bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heresy at Play: Academies and the Literary Underground in Counter-Reformation Siena*
Authors: McClure George 
Published: December 2010

AbstractThis article examines an anonymous manuscript from the Sienese academies, likely composed between 1584 and 1593, during the period in which these societies were closed by the Medici grand dukes. The work is a dialogue that depicts a contest between the emblems of the academies of the Intronati, the Accesi, and the Travagliati, all vying for cultural primacy. Purportedly written by a zealous monk who appraises these worldly emblems and mottoes in preposterously flattering, even blasphemous, religious terms, the dialogue is actually a hoax that mocks the proselytizing efforts of Counter-Reformation forces in the city. This article attempts to roughly date this underground work, identify its principal targets, and consider its importance: as a telling depiction of a contest between secular images and sacred symbols, as a parody of feigned orthodoxy, and as a possible expression of freethinking well before the Enlightenment.
Lady Hester Pulter'sThe Unfortunate Florinda:Race, Religion, and the Politics of Rape*
Authors: Herman Peter C. 
Published: December 2010

AbstractIn the mid-1990s a manuscript was discovered containing the poetry and prose of a previously unknown female author, Lady Hester Pulter. The poems, likely written during the 1640s–'50s, demonstrate Pulter's wide reading and her near-fanatical Royalism. The prose romance, The Unfortunate Florinda, however, displays a very different politics. Basing her fiction on the legends surrounding the Muslim conquest of Spain, I argue that Pulter adjusts her sources to present an alternative, Augustinian view of rape, one that blames the rapist, not the victim. The monarchs in Pulter's fiction use absolutist rhetoric to justify rape, and,contraher earlier poetic denunciations of Charles I's execution, rape now justifies regicide. I suggest that the sexual corruption of Charles II's court prompted Pulter to create a romance with distinctly republican overtones in which chastity is the highest value, sexual corruption the lowest vice, and rulers who commit such crimes forfeit both their right to rule and their right to live.
Improved predictions by Pcons.net using multiple templates
Authors: Larsson Per , Skwark Marcin J. , Wallner Björn , Elofsson Arne 
Published: December 2010

Abstract
Summary: Multiple templates can often be used to build more accurate homology models than models built from a single template. Here we introduce PconsM, an automated protocol that uses multiple templates to build protein models. PconsM has been among the top-performing methods in the recent CASP experiments and consistently perform better than the single template models used in Pcons.net. In particular for the easier targets with many alternative templates with a high degree of sequence identity, quality is readily improved with a few percentages over the highest ranked model built on a single template. PconsM is available as an additional pipeline within the Pcons.net protein structure prediction server.
Availability and implementation: PconsM is freely available from http://pcons.net/.
Contact: arne@bioinfo.se
Exploring metabolic pathways in genome-scale networks via generating flux modes
Authors: Rezola A. , de Figueiredo L. F. , Brock M. , Pey J. , Podhorski A. , Wittmann C. , Schuster S. , Bockmayr A. , Planes F. J. 
Published: December 2010

Abstract
Motivation: The reconstruction of metabolic networks at the genome scale has allowed the analysis of metabolic pathways at an unprecedented level of complexity. Elementary flux modes (EFMs) are an appropriate concept for such analysis. However, their number grows in a combinatorial fashion as the size of the metabolic network increases, which renders the application of EFMs approach to large metabolic networks difficult. Novel methods are expected to deal with such complexity.
Results: In this article, we present a novel optimization-based method for determining a minimal generating set of EFMs, i.e. a convex basis. We show that a subset of elements of this convex basis can be effectively computed even in large metabolic networks. Our method was applied to examine the structure of pathways producing lysine in Escherichia coli. We obtained a more varied and informative set of pathways in comparison with existing methods. In addition, an alternative pathway to produce lysine was identified using a detour via propionyl-CoA, which shows the predictive power of our novel approach.
Availability: The source code in C++ is available upon request.
Contact: fplanes@tecnun.es
Supplementary information: Supplementary data are available at Bioinformatics online.
The Bayesian lasso for genome-wide association studies
Authors: Li Jiahan , Das Kiranmoy , Fu Guifang , Li Runze , Wu Rongling 
Published: December 2010

