bluuebunny/crossref_metadata_2025_split huggingface dataset:
MeRIP-PF: An Easy-to-Use Pipeline for High-Resolution Peak-Finding in MeRIP-Seq Data
Authors: Li Yuli , Song Shuhui , Li Cuiping , Yu Jun 
Published: January 2013

Abstract
RNA modifications, especially methylation of the N6 position of adenosine (A)—m6A, represent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the controls and also calculates false discovery rate (FDR) as a cut off to differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation of m6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http://software.big.ac.cn/MeRIP-PF.html.
Levonorgestrel‐releasing intrauterine system versus conventional medical therapy for heavy menstrual bleeding in the Asia‐Pacific region
Authors: Lee Byung S. , Ling Xu , Asif Shaheena , Kraemer Peter , Hanisch Jens U. , Inki Pirjo 
Published: January 2013

AbstractObjectiveTo compare clinical outcomes, including cumulative continuation rate (CCR), in the treatment of idiopathic heavy menstrual bleeding (HMB) with the levonorgestrel‐releasing intrauterine system (LNG‐IUS) and with conventional medical therapies (CMTs), including combined oral contraceptives, oral progestins, and antifibrinolytics, either alone or in combination, in the Asia‐Pacific region.MethodsIn a prospective observational cohort study conducted between September 2008 and December 2010, 647 women (LNG‐IUS, n = 483; CMTs, n = 164), aged 18–45 years and diagnosed with HMB, were recruited from 8 countries and followed for up to 1 year. The primary outcome was the CCR at 12 months. Secondary outcomes included bleeding pattern, an assessment of treatment efficacy by the treating physician, and safety.ResultsThe CCR at 12 months was significantly higher for LNG‐IUS than for CMTs (87.6% vs 56.3% P < 0.05). Compared with CMTs, LNG‐IUS offered a better reduction in both subjectively assessed menstrual blood loss and the number of bleeding days, and had better efficacy for HMB, as determined by the physician's final evaluation.ConclusionThe present study provides information on the real‐life patterns of treatment of HMB in the Asia‐Pacific region. The efficacy of CMTs was inferior compared with LNG‐IUS in the clinical outcomes measured.ClinicalTrials.gov: NCT00864136.
Time between skin incision and delivery during cesarean
Authors: Rossouw Jana N. , Hall David , Harvey Justin 
Published: January 2013

AbstractObjectiveTo investigate factors influencing skin incision‐to‐delivery time (including sub‐divisions thereof) and the effect of these surgical intervals on immediate neonatal outcome.MethodsA prospective cohort analysis was conducted of all women undergoing cesarean delivery at Tygerberg Hospital, Cape Town, South Africa, from May 24 to November 2, 2010. Three surgical intervals were evaluated: skin incision to myometrium, myometrium to delivery, and skin incision to delivery. Neonatal outcome was assessed by the 5‐minute Apgar score.ResultsOf 1120 cesarean deliveries recorded during the study period, 77.2% were emergency procedures, which were performed more quickly at all surgical planes (P < 0.01). Adhesions in the surgical field were present in 7.4% of all primary procedures versus 67.7% of all third procedures (P < 0.001). The skin incision‐to‐delivery time was significantly extended among repeat procedures (P < 0.001) and increased progressively with degree of obesity (P < 0.001). Although the 3 surgical intervals were calculated individually, none of the median values correlated with a 5‐minute Apgar score below 7 for emergency deliveries.ConclusionRepeat procedures, adhesions, and obesity prolonged the time taken for cesarean delivery. Nevertheless, the effect of these factors on the 5‐minute Apgar score was minimal.
Detection of regional low myocardial perfusion helps predict a response to cardiac resynchronization therapy in patients with non‐ischemic cardiomyopathy: Results of the Find Index by Nuclear Imaging for Dyssynchrony (FIND) study
Authors: Keida Takehiko , Morishima Itsuro , Tsuchiya Taketsugu , Sagara Kouichi , Okishige Kaoru , Kumagai Kenta , Mibiki Yoshiaki , Nakamura Kentaro , Yamanaka Tamon , Yoshida Yukihiko , Yamamoto Akira , Takami Mitsuaki 
Published: January 2013

