bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occupational Exposure to High Molecular Weight Allergens and Lymphoma Risk Among Italian Adults
Authors: Mirabelli Maria C. , Zock Jan-Paul , D'Errico Angelo , Kogevinas Manolis , de Sanjosé Silvia , Miligi Lucia , Seniori Costantini Adele , Vineis Paolo 
Published: October 2009

AbstractObjectives. Exposure to high molecular weight (HMW) allergens that provoke immune reactivity through an IgE-mediated pathway has been associated with a decreased risk of B-cell lymphoma. The present analysis was conducted to assess the associations between occupational exposure to specific HMW allergens and the risk of B-cell, T-cell, and Hodgkin's lymphomas.Methods. We analyzed data from 2,290 incident lymphoma cases and 1,771 population-based controls enrolled in a multicenter study of hematolymphopoietic malignancies conducted in Italy between 1991 and 1993. All cases were histologically or cytologically confirmed. Controls were frequency-matched to cases based on age, sex, and study center. An industrial hygienist evaluated HMW occupational exposure classifications after an asthma-specific job exposure matrix was applied to participants' job histories. Unconditional logistic regression was used to assess associations between occupational exposures that occurred ≥10 years before the date of lymphoma diagnosis and B-cell, T-cell, and Hodgkin's lymphomas.Results. Ten percent of cases and 11% of controls were occupationally exposed to HMW allergens. Exposed individuals had a decreased risk for all lymphomas combined (odds ratio, 0.78; 95% confidence interval, 0.63-0.97), particularly for B-cell lymphomas (odds ratio, 0.75; 95% confidence interval, 0.59-0.94). The decreased risks for all lymphomas were also observed when HMW allergen exposure was limited to animal and latex allergens.Conclusions. These findings support the hypothesis that occupational exposure to immunologically active HMW allergens is inversely associated with the risk for lymphoma. The effect of exposure to specific allergens warrants further assessment. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2650–4)
Vitamin D Receptor Expression Is Associated with PIK3CA and KRAS Mutations in Colorectal Cancer
Authors: Kure Shoko , Nosho Katsuhiko , Baba Yoshifumi , Irahara Natsumi , Shima Kaori , Ng Kimmie , Meyerhardt Jeffrey A. , Giovannucci Edward L. , Fuchs Charles S. , Ogino Shuji 
Published: October 2009

Abstract
Vitamin D is associated with decreased risks of various cancers, including colon cancer. The vitamin D receptor (VDR) is a transcription factor, which plays an important role in cellular differentiation and inhibition of proliferation. A link between VDR and the RAS–mitogen-activated protein kinase (MAPK) or phosphatidylinositol 3-kinase (PI3K)–AKT pathway has been suggested. However, the prognostic role of VDR expression or its relationship with PIK3CA or KRAS mutation remains uncertain. Among 619 colorectal cancers in two prospective cohort studies, 233 (38%) tumors showed VDR overexpression by immunohistochemistry. We analyzed for PIK3CA and KRAS mutations and LINE-1 methylation by Pyrosequencing, microsatellite instability (MSI), and DNA methylation (epigenetic changes) in eight CpG island methylator phenotype (CIMP)–specific promoters [CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1] by MethyLight (real-time PCR). VDR overexpression was significantly associated with KRAS mutation (odds ratio, 1.55; 95% confidence interval, 1.11-2.16) and PIK3CA mutation (odds ratio, 2.17; 95% confidence interval, 1.36-3.47), both of which persisted in multivariate logistic regression analysis. VDR was not independently associated with body mass index, family history of colorectal cancer, tumor location (colon versus rectum), stage, tumor grade, signet ring cells, CIMP, MSI, LINE-1 hypomethylation, BRAF, p53, p21, β-catenin, or cyclooxygenase-2. VDR expression was not significantly related with patient survival, prognosis, or clinical outcome. In conclusion, VDR overexpression in colorectal cancer is independently associated with PIK3CA and KRAS mutations. Our data support potential interactions between the VDR, RAS–MAPK and PI3K–AKT pathways, and possible influence by KRAS or PIK3CA mutation on therapy or chemoprevention targeting VDR. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2765–72)
CYP19A1 Genetic Variation in Relation to Prostate Cancer Risk and Circulating Sex Hormone Concentrations in Men from the Breast and Prostate Cancer Cohort Consortium
Authors: Travis Ruth C. , Schumacher Fredrick , Hirschhorn Joel N. , Kraft Peter , Allen Naomi E. , Albanes Demetrius , Berglund Goran , Berndt Sonja I. , Boeing Heiner , Bueno-de-Mesquita H. Bas , Calle Eugenia E. , Chanock Stephen , Dunning Alison M. , Hayes Richard , Feigelson Heather Spencer , Gaziano J. Michael , Giovannucci Edward , Haiman Christopher A. , Henderson Brian E. , Kaaks Rudolf , Kolonel Laurence N. , Ma Jing , Rodriguez Laudina , Riboli Elio , Stampfer Meir , Stram Daniel O. , Thun Michael J. , Tjønneland Anne , Trichopoulos Dimitrios , Vineis Paolo , Virtamo Jarmo , Le Marchand Loïc , Hunter David J. 
Published: October 2009