AbstractMotivation: Despite their success in identifying genes that affect complex disease or traits, current genome-wide association studies (GWASs) based on a single SNP analysis are too simple to elucidate a comprehensive picture of the genetic architecture of phenotypes. A simultaneous analysis of a large number of SNPs, although statistically challenging, especially with a small number of samples, is crucial for genetic modeling.Method: We propose a two-stage procedure for multi-SNP modeling and analysis in GWASs, by first producing a ‘preconditioned’ response variable using a supervised principle component analysis and then formulating Bayesian lasso to select a subset of significant SNPs. The Bayesian lasso is implemented with a hierarchical model, in which scale mixtures of normal are used as prior distributions for the genetic effects and exponential priors are considered for their variances, and then solved by using the Markov chain Monte Carlo (MCMC) algorithm. Our approach obviates the choice of the lasso parameter by imposing a diffuse hyperprior on it and estimating it along with other parameters and is particularly powerful for selecting the most relevant SNPs for GWASs, where the number of predictors exceeds the number of observations.Results: The new approach was examined through a simulation study. By using the approach to analyze a real dataset from the Framingham Heart Study, we detected several significant genes that are associated with body mass index (BMI). Our findings support the previous results about BMI-related SNPs and, meanwhile, gain new insights into the genetic control of this trait.Availability: The computer code for the approach developed is available at Penn State Center for Statistical Genetics web site, http://statgen.psu.edu.Contact: rwu@hes.hmc.psu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Analyses of SORTING NEXINs Reveal Distinct Retromer-Subcomplex Functions in Development and Protein Sorting inArabidopsis thaliana
Authors: Pourcher Mikael , Santambrogio Martina , Thazar Nelcy , Thierry Anne-Marie , Fobis-Loisy Isabelle , Miège Christine , Jaillais Yvon , Gaude Thierry 
Published: December 2010

AbstractSorting nexins (SNXs) are conserved eukaryotic proteins that associate with three types of vacuolar protein sorting (VPS) proteins to form the retromer complex. How SNXs act in this complex and whether they might work independently of the retromer remains elusive. Here, we show by genetic and cell imaging approaches that the Arabidopsis thaliana SNX1 protein recruits SNX2 at the endosomal membrane, a process required for SNX1-SNX2 dimer activity. We report that, in contrast with the mammalian retromer, SNXs are dispensable for membrane binding and function of the retromer complex. We also show that VPS retromer components can work with or independently of SNXs in the trafficking of seed storage proteins, which reveals distinct functions for subcomplexes of the plant retromer. Finally, we provide compelling evidence that the combined loss of function of SNXs and VPS29 leads to embryo or seedling lethality, underlining the essential role of these proteins in development.
Lipopolysaccharide induces proinflammatory cytokines and chemokines in experimental otitis media through the prostaglandin D2 receptor (DP)-dependent pathway
Authors: Eguchi M , Kariya S , Okano M , Higaki T , Makihara S , Fujiwara T , Nagata K , Hirai H , Narumiya S , Nakamura M , Nishizaki K 
Published: December 2010

Summary
Otitis media is one of the most common and intractable ear diseases, and is the major cause of hearing loss, especially in children. Multiple factors affect the onset or development of otitis media. Prostaglandin D2 is the major prostanoid involved in infection and allergy. However, the role of prostaglandin D2 and prostaglandin D2 receptors on the pathogenesis of otitis media remains to be determined. Recent studies show that D prostanoid receptor (DP) and chemoattractant receptor-homologous molecule expressed on T helper type 2 (Th2) cells (CRTH2) are major prostaglandin D2 receptors. In this study, homozygous DP single gene-deficient (DP–/–) mice, CRTH2 single gene-deficient (CRTH2–/–) mice and DP/CRTH2 double gene-deficient (DP–/– CRTH2–/–) mice were used to investigate the role of prostaglandin D2 and its receptors in otitis media. We demonstrate that prostaglandin D2 is induced by lipopolysaccharide (LPS), a major component of Gram-negative bacteria, and that transtympanic injection of prostaglandin D2 up-regulates macrophage inflammatory protein 2 (MIP-2), interleukin (IL)-1β and IL-6 in the middle ear. We also show that middle ear inflammatory reactions, including infiltration of inflammatory cells and expression of MIP-2, IL-1β and IL-6 induced by LPS, are reduced significantly in DP–/– mice and DP–/– CRTH2–/– mice. CRTH2–/– mice display inflammatory reactions similar to wild-type mice. These findings indicate that prostaglandin D2 may play significant roles in LPS-induced experimental otitis media via DP.
Randomized controlled trial to improve childhood immunization adherence in rural Pakistan: redesigned immunization card and maternal education
Authors: Usman Hussain R. , Rahbar Mohammad H. , Kristensen Sibylle , Vermund Sten H. , Kirby Russell S. , Habib Faiza , Chamot Eric 
Published: December 2010