AbstractBackgroundThe aim of this study was to investigate the use of imaging techniques to predict the response to cardiac resynchronization therapy (CRT) in patients with non‐ischemic cardiomyopathy (NICM) by simultaneous assessment of left ventricular (LV) dyssynchrony and myocardial perfusion in a single nuclear scan of the heart.MethodsPatients indicated for CRT device implantation underwent a resting myocardial perfusion assessment with single photon emission computed tomography (MP‐SPECT) examination using technetium‐99 m methoxyisobutylisonitrile prior to device implantation. CardioGRAF and cardioBull software (FUJIFILM RI Pharma, Tokyo, Japan) were used to analyze the LV mechanical dyssynchrony and myocardial viability, respectively. Patient follow‐ups were performed at 6 months after device implantation. CRT response was defined as a ≥10% decrease in the LV end systolic volume.ResultsA total of 43 patients with NICM were analyzed. Using the cutoff points of 6.2 for the dyssynchrony index and 66% for LV myocardial perfusion, the combined indices predicted CRT response with a sensitivity of 77.8% and specificity of 91.2%.ConclusionCombined assessment of MP‐SPECT and a measure of LV mechanical dyssynchrony showed good predictive ability in patients with non‐ischemic heart failure.
Summability implies Collet–Eckmann almost surely
Authors: GAO BING , SHEN WEIXIAO 
Published: January 2013

AbstractWe provide a strengthened version of the famous Jakobson's theorem. Consider an interval map $f$ satisfying a summability condition. For a generic one-parameter family ${f}_{t} $ of maps with ${f}_{0} = f$, we prove that $t= 0$ is a Lebesgue density point of the set of parameters for which ${f}_{t} $ satisfies both the Collet–Eckmann condition and a strong polynomial recurrence condition.
Jacob Bronowski: a humanist intellectual for an atomic age, 1946–1956
Authors: DESMARAIS RALPH 
Published: January 2013

AbstractJacob (‘Bruno’) Bronowski (1908–1974), on the basis of having examined the effects of the atomic bombing of Japan in late 1945, became one of Britain's most vocal and best-known scientific intellectuals engaged in the cultural politics of the early atomic era. Witnessing Hiroshima helped transform him from pure mathematician–poet to scientific administrator; from obscurity to fame on the BBC airwaves and in print; and, crucially, from literary intellectual who promoted the superior truthfulness of poetry and poets to scientific humanist insisting that science and scientists were the standard-bearers of truth. A cornerstone of Bronowski's humanist ideology was that Hiroshima and the bomb had become symbols of the public's distrust of science, whereas, in reality, science was merely a scapegoat for society's loss of moral compass; more correctly, he stressed, science and scientists epitomized positive moral values. When discussing atomic energy, especially after 1949, Bronowski not only downplayed the bomb's significance but was deliberately vague regarding Britain's atomic weapon development programme; this lack of candour was compounded by Bronowski's evasiveness regarding his own prior involvement with wartime bombing. The net effect was a substantial contribution to British scientific intellectuals' influential yet frequently misleading accounts of the relations between science and war in the early atomic era.
Protective effect of ascorbic acid against ethanol-induced reproductive toxicity in male guinea pigs
Authors: Harikrishnan R. , Abhilash P. A. , Syam Das S. , Prathibha P. , Rejitha S. , John Febi , Kavitha S. , Indira M. 
Published: January 2013

