bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan
Authors: Lin Chien-Hsing , Lin Jen-Kou , Chang Shih-Ching , Chang Ya-Hui , Chang Hwey-May , Liu Jin-Hwang , Li Ling-Hui , Chen Yuan-Tsong , Tsai Shih-Feng , Chen Wei-Shone 
Published: June 2011

Abstract

Background
Colorectal cancer (CRC) is a major health concern worldwide, and recently becomes the most common cancer in Asia. The case collection of this study is one of the largest sets of CRC in Asia, and serves as representative data for investigating genomic differences between ethnic populations. We took comprehensive and high-resolution approaches to compare the clinicopathologic and genomic profiles of microsatellite instability (MSI) vs. microsatellite stability (MSS) in Taiwanese sporadic CRCs.

Methods
1,173 CRC tumors were collected from the Taiwan population, and sequencing-based microsatellite typing assay was used to determine MSI and MSS. Genome-wide SNP array was used to detect CN alterations in 16 MSI-H and 13 MSS CRCs and CN variations in 424 general controls. Gene expression array was used to evaluate the effects of CN alterations, and quantitative PCR methods were used to replicate the findings in independent clinical samples.

Results
These 1,173 CRC tumors can be classified into 75 high-frequency MSI (MSI-H) (6.4%), 96 low-frequency MSI (8.2%) and 1,002 MSS (85.4%). Of the 75 MSI-H tumors, 22 had a BRAF mutation and 51 showed MLH1 promoter hypermethylation. There were distinctive differences in the extent of CN alterations between CRC MSS and MSI-H subtypes (300 Mb vs. 42 Mb per genome, p-value < 0.001). Also, chr7, 8q, 13 and 20 gains, and 8p and 18 losses were frequently found in MSS but not in MSI-H. Nearly a quarter of CN alterations were smaller than 100 kb, which might have been missed in previous studies due to low-resolution technology. 514 expressed genes showed CN differences between subtypes, and 271 of them (52%) were differentially expressed.

Conclusions
Sporadic CRCs with MSI-H displayed distinguishable clinicopathologic features, which differ from those of MSS. Genomic profiling of the two types of sporadic CRCs revealed significant differences in the extent and distribution of CN alterations in the cancer genome. More than half of expressed genes showing CN differences can directly contribute to their expressional diversities, and the biological functions of the genes associated with CN changes in sporadic CRCs warrant further investigation to establish their possible clinical implications.
BMP signaling balances proliferation and differentiation of muscle satellite cell descendants
Authors: Friedrichs Melanie , Wirsdöerfer Florian , Flohé Stefanie B , Schneider Sabine , Wuelling Manuela , Vortkamp Andrea 
Published: June 2011

Abstract

Background
The capacity of muscle to grow or to regenerate after damage is provided by adult stem cells, so called satellite cells, which are located under the basement lamina of each myofiber. Upon activation satellite cells enter the cell cycle, proliferate and differentiate into myoblasts, which fuse to injured myofibers or form new fibers. These processes are tightly controlled by many growth factors.

Results
Here we investigate the role of bone morphogenetic proteins (BMPs) during satellite cell differentiation. Unlike the myogenic C2C12 cell line, primary satellite cells do not differentiate into osteoblasts upon BMP signaling. Instead BMP signaling inhibits myogenic differentiation of primary satellite cells ex vivo. In contrast, inhibition of BMP signaling results in cell cycle exit, followed by enhanced myoblast differentiation and myotube formation. Using an in vivo trauma model we demonstrate that satellite cells respond to BMP signals during the regeneration process. Interestingly, we found the BMP inhibitor Chordin upregulated in primary satellite cell cultures and in regenerating muscles. In both systems Chordin expression follows that of Myogenin, a marker for cells committed to differentiation.

Conclusion
Our data indicate that BMP signaling plays a critical role in balancing proliferation and differentiation of activated satellite cells and their descendants. Initially, BMP signals maintain satellite cells descendants in a proliferating state thereby expanding cell numbers. After cells are committed to differentiate they upregulate the expression of the BMP inhibitor Chordin thereby supporting terminal differentiation and myotube formation in a negative feedback mechanism.
Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence
Authors: Chen Yuansha , Stine O Colin , Badger Jonathan H , Gil Ana I , Nair G Balakrish , Nishibuchi Mitsuaki , Fouts Derrick E 
Published: June 2011

Abstract
Background
Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68.

Results
Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories.

