bluuebunny/crossref_metadata_2025_split huggingface dataset:
SEQMINER: An R‐Package to Facilitate the Functional Interpretation of Sequence‐Based Associations
Authors: Zhan Xiaowei , Liu Dajiang J. 
Published: September 2015

ABSTRACTNext‐generation sequencing has enabled the study of a comprehensive catalogue of genetic variants for their impact on various complex diseases. Numerous consortia studies of complex traits have publically released their summary association statistics, which have become an invaluable resource for learning the underlying biology, understanding the genetic architecture, and guiding clinical translations. There is great interest in the field in developing novel statistical methods for analyzing and interpreting results from these genotype‐phenotype association studies. One popular platform for method development and data analysis is R. In order to enable these analyses in R, it is necessary to develop packages that can efficiently query files of summary association statistics, explore the linkage disequilibrium structure between variants, and integrate various bioinformatics databases. The complexity and scale of sequence datasets and databases pose significant computational challenges for method developers. To address these challenges and facilitate method development, we developed the R package SEQMINER for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases. SEQMINER provides an infrastructure where novel methods can be distributed and applied to analyzing sequence datasets in practice. We illustrate the performance of SEQMINER using datasets from the 1000 Genomes Project. We show that SEQMINER is highly efficient and easy to use. It will greatly accelerate the process of applying statistical innovations to analyze and interpret sequence‐based associations. The R package, its source code and documentations are available from http://cran.r‐project.org/web/packages/seqminer and http://seqminer.genomic.codes/.
Predictors of psychiatric re‐hospitalization in older adults with severe mental illness
Authors: Yu Ching , Sylvestre Jean‐Daniel , Segal Marilyn , Looper Karl J. , Rej Soham 
Published: September 2015

ObjectiveMany patients with severe recurrent mental illness are approaching late life; however, little is known about psychiatric re‐hospitalization in this population. Our objective was to identify predictors of psychiatric re‐hospitalization.MethodsThis was a retrospective cohort study of all 226 geriatric patients (age ≥65 years) admitted to a tertiary care Canadian inpatient psychiatric unit between 2003 and 2008. The main outcome was psychiatric re‐hospitalization in 5‐year follow‐up post‐discharge (e.g. 2008–2013 if a patient had been first admitted in 2008). Multivariate Cox regression analyses were used to identify potential predictors of re‐hospitalization.ResultsOver 5‐year follow‐up, 32.3% (73/226) required psychiatric re‐hospitalization. Prior lifetime history of psychiatric admission, currently living in a supervised setting and bipolar disorder diagnosis all independently predicted a lower time to psychiatric re‐hospitalization (HRs > 2.0, p < 0.05).ConclusionsThe rate of psychiatric re‐hospitalization is high in older adults admitted for severe mental illness. Clinicians should be aware of the especially high rates of re‐hospitalization in geriatric psychiatric inpatients with bipolar disorder, previous psychiatric admissions, or those living in a supervised setting. Future research could investigate approaches to prevent psychiatric re‐hospitalization in these vulnerable sub‐populations. Copyright © 2015 John Wiley & Sons, Ltd.
Thyroid endocrine disruption of acetochlor on zebrafish (Danio rerio) larvae
Authors: Yang Mei , Hu Jingjin , Li Shuying , Ma Youning , Gui Wenjun , Zhu Guonian 
Published: September 2015