Abstract
Sex hormones, particularly the androgens, are important for the growth of the prostate gland and have been implicated in prostate cancer carcinogenesis, yet the determinants of endogenous steroid hormone levels remain poorly understood. Twin studies suggest a heritable component for circulating concentrations of sex hormones, although epidemiologic evidence linking steroid hormone gene variants to prostate cancer is limited. Here we report on findings from a comprehensive study of genetic variation at the CYP19A1 locus in relation to prostate cancer risk and to circulating steroid hormone concentrations in men by the Breast and Prostate Cancer Cohort Consortium (BPC3), a large collaborative prospective study. The BPC3 systematically characterized variation in CYP19A1 by targeted resequencing and dense genotyping; selected haplotype-tagging single nucleotide polymorphisms (htSNP) that efficiently predict common variants in U.S. and European whites, Latinos, Japanese Americans, and Native Hawaiians; and genotyped these htSNPs in 8,166 prostate cancer cases and 9,079 study-, age-, and ethnicity-matched controls. CYP19A1 htSNPs, two common missense variants and common haplotypes were not significantly associated with risk of prostate cancer. However, several htSNPs in linkage disequilibrium blocks 3 and 4 were significantly associated with a 5% to 10% difference in estradiol concentrations in men [association per copy of the two-SNP haplotype rs749292-rs727479 (A-A) versus noncarriers; P = 1 × 10-5], and with inverse, although less marked changes, in free testosterone concentrations. These results suggest that although germline variation in CYP19A1 characterized by the htSNPs produces measurable differences in sex hormone concentrations in men, they do not substantially influence risk of prostate cancer. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2734–44)
Associations between Smoking, Alcohol Consumption, and Colorectal Cancer, Overall and by Tumor Microsatellite Instability Status
Authors: Poynter Jenny N. , Haile Robert W. , Siegmund Kimberly D. , Campbell Peter T. , Figueiredo Jane C. , Limburg Paul , Young Joanne , Le Marchand Loic , Potter John D. , Cotterchio Michelle , Casey Graham , Hopper John L. , Jenkins Mark A. , Thibodeau Stephen N. , Newcomb Polly A. , Baron John A. ,   for the Colon Cancer Family Registry
Published: October 2009

