bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Real-Time PCR and a Microimmunofluorescence Serological Assay for Detection of Chlamydophila pneumoniae Infection in an Outbreak Investigation
Authors: Benitez Alvaro J. , Thurman Kathleen A. , Diaz Maureen H. , Conklin Laura , Kendig Newton E. , Winchell Jonas M. 
Published: October 2011

ABSTRACTWe assessed the performance of a recently validated real-time PCR assay and a commercially available microimmunofluorescence serologic test for the detection ofChlamydophila pneumoniaeinfection during an outbreak. Evaluation of specimens from 137 individuals suggests that real-time PCR holds greater utility as a diagnostic tool for earlyC. pneumoniaedetection.
Multiple Viral Ligands Naturally Presented by Different Class I Molecules in Transporter Antigen Processing-Deficient Vaccinia Virus-Infected Cells
Authors: Lorente Elena , Infantes Susana , Barnea Eilon , Beer Ilan , García Ruth , Lasala Fátima , Jiménez Mercedes , Vilches Carlos , Lemonnier François A. , Admon Arie , López Daniel 
Published: October 2011

ABSTRACTThe transporter associated with antigen processing (TAP) delivers the viral proteolytic products generated by the proteasome in the cytosol to the endoplasmic reticulum lumen that are subsequently recognized by cytotoxic T lymphocytes (CTLs). However, several viral epitopes have been identified in TAP-deficient models. Using mass spectrometry to analyze complex human leukocyte antigen (HLA)-bound peptide pools isolated from large numbers of TAP-deficient vaccinia virus-infected cells, we identified 11 ligands naturally presented by four different HLA-A, HLA-B, and HLA-C class I molecules. Two of these ligands were presented by two different HLA class I alleles, and, as a result, 13 different HLA-peptide complexes were formed simultaneously in the same vaccinia virus-infected cells. In addition to the high-affinity ligands, one low-affinity peptide restricted by each of the HLA-A, HLA-B, and HLA-C class I molecules was identified. Both high- and low-affinity ligands generated long-term memory CTL responses to vaccinia virus in an HLA-A2-transgenic mouse model. The processing and presentation of two vaccinia virus-encoded HLA-A2-restricted antigens took place via proteasomal and nonproteasomal pathways, which were blocked in infected cells with chemical inhibitors specific for different subsets of metalloproteinases. These data have implications for the study of the effectiveness of early empirical vaccination with cowpox virus against smallpox disease.
The TLR4-TRIF Pathway Protects against H5N1 Influenza Virus Infection
Authors: Shinya Kyoko , Ito Mutsumi , Makino Akiko , Tanaka Motoko , Miyake Kensuke , Eisfeld Amie J. , Kawaoka Yoshihiro 
Published: October 2011

ABSTRACT
Prestimulation of the TLR4 pathway with lipopolysaccharide (LPS) protects mice from lethal infection with H5N1 influenza virus. Here, we reveal that the TLR4-TRIF pathway is required for this protective effect by using mice whose TLR4-related molecules were knocked out. Microarray analysis of primary mouse lung culture cells that were LPS pretreated and infected with an H5N1 virus indicated that TLR3 mRNA was upregulated. Primary lung culture cells of TLR3 knockout mice showed no response to LPS pretreatment against H5N1 virus infection, suggesting that TLR3 is also involved in the preventive effect of LPS. Our data suggest that the TLR4-TRIF axis has an important role in stimulating protective innate immunity against H5N1 influenza A virus infection and that TLR3 signaling is involved in this pathway.
Loss of RKIP expression during the carcinogenic evolution of endometrial cancer
Authors: Martinho Olga , Faloppa Carlos Chaves , Neto Cristovam Scapulatempo , Longatto-Filho Adhemar , Baiocchi Glauco , da Cunha Isabela Werneck , Soares Fernando Augusto , Fregnani José Humberto Tavares Guerreiro , Reis Rui Manuel 
Published: October 2011

