. The application to COVID19 data will help researchers in other field to achieve better estimates and forecasting results.

The role of insulators and transcription in 3D chromatin organization of flies.

The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.

Balancing Gender Bias in Job Advertisements With Text-Level Bias Mitigation.

Despite progress toward gender equality in the labor market over the past few decades, gender segregation in labor force composition and labor market outcomes persists. Evidence has shown that job advertisements may express gender preferences, which may selectively attract potential job candidates to apply for a given post and thus reinforce gendered labor force composition and outcomes. Removing gender-explicit words from job advertisements does not fully solve the problem as certain implicit traits are more closely associated with men, such as ambitiousness, while others are more closely associated with women, such as considerateness. However, it is not always possible to find neutral alternatives for these traits, making it hard to search for candidates with desired characteristics without entailing gender discrimination. Existing algorithms mainly focus on the detection of the presence of gender biases in job advertisements without providing a solution to how the text should be (re)worded. To address this problem, we propose an algorithm that evaluates gender bias in the input text and provides guidance on how the text should be debiased by offering alternative wording that is closely related to the original input. Our proposed method promises broad application in the human resources process, ranging from the development of job advertisements to algorithm-assisted screening of job applications.

Single-molecule imaging reveals the concerted release of myosin from regulated thin filaments.

Regulated thin filaments (RTFs) tightly control striated muscle contraction through calcium binding to troponin, which enables tropomyosin to expose myosin-binding sites on actin. Myosin binding holds tropomyosin in an open position, exposing more myosin-binding sites on actin, leading to cooperative activation. At lower calcium levels, troponin and tropomyosin turn off the thin filament; however, this is antagonised by the high local concentration of myosin, questioning how the thin filament relaxes. To provide molecular details of deactivation, we used single-molecule imaging of green fluorescent protein (GFP)-tagged myosin-S1 (S1-GFP) to follow the activation of RTF tightropes. In sub-maximal activation conditions, RTFs are not fully active, enabling direct observation of deactivation in real time. We observed that myosin binding occurs in a stochastic step-wise fashion; however, an unexpectedly large probability of multiple contemporaneous detachments is observed. This suggests that deactivation of the thin filament is a coordinated active process.

BSC2 induces multidrug resistance via contributing to the formation of biofilm in Saccharomyces cerevisiae.

Biofilm plays an important role in fungal multidrug resistance (MDR). Our previous studies showed that BSC2 is involved in resistance to amphotericin B (AMB) through antioxidation in Saccharomyces cerevisiae. In this study, the overexpression of BSC2 and IRC23 induced strong MDR in S. cerevisiae. BSC2-overexpression affected cellular flocculation, cell surface hydrophobicity, biofilm formation and invasive growth. However, it failed to induce caspofungin (CAS) resistance and affect the invasive growth in FLO mutant strains (FLO11Δ, FLO1Δ, FLO8Δ and TUP1Δ). Furthermore, the overexpression of BSC2 compensated for chitin synthesis defects to maintain the cell wall integrity and significantly reduced the cell morphology abnormality induced by CAS. However, it could not repair the cell wall damage caused by CAS in the FLO mutant strains. Although BSC2 overexpression increased the level of mannose in the cell wall, DPM1 overexpression in both BY4741 and bsc2∆ could confer resistance to CAS and AMB. In addition, BSC2 overexpression significantly increased the mRNA expression of FLO11, FLO1, FLO8 and TUP1. BSC2 may function as a regulator of FLO genes and be involved in cell wall integrity in yeast. Taken together, our data demonstrate that BSC2 induces MDR in a FLO pathway-dependent manner via contributing to the formation of biofilms in S. cerevisiae. TAKE AWAYS: Overexpression of BSC2 induced strong MDR in S. cerevisiae. BSC2 affected cellular flocculation, CSH, biofilm formation and invasive growth. BSC2 could not repair the cell wall damage caused by CAS in the FLO mutants. BSC2 may function as a regulator of FLO genes to maintain cell wall integrity. BSC2 promotes biofilm formation in a FLO pathway-dependent manner to induce MDR.

Oncolytic HSV-Infected Glioma Cells Activate NOTCH in Adjacent Tumor Cells Sensitizing Tumors to Gamma Secretase Inhibition.

