Adaptively inferring human transcriptional subnetworks

Although the human genome has been sequenced, progress in understanding gene regulation in humans has been particularly slow. Many computational approaches developed for lower eukaryotes to identify cis-regulatory elements and their associated target genes often do not generalize to mammals, largely due to the degenerate and interactive nature of such elements. Motivated by the switch-like behavior of transcriptional responses, we present a systematic approach that allows adaptive determination of active transcriptional subnetworks (cis-motif combinations, the direct target genes and physiological processes regulated by the corresponding transcription factors) from microarray data in mammals, with accuracy similar to that achieved in lower eukaryotes. Our analysis uncovered several new subnetworks active in human liver and in cell-cycle regulation, with similar functional characteristics as the known ones. We present biochemical evidence for our predictions, and show that the recently discovered G2/M-specific E2F pathway is wider than previously thought; in particular, E2F directly activates certain mitotic genes involved in hepatocellular carcinomas. Additionally, we demonstrate that this method can predict subnetworks in a condition-specific manner, as well as regulatory crosstalk across multiple tissues. Our approach allows systematic understanding of how phenotypic complexity is regulated at the transcription level in mammals and offers marked advantage in systems where little or no prior knowledge of transcriptional regulation is available

A random forest approach to estimate daily particulate matter, nitrogen dioxide, and ozone at fine spatial resolution in Sweden

Air pollution is one of the leading causes of mortality worldwide. An accurate assessment of its spatial and temporal distribution is mandatory to conduct epidemiological studies able to estimate long-term (e.g., annual) and short-term (e.g., daily) health effects. While spatiotemporal models for particulate matter (PM) have been developed in several countries, estimates of daily nitrogen dioxide (NO 2 ) and ozone (O 3 ) concentrations at high spatial resolution are lacking, and no such models have been developed in Sweden. We collected data on daily air pollutant concentrations from routine monitoring networks over the period 2005-2016 and matched them with satellite data, dispersion models, meteorological parameters, and land-use variables. We developed a machine-learning approach, the random forest (RF), to estimate daily concentrations of PM 10 (PM<10 microns), PM 2.5 (PM<2.5 microns), PM 2.5-10 (PM between 2.5 and 10 microns), NO 2 , and O 3 for each squared kilometer of Sweden over the period 2005-2016. Our models were able to describe between 64% (PM 10 ) and 78% (O 3 ) of air pollutant variability in held-out observations, and between 37% (NO 2 ) and 61% (O 3 ) in held-out monitors, with no major differences across years and seasons and better performance in larger cities such as Stockholm. These estimates will allow to investigate air pollution effects across the whole of Sweden, including suburban and rural areas, previously neglected by epidemiological investigation

Life satisfaction amongst police officers working in the area of child abuse investigation

Child abuse investigation is an area of work reported to be associated with high levels of work stress. This potentially places professionals at risk of psychological harm and may lead to lower life satisfaction than in the general population. The current study examined this issue within a large sample of Australian police officers. Specifically, 214 officers working in the area of child abuse investigation responded to a single global measure of life satisfaction (LS) known to be highly related to other measures of subjective wellbeing as well as clinical depression. The results revealed that, irrespective of the officers&rsquo; gender or degree of exposure to child abuse cases, the mean score from LS score was within the expected adult normative range. Further, the overall incidence of low LS in this sample (1.9 per cent) was not significantly different from the general population (4.3 per cent). The implications of these findings for police organisations are discussed.<br /

A new way of valorizing biomaterials: the use of sunflower protein for 1 a-tocopherol microencapsulation

Biopolymer based microparticles were efficiently prepared from sunflower protein (SP) wall material and a-tocopherol (T) active core using a spray-drying technique. Protein enzymatic hydrolysis and/or N-acylation were carried out to make some structural modifications to the vegetable protein. Native and hydrolyzed SP were characterized by Asymmetrical Flow Field-Flow Fractionation (AsFlFFF). Results of AsFlFFF confirmed that size of proteinic macromolecules was influenced by degree of hydrolysis. The effect of protein modifications and the influence of wall/core ratio on both emulsions and microparticle properties were evaluated. Concerning emulsion properties, enzymatic hydrolysis involved a decrease in viscosity, whereas acylation did not significantly affect emulsion droplet size and viscosity. Microparticles obtained with hydrolyzed SP wall material showed lower retention efficiency (RE) than native SP microparticles (62-80% and 93% respectively). Conversely, acylation of both hydrolyzed SP and native SP allowed a higher RE to be reached (up to 100%). Increasing T concentration increased emulsion viscosity, emulsion droplet size, microparticle size, and enhanced RE. These results demonstrated the feasibility of high loaded (up to 79.2% T) microparticles

Reductions in cardiovascular, cerebrovascular, and respiratory mortality following the national Irish smoking ban: Interrupted time-series analysis