AbstractThe herbicide acetochlor is widely used and detected in the environment and biota, and has been suspected to disrupt the thyroid endocrine system, but underlying mechanisms have not yet been clarified. In the present study, zebrafish larvae (7 days post‐fertilization) were exposed to a series concentration of acetochlor (0, 1, 3, 10, 30, 100 and 300 µg l−1) within a 14‐day window until 21 days post‐fertilization. Thyroid hormones and mRNA expression profiles of genes involved in the hypothalamic–pituitary–thyroid (HPT) axis were analyzed. Exposure to the positive control, 3,5,3′‐triiodothyronine (T3), altered the mRNA expression, suggesting that the HPT axis in the critical window of zebrafish responded to chemical exposure and could be used to evaluate the effects of chemicals on the thyroid endocrine system. The mRNA expressions of genes involved in thyroid hormone synthesis (tshβ, slc5a5 and tpo) were upregulated significantly with acetochlor treatment, which might be responsible for the increased thyroxine concentrations. The downregulation of genes related to thyroid hormone metabolism (dio1 and ugt1ab) and transport (ttr) in zebrafish larvae exposed to acetochlor might further explain the increased thyroxine levels and decreased T3 levels. The mRNA expression of the thyroid hormone receptor (trα) was also upregulated upon acetochlor exposure. Results suggested that acetochlor altered mRNA expression of the HPT axis‐related genes and changed the whole body thyroid hormone levels in zebrafish larvae. It demonstrated that acetochlor could cause endocrine disruption of the thyroid system by simulating the biological activity of T3. Copyright © 2015 John Wiley & Sons, Ltd.
Osteology of Priocharax and remarkable developmental truncation in a miniature Amazonian fish (Teleostei: Characiformes: Characidae)
Authors: Mattox George M.T. , Britz Ralf , Toledo‐Piza Mônica 
Published: September 2015

ABSTRACTEstablishing phylogenetic relationships of miniature fishes is challenging in taxa with developmental truncation. Within the Characiformes, developmental truncation appears to be relatively rare, with the Neotropical genus Priocharax being an example. Priocharax includes three miniature species among the smallest of the order and has been hypothesized to belong to the Heterocharacinae. The pronounced reduction in its skeleton, however, prevented a clearer evaluation of its relationships. The present detailed osteological study was designed to address this question and revealed that 21 bones are absent and nine other skeletal structures are simplified in Priocharax when compared to other characids. Comparison of the skeleton of adult Priocharax with early developmental stages of other characids demonstrated that most of the absences and simplifications can be interpreted as developmental truncations. The most striking developmental truncations are in the pectoral girdle, in which the endoskeleton remains entirely cartilaginous. Other interesting truncations are in the ethmoid region of the skull, infraorbital series, and Weberian apparatus, in which the claustrum is absent. Our study also revealed some unusual sexual dimorphisms in the pelvic girdle. Two cladistic analyses were performed to assess the relationships of Priocharax within the Heterocharacinae. The first consisted of a traditional analysis in which all absences and reductions of Priocharax were coded in the same way as in the remaining taxa. This resulted in three equally most parsimonious topologies, all of which have Priocharax as the most basal taxon of the Heterocharacinae. The second analysis incorporated ontogenetic information, and most absences and reductions of Priocharax were reinterpreted as apomorphic conditions and thus, coded differently from similar conditions in outgroups. This resulted in a single phylogenetic hypothesis with Priocharax and Gnathocharax as sister groups based on seven synapomorphies. Our approach demonstrates the importance of developmental studies to better understand morphological evolution of miniaturized, truncated taxa, and to generate hypotheses of their relationships. J. Morphol. 277:65–85, 2016. © 2015 Wiley Periodicals, Inc.
The Impact of Infidelity on Combat‐Exposed Service Members
Authors: Kachadourian Lorig K. , Smith Brian N. , Taft Casey T. , Vogt Dawne 
Published: September 2015

AbstractThis study examined relationships between combat‐exposed Operation Enduring Freedom/Operation Iraqi Freedom veterans’ experiences related to infidelity during deployment (i.e., indicating that a partner was unfaithful or reporting concern about potential infidelity) and postdeployment mental health, as well as the role of subsequent stress exposure and social support in these associations. The sample consisted of 571 individuals (338 men). There were 128 participants (22.2%) who indicated that their partners were unfaithful during their most recent deployment. Of the remaining 443 participants, 168 (37.8%) indicated that they were concerned that their partners might have been unfaithful. Individuals who indicated that their partners were unfaithful exhibited higher levels of posttraumatic stress symptomatology (β = .08; f2= .18) and depression symptom severity (β = .09; f2 = .14), compared to individuals who did not indicate that their partners were unfaithful. For both men and women, reported infidelity was associated with mental health indirectly via postdeployment life stressors, whereas infidelity concerns were indirectly associated with mental health via postdeployment life stressors for men only. Findings suggested that infidelity can have a significant impact on combat‐exposed veterans’ mental health and highlight the need for additional research on this understudied topic within the military population.
A Genetic Algorithm–Based Method for the Optimization of Reduced Kinetics Mechanisms
Authors: Sikalo Nejra , Hasemann Olaf , Schulz Christof , Kempf Andreas , Wlokas Irenäus 
Published: September 2015

