bluuebunny/crossref_metadata_2025_split huggingface dataset:
Birt–Hogg–Dubé syndrome: novel FLCN frameshift deletion in daughter and father with renal cell carcinomas
Authors: Näf Ernst , Laubscher Dominik , Hopfer Helmut , Streit Markus , Matyas Gabor 
Published: September 2015

Abstract
Germline mutation of the FLCN gene causes Birt–Hogg–Dubé syndrome (BHD), a rare autosomal dominant condition characterized by skin fibrofolliculomas, lung cysts, spontaneous pneumothorax and renal tumours. We identified a hitherto unreported pathogenic FLCN frameshift deletion c.563delT (p.Phe188Serfs*35) in a family of a 46-year-old woman presented with macrohematuria due to bilateral chromophobe renal carcinomas. A heritable renal cancer was suspected due to the bilaterality of the tumour and as the father of this woman had suffered from renal cancer. Initially, however, BHD was overlooked by the medical team despite the highly suggestive clinical presentation. We assume that BHD is underdiagnosed, at least partially, due to low awareness of this variable condition and to insufficient use of appropriate genetic testing. Our study indicates that BHD and FLCN testing should be routinely considered in patients with positive family or personal history of renal tumours. In addition, we demonstrate how patients and their families can play a driving role in initiating genetic diagnosis, presymptomatic testing of at-risk relatives, targeted disease management, and genetic counselling of rare diseases such as BHD.
An Up-regulation of IRF-1 After a Spinal Cord Injury: Implications for Neuronal Apoptosis
Authors: Zhao Jian , Chen Chen , Xiao Jian-Ru , Wei Hai-Feng , Zhou Xu-hui , Mao Xing-Xing , Zhang Wei-dong , Qian Rong , Chen Xin-lei , He Ming-qing , Yu Xiao-Wei , Zhao Jian 
Published: September 2015

AbstractIRF-1, a kind of transcription factor, is expressed in many cell types, except in early embryonal cells. IRF-1 has played an essential role in various physiological and pathological processes, including tumor immune surveillance, viral infection, development of immunity system and pro-inflammatory injury. However, the expression and function of IRF-1 in spinal cord injury (SCI) are still unknown. In this study, we have performed an acute SCI model in adult rats and investigated the dynamic changes of IRF-1 expression in the spinal cord. Western blot have shown that IRF-1 protein levels gradually increased, reaching a peak at day 3 and then gradually declined to a normal level at day 14 after SCI. Double immunofluorescence staining showed that IRF-1 immunoreactivity was found in neurons, but not in astrocytes and microglia. Additionally, colocalization of IRF-1/active caspase-3 was detected in neurons. In vitro, IRF-1 depletion, by short interfering RNA, obviously decreases neuronal apoptosis. In conclusion, this is the first description of IRF-1 expression in spinal cord injury. Our results suggested that IRF-1 might play crucial roles in CNS pathophysiology after SCI.
Adolescent obesity and future substance use: Incorporating the psychosocial context
Authors: Lanza H. Isabella , Grella Christine E. , Chung Paul J. 
Published: September 2015

ABSTRACTA growing body of work has shown that obese adolescents are at risk of engaging in problematic substance use, but mixed findings highlight the complexity of the relationship. Incorporating the psychosocial context into this research may inform past discrepancies. The current study assessed whether obese adolescents had a higher likelihood of experiencing a psychosocial context that predicted problematic substance use in young adulthood. Latent class analysis on 10,637 adolescents from The National Longitudinal Study of Adolescent to Adult Health (Add Health) identified four psychosocial classes in adolescence: Adjusted, Deviant Peer/Victimization, Moderate Depression, and Maladjusted. Obese adolescents were more likely to belong to the Maladjusted class, characterized by higher levels of depression and deviant peer affiliation. Those in the Maladjusted class had the second highest levels of cigarette smoking and marijuana use in young adulthood. Obese adolescents' psychosocial context should be considered in future research linking obesity and substance use.
Music and Catholic culture in post-Reformation Lancashire: piety, protest, and conversion
Authors: Murphy Emilie K. M. 
Published: September 2015

AbstractThis essay adds to our existing understanding of what it meant to be a member of the English Catholic community during the late Elizabeth and early Stuart period by exploring Catholic musical culture in Lancashire. This was a uniquely Catholic village, which, like the majority of villages, towns and cities in early modern England, was filled with the singing of ballads. Ballads have almost exclusively been treated in scholarship as a ‘Protestant’ phenomenon and the ‘godly ballad’ associated with the very fabric of a distinctively Protestant Elizabethan and Stuart entertainment culture. By investigating the songs and ballads in two manuscript collections from the Catholic network surrounding the Blundell family this essay will show how Catholics both composed and ‘converted’ existing ballads to voice social, devotional, and political concerns. The ballads performed in Little Crosby highlight a vibrant Catholic community, where musical expression was fundamental. Performance widened the parochial religious divide, whilst enhancing Catholic integration. This essay uncovers the way Catholics used music to voice religious and exhort protest as much as prayer. Finally, by investigating the tunes and melodies preserved in the manuscripts, I demonstrate how priests serving this network used ballads as part of their missionary strategy.
Impact of Personal Relevance on Acquisition and Generalization of Script Training for Aphasia: A Preliminary Analysis
Authors: Cherney Leora R. , Kaye Rosalind C. , Lee Jaime B. , van Vuuren Sarel 
Published: September 2015

Purpose
The importance of personalization in script training in aphasia has been assumed but never tested. This study compared acquisition and generalization of personally relevant versus generic words or phrases appearing in the same scripts.

Method
Eight individuals (6 men; 2 women) with chronic aphasia received 3 weeks of intensive computer-based script training. For each participant, 2 scripts, a trained and an untrained generalization script, were embedded with 4 personally relevant word choices and 2–4 generic items that were similar across participants. Scripts were probed for accuracy at baseline and posttreatment. Significance testing was conducted on baseline and posttreatment scores, and for gains in personally relevant versus generic items. Effect sizes were computed.

Results

Both personally relevant and generic items improved significantly on trained scripts. Improvements on untrained scripts were smaller, with only personally relevant items reaching significance. There was no significant difference on gains made on personalized versus generic items for trained scripts (
p
= .059), but the effect size was large (
d
= 0.90). For generalization scripts, this effect was small (
d
= 0.25) and nonsignificant.

Conclusions
Personally relevant words and phrases were acquired, although not generalized, more successfully than generic words and phrases. Data supports the importance of personalization in script training, but the degree of that importance requires further investigation.
Cervical Myeloradiculopathy due to Ossification of the Posterior Longitudinal Ligament with versus without Diffuse Idiopathic Spinal Hyperostosis
Authors: Tauchi Ryoji , Lee Sang-Hun , Peters Colleen , Imagama Shiro , Ishiguro Naoki , Riew K. Daniel 
Published: September 2015

Study Design Retrospective study. Objectives Assess demographics, ossification characteristics, surgical outcomes, and complications in patients with both diffuse idiopathic spinal hyperostosis (DISH) and ossification of the posterior longitudinal ligament (OPLL) compared with patients who only have OPLL. Methods Clinical charts and radiographs of all patients treated surgically from February 2004 to July 2012 for cervical myeloradiculopathy due to DISH with OPLL or OPLL alone were reviewed retrospectively. All patients were observed for a minimum of 1 year. Pre- and postoperative Nurick grades were assessed for all patients. Results Forty-nine patients underwent surgical treatment for cervical myeloradiculopathy due to OPLL, and 8 also had DISH (average 58.9 years, range 37 to 70). The DISH with OPLL group had a significantly higher proportion of subjects with diabetes mellitus (50 versus 9.8% in the OPLL-only group). Everyone in the DISH with OPLL group had continuous or mixed-type OPLL, whereas 78% of patients in the OPLL-only group had primarily segmental type. Operative treatments for patients in the DISH with OPLL group included laminoplasty, anterior decompression and fusion, and posterior laminectomy with fusion. By Nurick grade, 5 patients improved and 3 showed no change. Conclusion Patients with both DISH and OPLL had a higher prevalence of diabetes mellitus and either continuous or mixed-type OPLL classifications. Surgical outcomes were mostly satisfactory; there was no aggravation of symptoms after surgery during the follow up period.
Correlations of Cervical Sagittal Alignment before and after Occipitocervical Fusion
Authors: Matsubayashi Yoshitaka , Shimizu Takachika , Chikuda Hirotaka , Takeshita Katsushi , Oshima Yasushi , Tanaka Sakae 
Published: September 2015

