bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunologic ignorance of vascular endothelial cells expressing minor histocompatibility antigen
Authors: Bolinger Beatrice , Krebs Philippe , Tian Yinghua , Engeler Daniel , Scandella Elke , Miller Simone , Palmer Douglas C. , Restifo Nicholas P. , Clavien Pierre-Alain , Ludewig Burkhard 
Published: January 2008

AbstractEndothelial cells (ECs) presenting minor histocompatibility antigen (mhAg) are major target cells for alloreactive effector CD8+ T cells during chronic transplant rejection and graft-versus-host disease (GVHD). The contribution of ECs to T-cell activation, however, is still a controversial issue. In this study, we have assessed the antigen-presenting capacity of ECs in vivo using a transgenic mouse model with beta-galactosidase (β-gal) expression confined to the vascular endothelium (Tie2-LacZ mice). In a GVHD-like setting with adoptive transfer of β-gal–specific T-cell receptor–transgenic T cells, β-gal expression by ECs was not sufficient to either activate or tolerize CD8+ T cells. Likewise, transplantation of fully vascularized heart or liver grafts from Tie2-LacZ mice into nontransgenic recipients did not suffice to activate β-gal–specific CD8+ T cells, indicating that CD8+ T-cell responses against mhAg cannot be initiated by ECs. Moreover, we could show that spontaneous activation of β-gal–specific CD8+ T cells in Tie2-LacZ mice was exclusively dependent on CD11c+ dendritic cells (DCs), demonstrating that mhAgs presented by ECs remain immunologically ignored unless presentation by DCs is granted.
LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Authors: Noirot Céline , Gaspin Christine , Schiex Thomas , Gouzy Jérôme 
Published: January 2008

Abstract

Background
In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs) in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules.

Results
LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation.

Conclusion
This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN
MeInfoText: associated gene methylation and cancer information from text mining
Authors: Fang Yu-Ching , Huang Hsuan-Cheng , Juan Hsueh-Fen 
Published: January 2008

Abstract

Background
DNA methylation is an important epigenetic modification of the genome. Abnormal DNA methylation may result in silencing of tumor suppressor genes and is common in a variety of human cancer cells. As more epigenetics research is published electronically, it is desirable to extract relevant information from biological literature. To facilitate epigenetics research, we have developed a database called MeInfoText to provide gene methylation information from text mining.

Description
MeInfoText presents comprehensive association information about gene methylation and cancer, the profile of gene methylation among human cancer types and the gene methylation profile of a specific cancer type, based on association mining from large amounts of literature. In addition, MeInfoText offers integrated protein-protein interaction and biological pathway information collected from the Internet. MeInfoText also provides pathway cluster information regarding to a set of genes which may contribute the development of cancer due to aberrant methylation. The extracted evidence with highlighted keywords and the gene names identified from each methylation-related abstract is also retrieved. The database is now available at http://mit.lifescience.ntu.edu.tw/.

Conclusion
MeInfoText is a unique database that provides comprehensive gene methylation and cancer association information. It will complement existing DNA methylation information and will be useful in epigenetics research and the prevention of cancer.
The midgut transcriptome of Lutzomyia longipalpis: comparative analysis of cDNA libraries from sugar-fed, blood-fed, post-digested and Leishmania infantum chagasi-infected sand flies
Authors: Jochim Ryan C , Teixeira Clarissa R , Laughinghouse Andre , Mu Jianbing , Oliveira Fabiano , Gomes Regis B , Elnaiem Dia-Eldin , Valenzuela Jesus G 
Published: January 2008

Abstract

Background
In the life cycle of Leishmania within the alimentary canal of sand flies the parasites have to survive the hostile environment of blood meal digestion, escape the blood bolus and attach to the midgut epithelium before differentiating into the infective metacyclic stages. The molecular interactions between the Leishmania parasites and the gut of the sand fly are poorly understood. In the present work we sequenced five cDNA libraries constructed from midgut tissue from the sand fly Lutzomyia longipalpis and analyzed the transcripts present following sugar feeding, blood feeding and after the blood meal has been processed and excreted, both in the presence and absence of Leishmania infantum chagasi.

