Developing clinical guidelines: a challenge to current methods.

Current methods for producing clinical guidelines are cumbersome and not always reliable. Could a more streamlined approach improve coverage and make decisions more transparent

Evaluating the potential risks and benefits of infant rotavirus vaccination in England.

Rotarix(®), a vaccine for the prevention of gastroenteritis in young children, was introduced in England in July 2013. At around this time, an elevated risk of intussusception (a cause of bowel obstruction) was reported among infants vaccinated in Australia and the USA. A risk-benefit analysis compared potential vaccine-related risks (additional intussusception admissions and deaths) with estimated vaccine benefits (prevented rotavirus general practitioner visits, emergency visits, admissions and deaths) in the 2012 birth cohort. Detailed data from England included the incidence of intussusception events aged <2 years by week of age, the coverage of vaccination aged <2 years by week of age, and the incidence of rotavirus gastroenteritis (RVGE) events aged <5 years by week of age. Recent estimates of vaccine-related risk from Australia were applied during the 1-21 day period after the first and second dose of vaccination. Rotarix(®) is estimated to cause one additional intussusception admission in every 18,551 vaccinated English infants (5th and 95th percentiles, 6728-93,952), equivalent to 35 (7-98) additional intussusception admissions each year. The vaccine is estimated to prevent three rotavirus deaths, 13,000 rotavirus admissions, 27,000 rotavirus emergency visits and 74,000 rotavirus GP consultations in children aged <5 years, and lead to annual savings of over £11 million, each year. We estimate 375 (136-1900) fewer RVGE admissions for every additional intussusception admission, and 88 (18-852) fewer RVGE deaths for every additional intussusception death. The estimated benefits of Rotarix(®) vaccination would greatly exceed the potential risk in England

Genotype and environment affect the grain quality and yield of winter oats (Avena sativa L.)

The extent to which the quality and yield of plant varieties are influenced by the environment is important for their successful uptake by end users particularly as climatic fluctuations are resulting in environments that are highly variable from one growing season to another. The genotype-by-environment interaction (GEI) of milling quality and yield was studied using four winter oat varieties in multi-locational trials over 4 years in the U.K. Significant differences across the 22 environments were found between physical grain quality and composition as well as grain yield, with the environment having a significant effect on all of the traits measured. Grain yield was closely related to grain number m−2 whereas milling quality traits were related to grain size attributes. Considerable genotype by environment interaction was obtained for all grain quality traits and stability analysis revealed that the variety Mascani was the least sensitive to the environment for all milling quality traits measured whereas the variety Balado was the most sensitive. Examination of environmental conditions at specific within-year stages of crop development indicated that both temperature and rainfall during grain development were correlated with grain yield and β-glucan content and with the ease of removing the hull (hullability)

Evaluation of work-based screening for early signs of alcohol-related liver disease in hazardous and harmful drinkers: the PrevAIL study

Background The direct cost of excessive alcohol consumption to health services is substantial but dwarfed by the cost borne by the workplace as a result of lost productivity. The workplace is also a promising setting for health interventions. The Preventing Alcohol Harm in Liverpool and Knowsley (PrevAIL) project aimed to evaluate a mechanism for detecting the prevalence of alcohol related liver disease using fibrosis biomarkers. Secondary aims were to identify the additive effect of obesity as a risk factor for early liver disease; to assess other impacts of alcohol on work, using a cross-sectional survey. Methods Participants (aged 36-55y) from 13 workplaces participated (March 2011–April 2012). BMI, waist circumference, blood pressure and self-reported alcohol consumption in the previous week was recorded. Those consuming more than the accepted UK threshold (men: >21 units; female: >14 units alcohol) provided a 20 ml venous blood sample for a biomarker test (Southampton Traffic Light Test) and completed an alcohol questionnaire (incorporating the Severity of Alcohol Dependence Questionnaire). Results The screening mechanism enrolled 363 individuals (52 % women), 39 % of whom drank above the threshold and participated in the liver screen (n = 141, complete data = 124 persons). Workplaces with successful participation were those where employers actively promoted, encouraged and facilitated attendance. Biomarkers detected that 30 % had liver disease (25 %, intermediate; 5 % probable). Liver disease was associated with the frequency of visits to the family physician (P = 0.036) and obesity (P = 0.052). Conclusions The workplace is an important setting for addressing alcohol harm, but there are barriers to voluntary screening that need to be addressed. Early detection and support of cases in the community could avert deaths and save health and social costs. Alcohol and obesity should be addressed simultaneously, because of their known multiplicative effect on liver disease risk, and because employers preferred a general health intervention to one that focused solely on alcohol consumption