AimsEndometrial cancer is one of the most common cancers in women worldwide, but there is a lack of diagnostic markers for early detection of these tumours. The raf kinase inhibitory protein (RKIP) negatively regulates the Raf/MEK/ERK pathway, and the downregulation of RKIP is associated with tumour progression and metastasis in several human neoplasms. The aim of this study was to assess the expression levels of RKIP in endometrial cancer and determine whether this expression correlates with clinical outcome in these patients.MethodsTissue microarrays constructed using tissue samples from 209 endometrial adenocarcinomas, 49 endometrial polyps and 48 endometrial hyperplasias were analysed for RKIP expression by immunohistochemistry.ResultsThe authors found that RKIP expression decreases significantly during malignant progression of endometrial cancer; it is highly expressed in non-neoplastic tissues (polyps 79.6%; hyperplasias 87.5%) and expressed at very low levels in endometrioid adenocarcinomas (29.7%). No correlations were observed between RKIP expression, clinicopathological data and survival.ConclusionThis study demonstrated for the first time that RKIP expression is lost during the carcinogenic evolution of endometrial tumours and that the loss of RKIP expression is associated with a malignant phenotype. Functional studies are needed to address the biological role of RKIP downregulation in endometrial cancer.
Hardness of Approximating Flow and Job Shop Scheduling Problems
Authors: Mastrolilli Monaldo , Svensson Ola 
Published: October 2011

We consider several variants of the job shop problem that is a fundamental and classical problem in scheduling. The currently best approximation algorithms have worse than logarithmic performance guarantee, but the only previously known inapproximability result says that it is NP-hard to approximate job shops within a factor less than 5/4. Closing this big approximability gap is a well-known and long-standing open problem.
This article closes many gaps in our understanding of the hardness of this problem and answers several open questions in the literature. It is shown the first nonconstant inapproximability result that almost matches the best-known approximation algorithm for acyclic job shops. The same bounds hold for the general version of flow shops, where jobs are not required to be processed on each machine. Similar inapproximability results are obtained when the objective is to minimize the sum of completion times. It is also shown that the problem with two machines and the preemptive variant with three machines have no PTAS.
The Influence of UGT1A6 Variants and Aspirin Use in a Randomized Trial of Celecoxib for Prevention of Colorectal Adenoma
Authors: Chan Andrew T. , Hsu Meier , Zauber Ann G. , Hawk Ernest T. , Bertagnolli Monica M. 
Published: October 2011

Abstract
Aspirin and celecoxib prevent colorectal adenoma recurrence. Genetic variants in the UGT1A6 enzyme are associated with delayed aspirin metabolism and greater chemopreventive efficacy. We examined the effect of combining aspirin and celecoxib in relation to UGT1A6 T181A and R184S variants among 1,647 patients in the Adenoma Prevention with Celecoxib (APC) trial who were stratified according to the use of low-dose aspirin after removal of adenomas and randomized to placebo, 200-mg twice daily, or 400-mg twice daily celecoxib for 3 years. Patients underwent follow-up colonoscopies at 1 and 3 years to assess on-treatment efficacy. At 5 years, 538 patients underwent a colonoscopy to assess risk of recurrence after treatment was discontinued for at least 1 year. During treatment, the relative risk (RR) of recurrent adenoma was 0.68 [95% confidence interval (CI), 0.59–0.79] for 200-mg twice daily celecoxib and 0.54 (95% CI, 0.46–0.64) for 400-mg twice daily celecoxib compared with placebo. Aspirin use was not independently associated with recurrent adenoma (RR, 0.98, 95% CI, 0.86–1.15). These results did not vary according to UGT1A6 genotype. However, among those with a variant UGT1A6 genotype on aspirin, the RR of adenoma was 1.60 (95% CI, 0.81–3.15) after withdrawal of 200-mg twice daily and 1.98 (95% CI, 1.06–3.70) after withdrawal of 400-mg twice daily celecoxib compared with withdrawal of placebo. In contrast, there was no increased risk associated with discontinuing celecoxib among any other groups. Concurrent use of low-dose aspirin does not influence the efficacy of celecoxib in adenoma prevention. However, discontinuing celecoxib among aspirin-using individuals who initially developed adenoma despite a UGT1A6 variant genotype resulted in rapid reemergence of disease. Cancer Prev Res; 5(1); 61–72. ©2011 AACR.
Mechanism of transfer of functional microRNAs between mouse dendritic cells via exosomes
Authors: Montecalvo Angela , Larregina Adriana T. , Shufesky William J. , Beer Stolz Donna , Sullivan Mara L. G. , Karlsson Jenny M. , Baty Catherine J. , Gibson Gregory A. , Erdos Geza , Wang Zhiliang , Milosevic Jadranka , Tkacheva Olga A. , Divito Sherrie J. , Jordan Rick , Lyons-Weiler James , Watkins Simon C. , Morelli Adrian E. 
Published: October 2011

