bluuebunny/crossref_metadata_2025_split huggingface dataset:
The “Iowa Get Screened” Colon Cancer Screening Program
Authors: Levy Barcey T. , Daly Jeanette M. , Luxon Bruce , Merchant Mary L. , Xu Yinghui , Levitz Carly E. , Wilbur Jason K. 
Published: March 2010

Objective: To implement a colon cancer screening program for uninsured or underinsured Iowans. Methods: All 1995 uninsured patients or patients with Iowa Care insurance aged 50 to 64 years attending the University of Iowa Clinic or the Iowa City Free Medical Clinic were mailed information about the project. Recruitment also took place in person, by having the clinic receptionist hand subjects a research packet, and through community posters. Individuals with colonic symptoms or who were up to date with screening were ineligible. Eligible subjects received a free fecal immunochemical test (FIT), and those with positive FITs were provided with a colonoscopy at no cost to them. Results: Of 449 individuals who completed eligibility forms (23% of the study population), 297 (66%) were eligible and were provided with an FIT. Two-hundred thirty-five (79%) returned a stool sample, with 49 (21%) testing positive. Thirty of the 49 (61%) individuals had a colonoscopy, and 20 individuals had at least 1 polyp biopsied. Thirteen individuals had at least 1 tubular adenoma; 2 had adenomas more than 1 cm in diameter, with no colon cancers identified. Face-to-face recruitment had the highest rate of returned FITs (72%) compared with handing the subject a research packet (3%) or a mailing only (9%) (Chi-square, P < .001). Conclusion: There was high interest in and compliance with colon cancer screening using a FIT among underinsured individuals. Although the FIT positivity rate was higher than expected, many individuals did not complete recommended follow-up colonoscopies. Population-based strategies for offering FIT could significantly increase colon cancer screening among disadvantaged individuals, but programs will have to develop sustainable mechanisms to include the necessary organization and address substantial costs of providing mass screening, as well as facilitating and providing colonoscopies for those who test positive.
A Transtheoretical, Case Management Approach to the Treatment of Pediatric Obesity
Authors: Crabtree Valerie McLaughlin , Moore Justin B. , Jacks Dean E. , Cerrito Patricia , Topp Robert V. 
Published: March 2010

Objective: The percentage of obese children in the United States has increased dramatically over the past three decades, particularly among ethnic/ racial minorities. This study sought to examine the impact of a clinical case-management intervention based upon the Transtheoretical Model (TTM) to reduce obesity and increase physical activity in children. Methods: Nineteen obese African-American children ages 8-12 were recruited from two pediatric clinics and were randomized to either a 12-week intervention group or a control group. Dependent variables included body mass index (BMI) percentile, physical activity, and stage of change for the child and parent. Results: In comparison to the control group, the intervention group demonstrated significant decreases in BMI and improvements in daily vigorous physical activity. The children in the intervention group demonstrated movement toward action/maintenance stages of change. Conclusions: A 12-week TTM-based case management intervention can have a favorable impact on obesity and physical activity in African-American child.
Patients in a Depression Collaborative Care Model of Care
Authors: Angstman Kurt B. , Williams Mark D. 
Published: March 2010

A collaborative care model (CCM) has been implemented for management of depression. This paper studies the impact that the CCM had on cost measures for the period of six months after initial diagnosis of depression compared to patients receiving usual care (UC). There was a significant increase in the CPT costs for the six months following diagnosis in the CCM group ($451.35 vs. $323.50, P < 0.001). The average CPT cost rank and CPT cost differential were also significantly increased in the CCM group. The adjusted means of the CPT costs were (when controlling for prior utilization) $452.11 for the CCM group and $322.09 for UC (P < 0.001). In the CCM group; there were 161 patients (73.5%) that achieved a clinical response for their depression compared to the UC group, which had a 15.1% (18/119) response rate (P < 0.001). There also was a significant difference between the groups in those who were symptoms free of their depression (PHQ-9 score < 5), with the CCM having 59.4% of the patients symptom-free compared to 10.9% of the UC group (P < 0.001). In this group of patients, CCM is associated with markedly improved clinical outcomes for depression, however with a modest short-term increase in CPT costs.
Differential characteristics of Waldenström macroglobulinemia according to patterns of familial aggregation
Authors: Royer Regan H. , Koshiol Jill , Giambarresi Therese R. , Vasquez Linda G. , Pfeiffer Ruth M. , McMaster Mary L. 
Published: March 2010

