bluuebunny/crossref_metadata_2025_split huggingface dataset:
One thousand genomes imputation in the national cancer institute breast and prostate cancer cohort consortium aggressive prostate cancer genome‐wide association study
Authors: Machiela Mitchell J. , Chen Constance , Liang Liming , Diver W. Ryan , Stevens Victoria L. , Tsilidis Konstantinos K. , Haiman Christopher A. , Chanock Stephen J. , Hunter David J. , Kraft Peter ,   on behalf of the National Cancer Institute Breast and Prostate Cancer Cohort Consortium
Published: December 2012

AbstractBACKGROUNDGenotype imputation substantially increases available markers for analysis in genome‐wide association studies (GWAS) by leveraging linkage disequilibrium from a reference panel. We sought to (i) investigate the performance of imputation from the August 2010 release of the 1000 Genomes Project (1000GP) in an existing GWAS of prostate cancer, (ii) look for novel associations with prostate cancer risk, (iii) fine‐map known prostate cancer susceptibility regions using an approximate Bayesian framework and stepwise regression, and (iv) compare power and efficiency of imputation and de novo sequencing.METHODSWe used 2,782 aggressive prostate cancer cases and 4,458 controls from the NCI Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer GWAS to infer 5.8 million well‐imputed autosomal single nucleotide polymorphisms (SNPs).RESULTSImputation quality, as measured by correlation between imputed and true allele counts, was higher among common variants than rare variants. We found no novel prostate cancer associations among a subset of 1.2 million well‐imputed low‐frequency variants. At a genome‐wide sequencing cost of $2,500, imputation from SNP arrays is a more powerful strategy than sequencing for detecting disease associations of SNPs with minor allele frequencies (MAF) above 1%.CONCLUSIONS1000GP imputation provided dense coverage of previously identified prostate cancer susceptibility regions, highlighting its potential as an inexpensive first‐pass approach to fine mapping in regions such as 5p15 and 8q24. Our study shows 1000GP imputation can accurately identify low‐frequency variants and stresses the importance of large sample size when studying these variants. Prostate 73: 677–689, 2013. © 2012 Wiley Periodicals, Inc.
Epigenetic Regulation of Nanog by MiR-302 Cluster-MBD2 Completes Induced Pluripotent Stem Cell Reprogramming
Authors: Lee Man Ryul , Prasain Nutan , Chae Hee-Don , Kim Young-June , Mantel Charlie , Yoder Mervin C. , Broxmeyer Hal E. 
Published: December 2012

Abstract
While most somatic cells undergoing induced pluripotent stem (iPS) cell reprogramming with Yamanaka factors accumulate at stable partially reprogrammed stages, the molecular mechanisms required to achieve full reprogramming are unknown. MicroRNAs (miRNAs) fine-tune mRNA translation and are implicated in reprogramming, but miRNA functional targets critical for complete iPS cell reprogramming remain elusive. We identified methyl-DNA binding domain protein 2 (MBD2) as an epigenetic suppressor, blocking full reprogramming of somatic to iPS cells through direct binding to NANOG promoter elements preventing transcriptional activation. When we overexpressed miR-302 cluster we observed a significant increase in conversion of partial to fully reprogrammed iPS cells by suppressing MBD2 expression, thereby increasing NANOG expression. Thus, expression of exogenous miR-302 cluster (without miR-367) is efficient in attaining a fully reprogrammed iPS state in partially reprogrammed cells by relieving MBD2-mediated inhibition of NANOG expression. Our studies provide a direct molecular mechanism involved in generating complete human iPS cell reprogramming to study disease pathogenesis, drug screening, and for potential cell-based therapies.
Good Candidates for a Third Liver Resection of Colorectal Metastasis
Authors: Yamazaki Shintaro , Takayama Tadatoshi , Okada Shunji , Iwama Atsuko , Midorikawa Yutaka , Moriguchi Masamichi , Nakayama Hisashi , Higaki Tokio , Sugutani Masahiko 
Published: December 2012