Abstract
Introduction: Both smoking and alcohol consumption have been associated with modestly increased risks of colorectal cancer (CRC). Reports have suggested that these associations may differ by tumor molecular subtype, with stronger associations for microsatellite unstable (MSI-H) tumors.
Methods: We used a population-based case-unaffected sibling design including 2,248 sibships (2,253 cases; 4,486 siblings) recruited to the Colon Cancer Family Registry to evaluate the association between smoking, alcohol consumption, and CRC. Associations were assessed using conditional logistic regression, treating sibship as the matching factor.
Results: Although there were no statistically significant associations between any smoking variable and CRC overall, smoking did confer an increased risk of certain types of CRC. We observed an association between pack-years of smoking and rectal cancer [odds ratio (OR), 1.85; 95% confidence interval (CI), 1.23-2.79 for &gt;40 pack-years versus nonsmokers; Ptrend = 0.03], and there was an increased risk of MSI-H CRC with increasing duration of smoking (OR, 1.94; 95% CI, 1.09-3.46 for &gt;30 years of smoking versus nonsmokers). Alcohol intake was associated with a modest increase in risk for CRC overall (OR, 1.21; 95% CI, 1.03-1.44 for 12+ drinks per week versus nondrinkers), with more marked increases in risk for MSI-L CRC (OR, 1.85; 95% CI, 1.06-3.24) and rectal cancer (OR, 1.48; 95% CI, 1.08-2.02).
Conclusions: We found associations between cigarette smoking and increased risks of rectal cancer and MSI-H CRC. Alcohol intake was associated with increased risks of rectal cancer and MSI-L CRC. These results highlight the importance of considering tumor phenotype in studies of risk factors for CRC. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2745–50)
Reduced Prediagnostic 25-Hydroxyvitamin D Levels in Women with Breast Cancer: A Nested Case-Control Study
Authors: Rejnmark Lars , Tietze Anna , Vestergaard Peter , Buhl Line , Lehbrink Melsene , Heickendorff Lene , Mosekilde Leif 
Published: October 2009

Abstract
Vitamin D status may affect risk of cancer. In a cross-sectional study with a nested case-control analysis, we determined whether risk of breast cancer is associated with prediagnostic plasma 25-hydroxyvitamin D (25OHD) levels and the effects of lifestyle characteristics known to influence vitamin D status on risk of breast cancer. We studied women without a prior history of breast cancer referred to a diagnostic mammography examination (n = 2,465). Cases were women diagnosed with an incident breast cancer (n = 142). Controls were women not diagnosed with a breast cancer matched to cases on age, menopausal status, and time of year of blood sampling (n = 420). Characteristics of cases and controls were assessed by a self-administrated questionnaire. Blood samples were collected prior to the diagnostic mammography examination. Cases had lower plasma 25OHD levels than controls. Compared with the lowest tertile of 25OHD levels, risk of breast cancer was significantly reduced among women in the highest tertile (relative risk, 0.52; 95% confidence interval, 0.32-0.85). Risk estimates were similar in women with an estrogen receptor–positive and estrogen receptor–negative breast cancer. Use of vitamin D supplements, sunbathing frequency, and fish intake was associated with 25OHD levels, but did not affect the risk of breast cancer. Accordingly, risk of breast cancer was inversely associated with 25OHD levels. Randomized controlled trials are warranted in order to assess whether a causal relationship exists. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2655–60)
An unstable social environment affects sex ratio in guinea pigs: an adaptive maternal effect?
Authors: Von Engelhardt Nikolaus , Kaiser Sylvia , Sachser Norbert , Kemme Kristina , Groothuis Ton , Wewers Dirk 
Published: October 2009

AbstractEvolutionary theory suggests that offspring sex should be adjusted to environmental conditions in order to maximize future reproductive success. In several animal taxa environmental factors indeed affect the secondary sex ratio. In humans, changes in the sex ratio at birth have been associated with population stressors like war, environmental disasters or economic strife during pregnancy. Here we compared litter sex ratios of female guinea pigs, exposed experimentally to a stable and an unstable social environment. In the latter group composition was changed every three days. Under unstable social conditions the sex ratio was significantly more biased towards daughters than in the stable social situation. This finding was consistent among four independent experiments, conducted independently from each other. Life expectancy can be dramatically reduced under conditions of social instability. Hence mothers in such conditions should bias their investment towards the sex that reaches sexual maturity first, which is the female sex in this species. Thus, to shift the offspring sex ratio towards more daughters under conditions of social instability may represent a maternal strategy to maximize future reproductive success.
The Synergistic Relationship between Soil Moisture and the Low-Level Jet and Its Role on the Prestorm Environment in the Southern Great Plains
Authors: Frye John D. , Mote Thomas L. 
Published: October 2009