The present study was undertaken to elucidate the effect of ascorbic acid on alcohol-induced reproductive toxicity and also to compare it with that of abstention. A total of thirty-six male guinea pigs were divided into two groups and were maintained for 90 d as control and ethanol-treated groups (4 g/kg body weight (b.wt.)). After 90 d, ethanol administration was stopped and animals in the control group were divided into two groups and then maintained for 30 d as the control and control+ascorbic acid groups and those in the ethanol-treated group as ethanol abstention and ethanol+ascorbic acid (25 mg/100 g b. wt.) groups. Animals treated with ethanol showed a significant decline in sperm quality (P< 0·001), decreased activity of steroidogenic enzymes (P< 0·05) and reduced serum testosterone (P< 0·05), luteinising hormone and follicle-stimulating hormone levels, decrease in the activity of testicular succinate dehydrogenase, adenosine triphosphatase, sorbitol dehydrogenase and reduction in fructose content (P< 0·05). It also caused an increase in testicular malondialdehyde levels (P< 0·05) and decrease in the levels of glutathione content (P< 0·001) of testes. Ascorbic acid levels in testes and plasma were also reduced (P< 0·001) in ethanol-fed animals. Ascorbic acid supplementation altered all these parameters and produced a better and faster recovery from alcohol-induced reproductive toxicity than abstention. The mechanism of action of ascorbic acid may be by reducing the oxidative stress and improving antioxidant status, which eventually changed the microenvironment of testes and enhanced the energy needed for motility of sperms, improved the sperm morphology and elevated the testosterone and gonadotropin levels.
The Effects of Early Years’ Childcare on Child Emotional and Behavioural Difficulties in Lone and Co-Parent Family Situations
Authors: ZAGEL HANNAH , KADAR-SATAT GITIT , JACOBS MYRTHE , GLENDINNING ANTHONY 
Published: January 2013

AbstractWith targeted childcare initiatives and welfare-to-work programmes policy-makers have sought to address employment activation of lone mothers and negative outcomes for children in lone parent households. The present study examines non-parental childcare use and maternal employment among children living in lone and co-parent family situations at ages three and four and emotional and behavioural difficulties at ages four and five. The results demonstrate that negative outcomes associated with lone motherhood are explained largely by mother's age, education, material circumstances and area deprivation; and that maternal employment does not relieve lone mothers’ disadvantages in a way that alleviates the risks of difficulties to their children. However, in any family constellation, mainly group-based formal pre-school childcare does have a positive impact on child difficulties compared to drawing on informal childcare arrangements as main provider. In addition, and specifically for the difficulties of children in lone mother family situations, any non-parental childcare – formal or informal − for at least twenty-five hours per week is beneficial. Study findings support policy agendas which tackle families’ material hardship beyond promoting mothers’ employment, and through investment in formal childcare provision, and also through arrangements allowing lone mothers to divide their weekly load of childcare with another main provider.
Organic-walled microfossils from the north-west Weddell Sea, Antarctica: records from surface sediments after the collapse of the Larsen-A and Prince Gustav Channel ice shelves
Authors: Pieńkowski Anna J. , Marret Fabienne , Scourse James D. , Thomas David N. 
Published: January 2013

AbstractSurface sediments from six box cores along the north-eastern Antarctic Peninsula document the dinoflagellate cyst (= dinocyst) and other non-pollen palynomorph (NPP) content soon after overlying ice shelves collapsed. Prince Gustav Channel (PGC) and Larsen-A (LA) areas exhibited markedly different dinocyst abundances, concentrations being low in LA (0–20 cysts g-1) and high in PGC (2600–9100 cysts g-1, average: c. 3800 cysts g-1). Since similar water masses impact both areas, differences may be due to low biological productivity, limited sediment accumulation, and/or restricted fine-grain deposition at Larsen-A. Islandinium minutum (Harland & Reid in Harland et al.) Head et al. dominated dinocyst assemblages, occurring as both excysted and encysted forms (lesser abundance). Other taxa (Echinidinium cf. transparantum Zonneveld, Impagidinium pallidum Bujak, Bitectatodinium tepikiense Wilson, Operculodinium centrocarpum Wall & Dale, Brigantedinium spp., Selenopemphix antarctica Marret & de Vernal, Polykrikos? sp. A, and Polykrikos schwartzii Bütschli) were rare. Such assemblage composition is unusual compared to previously published Southern Ocean data, but may be specific to ice shelf and/or recently ice-free environments. Alternatively, it may be attributable to excessive production facilitated by environmental factors and/or abundant food, or similar cyst morphologies produced by different dinoflagellates. Accompanying NPPs included zooplankton remains, acritarchs, and freshwater algae. Tintinnid loricae were most abundant (max. 800 g-1), followed by foraminiferal linings (max. 320 g-1), and the acritarch Palaeostomocystis fritilla (Bujak) Roncaglia (max. 150 g-1). Collectively, NPPs were more abundant in PGC compared to LA samples.
FOXgene cluster defects in alveolar capillary dysplasia associated with congenital heart disease
Authors: Laux Daniela , Malan Valérie , Bajolle Fanny , Boudjemline Younes , Amiel Jeanne , Bonnet Damien 
Published: January 2013

