Rituximab Treatment in Hepatitis C Infection: An In Vitro Model to Study the Impact of B Cell Depletion on Virus Infectivity

Hepatitis C virus (HCV) infected patients with vasculitis are often treated with the B-cell-depleting anti-CD20 antibody rituximab. Treatment reduces the cryoglobulins that cause vasculitis, yet it also leads to a transient increase in liver enzymes and HCV genomic RNA in the periphery. The mechanism underlying the increased viral load is unclear and both direct and indirect roles have been proposed for B cells in HCV infection. We previously reported that HCV can associate with B cells and can trans-infect hepatocytes. We established an in vitro assay to study the effect(s) of rituximab on B cell-associated HCV infectivity. Rituximab-mediated lysis of B cells in vitro increases the level of infectious HCV released from B cells. Our results, using a model where virus does not replicate in B cells, recapitulate observations seen in patients and may explain in part the rapid increase in blood HCV RNA observed after rituximab treatment

Change in maternal body mass index is associated with offspring body mass index: a 21-year prospective study

High body-mass index (BMI; defined as 25 kg/m(2) or greater) is associated with increased risk of cancer. To inform public health policy and future research, we estimated the global burden of cancer attributable to high BMI in 2012

Universal Alcohol/Drug Screening in Prenatal Care: A Strategy for Reducing Racial Disparities? Questioning the Assumptions

Agencies and organizations promoting universal screening for alcohol and drug use in prenatal care argue that universal screening will reduce White versus Black racial disparities in reporting to Child Protective Services (CPS) at delivery. Yet, no published research has assessed the impact of universal screening on reporting disparities or explored plausible mechanisms. This review defines two potential mechanisms: Equitable Surveillance and Effective Treatment and identifies assumptions underlying each mechanism. It reviews published literature relating to each assumption. Research relating to assumptions underlying each mechanism is primarily inconclusive or contradictory. Thus, available research does not support the claim that universal screening for alcohol and drug use in prenatal care reduces racial disparities in CPS reporting at delivery. Reducing these reporting disparities requires more than universal screening

An Essential Role for the Proximal but Not the Distal Cytoplasmic Tail of Glycoprotein M in Murid Herpesvirus 4 Infection

Murid herpesvirus-4 (MuHV-4) provides a tractable model with which to define common, conserved features of gamma-herpesvirus biology. The multi-membrane spanning glycoprotein M (gM) is one of only 4 glycoproteins that are essential for MuHV-4 lytic replication. gM binds to gN and is thought to function mainly secondary envelopment and virion egress, for which several predicted trafficking motifs in its C-terminal cytoplasmic tail could be important. We tested the contribution of the gM cytoplasmic tail to MuHV-4 lytic replication by making recombinant viruses with varying C-terminal deletions. Removing an acidic cluster and a distal YXXΦ motif altered the capsid distribution somewhat in infected cells but had little effect on virus replication, either in vitro or in vivo. In contrast, removing a proximal YXXΦ motif as well completely prevented productive replication. gM was still expressed, but unlike its longer forms showed only limited colocalization with co-transfected gN, and in the context of whole virus appeared to support gN expression less well. We conclude that some elements of the gM cytoplasmic tail are dispensible for MuHV-4 replication, but the tail as a whole is not

Accounting For Alignment Uncertainty in Phylogenomics

Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy

Growth Inhibition and Apoptosis Induced by Osthole, A Natural Coumarin, in Hepatocellular Carcinoma

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed tumors worldwide and is known to be resistant to conventional chemotherapy. New therapeutic strategies are urgently needed for treating HCC. Osthole, a natural coumarin derivative, has been shown to have anti-tumor activity. However, the effects of osthole on HCC have not yet been reported. METHODS AND FINDINGS: HCC cell lines were treated with osthole at various concentrations for 24, 48 and 72 hours. The proliferations of the HCC cells were measured by MTT assays. Cell cycle distribution and apoptosis were determined by flow cytometry. HCC tumor models were established in mice by subcutaneously injection of SMMC-7721 or Hepa1-6 cells and the effect of osthole on tumor growths in vivo and the drug toxicity were studied. NF-κB activity after osthole treatment was determined by electrophoretic mobility shift assays and the expression of caspase-3 was measured by western blotting. The expression levels of other apoptosis-related genes were also determined by real-time PCR (PCR array) assays. Osthole displayed a dose- and time-dependent inhibition of the HCC cell proliferations in vitro. It also induced apoptosis and caused cell accumulation in G2 phase. Osthole could significantly suppress HCC tumor growth in vivo with no toxicity at the dose we used. NF-κB activity was significantly suppressed by osthole at the dose- and time-dependent manner. The cleaved caspase-3 was also increased by osthole treatment. The expression levels of some apoptosis-related genes that belong to TNF ligand family, TNF receptor family, Bcl-2 family, caspase family, TRAF family, death domain family, CIDE domain and death effector domain family and CARD family were all increased with osthole treatment. CONCLUSION: Osthole could significantly inhibit HCC growth in vitro and in vivo through cell cycle arrest and inducing apoptosis by suppressing NF-κB activity and promoting the expressions of apoptosis-related genes

