Money Talks, Patients Walk?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71560/1/j.1525-1497.2001.10118.x.pd

Multiple sclerosis: time for early treatment with high-efficacy drugs

This review addresses current changes in the approach to treating patients with multiple sclerosis (MS). The widely practiced approach of utilizing agents with lower treatment efficacy (LETA) at onset with subsequent escalation has been challenged by new data suggesting that MS patients derive greater benefit when therapy is initiated with high-efficacy treatment agents (HETA). Several recent studies compared treatment efficacy and safety of early administration of HETA versus LETA. The results of randomized, double blind, phase III studies with LETA as a control arm and population-based larger and longer studies using propensity scoring, marginal structural modeling and weighted cumulative exposure analysis support the benefit of early treatment with HETA. Patients initiating their treatment with HETA, regardless of prognostic factors and MRI burden at baseline, showed significantly lower annualized relapse rate (ARR) and reduced disability progression in follow-up periods of up to 10–15 years. Moreover, the safety profile of recently approved HETA ameliorates concerns about off-target effects associated with a number of earlier high-efficacy drugs. Patient perception has also changed with an increasing preference for medication profiles that both improve symptoms and prevent disease progression. Accumulating data from randomized studies and the results of large population-based studies demonstrating short-term and longer-term patient benefits support the view that HETA should be more widely used. The adoption of early treatment with HETA capitalizes on a window of opportunity for anti-inflammatory drugs to maximally impact disease pathology and heralds a sea change in clinical practice toward pro-active management and away from a philosophy routed in generating clinical benefit as a consequence of treatment failure

Oxygen-dependent histone lysine demethylase 4 restricts hepatitis B virus replication

Mammalian cells have evolved strategies to regulate gene expression when oxygen is limited. Hypoxia-inducible factors (HIF) are the major transcriptional regulators of host gene expression. We previously reported that HIFs bind and activate hepatitis B virus (HBV) DNA transcription under low oxygen conditions; however, the global cellular response to low oxygen is mediated by a family of oxygenases that work in concert with HIFs. Recent studies have identified a role for chromatin modifiers in sensing cellular oxygen and orchestrating transcriptional responses, but their role in the HBV life cycle is as yet undefined. We demonstrated that histone lysine demethylase 4 (KDM4) can restrict HBV, and pharmacological or oxygen-mediated inhibition of the demethylase increases viral RNAs derived from both episomal and integrated copies of the viral genome. Sequencing studies demonstrated that KDM4 is a major regulator of the hepatic transcriptome, which defines hepatocellular permissivity to HBV infection. We propose a model where HBV exploits cellular oxygen sensors to replicate and persist in the liver. Understanding oxygen-dependent pathways that regulate HBV infection will facilitate the development of physiologically relevant cell-based models that support efficient HBV replication

Incremental bounded model checking for embedded software

Program analysis is on the brink of mainstream usage in embedded systems development. Formal verification of behavioural requirements, finding runtime errors and test case generation are some of the most common applications of automated verification tools based on bounded model checking (BMC). Existing industrial tools for embedded software use an off-the-shelf bounded model checker and apply it iteratively to verify the program with an increasing number of unwindings. This approach unnecessarily wastes time repeating work that has already been done and fails to exploit the power of incremental SAT solving. This article reports on the extension of the software model checker CBMC to support incremental BMC and its successful integration with the industrial embedded software verification tool BTC EMBEDDED TESTER. We present an extensive evaluation over large industrial embedded programs, mainly from the automotive industry. We show that incremental BMC cuts runtimes by one order of magnitude in comparison to the standard non-incremental approach, enabling the application of formal verification to large and complex embedded software. We furthermore report promising results on analysing programs with arbitrary loop structure using incremental BMC, demonstrating its applicability and potential to verify general software beyond the embedded domain

New methods for next generation sequencing based microRNA expression profiling

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer.</p> <p>Results</p> <p>High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. The sample preparation and E-miR pipeline were used to identify 37 cardiac enriched microRNAs in stage 16 chicken embryos. Isomir expression profiles between the heart and embryo were highly correlated for all miRNAs suggesting that tissue or cell specific miRNA modifications do not occur.</p> <p>Conclusions</p> <p>In conclusion, our alternative sample preparation method can successfully be applied to generate high quality miRNA sequencing libraries for the Illumina genome analyzer.</p

The Effect of Egg Embryonation on Field-Use of a Hookworm Benzimidazole-Sensitivity Egg Hatch Assay in Yunnan Province, People's Republic of China

With the implementation of mass drug administration programmes for the control of human soil transmitted helminths there is a need to develop drug sensitivity monitoring tools to detect the emergence of resistance. The present study aimed to use an egg hatch assay to measure benzimidazole sensitivity in human hookworms in a field setting in Yunnan province, People's Republic of China, in order to assess whether the assay offered a practical means of monitoring drug sensitivity in human hookworms in such a location. The assay proved able to generate dose response data, which allowed for the drug sensitivity of the hookworms in the local children to be described; the mean IC50 was 0.10 ug/ml thiabendazole. The study also found that practical issues associated with stool collection procedures, specifically the embryonation of some eggs during the time elapsing between stool deposition and egg recovery, can have an impact on the drug sensitivity data. We suggest means for data analysis that overcome the impact of egg embryonation on drug dose response data, which should allow for the use of such assays at different field sites worldwide

An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome

Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next Generation Sequencing to identify viral transcripts and splice junctions, however the fragmentation and selective amplification used in short read sequencing precludes the resolution of full length RNAs. Our study coupled an oligonucleotide enrichment protocol with state-of-the-art long read sequencing (PacBio) to identify the repertoire of HBV RNAs. This methodology provides sequencing libraries where up to 25 % of reads are of viral origin and enable the identification of canonical (unspliced), non-canonical (spliced) and chimeric viral-human transcripts. Sequencing RNA isolated from de novo HBV infected cells or those transfected with 1.3 × overlength HBV genomes allowed us to assess the viral transcriptome and to annotate 5′ truncations and polyadenylation profiles. The two HBV model systems showed an excellent agreement in the pattern of major viral RNAs, however differences were noted in the abundance of spliced transcripts. Viral-host chimeric transcripts were identified and more commonly found in the transfected cells. Enrichment capture and PacBio sequencing allows the assignment of canonical and non-canonical HBV RNAs using an open-source analysis pipeline that enables the accurate mapping of the HBV transcriptome