bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of prostate cancer risk with snps in regions containing androgen receptor binding sites captured by ChIP‐On‐chip analyses
Authors: Lu Yizhen , Sun Jielin , Kader Andrew K. , Kim Seong‐Tae , Kim Jin‐Woo , Liu Wennuan , Sun Jishan , Lu Daru , Feng Junjie , Zhu Yi , Jin Tao , Zhang Zheng , Dimitrov Latchezar , Lowey James , Campbell Kevin , Suh Edward , Duggan David , Carpten John , Trent Jeffrey M. , Gronberg Henrik , Zheng S. Lilly , Isaacs William B. , Xu Jianfeng 
Published: June 2011

AbstractBACKGROUNDGenome‐wide association studies (GWAS) have identified approximately three dozen single nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. Despite the reproducibility of these associations, the molecular mechanism for most of these SNPs has not been well elaborated as most lie within non‐coding regions of the genome. Androgens play a key role in prostate carcinogenesis. Recently, using ChIP‐on‐chip technology, 22,447 androgen receptor (AR) binding sites have been mapped throughout the genome, greatly expanding the genomic regions potentially involved in androgen‐mediated activity.METHODOLOGY/PRINCIPAL FINDINGSTo test the hypothesis that sequence variants in AR binding sites are associated with PCa risk, we performed a systematic evaluation among two existing PCa GWAS cohorts; the Johns Hopkins Hospital and the Cancer Genetic Markers of Susceptibility (CGEMS) study population. We demonstrate that regions containing AR binding sites are significantly enriched for PCa risk‐associated SNPs, that is, more than expected by chance alone. In addition, compared with the entire genome, these newly observed risk‐associated SNPs in these regions are significantly more likely to overlap with established PCa risk‐associated SNPs from previous GWAS. These results are consistent with our previous finding from a bioinformatics analysis that one‐third of the 33 known PCa risk‐associated SNPs discovered by GWAS are located in regions of the genome containing AR binding sites.CONCLUSIONS/SIGNIFICANCEThe results to date provide novel statistical evidence suggesting an androgen‐mediated mechanism by which some PCa associated SNPs act to influence PCa risk. However, these results are hypothesis generating and ultimately warrant testing through in‐depth molecular analyses. Prostate 72:376–385, 2012. © 2011 Wiley Periodicals, Inc.
Structural scaffold for eIF4E binding selectivity of 4E‐BP isoforms: crystal structure of eIF4E binding region of 4E‐BP2 and its comparison with that of 4E‐BP1
Authors: Fukuyo Ai , In Yasuko , Ishida Toshimasa , Tomoo Koji 
Published: June 2011

AbstractTo clarify the higher eukaryotic initiation factor 4E (eIF4E) binding selectivity of 4E‐binding protein 2 (4E‐BP2) than of 4E‐BP1, as determined by Trp fluorescence analysis, the crystal structure of the eIF4E binding region of 4E‐BP2 in complex with m7GTP‐bound human eIF4E has been determined by X‐ray diffraction analysis and compared with that of 4E‐BP1. The crystal structure revealed that the Pro47‐Ser65 moiety of 4E‐BP2 adopts a L‐shaped conformation involving extended and α‐helical structures and extends over the N‐terminal loop and two different helix regions of eIF4E through hydrogen bonds, and electrostatic and hydrophobic interactions; these features were similarly observed for 4E‐BP1. Although the pattern of the overall interaction of 4E‐BP2 with eIF4E was similar to that of 4E‐BP1, a notable difference was observed for the 60–63 sequence in relation to the conformation and binding selectivity of the 4E‐BP isoform, i.e. Met‐Glu‐Cys‐Arg for 4E‐BP1 and Leu‐Asp‐Arg‐Arg for 4E‐BP2. In this paper, we report that the structural scaffold of the eIF4E binding preference for 4E‐BP2 over 4E‐BP1 is based on the stacking of the Arg63 planar side chain on the Trp73 indole ring of eIF4E and the construction of a compact hydrophobic space around the Trp73 indole ring by the Leu59‐Leu60 sequence of 4E‐BP2. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Engineered Multifunctional Nanocarriers for Cancer Diagnosis and Therapeutics
Authors: Shi Donglu , Bedford Nicholas M. , Cho Hoon‐Sung 
Published: June 2011