AbstractBackgroundHaving three liver resections for colorectal metastases has long been considered to be associated with a high risk of postoperative complications. The present study was designed to assess the feasibility and survival benefits of three liver resections.MethodsBetween 2004 and 2011, data for 273 consecutive patients with colorectal metastases were analyzed. The patient characteristics, tumor status, operation‐related variables, degree of liver steatosis, and short‐ and long‐term outcomes were compared according to the number of liver resections.ResultsThe history of preoperative chemotherapy was higher for patients who had had three liver resections as compared with other resections: i.e., one resection 41.0 %, versus two resections 56.8 %, versus three resections 81.8 %; p = 0.04. Patients receiving three liver resections had a high rate of liver steatosis (17.9 vs. 32.4 vs. 59.1 %; p = 0.03). The median operative time for three resections was significantly longer than for the other resections (359 min [range: 115–579 min] vs. 395 min [range: 178–740 min], vs. 482 min [range: 195–616 min]; p = 0.04). However, the complication rate and the postoperative hospital stay did not differ among the three groups. The 1‐, 3‐ and 5‐year survival rates did not differ significantly among the three groups (83.3, 57.5, and 44.6 % for one resection vs. 92.3, 52.1, and 35.7 % for two resections vs. 93.3, 49.0, and 34.1 % for three resections). Patients who had <5 tumors at a third liver resection and a recurrence interval of ≥500 days from the second resection were good candidates for three resections.ConclusionsUndergoing three resections of colorectal metastasis is feasible and provides a similar survival benefit as one or two resections, without increasing morbidity or mortality.
Medial Versus Lateral Approach in Laparoscopic Colorectal Resection: A Systematic Review and Meta‐analysis
Authors: Ding Jie , Liao Guo‐qing , Xia Yu , Zhang Zhong‐min , Pan Yang , Liu Sheng , Zhang Yi , Yan Zhong‐shu 
Published: December 2012

AbstractBackgroundThe aim of this study was to investigate the safety and efficacy of the medial approach (MA) and the lateral approach (LA) in the treatment of colorectal disease.MethodsStudies published since 1994 that compared MA versus LA in laparoscopic colorectal resection were collected. Data on conversion rate, operative time, blood loss, number of harvested lymph nodes, hospital stay, complications, mortality, rate of recurrence, and hospitalization costs for MA and LA were meta‐analyzed using fixed‐effect and random‐effect models.ResultsFive cohort studies (2 randomized controlled trials and 3 retrospective studies) that included 881 patients were studied. Of these patients, 475 and 582 had undergone laparoscopic colorectal resection via MA and LA, respectively. There were significant reductions in conversion rate and operative time and possible reductions in blood loss and hospitalization costs for MA compared to LA; however, there were fewer harvested lymph nodes for MA compared with LA, which remains to be further studied. Other outcome variables such as postoperative complications, postoperative immune function, mortality, and rate of recurrence were not found to be statistically significant for either group. Sensitivity analysis on the pooled data from randomized controlled trials showed that the conversion rates were not significantly different between MA and LA.ConclusionsCompared with the lateral approach, the medial approach has the advantages of shorter operative time and possibly lower conversion rate; it also can be as safe as the lateral approach. Whether the MA has less blood loss and lower hospitalization costs remains to be confirmed, and its oncological safety and long‐term prognosis are not clear. Due to insufficient data from a limited number of studies, inadequate assessment of the results may arise.
Long‐term Outcome after Proximal Gastrectomy with Jejunal Interposition for Gastric Cancer Compared with Total Gastrectomy
Authors: Nozaki Isao , Hato Shinji , Kobatake Takaya , Ohta Koji , Kubo Yoshirou , Kurita Akira 
Published: December 2012

AbstractBackgroundProximal gastrectomy (PG) has been widely accepted as treatment for early gastric cancer located in the upper third of the stomach. Reconstruction by jejunal interposition has been known to reduce reflux esophagitis for PG patients. The aim of this study was to compare the long‐term outcomes of patients who underwent PG with jejunal interposition with those treated by total gastrectomy (TG).MethodsData on 102 cases of PG with jejunal interposition and 49 cases of TG with Roux‐Y reconstruction for gastric cancer were analyzed retrospectively in terms of overall survival, weight maintenance, anemia and nutritional status, and endoscopic findings.ResultsMedian follow‐up time was 59 months in the both groups. There was no significant difference in the overall 5‐year survival rate between the PG group (94 %) and the TG group (84 %). The PG group showed significantly better body weight maintenance at the first year. The laboratory blood tests showed that the PG group had a significantly better red blood cell count and hemoglobin and hematocrit levels at the second and third year. However, postoperative endoscopic surveillance detected reflux esophagitis (3 %), peptic ulcer (9 %), and metachronous gastric cancer (5 %) in the PG group.ConclusionsProximal gastrectomy maintains comparable oncological radicality to TG and is preferred over TG in terms of preventing postoperative anemia. However, periodic endoscopic follow‐up is necessary to monitor the upper gastrointestinal tract.
Changes in Developmental Contexts as Predictors of Transitions in HIV‐Risk Behaviors Among Young Men Who Have Sex with Men (YMSM)
Authors: Wong Carolyn F. , Schrager Sheree M. , Chou Chih-Ping , Weiss George , Kipke Michele D. 
Published: December 2012

