bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cue-selective adaptation operates on a separable encoding of stereo and texture information
Authors: Cesanek Evan , Domini Fulvio 
Published: February 2019

AbstractTo perform accurate movements, the sensorimotor system must maintain a delicate calibration of the mapping between visual inputs and motor outputs. Previous work has focused on the mapping between visual inputs and individual locations in egocentric space, but little attention has been paid to the mappings that support interactions with 3D objects. In this study, we investigated sensorimotor adaptation of grasping movements targeting the depth dimension of 3D paraboloid objects. Object depth was specified by separately manipulating binocular disparity (stereo) and texture gradients. At the end of each movement, the fingers closed down on a physical object consistent with one of the two cues, depending on the condition (haptic-for-texture or haptic-for-stereo). Unlike traditional adaptation paradigms, where relevant spatial properties are determined by a single dimension of visual information, this method enabled us to investigate whether adaptation processes can selectively adjust the influence of different sources of visual information depending on their relationship to physical depth. In two experiments, we found short-term changes in grasp performance consistent with a process of cue-selective adaptation: the slope of the grip aperture with respect to a reliable cue (correlated with physical reality) increased, whereas the slope with respect to the unreliable cue (uncorrelated with physical reality) decreased. In contrast, slope changes did not occur during exposure to a set of stimuli where both cues remained correlated with physical reality, but one was rendered with a constant bias of 10 mm; the grip aperture simply became uniformly larger or smaller, as in standard adaptation paradigms. Overall, these experiments support a model of cue-selective adaptation driven by correlations between error signals and input values (i.e., supervised learning), rather than mismatched haptic and visual signals.
Layer 5 circuits in V1 differentially control visuomotor behavior
Authors: Tang Lan , Higley Michael J. 
Published: February 2019

SummarySensory areas of the mammalian neocortex are thought to act as distribution hubs, transmitting information about the external environment to various cortical and subcortical structures in order to generate adaptive behavior. However, the exact role of cortical circuits in sensory perception remains unclear. Within primary visual cortex (V1), various populations of pyramidal neurons (PNs) send axonal projections to distinct targets, suggesting multiple cellular networks that may be independently engaged during the generation of behavior. Here, we investigated whether PN subpopulations differentially support sensory-guided performance by training mice in a visual detection task based on eyeblink conditioning. Applying 2-photon calcium imaging and optogenetic manipulation of anatomically-defined PNs in behaving animals, we show that layer 5 corticopontine neurons strongly encode task information and are selectively necessary for performance. These results contrast with recent observations of operant behavior showing a limited role for the neocortex in sensory detection. Instead, our findings support a model in which target-specific cortical subnetworks form the basis for adaptive behavior by directing relevant information to downstream brain areas. Overall, this work highlights the potential for neurons to form physically interspersed but functionally segregated networks capable of parallel, independent control of perception and behavior.
A charge-dependent phase transition determines interphase chromatin organization
Authors: Strickfaden Hilmar , Sharma Ajit K. , Hendzel Michael J. 
Published: February 2019

AbstractAn emerging principle of cellular compartmentalization is that liquid unmixing results in formation of compartments by phase separation. We used electron spectroscopic Imaging (ESI), a transmission electron microscopy technology, to distinguish chromatin and nucleoplasmic phases of mammalian cell lines and their responses towards different environmental changes. We tested the hypothesis that charge-dependent phase separation mediated by the histone N-termini could explain the organization of chromatin. 3D images of nuclear chromatin with electron spectroscopic imaging (ESI) demonstrates that the amount of chromatin proximal to the interchromatin compartment (IC) differs between cell types, reflecting major differences in chromatin organization. These differences were lost when cells were treated overnight with a histone deacetylase inhibitor. We show that drastic, reversible changes in chromatin mixing or unmixing with the nucleoplasm/interchromatin space can be induced by modulating osmolarity of the medium or acetylation status of the chromatin. In vitro phase separation experiments demonstrated that chromatin separated from solution through a phase transition towards a more solid chromatin state.
Caribbean multi-centre study of Klebsiella pneumoniae: whole genome sequencing, antimicrobial resistance and virulence factors
Authors: Heinz Eva , Brindle Richard , Morgan-McCalla Andrina , Peters Keisha , Thomson Nicholas R. 
Published: February 2019

