bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low Iodine Content in the Diets of Hospitalized Preterm Infants
Authors: Belfort Mandy B. , Pearce Elizabeth N. , Braverman Lewis E. , He Xuemei , Brown Rosalind S. 
Published: February 2012

Context:Iodine is critical for normal thyroid hormone synthesis and brain development during infancy, and preterm infants are particularly vulnerable to the effects of both iodine deficiency and excess. Use of iodine-containing skin antiseptics in intensive care nurseries has declined substantially in recent years, but whether the current dietary iodine intake meets the requirement for hospitalized preterm infants is unknown.Objective:The aim of the study was to measure the iodine content of enteral and parenteral nutrition products commonly used for hospitalized preterm infants and estimate the daily iodine intake for a hypothetical 1-kg infant.Methods:We used mass spectrometry to measure the iodine concentration of seven preterm infant formulas, 10 samples of pooled donor human milk, two human milk fortifiers (HMF) and other enteral supplements, and a parenteral amino acid solution and soy-based lipid emulsion. We calculated the iodine provided by typical diets based on 150 ml/kg · d of formula, donor human milk with or without HMF, and parenteral nutrition.Results:Preterm formula provided 16.4–28.5 μg/d of iodine, whereas unfortified donor human milk provided only 5.0–17.6 μg/d. Adding two servings (six packets) of Similac HMF to human milk increased iodine intake by 11.7 μg/d, whereas adding two servings of Enfamil HMF increased iodine intake by only 0.9 μg/d. The other enteral supplements contained almost no iodine, nor did a parenteral nutrition-based diet.Conclusions:Typical enteral diets for hospitalized preterm infants, particularly those based on donor human milk, provide less than the recommended 30 μg/d of iodine, and parenteral nutrition provides almost no iodine. Additional iodine fortification should be considered.
Effect of α-tocopherol on salivary reactive oxygen species and trace elements in oral submucous fibrosis
Authors: Chitra S , Balasubramaniam M , Hazra Jayram 
Published: February 2012

Background Oral submucous fibrosis (OSMF) is a chronic debilitating disease and a well-recognized, potentially malignant condition of the oral cavity associated with betel quid chewing. Betel quid chewing is a popular oral habit in India and shows strong association in the incidence of OSMF. The objective of the study was to determine the levels of trace elements, pro-oxidants and reactive oxygen species (ROS) in saliva of betel quid chewers and OSMF patients, which may help in the diagnosis of cancer progression in the oral cavity. Methods A total of 35 cases of OSMF and 35 cases of healthy individuals were included in the present study. The salivary status of ROS, pro-oxidants and some trace elements was studied in OSMF patients and normal healthy individuals. Results The levels of lipid peroxides ( P < 0.001), conjugated dienes ( P < 0.01), hydroxyl radicals ( P < 0.01), superoxide dismutase ( P < 0.05), copper ( P < 0.05), calcium ( P < 0.01), magnesium (NS), potassium ( P < 0.05) and iron ( P < 0.05) in OSMF patients were elevated when compared with normal healthy individuals. The levels of hydrogen peroxide ( P < 0.05) and sodium ( P < 0.01) in OSMF patients were found to be decreased when compared with control subjects. A significant alteration was noticed after supplementing with α-tocopherol in oral precancerous patients. Conclusion These parameters may help in the detection of the severity of oral diseases.
A Resource of Quantitative Functional Annotation forHomo sapiensGenes
Authors: Taşan Murat , Drabkin Harold J , Beaver John E , Chua Hon Nian , Dunham Julie , Tian Weidong , Blake Judith A , Roth Frederick P 
Published: February 2012