AbstractEmerging adulthood is a transitional time often marked by instability in many areas of life, including residential status, work, school, and romantic relationships. The purpose of this study is to examine transitions in HIV‐risk related behaviors among a cohort of ethnically‐diverse young men who have sex with men (YMSM) and to reveal how changes in developmental contexts during emerging adulthood might be associated with these behavioral changes. Hidden Markov models were used to examine movement across different stages of behavioral risk‐taking over time. Semi‐annual surveys were administered across 2 years; analyses included those with at least three of the five waves of data. Results indicated substantial movement at the individual‐level transitions. Additionally, high variability in sexual risk, alcohol misuse, and illicit drug‐risk behaviors was predicted by age, ethnicity, and correlates of emerging adulthood, such as residential status, work, post‐secondary school enrollment, and primary‐relationship status. Findings provide evidence of great change in risky behaviors among YMSM during this pivotal time, particularly among those who actively experiment in varying levels of risk‐taking. In order to prevent experimental behaviors from evolving into more serious risk, interventions must consider ways to assist YMSM to adjust to life changes brought on by emerging adulthood.
Nonlinear Dynamic Analysis for FGM Circular Plates
Authors: Dai H.-L. , Yan X. , Yang L. 
Published: December 2012

AbstractIn the paper, nonlinear dynamic analysis of a circular plate composed of functionally graded material (FGM) is presented. Considering a transverse shear deformation and geometric nonlinearity, the von Karman geometric relation of the FGM circular plate is established. Based on the theory of the first-order shear deformation, a new set of equilibrium equations is developed by the principle of minimum total energy. Applying the finite difference method and Newmark scheme, the nonlinear transient problem is solved by the iterative method. To validate the presented method, the transient problem of the FGM circular plate is compared with those of the existed literature, and good agreement is observed. The effects of the volume fraction index, boundary conditions, mechanical load and the ratio of thickness to radius on the nonlinear transient problem of the FGM circular plate are investigated.
Modern industrial policy and zoning: Chicago, 1910–1930
Authors: LEWIS ROBERT 
Published: December 2012

ABSTRACT:Industrial policy has long been considered a federal responsibility. Indeed, most scholars date modern local economic development programmes as starting in the 1960s. Before that, in this view, industrial policy wasad hoc, unco-ordinated and fragmented. In this article, I argue that the origins of modern industrial policy initiated by the local state slowly emerged at the beginning of the twentieth century in Chicago. Using an assortment of sources, I show that a new type of industrial policy was forged in the conflict over the 1923 zoning ordinance. The city's real-estate, financial and political elites were able to mobilize information, science, funding, individuals and arguments to convince industrialists that zoning was to their advantage. In the process, the city's industrial interests were able to frame the new zoning ordinance to their ends.
From ‘the people’ to ‘the citizen’: the emergence of the Edwardian municipal park in Manchester, 1902–1912
Authors: O'REILLY CAROLE 
Published: December 2012

ABSTRACT:This article argues that the Edwardian municipal park represents a significant transition from the highly regulated and formal space of the Victorian park. It takes as a case-study Heaton Park in Manchester purchased in late 1901 and suggests that this park represented a transition from a Victorian people's park to an Edwardian citizen's park in which each visitor accessed facilities and amenities appropriate to their individual or group leisure interests. It addresses the comparative neglect of the Edwardian park by urban historians and suggests the importance of the emerging concepts of citizenship and social responsibility.
Disputed transformations: deindustrialization and redevelopment of Cologne's Stollwerck factory, 1970–1980
Authors: HAUMANN SEBASTIAN 
Published: December 2012