Abstract
Changes in low-level moisture alter the convective parameters [e.g., convective available potential energy (CAPE), lifted index (LI), and convective inhibition (CIN)] as a result of alterations in the latent and sensible heat energy exchange. Two sources for low-level moisture exist in the southern Great Plains: 1) moisture advection by the low-level jet (LLJ) from the Gulf of Mexico and 2) evaporation and transpiration from the soils and vegetation in the region. The primary focus of this study is to examine the spatial distribution of soil moisture on a daily basis and to determine the effect it has on the convective parameters. The secondary objective is to investigate how the relationship between soil moisture and convective parameters is altered by the presence of an LLJ. The soil moisture data were obtained through newly developed procedures and advances in technology aboard the Tropical Rainfall Measuring Mission Microwave Imager. The convective parameter data were obtained through the North American Regional Reanalysis dataset. The study examined seven warm seasons (April–September) from 1998 to 2004 and found that the convective environment is more unstable (CAPE &gt; 900 J kg−1, LI &lt; −2°C) but more strongly capped (CIN &gt; 70 J kg−1) on days with an LLJ present. Spearman’s rank correlation analysis showed a less stable atmosphere with increased soil moisture, after soil moisture reached 5%, on most days. Additional analysis determined that on all synoptic-type days the probability of reaching various thresholds of convective intensity increased as soil moisture values increased. The probabilities were even greater on days with an LLJ present than on the days without an LLJ present. An examination of four days representing each synoptic-type day indicates that on the daily scale the intensity of the convective environment is closely related to the high soil moisture and the presence of an LLJ.
Oxidative modification of von Willebrand factor by neutrophil oxidants inhibits its cleavage by ADAMTS13
Authors: Chen Junmei , Fu Xiaoyun , Wang Yi , Ling Minhua , McMullen Brad , Kulman John , Chung Dominic W. , López José A. 
Published: October 2009

AbstractElevated plasma von Willebrand factor (VWF) and low ADAMTS13 activity have been reported in several inflammatory states, including sepsis and acute respiratory distress syndrome. One hallmark of inflammation is neutrophil activation and production of reactive oxygen species, including superoxide radical, hydrogen peroxide, and hypochlorous acid (HOCl). HOCl is produced from hydrogen peroxide and chloride ions through the action of myeloperoxidase. HOCl can oxidize methionine to methionine sulfoxide and tyrosine to chlorotyrosine. This is of interest because the ADAMTS13 cleavage site in VWF, the Tyr1605-Met1606 peptide bond, contains both oxidation-prone residues. We hypothesized that HOCl would oxidize either or both of these residues and possibly inhibit ADAMTS13-mediated cleavage. We therefore treated ADAMTS13 substrates with HOCl and examined their oxidative modification by mass spectrometry. Met1606 was oxidized to the sulfoxide in a concentration-dependent manner, with complete oxidation at 75μM HOCl, whereas only a miniscule percentage of Tyr1605 was converted to chlorotyrosine. The oxidized substrates were cleaved much more slowly by ADAMTS13 than the nonoxidized substrates. A similar result was obtained with multimeric VWF. Taken together, these findings indicate that reactive oxygen species released by activated neutrophils have a prothrombotic effect, mediated in part by inhibition of VWF cleavage by ADAMTS13.
Induction of B-cell development in adult mice reveals the ability of bone marrow to produce B-1a cells
Authors: Düber Sandra , Hafner Martin , Krey Martina , Lienenklaus Stefan , Roy Bishnudeo , Hobeika Elias , Reth Michael , Buch Thorsten , Waisman Ari , Kretschmer Karsten , Weiss Siegfried 
Published: October 2009