AbstractThe body of human genomic and proteomic evidence continues to grow at ever-increasing rates, while annotation efforts struggle to keep pace. A surprisingly small fraction of human genes have clear, documented associations with specific functions, and new functions continue to be found for characterized genes. Here we assembled an integrated collection of diverse genomic and proteomic data for 21,341 human genes and make quantitative associations of each to 4333 Gene Ontology terms. We combined guilt-by-profiling and guilt-by-association approaches to exploit features unique to the data types. Performance was evaluated by cross-validation, prospective validation, and by manual evaluation with the biological literature. Functional-linkage networks were also constructed, and their utility was demonstrated by identifying candidate genes related to a glioma FLN using a seed network from genome-wide association studies. Our annotations are presented—alongside existing validated annotations—in a publicly accessible and searchable web interface.
Transcriptome Atlases of Mouse Brain Reveals Differential Expression Across Brain Regions and Genetic Backgrounds
Authors: Sun Wei , Lee Seunggeun , Zhabotynsky Vasyl , Zou Fei , Wright Fred A , Crowley James J , Yun Zaining , Buus Ryan J , Miller Darla R , Wang Jeremy , McMillan Leonard , Pardo-Manuel de Villena Fernando , Sullivan Patrick F 
Published: February 2012

Abstract
Mouse models play a crucial role in the study of human behavioral traits and diseases. Variation of gene expression in brain may play a critical role in behavioral phenotypes, and thus it is of great importance to understand regulation of transcription in mouse brain. In this study, we analyzed the role of two important factors influencing steady-state transcriptional variation in mouse brain. First we considered the effect of assessing whole brain vs. discrete regions of the brain. Second, we investigated the genetic basis of strain effects on gene expression. We examined the transcriptome of three brain regions using Affymetrix expression arrays: whole brain, forebrain, and hindbrain in adult mice from two common inbred strains (C57BL/6J vs. NOD/ShiLtJ) with eight replicates for each brain region and strain combination. We observed significant differences between the transcriptomes of forebrain and hindbrain. In contrast, the transcriptomes of whole brain and forebrain were very similar. Using 4.3 million single-nucleotide polymorphisms identified through whole-genome sequencing of C57BL/6J and NOD/ShiLtJ strains, we investigated the relationship between strain effect in gene expression and DNA sequence similarity. We found that cis-regulatory effects play an important role in gene expression differences between strains and that the cis-regulatory elements are more often located in 5′ and/or 3′ transcript boundaries, with no apparent preference on either 5′ or 3′ ends.
Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross
Authors: Kelada Samir N P , Aylor David L , Peck Bailey C E , Ryan Joseph F , Tavarez Urraca , Buus Ryan J , Miller Darla R , Chesler Elissa J , Threadgill David W , Churchill Gary A , Pardo-Manuel de Villena Fernando , Collins Francis S 
Published: February 2012

Abstract
Hematological parameters, including red and white blood cell counts and hemoglobin concentration, are widely used clinical indicators of health and disease. These traits are tightly regulated in healthy individuals and are under genetic control. Mutations in key genes that affect hematological parameters have important phenotypic consequences, including multiple variants that affect susceptibility to malarial disease. However, most variation in hematological traits is continuous and is presumably influenced by multiple loci and variants with small phenotypic effects. We used a newly developed mouse resource population, the Collaborative Cross (CC), to identify genetic determinants of hematological parameters. We surveyed the eight founder strains of the CC and performed a mapping study using 131 incipient lines of the CC. Genome scans identified quantitative trait loci for several hematological parameters, including mean red cell volume (Chr 7 and Chr 14), white blood cell count (Chr 18), percent neutrophils/lymphocytes (Chr 11), and monocyte number (Chr 1). We used evolutionary principles and unique bioinformatics resources to reduce the size of candidate intervals and to view functional variation in the context of phylogeny. Many quantitative trait loci regions could be narrowed sufficiently to identify a small number of promising candidate genes. This approach not only expands our knowledge about hematological traits but also demonstrates the unique ability of the CC to elucidate the genetic architecture of complex traits.
Imputation of Single-Nucleotide Polymorphisms in Inbred Mice Using Local Phylogeny
Authors: Wang Jeremy R , de Villena Fernando Pardo-Manuel , Lawson Heather A , Cheverud James M , Churchill Gary A , McMillan Leonard 
Published: February 2012