AbstractFamilial aggregation of Waldenström macroglobulinemia (WM) and related B-cell disorders (BCDs) suggests a role for genetic factors, but few data address environmental influences. We designed a questionnaire-based study to examine clinical and environmental factors in a cohort of WM families with various patterns of case aggregation. We analyzed data on 103 WM patients and 272 unaffected relatives from 35 multiple-case WM and 46 mixed WM/BCD kindred and 28 nonfamilial (sporadic) WM patients, using logistic regression models with generalized estimating equations to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for association. In this study population, the WM disease process appeared similar among patients regardless of family history. Familial WM patients were more likely than unaffected relatives to report a history of autoimmune disease (OR, 2.27; 95% CI = 1.21-4.28) and infections (OR, 2.13; 95% CI = 1.25-3.64). Familial WM patients were also more likely to report exposure to farming (OR, 2.70; 95% CI = 1.34-5.42), pesticides (OR, 2.83; 95% CI = 1.56-5.11), wood dust (OR, 2.86; 95% CI = 1.54-5.33), and organic solvents (multiple-case WM OR, 4.21; 95% CI = 1.69-10.51) compared with unaffected family members. These data provide clues to both genetic and environmental factors that may influence development of WM. Well-designed case-control studies are needed to confirm these findings.
Modeling expression quantitative trait loci in data combining ethnic populations
Authors: Hsiao Ching-Lin , Lian Ie-Bin , Hsieh Ai-Ru , Fann Cathy SJ 
Published: March 2010

Abstract

Background
Combining data from different ethnic populations in a study can increase efficacy of methods designed to identify expression quantitative trait loci (eQTL) compared to analyzing each population independently. In such studies, however, the genetic diversity of minor allele frequencies among populations has rarely been taken into account. Due to the fact that allele frequency diversity and population-level expression differences are present in populations, a consensus regarding the optimal statistical approach for analysis of eQTL in data combining different populations remains inconclusive.

Results
In this report, we explored the applicability of a constrained two-way model to identify eQTL for combined ethnic data that might contain genetic diversity among ethnic populations. In addition, gene expression differences resulted from ethnic allele frequency diversity between populations were directly estimated and analyzed by the constrained two-way model. Through simulation, we investigated effects of genetic diversity on eQTL identification by examining gene expression data pooled from normal quantile transformation of each population. Using the constrained two-way model to reanalyze data from Caucasians and Asian individuals available from HapMap, a large number of eQTL were identified with similar genetic effects on the gene expression levels in these two populations. Furthermore, 19 single nucleotide polymorphisms with inter-population differences with respect to both genotype frequency and gene expression levels directed by genotypes were identified and reflected a clear distinction between Caucasians and Asian individuals.

Conclusions
This study illustrates the influence of minor allele frequencies on common eQTL identification using either separate or combined population data. Our findings are important for future eQTL studies in which different datasets are combined to increase the power of eQTL identification.
Identification of recurrent regions of copy-number variants across multiple individuals
Authors: Mei Teo Shu , Salim Agus , Calza Stefano , Seng Ku Chee , Seng Chia Kee , Pawitan Yudi 
Published: March 2010

Abstract

Background
Algorithms and software for CNV detection have been developed, but they detect the CNV regions sample-by-sample with individual-specific breakpoints, while common CNV regions are likely to occur at the same genomic locations across different individuals in a homogenous population. Current algorithms to detect common CNV regions do not account for the varying reliability of the individual CNVs, typically reported as confidence scores by SNP-based CNV detection algorithms. General methodologies for identifying these recurrent regions, especially those directed at SNP arrays, are still needed.