ABSTRACTThe surveillance of antimicrobial resistant isolates has proven to be one of the most valuable tools to understand the global rise of multidrug-resistant bacterial pathogens. We report the first insights into the current situation in the Caribbean, where a pilot project to monitor antimicrobial resistance through phenotypic resistance measurements combined with whole-genome sequencing was set up in collaboration with the Caribbean Public Health Agency (CARPHA). Our first study focused on Klebsiella pneumoniae, a highly relevant organism amongst the Gram-negative opportunistic pathogens world-wide today causing hospital, as well as community-acquired, infections. Our results show that not only carbapenem resistance, but also hypervirulent strains, are circulating in patients in the Caribbean. Our current data does not allow us to infer their prevalence in the population. We argue for the urgent need to further support antimicrobial resistance surveillance and stewardship in this almost uncharted territory, which can make a significant impact on the reduction of antimicrobial usage.DATA SUMMARY-Raw sequencing data is deposited at the sequence read archive (SRA), and assemblies are deposited at GenBank, accession numbers for all are given in Dataset S1.-The data of measured resistance phenotypes (Vitek) is also provided in Dataset S1.-The tree file and associated metadata can be investigated and downloaded through the free online platform microreact (https://microreact.org/project/S1-a7KAkV).✓ I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠Significance as a BioResource to the communityThis BioResource contains whole-genome sequence data of 270 Klebsiella pneumoniae isolates, information about encoded resistance genes and the phylogeny of the isolates, their distribution in the global K. pneumoniae population, and their resistance phenotype data as determined by the VITEK 2 compact system. The isolates are recent (2017 through 2018) and represent clinically relevant patient isolates from 15 different sites in 12 Caribbean states. These data will be of interest for researchers working on K. pneumoniae and other opportunistic pathogens as well as those interested in mobile genetic elements carrying antimicrobial resistance cassettes. Our data is the only recent survey of antimicrobial resistant opportunistic pathogens from multiple sites within the Caribbean, and is of high significance for the global surveillance of K. pneumoniae and antimicrobial resistance elements. This BioResource is made available through data tables provided with this article, as well deposition of the raw data in the relevant archives, and an interactive platform (microreact) to enquire and download analyses (phylogenetic tree, metadata).
Improving drug discovery using image-based multiparametric analysis of epigenetic landscape
Authors: Farhy Chen , Orozco Luis , Zeng Fu-Yue , Pass Ian , Ylanko Jarkko , Hariharan Santosh , Huang Chun-Teng , Andrews David , Terskikh Alexey V. 
Published: February 2019

AbstractWith the advent of automatic cell imaging and machine learning, high-content phenotypic screening has become the approach of choice for drug discovery due to its ability to extract drug specific multilayered data and compare it to known profiles. In the field of epigenetics such screening approaches has suffered from the lack of tools sensitive to selective epigenetic perturbations. Here we describe a novel approach Microscopic Imaging of Epigenetic Landscapes (MIEL) that captures patterns of nuclear staining of epigenetic marks (e.g. acetylated and methylated histones) and employs machine learning to accurately distinguish between such patterns (1). We demonstrated that MIEL has superior resolution compared to conventional intensity thresholding techniques and enables efficient detection of epigenetically active compounds, function-based classification, flagging possible off-target effects and even predict novel drug function. We validated MIEL platform across multiple cells lines and using dose-response curves to insure the robustness of this approach for the high content high throughput drug discovery.
Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems
Authors: Babenko V.V. , Golomidova A.K. , Ivanov P.A. , Letarova M.A. , Kulikov E.E. , Manolov A.I. , Prokhorov N.S. , Kostrukova E.S. , Matyushkina D.M. , Prilipov A.G. , Maslov S. , Belalov I.S. , Clokie M.R.J.C. , Letarov A.V. 
Published: February 2019

AbstractTailed bacteriophages (Caudovirales order) are omnipresent on our planet. Their impressive ecological and evolutionary success largely relies on the bacteriophage potential to adapt to great variety of the environmental conditions found in the Biosphere. It is believed that the adaptation of bacteriophages, including short time scale adaptation, is achieved almost exclusivelyviathe (micro)evolution processes. In order to analyze the major mechanisms driving adaptation of phage genomes in a natural habitat we used comparative genomics of G7C-like coliphage isolates obtained during 7 years period from the feces of the horses belonging to a local population. The data suggest that even at this relatively short time scale the impact of various recombination events overwhelms the impact of the accumulation of point mutations. The access to the large pool of the genes of a complex microbial and viral community of the animal gut had major effect on the evolutionary trajectories of these phages. Thus the “real world” bacteriophage evolution mechanisms may differ significantly from those observed in the simplified laboratory model systems.
OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes
Authors: Greiner Stephan , Lehwark Pascal , Bock Ralph 
Published: February 2019

