Baseline LHC machine parameters and configuration of the 2015 proton run

This paper shows the baseline LHC machine parameters for the 2015 start-up. Many systems have been upgraded during LS1 and in 2015 the LHC will operate at a higher energy than before and with a tighter filling scheme. Therefore, the 2015 commissioning phase risks to be less smooth than in 2012. The proposed starting configuration puts the focus on feasibility rather than peak performance and includes margins for operational uncertainties. Instead, once beam experience and a better machine knowledge has been obtained, a push in $\beta^*$ and performance can be envisaged. In this paper, the focus is on collimation settings and reach in $\beta^*$---other parameters are covered in greater depth by other papers in these proceedings.Comment: submitted for publication in a CERN yellow report (Proceedings of the LHC Performance Workshop - Chamonix 2014

The Efficacy of Vaginal Clindamycin for the Treatment of Abnormal Genital Tract Flora in Pregnancy

Objective: To assess the efficacy of 2% clindamycin vaginal cream (CVC) to treat bacterial vaginosis (BV) in pregnancy. Methods: A prospective, randomized, double-blind, placebo-controlled, tricenter study. Four hundred and four women with BV on Gram stain at their first antenatal clinic visit were randomized to receive a 3-day course of 2% CVC or placebo. The outcome was assessed using an intention to treat analysis at 3 weeks and 6 weeks post-treatment according to three different diagnostic methods based on five criteria (Gram stain and all four elements of clinical composite criteria: vaginal discharge, abnormal vaginal pH, clue cells, amine odor), three criteria (vaginal pH, clue cells, amine odor) or two criteria (clue cells and amine odor) to reflect stringency of diagnosis, historical precedence and government agency recommendations respectively. Results: Using five diagnostic criteria, 18% of CVC patients were cured and 70.8% either cured and/or improved compared to 1.6% and 12% of placebo patients respectively (p < 0.0001). Using three diagnostic criteria, 44.8% of CVC patients were cured and 77.3% were either cured and/or improved compared to 9.3% and 28.8% of placebo patients respectively (p < 0.0001). Using two diagnostic criteria, 75.0% of CVC patients were cured compared to 18.0% of placebo patients (p < 0.0001). Recurrence rates in those CVC patients successfully treated were approximately 6% at 6 weeks post baseline and 10% at 28 to 34 weeks gestation. Conclusions: A 3-day course of CVC appears to be well tolerated by the mother and statistically significantly more efficacious than placebo in the treatment of BV during the second trimester of pregnancy

SNP Discovery and Genomic Architecture of Highly Inbred Leghorn and Fayoumi Chicken Breeds Using Whole Genome Resequencing

Advances in the use of next generation sequencing (NGS) and ability to pool individuals into groups that represent distinct livestock populations has made it possible to examine trait differences between breeds of chicken. The breeds examined are very divergent when compared on their history of laying ability and immune response. The long-term objective is to understand the genetic differences between the Leghorn and Fayoumi breeds for use in developing more productive and disease resistant chickens. Statistical testing of the sequence of the two breeds along with Gene set enrichment analysis (GSEA) to make connections between the genetic variation seen in the NGS data and the breed specific traits of egg laying and heightened immune response can be used to characterize these two breeds. Genetic terms having the highest level of differentiation between the lines appear to group into metabolic processes, with terms over-enriched for immune system process, sexual reproduction, and growth for variants examined between lines. Terms for functions within the Fayoumi and Leghorn populations aligned to immune function and reproductive function, respectively. These results are consistent with known breed phenotypes and provide a means to focus on specific DNA variations and the birds’ genetic diversity that are potentially of more commercial importance

Design of a high power production target for the Beam Dump Facility at CERN

The Beam Dump Facility (BDF) project is a proposed general-purpose facility at CERN, dedicated to beam dump and fixed target experiments. In its initial phase, the facility is foreseen to be exploited by the Search for Hidden Particles (SHiP) experiment. Physics requirements call for a pulsed 400 GeV/c proton beam as well as the highest possible number of protons on target (POT) each year of operation, in order to search for feebly interacting particles. The target/dump assembly lies at the heart of the facility, with the aim of safely absorbing the full high intensity Super Proton Synchrotron (SPS) beam, while maximizing the production of charmed and beauty mesons. High-Z materials are required for the target/dump, in order to have the shortest possible absorber and reduce muon background for the downstream experiment. The high average power deposited on target (305 kW) creates a challenge for heat removal. During the BDF facility Comprehensive Design Study (CDS), launched by CERN in 2016, extensive studies have been carried out in order to define and assess the target assembly design. These studies are described in the present contribution, which details the proposed design of the BDF production target, as well as the material selection process and the optimization of the target configuration and beam dilution. One of the specific challenges and novelty of this work is the need to consider new target materials, such as a molybdenum alloy (TZM) as core absorbing material and Ta2.5W as cladding. Thermo-structural and fluid dynamics calculations have been performed to evaluate the reliability of the target and its cooling system under beam operation. In the framework of the target comprehensive design, a preliminary mechanical design of the full target assembly has also been carried out, assessing the feasibility of the whole target system.Comment: 17 pages, 18 figure

Gene Mapping by Chromosome Microdissection and Microisolation in the Chicken

A chromosome microdissection and microisolation technique in combination with filter hybridization was developed for chromosomal localization of cloned chicken genes. The DNA was obtained from microdissected chromosome regions of metaphase spreads. Dissected DNA was amplified by polymerase chain reaction (PCR). The chicken MHC gene located on the nucleolar chromosome and β-actin gene located on chromosome 2q were chosen as tests for the procedure and then detected by dot blot analysis using amplified chromosomal DNA probed with biotinylated DNA. The study establishes the technique of using chromosome microdissection and microisolation for localization of cloned genes as a complementary or alternative approach to both in situ DNA/chromosome hybridization and fluorescent in situ hybridization

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Background Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results Downstream fixation test (F ST ) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high F STvalues for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits

Biological survey of the Prince Edward Islands, December 2008

A biological survey of the Prince Edward Islands took place in December 2008. The survey repeated an earlier survey of the populations of surface-nesting seabirds on both islands and of fur seals (Arctocephalus spp.) and alien plants on Prince Edward Island in December 2001. Observations on burrowing seabirds, macro-invertebrates and plant communities on Prince Edward Island and an oceanographic survey of surrounding waters were also included. The survey confirmed many of the observations made on the earlier survey and permitted an assessment of trends in the abundance and distribution of biota since 2001