SummaryObjective  A substantial dropout from the first dose of diphtheria‐tetanus‐pertussis (DTP1) to the 3rd dose of DTP (DTP3) immunization has been recorded in Pakistan. We conducted a randomized controlled trial to assess the effects of providing a substantially redesigned immunization card, centre‐based education, or both interventions together on DTP3 completion at six rural expanded programme on immunization (EPI) centres in Pakistan.Methods  Mother‐child pairs were enrolled at DTP1 and randomized to four study groups: redesigned card, centre‐based education, combined intervention and standard care. Each child was followed up for 90 days to record the dates of DTP2 and DTP3 visits. The study outcome was DTP3 completion by the end of follow‐up period in each study group.Results  We enrolled 378 mother–child pairs in redesigned card group, 376 in centre‐based education group, 374 in combined intervention group and 378 in standard care group. By the end of follow‐up, 39% of children in standard care group completed DTP3. Compared to this, a significantly higher proportion of children completed DTP3 in redesigned card group (66%) (crude risk ratio [RR] = 1.7; 95% CI = 1.5, 2.0), centre‐based education group (61%) (RR = 1.5; 95% CI = 1.3, 1.8) and combined intervention group (67%) (RR = 1.7; 95% CI = 1.4, 2.0).Conclusions  Improved immunization card alone, education to mothers alone, or both together were all effective in increasing follow‐up immunization visits. The study underscores the potential of study interventions’ public health impact and necessitates their evaluation for complete EPI schedule at a large scale in the EPI system.
Out‐of‐reach obscure bleeding: Single‐balloon enteroscopy to diagnose and treat varices in hepaticojejunostomy after pediatric liver transplant
Authors: Curcio Gabriele , Sciveres Marco , Mocciaro Filippo , Riva Silvia , Spada Marco , Tarantino Ilaria , Barresi Luca , Traina Mario 
Published: December 2010

Curcio G, Sciveres M, Mocciaro F, Riva S, Spada M, Tarantino I, Barresi L, Traina M. Out‐of‐reach obscure bleeding: Single‐balloon enteroscopy to diagnose and treat varices in hepaticojejunostomy after pediatric liver transplant.Abstract:  Obscure gastrointestinal (GI) bleeding is defined as bleeding from the GI tract that persists or recurs, with no obvious etiology, after esophagogastroduodenoscopy (EGD), colonoscopy, and radiologic evaluation of the small bowel. We present the case of a 17‐yr‐old girl who for two years had been suffering from recurrent episodes of melena and/or enterorrhagia. Fifteen yr earlier she had undergone a split‐liver transplant with Roux‐en‐Y biliary reconstruction. A series of endoscopic and radiologic investigations had failed to find the source of the bleeding. Suspecting the presence of ectopic varices, we decided to perform single‐balloon enteroscopy (SBE). We observed and aspirated a large amount of fresh red blood in the afferent loop until we found the hepaticojejunostomy. On the edge of the biliary‐enteric anastomosis we observed a vascular lesion 5 mm in diameter. Judging this ectopic varix to be the source of bleeding, we placed two endoclips. The second clip placement caused varix rupture with a consequent massive hemorrhage, emergently and successfully treated with cyanoacrylate sclerotherapy. No episodes of rebleeding were observed, and no complications occurred during the entire hospital stay, and after six months of follow‐up. This report highlights the importance of afferent loop examination in patients with obscure GI bleeding who have undergone liver transplant with Roux‐en‐Y biliary reconstruction.
Reduced light availability and increased competition diminish the reproductive success of wet forest sedge Carex loliacea L.
Authors: KULL THEA , KULL TIIU , SAMMUL MAREK 
Published: December 2010