Conclusions
Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.
Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques
Authors: Moreland Anna J , Guethlein Lisbeth A , Reeves R Keith , Broman Karl W , Johnson R Paul , Parham Peter , O'Connor David H , Bimber Benjamin N 
Published: June 2011

Abstract

Background
Human killer immunoglobulin-like receptors (KIRs) play a critical role in governing the immune response to neoplastic and infectious disease. Rhesus macaques serve as important animal models for many human diseases in which KIRs are implicated; however, the study of KIR activity in this model is hindered by incomplete characterization of KIR genetics.

Results
Here we present a characterization of KIR genetics in rhesus macaques (Macaca mulatta). We conducted a survey of KIRs in this species, identifying 47 novel full-length KIR sequences. Using this expanded sequence library to build upon previous work, we present evidence supporting the existence of 22 Mamu-KIR genes, providing a framework within which to describe macaque KIRs. We also developed a novel pyrosequencing-based technique for KIR genotyping. This method provides both comprehensive KIR genotype and frequency estimates of transcript level, with implications for the study of KIRs in all species.

Conclusions
The results of this study significantly improve our understanding of macaque KIR genetic organization and diversity, with implications for the study of many human diseases that use macaques as a model. The ability to obtain comprehensive KIR genotypes is of basic importance for the study of KIRs, and can easily be adapted to other species. Together these findings both advance the field of macaque KIRs and facilitate future research into the role of KIRs in human disease.
Computational classifiers for predicting the short-term course of Multiple sclerosis
Authors: Bejarano Bartolome , Bianco Mariangela , Gonzalez-Moron Dolores , Sepulcre Jorge , Goñi Joaquin , Arcocha Juan , Soto Oscar , Carro Ubaldo Del , Comi Giancarlo , Leocani Letizia , Villoslada Pablo 
Published: June 2011

Abstract

Background
The aim of this study was to assess the diagnostic accuracy (sensitivity and specificity) of clinical, imaging and motor evoked potentials (MEP) for predicting the short-term prognosis of multiple sclerosis (MS).

Methods
We obtained clinical data, MRI and MEP from a prospective cohort of 51 patients and 20 matched controls followed for two years. Clinical end-points recorded were: 1) expanded disability status scale (EDSS), 2) disability progression, and 3) new relapses. We constructed computational classifiers (Bayesian, random decision-trees, simple logistic-linear regression-and neural networks) and calculated their accuracy by means of a 10-fold cross-validation method. We also validated our findings with a second cohort of 96 MS patients from a second center.

Results
We found that disability at baseline, grey matter volume and MEP were the variables that better correlated with clinical end-points, although their diagnostic accuracy was low. However, classifiers combining the most informative variables, namely baseline disability (EDSS), MRI lesion load and central motor conduction time (CMCT), were much more accurate in predicting future disability. Using the most informative variables (especially EDSS and CMCT) we developed a neural network (NNet) that attained a good performance for predicting the EDSS change. The predictive ability of the neural network was validated in an independent cohort obtaining similar accuracy (80%) for predicting the change in the EDSS two years later.

Conclusions
The usefulness of clinical variables for predicting the course of MS on an individual basis is limited, despite being associated with the disease course. By training a NNet with the most informative variables we achieved a good accuracy for predicting short-term disability.
SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation
Authors: Acun Tolga , Oztas Emin , Yagci Tamer , Yakicier Mustafa C 
Published: June 2011

Abstract

Background
Smad interacting protein-1 is a transcription factor that is implicated in transforming growth factor-β/bone morphogenetic protein signaling and a repressor of E-cadherin and human telomerase reverse transcriptase. It is also involved in epithelial-mesenchymal transition and tumorigenesis. However, genetic and epigenetic alterations of SIP1 have not been fully elucidated in cancers. In this study, we investigated mutations and promoter hypermethylation of the SIP1 gene in human hepatocellular carcinomas.

Methods

SIP1 expression was analyzed in HCC cell lines and primary tumors in comparison to normal and non-tumor liver tissues by using semi-quantitative RT-PCR, quantitative real-time RT-PCR and immunohistochemistry. Mutation and deletion screening of the SIP1 gene were performed by direct sequencing in HCC-derived cells. Restoration of SIP1 expression was sought by treating HCC cell lines with the DNA methyl transferase inhibitor, 5-AzaC, and the histone deacetylase inhibitor, TSA. SIP1 promoter methylation was analyzed by the combined bisulfite restriction analysis assay in in silico-predicted putative promoter and CpG island regions.

