Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics

This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014

Analyses of odours from concentrated animal feeding operations: a review

Concentrated Animal Feeding Operations (CAFOs) are widely present all over the world due to the high population demand for food and products of animal origin. However, they have generated several environmental concerns, including odour nuisance, which affects people health and quality of life. Odours from livestock are a very complex mixtures of molecules and their analytical investigation is highly demanding. Many works have been published regarding the study of odours from CAFOs, using different techniques and technologies to face the issue. Thus, the aim of this review paper is to summarize all the ways to study odours from CAFOs, starting from the sampling methods and then treating in general the principles of Dynamic Olfactometry, Gas Chromatography coupled with Mass Spectrometry and Electronic Noses. Finally, a deep literature summary of Gas Chromatography coupled with Mass Spectrometry and Electronic Noses applied to odours coming from poultry, dairy and swine feeding operations is reported. This work aims to make some order in this field and it wants to help future researchers to deal with this environmental problem, constituting a state-of-the-art in this field

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations

Steps towards the hyperfine splitting measurement of the muonic hydrogen ground state: pulsed muon beam and detection system characterization

The high precision measurement of the hyperfine splitting of the muonic-hydrogen atom ground state with pulsed and intense muon beam requires careful technological choices both in the construction of a gas target and of the detectors. In June 2014, the pressurized gas target of the FAMU experiment was exposed to the low energy pulsed muon beam at the RIKEN RAL muon facility. The objectives of the test were the characterization of the target, the hodoscope and the X-ray detectors. The apparatus consisted of a beam hodoscope and X-rays detectors made with high purity Germanium and Lanthanum Bromide crystals. In this paper the experimental setup is described and the results of the detector characterization are presented.Comment: 22 pages, 14 figures, published and open access on JINS

Estrogen-dependent dynamic profile of eNOS-DNA associations in prostate cancer

In previous work we have documented the nuclear translocation of endothelial NOS (eNOS) and its participation in combinatorial complexes with Estrogen Receptor Beta (ERβ) and Hypoxia Inducible Factors (HIFs) that determine localized chromatin remodeling in response to estrogen (E2) and hypoxia stimuli, resulting in transcriptional regulation of genes associated with adverse prognosis in prostate cancer (PCa). To explore the role of nuclear eNOS in the acquisition of aggressive phenotype in PCa, we performed ChIP-Sequencing on chromatin-associated eNOS from cells from a primary tumor with poor outcome and from metastatic LNCaP cells. We found that: 1. the eNOS-bound regions (peaks) are widely distributed across the genome encompassing multiple transcription factors binding sites, including Estrogen Response Elements. 2. E2 increased the number of peaks, indicating hormone-dependent eNOS re-localization. 3. Peak distribution was similar with/without E2 with ≈ 55% of them in extragenic DNA regions and an intriguing involvement of the 5′ domain of several miRs deregulated in PCa. Numerous potentially novel eNOS-targeted genes have been identified suggesting that eNOS participates in the regulation of large gene sets. The parallel finding of downregulation of a cluster of miRs, including miR-34a, in PCa cells associated with poor outcome led us to unveil a molecular link between eNOS and SIRT1, an epigenetic regulator of aging and tumorigenicity, negatively regulated by miR-34a and in turn activating eNOS. E2 potentiates miR-34a downregulation thus enhancing SIRT1 expression, depicting a novel eNOS/SIRT1 interplay fine-tuned by E2-activated ER signaling, and suggesting that eNOS may play an important role in aggressive PCa

A Large Hadron Electron Collider at CERN

This document provides a brief overview of the recently published report on the design of the Large Hadron Electron Collider (LHeC), which comprises its physics programme, accelerator physics, technology and main detector concepts. The LHeC exploits and develops challenging, though principally existing, accelerator and detector technologies. This summary is complemented by brief illustrations of some of the highlights of the physics programme, which relies on a vastly extended kinematic range, luminosity and unprecedented precision in deep inelastic scattering. Illustrations are provided regarding high precision QCD, new physics (Higgs, SUSY) and electron-ion physics. The LHeC is designed to run synchronously with the LHC in the twenties and to achieve an integrated luminosity of O(100) fb$^{-1}$. It will become the cleanest high resolution microscope of mankind and will substantially extend as well as complement the investigation of the physics of the TeV energy scale, which has been enabled by the LHC

The SM and NLO multileg working group: Summary report

This report summarizes the activities of the SM and NLO Multileg Working Group of the Workshop "Physics at TeV Colliders", Les Houches, France 8-26 June, 2009.Comment: 169 pages, Report of the SM and NLO Multileg Working Group for the Workshop "Physics at TeV Colliders", Les Houches, France 8-26 June, 200

Recoil and Threshold Corrections in Short-distance Cross Sections

We identify and resum corrections associated with the kinematic recoil of the hard scattering against soft-gluon emission in single-particle inclusive cross sections. The method avoids double counting and conserves the flow of partonic energy. It reproduces threshold resummation for high-p_T single-particle cross sections, when recoil is neglected, and Q_T-resummation at low Q_T, when higher-order threshold logarithms are suppressed. We exhibit explicit resummed cross sections, accurate to next-to-leading logarithm, for electroweak annihilation and prompt photon inclusive cross sections.Comment: minor modifications of the text, some references added. 51 pages, LaTeX, 6 figures as eps file

First FAMU observation of muon transfer from \u3bcp atoms to higher-Z elements

Abstract: The FAMU experiment aims to accurately measure the hyperfine splitting of the ground state of the muonic hydrogen atom. A measurement of the transfer rate of muons from hydrogen to heavier gases is necessary for this purpose. In June 2014, within a preliminary experiment, a pressurized gas-target was exposed to the pulsed low-energy muon beam at the RIKEN RAL muon facility (Rutherford Appleton Laboratory, U.K.). The main goal of the test was the characterization of both the noise induced by the pulsed beam and the X-ray detectors. The apparatus, to some extent rudimental, has served admirably to this task. Technical results have been published that prove the validity of the choices made and pave the way for the next steps. This paper presents the results of physical relevance of measurements of the muon transfer rate to carbon dioxide, oxygen, and argon from non-thermalized excited \u3bcp atoms. The analysis methodology and the approach to the systematics errors are useful for the subsequent study of the transfer rate as function of the kinetic energy of the \u3bcp currently under way

QCD analysis of W- and Z-boson production at Tevatron

Recent measurements of the W-boson charge asymmetry and of the Z-boson production cross sections, performed at the Tevatron collider in Run II by the D0 and CDF collaborations, are studied using the HERAFitter framework to assess their impact on the proton parton distribution functions (PDFs). The Tevatron measurements, together with deep-inelastic scattering data from HERA, are included in a QCD analysis performed at next-to-leading order, and compared to the predictions obtained using other PDF sets from different groups. Good agreement between measurements and theoretical predictions is observed. The Tevatron data provide significant constraints on the d-valence quark distribution