Ti-ordered reflections

[EN] We present a construction which shows that the Ti-ordered reflection (i ϵ {0, 1, 2}) of a partially ordered topological space (X, , τ, ≤) exists and is an ordered quotient of (X, τ, ≤). We give an explicit construction of the T0-ordered reflection of an ordered topological space (X, τ, ≤), and characterize ordered topological spaces whose T0-ordered reflection is T1-ordered.The first author would like to thank the South African Research Foundation for partial financial support under Grant Number 2068799.Künzi, HA.; Richmond, TA. (2005). Ti-ordered reflections. Applied General Topology. 6(2):207-216. https://doi.org/10.4995/agt.2005.1955SWORD2072166

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300- 05645 to GJM

Dynamic Stability Instrumentation System (DSIS)

The paper is an operating manual for the Dynamic Stability Instrumentation System in specific NASA Langley wind tunnels. The instrumentation system performs either a synchronous demodulation or a Fast Fourier Transform on dynamic balance strain gage signals, and ultimately computes aerodynamic coefficients. The dynamic balance converts sting motor rotation into pitch or yaw plane or roll axis oscillation, with timing information provided by a shaft encoder. Additional instruments control model attitude and balance temperature and monitor sting vibrations. Other instruments perform self-calibration and diagnostics. Procedures for conducting calibrations and wind-off and wind-on tests are listed

The Amateur Sky Survey Mark III Project

The Amateur Sky Survey (TASS) is a loose confederation of amateur and professional astronomers. We describe the design and construction of our Mark III system, a set of wide-field drift-scan CCD cameras which monitor the celestial equator down to thirteenth magnitude in several passbands. We explain the methods by which images are gathered, processed, and reduced into lists of stellar positions and magnitudes. Over the period October, 1996, to November, 1998, we compiled a large database of photometric measurements. One of our results is the "tenxcat" catalog, which contains measurements on the standard Johnson-Cousins system for 367,241 stars; it contains links to the light curves of these stars as well.Comment: 20 pages, including 4 figures; additional JPEG files for Figures 1, 2. Submitted to PAS

Methods for Linking Community Views to Measureable Outcomes in a Youth Violence Prevention Program

Background: All parties in community–academic partnerships have a vested interest prevention program success. Markers of success that reflect community’s experiences of programmatic prevention success are not always measurable, but critically speak to community-defined needs. Objective: The purpose of this manuscript was to (1) describe our systematic process for linking locally relevant community views (community-defined indicators) to measurable outcomes in the context of a youth violence prevention program and (2) discuss lessons learned, next steps, and recommendations for others trying to replicate a similar process. Methods: A research team composed of both academic and community researchers conducted a systematic process of matching community-defined indicators of youth violence prevention programmatic success to standardized youth survey items being administered in the course of a program evaluation. The research team of three community partners and five academic partners considered 43 community-defined indicators and 208 items from the youth surveys being utilized within the context of a community-based aggression prevention program. At the end of the matching process, 92 youth survey items were identified and agreed upon as potential matches to 11 of the community-defined indicators. Conclusions: We applied rigorous action steps to match community-defined indicators to survey data collected in the youth violence prevention intervention. We learned important lessons that inform recommendations for others interested in such endeavors. The process used to derive and assess community-defined indicators of success emphasized the principles of community-based participatory research (CBPR) and use of existing and available data to reduce participant burden

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

An update on oral cavity cancer:epidemiological trends, prevention strategies and novel approaches in diagnosis and prognosis

In the UK, the incidence of oral cavity cancer continues to rise, with an increase of around 60% over the past 10 years. Many patients still present with advanced disease, often resulting in locoregional recurrence and poor outcomes, which has not changed significantly for over four decades. Changes in aetiology may also be emerging, given the decline of smoking in developed countries. Therefore, new methods to better target prevention, improve screening and detect recurrence are needed. High-throughput ‘omics’ technologies appear promising for future individual-level diagnosis and prognosis. However, given this is a relatively rare cancer with significant intra-tumour heterogeneity and variation in patient response, reliable biomarkers have been difficult to elucidate. From a public health perspective, implementing these novel technologies into current services would require substantial practical, financial and ethical considerations. This may be difficult to justify and implement at present, therefore focus remains on early detection using new patient-led follow-up strategies. This paper reviews the latest evidence on epidemiological trends in oral cavity cancer to help identify at risk groups, population-based approaches for prevention, in addition to potential cutting-edge approaches in the diagnosis and prognosis of this disease. Keywords: Epidemiology, Oral Cancer, Survival, Risk Factors, Squamous Cell Carcinoma, Mouth Neoplasm

Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: A case-control study protocol

Introduction: Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies. Methods and analysis: We are conducting a prospective case-control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case-control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR; pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined; relationships between pathogen load and disease status and severity will be explored. Ethics and dissemination: This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals

Synthesis of Sensor Fish Data for Assessment of Fish Passage Conditions at Turbines, Spillways, and Bypass Facilities – Phase 1: The Dalles Dam Spillway Case Study

This report summarizes the characterization of spillway passage conditions at The Dalles Dam in 2006 and the effort to complete a comprehensive database for data sets from The Dalles Dam spillway Sensor Fish and balloon-tagged live fish experiments. Through The Dalles Dam spillway case study, Pacific Northwest National Laboratory (PNNL) researchers evaluated the database as an efficient means for accessing and retrieving system-wide data for the U.S Army Corps of Engineers (USACE)

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND: There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS: A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS: We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes