bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of a csoR-cueA divergon in Bradyrhizobium liaoningense CCNWSX0360, involved in copper, zinc and cadmium cotolerance
Authors: Liang Jianqiang , Zhang Mingzhe , Lu Mingmei , Li Zhefei , Shen Xihui , Chou Minxia , Wei Gehong 
Published: October 2016

AbstractRandom mutagenesis in a symbiotic nitrogen-fixing Bradyrhizobium liaoningense CCNWSX0360 (Bln0360) using Tn5 identified five copper (Cu) resistance-related genes. They were functionally sorted into three groups: transmembrane transport (cueA and tolC); oxidation (copA); and protection of the membrane barrier (lptE and ctpA). The gene cueA, together with the upstream csoR (Cu-sensitive operon repressor), constituted a csoR-cueA divergon which plays a crucial role in Cu homeostasis. Deletion of cueA decreased the Cu tolerance of cells, and complementation of this mutant restored comparable Cu resistance to that of the wild-type. Transcriptional and fusion expression analysis demonstrated that csoR-cueA divergon was up-regulated by both the monovalent Cu+ and divalent Zn2+/Cd2+, and negatively regulated by transcriptional repressor CsoR, via a bidirectional promoter. Deletion of csoR renders the cell hyper-resistant to Cu, Zn and Cd. Although predicted to encode a Cu transporting P-type ATPase (CueA), cueA also conferred resistance to zinc and cadmium; two putative N-MBDs (N-terminal metal binding domains) of CueA were required for the Cu/Zn/Cd tolerance. Moreover, cueA is needed for nodulation competitiveness of B. liaoningense in Cu rich conditions. Together, the results demonstrated a crucial role for the csoR-cueA divergon as a component of the multiple-metal resistance machinery in B. liaoningense.
Cu3P/RGO Nanocomposite as a New Anode for Lithium-Ion Batteries
Authors: Liu Shuling , He Xiaodong , Zhu Jianping , Xu Liqiang , Tong Jianbo 
Published: October 2016

AbstractCu3P/reduced graphene oxide (Cu3P/RGO) nanocomposite was successfully synthesized by a facile one-pot method as an advanced anode material for high-performance lithium-ion batteries. Cu3P nanostructures with a polyhedral shape with the mean diameter (80–100 nm) were homogeneously anchored on the surface of RGO. The flexible RGO sheets acted as elastic buffering layer which not only reduced the volume change, but also prevented the aggregation of Cu3P nanostructures, the cracking and crumbing of electrodes. On the other hand, the presence of Cu3P nanostructures could also avoid the agglomeration of RGO sheets and retain their highly active surface area. Therefore, as an advanced anode material for high-performance lithium-ion batteries, the as-prepared Cu3P/RGO exhibited high capacity of 756.15 mAhg−1 at the current density 500 mAg−1 after 80 cycles, superior cyclic stability and good rate capability.
A new class of optical sensors: a random laser based device
Authors: Ignesti Emilio , Tommasi Federico , Fini Lorenzo , Martelli Fabrizio , Azzali Niccolò , Cavalieri Stefano 
Published: October 2016

AbstractIn a random laser the optical feedback is provided by scattering rather than by an optical cavity. Then, since its emission characteristics are very susceptible to the scattering details, it is a natural candidate for making active sensors to use as a diagnostic tool for disordered media like biological samples. However, the methods reported up to now, requiring the injection of toxic substances in the sample, have the drawback of altering the physical-chemical composition of the medium and are not suitable for in-vivo measurements. Here we present a random laser based sensor that overcomes these problems by keeping gain and diffusion separated. We provide an experimental characterisation of the sensor by using a reference diffusive liquid phantom and we show that, compared to a passive method, this sensor takes advantage of the gain and spectral properties of the random laser principle.
Alterations in the functional neural circuitry supporting flexible choice behavior in autism spectrum disorders
Authors: D'Cruz A-M , Mosconi M W , Ragozzino M E , Cook E H , Sweeney J A 
Published: October 2016

