bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spousal resemblance in psychopathology: A comparison of parents of children with and without psychopathology
Authors: Wesseldijk LW , Dieleman GC , Lindauer RJL , Bartels M , Willemsen G , Hudziak JJ , Boomsma DI , Middeldorp CM 
Published: February 2016

AbstractBackgroundSpouses resemble each other for psychopathology, but data regarding spousal resemblance in externalizing psychopathology, and data regarding spousal resemblance across different syndromes (e.g. anxiety in wives and attention deficit/hyperactivity disorder [ADHD] in husbands) are limited. Moreover, knowledge is lacking regarding spousal resemblance in parents of children with psychiatric disorders. We investigated and compared spousal resemblance within and across internalizing and externalizing symptom domains in parents of children with and without psychopathology.MethodsSymptoms of depression, anxiety, avoidant personality, ADHD, and antisocial personality were assessed with the Adult Self Report in 728 mothers and 544 fathers of 778 children seen in child and adolescent psychiatric outpatient clinics and in 2075 mothers and 1623 fathers of 2784 children from a population-based sample. Differences in symptom scores and spousal correlations between the samples were tested.ResultsParents in the clinical sample had higher symptom scores than in the population-based sample. In both samples, correlations within and across internalizing and externalizing domains of psychopathology were significant. Importantly, correlations were significantly higher in the clinical sample (P = 0.03). Correlations, within and across symptoms, ranged from 0.14 to 0.30 in the clinical sample and from 0.05 to 0.23 in the population-based sample.ConclusionsThis large study shows that spousal resemblance is not only present within but also across symptom domains. Especially in the clinical sample, ADHD symptoms in fathers and antisocial personality symptoms in mothers were correlated with a range of psychiatric symptoms in their spouses. Clinicians need to be alert of these multiple affected families.
Dysfunctional default mode network and executive control network in people with Internet gaming disorder: Independent component analysis under a probability discounting task
Authors: Wang L , Wu L , Lin X , Zhang Y , Zhou H , Du X , Dong G 
Published: February 2016

AbstractBackgroundThe present study identified the neural mechanism of risky decision-making in Internet gaming disorder (IGD) under a probability discounting task.MethodsIndependent component analysis was used on the functional magnetic resonance imaging data from 19 IGD subjects (22.2 ± 3.08 years) and 21 healthy controls (HC, 22.8 ± 3.5 years).ResultsFor the behavioral results, IGD subjects prefer the risky to the fixed options and showed shorter reaction time compared to HC. For the imaging results, the IGD subjects showed higher task-related activity in default mode network (DMN) and less engagement in the executive control network (ECN) than HC when making the risky decisions. Also, we found the activities of DMN correlate negatively with the reaction time and the ECN correlate positively with the probability discounting rates.ConclusionsThe results suggest that people with IGD show altered modulation in DMN and deficit in executive control function, which might be the reason for why the IGD subjects continue to play online games despite the potential negative consequences.
Quantification of active mitochondrial permeability transition pores using GNX-4975 inhibitor titrations provides insights into molecular identity
Authors: Richardson Andrew P. , Halestrap Andrew P. 
Published: February 2016

Inhibition of the mitochondrial permeability transition pore (MPTP) by the novel inhibitor GNX-4975 was characterized. Titration of MPTP activity in de-energized rat liver mitochondria allowed determination of the number of GNX-4975-binding sites and their dissociation constant (Ki). Binding sites increased in number when MPTP opening was activated by increasing [Ca2+], phenylarsine oxide (PAO) or KSCN, and decreased when MPTP opening was inhibited with bongkrekic acid (BKA) or ADP. Values ranged between 9 and 50 pmol/mg of mitochondrial protein, but the Ki remained unchanged at ∼1.8 nM when the inhibitor was added before Ca2+. However, when GNX-4975 was added after Ca2+ it was much less potent with a Ki of ∼140 nM. These data imply that a protein conformational change is required to form the MPTP complex and generate the GNX-4975-binding site. Occupation of the latter with GNX-4975 prevents the Ca2+ binding that triggers pore opening. We also demonstrated that GNX-4975 stabilizes an interaction between the adenine nucleotide translocase (ANT), held in its ‘c’ conformation with carboxyatractyloside (CAT), and the phosphate carrier (PiC) bound to immobilized PAO. No components of the F1Fo-ATP synthase bound significantly to immobilized PAO. Our data are consistent with our previous proposal that the MPTP may form at an interface between the PiC and ANT (or other similar mitochondrial carrier proteins) when they adopt novel conformations induced by factors that sensitize the MPTP to [Ca2+]. We propose that GNX-4975 binds to this interface preventing a calcium-triggered event that opens the interface into a pore.
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra
Authors: Mohamed Ahmed , Nguyen Canh Hao , Mamitsuka Hiroshi 
Published: February 2016