Results
In this paper, we describe two new approaches for identifying common CNV regions based on (i) the frequency of occurrence of reliable CNVs, where reliability is determined by high confidence scores, and (ii) a weighted frequency of occurrence of CNVs, where the weights are determined by the confidence scores. In addition, motivated by the fact that we often observe partially overlapping CNV regions as a mixture of two or more distinct subregions, regions identified using the two approaches can be fine-tuned to smaller sub-regions using a clustering algorithm. We compared the performance of the methods with sequencing-based results in terms of discordance rates, rates of departure from Hardy-Weinberg equilibrium (HWE) and average frequency and size of the identified regions. The discordance rates as well as the rates of departure from HWE decrease when we select CNVs with higher confidence scores. We also performed comparisons with two previously published methods, STAC and GISTIC, and showed that the methods we consider are better at identifying low-frequency but high-confidence CNV regions.

Conclusions
The proposed methods for identifying common CNV regions in multiple individuals perform well compared to existing methods. The identified common regions can be used for downstream analyses such as group comparisons in association studies.
Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome
Authors: Kissen Ralph , Winge Per , Tran Diem Hong Thi , Jørstad Tommy S , Størseth Trond R , Christensen Tone , Bones Atle M 
Published: March 2010

AbstractBackgroundGlutamate plays a central position in the synthesis of a variety of organic molecules in plants and is synthesised from nitrate through a series of enzymatic reactions. Glutamate synthases catalyse the last step in this pathway and two types are present in plants: NADH- or ferredoxin-dependent. Here we report a genome wide microarray analysis of the transcriptional reprogramming that occurs in leaves and roots of theA. thalianamutantglu1-2knocked-down in the expression ofFd-GOGAT1(GLU1;At5g04140), one of the two genes ofA. thalianaencoding ferredoxin-dependent glutamate synthase.ResultsTranscriptional profiling ofglu1-2revealed extensive changes with the expression of more than 5500 genes significantly affected in leaves and nearly 700 in roots. Both genes involved in glutamate biosynthesis and transformation are affected, leading to changes in amino acid compositions as revealed by NMR metabolome analysis. An elevated glutamine level in theglu1-2mutant was the most prominent of these changes. An unbiased analysis of the gene expression datasets allowed us to identify the pathways that constitute the secondary response of anFdGOGAT1/GLU1knock-down. Among the most significantly affected pathways, photosynthesis, photorespiratory cycle and chlorophyll biosynthesis show an overall downregulation inglu1-2leaves. This is in accordance with their slight chlorotic phenotype. Another characteristic of theglu1-2transcriptional profile is the activation of multiple stress responses, mimicking cold, heat, drought and oxidative stress. The change in expression of genes involved in flavonoid biosynthesis is also revealed. The expression of a substantial number of genes encoding stress-related transcription factors, cytochrome P450 monooxygenases, glutathione S-transferases and UDP-glycosyltransferases is affected in theglu1-2mutant. This may indicate an induction of the detoxification of secondary metabolites in the mutant.ConclusionsAnalysis of theglu1-2transcriptome reveals extensive changes in gene expression profiles revealing the importance of Fd-GOGAT1, and indirectly the central role of glutamate, in plant development. Besides the effect on genes involved in glutamate synthesis and transformation, theglu1-2mutant transcriptome was characterised by an extensive secondary response including the downregulation of photosynthesis-related pathways and the induction of genes and pathways involved in the plant response to a multitude of stresses.
Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)
Authors: Hubert Sophie , Higgins Brent , Borza Tudor , Bowman Sharen 
Published: March 2010

Abstract

Background
Atlantic cod (Gadus morhua) is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs) is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST) program, focusing on fish originating from Canadian waters.

Results
A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%). 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26%) SNPs were monomorphic for all populations tested. In total, 64 (4%) of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620) were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141). Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141), we determined that 36% (51) are non-synonymous. Many loci (1033 SNPs; 64%) are polymorphic in all populations tested. However a small number of SNPs (184) that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs.

Conclusions
These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. Genes that map within QTL intervals can be prioritized for testing to determine whether they contribute to observed phenotypes.
Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21
Authors: Pironon Nathalie , Puechberty Jacques , Roizès Gérard 
Published: March 2010

Abstract

Background
The mode of evolution of the highly homogeneous Higher-Order-Repeat-containing alpha satellite arrays is still subject to discussion. This is also true of the CENP-A associated repeats where the centromere is formed.