Copyright @ 2013 Stallings-Smith et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.This article has been made available through the Brunel Open Access Publishing Fund.Background: Previous studies have shown decreases in cardiovascular mortality following the implementation of comprehensive smoking bans. It is not known whether cerebrovascular or respiratory mortality decreases post-ban. On March 29, 2004, the Republic of Ireland became the first country in the world to implement a national workplace smoking ban. The aim of this study was to assess the effect of this policy on all-cause and cause-specific, non-trauma mortality. Methods: A time-series epidemiologic assessment was conducted, utilizing Poisson regression to examine weekly age and gender-standardized rates for 215,878 non-trauma deaths in the Irish population, ages ≥35 years. The study period was from January 1, 2000, to December 31, 2007, with a post-ban follow-up of 3.75 years. All models were adjusted for time trend, season, influenza, and smoking prevalence. Results: Following ban implementation, an immediate 13% decrease in all-cause mortality (RR: 0.87; 95% CI: 0.76-0.99), a 26% reduction in ischemic heart disease (IHD) (RR: 0.74; 95% CI: 0.63-0.88), a 32% reduction in stroke (RR: 0.68; 95% CI: 0.54-0.85), and a 38% reduction in chronic obstructive pulmonary disease (COPD) (RR: 0.62; 95% CI: 0.46-0.83) mortality was observed. Post-ban reductions in IHD, stroke, and COPD mortalities were seen in ages ≥65 years, but not in ages 35-64 years. COPD mortality reductions were found only in females (RR: 0.47; 95% CI: 0.32-0.70). Post-ban annual trend reductions were not detected for any smoking-related causes of death. Unadjusted estimates indicate that 3,726 (95% CI: 2,305-4,629) smoking-related deaths were likely prevented post-ban. Mortality decreases were primarily due to reductions in passive smoking. Conclusions: The national Irish smoking ban was associated with immediate reductions in early mortality. Importantly, post-ban risk differences did not change with a longer follow-up period. This study corroborates previous evidence for cardiovascular causes, and is the first to demonstrate reductions in cerebrovascular and respiratory causes

Pacific island regional preparedness for El Niño

The El Niño Southern Oscillation (ENSO) cycle is often blamed for disasters in Pacific island communities. From a disaster risk reduction (DRR) perspective, the challenges with the El Niño part of the ENSO cycle, in particular, are more related to inadequate vulnerability reduction within development than to ENSO-induced hazard influences. This paper analyses this situation, filling in a conceptual and geographic gap in El Niño-related research, by reviewing El Niño-related preparedness (the conceptual gap) for Pacific islands (the geographic gap). Through exploring El Niño impacts on Pacific island communities alongside their vulnerabilities, resiliences, and preparedness with respect to El Niño, El Niño is seen as a constructed discourse rather than as a damaging phenomenon, leading to suggestions for El Niño preparedness as DRR as part of development. Yet the attention which El Niño garners might bring resources to the Pacific region and its development needs, albeit in the short term while El Niño lasts. Conversely, the attention given to El Niño could shift blame from underlying causes of vulnerability to a hazard-centric viewpoint. Instead of focusing on one hazard-influencing phenomenon, opportunities should be created for the Pacific region to tackle wider DRR and development concerns

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

The association between secondhand smoke and the risk of developing acute coronary syndromes, among non-smokers, under the presence of several cardiovascular risk factors: The CARDIO2000 case-control study

BACKGROUND: The purpose of this study was to investigate the association between secondhand smoke and the risk of developing a first event of acute coronary syndromes (ACS), i.e. acute myocardial infarction or unstable angina, among non-smokers, in relation to the presence of several other cardiovascular risk factors. METHODS: Eight hundred and forty-eight patients with first event of ACS and 1078 cardiovascular disease-free matched controls completed a detailed questionnaire regarding their exposure to secondhand smoke, among other investigated parameters. RESULTS: Two hundred and ninety–seven (35%) of the patients and 259 (24%) of the controls were defined as secondhand smokers. After controlling for several potential confounders, the results showed that non-smokers occasionally (< 3 time per week) exposed to cigarette smoke were associated with 26% higher risk of ACS (OR = 1.26, P-value < 0.01) compared to non-smokers not exposed to smoke, while regular exposure is associated with 99% higher risk of developing ACS (OR = 1.99, P-value < 0.001). Moreover, the previous risk increases progressively from 15% to 256% if one or more of the classical cardiovascular risk factors (i.e. hypertension, hypercholesterolemia, diabetes mellitus, sedentary life and family history of premature coronary heart disease) are present. CONCLUSIONS: Consequently, this study supports the hypothesis that even occasional secondhand smoke increases the risk of developing acute coronary syndromes, especially when other risk factors are present. Given the high prevalence of cigarette smoking, the public health consequences of passive smoking with regard to coronary heart disease are important