ABSTRACT:Urban development corresponds with economic shifts. In the second half of the twentieth century, when traditional forms of industrial production declined in many western cities, this posed new kinds of challenges. Cities were in need of a new economic base and at the same time had to cope with the abandonment of industrial sites. This article highlights the agency of local societies in shaping this process of deindustrialization and redevelopment. It interprets deindustrialization and redevelopment as a process of transformation which was open-ended and a matter of intense negotiation between diverging interests at the local level. In analysing the highly contentious case of the disused Stollwerck chocolate factory in Cologne, the article traces a complex set of site-specific factors of deindustrialization and redevelopment.
Gender effect on the relationship between stress hormones and panic-agoraphobic spectrum dimensions in healthy subjects
Authors: Dell'Osso Liliana , Marazziti Donatella , Da Pozzo Eleonora , Conversano Ciro , Baroni Stefano , Massimetti Gabriele , Martini Claudia , Carmassi Claudia 
Published: December 2012

IntroductionAlterations of the hypothalamic-pituitary-adrenal (HPA) axis and of its peripheral indices have been reported in both normal and pathological anxiety with controversial findings. The aim of the present study was to investigate the possible correlations between serum cortisol and dehydroepiandrosterone-sulfate (DHEA-S) levels and DHEA-S/cortisol ratio, and panic-agoraphobic spectrum dimensions in a sample of healthy subjects.MethodsForty-two healthy subjects of both sexes, with no current or lifetime psychiatric disorders, were assessed by means of the Structured Clinical Interview for DSM-IV (SCID-I/P) and the so-called Panic Agoraphobic Spectrum-Self Report lifetime version (PAS-SR).ResultsSignificant, negative correlations were found between cortisol levels and the total score of the separation sensitivity, panic-like symptoms, and medication/substance sensitivity PAS-SR domains. The PAS-SR total and the panic-like symptoms domain scores were positively related to the DHEAS/cortisol ratio. When the sample was divided in women and men, these correlations were present in women only.DiscussionThese findings, while indicating the presence of significant relationships between panic-agoraphobic traits and some indices of HPA axis functioning in healthy women, would suggest this as one of the factors explaining the greater vulnerability of women to cross the line between normal and pathological anxiety.ConclusionsFurther studies are needed to explore gender differences in the relationships between HPA axis alterations and the panic-agoraphobic spectrum dimensions.
Neoliberalism, Race, and the American Welfare State
Authors: Ernst Rose 
Published: December 2012

Disciplining the Poor: Neoliberal Paternalism and the Persistent Power of Race.By Joe Soss, Richard C. Fording, and Sanford F. Schram. Chicago: University of Chicago Press, 2011. 368p. $75.00 cloth, $25.00 paper.It is more than 15 years since the Personal Responsibility and Work Opportunity Act was passed in 1996, famously described by then-President Bill Clinton as “the end of welfare as we know it.” InDisciplining the Poor, Joe Soss, Richard Fording, and Sanford Schram analyze recent changes in US welfare policy as reflections of broader transformations of the “governance” of poverty, arguing that these transformations represent a new form of “neoliberal paternalism” in which race continues to be an important element. In this symposium, a diverse group of political scientists working on welfare issues have been asked to critically assess the book's account and to comment more broadly on the importance of the “governance of poverty” to the future of American politics.—Jeffrey C. Isaac, Editor
Production and Associated Economics of Fingerling-to-Stocker and Stocker-to-Grow-Out Modular Phases for Farming Channel Catfish in Commercial-Size Ponds
Authors: D’Abramo Louis R , Hanson Terrill R , Kingsbury Susan K , Steeby James A , Tucker Craig S 
Published: December 2012