AbstractObjectiveThe objective was to report two new patients with the diagnosis of alveolar capillary dysplasia and congenital heart disease, to describe the associated cardiac defects seen in these cases and in the literature, and to consider recent genetic advances concerning theFOXtranscription factor gene cluster in chromosome 16q24.1q24.2.MethodsWe retrospectively analysed the records of all patients with congenital heart disease and alveolar capillary dysplasia seen in the Pediatric Cardiology Department between 2005 and 2010. We reviewed all literature published in the English language relating to cases of alveolar capillary dysplasia and congenital heart disease.ResultsTwo infants with alveolar capillary dysplasia and cardiac malformation were identified: one had an atrioventricular septal defect and a de novo balanced reciprocal translocation t(1;16)(q32;q24), the second infant had a ventricular septal defect. Analysis of 31 cases of the literature including these new cases showed a predominant association of alveolar capillary dysplasia with obstructive left heart disease (35%), as well as an atrioventricular septal defect (29%).FOXgene cluster defects were identified in eight of these patients.DiscussionGenetic background of alveolar capillary dysplasia is discussed in the light of the balanced reciprocal translocation t(1;16)(q32;q24) identified in the first child of this report. Alveolar capillary dysplasia should be suspected in neonates with congenital heart disease and unexpectedly elevated pulmonary vascular resistances, especially in cases of obstructive left heart disease or atrioventricular septal defect. DetectingFOXgene cluster defects should be considered in infants with alveolar capillary dysplasia with or without congenital heart disease.
Working Memory and Intelligence Are Associated with Victoria Symptom Validity Test Hard Item Performance in Patients With Intractable Epilepsy
Authors: Keary Therese A. , Frazier Thomas W. , Belzile Catherine J. , Chapin Jessica S. , Naugle Richard I. , Najm Imad M. , Busch Robyn M. 
Published: January 2013

AbstractLoring et al. (Journal of Clinical and Experimental Neuropsychology, 2005:27;610–617) observed relationships between VSVT hard item performance and IQ and memory indices in epilepsy surgical candidates, with a potential confound of low FSIQ on VSVT performance. The present study replicated the Loring et al. study in a larger sample and extended their findings by examining the relationships among VSVT performance, FSIQ, and working memory. A total of 404 patients with medically intractable epilepsy completed a comprehensive neuropsychological assessment. Differences in WAIS-III and WMS-III performance were examined as a function of VSVT hard score categories as determined by Grote et al. (2000)—that is,valid, >20/24;questionable, 18–20; orinvalid, <18. Quantile regression models were constructed to compare the strength of the relationship between FSIQ and VSVT at various points of the FSIQ distribution. Linear regression analyses examined working memory as a potential mediator between FSIQ and VSVT performance. Theinvalidgroup performed more poorly than thevalidandquestionablegroups on multiple measures of intelligence and memory. The strength of the relationship between FSIQ and VSVT hard item performance decreased as FSIQ increased, and working memory mediated this relationship. Results suggest VSVT hard item scores may be impacted by working memory difficulties and/or low intellectual functioning. (JINS, 2013,19, 1–10)
B-Raf is required for positive selection and survival of DP cells, but not for negative selection of SP cells
Authors: Dillon Tara J. , Takahashi Maho , Li Yanping , Tavisala Srilatha , Murray Susan E. , Moran Amy E. , Parker David C. , Stork Philip J. S. 
Published: January 2013

