bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and application of a zebrafish array comparative genomic hybridization platform
Authors: Freeman Jennifer L. , Ceol Craig , Feng Hui , Langenau David M. , Belair Cassandra , Stern Howard M. , Song Anhua , Paw Barry H. , Look A. Thomas , Zhou Yi , Zon Leonard I. , Lee Charles 
Published: October 2008

AbstractThe zebrafish is emerging as a prominent model system for studying the genetics of human development and disease. Genetic alterations that underlie each mutant model can exist in the form of single base changes, balanced chromosomal rearrangements, or genetic imbalances. To detect genetic imbalances in an unbiased genome‐wide fashion, array comparative genomic hybridization (CGH) can be used. We have developed a 5‐Mb resolution array CGH platform specifically for the zebrafish. This platform contains 286 bacterial artificial chromosome (BAC) clones, enriched for orthologous sequences of human oncogenes and tumor suppressor genes. Each BAC clone has been end‐sequenced and cytogenetically assigned to a specific location within the zebrafish genome, allowing for ease of integration of array CGH data with the current version of the genome assembly. This platform has been applied to three zebrafish cancer models. Significant genomic imbalances were detected in each model, identifying different regions that may potentially play a role in tumorigenesis. Hence, this platform should be a useful resource for genetic dissection of additional zebrafish developmental and disease models as well as a benchmark for future array CGH platform development. © 2008 Wiley‐Liss, Inc.
ERK5 is a target for gene amplification at 17p11 and promotes cell growth in hepatocellular carcinoma by regulating mitotic entry
Authors: Zen Keika , Yasui Kohichiroh , Nakajima Tomoaki , Zen Yoh , Zen Kan , Gen Yasuyuki , Mitsuyoshi Hironori , Minami Masahito , Mitsufuji Shoji , Tanaka Shinji , Itoh Yoshito , Nakanuma Yasuni , Taniwaki Masafumi , Arii Shigeki , Okanoue Takeshi , Yoshikawa Toshikazu 
Published: October 2008

AbstractUsing high‐density oligonucleotide microarrays, we investigated DNA copy‐number aberrations in cell lines derived from hepatocellular carcinomas (HCCs) and detected a novel amplification at 17p11. To identify the target of amplification at 17p11, we defined the extent of the amplicon and examined HCC cell lines for expression of all seven genes in the 750‐kb commonly amplified region. Mitogen‐activated protein kinase (MAPK) 7, which encodes extracellular‐regulated protein kinase (ERK) 5, was overexpressed in cell lines in which the gene was amplified. An increase in MAPK7 copy number was detected in 35 of 66 primary HCC tumors. Downregulation of MAPK7 by small interfering RNA suppressed the growth of SNU449 cells, the HCC cell line with the greatest amplification and overexpression of MAPK7. ERK5, phosphorylated during the G2/M phases of the cell cycle, regulated entry into mitosis in SNU449 cells. In conclusion, our results suggest that MAPK7 is likely the target of 17p11 amplification and that the ERK5 protein product of MAPK7 promotes the growth of HCC cells by regulating mitotic entry. © 2008 Wiley‐Liss, Inc.
The galanin signaling cascade is a candidate pathway regulating oncogenesis in human squamous cell carcinoma
Authors: Sugimoto Takashi , Seki Naohiko , Shimizu Satoya , Kikkawa Naoko , Tsukada Jun , Shimada Hideaki , Sasaki Keita , Hanazawa Toyoyuki , Okamoto Yoshitaka , Hata Akira 
Published: October 2008

AbstractTo identify putative biomarkers in squamous cell carcinoma (SCC), a survey of parallel chromosomal alterations and gene expression studies in 10 SCC cell lines were performed using array–comparative genomic hybridization (CGH) and oligo‐microarray techniques. The most frequent changes were gains of 11q13.1‐13.3 and losses of 18q12.1‐23 in SCC. Furthermore, the expression levels of the sets of genes at both these loci in SCC were measured using microarray analysis. By combining the array‐CGH with the microarray data, 10 genes at 11q13.1‐13.3 and 6 genes at 18q12.1‐23 whose expression correlated with chromosomal alterations were identified. To verify the expression levels of the identified genes, we used expression analysis data derived from our earlier study of clinical specimens. In clinical samples, six genes (GAL, GSTP1, MRPL11, MRPL21, SF3B2, and YIF1A) at 11q13.1‐13.3 and one gene (GALR1) at 18q23 showed a significant difference between normal and tumor samples. GAL, coding for the neuropeptide galanin, and GALR1, a galanin receptor, were identified as candidate genes of oncogenesis in SCC. The expression levels of GAL, GALR1, GALR2, and GALR3 were confirmed by real‐time PCR. The expression ratio between GAL and GALR1 showed a significant negative correlation. GALR1 is a G‐protein‐coupled receptor that activates GTP‐binding proteins to trigger signaling cascades such as the mitogen‐activated protein kinase pathway, and is a well‐established mitogenic pathway. This further supports the hypothesis that the genes involved in the GAL signaling cascade are candidates for regulation of oncogenesis in SCC. © 2008 Wiley‐Liss, Inc.
Discrete choice experiments for complex health‐care decisions: does hierarchical information integration offer a solution?
Authors: van Helvoort‐Postulart Debby , Dellaert Benedict G. C. , van der Weijden Trudy , von Meyenfeldt Maarten F. , Dirksen Carmen D. 
Published: October 2008

