Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

Combination of gefitinib and methotrexate to treat tubal ectopic pregnancy (GEM3): a multicentre, randomised, double-blind, placebo-controlled trial

BACKGROUND: Tubal ectopic pregnancies can cause substantial morbidity or even death. Current treatment is with methotrexate or surgery. Methotrexate treatment fails in approximately 30% of women who subsequently require rescue surgery. Gefitinib, an epidermal growth factor receptor inhibitor, might improve the effects of methotrexate. We assessed the efficacy of oral gefitinib with methotrexate, versus methotrexate alone, to treat tubal ectopic pregnancy. METHODS: We performed a multicentre, randomised, double-blind, placebo-controlled trial across 50 UK hospitals. Participants diagnosed with tubal ectopic pregnancy were administered a single dose of intramuscular methotrexate (50 mg/m2) and randomised (1:1 ratio) to 7 days of additional oral gefitinib (250 mg daily) or placebo. The primary outcome, analysed by intention to treat, was surgical intervention to resolve the ectopic pregnancy. Secondary outcomes included time to resolution of ectopic pregnancy and serious adverse events. This trial is registered at the ISRCTN registry, ISCRTN 67795930. FINDINGS: Between Nov 2, 2016, and Oct 6, 2021, 328 participants were allocated to methotrexate and gefitinib (n=165) or methotrexate and placebo (n=163). Three participants in the placebo group withdrew. Surgical intervention occurred in 50 (30%) of 165 participants in the gefitinib group and in 47 (29%) of 160 participants in the placebo group (adjusted risk ratio 1·15, 95% CI 0·85 to 1·58; adjusted risk difference -0·01, 95% CI -0·10 to 0·09; p=0·37). Without surgical intervention, median time to resolution was 28·0 days in the gefitinib group and 28·0 days in the placebo group (subdistribution hazard ratio 1·03, 95% CI 0·75 to 1·40). Serious adverse events occurred in five (3%) of 165 participants in the gefitinib group and in six (4%) of 162 participants in the placebo group. Diarrhoea and rash were more common in the gefitinib group. INTERPRETATION: In women with a tubal ectopic pregnancy, adding oral gefitinib to parenteral methotrexate does not offer clinical benefit over methotrexate and increases minor adverse reactions. FUNDING: National Institute of Health Research

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

(Re)imagining the ‘backstreet’:Anti-abortion campaigning against decriminalisation in the UK

The risk of death or serious injury from ‘backstreet abortions’ was an important narrative in the 20th century campaign to liberalise abortion in the UK. Since then, clinical developments have reduced the overall health risks of abortion, and international health organisations have been set up to provide cross-border, medically safe abortions to places where it is unlawful, offering advice and, where possible, supplying abortion pills. These changes mean that pro-choice campaigns in Europe have often moved away from the risks of ‘backstreet abortions’ as a central narrative when campaigning for abortion liberalisation. In contrast, in the UK, anti-abortion activists are increasingly using ideas about ‘backstreet abortions’ to resist further liberalisation. These claims can be seen to fit within a broader shift from morals to risk within moral regulation campaigns and build on anti-abortion messages framed as being ‘pro-women’, with anti-abortion activists claiming to be the ‘savers’ of women. Using a parliamentary debate as a case study, this article will illustrate these trends and show how the ‘backstreet’ metaphor within anti-abortion campaigns builds on three interconnected themes of ‘abortion-as-harmful’, ‘abortion industry’, and ‘abortion culture’. This article will argue that the anti-abortion movement’s adoption of risk-based narratives contains unresolved contradictions due to the underlying moral basis of their position. These are exacerbated by the need, in this case, to defend legislation that they fundamentally disagree with. Moreover, their attempts to construct identifiable ‘harms’ and vulnerable ‘victims’, which are components of moral regulation campaigns, are unlikely to be convincing in the context of widespread public support for abortion

Developing an award program for children's settings to support healthy eating and physical activity and reduce the risk of overweight and obesity