Study Design Retrospective radiographic study. Objective To investigate changes and correlations of cervical sagittal alignment including T1 slope before and after occipitocervical corrective surgery. We also investigated the relevance for preoperative planning. Methods We conducted a retrospective radiographic analysis of 27 patients who underwent surgery for occipitocervical deformity. There were 7 men and 20 women with a mean age of 56.0 years. Mean follow-up was 68.0 months (range 24 to 120). The radiographic parameters measured before surgery and at final follow-up included McGregor slope, T1 slope, occipito (O)–C2 angle, O–C7 angle, and C2–C7 angle. Pearson correlation coefficient was used to examine the correlation between the radiographic parameters. Results There was a stronger positive correlation between the T1 slope and the O–C7 angle both preoperatively and postoperatively ( r = 0.72 and r = 0.83, respectively) than between the T1 slope and the C2–C7 angle ( r = 0.60 and r = 0.76, respectively). The O–C2 angle and C2–C7 angle had inverse correlations to each other both pre- and postoperatively ( r = − 0.50 and −0.45). McGregor slope and T1 slope did not significantly change postoperatively at final follow-up. Increase in O–C2 angle after surgery (mean change, 10.7 degrees) inversely correlated with decrease in postoperative C2–C7 angle (mean change, 12.2 degrees). As result of these complementary changes, O–C7 angle did not statistically change. Conclusions Our results suggest that the O–C7 angle is regulated by T1 slope and the corresponding O–C7 angle is divided into the O–C2 and C2–C7 angles, which have inverse correlation to each other and then maintain McGregor slope (horizontal gaze).
Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis
Authors: Gao Qiaozi , Ostendorf Elisabeth , Cruz Jeffrey A. , Jin Rong , Kramer David M , Chen Jin 
Published: September 2015

Abstract
Motivation: Phenomics is the study of the properties and behaviors of organisms (i.e. their phenotypes) on a high-throughput scale. New computational tools are needed to analyze complex phenomics data, which consists of multiple traits/behaviors that interact with each other and are dependent on external factors, such as genotype and environmental conditions, in a way that has not been well studied.
Results: We deployed an efficient framework for partitioning complex and high dimensional phenotype data into distinct functional groups. To achieve this, we represented measured phenotype data from each genotype as a cloud-of-points, and developed a novel non-parametric clustering algorithm to cluster all the genotypes. When compared with conventional clustering approaches, the new method is advantageous in that it makes no assumption about the parametric form of the underlying data distribution and is thus particularly suitable for phenotype data analysis. We demonstrated the utility of the new clustering technique by distinguishing novel phenotypic patterns in both synthetic data and a high-throughput plant photosynthetic phenotype dataset. We biologically verified the clustering results using four Arabidopsis chloroplast mutant lines.
Availability and implementation: Software is available at www.msu.edu/~jinchen/NPM.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: jinchen@msu.edu, kramerd8@cns.msu.edu or rongjin@cse.msu.edu
Evolutionary quantitative genomics ofPopulus trichocarpa
Authors: Porth Ilga , Klápště Jaroslav , McKown Athena D. , Mantia Jonathan La , Guy Robert D. , Ingvarsson Pär K. , Hamelin Richard , Mansfield Shawn D. , Ehlting Jüergen , Douglas Carl J. , El-Kassaby Yousry A. 
Published: September 2015