Results
In this paper, we show that the molecular mechanisms by which these arrays evolve are identical in multiple chromosomes: i) accumulation of crossovers that homogenise and expand the arrays into different domains and subdomains that are mostly unshared between homologues and ii) sporadic mutations and conversion events that simultaneously differentiate them from one another. Individual arrays are affected by these mechanisms to different extents that presumably increase with time. Repeats associated with CENP-A, where the centromere is formed, are subjected to the same evolutionary mechanisms, but constitute minor subsets that exhibit subtle sequence differences from those of the bulk repeats. While the DNA sequence per se is not essential for centromere localisation along an array, it appears that certain sequences can be selected against. On chromosomes 1 and 19, which are more affected by the above evolutionary mechanisms than are chromosomes 21 and 5, CENP-A associated repeats were also recovered from a second homogeneous array present on each chromosome. This could be a way for chromosomes to sustain mitosis and meiosis when the normal centromere locus is ineluctably undermined by the above mechanisms.

Conclusion
We discuss, in light of these observations, possible scenarios for the normal evolutionary fates of human centromeric regions.
Characterization of 13 multi-drug resistant Salmonella serovars from different broiler chickens associated with those of human isolates
Authors: Chiu Lan-Ho , Chiu Cheng-Hsun , Horn Yan-Ming , Chiou Chien-Shun , Lee Chien-Yu , Yeh Chia-Ming , Yu Chang-You , Wu Chean-Ping , Chang Chao-Chin , Chu Chishih 
Published: March 2010

Abstract

Background

Salmonella are frequently isolated from chickens and their products. Prevalent serogroups and serovars of Salmonella as well as their genotypes and antibiograms were determined for cloacal samples from 1595 chickens. To understand the possible serovar and H antigens for transmission between chicken and human, serovars and their H antigens of 164 chicken and 5314 human isolates were compared.

Results
Prevalence of Salmonella differed among chicken lines and ages. Chicken and human isolates belonged mainly to serogroup B, C1, C2-C3, D, and E. 13 serovars and 66 serovars were identified for chicken and human isolates respectively. The common serovars for chicken and human isolates were S. Typhimurium, S. Enteritidis, S. Albany, S. Derby, and S. Anatum and shared common H1 antigens "g complex; i; e,h; and z4,z24" and H2 antigens "1 complex and -". In human isolates, H1 antigen "i" and H2 antigen "-" were common in all serogroups. In chicken, antimicrobial susceptibility differed among serogroups, serovars and three counties. All isolates were susceptible to cefazolin and ceftriaxone, but highly resistant to ampicillin, chloramphenicol, flumequine, streptomycin, sulfamethoxazole-trimethoprim, and tetracycline. Except those isolates of serogroup C1 of Chick group and serogroup G, all isolates were multi-drug resistance. Only S. Kubacha, S. Typhimurium, S. Grampian, and S. Mons were resistant to ciprofloxacin and/or enrofloxacin.

Conclusion
In chicken, prevalent serogroups and serovars were associated with chicken ages, lines and regions; and flouroquinolone-resistant and MDR isolates emerged. H1 antigens "g complex and i" and H2 antigens "1 complex and -" might be important for transmission of Salmonella between chicken and human.
Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data
Authors: Artico Sinara , Nardeli Sarah M , Brilhante Osmundo , Grossi-de-Sa Maria Fátima , Alves-Ferreira Marcio 
Published: March 2010

AbstractBackgroundNormalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.ResultsBy the use of two distinct algorithms, implemented bygeNormandNormFinder, we have assessed the gene expression of nine candidate reference genes in cotton:GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3andGhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression ofGhPP2A1andGhUBQ14genes were the most stable across all samples and also when distinct plants organs are examined.GhACT4andGhUBQ14present more stable expression during flower development,GhACT4andGhFBX6in the floral verticils andGhMZAandGhPTBduring fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development.ConclusionWe have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use ofGhUBQ14andGhPP2A1housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs;GhACT4andGhUBQ14for flower development,GhACT4andGhFBX6for the floral organs andGhMZAandGhPTBfor fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.