bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular chaperone accumulation as a function of stress evidences adaptation to high hydrostatic pressure in the piezophilic archaeon Thermococcus barophilus
Authors: Cario Anaïs , Jebbar Mohamed , Thiel Axel , Kervarec Nelly , Oger Phil M. 
Published: July 2016

AbstractThe accumulation of mannosyl-glycerate (MG), the salinity stress response osmolyte of Thermococcales, was investigated as a function of hydrostatic pressure in Thermococcus barophilus strain MP, a hyperthermophilic, piezophilic archaeon isolated from the Snake Pit site (MAR), which grows optimally at 40 MPa. Strain MP accumulated MG primarily in response to salinity stress, but in contrast to other Thermococcales, MG was also accumulated in response to thermal stress. MG accumulation peaked for combined stresses. The accumulation of MG was drastically increased under sub-optimal hydrostatic pressure conditions, demonstrating that low pressure is perceived as a stress in this piezophile, and that the proteome of T. barophilus is low-pressure sensitive. MG accumulation was strongly reduced under supra-optimal pressure conditions clearly demonstrating the structural adaptation of this proteome to high hydrostatic pressure. The lack of MG synthesis only slightly altered the growth characteristics of two different MG synthesis deletion mutants. No shift to other osmolytes was observed. Altogether our observations suggest that the salinity stress response in T. barophilus is not essential and may be under negative selective pressure, similarly to what has been observed for its thermal stress response.
Evidence for social cooperation in rodents by automated maze
Authors: Avital Avi , Aga-Mizrachi Shlomit , Zubedat Salman 
Published: July 2016

AbstractSocial cooperation is defined as a joint action for mutual benefit that depends on the individual and the counterparts’ behaviors. To gain valid evidence for social cooperation behavior we conducted a series of experiments in our suggested fully automated non-conditioned maze and depicted three major findings: (i) During 18 days of training the rats showed a progressive social learning curve as well as latent social learning; (ii) Examining the perceptual communication between the cooperating partners, we found a correlation between the available perceptual modalities and the social cooperation performance; and (iii) Investigating contextual learning as a competing process to the social cooperation, we found that additional contextual cues impaired the social cooperation performance. In conclusion, our suggested automated cooperation maze is designed to further our understanding of social cooperation under normal conditions, such as decision-making and to examine the neural basis of social cooperation. A variety of neuropsychiatric disorders are characterized by disruptions in social behavior and social cognition, including depression, autism spectrum disorders, obsessive-compulsive disorder and schizophrenia. Thus, on the pathological end, our maze for social cooperation evaluation can contribute significantly to the investigation of a wide range of social cooperation impairments in a rodent model.
Methylation of the leukocyte glucocorticoid receptor gene promoter in adults: associations with early adversity and depressive, anxiety and substance-use disorders
Authors: Tyrka A R , Parade S H , Welch E S , Ridout K K , Price L H , Marsit C , Philip N S , Carpenter L L 
Published: July 2016

AbstractEarly adversity increases risk for developing psychopathology. Epigenetic modification of stress reactivity genes is a likely mechanism contributing to this risk. The glucocorticoid receptor (GR) gene is of particular interest because of the regulatory role of the GR in hypothalamic–pituitary–adrenal (HPA) axis function. Mounting evidence suggests that early adversity is associated with GR promoter methylation and gene expression. Few studies have examined links between GR promoter methylation and psychopathology, and findings to date have been mixed. Healthy adult participants (N=340) who were free of psychotropic medications reported on their childhood experiences of maltreatment and parental death and desertion. Lifetime depressive and anxiety disorders and past substance-use disorders were assessed using the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition. Methylation of exon 1F of the GR gene (NR3C1) was examined in leukocyte DNA via pyrosequencing. On a separate day, a subset of the participants (n=231) completed the dexamethasone/corticotropin-releasing hormone (Dex/CRH) test. Childhood adversity and a history of past substance-use disorder and current or past depressive or anxiety disorders were associated with lower levels of NR3C1 promoter methylation across the region as a whole and at individual CpG sites (P<0.05). The number of adversities was negatively associated with NR3C1 methylation in participants with no lifetime disorder (P=0.018), but not in those with a lifetime disorder. GR promoter methylation was linked to altered cortisol responses to the Dex/CRH test (P<0.05). This study presents evidence of reduced methylation of NR3C1 in association with childhood maltreatment and depressive, anxiety and substance-use disorders in adults. This finding stands in contrast to our prior work, but is consistent with emerging findings, suggesting complexity in the regulation of this gene.
Identification of learning-induced changes in protein networks in the hippocampi of a mouse model of Alzheimer’s disease
Authors: Ferreira E , Shaw D M , Oddo S 
Published: July 2016