Abstract
Summary: The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization.
Availability and implementation: Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/
Contact: mohamed@kuicr.kyoto-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony
Authors: Jacox Edwin , Chauve Cedric , Szöllősi Gergely J. , Ponty Yann , Scornavacca Celine 
Published: February 2016

Abstract
Summary: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation.
Availability and implementation: ecceTERA is freely available under http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.
Contact: celine.scornavacca@umontpellier.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Authors: Katoh Kazutaka , Standley Daron M. 
Published: February 2016

Abstract
Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction.
Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment.
Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/
Contact: katoh@ifrec.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Computational clustering for viral reference proteomes
Authors: Chen Chuming , Huang Hongzhan , Mazumder Raja , Natale Darren A. , McGarvey Peter B. , Zhang Jian , Polson Shawn W. , Wang Yuqi , Wu Cathy H. ,   UniProt Consortium
Published: February 2016

Abstract
Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.
Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.
Availability and implementation: http://proteininformationresource.org/rps/viruses/
Contact: chenc@udel.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules
Authors: Wala Jeremiah , Zhang Cheng-Zhong , Meyerson Matthew , Beroukhim Rameen 
Published: February 2016

Abstract
We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis.
Availability and implementation: VariantBam and full documentation are available at github.com/jwalabroad/VariantBam.
Contact: rameen@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
Authors: Elhanati Yuval , Marcou Quentin , Mora Thierry , Walczak Aleksandra M. 
Published: February 2016

Abstract
Motivation: The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events—choices of gene templates, base pair deletions and insertions—described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence.
Results: We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum–Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be ≈1023 for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires.
Availability and implementation: Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads.
Contact: elhanati@lpt.ens.fr or tmora@lps.ens.fr or awalczak@lpt.ens.fr
Mycobacterial r32-kDa antigen-specific T-cell responses correlate with successful treatment and a heightened anti-microbial response in human leprosy patients
Authors: Neela Venkata Sanjeev Kumar , Devalraju Kamakshi Prudhula , Pydi Satya Sudheer , Sunder Sharada Ramaseri , Adiraju Kameswara Rao , Singh Surya Satyanarayana , Anandaraj M. P. J. S. , Valluri Vijaya Lakshmi 
Published: February 2016

Abstract

Background:
Immunological characterization of mycobacterial peptides may help not only in the preparation of a vaccine for leprosy but also in developing in vitro T-cell assays that could perhaps be used as an in vitro correlate for treatment outcome. The main goal of this study was to evaluate the use of Mycobacterium bovis recombinant 32-kDa protein (r32-kDa) antigen-stimulated T-cell assay as a surrogate marker for treatment outcome and monitor vitamin D receptor (VDR)-mediated anti-microbial responses during multidrug therapy (MDT) in leprosy.

Methods:
Newly diagnosed tuberculoid and lepromatous leprosy patients were enrolled and followed up during their course of MDT at 6 and 12 months. IFN-γ, IL-10, IL-17 and IL-23 levels in culture supernatants and expression of VDR, TLR2, LL37 and DEFB in r32-kDa-stimulated PBMCs were measured. Controls comprised household contacts (HHCs) and healthy endemic subjects (HCs).