AbstractTo study B-cell development from bone marrow (BM), we generated recombination-activating gene 1 (Rag1)–targeted mice lacking mature lymphocytes. B-cell development can be induced in such mice by B cell–specific restoration of a functional Rag1 transcription unit. Follicular and marginal zone B cells populated the spleen when Rag1 expression was permitted. Notably, the peritoneal cavity was dominated by bona fide B-1a cells, as judged by surface markers and functional properties. These BM-derived B-1a cells exhibited a polyclonal VDJ repertoire with substantial N nucleotide insertions. Nevertheless, physiologic frequencies of phosphatidylcholine-specific B cells were detected. Importantly, the BM of young and 5-month-old mice was indistinguishable with regard to the potential to generate B-1a cells.
Primary radiotherapy showed favorable outcome in treating extranodal nasal-type NK/T-cell lymphoma in children and adolescents
Authors: Wang Zhao-Yang , Li Ye-Xiong , Wang Wei-Hu , Jin Jing , Wang Hua , Song Yong-Wen , Liu Qing-Feng , Wang Shu-Lian , Liu Yue-Ping , Qi Shu-Nan , Fang Hui , Liu Xin-Fan , Yu Zi-Hao 
Published: October 2009

Abstract
Extranodal nasal-type natural killer (NK)/T-cell lymphoma is rarely observed in children and adolescents. We aim to investigate the clinical features, prognosis, and treatment outcomes in these patients. Thirty-seven patients were reviewed. There were 19, 14, 2, and 2 patients with stage I, stage II, stage III, and stage IV diseases, respectively. Among the patients with stage I and II disease, 19 patients received initial radiotherapy with or without chemotherapy, and 14 patients received chemotherapy followed by radiotherapy. The 4 patients with stage III and IV disease received primary chemotherapy and radiation of the primary tumor. Children and adolescents with extranodal nasal-type NK/T-cell lymphoma usually presented with early-stage disease, high frequency of B symptoms, good performance, low-risk age-adjusted international prognostic index, and chemoresistance. The complete response rate after initial radiotherapy was 73.7%, which was significantly higher than the response rate after initial chemotherapy (16.7%; P = .002). The 5-year overall survival (OS) and progression-free survival (PFS) rates for all the patients were 77.0% and 68.5%, respectively. The corresponding OS and PFS rates for patients with stage I and II disease were 77.6% and 72.3%, respectively. Children and adolescents with early-stage extranodal nasal-type NK/T-cell lymphoma treated with primary radiotherapy had a favorable prognosis.
Riboswitch Detection Using Profile Hidden Markov Models
Authors: Singh Payal , Bandyopadhyay Pradipta , Bhattacharya Sudha , Krishnamachari A , Sengupta Supratim 
Published: October 2009

Abstract

Background
Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.

Results
Our method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.

Conclusion
Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
Authors: Li Zhiguang , Su Zhenqiang , Wen Zhining , Shi Leming , Chen Tao 
Published: October 2009

Abstract

Background
Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platforms. Both high and low consistencies were demonstrated across different platforms in terms of genes with significantly differential expression. Array studies for gene expression are used to explore biological causes and effects. Therefore, consistency should eventually be evaluated in a biological setting to reveal the functional differences between the examined samples, not just a list of differentially expressed genes (DEG). In this study, we investigated whether different platforms had a high consistency from the biologically functional perspective.

Results
DEG data without filtering the different probes in microarrays from different platforms generated from kidney samples of rats treated with the kidney carcinogen, aristolochic acid, in five test sites using microarrays from Affymetrix, Applied Biosystems, Agilent, and GE health platforms (two sites using Affymetrix for intra-platform comparison) were input into the Ingenuity Pathway Analysis (IPA) system for functional analysis. The functions of the DEG lists determined by IPA were compared across the four different platforms and two test sites for Affymetrix platform. Analysis results showed that there is a very high level of consistency between the two test sites using the same platform or among different platforms. The top functions determined by the different platforms were very similar and reflected carcinogenicity and toxicity of aristolochic acid in the rat kidney.

Conclusion
Our results demonstrate that highly consistent biological information can be generated from different microarray platforms.