AbstractWet forest ecosystems in temperate regions have been heavily drained and logged, often with significant negative consequences for biodiversity in these habitats. Our research focused on population maintenance mechanisms of a declining wet forest sedge Carex loliacea L. We studied germination under different light regimes and seedling survival under different vegetation densities using an in situ removal experiment. For successful germination, seeds of C. loliacea need light; germination in reduced light conditions is depressed. The seeds of C. loliacea are able to accumulate a seed bank and exhibit seasonal dormancy cycles. Survival of seedlings strongly depends on competition with other plant species. Our results imply that changes in habitat conditions (draining, forest cutting) affect the successful generative reproduction of C. loliacea primarily via a change in light conditions, which is a strong factor both at the stage of germination and seedling growth. However, adult plants are able to persist over a much broader range of habitat conditions without detectable vitality loss.
Stem tissue mass density is linked to growth and resistance to a stem‐boring insect in Alternanthera philoxeroides
Authors: PAN XIAOYUN , JIA XIN , ZENG JING , SOSA ALEJANDRO , LI BO , CHEN JIAKUAN 
Published: December 2010

AbstractTo investigate how stem anatomical structure is linked to growth and resistance to stem‐boring insects in a herbaceous species, six populations of alligatorweed (Alternanthera philoxeroides) were grown in a common garden. Stem growth rate (GR) of A. philoxeroides and pupation rate as an estimate of resistance to a stem‐boring insect (Agasicles hygrophila) were quantified. Stem tissue mass density (TMD) was measured and stem anatomical traits were analysed on cross‐sectional areas (CSA). Stem TMD was positively correlated with resistance (i.e. negatively correlated with pupation rate) and negatively correlated with GR. Stem cortex CSA (%) and vascular bundle (VB) density (no./mm2) were positively related to stem TMD and negatively related to pupation rate. The GR was positively related to VB CSA (%) and negatively related to VB density. These results suggest that stem TMD, which results from a high fraction in cortex CSA and high VB density, is a key determinant of resistance to a stem‐boring specialist in A. philoxeroides. The high resistance of plants with higher stem TMD may partially impose a cost to plant growth.
MTHFR C677T and A1298C polymorphisms as a risk factor for congenital heart defects in Down syndrome
Authors: Babić Božović Ivana , Vraneković Jadranka , StarčevićČizmarević Nada , Mahulja‐Stamenković Vesna , Prpić Igor , Brajenović‐Milić Bojana 
Published: December 2010

AbstractBackground:  Congenital heart defects (CHD) are present in most, but not all, cases of Down syndrome (DS). The presence of methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms has been reported as a risk factor for CHD in DS. The aims of the present study were to assess (i) the frequency of MTHFR C677T and A1298C polymorphisms in DS individuals in the Croatian population; (ii) the relationship between the two maternal MTHFR polymorphisms and CHD‐affected DS children; and (iii) the transmission frequencies of the variant alleles of the two MTHFR polymorphisms in CHD‐affected DS.Methods:  The study population included 112 DS subjects and 221 controls. CHD were present in 48% of the DS subjects (54/112). The mothers of 107 DS individuals were available for the study; none was a periconceptional folic acid user. Allele transmission was analyzed in 34 complete parent–offspring triads.Results:  The frequencies of the allele, individual, and combined genotypes of MTHFR C677T and A1298C in DS subjects were not statistically different compared to the normal healthy Croatian controls. The maternal MTHFR polymorphisms were not found to be a risk factor for DS‐related CHD. The allele transmission of the two MTHFR polymorphisms showed no deviations from random segregation.Conclusions:  Because the fetus is lost in a great proportion of trisomy 21 pregnancies, both maternal and fetal, not only live‐born MTHFR C677T and A1298C, as well as maternal nutrition and lifestyle during pregnancy, should be analyzed to asses the impact on CHD in DS.
Problems with body mass index as an index to evaluate physical status of children in puberty
Authors: Sugiura Reiko , Murata Mitsunori 
Published: December 2010

