bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice
Authors: Bottomly Daniel , Ferris Martin T , Aicher Lauri D , Rosenzweig Elizabeth , Whitmore Alan , Aylor David L , Haagmans Bart L , Gralinski Lisa E , Bradel-Tretheway Birgit G , Bryan Janine T , Threadgill David W , de Villena Fernando Pardo-Manuel , Baric Ralph S , Katze Michael G , Heise Mark , McWeeney Shannon K 
Published: February 2012

Abstract
Outbreaks of influenza occur on a yearly basis, causing a wide range of symptoms across the human population. Although evidence exists that the host response to influenza infection is influenced by genetic differences in the host, this has not been studied in a system with genetic diversity mirroring that of the human population. Here we used mice from 44 influenza-infected pre-Collaborative Cross lines determined to have extreme phenotypes with regard to the host response to influenza A virus infection. Global transcriptome profiling identified 2671 transcripts that were significantly differentially expressed between mice that showed a severe (“high”) and mild (“low”) response to infection. Expression quantitative trait loci mapping was performed on those transcripts that were differentially expressed because of differences in host response phenotype to identify putative regulatory regions potentially controlling their expression. Twenty-one significant expression quantitative trait loci were identified, which allowed direct examination of genes associated with regulation of host response to infection. To perform initial validation of our findings, quantitative polymerase chain reaction was performed in the infected founder strains, and we were able to confirm or partially confirm more than 70% of those tested. In addition, we explored putative causal and reactive (downstream) relationships between the significantly regulated genes and others in the high or low response groups using structural equation modeling. By using systems approaches and a genetically diverse population, we were able to develop a novel framework for identifying the underlying biological subnetworks under host genetic control during influenza virus infection.
Ten Years of the Collaborative Cross
Authors: Threadgill David W , Churchill Gary A 
Published: February 2012

Abstract
The February 2012 issues of GENETICS and G3: Genes, Genomes, Genetics present a collection of articles reporting recent advances from the international Collaborative Cross (CC) project. The goal of the CC project is to develop a new resource that will enhance quantitative trait locus (QTL) and systems genetic analyses in mice. The CC consists of hundreds of independently bred, octo-parental recombinant inbred lines (Figure 1). The work reported in these issues represents progress toward completion of the CC, proof-of-principle experiments using incipient inbred CC mice, and new research areas and complementary resources facilitated by the CC project.
Chromatin and Transcription in Yeast
Authors: Rando Oliver J , Winston Fred 
Published: February 2012

Abstract
Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.
High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
Authors: Svenson Karen L , Gatti Daniel M , Valdar William , Welsh Catherine E , Cheng Riyan , Chesler Elissa J , Palmer Abraham A , McMillan Leonard , Churchill Gary A 
Published: February 2012

Abstract
The JAX Diversity Outbred population is a new mouse resource derived from partially inbred Collaborative Cross strains and maintained by randomized outcrossing. As such, it segregates the same allelic variants as the Collaborative Cross but embeds these in a distinct population architecture in which each animal has a high degree of heterozygosity and carries a unique combination of alleles. Phenotypic diversity is striking and often divergent from phenotypes seen in the founder strains of the Collaborative Cross. Allele frequencies and recombination density in early generations of Diversity Outbred mice are consistent with expectations based on simulations of the mating design. We describe analytical methods for genetic mapping using this resource and demonstrate the power and high mapping resolution achieved with this population by mapping a serum cholesterol trait to a 2-Mb region on chromosome 3 containing only 11 genes. Analysis of the estimated allele effects in conjunction with complete genome sequence data of the founder strains reduced the pool of candidate polymorphisms to seven SNPs, five of which are located in an intergenic region upstream of the Foxo1 gene.
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
Authors:   Collaborative Cross Consortium
Published: February 2012

AbstractThe Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multiparental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND). These institutions aim to make publicly available the completed CC lines and their genotypes and sequence information. We genotyped, and report here, results from 458 extant lines from UNC, TAU, and GND using a custom genotyping array with 7500 SNPs designed to be maximally informative in the CC and used a novel algorithm to infer inherited haplotypes directly from hybridization intensity patterns. We identified lines with breeding errors and cousin lines generated by splitting incipient lines into two or more cousin lines at early generations of inbreeding. We then characterized the genome architecture of 350 genetically independent CC lines. Results showed that founder haplotypes are inherited at the expected frequency, although we also consistently observed highly significant transmission ratio distortion at specific loci across all three populations. On chromosome 2, there is significant overrepresentation of WSB/EiJ alleles, and on chromosome X, there is a large deficit of CC lines with CAST/EiJ alleles. Linkage disequilibrium decays as expected and we saw no evidence of gametic disequilibrium in the CC population as a whole or in random subsets of the population. Gametic equilibrium in the CC population is in marked contrast to the gametic disequilibrium present in a large panel of classical inbred strains. Finally, we discuss access to the CC population and to the associated raw data describing the genetic structure of individual lines. Integration of rich phenotypic and genomic data over time and across a wide variety of fields will be vital to delivering on one of the key attributes of the CC, a common genetic reference platform for identifying causative variants and genetic networks determining traits in mammals.
Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
Authors: Broman Karl W 
Published: February 2012