ABSTRACTThis paper describes an automatic method for the optimization of reaction rate constants of reduced reaction mechanisms. The optimization technique is based on a genetic algorithm that aims at finding new reaction rate coefficients that minimize the error introduced by the preceding reduction process. The error is defined by an objective function that covers regions of interest where the reduced mechanism may deviate from the original mechanism. The mechanism's performance is assessed for homogeneous reactor or laminar‐flame simulations against the results obtained from a given reference—the original mechanism, another detailed mechanism, or experimental data, if available. The overall objective function directs the search towards more accurate reduced mechanisms that are valid for a given set of operating conditions. An optional feature to the objective function is a penalty term that permits to minimize the change to the reaction coefficients, keeping them as close as possible to the original value. This means that the penalty function can be used to constrain the reaction rates modifications during the optimization if needed. It is demonstrated that the penalty function is successful and can be combined with predefined uncertainty bounds for each reaction of the mechanism. In addition, the penalty function can be modified to achieve a further reduction of the mechanism. The algorithm is demonstrated for the optimization of a previously reduced variant of the GRI‐Mech 3.0, a tert‐butanol combustion mechanism by Sarathy et al. (Combust. Flame, 2012, 159, 2028–2055) and a hydrogen mechanism by Konnov (Combust. Flame, 2008, 152, 507–528), for which the complete uncertainty vector is known. The method has shown to be, robust, flexible, and suitable for a wide range of operating conditions by using multiple criteria simultaneously.
Quantifying the distribution and influence of non‐uniform bed properties in shallow coastal bays
Authors: Wiberg Patricia L. , Carr Joel A. , Safak Ilgar , Anutaliya Arachaporn 
Published: September 2015

AbstractSediment resuspension and related increases in turbidity in shallow coastal bays are strongly controlled by local bed properties. However, knowledge of bed properties in coastal bays is typically sparse at best. In this study, we developed a method to estimate the spatial distribution of bed properties in shallow coastal bays using a combination of bed sediment measurements and residence time calculations that requires neither extensive dedicated modeling nor extensive sampling. We found a strong relationship between water residence times derived from a coastal hydrodynamic model and observed bed grain size fractions in a system of coastal bays and used that relationship to transform maps of residence time to maps of grain size fractions throughout the bays. Because grain‐size fractions are related to other bed properties such as organic fraction, permeability and cohesion, these maps provide valuable information for habitat studies as well as morphodynamic modeling. We used our maps of grain size distributions to initialize a 2‐month‐long model simulation of currents, waves and suspended sediment forced with measured wind and tides. Spatial variations in suspended sediment concentration (SSC) reflected spatial gradients in sand and mud abundance in the bed. Lower SSC in sandier regions of the bays, near barrier islands and inlets, resulted in higher benthic light availability but lower sediment supply for deposition on back‐barrier marshes. Higher SSC in more landward, muddier regions resulted in greater light attenuation and sediment availability for deposition on mainland fringing marshes. The proposed methodology facilitates quantification of these bed‐dependent spatial variations in SSC.
Nomogram for determining the lower normal limits for radial sensory nerve action potentials
Authors: Panagiotis Kokotis , Alexandra Antelli , Nikos Karandreas 
Published: September 2015

ABSTRACTIntroduction: In this study we aimed to determine the normal lower limits of sensory nerve action potential (SNAP) amplitude of the radial nerve by taking into account age, height, weight, and body mass index (BMI). Methods: Three hundred thirty‐four volunteers, 168 men and 166 women, were recruited. Sensory nerve conduction studies of the radial nerve were performed, and reproducible waveforms were obtained. Results: The mean radial SNAP amplitude was 44.87 ± 14.58 (range 24–92) μV. SNAP amplitude had a statistically strong negative correlation with age, height, weight, and BMI of the subjects. A multiple linear correlation equation was computed, based on age and BMI of the subjects, to calculate the lower normal limits of radial SNAP and to construct the corresponding nomogram. Conclusion The lower limit of normal SNAP amplitude of the radial nerve, determined in individual subjects using the nomogram, is a useful tool for detection of polyneuropathy. Muscle Nerve 53: 136–139, 2016
Pelvic floor muscle training for female stress urinary incontinence: Five years outcomes
Authors: Beyar Netta , Groutz Asnat 
Published: September 2015