AbstractThis article reviews advances in the design and development of multifunctional carbon‐based and/or magnetic nanoparticle systems (or simply ‘nanocarriers’) for early cancer diagnosis and spatially and temporally controlled therapy. The critical issues in cancer diagnosis and treatment are addressed based on novel nanotechnologies such as real‐time in‐vivo imaging, drug storage and release, and specific cancer‐cell targeting. The implementation of nanocarriers into animal models and the subsequent effectiveness in treating tumors is also reviewed. Recommendations for future research are given.
Design patterns: a survey on their micro‐structures
Authors: Fontana Francesca Arcelli , Maggioni Stefano , Raibulet Claudia 
Published: June 2011

SUMMARYDesign patterns play a significant role in reverse engineering by providing information not only on how but also on why a solution has been implemented in a specific way because of their semantics. The application of design patterns leads to their personalization to a specific context, hence to the generation of variants. This makes their recognition a challenging task, which may be addressed through the understanding and detection of the micro‐structures design patterns are made of. This is very useful for the detection as well as for the application of design patterns. The principal aim of this paper is to present a survey on these micro‐structures and a comparison among them in the perspective of reverse engineering. Because of their less complex structure and behavior, as well as closer link to the source code, the recognition of these micro‐structures may be automated, which can be considered a step towards the automatic recognition of the more complex design patterns. In this paper, we consider four of the most significant types of micro‐structures: elemental design patterns, clues, sub‐patterns, and micro patterns. To analyze the role of the micro‐structures in the design pattern detection process, we make a comparison among these four types of micro‐structures and among the micro‐structures of various types in order to identify the relations among them. Copyright © 2011 John Wiley & Sons, Ltd.
Multivariate U‐statistics: a tutorial with applications
Authors: Yu Q. , Tang W. , Kowalski J. , Tu X. M. 
Published: June 2011

AbstractU‐statistics represent an important class of statistics arising from modeling quantities of interest defined by multi‐subject responses such as the classic Mann–Whitney–Wilcoxon rank tests. However, classic applications of U‐statistics are largely limited to univariate outcomes within a cross‐sectional data setting. As longitudinal study designs become increasingly popular in today's research, it is imperative to generalize the classic theory of U‐statistics to such a study setting to meet the challenges of modern clinical and translational research. In this article, we focus on applications of U‐statistics to longitudinal study data. We first give a brief overview of U‐statistics and then discuss how to apply this powerful class of statistics to model quantities of interest with a longitudinal data setting. In addition to generalizing U‐statistics and associated inference theory to longitudinal data analysis, we also discuss a class of function response models (FRM) to bring the power of U‐statistics to uncharted territory. We illustrate applications of generalized U‐statistics and FRM with data from some real longitudinal studies.WIREs Comp Stat2011 3 457–471 DOI: 10.1002/wics.178This article is categorized under:Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Preoperative biliary stents in pancreatic cancer
Authors: Bonin Eduardo A. , Baron Todd H. 
Published: June 2011

AbstractBackgroundPancreatic cancer is a common digestive cancer with high mortality, and surgical resection is the only potential curative treatment option. Pancreatic head cancer is usually accompanied by biliary obstruction, which potentially increases surgical complications following pancreaticoduodenectomy. Thus, preoperative biliary drainage has long been advocated.MethodsA review of the literature using Medline, Embase and Cochrane databases was undertaken.ResultsEndoscopic or percutaneous biliary stent placement is technically successful in most patients. The use of routine preoperative biliary drainage in the setting of pancreatic cancer with biliary obstruction is controversial. Prospective studies have shown that complications related to preoperative biliary drainage using endoscopic placement of traditional plastic endoprostheses increase the overall morbidity compared to pancreaticoduodenectomy alone. Placement of self‐expandable metal stents could reduce stent‐related complication rates such as early occlusion because of prolonged patency, especially when surgery is delayed.ConclusionPancreatic cancer patients with deep jaundice and expected delay prior to curative intent surgery are potential candidates for temporary biliary drainage. Cholangitis remains a formal indication for early, urgent preoperative biliary decompression for patients with pancreatic cancer.
Covered metallic stenting for malignant distal biliary obstruction: clinical results according to stent type
Authors: Isayama Hiroyuki , Nakai Yousuke , Kawakubo Kazumichi , Kogure Hirofumi , Togawa Osamu , Hamada Tsuyoshi , Ito Yukiko , Sasaki Takashi , Yamamoto Natsuyo , Sasahira Naoki , Hirano Kenji , Tsujino Takeshi , Tada Minoru , Koike Kazuhiko 
Published: June 2011