Abstract
The mouse Collaborative Cross (CC) is a panel of eight-way recombinant inbred lines: eight diverse parental strains are intermated, followed by repeated sibling mating, many times in parallel, to create a new set of inbred lines whose genomes are random mosaics of the genomes of the original eight strains. Many generations are required to reach inbreeding, and so a number of investigators have sought to make use of phenotype and genotype data on mice from intermediate generations during the formation of the CC lines (so-called pre-CC mice). The development of a hidden Markov model for genotype reconstruction in such pre-CC mice, on the basis of incompletely informative genetic markers (such as single-nucleotide polymorphisms), formally requires the two-locus genotype probabilities at an arbitrary generation along the path to inbreeding. In this article, I describe my efforts to calculate such probabilities. While closed-form solutions for the two-locus genotype probabilities could not be derived, I provide a prescription for calculating such probabilities numerically. In addition, I present a number of useful quantities, including single-locus genotype probabilities, two-locus haplotype probabilities, and the fixation probability and map expansion at each generation along the course to inbreeding.
Preparation of amorphous aluminium ammonium phosphates
Authors: Grzmil Barbara , Łuczka Kinga , Gleń Marta 
Published: February 2012

ABSTRACTA method for obtaining of amorphous aluminium ammonium phosphates is developed. The statistical program STATISTICA 9 is used for planning and evaluation of the experiments. Research is carried out according to the Box-Behnken model for the following values of independent variables (input factors): pH: 6.0 ± 2; concentration of reagents: 40 ± 10 wt%, molar ratio of NH4+:PO43- in substrates (2 ± 1:1) i.e. Al3+:NH4+:PO43- (0.66:1-3:1). On the basis of this research, process parameters are determined, in which materials with the expected physicochemical properties (chemical composition, specific surface area, oil absorption number) can be obtained.
Effect of manganese on the thermostability and reducibility of cobalt nanomaterials.
Authors: Lendzion-Bieluń Zofia 
Published: February 2012

ABSTRACTCobalt nanomaterials with promoters have been prepared by precipitation followed by calcination and impregnation method. The obtained materials are characterized by ICP, H2-TPR, BET and XRD. A small addition of manganese increases the specific surface area of cobalt nanomaterials and thermostability under reduction atmosphere. Bulk Co3O4 has been reduced in two steps (Co3+→Co2+→Co). A small addition of manganese to the cobalt oxide shifts the reduction peaks to high temperatures.
Associations Between Socioeconomic Status and Allostatic Load: Effects of Neighborhood Poverty and Tests of Mediating Pathways
Authors: Schulz Amy J. , Mentz Graciela , Lachance Laurie , Johnson Jonetta , Gaines Causandra , Israel Barbara A. 
Published: February 2012

Objectives. We examined relationships between neighborhood poverty and allostatic load in a low- to moderate-income multiracial urban community. We tested the hypothesis that neighborhood poverty is associated with allostatic load, controlling for household poverty. We also examined the hypotheses that this association was mediated by psychosocial stress and health-related behaviors. Methods. We conducted multilevel analyses using cross-sectional data from a probability sample survey in Detroit, Michigan (n = 919) and the 2000 US Census. The outcome measure was allostatic load. Independent variables included neighborhood and household poverty, psychosocial stress, and health-related behaviors. Covariates included neighborhood and individual demographic characteristics. Results. Neighborhood poverty was positively associated with allostatic load (P < .05), independent of household poverty and controlling for potential confounders. Relationships between neighborhood poverty were mediated by self-reported neighborhood environment stress but not by health-related behaviors. Conclusions. Neighborhood poverty is associated with wear and tear on physiological systems, and this relationship is mediated through psychosocial stress. These relationships are evident after accounting for household poverty levels. Efforts to promote health equity should focus on neighborhood poverty, associated stressful environmental conditions, and household poverty.
Syndemic Theory and HIV-Related Risk Among Young Transgender Women: The Role of Multiple, Co-Occurring Health Problems and Social Marginalization
Authors: Brennan Julia , Kuhns Lisa M. , Johnson Amy K. , Belzer Marvin , Wilson Erin C. , Garofalo Robert ,   the Adolescent Medicine Trials Network for HIV/AIDS Interventions
Published: February 2012