Results
We found that the expression of SIP1 was completely lost or reduced in five of 14 (36%) HCC cell lines and 17 of 23 (74%) primary HCC tumors. Immunohistochemical analysis confirmed that SIP1 mRNA downregulation was associated with decreased expression of the SIP1 protein in HCC tissues (82.8%). No somatic mutation was observed in SIP1 exons in any of the 14 HCC cell lines. Combined treatment with DNA methyl transferase and histone deacetylase inhibitors synergistically restored SIP1 expression in SIP1-negative cell lines. Analysis of three putative gene regulatory regions revealed tumor-specific methylation in more than half of the HCC cases.

Conclusions
Epigenetic mechanisms contribute significantly to the downregulation of SIP1 expression in HCC. This finding adds a new level of complexity to the role of SIP1 in hepatocarcinogenesis.
Clinical symptoms and chemotherapy completion in elderly patients with newly diagnosed acute leukemia: a retrospective comparison study with a younger cohort
Authors: Hu Rong , Wu Yong , Jiang Xiaoying , Zhang Wenteng , Xu Le 
Published: June 2011

Abstract

Background
Cancer affects older adults disproportionately. The disease is often difficult to diagnose and treat due to co-morbidities and performance status, and patients tend to discontinue chemotherapy prematurely. There are no systemic studies of the reasons and factors that create a higher withdrawal rate in older acute leukemia patients. This study tried to understand the initial characteristics, blood counts and bone marrow measurements in older acute leukemia patients by comparing them with a younger group to provide information and assistance in early clinical diagnosis, treatment and reasons for treatment withdrawal.

Methods
Using retrospective medical record reviews, we examined clinical characteristics and chemotherapy completion status in the patients of two groups (age ≥ 60, n = 183 and age <60, n = 183) who were diagnosed with acute leukemia for the first time and were hospitalized in Union Hospital Affiliated with Fujian Medical University from 2004 to 2008.

Results
There were no statistical differences in initial presenting symptoms of fatigue (67.2% vs. 57.9%, P>0.05) and pallor (53% vs. 59.6%, P>0.05) between the two groups, but older patients demonstrated more underlying diseases including lung infections (25.7%, P = <0.001), cardiovascular disease (4.4%, P = 0.007), and hypertension (20.8%, P =< 0.001). The complete remission rate after chemotherapy (1 to 2 courses) was 49.5% in the older group and 66.7% in the younger group (χ2 = 6.202, P = 0.013). The percentage of patients age 60 and older who prematurely discontinued chemotherapy (50.3%), mainly due to the influences of traditional Chinese concept of critical illness, financial difficulties, and intolerance to adverse reactions to chemotherapy, was significantly higher than that of younger patients (37.7%) (χ2 = 5.866, P = 0.015).

Conclusions
A comprehensive approach to diagnosis, treatment selection, and toxicity management, and implementing strategies to enhance treatment compliance may improve outcomes in older adults with acute leukemia.
Safety during the monitoring of diabetic patients: trial teaching course on health professionals and diabetics - SEGUDIAB study
Authors: Cabré Juan J , Ripoll Marta , Hernández Josep M , Basora Josep , Bejarano Ferran , Arija Victoria 
Published: June 2011

AbstractBackgroundSafety for diabetic patients means providing the most suitable treatment for each type of diabetic in order to improve monitoring and to prevent the adverse effects of drugs and complications arising from the disease. The aim of this study is to analyze the effect of imparting educational interventions to health professionals regarding the safety of patients with Diabetes Mellitus (DM).MethodsDesign: A cluster randomized trial with a control group.Setting and sample: The study analyzed ten primary healthcare centres (PHC) covering approximately 150,000 inhabitants. Two groups of 5 PHC were selected on the basis of their geographic location (urban, semi-urban and rural), their socio-economic status and the size of their PHC, The interventions and control groups were assigned at random. The study uses computerized patient records to individually assess subjects aged 45 to 75 diagnosed with type 1 and type 2 DM, who met the inclusion conditions and who had the variables of particular interest to the study.Trial: The educational interventions consisted of a standardized teaching course aimed at doctors and nurses. The course lasted 6 hours and was split into three 2-hour blocks with subsequent monthly refresher courses.Measurement: For the health professionals, the study used theDiabetes Attitude Scale(DAS-3) to assess their attitudes and motivation when monitoring diabetes. For the patients, the study assessed factors related to their degree of control over the disease at onset, 6, 12 and 24 months.Main variables: levels of HbA1c.Analysis: The study analyzed the effect of the educational interventions both on the attitudes and motivations of health professionals and on the degree of control over the diabetes in both groups.DiscussionImparting educational interventions to health professionals would improve the monitoring of diabetic patients. The most effective model involves imparting the course to both doctors and nurses. However, these models have not been tested on our Spanish population within the framework of primary healthcare.Trial registrationClinicalTrials.gov:NCT01087541
Socio-demographic and lifestyle factors associated with overweight in a representative sample of 11-15 year olds in France: Results from the WHO-Collaborative Health Behaviour in School-aged Children (HBSC) cross-sectional study
Authors: Dupuy Marie , Godeau Emmanuelle , Vignes Céline , Ahluwalia Namanjeet 
Published: June 2011