AbstractRestricted and repetitive behaviors, and a pronounced preference for behavioral and environmental consistency, are distinctive characteristics of autism spectrum disorder (ASD). Alterations in frontostriatal circuitry that supports flexible behavior might underlie this behavioral impairment. In an functional magnetic resonance imaging study of 17 individuals with ASD, and 23 age-, gender- and IQ-matched typically developing control participants, reversal learning tasks were used to assess behavioral flexibility as participants switched from one learned response choice to a different response choice when task contingencies changed. When choice outcome after reversal was uncertain, the ASD group demonstrated reduced activation in both frontal cortex and ventral striatum, in the absence of task performance differences. When the outcomes of novel responses were certain, there was no difference in brain activation between groups. Reduced activation in frontal cortex and ventral striatum suggest problems in decision-making and response planning, and in processing reinforcement cues, respectively. These processes, and their integration, are essential for flexible behavior. Alterations in these systems may therefore contribute to a rigid adherence to preferred behavioral patterns in individuals with an ASD. These findings provide an additional impetus for the use of reversal learning paradigms as a translational model for treatment development targeting the domain of restricted and repetitive behaviors in ASD.
Nitrile versus isonitrile adsorption at interstellar grains surfaces
Authors: Bertin M. , Doronin M. , Fillion J.-H. , Michaut X. , Philippe L. , Lattelais M. , Markovits A. , Pauzat F. , Ellinger Y. , Guillemin J.-C. 
Published: October 2016

Context. Almost 20% of the ~200 different species detected in the interstellar and circumstellar media present a carbon atom linked to nitrogen by a triple bond. Among these 37 molecules, 30 are nitrile R-CN compounds, the remaining seven belonging to the isonitrile R-NC family. How these species behave in presence of the grain surfaces is still an open question.
Aims. In this contribution we investigate whether the difference between nitrile and isonitrile functional groups may induce differences in the adsorption energies of the related isomers at the surfaces of interstellar grains of different nature and morphologies.
Methods. The question was addressed by means of a concerted experimental and theoretical study of the adsorption energies of CH3CN and CH3NC on the surface water ice and silica. The experimental determination of the molecule – surface interaction energies was carried out using temperature programmed desorption (TPD) under an ultra-high vacuum (UHV) between 70 and 160 K. Theoretically, the question was addressed using first principle periodic density functional theory (DFT) to represent the organized solid support.
Results. The most stable isomer (CH3CN) interacts more efficiently with the solid support than the higher energy isomer (CH3NC) for water ice and silica. Comparing with the HCN and HNC pair of isomers, the simulations show an opposite behaviour, in which isonitrile HNC are more strongly adsorbed than nitrile HCN provided that hydrogen bonds are compatible with the nature of the model surface.
Conclusions. The present study confirms that the strength of the molecule surface interaction between isomers is not related to their intrinsic stability but instead to their respective ability to generate different types of hydrogen bonds. Coupling TPD to first principle simulations is a powerful method for investigating the possible role of interstellar surfaces in the release of organic species from grains, depending on the environment.
La naissance de l’Edgewise ou le dernier et le meilleur
mécanisme d’Angle
Authors: Philippe Julien 
Published: October 2016

Introduction : L’application de forces mécaniques sur les dents constitue
une part non négligeable du traitement orthodontique. La mécanique la plus utilisée,
l’« Edgewise », née il y a 88 ans, s’est imposée à travers le monde. Son invention par E.H.
Angle en 1928 représente, pour l’histoire de l’orthodontie, un évènement qui mérite d’être
rappelé. Matériels et méthodes : Cet article expose brièvement les raisons
qui ont poussé Angle à mettre au point une nouvelle mécanique. Résultats :
Pour présenter le premier système mécanique agissant dans les trois plans de
l’espace, Angle a montré des schémas et donner des modes d’emploi précis, rappelant à
plusieurs reprises que sa mécanique n’est pas compliquée et qu’une étude attentive doit
permettre d’en surmonter toutes les difficultés. Discussion : La conception
thérapeutique d’Angle n’a été suivie que pendant une courte période, son auteur étant
décédé peu de temps après sa présentation. Mais les mécaniques inventées par la suite
conservèrent les principes de l’Edgewise, rendant ainsi hommage à une grande invention.
Radical new paradigm for heme degradation in
Escherichia coli
O157:H7
Authors: LaMattina Joseph W. , Nix David B. , Lanzilotta William Nicholas 
Published: October 2016