AimTo evaluate the clinical status, lower urinary tract symptoms (LUTS) and quality of life (QOL) 5 years after completion of a pelvic floor muscle training (PFMT) program for female stress urinary incontinence (SUI).MethodsTwo hundred and eight consecutive women who underwent a guided PFMT program as first‐line management of SUI were invited to participate in a questionnaire‐based outcome study 5 years after treatment. Primary outcome measures comprised of adherence to PFMT, interim surgery for SUI, and patients’ self‐assessment of LUTS and QOL.ResultsOne hundred and thirty‐two (63%) women completed all questionnaires, 55 of whom (41.7%, mean age 52.1 ± 10.8) reported adherence to PFMT, 75 (56.8%, mean age 49.8 ± 10.8) discontinued training, and two (1.5%) underwent surgery. Further analysis of the 76 non‐responders revealed six more patients who underwent surgery. Thus, overall, eight patients (3.8% of the original cohort) underwent surgery within 5 years after completion of the training program. Except for those who underwent surgery, almost all women reported SUI, however their ICIQ‐UI scores for frequency and amount of leakage were low (2.2 ± 0.9, 1.18 ± 1.04, respectively) and I‐QOL score was high (96.2 ± 13.6). All investigated parameters and domains, in each of the three questionnaires and among all women, consistently demonstrated low severity of LUTS and relatively high continence‐associated QOL. There were no statistically significant differences in favor of adherence to PFMT.ConclusionsAlthough relatively high rates of 5‐year adherence to training were demonstrated among our patients, this adherence was not associated with superior treatment outcomes. Further studies are needed to establish the long‐term efficacy of PFMT for SUI. Neurourol. Urodynam. 36:132–135, 2017. © 2015 Wiley Periodicals, Inc.
Biocultural Consequences of Spanish Contact in the Lambayeque Valley Region of Northern Peru: Internal Enamel Micro‐Defects as Indicators of Early Life Stress
Authors: Garland C. J. , Turner B. L. , Klaus H. D. 
Published: September 2015

AbstractThe present study utilises dental histological methods to analyse enamel micro‐defects as indicators of early life stress in indigenous Muchik individuals interred at two sites: La Capilla Santa María Magdalena de Eten (CSMME) (n = 15) and La Capilla del Niño Serranito (CNS) (n = 15), both located in the Lambayeque Valley region of northern Peru. Individuals interred at CNS date to the Early Colonial Period (AD 1533–1610), and individuals interred at CSMME date to the Middle/Late Colonial Period (AD 1625–1760), thus permitting comparison of childhood stress events between the Early and Middle/Late Colonial Periods. Results reveal a high prevalence of Wilson bands at both sites, although a lower prevalence at the CSMME was observed in comparison with the CNS. This indicates that, over time, Muchik individuals in this town may have been able to acclimate to life under Spanish oppression. Stress chronologies suggest that early life stress possibly resulted from inadequate and less than desirable food and/or water available for supplemental feeding during early infancy, especially around the ages of 4 and 5 months. Furthermore, results show that individuals with enamel defects in the form of Wilson bands at both the CNS and CSMME had an earlier mean age‐at‐death (9.6 and 4.05 years, respectively) in comparison with those without observed Wilson bands (19.75 and 8.8 years, respectively). These results underscore the importance of not only regional and temporal studies of the biological consequences of Spanish contact in the Americas but also of investigating the relationship between early life stress and adult health and longevity in archaeological populations. Copyright © 2015 John Wiley & Sons, Ltd.
Pharmacodynamic and genomic markers associated with response to the XPO1/CRM1 inhibitor selinexor (KPT‐330): A report from the pediatric preclinical testing program
Authors: Attiyeh Edward F. , Maris John M. , Lock Richard , Reynolds C. Patrick , Kang Min H. , Carol Hernan , Gorlick Richard , Kolb E. Anders , Keir Stephen T. , Wu Jianrong , Landesman Yosef , Shacham Sharon , Lyalin Dmitry , Kurmasheva Raushan T. , Houghton Peter J. , Smith Malcolm A. 
Published: September 2015