AbstractThis paper describes an application of hierarchical information integration (HII) discrete choice experiments. We assessed theoretical and construct validity, as well as internal consistency, to investigate whether HII can be used to investigate complex multi‐faceted health‐care decisions (objective 1). In addition, we incorporated recent advances in mixed logit modelling (objective 2). Finally, we determined the response rate and predictive ability to study the feasibility of HII to support health‐care management (objective 3). The clinical subject was the implementation of the guideline for breast cancer surgery in day care, which is a complex process that involves changes at the organizational and management levels, as well as the level of health‐care professionals and that of patients.We found good theoretical and construct validity and satisfactory internal consistency. The proposed mixed logit model, which included repeated measures corrections and subexperiment error scale variations, also performed well. We found a poor response, but the model had satisfactory predictive ability. Therefore, we conclude that HII can be used successfully to study complex multi‐faceted health‐care decisions (objectives 1 and 2), but that the feasibility of HII to support health‐care management, in particular in challenging implementation projects, seems less favourable (objective 3). Copyright © 2008 John Wiley & Sons, Ltd.
Geomorphologic control on pollutant retardation at the groundwater–surface water interface
Authors: Smith J.W.N. , Lerner D.N. 
Published: October 2008

AbstractThe results of research on the pollutant retardation potential of permeable riverbed sediments in catchments with significant groundwater–surface water (GW‐SW) interaction are presented. The fraction of organic carbon and cation exchange capacity of fluvial sediments in various geomorphologic environments have been quantified. Sediments in selected reaches of the rivers Tern and Leith (UK), from the underlying Permian sandstone aquifers, and from along the length of the rivers Severn and Eden into which the Tern and Leith discharge have been investigated. Statistical analyses show significant variation in the geochemistry and pollutant retardation potential of sediments from different geomorphologic features, and between upland and lowland rivers. The sorption potential of fine‐grained sediments deposited in pools was greater than sand in runs and coarser deposits in riffles. Similarly, sediments in lowland rivers were found to have a greater retardation potential than those in upland rivers. There was generally greater retardation potential in fluvial sediments of all types than in the underlying aquifers, and in lowland rivers the fluvial sediment retardation potential greatly dominated that of the aquifer. The findings demonstrate the potential for pollutant retardation processes in riverbed sediments of sandstone catchments, and suggest that consideration of retardation processes at the groundwater–surface water interface should be included into environmental risk‐assessment studies, in order to better assess and manage the effects of contaminated groundwater discharges to rivers, particularly in lowland catchments. Copyright © 2008 John Wiley & Sons, Ltd.
The effect of climate and land use change on flow duration in the Maryland Piedmont region
Authors: Hejazi Mohamad I. , Moglen Glenn E. 
Published: October 2008

AbstractThis paper describes the use of a continuous streamflow model to examine the effects of climate and land use change on flow duration in six urbanizing watersheds in the Maryland Piedmont region. The hydrologic model is coupled with an optimization routine to achieve an agreement between observed and simulated streamflow. Future predictions are made for three scenarios: future climate change, land use change, and jointly varying climate and land use. Future climate is modelled using precipitation and temperature predictions for the Canadian Climate Centre (CCC) and Hadley climate models. Results show that a significant increase in temperature under the CCC climate predictions produces a decreasing trend in low flows. A significant increasing trend in precipitation under the Hadley climate predictions produces an increasing trend in peak flows. Land use change by itself, as simulated by an additional 10% increase in imperviousness (from 20·5 to 30·5%), produces no significant changes in the simulated flow durations. However, coupling the effects of land use change with climate change leads to more significant decreasing trends in low flows under the CCC climate predictions and more significant increasing trends in peak flows under Hadley climate predictions than when climate change alone is employed. These findings indicate that combined land use and climate change can result in more significant hydrologic change than either driver acting alone. Copyright © 2008 John Wiley & Sons, Ltd.
Breast cancer susceptibility alleles and ovarian cancer risk in 2 study populations
Authors: Gates Margaret A. , Tworoger Shelley S. , Terry Kathryn L. , De Vivo Immaculata , Hunter David J. , Hankinson Susan E. , Cramer Daniel W. 
Published: October 2008