Significance
The ability of pathogenic microorganisms to acquire iron from heme has been shown to be a valid antimicrobial target. However, all of the known mechanisms for heme catabolism that lead to iron release in bacteria and higher eukaryotes are dependent on molecular oxygen as a cosubstrate. The human gut is dominated by strictly anaerobic bacteria, and in this work, we provide evidence for anaerobic heme degradation in enteric pathogens. The anaerobic mechanism is significantly different from what has been observed in other bacteria and may provide a unique opportunity for a new class of antimicrobial compounds.
Human amygdala engagement moderated by early life stress exposure is a biobehavioral target for predicting recovery on antidepressants
Authors: Goldstein-Piekarski Andrea N. , Korgaonkar Mayuresh S. , Green Erin , Suppes Trisha , Schatzberg Alan F. , Hastie Trevor , Nemeroff Charles B. , Williams Leanne M. 
Published: October 2016

Significance
Amygdala reactivity and early life stress (ELS) are both strongly implicated in the mechanisms of depression in animal and human models. Despite these mechanistic foundations, amygdala reactivity and ELS have not been investigated as biobehavioral targets for predicting functional remission in depression. We addressed this issue by integrating human imaging and ELS measures within a controlled trial of antidepressant outcomes. We demonstrate that the interaction between ELS and amygdala engagement predicts functional remission on antidepressants with a greater than 80% cross-validated accuracy. In depressed people exposed to high ELS, a greater likelihood of remission was predicted by amygdala hyperreactivity to socially rewarding stimuli, whereas for those with low-ELS exposure, amygdala hyporeactivity to both rewarding and threat-related stimuli predicted remission.
Resource scarcity drives lethal aggression among prehistoric hunter-gatherers in central California
Authors: Allen Mark W. , Bettinger Robert Lawrence , Codding Brian F. , Jones Terry L. , Schwitalla Al W. 
Published: October 2016

SignificanceFrom warfare to homicide, lethal violence is an all too common aspect of the human experience, yet we still do not have a clear explanation of why individuals kill one another. We suggest the search for an answer should begin with an empirical understanding of where and when individuals are more prone to experience violence. Examining patterns of lethal trauma among hunter-gatherer populations in prehistoric central California, this study reveals that violence is explained by resource scarcity and not political organization. This finding provides a clear rationale to understand why violence may be greater in specific times or places through human history, which can help predict where and when it may arise in the future.
The physics and technology basis entering European system code studies for DEMO
Authors: Wenninger R. , Kembleton R. , Bachmann C. , Biel W. , Bolzonella T. , Ciattaglia S. , Cismondi F. , Coleman M. , Donné A.J.H. , Eich T. , Fable E. , Federici G. , Franke T. , Lux H. , Maviglia F. , Meszaros B. , Pütterich T. , Saarelma S. , Snickers A. , Villone F. , Vincenzi P. , Wolff D. , Zohm H. 
Published: October 2016

Abstract
A large scale program to develop a conceptual design for a demonstration fusion power plant (DEMO) has been initiated in Europe. Central elements are the baseline design points, which are developed by system codes. The assessment of the credibility of these design points is often hampered by missing information. The main physics and technology content of the central European system codes have been published (Kovari et al 2014 Fusion Eng. Des. 89 3054–69, 2016 Fusion Eng. Des. 104 9–20, Reux et al 2015 Nucl. Fusion
55 073011). In addition, this publication discusses key input parameters for the pulsed and conservative design option

EU DEMO1 2015

and provides justifications for the parameter choices. In this context several DEMO physics gaps are identified, which need to be addressed in the future to reduce the uncertainty in predicting the performance of the device.
Also the sensitivities of net electric power and pulse duration to variations of the input parameters are investigated. The most extreme sensitivity is found for the elongation (

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LDAP: a web server for lncRNA-disease association prediction
Authors: Lan Wei , Li Min , Zhao Kaijie , Liu Jin , Wu Fang-Xiang , Pan Yi , Wang Jianxin 
Published: October 2016

Abstract

Motivation
Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource.

Results
In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources. Then, we implement this method as a web server for lncRNA-disease association prediction (LDAP). The input of the LDAP server is the lncRNA sequence. The LDAP predicts potential lncRNA-disease associations by using a bagging SVM classifier based on lncRNA similarity and disease similarity.