Abstract
We present full-genome genotype imputations for 100 classical laboratory mouse strains, using a novel method. Using genotypes at 549,683 SNP loci obtained with the Mouse Diversity Array, we partitioned the genome of 100 mouse strains into 40,647 intervals that exhibit no evidence of historical recombination. For each of these intervals we inferred a local phylogenetic tree. We combined these data with 12 million loci with sequence variations recently discovered by whole-genome sequencing in a common subset of 12 classical laboratory strains. For each phylogenetic tree we identified strains sharing a leaf node with one or more of the sequenced strains. We then imputed high- and medium-confidence genotypes for each of 88 nonsequenced genomes. Among inbred strains, we imputed 92% of SNPs genome-wide, with 71% in high-confidence regions. Our method produced 977 million new genotypes with an estimated per-SNP error rate of 0.083% in high-confidence regions and 0.37% genome-wide. Our analysis identified which of the 88 nonsequenced strains would be the most informative for improving full-genome imputation, as well as which additional strain sequences will reveal more new genetic variants. Imputed sequences and quality scores can be downloaded and visualized online.
Varying Coefficient Models for Mapping Quantitative Trait Loci Using Recombinant Inbred Intercrosses
Authors: Gong Yi , Zou Fei 
Published: February 2012

AbstractThere has been a great deal of interest in the development of methodologies to map quantitative trait loci (QTL) using experimental crosses in the last 2 decades. Experimental crosses in animal and plant sciences provide important data sources for mapping QTL through linkage analysis. The Collaborative Cross (CC) is a renewable mouse resource that is generated from eight genetically diverse founder strains to mimic the genetic diversity in humans. The recombinant inbred intercrosses (RIX) generated from CC recombinant inbred (RI) lines share similar genetic structures of F2 individuals but with up to eight alleles segregating at any one locus. In contrast to F2 mice, genotypes of RIX can be inferred from the genotypes of their RI parents and can be produced repeatedly. Also, RIX mice typically do not share the same degree of relatedness. This unbalanced genetic relatedness requires careful statistical modeling to avoid false-positive findings. Many quantitative traits are inherently complex with genetic effects varying with other covariates, such as age. For such complex traits, if phenotype data can be collected over a wide range of ages across study subjects, their dynamic genetic patterns can be investigated. Parametric functions, such as sigmoidal or logistic functions, have been used for such purpose. In this article, we propose a flexible nonparametric time-varying coefficient QTL mapping method for RIX data. Our method allows the QTL effects to evolve with time and naturally extends classical parametric QTL mapping methods. We model the varying genetic effects nonparametrically with the B-spline bases. Our model investigates gene-by-time interactions for RIX data in a very flexible nonparametric fashion. Simulation results indicate that the varying coefficient QTL mapping has higher power and mapping precision compared to parametric models when the assumption of constant genetic effects fails. We also apply a modified permutation procedure to control overall significance level.
A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains
Authors: Lenarcic Alan B , Svenson Karen L , Churchill Gary A , Valdar William 
Published: February 2012

AbstractThe classic diallel takes a set of parents and produces offspring from all possible mating pairs. Phenotype values among the offspring can then be related back to their respective parentage. When the parents are diploid, sexed, and inbred, the diallel can characterize aggregate effects of genetic background on a phenotype, revealing effects of strain dosage, heterosis, parent of origin, epistasis, and sex-specific versions thereof. However, its analysis is traditionally intricate, unforgiving of unplanned missing information, and highly sensitive to imbalance, making the diallel unapproachable to many geneticists. Nonetheless, imbalanced and incomplete diallels arise frequently, albeit unintentionally, as by-products of larger-scale experiments that collect F1 data, for example, pilot studies or multiparent breeding efforts such as the Collaborative Cross or the Arabidopsis MAGIC lines. We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imbalance, missing data, and small sample size. We further present a model selection procedure for weighing evidence for or against the inclusion of those components in a predictive model. We evaluate our method through simulation and apply it to incomplete diallel data on the founders and F1's of the Collaborative Cross, robustly characterizing the genetic architecture of 48 phenotypes.
Rates and Fitness Consequences of New Mutations in Humans
Authors: Keightley Peter D 
Published: February 2012