Abstract
The duration of signaling through the MAP kinase (or ERK pathway) cascade has been implicated in thymic development, particularly positive and negative selection. In T cells, two isoforms of the MAP kinase kinase kinase Raf function to transmit signals from the T-cell receptor to ERK: C-Raf and B-Raf. In this study, we conditionally ablated B-Raf expression within thymocytes to assess the effects on ERK activation and thymocyte development. The complete loss of B-Raf is accompanied by a dramatic loss of ERK activation in both the double positive (DP) and single positive (SP) thymocytes, as well as peripheral splenocytes. There was a significant decrease in the cellularity of KO thymi, largely due to a loss of pre-selected DP cells, a decrease in DP cells undergoing positive selection, and a defect in SP maturation. B-Raf plays significant roles in survival of DP thymocytes and function of SP cells in the periphery. Surprisingly, we saw no effect of B-Raf deficiency on negative selection of autoreactive SP thymocytes, despite the greatly reduced ERK activation in these cells.
Association of human leukocyte antigen class I antigens in Iranian patients with pemphigus vulgaris
Authors: Mortazavi Hossein , Amirzargar Ali Akbar , Esmaili Nafiseh , Toofan Hesam , Ehsani Amir Hooshang , Hosseini Seyed Hamed , Rezaei Nima 
Published: January 2013

AbstractThere are a limited number of reports indicating the role of human leukocyte antigen (HLA) class I alleles in pemphigus vulgaris. This study was designed to highlight the association of HLA class I alleles with pemphigus vulgaris in Iran. Fifty patients with pemphigus vulgaris, diagnosed based on clinical, histological and direct immunofluorescence findings were enrolled into this study. The control group consisted of 50 healthy, age‐ and sex‐matched individuals. HLA typing of class I (A, B and C alleles) was carried out using polymerase chain reaction based on the sequence‐specific primer method. This study showed the higher frequency of HLA‐B*44:02 (P = 0.007), ‐C*04:01 (P < 0.001), ‐C*15:02 (P < 0.001) and ‐C*16:01 (P = 0.027) in the patient group, compared to the controls, while the frequency of HLA‐C*06:02 (P < 0.001) and ‐C*18:01 (P = 0.008) in the patients with pemphigus vulgaris was significantly lower than the controls. Regarding the linkage disequilibrium between HLA class I alleles, the HLA‐A*03:01, ‐B*51:01, ‐C*16:02 haplotype (4% vs 0%, P = 0.04) is suggested to be a predisposing factor, whereas HLA‐A*26:01, ‐B*38, ‐C*12:03 haplotype (0% vs 6%, P = 0.01) is suggested to be a protective factor. In conclusion, it is suggested that HLA‐B*44:02, ‐C*04:01, ‐C*15:02 alleles and HLA‐A*03:01, ‐B*51:01, ‐C*16:02 haplotype are susceptibility factors for development of pemphigus vulgaris in the Iranian population, while HLA‐C*06:02, ‐C*18:01 alleles and HLA‐A*26:01, ‐B*38, ‐C*12:03 haplotype may be considered as protective alleles.
Spatial spread of Eurasian beavers in river networks: a comparison of range expansion rates
Authors: Barták Vojtěch , Vorel Aleš , Šímová Petra , Puš Vladimír 
Published: January 2013

Summary

Accurately measuring the rate of spread for expanding populations is important for reliably predicting their future spread, as well as for evaluating the effect of different conditions and management activities on that rate of spread.

Although a number of methods have been developed for such measurement, all these are designed only for one‐ or two‐dimensional spread. Species dispersing along rivers, however, require specific methods due to the distinctly branching structure of river networks.

In this study, we analyse data regarding Eurasian beavers' modern recolonization of the Czech Republic. We developed a new methodology for quantifying spread of species dispersing along streams based on representation of the river network by means of a weighted graph.

We defined two different network‐based spread rate measures, one estimating the rate of range expansion, with the range defined as the total length of occupied streams, and the second, named range diameter, quantifying the progress along one or several main streams. In addition, we estimated the population growth rates, and, dividing the population size by the range size, we measured the density of beaver records within their overall range. Using linear regression, we compared four beaver populations under different environmental conditions in terms of each of these measures. Finally, we discuss the differences between our method and the classical approaches.

Our method provided substantially higher spread rate values than did the classical methods. Both population growth and range expansion were found to follow logistic growth. In cases of there being no considerable barriers in dispersal routes, the rate of progress along main streams did not differ significantly among populations. In homogeneous environments, population densities remained relatively constant over time even though overall population sizes increased. This indicates that at large spatial scales, the population growth of beavers occurs through progressive space filling rather than increasing population density.