Availability and Implementation
The web server is available at http://bioinformatics.csu.edu.cn/ldap

Supplementary information
Supplementary data are available at Bioinformatics online.
CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data
Authors: Russo Daniel P , Kim Marlene T , Wang Wenyi , Pinolini Daniel , Shende Sunil , Strickland Judy , Hartung Thomas , Zhu Hao 
Published: October 2016

Abstract

Summary
We have developed a public Chemical In vitro–In vivo Profiling (CIIPro) portal, which can automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds. For compounds with in vivo target activity data (e.g. animal toxicity testing results), the integrated cheminformatics algorithm will optimize the extracted biological data using in vitro–in vivo correlations. The resulting in vitro biological data for target compounds can be used for read-across risk assessment of target compounds. Additionally, the CIIPro portal can identify the most similar compounds based on their optimized bioprofiles. The CIIPro portal provides new powerful assessment capabilities to the scientific community and can be easily integrated with other cheminformatics tools.

Availability and Implementation
ciipro.rutgers.edu.
simPATHy: a new method for simulating data from perturbed biological PATHways
Authors: Salviato Elisa , Djordjilović Vera , Chiogna Monica , Romualdi Chiara 
Published: October 2016

Abstract

Summary
In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data – gene expression, RPKM/FPKM or protein abundances – from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological approaches.

Availability and Implementation
The simPATHy is an R package, it is open source and freely available on CRAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improving cross-study prediction through addon batch effect adjustment or addon normalization
Authors: Hornung Roman , Causeur David , Bernau Christoph , Boulesteix Anne-Laure 
Published: October 2016

Abstract

Motivation
To date most medical tests derived by applying classification methods to high-dimensional molecular data are hardly used in clinical practice. This is partly because the prediction error resulting when applying them to external data is usually much higher than internal error as evaluated through within-study validation procedures. We suggest the use of addon normalization and addon batch effect removal techniques in this context to reduce systematic differences between external data and the original dataset with the aim to improve prediction performance.

Results
We evaluate the impact of addon normalization and seven batch effect removal methods on cross-study prediction performance for several common classifiers using a large collection of microarray gene expression datasets, showing that some of these techniques reduce prediction error.

Availability and Implementation
All investigated addon methods are implemented in our R package bapred.

Supplementary information
Supplementary data are available at Bioinformatics online.
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
Authors: Shah Ankeeta , Qian Yingzhi , Weyn-Vanhentenryck Sebastien M , Zhang Chaolin 
Published: October 2016

Abstract

Summary
UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package.

Availability and Implementation
The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2.columbia.edu/index.php/CTK.
Electrical remodelling in patients with iatrogenic left bundle branch block
Authors: Engels Elien B. , Poels Thomas T. , Houthuizen Patrick , de Jaegere Peter P.T. , Maessen Jos G. , Vernooy Kevin , Prinzen Frits W. 
Published: October 2016

Aims
Left bundle branch block (LBBB) is induced in approximately one-third of all transcatheter aortic valve implantation (TAVI) procedures. We investigated electrophysiological remodelling in patients with TAVI-induced LBBB.

Methods and results
This retrospective study comprises 107 patients with initially narrow QRS complex of whom 40 did not and 67 did develop persistent LBBB after TAVI. 12-lead electrocardiograms (ECGs) taken before TAVI, within 24 hours (‘acute’), and 1–12 months after TAVI (‘chronic’) were used to reconstruct vectorcardiograms. From these vectorcardiograms, QRS and T-wave area were calculated as comprehensive indices of depolarization and repolarization abnormalities, respectively. TAVI-induced LBBB resulted in significant acute depolarization and repolarization changes while further repolarization changes were observed with longer lasting LBBB. The amount of long-term repolarization changes (remodelling) was highly variable between patients. The change in T-wave area between acute and chronic LBBB ranged from +57% to − 77%. After dividing the LBBB cohort into tertiles based on the change in T-wave area, only baseline QRS area was larger in the tertile with no significant change in T-wave area. During longer lasting LBBB, the spatial vector gradient (SVG) changed orientation towards the direction of the QRS-vector, indicating that later-activated regions developed shorter action potential duration.

Conclusion
This study in patients with TAVI-induced LBBB shows that repolarization changes develop within months after onset of LBBB, and that these changes are highly variable between individual patients.
Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses
Authors: Rahaman Jordon , Siltberg-Liberles Jessica 
Published: October 2016

AbstractWithin the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the &gt;10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.