Results:
Significant differences were observed in the levels of IFN-γ, IL-17, IL-23, VDR and anti-microbial peptides LL37 and DEFB after treatment and when compared with that of HHCs and HCs, respectively.

Conclusions:
These findings suggest that responses to r32-kDa antigen reflect an improved immunological and anti-microbial response in leprosy patients during therapy, thereby indicating its potential use as an immune correlate in the treatment of leprosy patients.
Systematic revision of the pocket gopher genus Orthogeomys
Authors: Spradling Theresa A. , Demastes James W. , Hafner David J. , Milbach Paige L. , Cervantes Fernando A. , Hafner Mark S. 
Published: February 2016

AbstractPocket gophers of the genus Orthogeomys show unusually high morphological and ecological diversity compared to other genera in the family Geomyidae. Whereas this diverse group once was divided into 3 genera ( Merriam 1895 ), a revision by Russell (1968) recognized only Orthogeomys , with Merriam’s original genera relegated to subgeneric status as Heterogeomys , Macrogeomys , and Orthogeomys . Recent studies have called into question the monophyly of Orthogeomys , as well as the validity of 4 currently recognized Orthogeomys species. To date, the taxonomic validity of only 1 of these species has been verified ( Hafner et al. 2014 ). In this analysis, the first to include all 11 recognized species of the genus, we examine 3 mitochondrial and 2 nuclear gene sequences (4,352 base pairs) and analyze cranial morphology to explore relationships within the genus. Our data support a taxonomic revision that restricts the genus Orthogeomys to a single species ( O. grandis ) and combines the subgenera Heterogeomys and Macrogeomys into the resurrected genus, Heterogeomys (7 species). In addition, 3 currently recognized species of Orthogeomys are synonymized as follows: O. cuniculus with O. grandis ; H. thaeleri with H. dariensis ; and H. matagalpae with H. cherriei . A synonymy and a key to the species of the genera Orthogeomys and Heterogeomys are provided.Las tuzas del género Orthogeomys muestran una diversidad morfológica y ecológica inusual en comparación con otros géneros de la familia Geomyidae. Aunque este diverso grupo fue alguna vez dividido en 3 géneros ( Merriam 1895 ), la revisión de Russell (1968) reconoció solo a Orthogeomys , mientras que los géneros originales de Merriam fueron relegados a estatus subgenérico como Heterogeomys , Macrogeomys y Orthogeomys . Estudios recientes han cuestionado la monofilia de Orthogeomys , así como la validez de 4 de las especies actualmente reconocidas. A la fecha, la validez taxonómica de sólo una de estas especies ha sido verificada. En este análisis, el primero en incluir las 11 especies reconocidas en el género, examinamos secuencias de 3 genes mitocondriales y 2 nucleares y analizamos la morfología craneal para explorar las relaciones dentro del género. Nuestras 4,352 pares de bases de secuencias de ADN apoyan una revisión taxonómica que retiene al género Orthogeomys (incluyendo sólo a O. grandis ) y combina los subgéneros Heterogeomys y Macrogeomys en un género recuperado, Heterogeomys (7 especies). Además, 3 especies de Orthogeomys actualmente reconocidas son sinonimizadas de la siguiente forma: O. cuniculus con O. grandis ; H. thaeleri con H. dariensis ; y H. matagalpae con H. cherriei . Se incluye sinonimia y una clave para las especies de los géneros Orthogeomys y Heterogeomys .
Neural Correlates of Phonetic Learning in Postlingually Deafened Cochlear Implant Listeners
Authors: Miller Sharon , Zhang Yang , Nelson Peggy 
Published: February 2016

Objective:
The present training study aimed to examine the fine-scale behavioral and neural correlates of phonetic learning in adult postlingually deafened cochlear implant (CI) listeners. The study investigated whether high variability identification training improved phonetic categorization of the /ba/–/da/ and /wa/–/ja/ speech contrasts and whether any training-related improvements in phonetic perception were correlated with neural markers associated with phonetic learning. It was hypothesized that training would sharpen phonetic boundaries for the speech contrasts and that changes in behavioral sensitivity would be associated with enhanced mismatch negativity (MMN) responses to stimuli that cross a phonetic boundary relative to MMN responses evoked using stimuli from the same phonetic category.