PURPOSE: To examine the effect of oncolytic herpes simplex virus (oHSV) on NOTCH signaling in central nervous system tumors. EXPERIMENTAL DESIGN: Bioluminescence imaging, reverse phase protein array proteomics, fluorescence microscopy, reporter assays, and molecular biology approaches were used to evaluate NOTCH signaling. Orthotopic glioma-mouse models were utilized to evaluate effects in vivo. RESULTS: We have identified that herpes simplex virus-1 (HSV-1; oncolytic and wild-type)-infected glioma cells induce NOTCH signaling, from inside of infected cells into adjacent tumor cells (inside out signaling). This was canonical NOTCH signaling, which resulted in activation of RBPJ-dependent transcriptional activity that could be rescued with dnMAML. High-throughput screening of HSV-1-encoded cDNA and miRNA libraries further uncovered that HSV-1 miR-H16 induced NOTCH signaling. We further identified that factor inhibiting HIF-1 (FIH-1) is a direct target of miR-H16, and that FIH-1 downregulation by virus encoded miR-H16 induces NOTCH activity. FIH-1 binding to Mib1 has been reported, but this is the first report that shows FIH-1 sequester Mib1 to suppress NOTCH activation. We observed that FIH-1 degradation induced NOTCH ligand ubiquitination and NOTCH activity. REMBRANDT and The Cancer Genome Atlas data analysis also uncovered a significant negative regulation between FIH-1 and NOTCH. Furthermore, combination of oHSV with NOTCH-blocking gamma secretase inhibitor (GSI) had a therapeutic advantage in two different intracranial glioma models treated with oncolytic HSV, without affecting safety profile of the virus in vivo. CONCLUSIONS: To our knowledge this is the first report to identify impact of HSV-1 on NOTCH signaling and highlights the significance of combining oHSV and GSI for glioblastoma therapy.

An oncolytic herpesvirus expressing E-cadherin improves survival in mouse models of glioblastoma.

The efficacy of oncolytic herpes simplex virus (oHSV) is limited by rapid viral clearance by innate immune effector cells and poor intratumoral viral spread. We combine two approaches to overcome these barriers: inhibition of natural killer (NK) cells and enhancement of intratumoral viral spread. We engineered an oHSV to express CDH1, encoding E-cadherin, an adherent molecule and a ligand for KLRG1, an inhibitory receptor expressed on NK cells. In vitro, infection with this engineered virus, named OV-CDH1, induced high surface E-cadherin expression on infected glioblastoma (GBM) cells, which typically lack endogenous E-cadherin. Ectopically expressed E-cadherin enhanced the spread of OV-CDH1 by facilitating cell-to-cell infection and viral entry and reduced viral clearance by selectively protecting OV-CDH1-infected cells from KLRG1+ NK cell killing. In vivo, OV-CDH1 treatment substantially prolonged the survival in GBM-bearing mouse models, primarily because of improved viral spread rather than inhibition of NK cell activity. Thus, virus-induced overexpression of E-cadherin may be a generalizable strategy for improving cancer virotherapy.

Refining value-at-risk estimates using a Bayesian Markov-switching GJR-GARCH copula-EVT model.

In this paper, we propose a model for forecasting Value-at-Risk (VaR) using a Bayesian Markov-switching GJR-GARCH(1,1) model with skewed Student's-t innovation, copula functions and extreme value theory. A Bayesian Markov-switching GJR-GARCH(1,1) model that identifies non-constant volatility over time and allows the GARCH parameters to vary over time following a Markov process, is combined with copula functions and EVT to formulate the Bayesian Markov-switching GJR-GARCH(1,1) copula-EVT VaR model, which is then used to forecast the level of risk on financial asset returns. We further propose a new method for threshold selection in EVT analysis, which we term the hybrid method. Empirical and back-testing results show that the proposed VaR models capture VaR reasonably well in periods of calm and in periods of crisis.

Molecular Basis for the Recognition of Herpes Simplex Virus Type 1 Infection by Human Natural Killer Cells.