Abstract
A 2-year study was conducted to evaluate two phases (phase 2: fingerling to stocker; phase 3: stocker to grow out) of a three-phase modular production system for Channel Catfish Ictalurus punctatus in commercial-scale ponds. Fingerlings (mean = 14.3 kg/1,000 fish; 11.9 cm TL) were stocked into each of six 1.62-ha earthen ponds at a density of 123,500 fish/ha and were fed a 35% crude protein floating feed daily to satiation. After 142 d, the mean weight of harvested stockers ranged from 108.9 to 158.8 g and survival ranged from 38.8% to 62.0%. These fish were subsequently stocked (at either 12,350 or 16,055 fish/ha) into 1.62-ha ponds for grow out to food-size fish (≥567.5 kg) and were fed a 35% crude protein floating feed to satiation. A partial (selective) harvest was conducted at 105–130 d poststocking by using an in-pond grader, and a final harvest was conducted at 207–245 d poststocking. Combined production means were 7,124 kg/ha for the 12,350-fish/ha treatment and 7,210 kg/ha for the 16,055-fish/ha treatment. Survival (range = 84.3–105.5%) and feed conversion ratios (range = 2.25–2.65) were not significantly different. Mean weight (659.5 g) and length (41.8 cm) of fish harvested from the 12,350-fish/ha treatment ponds were significantly greater than those of fish harvested from the 16,055-fish/ha treatment (474.8 g; 38.4 cm). Cost of producing a 142-g stocker was $0.409. For the economic analysis, phase-2 production area was based on producing sufficient stockers for all phase-3 ponds within a representative 445-ha operation. Enterprise budgets were developed for the 12,350- and 16,055-fish/ha treatments; the incomes above variable cost were $1,450 and $108 per hectare, respectively, and net returns to land were $399 and −$943 per hectare, respectively. Low survival in phase-2 stocker production reduced the returns. The three-phase modular system should provide additional management benefits that were not valued in this analysis.
Captive Volitional Spawning and Larval Rearing of Pigfish
Authors: DiMaggio Matthew A , Broach Jason S , Ohs Cortney L , Grabe Scott W 
Published: December 2012

Abstract
Pigfish Orthopristis chrysoptera have been identified as a species with potential for commercial production; however, lack of established culture protocols remain a major obstacle. To date, there is no scientific literature that adequately examines captive spawning and culture of this species. The purpose of this study was to evaluate volitional spawning and larval culture of Pigfish. Additionally, a preliminary larval feeding regime was investigated and growth and development of Pigfish larvae were documented. A fecundity of 1,147,149 eggs per female (2,959 eggs/g body weight) was calculated based on 58 recorded volitional spawning events. Larval survival ranged from 6.5% to 100% through 25-d posthatch (DPH). Larvae were observed to initiate swim bladder inflation by 9 DPH, and 100% percent of larvae exhibited notochord flexion by 19 DPH. An effective feeding regime was established that incorporated the nauplii of the copepod Pseudodiaptomus pelagicus, the rotifer Brachionus plicatilis, and Artemia. This study represents the first published report of repeated captive volitional spawning of Pigfish with successful protracted larval rearing.
SAUR36, a SMALL AUXIN UP RNA Gene, Is Involved in the Promotion of Leaf Senescence in Arabidopsis
Authors: Hou Kai , Wu Wei , Gan Su-Sheng 
Published: December 2012

Abstract
Small Auxin Up RNA genes (SAURs) are early auxin-responsive genes, but whether any of them are involved in leaf senescence is not known. Auxin, on the other hand, has been shown to have a role in leaf senescence. Some of the external application experiments indicated that auxin can inhibit leaf senescence, whereas other experiments indicated that auxin can promote leaf senescence. Here, we report the identification and characterization of an Arabidopsis (Arabidopsis thaliana) leaf senescence-associated gene named SAG201, which is highly up-regulated during leaf senescence and can be induced by 1-naphthaleneacetic acid, a synthetic auxin. It encodes a functionally uncharacterized SAUR that has been annotated as SAUR36. Leaf senescence in transfer DNA insertion saur36 knockout lines was delayed as revealed by analyses of chlorophyll content, F v/F m ratio (a parameter for photosystem II activity), ion leakage, and the expression of leaf senescence marker genes. In contrast, transgenic Arabidopsis plants overexpressing SAUR36 (without its 3′ untranslated region [UTR]) displayed an early leaf senescence phenotype. However, plants overexpressing SAUR36 with its 3′ UTR were normal and did not exhibit the early-senescence phenotype. These data suggest that SAUR36 is a positive regulator of leaf senescence and may mediate auxin-induced leaf senescence and that the 3′ UTR containing a highly conserved downstream destabilizes the SAUR36 transcripts in young leaves.