AbstractDendritic cells (DCs) are the most potent APCs. Whereas immature DCs down-regulate T-cell responses to induce/maintain immunologic tolerance, mature DCs promote immunity. To amplify their functions, DCs communicate with neighboring DCs through soluble mediators, cell-to-cell contact, and vesicle exchange. Transfer of nanovesicles (< 100 nm) derived from the endocytic pathway (termed exosomes) represents a novel mechanism of DC-to-DC communication. The facts that exosomes contain exosome-shuttle miRNAs and DC functions can be regulated by exogenous miRNAs, suggest that DC-to-DC interactions could be mediated through exosome-shuttle miRNAs, a hypothesis that remains to be tested. Importantly, the mechanism of transfer of exosome-shuttle miRNAs from the exosome lumen to the cytosol of target cells is unknown. Here, we demonstrate that DCs release exosomes with different miRNAs depending on the maturation of the DCs. By visualizing spontaneous transfer of exosomes between DCs, we demonstrate that exosomes fused with the target DCs, the latter followed by release of the exosome content into the DC cytosol. Importantly, exosome-shuttle miRNAs are functional, because they repress target mRNAs of acceptor DCs. Our findings unveil a mechanism of transfer of exosome-shuttle miRNAs between DCs and its role as a means of communication and posttranscriptional regulation between DCs.
Snat: a SNP annotation tool for bovine by integrating various sources of genomic information
Authors: Jiang Jicai , Jiang Li , Zhou Bin , Fu Weixuan , Liu Jian-Feng , Zhang Qin 
Published: October 2011

Abstract

Background
Most recently, with maturing of bovine genome sequencing and high throughput SNP genotyping technologies, a large number of significant SNPs associated with economic important traits can be identified by genome-wide association studies (GWAS). To further determine true association findings in GWAS, the common strategy is to sift out most promising SNPs for follow-up replication studies. Hence it is crucial to explore the functional significance of the candidate SNPs in order to screen and select the potential functional ones. To systematically prioritize these statistically significant SNPs and facilitate follow-up replication studies, we developed a bovine SNP annotation tool (Snat) based on a web interface.

Results
With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO), KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA). Snat provides two different applications, including a CGI-based web utility and a command-line version, to access the integrated database, target any single nucleotide loci of interest and perform multi-level functional annotations. For further validation of the practical significance of our study, SNPs involved in two commercial bovine SNP chips, i.e., the Affymetrix Bovine 10K chip array and the Illumina 50K chip array, have been annotated by Snat, and the corresponding outputs can be directly downloaded from Snat website. Furthermore, a real dataset involving 20 identified SNPs associated with milk yield in our recent GWAS was employed to demonstrate the practical significance of Snat.

Conclusions
To our best knowledge, Snat is one of first tools focusing on SNP annotation for livestock. Snat confers researchers with a convenient and powerful platform to aid functional analyses and accurate evaluation on genes/variants related to SNPs, and facilitates follow-up replication studies in the post-GWAS era.
Protein and lipid MALDI profiles classify breast cancers according to the intrinsic subtype
Authors: Kang Han Sung , Lee Seok Cheol , Park Young Seung , Jeon Young Eun , Lee Jeong Hwa , Jung So-Youn , Park In Hae , Jang Seok Hoon , Park Hye Min , Yoo Chong Woo , Park Seok Hee , Han Sang Yun , Kim Kwang Pyo , Kim Young Hwan , Ro Jungsil , Kim Hark Kyun 
Published: October 2011

Abstract

Background
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of common solid tumors. Using recently developed MALDI matrices for lipid profiling, we evaluated whether direct tissue MALDI MS analysis on proteins and lipids may classify human breast cancer samples according to the intrinsic subtype.