Primary infection with Herpes simplex virus type 1 (HSV1) is subclinical or only mildly symptomatic in normal individuals, yet the reason for the body's effective immune defense against this pathogen in the absence of antigen-specific immunity has not been well understood. It is clear that human natural killer (NK) cells recognize and kill HSV1-infected cells, and those individuals who either lack or have functionally impaired NK cells can suffer severe, recurrent, and sometimes fatal HSV1 infection. In this article, we review what is known about the recognition of HSV1 by NK cells, and describe a novel mechanism of innate immune surveillance against certain viral pathogens by NK cells called Fc-bridged cell-mediated cytotoxicity.

The Fc Domain of Immunoglobulin Is Sufficient to Bridge NK Cells with Virally Infected Cells.

Clearance of pathogens or tumor cells by antibodies traditionally requires both Fab and Fc domains of IgG. Here, we show the Fc domain of IgG alone mediates recognition and clearance of herpes simplex virus (HSV1)-infected cells. The human natural killer (NK) cell surface is naturally coated with IgG bound by its Fc domain to the Fcγ receptor CD16a. NK cells utilize the Fc domain of bound IgG to recognize gE, an HSV1-encoded glycoprotein that also binds the Fc domain of IgG but at a site distinct from CD16a. The bridge formed by the Fc domain between the HSV1-infected cell and the NK cell results in NK cell activation and lysis of the HSV1-infected cell in the absence of HSV1-specific antibody in vitro and prevents fatal HSV1 infection in vivo. This mechanism also explains how bacterial IgG-binding proteins regulate NK cell function and may be broadly applicable to Fcγ-receptor-bearing cells.

Bortezomib Treatment Sensitizes Oncolytic HSV-1-Treated Tumors to NK Cell Immunotherapy.

PURPOSE: Both the proteasome inhibitor bortezomib and an oncolytic herpes simplex virus-1 (oHSV)-expressing GM-CSF are currently FDA approved. Although proteasome blockade can increase oHSV replication, immunologic consequences, and consequent immunotherapy potential are unknown. In this study, we investigated the impact of bortezomib combined with oHSV on tumor cell death and sensitivity to natural killer (NK) cell immunotherapy. EXPERIMENTAL DESIGN: Western blot, flow cytometry, and caspase 3/7 activity assays were used to evaluate the induction of apoptosis/autophagy and/or necroptotic cell death. Cellular and mitochondrial reactive oxygen species (ROS) production was measured using CellROX and MitoSOX. Inhibitors/shRNA-targeting ROS, JNK and RIP1 kinase (RIPK1) were used to investigate the mechanism of cell killing. The synergistic interaction between oHSV and bortezomib was calculated using a Chou-Talalay analysis. NK cells isolated from normal human blood were co-cultured with tumor cells to evaluate cellular interactions. Q-PCR, ELISA, and FACS analysis were used to evaluate NK cell activation. Intracranial tumor xenografts were used to evaluate antitumor efficacy. RESULTS: Combination treatment with bortezomib- and oHSV-induced necroptotic cell death and increased the production of mitochondrial ROS and JNK phosphorylation. Inhibitors/shRNA of RIPK1 and JNK rescued synergistic cell killing. Combination treatment also significantly enhanced NK cell activation and adjuvant NK cell therapy of mice treated with bortezomib and oHSV improved antitumor efficacy. CONCLUSIONS: This study provides a significant rationale for triple combination therapy with bortezomib, oHSV, and NK cells to improve efficacy, in glioblastoma patients. Clin Cancer Res; 22(21); 5265-76. ©2016 AACRSee related commentary by Suryadevara et al., p. 5164.

Joint longitudinal and survival-cure models in tumour xenograft experiments.

In tumour xenograft experiments, treatment regimens are administered, and the tumour volume of each individual is measured repeatedly over time. Survival data are recorded because of the death of some individuals during the observation period. Also, cure data are observed because of a portion of individuals who are completely cured in the experiments. When modelling these data, certain constraints have to be imposed on the parameters in the models to account for the intrinsic growth of the tumour in the absence of treatment. Also, the likely inherent association of longitudinal and survival-cure data has to be taken into account in order to obtain unbiased estimators of parameters. In this paper, we propose such models for the joint modelling of longitudinal and survival-cure data arising in xenograft experiments. Estimators of parameters in the joint models are obtained using a Markov chain Monte Carlo approach. Real data analysis of a xenograft experiment is carried out, and simulation studies are also conducted, showing that the proposed joint modelling approach outperforms the separate modelling methods in the sense of mean squared errors.