AbstractRecent genome‐wide scans identified several novel breast cancer risk alleles, including variants of the FGFR2, MAP3K1 and LSP1 genes, and a study of associations between these alleles and characteristics of breast cancer patients reported a borderline significant correlation between the number of FGFR2 minor alleles and family history of breast/ovarian cancer. Given these results and similarities in the etiology of breast and ovarian cancer, we examined the association between 7 novel breast cancer susceptibility alleles and epithelial ovarian cancer risk in 2 large study populations. Our analysis included 1,173 cases and 1,201 controls from a New England‐based Case–Control study and 210 cases and 603 controls from the prospective Nurses' Health Study. We used logistic regression to estimate the odds ratio (OR) for individuals heterozygous or homozygous for the minor allele at each locus, compared to individuals with the wild‐type genotype. We examined the associations separately in each population and, after testing for heterogeneity in the results, pooled the estimates using a random effects model. There was no clear association between these polymorphisms and ovarian cancer risk in either population. The pooled per allele OR for FGFR2 was 1.06 (95% confidence interval (CI) = 0.95–1.18) for rs1219648 and 1.04 (95% CI = 0.93–1.15) for rs2981582. We had more than 80% power to detect a log‐additive OR of 1.16–1.18 per allele at the alpha = 0.05 level in the pooled analysis. Our results do not provide strong support for an association between these breast cancer susceptibility alleles and epithelial ovarian cancer risk. © 2008 Wiley‐Liss, Inc.
Risk of contralateral testicular cancer among men with unilaterally undescended testis: A meta analysis
Authors: Akre Olof , Pettersson Andreas , Richiardi Lorenzo 
Published: October 2008

AbstractThe association between undescended testis (cryptorchidism) and testicular cancer is established, but it is not known whether the risk of testicular cancer among men with unilateral maldescent is increased in both testes, or only on the undescended side. This is a meta‐analysis of 11 case‐control studies and 1 cohort study that all assessed the risk of testicular cancer separately for the undescended and descended testis. We used fixed‐effects meta‐analysis to calculate pooled estimates and 95% confidence intervals (CIs) for the relative risk. Of 199 tumors in men with unilateral cryptorchidism, 158 (79%) were on the ipsilateral side and 41 (21%) on the contralateral side. The pooled relative risks for testicular cancer in the ipsilateral and contralateral testis were 6.33 (95% CI, 4.30 to 9.31) and 1.74 (95% CI, 1.01 to 2.98), respectively. We conclude that in 1‐sided undescended testis, the risk of testicular cancer may be increased in both testes, although to a much greater extent on the ipsilateral side. © 2008 Wiley‐Liss, Inc.
MicroRNA profiling in human medulloblastoma
Authors: Ferretti Elisabetta , De Smaele Enrico , Po Agnese , Di Marcotullio Lucia , Tosi Emanuele , Espinola Maria Salome B. , Di Rocco Concezio , Riccardi Riccardo , Giangaspero Felice , Farcomeni Alessio , Nofroni Italo , Laneve Pietro , Gioia Ubaldo , Caffarelli Elisa , Bozzoni Irene , Screpanti Isabella , Gulino Alberto 
Published: October 2008