Methods
Thirty-four pairs of frozen, resected breast cancer and adjacent normal tissue samples were analyzed using histology-directed, MALDI MS analysis. Sinapinic acid and 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells to identify lipid profiles, and mass spectra were acquired using a MALDI-time of flight instrument.

Results
Protein and lipid profiles distinguish cancer from adjacent normal tissue samples with the median prediction accuracy of 94.1%. Luminal, HER2+, and triple-negative tumors demonstrated different protein and lipid profiles, as evidenced by permutation P values less than 0.01 for 0.632+ bootstrap cross-validated misclassification rates with all classifiers tested. Discriminatory proteins and lipids were useful for classifying tumors according to the intrinsic subtype with median prediction accuracies of 80.0-81.3% in random test sets.

Conclusions
Protein and lipid profiles accurately distinguish tumor from adjacent normal tissue and classify breast cancers according to the intrinsic subtype.
Dynamic Behavior of Sand/Rubber Mixtures. Part I: Effect of Rubber Content and Duration of Confinement on Small-Strain Shear Modulus and Damping Ratio
Authors: Anastasiadis Anastasios , Senetakis Kostas , Pitilakis Kyriazis , Gargala Chrysanthi , Karakasi Iphigeneia 
Published: October 2011

Abstract
The paper examines the small-strain dynamic properties of mixtures composed of sandy soils with recycled tire rubber. For this purpose, the experimental results stemming from a torsional resonant column testing program on twenty four [24] saturated and dry specimens are analyzed. The percentages of rubber used range between 0 and 35 % by mixture weight. GO values increase whereas DTO values decrease systematically as the content of rubber decreases and the mean confining pressure increases. Based on the experimental results we propose an analytical relationship for the estimation of GO, which is expressed in terms of an equivalent void ratio that considers the volume of rubber solids as part of the total volume of voids, along with an analytical relationship for the estimation of DTO. Finally, the effect of the specimen’s size and the duration of confinement on the initial shear modulus and damping ratio of the mixtures are also discussed.
The Relationship between Body Mass Index, the Use of Second-Generation Antipsychotics, and Dental Caries among Hospitalized Patients with Schizophrenia
Authors: Chu Kuan-Yu , Yang Nan-Ping , Chou Pesus , Chi Lin-Yang , Chiu Hsien-Jane 
Published: October 2011

Objective: Weight gain is common in schizophrenia due to use of the second-generation antipsychotic medicines (SGAs). Studies have also shown that body mass index (BMI) and the side effect of SGAs, such as anticholinergic activity, are related to the risk of dental caries. This study aims to investigate the relationship between BMI, the use of the SGAs, and the decayed, missing, and filled tooth index (DMFT) among hospitalized patients with schizophrenia. Methods: A cross-sectional survey of oral health was conducted in a psychiatric long-term care hospital in Taiwan in 2006. A total of 878 schizophrenic inpatients participated in this survey. The DMFT index was used to assess dental caries, the use of SGAs of subjects were recorded, and the BMI classification was done in accordance with Asian standard scales. Multiple regression models were used to measure the effects of SGAs or BMI on the DMFT index in each subject. Results: Among the subjects with schizophrenia, DMFT is significantly related to independent variables such as age, length of stay, BMI, education, marital status, and grade of disability. Consequent multiple linear regression showed that being underweight (β = 0.07, p = 0.041) and age were the most significant factors that influence the DMFT score. Conclusions: We found that the use of SGAs was not significantly associated with the DMFT index. After adjusting for age, being underweight is a significant factor associated with the increased risk of dental caries in hospitalized patients with schizophrenia. Psychologists and dentists should pay more attention to the relation between BMI and dental caries in this population.
Harmonicity of vector fields on four-dimensional generalized symmetric spaces
Authors: Calvaruso Giovanni 
Published: October 2011

Abstract
Let (M = G/H;g)denote a four-dimensional pseudo-Riemannian generalized symmetric space and g = m + h the corresponding decomposition of the Lie algebra g of G. We completely determine the harmonicity properties of vector fields belonging to m. In some cases, all these vector fields are critical points for the energy functional restricted to vector fields. Vector fields defining harmonic maps are also classified, and the energy of these vector fields is explicitly calculated.
Detection of the near surface structure through a multidisciplinary geophysical approach
Authors: Kokinou Eleni , Sarris Apostolos 
Published: October 2011