Developing H++ climate change scenarios for heat waves, droughts, floods, windstorms and cold snaps

This report describes the results of a project to investigate the development of plausible high-end climate change scenarios. It covers the following climate hazards: heat waves, cold snaps, low and high rainfall, droughts, floods and windstorms. The scope of the project does not extend into defining the consequences of these hazards such as mortality, property damage or impacts on the natural environment. The scenarios created for this report are referred to as H++ scenarios, and are typically more extreme climate change scenarios on the margins or outside of the 10th to 90th percentile range presented in the 2009 UK climate change projections (also known as ‘UKCP09’)

Scalable downstream purification of recombinant adeno-associated viral vectors

Scalable manufacturing technologies are essential for ensuring modern medicines can be produced to meet the needs of clinical trials, process development, and commercial manufacture. Recent advances in in vivo gene therapies have resulted in multiple regulatory approvals of rAAV vectors for gene transfer in humans. These vectors can be produced using transient transfection of mammalian cells, baculovirus infection of insect cells or produced via engineered stable producer cells. These production methods are performed in single-use bioreactors and utilize other scalable technologies as used in commercial monoclonal antibody manufacture. In this work, we evaluated the use of existing single-use filtration and separation technologies for downstream purification of an rAAV5 viral vector. rAAV5 vector was produced by transient transfection of HEK293 cells in the Pall iCELLis® Nano bioreactor. Bioreactor harvest lysis material was clarified using direct flow filtration with both depth and sterilizing grade filters. The product was concentrated 10x using 100kD OmegaTM flat-sheet tangential flow-filtration (TFF) before primary purification using affinity chromatography. The rAAV5 vector was then polished using Mustang® Q membrane chromatography to enrich for full capsids. A second TFF step was performed to concentrate and buffer exchange with flat sheet TFF with the same 100KD Omega membrane. Final sterile filtration was performed using Supor® EKV validated sterilizing grade filters. All downstream unit operations resulted in acceptable performance. Feasibility of a complete downstream process was established with a theoretical whole process yield of ~25%. This process results in a very low contaminant profile as host cell protein (HCP) and host cell DNA were reduced to near and below the assays’ limits of quantitation during purification. Of particular interest, Mustang Q polishing resulted in retention of only ~10% of total capsids, while recovering ~50% of full capsids enriching the ratio of full capsids to empty capsids by 4.5 fold

Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis.

Microbes unculturable in vitro remain diagnostically challenging, dependent historically on clinical findings, histology, or targeted molecular detection. We applied whole-genome sequencing directly from tissue to diagnose infections with mycobacteria (leprosy) and parasites (coenurosis). Direct pathogen DNA sequencing provides flexible solutions to diagnosis of difficult pathogens in diverse contexts

FracPaQ: A MATLAB™ toolbox for the quantification of fracture patterns

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, and spatial distributions often exhibit some kind of order. In detail, relationships may exist among the different fracture attributes, e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture attributes and patterns. This paper describes FracPaQ, a new open source, cross-platform toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on previously published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity.An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales, rock types and tectonic settings. The implemented methods presented are inherently scale independent, and a key task where applicable is analysing and integrating quantitative fracture pattern data from micro-to macro-scales. The toolbox was developed in MATLAB™ and the source code is publicly available on GitHub™ and the Mathworks™ FileExchange. The code runs on any computer with MATLAB installed, including PCs with Microsoft Windows, Apple Macs with Mac OS X, and machines running different flavours of Linux. The application, source code and sample input files are available in open repositories in the hope that other developers and researchers will optimise and extend the functionality for the benefit of the wider community