AbstractForest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management.Merging quantitative genetics and population genomics, we studied the molecular basis of climate adaptation in 433Populus trichocarpa(black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparingQST-FST) using clustering of individuals by climate of origin. 29,354 SNPs were investigated employing three different outlier detection methods.Narrow-sense QSTfor 53% of distinct fieldQSTtraits was significantly divergent from expectations of neutrality (indicatingadaptivetrait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significantQST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance.Evolutionary quantitative genomics inP. trichocarpaprovides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees. We highlight that important loci underlyingadaptivetrait variation also show relationship to climate of origin.Author summaryComparisons between population differentiation on the basis of quantitative traits and neutral genetic markers inform about the importance of natural selection, genetic drift and gene flow for local adaptation of populations. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Marker-inferred relatedness was estimated to obtain thenarrow-senseestimate of population differentiation in wild populations. We analyzed an unstructured population of common garden grownPopulus trichocarpaindividuals to uncover different extents of variation for a suite of field traits, wood quality and pathogen resistance with temperature and precipitation. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species’ potential adaptive capacity to future climatic scenarios.
Facilitating systematic reviews, data extraction and meta‐analysis with the metagear package for r
Authors: Lajeunesse Marc J. 
Published: September 2015

Summary

The r package ecosystem is rich in tools for the statistics of meta‐analysis. However, there are few resources available to facilitate research synthesis as a whole.

Here, I present the metagear package for r. It is a comprehensive, multifunctional toolbox with capabilities aimed to cover much of the research synthesis taxonomy: from applying a systematic review approach to objectively assemble and screen the literature, to extracting data from studies, and to finally summarize and analyse these data with the statistics of meta‐analysis.

Current functionalities of metagear include the following: an abstract screener GUI to efficiently sieve bibliographic information from large numbers of candidate studies; tools to assign screening effort across multiple collaborators/reviewers and to assess inter‐reviewer reliability using kappa statistics; PDF downloader to automate the retrieval of journal articles from online data bases; automated data extractions from scatter‐plots, box‐plots and bar‐plots; PRISMA flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random‐effects sizes for Hedges' d, log response ratio, odds ratio and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g. with a common control, phylogenetic correlations); and finally, summaries that replicate analyses and outputs from widely used but no longer updated meta‐analysis software.

Research synthesis practices are vital to many disciplines in the sciences, including ecology and evolutionary biology, and metagear aims to enrich the scope, quality and reproducibility of what can be achieved with the systematic review and meta‐analysis of research outcomes.
Body posture during simulated tracheal intubation: GlideScope® videolaryngoscopy vs Macintosh direct laryngoscopy for novices and experts
Authors: Grundgeiger T. , Roewer N. , Grundgeiger J. , Hurtienne J. , Happel O. 
Published: September 2015

SummaryTracheal intubation requires the anaesthetist to adopt an awkward body posture. To investigate how posture may be improved, we compared the effects of laryngoscopy technique (GlideScope® vs Macintosh blade) and experience (novices vs experts) on body posture angles and the Rapid Entire Body Assessment postural analysis score. Novices (25 medical students) and experts (26 anaesthetists) were video‐recorded performing intubation in a manikin using both devices. The GlideScope resulted in smaller deflections for all analysed posture angles (all p values < 0.001) except the wrist compared with the Macintosh blade. Novices showed more trunk (p < 0.001) and neck (p = 0.002) flexion than experts. Using the GlideScope resulted in a lower Rapid Entire Body Assessment score compared with using the Macintosh blade (p < 0.001), indicating that the GlideScope resulted in body posture less likely to induce musculoskeletal injuries. From an ergonomic point of view, the GlideScope should be the preferred technique for laryngoscopy.
Recurrence of gestational diabetes in primiparous women
Authors: Kruse Anne R. , Darling Mette S. , Hansen Mia K. L. , Markman Miriam J. , Lauszus Finn F. , Wielandt Hanne B. 
Published: September 2015