AbstractMemory loss is the most profound clinical manifestation in Alzheimer’s disease (AD); however, the molecular mechanisms underlying these deficits are poorly understood. Identification of the molecular pathways involved in the onset of cognitive deficits may lead to the identification of key events in the pathogenesis of AD. Using isobaric tags for relative and absolute quantitation (iTRAQ) and proteomic methods, here we identified learning-induced changes in the hippocampal proteome of non-transgenic (NonTg) and 3 × Tg-AD mice, a widely used animal model of AD. We found that expression of 192 proteins was differentially regulated by learning in NonTg mice. Notably, of these 192 proteins, only 28 were also differentially regulated by learning in 3 × Tg-AD mice, whereas the levels of 164 proteins were uniquely changed in NonTg mice but not in 3 × Tg-AD mice. These data suggest that during learning, 3 × Tg-AD mice fail to differentially regulate 164 proteins. Gene ontology and protein interaction analyses indicated that these proteins were overrepresented in RNA processing, specifically RNA transport, splicing and mRNA translation initiation pathways. These findings suggest that mRNA-processing events that take place during learning and memory are significantly altered in 3 × Tg-AD mice.
Epigenetics changes caused by the fusion of human embryonic stem cell and ovarian cancer cells
Authors: He Ke , Qu Hu , Xu Li-Nan , Gao Jun , Cheng Fu-Yi , Xiang Peng , Zhou Can-Quan 
Published: July 2016

To observe the effect of gene expression and tumorigenicity in hybrid cells of human embryonic stem cells (hESCs) and ovarian cancer cells in vitro and in vivo using a mouse model, and to determine its feasibility in reprogramming tumour cells growth and apoptosis, for a potential exploration of the role of hESCs and tumour cells fusion in the management of ovarian cancer. Stable transgenic hESCs (H1) and ovarian cancer cell line OVCAR-3 were established before fusion, and cell fusion system was established to analyse the related indicators. PTEN expression in HO-H1 cells was higher than those in the parental stem cells and lower than those in parental tumour cells; the growth of OV-H1 (RFP+GFP) hybrid cells with double fluorescence expressions were obviously slower than that of human embryonic stem cells and OVCAR-3 ovarian cancer cells. The apoptosis signal of the OV-H1 hybrid cells was significantly higher than that of the hESCs and OVCAR-3 ovarian cancer cells. In vivo results showed that compared with 7 days, 28 days and 35 days after inoculation of OV-H1 hybrid cells; also, apoptotic cell detection indicated that much stronger apoptotic signal was found in OV-H1 hybrid cells inoculated mouse. The hESCs can inhibit the growth of OVCAR-3 cells in vitro by suppressing p53 and PTEN expression to suppress the growth of tumour that may be achieved by inducing apoptosis of OVCAR-3 cells. The change of epigenetics after fusion of ovarian cancer cells and hESCs may become a novel direction for treatment of ovarian cancer.
Use of Language Sample Analysis by School-Based SLPs: Results of a Nationwide Survey
Authors: Pavelko Stacey L. , Owens Robert E. , Ireland Marie , Hahs-Vaughn Debbie L. 
Published: July 2016

Purpose
This article examines use of language sample analysis (LSA) by school-based speech-language pathologists (SLPs), including characteristics of language samples, methods of transcription and analysis, barriers to LSA use, and factors affecting LSA use, such as American Speech-Language-Hearing Association certification, number of years' experience, and caseload characteristics.