Interleukin 6 increases production of cytokines by colonic innate lymphoid cells in mice and patients with chronic intestinal inflammation

Background & Aims: Innate lymphoid cells (ILCs) are a heterogeneous group of mucosal inflammatory cells that participate in chronic intestinal inflammation. We investigated the role of interleukin 6 (IL6) in inducing activation of ILCs in mice and in human beings with chronic intestinal inflammation. Methods: ILCs were isolated from colons of Tbx21-/- × Rag2-/- mice (TRUC), which develop colitis; patients with inflammatory bowel disease (IBD); and patients without colon inflammation (controls). ILCs were characterized by flow cytometry; cytokine production was measured by enzyme-linked immunosorbent assay and cytokine bead arrays. Mice were given intraperitoneal injections of depleting (CD4, CD90), neutralizing (IL6), or control antibodies. Isolated colon tissues were analyzed by histology, explant organ culture, and cell culture. Bacterial DNA was extracted from mouse fecal samples to assess the intestinal microbiota. Results: IL17A- and IL22-producing, natural cytotoxicity receptor-negative, ILC3 were the major subset of ILCs detected in colons of TRUC mice. Combinations of IL23 and IL1α induced production of cytokines by these cells, which increased further after administration of IL6. Antibodies against IL6 reduced colitis in TRUC mice without significantly affecting the structure of their intestinal microbiota. Addition of IL6 increased production of IL17A, IL22, and interferon-γ by human intestinal CD3-negative, IL7-receptor-positive cells, in a dose-dependent manner. Conclusions: IL6 contributes to activation of colonic natural cytotoxicity receptor-negative, CD4-negative, ILC3s in mice with chronic intestinal inflammation (TRUC mice) by increasing IL23- and IL1α-induced production of IL17A and IL22. This pathway might be targeted to treat patients with IBD because IL6, which is highly produced in colonic tissue by some IBD patients, also increased the production of IL17A, IL22, and interferon-γ by cultured human colon CD3-negative, IL7-receptor-positive cells

Removal of Misincorporated Ribonucleotides from Prokaryotic Genomes: An Unexpected Role for Nucleotide Excision Repair

Stringent steric exclusion mechanisms limit the misincorporation of ribonucleotides by high-fidelity DNA polymerases into genomic DNA. In contrast, low-fidelity Escherichia coli DNA polymerase V (pol V) has relatively poor sugar discrimination and frequently misincorporates ribonucleotides. Substitution of a steric gate tyrosine residue with alanine (umuC_Y11A) reduces sugar selectivity further and allows pol V to readily misincorporate ribonucleotides as easily as deoxynucleotides, whilst leaving its poor base-substitution fidelity essentially unchanged. However, the mutability of cells expressing the steric gate pol V mutant is very low due to efficient repair mechanisms that are triggered by the misincorporated rNMPs. Comparison of the mutation frequency between strains expressing wild-type and mutant pol V therefore allows us to identify pathways specifically directed at ribonucleotide excision repair (RER). We previously demonstrated that rNMPs incorporated by umuC_Y11A are efficiently removed from DNA in a repair pathway initiated by RNase HII. Using the same approach, we show here that mismatch repair and base excision repair play minimal back-up roles in RER in vivo. In contrast, in the absence of functional RNase HII, umuC_Y11A-dependent mutagenesis increases significantly in ΔuvrA, uvrB5 and ΔuvrC strains, suggesting that rNMPs misincorporated into DNA are actively repaired by nucleotide excision repair (NER) in vivo. Participation of NER in RER was confirmed by reconstituting ribonucleotide-dependent NER in vitro. We show that UvrABC nuclease-catalyzed incisions are readily made on DNA templates containing one, two, or five rNMPs and that the reactions are stimulated by the presence of mispaired bases. Similar to NER of DNA lesions, excision of rNMPs proceeds through dual incisions made at the 8th phosphodiester bond 5′ and 4th-5th phosphodiester bonds 3′ of the ribonucleotide. Ribonucleotides misinserted into DNA can therefore be added to the broad list of helix-distorting modifications that are substrates for NER