AbstractBackgroundIn the endoscopic management of unresectable malignant biliary obstructions, covered metallic stents (CMSs) showed longer patency and lower incidence of stent occlusion than uncovered metallic stents (UMCs). However, there are very few reports on factors influencing the results of inserting CMSs. We evaluated differences in clinical results according to stent type.MethodsWe reviewed the results of four types of CMS (polyurethane‐covered Diamond stent (PCD), silicone‐covered WALLSTENT (SCW), ComVi stent, and VIABIL biliary stent) and an uncovered MS (UMS), based on our experience and the literature. CMSs were characterized according to the axial and radial forces, covering (partial, full), smoothness of the inner surface, and presence of an anti‐migration system.ResultsCMSs were patent significantly longer than UMSs. There were differences in stent patency among the CMSs, including the cause of occlusion and other complications. The PCD had good patency and a low incidence of migration. The ComVi stent occluded early due to food impaction, but had the longest median stent patency and a low migration rate. The incidence of migration of SCW was relatively high and the SCW was occluded primarily by sludge.ConclusionsWe should assess the differences between the various CMSs and select the best one for each patient.
Bacterial expression of mutant argininosuccinate lyase reveals imperfect correlation of in‐vitro enzyme activity with clinical phenotype in argininosuccinic aciduria
Authors: Engel Katharina , Vuissoz Jean‐Marc , Eggimann Sandra , Groux Murielle , Berning Christoph , Hu Liyan , Klaus Vera , Moeslinger Dorothea , Mercimek‐Mahmutoglu Saadet , Stöckler Sylvia , Wermuth Bendicht , Häberle Johannes , Nuoffer Jean‐Marc 
Published: June 2011

AbstractBackgroundThe urea cycle defect argininosuccinate lyase (ASL) deficiency has a large spectrum of presentations from highly severe to asymptomatic. Enzyme activity assays in red blood cells or fibroblasts, although diagnostic of the deficiency, fail to discriminate between severe, mild or asymptomatic cases. Mutation/phenotype correlation studies are needed to characterize the effects of individual mutations on the activity of the enzyme.MethodsBacterial in‐vitro expression studies allowed the enzyme analysis of purified mutant ASL proteins p.I100T (c.299 T > C), p.V178M (c.532 G > A), p.E189G (c.566A > G), p.Q286R (c.857A > G), p.K315E (c.943A > G), p.R379C (c.1135 C > T) and p.R385C (c.1153 C > T) in comparison to the wildtype protein.ResultsIn the bacterial in‐vitro expression system, ASL wild‐type protein was successfully expressed. The known classical p.Q286R, the novel classical p.K315E and the known mutations p.I100T, p.E189G and p.R385C, which all have been linked to a mild phenotype, showed no significant residual activity. There was some enzyme activity detected with the p.V178M (5 % of wild‐type) and p.R379C (10 % of wild‐type) mutations in which Km values for argininosuccinic acid differed significantly from the wild‐type ASL protein.ConclusionThe bacterially expressed enzymes proved that the mutations found in patients and studied here indeed are detrimental. However, as in the case of red cell ASL activity assays, some mutations found in genetically homozygous patients with mild presentations resulted in virtual loss of enzyme activity in the bacterial system, suggesting a more protective environment for the mutant enzyme in the liver than in the heterologous expression system and/or in the highly dilute assays utilized here.
Species turnover of amphibians and reptiles in eastern China: disentangling the relative effects of geographic distance and environmental difference
Authors: Chen Shengbin , Jiang Gaoming , Zhang Jinlong , Li Yonggeng , Qian Hong 
Published: June 2011