Results
Comparative analysis of the transcripts from sugar-fed and blood-fed cDNA libraries resulted in the identification of transcripts differentially expressed during blood feeding. This included upregulated transcripts such as four distinct microvillar-like proteins (LuloMVP1, 2, 4 and 5), two peritrophin like proteins, a trypsin like protein (Lltryp1), two chymotrypsin like proteins (LuloChym1A and 2) and an unknown protein. Downregulated transcripts by blood feeding were a microvillar-like protein (LuloMVP3), a trypsin like protein (Lltryp2) and an astacin-like metalloprotease (LuloAstacin). Furthermore, a comparative analysis between blood-fed and Leishmania infected midgut cDNA libraries resulted in the identification of the transcripts that were differentially expressed due to the presence of Leishmania in the gut of the sand fly. This included down regulated transcripts such as four microvillar-like proteins (LuloMVP1,2, 4 and 5), a Chymotrypsin (LuloChym1A) and a carboxypeptidase (LuloCpepA1), among others. Upregulated midgut transcripts in the presence of Leishmania were a peritrophin like protein (LuloPer1), a trypsin-like protein (Lltryp2) and an unknown protein.

Conclusion
This transcriptome analysis represents the largest set of sequence data reported from a specific sand fly tissue and provides further information of the transcripts present in the sand fly Lutzomyia longipalpis. This analysis provides the detailed information of molecules present in the midgut of this sand fly and the transcripts potentially modulated by blood feeding and by the presence of the Leishmania parasite. More importantly, this analysis suggests that Leishmania infantum chagasi alters the expression profile of certain midgut transcripts in the sand fly during blood meal digestion and that this modulation may be relevant for the survival and establishment of the parasite in the gut of the fly. Moreover, this analysis suggests that these changes may be occurring during the digestion of the blood meal and not afterwards.
Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family
Authors: Joannin Nicolas , Abhiman Saraswathi , Sonnhammer Erik L , Wahlgren Mats 
Published: January 2008

Abstract

Background
Parasitic protozoans possess many multicopy gene families which have central roles in parasite survival and virulence. The number and variability of members of these gene families often make it difficult to predict possible functions of the encoded proteins. The families of extra-cellular proteins that are exposed to a host immune response have been driven via immune selection to become antigenically variant, and thereby avoid immune recognition while maintaining protein function to establish a chronic infection.

Results
We have combined phylogenetic and function shift analyses to study the evolution of the RIFIN proteins, which are antigenically variant and are encoded by the largest multicopy gene family in Plasmodium falciparum. We show that this family can be subdivided into two major groups that we named A- and B-RIFIN proteins. This suggested sub-grouping is supported by a recently published study that showed that, despite the presence of the Plasmodium export (PEXEL) motif in all RIFIN variants, proteins from each group have different cellular localizations during the intraerythrocytic life cycle of the parasite. In the present study we show that function shift analysis, a novel technique to predict functional divergence between sub-groups of a protein family, indicates that RIFINs have undergone neo- or sub-functionalization.

Conclusion
These results question the general trend of clustering large antigenically variant protein groups into homogenous families. Assigning functions to protein families requires their subdivision into meaningful groups such as we have shown for the RIFIN protein family. Using phylogenetic and function shift analysis methods, we identify new directions for the investigation of this broad and complex group of proteins.
Combined effect of CCND1 and COMT polymorphisms and increased breast cancer risk
Authors: Onay Ummiye V , Aaltonen Kirsimari , Briollais Laurent , Knight Julia A , Pabalan Noel , Kilpivaara Outi , Andrulis Irene L , Blomqvist Carl , Nevanlinna Heli , Ozcelik Hilmi 
Published: January 2008

Abstract

Background
Estrogens are crucial tumorigenic hormones, which impact the cell growth and proliferation during breast cancer development. Estrogens are metabolized by a series of enzymes including COMT, which converts catechol estrogens into biologically non-hazardous methoxyestrogens. Several studies have also shown the relationship between estrogen and cell cycle progression through activation of CCND1 transcription.