Objectives. We assessed whether multiple psychosocial factors are additive in their relationship to sexual risk behavior and self-reported HIV status (i.e., can be characterized as a syndemic) among young transgender women and the relationship of indicators of social marginalization to psychosocial factors. Methods. Participants (n = 151) were aged 15 to 24 years and lived in Chicago or Los Angeles. We collected data on psychosocial factors (low self-esteem, polysubstance use, victimization related to transgender identity, and intimate partner violence) and social marginalization indicators (history of commercial sex work, homelessness, and incarceration) through an interviewer-administered survey. Results. Syndemic factors were positively and additively related to sexual risk behavior and self-reported HIV infection. In addition, our syndemic index was significantly related to 2 indicators of social marginalization: a history of sex work and previous incarceration. Conclusions. These findings provide evidence for a syndemic of co-occurring psychosocial and health problems in young transgender women, taking place in a context of social marginalization.
Contribution of Communication Inequalities to Disparities in Human Papillomavirus Vaccine Awareness and Knowledge
Authors: Kontos Emily Z. , Emmons Karen M. , Puleo Elaine , Viswanath K. 
Published: February 2012

Objectives. We examined the association of Internet-related communication inequalities on human papillomavirus (HPV) vaccine awareness and infection knowledge. Methods. We drew data from National Cancer Institute’s 2007 Health Information National Trends Survey (n = 7674). We estimated multivariable logistic regression models to assess Internet use and Internet health information seeking on HPV vaccine awareness and infection knowledge. Results. Non–Internet users, compared with general Internet users, had significantly lower odds of being aware of the HPV vaccine (odds ratio [OR] = 0.42; 95% confidence interval [CI] = 0.34, 0.51) and knowing that HPV causes cervical cancer (OR = 0.70; 95% CI = 0.52, 0.95). Among general health information seekers, non–Internet seekers compared with Internet information seekers exhibit significantly lower odds of HPV vaccine awareness (OR = 0.59; 95% CI = 0.46, 0.75), and of knowing about the link between HPV infection and cervical cancer (OR = 0.79; 95% CI = 0.63, 0.99) and the sexual transmission of HPV (OR = 0.71; 95% CI = 0.57, 0.89). Among cancer information seekers, there were no differences in outcomes between Internet seekers and non–Internet seekers. Conclusions. Use of a communication channel, such as the Internet, whose use is already socially and racially patterned, may widen observed disparities in vaccine completion rates.
The Effects of Smoking-Related Television Advertising on Smoking and Intentions to Quit Among Adults in the United States: 1999–2007
Authors: Emery Sherry , Kim Yoonsang , Choi Young Ku , Szczypka Glen , Wakefield Melanie , Chaloupka Frank J. 
Published: February 2012

Objectives. We investigated whether state-sponsored antitobacco advertisements are associated with reduced adult smoking, and interactions between smoking-related advertising types. Methods. We measured mean exposure to smoking-related advertisements with television ratings for the top-75 US media markets from 1999 to 2007. We combined these data with individual-level Current Population Surveys Tobacco Use Supplement data and state tobacco control policy data. Results. Higher exposure to state-sponsored, Legacy, and pharmaceutical advertisements was associated with less smoking; higher exposure to tobacco industry advertisements was associated with more smoking. Higher exposure to state- and Legacy-sponsored advertisements was positively associated with intentions to quit and having made a past-year quit attempt; higher exposure to ads for pharmaceutical cessation aids was negatively associated with having made a quit attempt. There was a significant negative interaction between state- and Legacy-sponsored advertisements. Conclusions. Exposure to state-sponsored advertisements was far below Centers for Disease Control and Prevention–recommended best practices. The significant negative relationships between antismoking advertising and adult smoking provide strong evidence that tobacco-control media campaigns help reduce adult smoking. The significant negative interaction between state- and Legacy-sponsored advertising suggests that the campaigns reinforce one another.
Continued Increases in the Relative Risk of Death From Smoking
Authors: Mehta Neil , Preston Samuel 
Published: February 2012