AbstractMedulloblastoma is an aggressive brain malignancy with high incidence in childhood. Current treatment approaches have limited efficacy and severe side effects. Therefore, new risk‐adapted therapeutic strategies based on molecular classification are required. MicroRNA expression analysis has emerged as a powerful tool to identify candidate molecules playing an important role in a large number of malignancies. However, no data are yet available on human primary medulloblastomas. A high throughput microRNA expression profiles was performed in human primary medulloblastoma specimens to investigate microRNA involvement in medulloblastoma carcinogenesis. We identified specific microRNA expression patterns which distinguish medulloblastoma differing in histotypes (anaplastic, classic and desmoplastic), in molecular features (ErbB2 or c‐Myc overexpressing tumors) and in disease‐risk stratification. MicroRNAs expression profile clearly differentiates medulloblastoma from either adult or fetal normal cerebellar tissues. Only a few microRNAs displayed upregulated expression, while most of them were downregulated in tumor samples, suggesting a tumor growth‐inhibitory function. This property has been addressed for miR‐9 and miR‐125a, whose rescued expression promoted medulloblastoma cell growth arrest and apoptosis while targeting the proproliferative truncated TrkC isoform. In conclusion, misregulated microRNA expression profiles characterize human medulloblastomas, and may provide potential targets for novel therapeutic strategies. © 2008 Wiley‐Liss, Inc.
Genomic events associated with progression of pleural malignant mesothelioma
Authors: Ivanov Sergey V. , Miller Jeremy , Lucito Robert , Tang Chunlao , Ivanova Alla V. , Pei Jianming , Carbone Michele , Cruz Christina , Beck Amanda , Webb Craig , Nonaka Daisuke , Testa Joseph R. , Pass Harvey I. 
Published: October 2008

AbstractPleural malignant mesothelioma (MM) is an aggressive cancer with a very long latency and a very short median survival. Little is known about the genetic events that trigger MM and their relation to poor outcome. The goal of our study was to characterize major genomic gains and losses associated with MM origin and progression and assess their clinical significance. We performed Representative Oligonucleotide Microarray Analysis (ROMA) on DNA isolated from tumors of 22 patients who recurred at variable interval with the disease after surgery. The total number of copy number alterations (CNA) and frequent imbalances for patients with short time (<12 months from surgery) and long time to recurrence were recorded and mapped using the Analysis of Copy Errors algorithm. We report a profound increase in CNA in the short‐time recurrence group with most chromosomes affected, which can be explained by chromosomal instability associated with MM. Deletions in chromosomes 22q12.2, 19q13.32 and 17p13.1 appeared to be the most frequent events (55‐74%) shared between MM patients followed by deletions in 1p, 9p, 9q, 4p, 3p and gains in 5p, 18q, 8q and 17q (23‐55%). Deletions in 9p21.3 encompassing CDKN2A/ARF and CDKN2B were characterized as specific for the short‐term recurrence group. Analysis of the minimal common areas of frequent gains and losses identified candidate genes that may be involved in different stages of MM: OSM (22q12.2), FUS1 and PL6 (3p21.3), DNAJA1 (9p21.1) and CDH2 (18q11.2‐q12.3). Imbalances seen by ROMA were confirmed by Affymetrix genome analysis in a subset of samples. © 2008 Wiley‐Liss, Inc.
Marine n‐3 and saturated fatty acids in relation to risk of colorectal cancer in Singapore Chinese: A prospective study
Authors: Butler Lesley M. , Wang Renwei , Koh Woon‐Puay , Stern Mariana C. , Yuan Jian‐Min , Yu Mimi C. 
Published: October 2008

AbstractExperimental data support multiple roles for fatty acids in colorectal carcinogenesis. We examined dietary fatty acids and incidence of colorectal cancer, and evaluated effect modification by sex and stage of disease among a population‐based cohort of 61,321 Singapore Chinese that was established between 1993 and 1998. As of December 31, 2005, 961 incident colorectal cancers were diagnosed. Presented hazard ratios (HRs) are for highestversuslowest quartiles with adjustment for potential confounders. Among women, we observed a dose‐dependent, positive association between saturated fat and localized colorectal cancer (Dukes A or B) [(HR = 1.69, 95% confidence interval (CI) = 1.08–2.63,pfor trend = 0.01)]. No such associations were noted in men (pfor interaction by sex = 0.04). Marine n‐3 polyunsaturated fatty acid (PUFA) intake was positively associated with advanced disease (Dukes C or D) (HR = 1.33, 95% CI = 1.05–1.70,pfor trend = 0.01), regardless of sex. The association with marine n‐3 PUFAs was strongest among those with the shortest (≤5 years) duration of follow‐up (HR = 1.49, 95% CI = 1.00–2.21,pfor trend = 0.04). In contrast, we observed a small, albeit imprecise, inverse association with marine n‐3 PUFAs for localized colorectal cancer among those with the longest duration of follow‐up (>10 years) (HR = 0.62, 95% CI = 0.29–1.34,pfor trend = 0.55). Our findings suggest that subtypes of fatty acids may differentially influence risk of colorectal cancer of a specified stage. © 2008 Wiley‐Liss, Inc.
Coffee consumption and risk of colorectal cancer: A systematic review and meta‐analysis of prospective cohort studies
Authors: Je Youjin , Liu Wei , Giovannucci Edward 
Published: October 2008