Key pointsOGDRAW has become the standard tool for displaying maps of organellar genomesit converts GenBank entries into graphical mapsa new version with improved functionality has been releasedAbstractOrganellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here were present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW has now access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.
Biomarker-based outcome prediction in prostate adenocarcinoma depends on theTMPRSS2-ERGstatus
Authors: Gerke Julia S. , Orth Martin F. , Tolkach Yuri , Romero-Pérez Laura , Wehweck Fabienne , Stein Stefanie , Musa Julian , Knott Maximilian M. L. , Hölting Tilman L. B. , Li Jing , Sannino Giuseppina , Marchetto Aruna , Ohmura Shunya , Cidre-Aranaz Florencia , Müller-Nurasyid Martina , Strauch Konstantin , Stief Christian , Kristiansen Glen , Kirchner Thomas , Buchner Alexander , Grünewald Thomas G. P. 
Published: February 2019

ABSTRACTBackgroundProstate adenocarcinoma (PCa) with/without theTMPRSS2-ERG(T2E)-fusion represent distinct molecular subtypes.ObjectiveTo investigate gene-signatures associated with metastasis in T2E-positive and -negative PCa, and to identify and validate subtype-specific prognostic biomarkers.Design, setting and participantsGene expression and clinicopathological data of two discovery PCa cohorts (totaln=783) were separately analyzed regarding the T2E-status. Selected subtype-specific biomarkers were validated in two additional cohorts (totaln=405).Outcome measurements and statistical analysisFrom both discovery cohorts, we generated two gene lists ranked by their differential intratumoral expression in patients with/without metastases stratified by T2E-status, which were subjected to gene set enrichment and leading-edge analyses. The resulting top 20 gene-signatures of both gene lists associated with metastasis were analyzed for overlaps between T2E-positive and -negative cases. Genes shared by several functional gene-signatures were tested for their association with event-free survival using the Kaplan-Meier method in a validation cohort. Immunohistochemistry was performed in another validation cohort.Results and limitationsMetastatic T2E-positive and -negative PCa are characterized by different gene-signatures. Five genes (ASPN, BGN, COL1A1, RRM2andTYMS) were identified whose high expression was significantly associated with worse outcome exclusively in T2E-negative PCa. This was validated in an independent cohort for all genes and additionally for RRM2 by immunohistochemistry in a separate validation cohort. No prognostic biomarkers were identified exclusively for T2E-positive tumors.ConclusionsOur study demonstrates that the prognostic value of biomarkers critically depends on the molecular subtype, i.e. the T2E-status, which should be considered when screening for and applying novel prognostic biomarkers for outcome prediction in PCa.Patient summaryOutcome prediction for PCa is complex. The results of this study highlight that the validity of prognostic biomarkers depends on the molecular subtype, specifically the presence/absence of T2E. The reported new subtype-specific biomarkers exemplify that biomarker-based outcome prediction in PCa should consider the T2E-status.
The Out of East Asia model versus the African Eve model of modern human origins in light of ancient mtDNA findings
Authors: Zhang Ye , Huang Shi 
Published: February 2019

AbstractThe first molecular model of modern human origins published in 1983 had the mtDNA phylogenetic tree rooted in Asia. This model was subsequently overlooked and superseded by the African Eve model in 1987 that was premised on the unrealistic infinite site assumption and the now failed molecular clock hypothesis. We have recently developed a new framework of molecular evolution, the maximum genetic diversity (MGD) hypothesis, which has in turn led us to discover a new model of modern human origins with the roots of uniparental DNAs placed in East Asia. While the African mtDNA Eve model has haplotype N as ancestral to R, our Asia model places R as the ancestor of all. We here examined ancient mtDNAs from the literature focusing on the relationship between N and R. The data showed that all three oldest mtDNAs were R with the 45000 year old Ust-Ishim a basal type and the two ~40000 year old samples sub-branch of R. Among the numerous mtDNAs of 39500-30000 year old, most were R subtype U and only two were N samples, the 39500 year old Oase1 and the 34425 year old Salkhit. These N types are basal and hence likely close to the root of N. These ancient DNA findings suggest that basal R is ~5000 years older than basal N, thereby confirming the East Asia model and invalidating the African Eve model.
The effect of sword bean extract on the relationship between rheumatoid arthritis and periodontitis in mice
Authors: Matsumoto Kosei , Nakatsuka Yuko , Shirai Kaname , Shimizu Shintaro , Yanase Shunshuke , Abiko Yoshihiro , Furuichi Yasushi 
Published: February 2019