Methods
In this study, we have investigated the independent and the combined effects of commonly occurring CCND1 (Pro241Pro, A870G) and COMT (Met108/158Val) polymorphisms to breast cancer risk in two independent Caucasian populations from Ontario (1228 breast cancer cases and 719 population controls) and Finland (728 breast cancer cases and 687 population controls). Both COMT and CCND1 polymorphisms have been previously shown to impact on the enzymatic activity of the coded proteins.

Results
Here, we have shown that the high enzymatic activity genotype of CCND1High (AA) was associated with increased breast cancer risk in both the Ontario [OR: 1.3, 95%CI (1.0–1.69)] and the Finland sample [OR: 1.4, 95%CI (1.01–1.84)]. The heterozygous COMTMedium (MetVal) and the high enzymatic activity of COMTHigh (ValVal) genotype was also associated with breast cancer risk in Ontario cases, [OR: 1.3, 95%CI (1.07–1.68)] and [OR: 1.4, 95%CI (1.07–1.81)], respectively. However, there was neither a statistically significant association nor increased trend of breast cancer risk with COMTHigh (ValVal) genotypes in the Finland cases [OR: 1.0, 95%CI (0.73–1.39)]. In the combined analysis, the higher activity alleles of the COMT and CCND1 is associated with increased breast cancer risk in both Ontario [OR: 2.22, 95%CI (1.49–3.28)] and Finland [OR: 1.73, 95%CI (1.08–2.78)] populations studied. The trend test was statistically significant in both the Ontario and Finland populations across the genotypes associated with increasing enzymatic activity.

Conclusion
Using two independent Caucasian populations, we have shown a stronger combined effect of the two commonly occurring CCND1 and COMT genotypes in the context of breast cancer predisposition.
Risk adjustment performance of Charlson and Elixhauser comorbidities in ICD-9 and ICD-10 administrative databases
Authors: Li Bing , Evans Dewey , Faris Peter , Dean Stafford , Quan Hude 
Published: January 2008

Abstract

Background
The performance of the Charlson and Elixhauser comorbidity measures in predicting patient outcomes have been well validated with ICD-9 data but not with ICD-10 data, especially in disease specific patient cohorts. The objective of this study was to assess the performance of these two comorbidity measures in the prediction of in-hospital and 1 year mortality among patients with congestive heart failure (CHF), diabetes, chronic renal failure (CRF), stroke and patients undergoing coronary artery bypass grafting (CABG).

Methods
A Canadian provincial hospital discharge administrative database was used to define 17 Charlson comorbidities and 30 Elixhauser comorbidities. C-statistic values were calculated to evaluate the performance of two measures. One year mortality information was obtained from the provincial Vital Statistics Department.

Results
The absolute difference between ICD-9 and ICD-10 data in C-statistics ranged from 0 to 0.04 across five cohorts for the Charlson and Elixhauser comorbidity measures predicting in-hospital or 1 year mortality. In the models predicting in-hospital mortality using ICD-10 data, the C-statistics ranged from 0.62 (for stroke) – 0.82 (for diabetes) for Charlson measure and 0.62 (for stroke) to 0.83 (for CABG) for Elixhauser measure.

Conclusion
The change in coding algorithms did not influence the performance of either the Charlson or Elixhauser comorbidity measures in the prediction of outcome. Both comorbidity measures were still valid prognostic indicators in the ICD-10 data and had a similar performance in predicting short and long term mortality in the ICD-9 and ICD-10 data.
Correlates of current cigarette smoking among school-going adolescents in Punjab, India: results from the Global Youth Tobacco Survey 2003
Authors: Siziya Seter , Muula Adamson S , Rudatsikira Emmanuel 
Published: January 2008

Abstract

Background
Smoking is a leading cause of morbidity and mortality globally. There is therefore need to identify relevant factors associated with smoking among adolescents in order to better tailor public health interventions aimed at preventing smoking.