AbstractSpatial turnover of species lies at the heart of macroecology and conservation biogeography. However, our knowledge of the causes of species turnover remains poor, particularly for herpetofaunas including amphibians and reptiles. Here, using regression, variance partitioning, and hierarchical partitioning analyses, we examine the relationships of species turnover in herpetofaunas among provinces in eastern China with respect to geographic distance and environmental difference. We found that species turnover in herpetofaunas is moderately to strongly correlated with geographic distance and difference in most environmental variables examined between provinces. Geographic distance and environmental difference together explain 87.1 and 89.9% of the variance of species turnover for amphibians and reptiles, respectively. Variance partitioning analysis indicated that most variance in species turnover is explained by the joint effect of geographic distance and environmental difference. Beyond this shared variance, environmental difference is a stronger predictor of species turnover than geographic distance, particularly for reptiles. Hierarchical partitioning analysis showed that energy‐related variables explained more variance in species turnover for both amphibians and reptiles, compared with water‐related variables. The independent effects of water‐related variables are slightly higher for amphibians than for reptiles whereas the independent effects of energy‐related variables are slightly higher for reptiles than amphibians. These patterns are consistent with different ecophysiological requirements of the two taxa. Our results have important implications for predicting changes in biodiversity of herpetofaunas under climate change scenarios. Global warming will affect the immigration and local extinction of both amphibians and reptiles, and precipitation change may affect amphibians more strongly, compared with its effect on reptiles.
Testostérone et contrôle central de l’érection
Authors: Raskin K. , Mhaouty-Kodja S. 
Published: June 2011

RésuméLa testostérone orchestre l’organisation périnatale et l’activation adulte des structures nerveuses cérébrales et spinales impliquées dans l’expression du comportement sexuel mâle. Cette revue décrit brièvement les différents effets de la testostérone dans la régulation de la motivation sexuelle et de l’érection, et les modèles génétiques générés, jusqu’à présent, dans le but d’élucider ses mécanismes d’action centraux.
National Diet and Nutrition Survey: UK food consumption and nutrient intakes from the first year of the rolling programme and comparisons with previous surveys
Authors: Whitton Clare , Nicholson Sonja K. , Roberts Caireen , Prynne Celia J. , Pot Gerda K. , Olson Ashley , Fitt Emily , Cole Darren , Teucher Birgit , Bates Beverley , Henderson Helen , Pigott Sarah , Deverill Claire , Swan Gillian , Stephen Alison M. 
Published: June 2011

The National Diet and Nutrition Survey (NDNS) is a cross-sectional survey designed to gather data representative of the UK population on food consumption, nutrient intakes and nutritional status. The objectives of the present paper were to identify and describe food consumption and nutrient intakes in the UK from the first year of the NDNS rolling programme (2008–09) and compare these with the 2000–01 NDNS of adults aged 19–64 years and the 1997 NDNS of young people aged 4–18 years. Differences in median daily food consumption and nutrient intakes between the surveys were compared by sex and age group (4–10 years, 11–18 years and 19–64 years). There were no changes in energy, total fat or carbohydrate intakes between the surveys. Children aged 4–10 years had significantly lower consumption of soft drinks (not low calorie), crisps and savoury snacks and chocolate confectionery in 2008–09 than in 1997 (all P < 0·0001). The percentage contribution of non-milk extrinsic sugars to food energy was also significantly lower than in 1997 in children aged 4–10 years (P < 0·0001), contributing 13·7–14·6 % in 2008–09 compared with 16·8 % in 1997. These changes were not as marked in older children and there were no changes in these foods and nutrients in adults. There was still a substantial proportion (46 %) of girls aged 11–18 years and women aged 19–64 years (21 %) with mean daily Fe intakes below the lower reference nutrient intake. Since previous surveys there have been some positive changes in intakes especially in younger children. However, further attention is required in other groups, in particular adolescent girls.
The Past as Destiny: Historical Visions in Samʾal and Judah under Assyrian Hegemony
Authors: Hamilton Mark W. 
Published: June 2011

In his groundbreaking study of the literary ramifications of the experience of western imperialism for both conquerors and the conquered, Edward Said remarks:Appeals to the past are among the commonest of strategies in interpretations of the present. What animates such appeals is not only disagreement about what happened in the past and what the past was, but uncertainty about whether the past really is past.
Condemnation of the Impious in Xenophon'sHellenica
Authors: Pownall Frances Skoczylas 
Published: June 2011