Method
School-based SLPs responded to an invitation to complete an electronic survey related to LSA.

Results
One third of respondents indicated they did not use LSA during the 2012–2013 school year. SLPs who served middle and high school students were less likely to use LSA. Most respondents reported using conversation to analyze fewer than 10 samples and transcribing in real time. Additional analyses revealed that SLPs who had 3 or fewer years of experience and who analyzed fewer than 20 language samples per year were statistically less likely to report using real-time transcription. The most frequently cited barrier to using LSA was “LSA is too time-consuming.”

Conclusion
Many school-based SLPs do not routinely use LSA. Further, many did not report engaging in evidence-based practices, such as recording samples, using established protocols, or using tasks designed to elicit complex syntax. These results indicate a continued need for professional development regarding evidenced-based practices relative to LSA use.
Non-monotonic growth rates of sawtooth precursors evidenced with a new method on ASDEX Upgrade
Authors: Vezinet D. , Igochine V. , Weiland M. , Yu Q. , Gude A. , Meshcheriakov D. , Sertoli M. 
Published: July 2016

Abstract
This paper describes a new method to derive, from soft x-ray (SXR) tomography, robust estimates of the core displacement, growth rate and frequency of a 1/1 sawtooth crash precursor. The method is valid for very peaked SXR profiles and is robust against both the inversion algorithm and the presence of tungsten in a rotating plasma. Three typical ASDEX Upgrade crashes are then analysed. In all cases a postcursor is observed, suggesting incomplete reconnection. Despite different dynamics, in all three cases the growth rate of the core displacement shows similar features. First, it is not constant, supporting the idea of non-linear growth. Second, it can be divided into clearly identified phases with quasi-constant growth rates, suggesting sudden change of growth regime rather than smooth transitions. Third, its evolution is non-monotonic, with phases of accelerated growth followed by damped phases. This damping is interpreted for two cases respectively as an effect of fast ions and of mode coupling, based on the result of a MHD simulation. The mode frequency is observed in all cases to be closely related to the plasma bulk rotation profile, with little or no visible effect of the electron diamagnetic drift frequency. The onset criterion could not be clearly identified and it is shown that the role of the pressure gradient is not as expected from a naive extrapolation of the linear stability theory.
Non-axisymmetric ideal equilibrium and stability of ITER plasmas with rotating RMPs
Authors: Ham C.J. , Cramp R.G.J. , Gibson S. , Lazerson S.A. , Chapman I.T. , Kirk A. 
Published: July 2016

Abstract
The magnetic perturbations produced by the resonant magnetic perturbation (RMP) coils will be rotated in ITER so that the spiral patterns due to strike point splitting which are locked to the RMP also rotate. This is to ensure even power deposition on the divertor plates. VMEC equilibria are calculated for different phases of the RMP rotation. It is demonstrated that the off harmonics rotate in the opposite direction to the main harmonic. This is an important topic for future research to control and optimize ITER appropriately. High confinement mode (H-mode) is favourable for the economics of a potential fusion power plant and its use is planned in ITER. However, the high pressure gradient at the edge of the plasma can trigger periodic eruptions called edge localized modes (ELMs). ELMs have the potential to shorten the life of the divertor in ITER (Loarte et al 2003 Plasma Phys. Control. Fusion
45 1549) and so methods for mitigating or suppressing ELMs in ITER will be important. Non-axisymmetric RMP coils will be installed in ITER for ELM control. Sampling theory is used to show that there will be significant a

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harmonic sideband. There are nine coils toroidally in ITER so

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. This results in a significant n  =  6 component to the

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applied field and a significant n  =  5 component to the

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applied field. Although the vacuum field has similar amplitudes of these harmonics the plasma response to the various harmonics dictates the final equilibrium. Magnetic perturbations with toroidal mode number n  =  3 and n  =  4 are applied to a 15 MA,