<p>Abstract</p> <p>Background</p> <p>This paper aimed to identify the best way to engage, motivate and support early childhood services (ECS) and primary schools (PS) to create policy and practise changes to promote healthy eating and physical activity. This information would be used to develop a suitable program to implement within these children's settings to reduce the risk of childhood overweight and obesity.</p> <p>Methods</p> <p>The Medical Research Council's (UK) framework for the design and evaluation of complex interventions was used to guide the development of the healthy eating and physical activity program suitable for ECS and PS. Within this framework a range of evaluation methods, including stakeholder planning, in-depth interviews with ECS and PS staff and acceptability and feasibility trials in one local government area, were used to ascertain the best way to engage and support positive changes in these children's settings.</p> <p>Results</p> <p>Both ECS and PS identified that they had a role to play to improve children's healthy eating and physical activity. ECS identified their role in promoting healthy eating and physical activity as important for children's health, and instilling healthy habits for life. PS felt that these were health issues, rather than educational issues; however, schools saw the link between healthy eating and physical activity and student learning outcomes. These settings identified that a program that provides a simple guide that recognises good practise in these settings, such as an award scheme using a health promoting schools approach, as a feasible and acceptable way for them to support children's healthy eating and physical activity.</p> <p>Conclusion</p> <p>Through the process of design and evaluation a program - <it>Kids - 'Go for your life'</it>, was developed to promote and support children's healthy eating and physical activity and reduce the risk of childhood overweight and obesity. <it>Kids - 'Go for your life' </it>used an award program, based on a health promoting schools approach, which was demonstrated to be a suitable model to engage ECS and PS and was acceptable and feasible to create policy and practise changes to support healthy eating and physical activity for children.</p

CTGF drives autophagy, glycolysis and senescence in cancer-associated fibroblasts via HIF1 activation, metabolically promoting tumor growth

Previous studies have demonstrated that loss of caveolin-1 (Cav-1) in stromal cells drives the activation of the TGF-β signaling, with increased transcription of TGF-β target genes, such as connective tissue growth factor (CTGF). In addition, loss of stromal Cav-1 results in the metabolic reprogramming of cancer-associated fibroblasts, with the induction of autophagy and glycolysis. However, it remains unknown if activation of the TGF-β / CTGF pathway regulates the metabolism of cancer-associated fibroblasts. Therefore, we investigated whether CTGF modulates metabolism in the tumor microenvironment. For this purpose, CTGF was overexpressed in normal human fibroblasts or MDA-MB-231 breast cancer cells. Overexpression of CTGF induces HIF-1α-dependent metabolic alterations, with the induction of autophagy/mitophagy, senescence, and glycolysis. Here, we show that CTGF exerts compartment-specific effects on tumorigenesis, depending on the cell-type. In a xenograft model, CTGF overexpressing fibroblasts promote the growth of co-injected MDA-MB-231 cells, without any increases in angiogenesis. Conversely, CTGF overexpression in MDA-MB-231 cells dramatically inhibits tumor growth in mice. Intriguingly, increased extracellular matrix deposition was seen in tumors with either fibroblast or MDA-MB-231 overexpression of CTGF. Thus, the effects of CTGF expression on tumor formation are independent of its extracellular matrix function, but rather depend on its ability to activate catabolic metabolism. As such, CTGF-mediated induction of autophagy in fibroblasts supports tumor growth via the generation of recycled nutrients, whereas CTGF-mediated autophagy in breast cancer cells suppresses tumor growth, via tumor cell self-digestion. Our studies shed new light on the compartment-specific role of CTGF in mammary tumorigenesis, and provide novel insights into the mechanism(s) generating a lethal tumor microenvironment in patients lacking stromal Cav-1. As loss of Cav-1 is a stromal marker of poor clinical outcome in women with primary breast cancer, dissecting the downstream signaling effects of Cav-1 are important for understanding disease pathogenesis, and identifying novel therapeutic targets