Methods
We used data from the Global Youth Tobacco Survey (GYTS) conducted in 2003 in Punjab, India, on 2014 adolescents of whom 58.9% were males. We conducted a weighted logistic regression analysis, adjusting for age and sex, to determine associations between predictor variables and current tobacco smoking status.

Results
A total of 2014 adolescents participated in the survey in 2003, and of these 58.9% were males. Male respondents tended to be older than females (21.2% of males, and 13.1% of females were of age 16 years or above). The percent of males and females in the other age groups were: 23.0% and 28.6% for <14 years, 27.3% and 31.0% for 14 years, and 28.4% and 27.0% for 15 years, respectively. The following factors were positively associated with smoking: adolescents who received pocket money; adolescents who had parents who smoked, chewed or applied tobacco; adolescents who said that boys or girls who smoke or chew tobacco have more friends; adolescents who said that smoking or chewing tobacco makes boys look less attractive; adolescents who said that there is no difference in weight between smokers and non-smokers; adolescents who said that smoking makes one gain weight; and adolescents who had most or all of their closest friends who smoked. The factors that were negatively associated with smoking were: adolescents who said that boys or girls who smoke or chew tobacco have less number of friends; adolescents who said that girls who smoke or chew tobacco are less attractive; and adolescents who had some of their closest friends who smoked.

Conclusion
The observed associations between current smoking on one hand and peer smoking, and perception that boys who smoke are less attractive on the other, deserve further studies. The factors reported in the current study should be considered in the design of public health interventions aimed to reduce adolescent cigarette smoking.
Var transcription profiling of Plasmodium falciparum 3D7: assignment of cytoadherent phenotypes to dominant transcripts
Authors: Gölnitz Uta , Albrecht Letusa , Wunderlich Gerhard 
Published: January 2008

AbstractBackgroundCytoadherence ofPlasmodium falciparum-infected red blood cells is mediated byvargene-encodedP. falciparumerythrocyte membrane protein-1 and host receptor preference depends in most cases on which of the 50–60vargenes per genome is expressed. Enrichment of phenotypically homogenous parasites by panning on receptor expressing cells is fundamental for the identification of the correspondingvartranscript.MethodsP. falciparum3D7 parasites were panned on several transfected CHO-cell lines and theirvartranscripts analysed by i) reverse transcription/PCR/cloning/sequencing using a universal DBLα specific oligonucleotide pair and ii) by reverse transcription followed by quantitative PCR using 57 different oligonucleotide pairs.ResultsEach cytoadherence selected parasite line also adhered to untransfected CHO-745 cells and upregulation of thevargene PFD995/PFD1000c was consistently associated with cytoadherence to all but one CHO cell line. In addition, parasites panned on different CHO cell lines revealed candidatevargenes which reproducibly associated to the respective cytoadherent phenotype. The transcription profile obtained by RT-PCR/cloning/sequencing differed significantly from that of RT-quantitative PCR.ConclusionTransfected CHO cell lines are of limited use for the creation of monophenotypic cytoadherent parasite lines. Nevertheless, 3D7 parasites can be reproducibly selected for the transcription of different determinedvargenes without genetic manipulation. Most importantly,vartranscription analysis by RT-PCR/cloning/sequencing may lead to erroneous interpretation ofvartranscription profiles.
Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile
Authors: Cifola Ingrid , Spinelli Roberta , Beltrame Luca , Peano Clelia , Fasoli Ester , Ferrero Stefano , Bosari Silvano , Signorini Stefano , Rocco Francesco , Perego Roberto , Proserpio Vanessa , Raimondo Francesca , Mocarelli Paolo , Battaglia Cristina 
Published: January 2008