Objectives. We examined changes in the relative risk of death among current and former smokers over recent decades in the United States. Methods. Data from the National Health Interview Survey (NHIS) and National Health and Nutrition Examination Survey (NHANES) were linked to subsequent deaths. We calculated age-standardized death rates by gender and smoking status, and estimated multivariate discrete time logit regression models. Results. The risk of death for a smoker compared with that for a never-smoker increased by 25.4% from 1987 to 2006 based on NHIS data. Analysis of NHANES data from 1971 to 2006 showed an even faster annual increase in the relative risk of death for current smokers. Former smokers also showed an increasing relative risk of death, although the increase was slower than that among current smokers and not always statistically significant. These trends were not related to increasing educational selectivity of smokers or increased smoking intensity or duration among current smokers. Smokers may have become more adversely selected on other health-related variables. Conclusions. A continuing increase in the relative risk of death for current and former smokers suggests that the contribution of smoking to national mortality patterns is not decreasing as rapidly as would be implied by the decreasing prevalence of smoking among Americans.
Benefits and Effectiveness of Administering Pneumococcal Polysaccharide Vaccine With Seasonal Influenza Vaccine: An Approach for Policymakers
Authors: Gilchrist Shawn A. N. , Nanni Angeline , Levine Orin 
Published: February 2012

For the influenza pandemic of 2009–2010, countries responded to the direct threat of influenza but may have missed opportunities and strategies to limit secondary pneumococcal infections. Delivering both vaccines together can potentially increase pneumococcal polysaccharide vaccine (PPV23) immunization rates and prevent additional hospitalizations and mortality in the elderly and other high-risk groups. We used PubMed to review the literature on the concomitant use of PPV23 with seasonal influenza vaccines. Eight of 9 clinical studies found that a concomitant program conferred clinical benefits. The 2 studies that compared the cost-effectiveness of different strategies found concomitant immunization to be more cost-effective than either vaccine given alone. Policymakers should consider a stepwise strategy to reduce the burden of secondary pneumococcal infections during seasonal and pandemic influenza outbreaks.
Exposure to Natural Cold and Heat: Hypothermia and Hyperthermia Medicare Claims, United States, 2004–2005
Authors: Noe Rebecca S. , Jin Jill O. , Wolkin Amy F. 
Published: February 2012

Objectives. We measured the burden of hypothermia- and hyperthermia-related health care visits, identified risk factors, and determined the health care costs associated with environmental heat or cold exposure among Medicare beneficiaries. Methods. We obtained Medicare fee-for-service claims data of inpatient and outpatient health care visits for hypothermia and hyperthermia from 2004 to 2005. We examined the distribution and differences of visits by age, sex, race, geographic regions, and direct costs. We estimated rate ratios to determine risk factors. Results. Hyperthermia-related visits (n = 10 007) were more frequent than hypothermia-related visits (n = 8761) for both years. However, hypothermia-related visits resulted in more deaths (359 vs 42), higher mortality rates (0.50 per 100 000 vs 0.06 per 100 000), higher inpatient rates (5.29 per 100 000 vs 1.76 per 100 000), longer hospital stays (median days = 4 vs 2), and higher total health care costs ($98 million vs $36 million). Conclusions. This study highlighted the magnitude of these preventable conditions among older adults and disabled persons and the burden on the Medicare system. These results can help target public education and preparedness activities for extreme weather events.
Destigmatizing Alcohol Dependence: The Requirement for an Ethical (Not Only Medical) Remedy
Authors: Williamson Laura 
Published: February 2012

The disease model of alcohol dependence or “alcoholism” is often presented as the linchpin in addressing the condition successfully. It has been argued, for example, that adopting a medical approach will reduce the stigma that impedes the provision and acceptance of treatment. However, the medical paradigm has existed for many years without significantly affecting the negative social attitudes that surround dependence. I argue that a reductive scientific approach is not equipped to address the socioethical tensions that dependence creates. To lessen the stigmatization of dependence, it is important to integrate ethical analysis into policy debates on the condition.
Auditor Resignations and the Importance of Monitoring Client Acceptance Risk
Authors: Irving James H. , Walker Paul L. 
Published: February 2012

SUMMARY
We summarize our recently published study in Accounting Horizons (Catanach et al. 2011) that examines client acceptance patterns and client outcomes following auditor resignations. We used a sample of auditor resignations to examine two issues: (1) why accounting firms assume the role of successor auditor on these presumably risky engagements, and (2) the future outcomes of clients accepted by these successor auditors. We find that smaller accounting firms accept the successor auditor role for resigned clients at a considerably greater rate than do larger firms. Additionally, resigned clients accepted by smaller firms are riskier on several dimensions than those accepted by larger firms. Furthermore, resigned clients accepted by smaller firms are associated with weaker long-term financial ratios, shorter survival tenures, and a greater likelihood of adverse outcomes relative to those accepted by larger firms. We offer related insights for practitioners.