Abstract

Background
The prevalence of overweight in children and adolescents is high and overweight is associated with poor health outcomes over short- and long-term. Lifestyle factors can interact to influence overweight. Comprehensive studies linking overweight concomitantly with several demographic and potentially-modifiable lifestyle factors and health-risk behaviours are limited in adolescents - an age-group characterized by changes in lifestyle behaviours and high prevalence of overweight. Thus, the objective of the current study was to examine the association of overweight with several socio-demographic and lifestyle variables simultaneously in a representative sample of adolescents.

Methods
A nationally representative sample of 11-15 year-olds (n = 7154) in France participated as part of the WHO-Collaborative Health Behaviour in School-aged Children (HBSC) study. Students reported data on their age, height, weight, socio-demographic variables, lifestyle factors including nutrition practices, physical activity at two levels of intensity (moderate and vigorous), sedentary behaviours, as well as smoking and alcohol consumption patterns using standardized HBSC protocols. Overweight (including obesity) was defined using the IOTF reference. The multivariate association of overweight with several socio-demographic and lifestyle factors was examined with logistic regression models.

Results
The adjusted odds ratios for the association with overweight were: 1.80 (95% CI: 1.37-2.36) for low family affluence; 0.73 (0.60-0.88) for eating breakfast daily; 0.69 (0.56-0.84) for moderate to vigorous physical activity (MVPA); and 0.71 (0.59-0.86) for vigorous physical activity (VPA). Significant interactions between age and gender as well as television (TV) viewing and gender were noted: for boys, overweight was not associated with age or TV viewing; in contrast, for girls overweight correlated negatively with age and positively with TV viewing. Fruit and vegetable intake, computer and video-games use, smoking and alcohol consumption were not associated with overweight.

Conclusions
In multivariate model, family affluence, breakfast consumption and moderate to vigorous as well as vigorous physical activity were negatively associated with overweight. These findings extend previous research to a setting where multiple risk and protective factors were simultaneously examined and highlight the importance of multi-faceted approaches promoting physical activity and healthy food choices such as breakfast consumption for overweight prevention in adolescents.
Happiness and health behaviours in Chilean college students: A cross-sectional survey
Authors: Piqueras José A , Kuhne Walter , Vera-Villarroel Pablo , van Straten Annemieke , Cuijpers Pim 
Published: June 2011

Abstract

Background
Happiness has been associated with a range of favourable health outcomes through two pathways: its relationship with favourable biological responses to stress and with healthy lifestyles and prudent health behaviours. There are a substantial number of cross-cultural studies about happiness, but none of them has studied the association of happiness with perceived stress and health behaviours in Latin American samples. Therefore, the aim of this study was to examine the association between general happiness and these variables in a Latin American sample.

Methods
We conducted a survey to examine the status of 3461 students aged between 17 and 24 years old (mean age = 19.89; SD = 1.73) who attended University of Santiago de Chile during 2009. The healthy behaviours indexes assessed were the frequency of daily physical exercise, fruits/vegetables intake, breakfast and lunch intake, smoking, alcohol and other drugs consumption. We also included the assessment of perceived stress and Body Mass Index. All of them were evaluated using a self-report questionnaire.

Results
The univariate and multivariate binary logistic regression analyses showed that being female and younger was related to a higher happiness, as well as that people self-reporting daily physical activity, having lunch and fruits and vegetables each day had a higher likelihood (OR between 1.33 and 1.40) of being classified as "very happy". Those who informed felt stressed in normal circumstances and during tests situations showed a lower likelihood (0.73 and 0.82, respectively) of being considered "very happy". Regarding drug consumption, taking tranquilizers under prescription was negative related to "subjective happiness" (OR = 0.62), whereas smoking was positive associated (OR = 1.20).

Conclusions
The findings of this study mainly support the relationship between happiness and health outcomes through the two pathways previously mentioned. They also underscore the importance of that some healthy behaviours and person's cognitive appraisal of stress are integrated into their lifestyle for college students. Additionally, highlight the importance of taking into account these variables in the design of strategies to promote health education in university setting.