AbstractBackgroundClear cell renal carcinoma (RCC) is the most common and invasive adult renal cancer. For the purpose of identifying RCC biomarkers, we investigated chromosomal regions and individual genes modulated in RCC pathology. We applied the dual strategy of assessing and integrating genomic and transcriptomic data, today considered the most effective approach for understanding genetic mechanisms of cancer and the most sensitive for identifying cancer-related genes.ResultsWe performed the first integrated analysis of DNA and RNA profiles of RCC samples using Affymetrix technology. Using 100K SNP mapping arrays, we assembled a genome-wide map of DNA copy number alterations and LOH areas. We thus confirmed the typical genetic signature of RCC but also identified other amplified regions (e.g. on chr. 4, 11, 12), deleted regions (chr. 1, 9, 22) and LOH areas (chr. 1, 2, 9, 13). Simultaneously, using HG-U133 Plus 2.0 arrays, we identified differentially expressed genes (DEGs) in tumor vs. normal samples. Combining genomic and transcriptomic data, we identified 71 DEGs in aberrant chromosomal regions and observed, in amplified regions, a predominance of up-regulated genes (27 of 37 DEGs) and a trend to clustering. Functional annotation of these genes revealed some already implicated in RCC pathology and other cancers, as well as others that may be novel tumor biomarkers.ConclusionBy combining genomic and transcriptomic profiles from a collection of RCC samples, we identified specific genomic regions with concordant alterations in DNA and RNA profiles and focused on regions with increased DNA copy number. Since the transcriptional modulation of up-regulated genes in amplified regions may be attributed to the genomic alterations characteristic of RCC, these genes may encode novel RCC biomarkers actively involved in tumor initiation and progression and useful in clinical applications.
Low-volume muscular endurance and strength training during 3-week forearm immobilization was effective in preventing functional deterioration
Authors: Matsumura Mika , Ueda Chihoko , Shiroishi Kiyoshi , Esaki Kazuki , Ohmori Fumiko , Yamaguchi Kuniko , Ichimura Shiro , Kurosawa Yuko , Kime Ryotaro , Osada Takuya , Murase Norio , Katsumura Toshihito , Hoshika Akinori , Hamaoka Takafumi 
Published: January 2008

Abstract

Purpose
The purpose of this study was to determine whether endurance and strength hand grip exercises during 3-week upper limb immobilization preserve muscle oxidative capacity, endurance performance and strength.

Methods
Ten healthy adult men underwent non-dominant forearm immobilization by plaster cast for 21 days. Five healthy adult subjects were designated as the immobilization (IMM) group and five were designated as the immobilization + training (IMM+TRN) group. Grip strength, forearm circumference, dynamic handgrip endurance and muscle oxygenation response were measured before and after the 21 day immobilization period. Using near-infrared spectroscopy (NIRS), muscle oxygen consumption recovery (VO2mus) was recorded after a submaximal exercise and the recovery time constant (TcVO2mus) was calculated. Reactive hyperemic oxygenation recovery was evaluated after 5 minutes ischemia. Two training programs were performed by the IMM+TRN group twice a week. One exercise involved a handgrip exercise at 30% maximum voluntary contraction (MVC) at a rate of 1 repetition per 1 second until exhaustion (about 60 seconds). The other involved a handgrip exercise at 70% MVC for 2 seconds with a 2 second rest interval, repeated 10 times (40 seconds).

Results
There was a significant group-by-time interaction between the IMM and IMM+TRN groups in the TcVO2mus (p = 0.032, F = 6.711). A significant group-by-time interaction was observed between the IMM and IMM+TRN groups in the MVC (p = 0.001, F = 30.415) and in grip endurance (p = 0.014, F = 9.791). No significant group-by-time interaction was seen in forearm circumference and reactive hyperemic oxygenation response either in IMM or IMM+TRN group.

Conclusion
The training programs during immobilization period used in this experiment were effective in preventing a decline in muscle oxidative function, endurance and strength.