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs

Background A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the alignment used, and neglecting the uncertainty in the alignment can lead to significant bias in the resulting inference. In recent years, a number of approaches have been developed for probabilistic sampling of alignments, rather than simply generating a single optimum. However, this type of probabilistic information is currently not widely used in the context of downstream inference, since most existing algorithms are set up to make use of a single alignment. Results In this work we present a framework for representing a set of sampled alignments as a directed acyclic graph (DAG) whose nodes are alignment columns; each path through this DAG then represents a valid alignment. Since the probabilities of individual columns can be estimated from empirical frequencies, this approach enables sample-based estimation of posterior alignment probabilities. Moreover, due to conditional independencies between columns, the graph structure encodes a much larger set of alignments than the original set of sampled MSAs, such that the effective sample size is greatly increased. Conclusions The alignment DAG provides a natural way to represent a distribution in the space of MSAs, and allows for existing algorithms to be efficiently scaled up to operate on large sets of alignments. As an example, we show how this can be used to compute marginal probabilities for tree topologies, averaging over a very large number of MSAs. This framework can also be used to generate a statistically meaningful summary alignment; example applications show that this summary alignment is consistently more accurate than the majority of the alignment samples, leading to improvements in downstream tree inference. Implementations of the methods described in this article are available at http://statalign.github.io/WeaveAlign webcite

The ionizing photon production efficiency at z ∼6 for Lyman-Alpha emitters using JEMS and MUSE

We study the ionizing photon production efficiency at the end of the Epoch of Reionization (z ∼5.4-6.6) for a sample of 30 Ly α emitters. This is a crucial quantity to infer the ionizing photon budget of the universe. These objects were selected to have reliable spectroscopic redshifts, assigned based on the profile of their Ly α emission line, detected in the MUSE deep fields. We exploit medium-band observations from the JWST Extragalactic Medium-band Survey (JEMS) to find the flux excess corresponding to the redshifted Hα emission line. We estimate the ultraviolet (UV) luminosity by fitting the full JEMS photometry, along with several HST photometric points, with Prospector. We find a median UV continuum slope of, indicating young stellar populations with little-To-no dust attenuation. Supported by this, we derive ζion,0 with no dust attenuation and find a median value of log. If we perform dust attenuation corrections and assume a Calzetti attenuation law, our values are lowered by ∼0.1 dex. Our results suggest Ly α emitters at the Epoch of Reionization have slightly enhanced ζion,0 compared to previous estimations from literature, in particular, when compared to the non-Ly α emitting population. This initial study provides a promising outlook on the characterization of ionizing photon production in the early universe. In the future, a more extensive study will be performed on the entire data set provided by the JWST Advanced Deep Extragalactic Survey (JADES). Thus, for the first time, allowing us to place constraints on the wider galaxy populations driving reionization

Patterns of Non-injection Drug Use Associated with Injection Cessation among Street-Involved Youth in Vancouver, Canada

Although abstinence from drug use is often a key goal of youth substance use treatment, transitioning to less harmful routes and types of drug use is desirable from both a clinical and public health perspective. Despite this, little is known about the trajectories of youth who inject drugs including changes in patterns of non-injection drug use. The At-Risk Youth Study (ARYS) is a longitudinal cohort of street-involved youth who use drugs in Vancouver, Canada. We used linear growth curve modeling to compare changes in non-injection drug use among participants who ceased injecting drugs for at least one 6-month period between September 2005 and May 2015 to matched controls who continued injecting over the same period. Of 387 eligible participants, 173 (44.7%) reported ceasing drug injection at least once. Non-injection drug use occurred during 160 (79.6%) periods of injection cessation. In adjusted linear growth curve analyses, the only non-injection drug use pattern observed to decrease significantly more than controls following injection cessation was daily crack/cocaine use (p = 0.024). With the exception of frequent crack/cocaine use, transitions out of injection drug use did not appear to coincide with increased reductions in patterns of non-injection drug use. Our findings indicate that most (80%) of the observed injection cessation events occurred in the context of ongoing substance use. Given that transitioning out of drug injection represents a significant reduction in risk and harm, efforts supporting vulnerable youth to move away from injecting may benefit from approaches that allow for ongoing non-injection drug use. &nbsp