Abstract
The human mutation rate per nucleotide site per generation (μ) can be estimated from data on mutation rates at loci causing Mendelian genetic disease, by comparing putatively neutrally evolving nucleotide sequences between humans and chimpanzees and by comparing the genome sequences of relatives. Direct estimates from genome sequencing of relatives suggest that μ is about 1.1 × 10−8, which is about twofold lower than estimates based on the human–chimp divergence. This implies that an average of ∼70 new mutations arise in the human diploid genome per generation. Most of these mutations are paternal in origin, but the male:female mutation rate ratio is currently uncertain and might vary even among individuals within a population. On the basis of a method proposed by Kondrashov and Crow, the genome-wide deleterious mutation rate (U) can be estimated from the product of the number of nucleotide sites in the genome, μ, and the mean selective constraint per site. Although the presence of many weakly selected mutations in human noncoding DNA makes this approach somewhat problematic, estimates are U ≈ 2.2 for the whole diploid genome per generation and ∼0.35 for mutations that change an amino acid of a protein-coding gene. A genome-wide deleterious mutation rate of 2.2 seems higher than humans could tolerate if natural selection is “hard,” but could be tolerated if selection acts on relative fitness differences between individuals or if there is synergistic epistasis. I argue that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations.
James F. Crow and the Stochastic Theory of Population Genetics
Authors: Ewens Warren J 
Published: February 2012

AbstractResearch in population genetics theory has two main strands. The first is deterministic theory, where random changes in allelic frequencies are ignored and attention focuses on the evolutionary effects of selection and mutation. The second strand, stochastic theory, takes account of these random changes and thus is more complete than deterministic theory. This essay is one in the series of Perspectives and Reviews honoring James F. Crow on the occasion of his 95th birthday. It concerns his contributions to, and involvement with, the stochastic theory of evolutionary population genetics.
The Influence of Thermal Annealing on Microstructure and Mechanical Properties in High Performance Liquid Crystal Copolyesters
Authors: Reyes-Mayer Adriana , Constant Amaury , Romo-Uribe Angel , Jaffe Michael 
Published: February 2012

ABSTRACTIn this research we have focused on the influence of thermal treatment for periods of time on the thermal and mechanical properties of extruded films of a series of high-performance thermotropic liquid crystal polymers (LCPs). The dependence of microstructure, thermal and mechanical properties on the extent of thermal treatment is investigated. Especially synthesized wholly aromatic LCPs based on hydroxybenzoic acid (B), hydroxynaphthoic acid (N), terephthalic acid (TA) and biphenol (BP) are kindly supplied by Hoechst Celanese Research Corp in the form of 50 μm thick extruded films. Thus, the influence of monomer composition is also studied in order to contrast the influence of molecular conformation. Thermal treatments are carried out at temperatures close to the solid-to-nematic transition (Ts→n) for up to several hours under dry air conditions. The results show a profound influence of thermal annealing on morphology and mechanical modulus when annealing is carried out c.a. 40ºC below Ts→n, where solid-to-nematic transition and Young’s modulus are significantly increased.
Improvement of Electrochemical Activity of Pt/MWCNT Catalyst for Proton Exchange Membrane Fuel Cell
Authors: Baatar Battsengel , Jamiyansuren Bayardulam , Myakhlai Munkhshur , Myagmarsuren Baasandorj 
Published: February 2012