BackgroundSelinexor (KPT‐330) is an inhibitor of the major nuclear export receptor, exportin 1 (XPO1, also termed chromosome region maintenance 1, CRM1) that has demonstrated activity in preclinical models and clinical activity against several solid and hematological cancers.ProceduresSelinexor was tested against the Pediatric Preclinical Testing Program (PPTP) in vitro cell line panel at concentrations from 1.0 nM to 10 μM and against the PPTP in vivo xenograft panels administered orally at a dose of 10 mg/kg thrice weekly for 4 weeks.ResultsSelinexor demonstrated cytotoxic activity in vitro, with a median relative IC50 value of 123 nM (range 13.0 nM to >10 μM). Selinexor induced significant differences in event‐free survival (EFS) distribution in 29 of 38 (76%) of the evaluable solid tumor xenografts and in five of eight (63%) of the evaluable ALL xenografts. Objective responses (partial or complete responses, PR/CR) were observed for 4 of 38 solid tumor xenografts including Wilms tumor, medulloblastoma (n = 2), and ependymoma models. For the ALL panel, two of eight (25%) xenografts achieved either CR or maintained CR. Two responding xenografts had FBXW7 mutations at R465 and two had SMARCA4 mutations. Selinexor induced p53, p21, and cleaved PARP in several solid tumor models.ConclusionsSelinexor induced regression against several solid tumor and ALL xenografts and slowed tumor growth in a larger number of models. Pharmacodynamic effects for XPO1 inhibition were noted. Defining the relationship between selinexor systemic exposures in mice and humans will be important in assessing the clinical relevance of these results. Pediatr Blood Cancer © 2015 Wiley Periodicals, Inc.
Follow‐up care of adolescent survivors of childhood cancer: The role of health beliefs
Authors: Lupatsch Judith E. , Wengenroth Laura , Rueegg Corina S. , Teuffel Oliver , Gumy‐Pause Fabienne , Kuehni Claudia E. , Michel Gisela ,   for the Swiss Paediatric Oncology Group (SPOG)
Published: September 2015

BackgroundLittle is known about follow‐up care attendance of adolescent survivors of childhood cancer, and which factors foster or hinder attendance. Attending follow‐up care is especially important for adolescent survivors to allow for a successful transition into adult care. We aimed to (i) describe the proportion of adolescent survivors attending follow‐up care; (ii) describe adolescents' health beliefs; and (iii) identify the association of health beliefs, demographic, and medical factors with follow‐up care attendance.ProcedureOf 696 contacted adolescent survivors diagnosed with cancer at ≤16 years of age, ≥5 years after diagnosis, and aged 16–21 years at study, 465 (66.8%) completed the Swiss Childhood Cancer Survivor Study questionnaire. We assessed follow‐up care attendance and health beliefs, and extracted demographic and medical information from the Swiss Childhood Cancer Registry. Cross‐sectional data were analyzed using descriptive statistics and logistic regression models.ResultsOverall, 56% of survivors reported attending follow‐up care. Most survivors (80%) rated their susceptibility for late effects as low and believed that follow‐up care may detect and prevent late effects (92%). Few (13%) believed that follow‐up care is not necessary. Two health beliefs were associated with follow‐up care attendance (perceived benefits: odds ratio [OR]: 1.56; 95% confidence interval [CI]: 1.07–2.27; perceived barriers: OR: 0.70; 95%CI: 0.50–1.00).ConclusionsWe show that health beliefs are associated with actual follow‐up care attendance of adolescent survivors of childhood cancer. A successful model of health promotion in adolescent survivors should, therefore, highlight the benefits and address the barriers to keep adolescent survivors in follow‐up care. Pediatr Blood Cancer © 2015 Wiley Periodicals, Inc.