In theHellenica, Xenophon prefaces his account of the liberation of Thebes from Spartan occupation by making the following gnomic observation:One could tell also of many other incidents, both Greek and barbarian, showing that the gods are not unmindful either of those who are impious or of those who commit unholy acts. Now, at any rate, I shall tell only of the events at hand.
An abattoir-based study on the prevalence of hydatidosis in livestock in Mashhad, Iran
Authors: Borji H. , Azizzadeh M. , Afsai A. 
Published: June 2011

AbstractA 6-year (2004–2010) retrospective study was carried out to determine the prevalence of hydatidosis in livestock slaughtered in Mashhad abattoir, Mashhad, in north-eastern Iran and the capital of Khorasan province. Between 20 March 2004 and 19 March 2010, 5,131,485 animals (411,163 cattle; 4,547,618 sheep; 172,704 goats) were slaughtered in the study area and 388,399 (7.5%) livers and 1,139,529 (22.2%) lungs were discarded. Hydatidosis was responsible for 4% and 6.5% of total livers and lungs inspected, respectively. Of the cattle livers and lungs inspected over the survey period, 5.5% and 7.9% were condemned, respectively, because they held hydatid cysts. The corresponding values for livers and lungs of sheep (2%, 4%) and of goats (4.5%, 7.8%), respectively, were also condemned due to hydatidosis. Data showed a prominent seasonal pattern for hydatidosis. Liver condemnations due to hydatidosis were higher in winter and autumn for cattle and sheep, respectively, whereas lung condemnations were higher in summer for sheep and cattle. In goats, liver and lung condemnations were higher in winter. This could be attributed to various factors, such as sources of slaughtered animals, changes in management practice and ecological factors. The present survey provides baseline data for the future monitoring of this potentially important parasitic disease in the region.
The Late Minoan II–III and Mycenaean Pottery from the 1911 Excavations at Phylakopi on Melos
Authors: Mountjoy P.A. 
Published: June 2011

This article presents the Late Minoan II–III B and the Late Helladic I–III C pottery from the 1911 excavations of J. Dawkins and J. Droop at Phylakopi on Melos.The material from the 1911 excavations fills gaps in the corpus of pottery provided by the 1896–9 excavations and the 1974–7 excavations. It fills out our knowledge of the LH III A2 pottery and adds a considerable amount of LH III A1 and LH III C material. A small group of vessels caught in a LM I B/LH II A destruction confirms the supposition that full Marine Style was circulating together with open ground Marine Style and Alternating Style vases. The LH III C pottery adds some more parallels to the pottery from Koukounaries on Paros and also has one or two parallels to pottery from the east Aegean and pottery exported from there to the Levant.Σε αυτό το άρθρο παρουσιάζεται η Υστερομινωική II–III B και η Υστεροελλαδική I–III Γ κεραμική από τις ανασκαφές των J. Dawkins και J. Droop το 1911 στη Φυλακωπή της Μήλου.Το υλικό από τις ανασκαφές του 1911 συμπληρώνει τα κενά των δημοσιεύσεων της κεραμικής από τις ανασκαφικές περιόδους 1896–99 και 1974–77. Συμπληρώνει τη γνώση μας για την YE III A2 κεραμική και προστέτει μία σημαντική ποσόθητα υλικού της YE III A1 και YE III Γ. Ένας μικρός αριθμός αγγείων, που εντοπίστηκε στην YM I B / YE II A καταστροφή, επιβεβαιώνει την υπόθεση ότι ο πλήρης θαλάσσιος ρυθμός ήταν διαδεδομένος συγχρόνως με το θαλάσσιο ρυθμό επί ανοικτού βάθους και με τα αγγεία του εναλλασόμενου στυλ. H YE III Γ κεραμική προσθέτει ορισμένα ακόμη παράλληλα στην κεραμική από τις Κουκουναριές της Πάρου. Επιπλέον παρουσιάζει ένα ή δύο παράλληλα με την κεραμική του ανατολικού Αιγαίου, όπως και με την εξαγόμενη από εκεί κεραμική προς τη Συροπαλαιστίνη.