ABSTRACTIn last years, the carbon nanotubes have been studied as an advanced metal catalyst support for proton exchange membrane fuel cell. This study focuses on the sonochemical treatment of multi walled carbon nanotubes (MWCNTs) as a platinum supporting material for proton exchange membrane fuel cell (PEMFC) by mixture of sulfuric acid and nitric acid and mixture of sulfuric acid and hydrogen peroxide. X-ray diffraction (XRD) and Infrared (IR) spectroscopy were used to characterize the surface of sonochemically treated MWCNT and nanostructured electrocatalyst Pt/MWCNT. According to the experimental results of this work, the surface of MWCNT can be more successfully functionalized with hydroxyl and carboxyl groups after sonochemical treatment by mixture of sulfuric acid and nitric acid. The particle size of prepared Pt -electrocatalyst on MWCNT was determined 3.4 nm by XRD.
New Developments for Lignocellulosics-Nanocomposites with Low Carbon Footprint
Authors: Leao Alcides L. , Cherian Bibin M. , Souza Sivoney F. , Sain Mohini , Narine Suresh 
Published: February 2012

ABSTRACTCellulose nanofibrils have been evaluated as reinforcement material in polymeric matrixes due to their potential to improve the mechanical, optical, and dielectric properties of these matrixes as well as its environmental positive footprint. This work describes how banana nanocellulose can be used to replace others not so friendly materials in many applications including, biomaterials, automotive industries and packaging by proved with their mechanical properties. The process used is very mild to the environment and consists of a high pressure fibrillation followed by a chemical purification which affects the fiber morphology. Many fibers characterization processes were used including microscopy techniques and X-ray diffraction to study the structure and properties of the prepared nanofibers and composites. Microscopy studies showed that the used individualization processes lead to a unique morphology of interconnected web-like structure of the fibers.
Trends in Risk Perceptions and Vaccination Intentions: A Longitudinal Study of the First Year of the H1N1 Pandemic
Authors: Gidengil Courtney A. , Parker Andrew M. , Zikmund-Fisher Brian J. 
Published: February 2012

Objectives. We sought to evaluate longitudinal trends in people’s risk perceptions and vaccination intentions during the 2009 H1N1 pandemic. Methods. We used data from 10 waves of a US national survey focusing on the H1N1 pandemic (administered between May 2009 and January 2010) to conduct a longitudinal analysis of adult respondents’ risk perceptions and vaccination intentions. Results. Self-reported perceived risk of becoming infected with H1N1 paralleled H1N1 activity throughout the pandemic’s first year. However, intention to be vaccinated declined from 50% (May 2009) to 16% (January 2010) among those who remained unvaccinated (27% had been vaccinated by January 2010). Respondents who indicated that they had previously been vaccinated against seasonal influenza reported significantly higher H1N1 vaccination intentions than those who had not been vaccinated (67% vs 26%; P < .001). Conclusions. Reported intention to be vaccinated declined well before vaccine became available and decreased throughout the pandemic year. To the extent that prior vaccination for seasonal influenza vaccination is a strong correlate of H1N1 risk perceptions, encouraging seasonal influenza vaccination may benefit pandemic preparedness efforts.
Worrying About Terrorism and Other Acute Environmental Health Hazard Events
Authors: Greenberg Michael , Babcock-Dunning Lauren 
Published: February 2012

Objectives. To better understand why some people worry more about terrorism compared with others, we measured how much US residents worried about a terrorist event in their area and examined the association of their fears with their concerns about acute and chronic hazards and other correlates. Methods. In 2008 (n = 600) and 2010 (n = 651), we performed a random-digit dialing national landline telephone survey. We asked about worries about terrorism and 5 other environmental health hazard issues. We also collected demographic and socioeconomic data. Results. Only 15% worried “a great deal” about a terrorist event in their area and 18% to 33% were greatly concerned about other environmental issues. Fear about acute hazard events was a stronger predictor of a great deal of concern about terrorism than were age, race/ethnicity, gender, educational achievement, and other correlates. Conclusions. Those who worried most about acute environmental health hazard events were most likely to worry about terrorism. Also, those who were older, poorer, Blacks, or Latinos, or who lived in populous urban areas felt they were most vulnerable to terrorist attacks. We recommend methods to involve US citizens as part of disaster planning.