AbstractIntroductionGestational diabetes mellitus (GDM) increases the risk for diabetes in the next pregnancy and later in life. Thus, estimating the risk of GDM in further pregnancies provides a time frame for possible preventive measures. We aimed to calculate the recurrence rate of GDM in primiparous women and evaluate the factors involved such as age, body mass index, weight gain, time between pregnancy and postpartum OGTT results.Material and methodsWe established a prospective cohort during a 5‐year period at the Department of Obstetrics at Kolding Hospital. Women with diet‐treated GDM in their first pregnancy and a subsequent pregnancy constituted our study population. Multiparity and insulin‐treated GDM were exclusion criteria.ResultsAmong 15 735 deliveries, 535 women were diagnosed with GDM (3.4%). Of these, 209 (39.1%) were nulliparous women, treated with diet only. Seventy‐two of these women had a subsequent pregnancy and they all attended the recommended screening procedure, a 75‐g oral glucose tolerance test at 14–20 (early) or 27–30 (late) weeks' gestation. The recurrence rate of GDM was 47.2%. The risk of recurrence was less in women who lost weight between the first and the subsequent pregnancy.ConclusionsRecurrence of diet‐treated GDM was 47.2% in primiparous women with previous GDM and the recurrence was associated with weight gain between pregnancies.
Pharmaceutical and clinical development of a novel progesterone formulation
Authors: Cometti Barbara 
Published: September 2015

AbstractProgesterone plays an essential role in reproductive events. Its use for luteal support in patients undergoing infertility treatment is an established practice. The different routes used to administer progesterone impact on its efficacy in luteal support: oral administration has been shown to be ineffective due to an extensive first‐pass metabolism in the liver; vaginal application has a good efficacy but has drawbacks such as vaginal leakage, irritation, discomfort and uncertainty about the real dose adsorbed; finally, intramuscular administration ensures a precise dosage but can be extremely painful with, in some cases, formation of sterile abscesses. A new progesterone preparation is now available in several European and extra‐European countries that combines the precise dosage of the injectable formulation with the comfort of a well‐tolerated subcutaneous self‐administration. The pharmacokinetic and pharmacodynamic properties of this new product are reviewed here, together with the clinical evidence obtained in two multicenter randomized clinical trials.
A comparison of postoperative pain after transumbilical single‐port access and conventional three‐port total laparoscopic hysterectomy: a randomized controlled trial
Authors: Chung Ji‐Hyun , Baek Jong Min , Chung Kyudon , Park Eun Kyung , Jeung In Cheul , Chang Hyun Tae , Choi Ji Hyang , Kim Chan Joo , Lee Yong Seok 
Published: September 2015

AbstractIntroductionThe objective of this study was to compare postoperative pain between single‐port access total laparoscopic hysterectomy (SPA‐TLH) using a transumbilical single‐port system and conventional multi (three)‐port access total laparoscopic hysterectomy (MPA‐TLH).Material and methodsA randomized controlled trial was conducted on 60 women who underwent SPA‐TLH and MPA‐TLH for benign gynecologic diseases between March 2014 and January 2015. Patients were randomly assigned to undergo SPA‐TLH (n = 30) or MPA‐TLH (n = 30). The variables measured included surgical outcomes and postoperative pain at 30 min and 1, 12, 24, and 48 h after surgery, assessed by the visual analog scale, bolus requirement of intravenous patient‐controlled analgesia, and additional analgesic use.ResultsThe two study groups did not differ in terms of patient demographics or surgical outcomes except for operative time. The SPA‐TLH group had a longer operative time (p < 0.0001) compared with the MPA‐TLH groups. There were no differences in pain scores between the two groups. The SPA‐TLH group had significantly more intravenous analgesia requests during the 12–24 h after surgery (2.17 ± 3.05 vs. 0.79 ± 1.99; p = 0.047), more 24–48 h postoperative analgesics (0.21 ± 0.41 vs. 0.03 ± 0.19; p = 0.045), and more total additional analgesics (0.97 ± 0.94 vs. 0.45 ± 0.87; p = 0.034).ConclusionSPA‐TLH was feasible compared with MPA‐TLH but the SPA‐TLH group had a longer operative time. Although there is no difference in pain based on the visual analog scale pain score, the SPA‐TLH group required more analgesia to give the same postoperative pain control.