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≈
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burning ITER plasma. We use a three-dimensional ideal magnetohydrodynamic model (VMEC) to calculate ITER equilibria with applied RMPs and to determine growth rates of infinite n ballooning modes (COBRA). The

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case shows little change in ballooning mode growth rate as the RMP is rotated, however there is a change with rotation for the

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case.
Unbiased classification of spatial strategies in the Barnes maze
Authors: Illouz Tomer , Madar Ravit , Clague Charlotte , Griffioen Kathleen J. , Louzoun Yoram , Okun Eitan 
Published: July 2016

Abstract
Motivation: Spatial learning is one of the most widely studied cognitive domains in neuroscience. The Morris water maze and the Barnes maze are the most commonly used techniques to assess spatial learning and memory in rodents. Despite the fact that these tasks are well-validated paradigms for testing spatial learning abilities, manual categorization of performance into behavioral strategies is subject to individual interpretation, and thus to bias. We have previously described an unbiased machine-learning algorithm to classify spatial strategies in the Morris water maze.
Results: Here, we offer a support vector machine—based, automated, Barnes-maze unbiased strategy (BUNS) classification algorithm, as well as a cognitive score scale that can be used for memory acquisition, reversal training and probe trials. The BUNS algorithm can greatly benefit Barnes maze users as it provides a standardized method of strategy classification and cognitive scoring scale, which cannot be derived from typical Barnes maze data analysis.
Availability and Implementation: Freely available on the web at http://okunlab.wix.com/okunlab as a MATLAB application.
Contact: eitan.okun@biu.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
ChAsE: chromatin analysis and exploration tool
Authors: Younesy Hamid , Nielsen Cydney B. , Lorincz Matthew C. , Jones Steven J.M. , Karimi Mohammad M. , Möller Torsten 
Published: July 2016

Abstract
Summary : We present ChAsE, a cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and bioinformaticians with a focus on usability and interactivity. Data can be analyzed through k-means clustering, specifying presence or absence of signal in epigenetic data and performing set operations between clusters. Results can be explored in an interactive heat map and profile plot interface and exported for downstream analysis or as high quality figures suitable for publications.
Availability and Implementation: Software, source code (MIT License), data and video tutorials available at http://chase.cs.univie.ac.at .
Contact : mkarimi@brc.ubc.ca or torsten.moeller@univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes
Authors: Weinmaier Thomas , Platzer Alexander , Frank Jeroen , Hellinger Hans-Jörg , Tischler Patrick , Rattei Thomas 
Published: July 2016

Abstract
Motivation: The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial and re-annotation. Here we present ConsPred, a prokaryotic genome annotation framework that performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a consensus annotation. ConsPred achieves comprehensive, high-quality annotations based on rules and priorities, similar to decision-making in manual curation and avoids conflicting predictions. Parameters controlling the annotation process are configurable by the user. ConsPred has been used in the institutions of the authors for longer than 5 years and can easily be extended and adapted to specific needs.
Summary: The ConsPred algorithm for producing a consensus from the varying scores of multiple gene prediction programs approaches manual curation in accuracy. Its rule-based approach for choosing final predictions avoids overriding previous manual curations.
Availability and implementation: ConsPred is implemented in Java, Perl and Shell and is freely available under the Creative Commons license as a stand-alone in-house pipeline or as an Amazon Machine Image for cloud computing, see https://sourceforge.net/projects/conspred/.
Contact: thomas.rattei@univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
Recognizing metal and acid radical ion-binding sites by integrating
ab initio
modeling with template-based transferals
Authors: Hu Xiuzhen , Dong Qiwen , Yang Jianyi , Zhang Yang 
Published: July 2016