AbstractAn inverse association between coffee consumption and the risk of colorectal cancer has been found in several case‐control studies, but such an association was not consistent in prospective cohort studies. We conducted a systematic meta‐analysis of prospective cohort studies on coffee consumption and colorectal cancer published up to June 2008. We combined relative risks (RR) for colorectal cancer comparing high vs. low categories of coffee consumption using random‐effects models. We identified 12 eligible cohort studies, which included 646,848 participants and 5,403 cases for colorectal cancer. The summarized result of the meta‐analysis comparing high‐ vs. low‐consumption categories showed no significant effect of coffee consumption on colorectal cancer risk (RR = 0.91; 95% confidence intervals [CI]: 0.81–1.02). The RR was 0.93 (95% CI: 0.71–1.22) when considering 4 studies conducted in the United States of America, 0.91 (95% CI: 0.76–1.10) for 5 studies from Europe, and 0.83 (95% CI: 0.62–1.10) for 3 Japanese studies. No significant differences by sex and cancer‐site were found, but there was a slight suggestion of an inverse association between coffee consumption and colon cancer in women (RR = 0.79; 95% CI: 0.60–1.04), especially Japanese women (RR = 0.62; 95% CI: 0.37–1.05). The suggestive inverse associations were slightly stronger in studies that controlled for smoking and alcohol, and in studies with shorter follow‐up times. Information on coffee type, its serving size, or brewing method may provide a better understanding of this reassuring result and the real role of coffee on colorectal cancer risk. © 2008 Wiley‐Liss, Inc.
Surface endotoxin contamination and hemocompatibility evaluation of materials
Authors: Maitz Manfred F. , Teichmann Juliane , Sperling Claudia , Werner Carsten 
Published: October 2008

AbstractTo evaluate the blood compatibility of new materials, a clear distinction between properties of the materials and effects due to surface contamination by adsorbed endotoxins is essential. This study compares direct contact approaches and elution methods with water, organic solvents, nonionic, and zwitterionic detergents for determination of surface‐adsorbed endotoxin by the limulus amoebocyte lysate (LAL) test and determines the blood compatibility of various surfaces with controlled endotoxin contamination in vitro. The LAL test in direct contact with an endotoxin‐contaminated surface was concluded to be not practicable for most devices and its sensitivity showed a high dependence on surface characteristics. Among the elution methods, 0.2% Tween‐20 showed most stable elution characteristics and appears therefore preferable. Biological reactions at in vitro blood exposure were found to be only minimally influenced by adsorbed endotoxin during the time window of 2 h, allowing for a straightforward discrimination between materials and endotoxin‐dependent reactions. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
The effect of paraformaldehyde fixation on the Delayed Gadolinium‐Enhanced MRI of Cartilage (dGEMRIC) measurement
Authors: Dugar Arushi , Farley Michelle L. , Wang Angeline L. , Goldring Mary B. , Goldring Steven R. , Swaim Bryan H. , Bierbaum Benjamin E. , Burstein Deborah , Gray Martha L. 
Published: October 2008

AbstractThe delayed Gadolinium‐Enhanced Magnetic Resonance Imaging of Cartilage (dGEMRIC) method allows for both qualitative and quantitative measurement of the spatial distribution of glycosaminoglycan [GAG] in excised cartilage. The objective of this study was to determine the effect of paraformaldehyde fixation on dGEMRIC measurements. Five bovine and seven human cartilage pieces were punched into 5‐mm plugs, fixed for 18 h in 4% paraformaldehyde solution, and washed. The magnetic resonance imaging (MRI) parameter T1 was measured prior and post fixation in cartilage without (T10) and with (T1Gd), the ionically charged MRI contrast agent Gd(DTPA)2−. Images of tissue before and after fixation were qualitatively very similar. The ratios of T10, T1Gd, and calculated [GAG] after fixation, relative to before fixation, were near or slightly higher than 1 for both bovine cartilage (1.01 ± 0.01, 1.04 ± 0.02, 1.05 ± 0.03, respectively) and for human cartilage (0.96 ± 0.11, 1.03 ± 0.05, 1.09 ± 0.13). Thus, these data suggest that dGEMRIC can be used on previously fixed samples to assess the three dimensional spatial distribution of GAG. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 536–539, 2009