High temperature AlInP X-ray spectrometers

Two custom-made Al0.52In0.48P p+-i-n+ mesa photodiodes with different diameters (217 µm ± 15 µm and 409 µm ± 28 µm) and i layer thicknesses of 6 µm have been electrically characterised over the temperature range 0 °C to 100 °C. Each photodiode was then investigated as a high-temperature-tolerant photon counting X-ray detector by connecting it to a custom-made low-noise charge-sensitive preamplifier and illuminating it with an 55Fe radioisotope X-ray source (Mn Kα = 5.9 keV; Mn Kβ = 6.49 keV). At 100 °C, the best energy resolutions (full width at half maximum at 5.9 keV) achieved using the 217 µm ± 15 µm diameter photodiode and the 409 µm ±28 µm diameter photodiode were 1.31 keV ± 0.04 keV and 1.64 keV ±0.08 keV, respectively. Noise analysis of the system is presented. The dielectric dissipation factor of Al0.52In0.48P was estimated as a function of temperature, up to 100 °C. The results show the performance of the thickest Al0.52In0.48P X-ray detectors so far reported at high temperature. The work has relevance for the development of novel space science instrumentation for use in hot space environments and extreme terrestrial applications

Similarities and differences in the dolomitization history of two coeval Middle Triassic carbonate platforms, Balaton Highland, Hungary

Dolomitization of platform carbonates is commonly the result of multiphase processes. Documentation of the complex dolomitization history is difficult if completely dolomitized sections are studied. Two Middle Anisian sections representing two coeval carbonate platforms were investigated and compared in the present study. Both sections are made up of meter-scale peritidal–lagoonal cycles with significant pedogenic overprint. One of the sections contains non-dolomitized, partially dolomitized, and completely dolomitized intervals, whereas the other is completely dolomitized. Based on investigations of the partially dolomitized section, penecontemporaneous dolomite formation and/or very early post-depositional dolomitization were identified in various lithofacies types. In shallow subtidal facies, porphyrotopic dolomite was found preferentially in microbial micritic fabrics. Microbially induced dolomite precipitation and/or progressive replacement of carbonate sediments could be interpreted for stromatolites. Cryptocrystalline to very finely crystalline dolomite, probably of pedogenic origin, was encountered in paleosoil horizons. Fabric-destructive dolomite commonly found below these horizons was likely formed via reflux of evaporated seawater. As a result of the different paleogeographic settings of the two platforms, their shallow-burial conditions were significantly different. One of the studied sections was located at the basinward platform margin where pervasive fabric-retentive dolomitization took place in a shallow-burial setting, probably via thermal convection. In contrast, in the area of the other, smaller platform shallow-water carbonates were covered by basinal deposits, preventing fluid circulation and accordingly pervasive shallow-burial dolomitization. In the intermediate to deep burial zone, recrystallization of partially dolomitized limestone and occlusion of newly opened fractures and pores by coarsely crystalline dolomite took place

Prevalence of obesity in preschool Greek children, in relation to parental characteristics and region of residence

<p>Abstract</p> <p>Background</p> <p>The aim of this retrospective cohort study was to record the prevalence of overweight and obesity in relation to parental education level, parental body mass index and region of residence, in preschool children in Greece.</p> <p>Methods</p> <p>A total of 2374 children (1218 males and 1156 females) aged 1–5 years, stratified by parental educational level (Census 1999), were examined from 105 nurseries in five counties, from April 2003 to July 2004, Weight (kg) and height (cm) were obtained and BMI (kg/m²) was calculated. Both the US Centers for Disease Control (CDC) and the International Obesity Task Force (IOTF) methods were used to classify each child as "normal", "at risk of overweight" and "overweight". Parental demographic characteristics, such as age and educational level and parental anthropometrical data, such as stature and body weight, were also recorded with the use of a specifically designed questionnaire.</p> <p>Results</p> <p>The overall estimates of at risk of overweight and overweight using the CDC method was 31.9%, 10.6 percentage points higher than the IOTF estimate of 21.3% and this difference was significant (p < 0.001). Children with one obese parent had 91% greater odds for being overweight compared to those with no obese parent, while the likelihood for being overweight was 2.38 times greater for children with two obese parents in the multivariate model.</p> <p>Conclusion</p> <p>Both methods used to assess prevalence of obesity have demonstarted that a high percentage of the preschool children in our sample were overweight. Parental body mass index was also shown to be an obesity risk factor in very young children.</p