Abstract
Motivation: More than half of proteins require binding of metal and acid radical ions for their structure and function. Identification of the ion-binding locations is important for understanding the biological functions of proteins. Due to the small size and high versatility of the metal and acid radical ions, however, computational prediction of their binding sites remains difficult.
Results: We proposed a new ligand-specific approach devoted to the binding site prediction of 13 metal ions (Zn 2+ , Cu 2+ , Fe 2+ , Fe 3+ , Ca 2+ , Mg 2+ , Mn 2+ , Na + , K + ) and acid radical ion ligands (CO3 2− , NO2 − , SO4 2− , PO4 3− ) that are most frequently seen in protein databases. A sequence-based ab initio model is first trained on sequence profiles, where a modified AdaBoost algorithm is extended to balance binding and non-binding residue samples. A composite method IonCom is then developed to combine the ab initio model with multiple threading alignments for further improving the robustness of the binding site predictions. The pipeline was tested using 5-fold cross validations on a comprehensive set of 2,100 non-redundant proteins bound with 3,075 small ion ligands. Significant advantage was demonstrated compared with the state of the art ligand-binding methods including COACH and TargetS for high-accuracy ion-binding site identification. Detailed data analyses show that the major advantage of IonCom lies at the integration of complementary ab initio and template-based components. Ion-specific feature design and binding library selection also contribute to the improvement of small ion ligand binding predictions.
Availability and Implementation : http://zhanglab.ccmb.med.umich.edu/IonCom
Contact: hxz@imut.edu.cn or zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The SMAL web server: global multiple network alignment from pairwise alignments
Authors: Dohrmann Jakob , Singh Rahul 
Published: July 2016

Abstract
Motivation: Alignments of protein-protein interaction networks (PPIN) can be used to predict protein function, study conserved aspects of the interactome, and to establish evolutionary correspondences. Within this problem context, determining multiple network alignments (MNA) is a significant challenge that involves high computational complexity. A limited number of public MNA implementations are available currently and the majority of the pairwise network alignment (PNA) algorithms do not have MNA counterparts. Furthermore, current MNA algorithms do not allow choosing a specific PPIN relative to which an MNA could be constructed. Also, once an MNA is obtained, it cannot easily be modified, such as through addition of a new network, without expensive re-computation of the entire MNA.
Results: SMAL (Scaffold-Based Multiple Network Aligner) is a public, open-source, web-based application for determining MNAs from existing PNAs that addresses all the aforementioned challenges. With SMAL, PNAs can be combined rapidly to obtain an MNA. The software also supports visualization and user-data interactions to facilitate exploratory analysis and sensemaking. SMAL is especially useful when multiple alignments relative to a particular PPIN are required; furthermore, SMAL alignments are persistent in that existing correspondences between networks (obtained during PNA or MNA) are not lost as new networks are added. In comparative studies alongside existent MNA techniques, SMAL MNAs were found to be superior per a number of measures, such as the total number of identified homologs and interologs as well as the fraction of all identified correspondences that are functionally similar or homologous to the scaffold. While directed primarily at PPIN-alignment, SMAL is a generic network aligner and may be applied to arbitrary networks.
Availability information: The SMAL web server and source code is available at: http://haddock6.sfsu.edu/smal/
Contact: rahul@sfsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MetaCycle: an integrated R package to evaluate periodicity in large scale data
Authors: Wu Gang , Anafi Ron C. , Hughes Michael E. , Kornacker Karl , Hogenesch John B. 
Published: July 2016

Abstract
Summary: Detecting periodicity in large scale data remains a challenge. While efforts have been made to identify best of breed algorithms, relatively little research has gone into integrating these methods in a generalizable method. Here, we present MetaCycle, an R package that incorporates ARSER, JTK_CYCLE and Lomb-Scargle to conveniently evaluate periodicity in time-series data. MetaCycle has two functions, meta2d and meta3d, designed to analyze two-dimensional and three-dimensional time-series datasets, respectively. Meta2d implements N-version programming concepts using a suite of algorithms and integrating their results.
Availability and implementation: MetaCycle package is available on the CRAN repository ( https://cran.r-project.org/web/packages/MetaCycle/index.html ) and GitHub ( https://github.com/gangwug/MetaCycle ).
Contact: hogenesch@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.