Design:
A computer-based training program was developed that featured multitalker variability and adaptive listening. The program was designed to help CI listeners attend to the important second formant transition cue that categorizes the /ba/–/da/ and /wa/–/ja/ contrasts. Nine adult CI listeners completed the training and 4 additional CI listeners that did not undergo training were included to assess effects of procedural learning. Behavioral pre-post tests consisted of identification and discrimination of the synthetic /ba/–/da/ and /wa/–/ja/ speech continua. The electrophysiologic MMN response elicited by an across phoneme category pair and a within phoneme category pair that differed by an acoustically equivalent amount was derived at pre-post test intervals for each speech contrast as well.

Results:
Training significantly enhanced behavioral sensitivity across the phonetic boundary and significantly altered labeling of the stimuli along the /ba/–/da/ continuum. While training only slightly altered identification and discrimination of the /wa/–/ja/ continuum, trained CI listeners categorized the /wa/–/ja/ contrast more efficiently than the /ba/–/da/ contrast across pre-post test sessions. Consistent with behavioral results, pre-post EEG measures showed the MMN amplitude to the across phoneme category pair significantly increased with training for both the /ba/–/da/ and /wa/–/ja/ contrasts, but the MMN was unchanged with training for the corresponding within phoneme category pairs. Significant brain–behavior correlations were observed between changes in the MMN amplitude evoked by across category phoneme stimuli and changes in the slope of identification functions for the trained listeners for both speech contrasts.

Conclusions:
The brain and behavior data of the present study provide evidence that substantial neural plasticity for phonetic learning in adult postlingually deafened CI listeners can be induced by high variability identification training. These findings have potential clinical implications related to the aural rehabilitation process following receipt of a CI device.
Frequency of Jackhammer Esophagus as the Extreme Phenotypes of Esophageal Hypercontractility Based on the New Chicago Classification
Authors: Jia Yi , Arenas Juan , Hejazi Reza A. , Elhanafi Sherif , Saadi Mohammed , McCallum Richard W. 
Published: February 2016

Background:
Jackhammer Esophagus is defined as intact esophageal peristaltic contractions with extremely elevated amplitudes. We conducted a retrospective study to identify the frequency of esophageal hypercontractility and the clinical characteristics of Jackhammer Esophagus.

Methods:
Charts for the patients referred for manometric study at a tertiary-care motility center were reviewed. Data were collected utilizing the new Chicago classification criteria for Jackhammer Esophagus. Concomitant clinical variables were also explored.

Results:
Eight patients were identified with Jackhammer Esophagus from a total of 205 (127 female/77 male) patients referred for high-resolution esophageal manometry. Jackhammer patients had an average distal contractile integral (DCI) of 9061 mmHg/ sec/ cm and median maximal DCI of 16,433 mmHg/ sec/ cm. The greatest DCI from 15 swallows was 28,875 mmHg/ sec/ cm. Hypercontractility was associated with multipeaked contractions in every Jackhammer patient. The mean lower esophageal sphincter (LES) pressure was 41 mm Hg with 4 patients having a hypertensive pressure of >40 mm Hg. Three of the 8 (37.5%) Jackhammer group had incomplete LES relaxation by integrated relaxation pressure criteria (>15 mm Hg residual pressure). Dysphagia (8/8) was the dominant indication for the manometric study, whereas the clinical background setting was gastroesophageal reflux disease (4/8) and hiatal hernia (1/8). Treatments included smooth muscle relaxation, antireflux regimens, and pneumatic dilation of the LES.

Conclusions:
Jackhammer Esophagus, an extreme manometric phenotype, was identified in 4.0% of patients referred to a University Motility Center. The patients with these esophageal hypercontractility states present mainly with dysphagia. A subgroup of Jackhammer did have accompanying incomplete LES relaxation and responded to targeted therapy with pneumatic dilatation.