AbstractThe present survey aimed to image the subsurface structure, including karstic voids, and to evaluate the extent of the heterogeneities that can result in potentially dangerous collapse of road segments overlying these features. A multidisciplinary geophysical approach (seismic refraction, frequency domain electromagnetic and ground penetrating radar) in combination with a detailed geological survey indicated the presence of tectonic faults as well as velocity and conductivity anomalies along an old road within the area of Akrotiri at Chania (Crete). Due to the presence of subsurface fuel pipes, perpendicular to the direction of the road, 2D resistivity imaging was excluded from the applied geophysical methods.Interpretation of the geophysical data revealed that the section of the road investigated overlies prominent voids attributed mostly to karst features. The conductivity and velocity anomalies are interpreted to indicate an area where the host limestone rock has been downthrown by faulting and associated karstification. The continuation of this fault zone was observed in the slope of the road during later excavations. Interpretation, using geographic information systems (GIS) to integrate data, allowed these controls and relationships to be understood and monitored. The above methodology was proved successful for areas where the application of resistivity method is not possible.
Populations et tendances démographiques des pays européens (1980-2010)
Authors: Avdeev Alexandre , Eremenko Tatiana , Festy Patrick , Gaymu Joëlle , Le Bouteillec Nathalie , Springer Sabine 
Published: October 2011

Résumé	Au cours des trente dernières années, la croissance de la population européenne s’est effectuée à un rythme de plus en plus ralenti. L’excédent naturel des naissances sur les décès n’a cessé de reculer, et l’excédent migratoire représente désormais un apport substantiel, parfois décisif pour le maintien d’une croissance positive. Cette tendance générale est largement partagée par la plupart des pays, à travers un mouvement qui combine recul de la fécondité, progression des espérances de vie et solde migratoire positif en augmentation. À un niveau plus fin d’analyse, on observe une évolution semblable des formes familiales vers moins de mariages et davantage de situations de fait, et un même recul des causes majeures de mortalité, cancéreuses ou cardiovasculaires. Pourtant, il y a moins convergence de ces tendances à travers l’espace européen que répétition à quelques années d’intervalle de ces transformations, les écarts se maintenant entre les pays ou les régions du continent. L’avenir de la population européenne dépendra largement du niveau de la fécondité future?: croissance ou décroissance selon qu’elle sera élevée ou faible, quasi-stabilité si elle reste moyenne. Quelle que soit la fécondité des quarante ans à venir, le vieillissement de la population européenne est inéluctable, y compris en cas de poursuite de l’immigration, et des différences notables vont perdurer à travers l’Europe.
Penser l'informel
Authors: Geoffroy François 
Published: October 2011

Résumé Le présent travail vise à expliquer la notion d’informel au sein des organisations en s’appuyant sur deux théories complémentaires : la théorie des organisations et la théorie des institutions. Malgré ces apports incontestables, l’informel reste une notion inévitablement attachée à une autre telle que l’organisation et l’institution. Peu de recherches considèrent l’informel comme objet théorique à part entière. Ainsi, nous essayons de théoriser l’informel pour comprendre cette notion tant discutée et discutable. Nous concluons que l’informel, du fait de son importance et de sa transdisciplinarité, doit être appréhendé comme un méta-concept dans l’étude des organisations.
Sur la nature interstitielle de l'agir
Authors: Bibard Laurent 
Published: October 2011

Résumé L’action est actuellement structurellement empêchée au sein des organisations : pris dans les injonctions contradictoires spécifiques à la tension entre court et long terme, les acteurs doivent se frayer un chemin entre des impossibilités de plus en plus nombreuses. Outre une action d’ordre politique, cette évolution de la vie économique demande de penser les raisons de la possibilité de ces contradictions. L’on montre que c’est parce que le « sujet » de l’action est structurellement double - et féminin et masculin – qu’il est à la fois susceptible d’être saisi dans de douloureuses contradictions et de les dépasser.