AbstractBackground:  The aim of the present study was to examine the problems associated with using body mass index (BMI) for evaluating the physical status of children during puberty and the problems associated with establishing international standard values as cut‐off points for obesity and thinness in children.Methods:  A cohort study was undertaken on BMI as an indicator of physical status in puberty based on the data in the 2000 Annual Report of School Health Statistics. The subjects were 695,600 children from 5 to 17 years of age.Results:  In puberty, even in those with the optimal weight for their sex and age, BMI increases as height increases; therefore, a considerable variation in the range of BMI is observed in normal individuals of the same degree of fatness. For this reason, there is considerable overlap in the “healthy weight”, “overweight” and “obese” groups defined by the CDC using BMI percentile with regard to fatness in puberty. When the pubertal growth patterns are different among children from different countries, it is difficult to determine internationally average BMI by sex and age.Conclusions:  Distinguishing the respective healthy weight, overweight, and obese groups based on cut‐off points using BMI percentile during puberty is difficult. If differences exist in the socioeconomic status of the subject cohorts and in the passage through puberty among children from different countries, we must consider that average values of BMI for the same age of children in puberty will have different meanings. With regard to evaluation of physical status in pubertal children, only BMI average values for the same stage of pubertal development are meaningful, rather than individual values.
The prognostic significance of human equilibrative nucleoside transporter 1 expression in patients with metastatic bladder cancer treated with gemcitabine‐cisplatin‐based combination chemotherapy
Authors: Matsumura Nagahide , Nakamura Yasushi , Kohjimoto Yasuo , Inagaki Takeshi , Nanpo Yoshihito , Yasuoka Hironao , Ohashi Yasuo , Hara Isao 
Published: December 2010

What’s known on the subject? and What does the study add? The expression of hENT1 was significantly associated with prolonged survival in advanced bladder cancer treated with gemcitabine–cisplatin‐based combination chemotherapy.The mechanism‐based approach to the chemotherapeutic agents may be helpful to personalize medicine for the individual advanced bladder cancer patient.OBJECTIVETo evaluate the expression of the human equilibrative nucleoside transporter 1 (hENT1) and excision repair cross complementing 1 (ERCC1) as possible prognostic factors for patients with metastatic bladder cancer treated with gemcitabine–cisplatin‐based combination chemotherapy.PATIENTS AND METHODSThe present study retrospectively evaluated the expression of hENT1 and ERCC1 by immunostaining in chemo‐naive primary bladder tumour specimens from 40 patients with metastatic bladder cancer who received treatment with gemcitabine–cisplatin‐based combination chemotherapy at Wakayama Medical University Hospital and affiliated hospitals from May 2002 to July 2009. Immunohistochemistry on formalin‐fixed, paraffin‐embedded tissues was performed with specific hENT1 and ERCC1 antibodies scored by two pathologists who were blinded to clinical outcomes. The clinical and histopathological variables were analyzed to evaluate predictive values for survival.RESULTSThe median survival time in patients with high and low hENT1 expression was 17.3 and 11.6 months, respectively (log‐rank test, P= 0.003). This contrasted with the median survival in patients with high and low ERCC1 expressions, which did not differ significantly (high ERCC1, 13.6 months; low ERCC1, 17.1 months; P= 0.178). In univariate Cox regression analyses for pretreatment clinicopathological variables, performance status (P= 0.02) and hENT1 expression (P= 0.004), but not ERCC1 expression (P= 0.182), were associated with overall survival. Multivariate analysis using a Cox proportional hazards model showed that hENT1 expression was an independent prognostic factor (P= 0.008).CONCLUSIONThe data obtained in the present study show that high expression of hENT1 in tumour cells is associated with prolonged survival in patients with metastatic bladder cancer treated with gemcitabine–cisplatin‐based combination chemotherapy.
Current debate on the use of antibiotic prophylaxis for caesarean section
Authors: Lamont RF , Sobel JD , Kusanovic JP , Vaisbuch E , Mazaki‐Tovi S , Kim SK , Uldbjerg N , Romero R 
Published: December 2010

Please cite this paper as: Lamont R, Sobel J, Kusanovic J, Vaisbuch E, Mazaki‐Tovi S, Kim S, Uldbjerg N, Romero R. Current debate on the use of antibiotic prophylaxis for caesarean section. BJOG 2011;118:193–201.Caesarean delivery is frequently complicated by surgical site infections, endometritis and urinary tract infection. Most surgical site infections occur after discharge from the hospital, and are increasingly being used as performance indicators. Worldwide, the rate of caesarean delivery is increasing. Evidence‐based guidelines recommended the use of prophylactic antibiotics before surgical incision. An exception is made for caesarean delivery, where narrow‐range antibiotics are administered after umbilical cord clamping because of putative neonatal benefit. However, recent evidence supports the use of pre‐incision, broad‐spectrum antibiotics, which result in a lower rate of maternal morbidity with no disadvantage to the neonate.