Directed evolution of a virus exclusively utilizing human epidermal growth factor receptor as the entry receptor.

Rational design and directed evolution are powerful tools to generate and improve protein function; however, their uses are mostly limited to enzyme and antibody engineering. Here we describe a directed-evolution strategy, named the tandem selection and enrichment system (TSES), and its use in generating virus with exclusive specificity for a particular cellular receptor. In TSES, evolving viruses are sequentially and iteratively transferred between two different host cells, one for selection of receptor specificity and the other for enrichment of the fittest virus. By combining rational design and TSES, we generated human epidermal growth factor receptor (EGFR)-specific virus 1 (ESV1). ESV1 has the backbone of Sindbis virus (SINV) and displays an EGF domain engrafted onto structural protein E2 after residue Pro192, together with eight amino acid changes stabilizing the E2-EGF chimera. ESV1 uses EGFR to initiate infection and has lost the capacity to interact with all known SINV receptors. A 12.2-Å cryoelectron microscopic (cryoEM) reconstruction of ESV1 reveals that the E2-EGF fusion adopts a fixed conformation, with EGF sitting at the top of the E2 spike; The EGFR binding interface faces outward, and the EGF domain completely masks SINV receptor binding. The cryoEM structure of ESV1 explains the desirable properties of ESV1 and provides insights for its further modification. TSES expands the scope of directed evolution and can be easily extended to other targeting molecules and viral systems.

Accelerated failure time models for censored survival data under referral bias.

The estimation of progression to liver cirrhosis and identifying its risk factors are often of epidemiological interest in hepatitis C natural history study. In most hepatitis C cohort studies, patients were usually recruited to the cohort with a referral bias because clinically the patients with more rapid disease progression were preferentially referred to liver clinics. A pair of correlated event times may be observed for each patient, time to development of cirrhosis and time to referral to a cohort. This paper considers accelerated failure time models to study the effects of covariates on progression to cirrhosis. A new non-parametric estimator is proposed to handle a flexible bivariate distribution of the cirrhosis and referral times and to take the referral bias into account. The asymptotic normality of the proposed estimator is also provided. Numerical studies show that the coefficient estimator and its covariance function estimator perform well.

[Study on the mechanism of enhancing homing efficiency of human hematopoietic stem/progenitor cells into bone marrow after manipulation with tumor necrosis factor alpha in xenotransplanted BALB/c mouse model].

OBJECTIVE: To investigate the role of tumor necrosis factor (TNF) alpha on the homing efficiency of hematopoietic stem/progenitor cells (HS/PC) into bone marrow and its mechanism. METHODS: CFSE-labeled umbilical cord blood (UCB) CD34+ cells were transplanted into irradiated (control group) or combined with TNF alpha prepared (experimental group) BALB/c recipient mice. The distribution in peripheral blood, liver, lung and homing characteristics in bone marrow and spleen of UCB CD34+ cells, in BALB/c recipient mice were determined 20 hours after xenotransplantation by flow cytometry (FACS) and their homing efficiency was calculated. ELISA was used to measure serum SDF-1 alpha level. CXCR4 expression levels of on UCB CD34+ cells were assessed by FACS pre-/post-manipulation with TNF alpha. SDF-1 alpha expression level in bone marrow and spleen was tested by immunohistochemistry. RESULTS: UCB CD34+ cells mainly home into recipient mice bone marrow and spleen; The homing efficiency in experimental group bone marrow [(0.65 +/- 0.13)%] was significantly higher than that in control ones [(0.30 +/- 0.09)%, P < 0.01], whereas the homing efficiency in experimental group spleen was dramatically lower than that in control ones (P < 0.01); Treatment with TNF alpha did not affect recipient serum SDF-1 alpha level; After 18 hours co-cultured with TNF alpha, the CXCR4e expression level on UCB CD34+ cells was similar to that on fresh ones; TNF alpha treatment induced significantly higher SDF-1 alpha expression on osteoblastic and stromal cells in bone marrow, and reversed spleen SDF-1 alpha gradient that was originally favorable for CD34+ cells homing. CONCLUSION: TNF alpha enhances the homing efficiency of HS/PC via up-regulating SDF-1 alpha gradient in bone marrow, and might be an useful enhancer for HS/PC homing in clinical practice.