AbstractObjectivesSeveral studies in humans and experimental animals have reported an interaction between rheumatoid arthritis (RA) and periodontitis (PD). We previously showed that extracts of Canavalia gladiata (sword bean extract, SBE) can treat PD in rats. Here, we investigated the relationship between RA and PD and the effects of SBE in an experimental mouse model.MethodsFemale SKG mice were assigned to eight groups (n=6/group): (1) Untreated controls, (2) RA (induced at 6 weeks of age), (3) PD (induced at 10 weeks of age), (4) RA + PD, (5) SBE (2 mg/ml in drinking water starting at 5 weeks of age), (6) PD + SBE, (7) RA + SBE, and (8) RA + PD + SBE. Mice were sacrificed at 13 weeks of age, and alveolar bone resorption, periodontal tissue inflammation, and paw joint inflammation were assessed by histology and immunohistochemistry.ResultsMice in the RA + PD group exhibited significantly higher inflammation scores in the joint tissues as well as more abundant IL-17-positive cells and cathepsin K-positive osteoclasts in the radial bone compared with the RA mice. Alveolar bone resorption was also significantly more severe in the RA + PD mice than in the PD mice. SBE treatment significantly improved all bone resorption and tissue inflammation scores in mice with RA + PD.ConclusionConcomitant RA and PD exacerbates the tissue destruction symptomatic of each condition. SBE suppresses all parameters evaluated, suggesting that it is has anti-inflammatory activities in both RA and PD.
Effects of reduced sulfur on passive film properties of steam generator (SG) tubing: an overview
Authors: Xia Da-Hai , Luo Jing-Li 
Published: February 2019

Purpose
Corrosion is considered as one of the issues that threaten the safe operation of steam generator (SG) tubing. Some sulfur-related specie can cause corrosion degradation of SG tubing. Sulfur-induced corrosion of SG alloys in high temperature and high-pressure water is one of the most complicated processes. The purpose of this study is to study the effect of reduced sulphur on passive film properties of steam generator (SG) tubing.

Design/methodology/approach
In this paper, the effects of reduced sulfur on passive film properties of SG tubing were reviewed from the aspects of thermodynamic calculations and experimental.

Findings
Thermodynamic calculations are mainly presented by E-pH diagrams, volt equivalent diagrams and species distribution curves. The stability of sulphur species highly depends on temperature, solution pH, and electrochemical potential. Experimental data indicated that reduced sulfur species can interact with the passive film, which led to changes in film thickness, film structure, semiconductivity and pitting growth rate.

Originality/value
The state-of-the-art discussed in this paper gives basis for resolving engineering problems regarding with sulfur-induced corrosion.
The impact of perceived CSR on corporate reputation and purchase intention
Authors: Bianchi Enrique , Bruno Juan Manuel , Sarabia-Sanchez Francisco J. 
Published: February 2019

Purpose
The purpose of this paper is to examine the influence of consumers’ perceived corporate social responsibility (CSR). The aim is to provide insight into the effect of perceived CSR on purchase intention (short-term effect) and corporate reputation (long-term effect), whilst considering the role of brand image, satisfaction (affective and cognitive) and brand loyalty.

Design/methodology/approach
The sample comprised 429 consumers selected using non-probabilistic sampling with age and gender quotas. Confirmatory factor analysis was used to validate the measurement model. Structural equation modelling was used to validate the research hypotheses.

Findings
All direct and mediated influences in the model were significant, except for the effects of perceived CSR on affective satisfaction. Thus, the proposed causal chain is valuable to understand how perceptions of CSR influence purchase intention and perceived reputation.

Research limitations/implications
Perception is considered a dual phenomenon (cognitive and affective). It would be advisable to consider both dimensions in the future. The same is true of affective satisfaction.

Originality/value
Direct and mediated relationships that have previously been studied separately are considered together in a single model. This approach provides a better understanding of how perceived CSR influences purchase intention and reputation.
Forensic analysis of Google Allo messenger on Android platform
Authors: Agrawal Vinayak , Tapaswi Shashikala 
Published: February 2019

Purpose
The purpose of this paper is to conduct a forensic analysis of Google Allo messenger on an Android-based mobile phone. The focus was on the analysis of the data stored by this application in the internal memory of the mobile device, with minimal use of third-party applications. The findings were compared with the already existing works on this topic. Android is the most popular operating system for mobile devices, and these devices often contain a massive amount of personal information about the user such as photos and contact details. Analysis of these applications is required in case of a forensic investigation and makes the process easier for forensic analysts.

Design/methodology/approach
Logical acquisition of the data stored by these applications was performed. A locked Android device was used for this purpose. Some scripts are presented to help in data acquisition using Android Debug Bridge (ADB). Manual forensic analysis of the device image was performed to see whether the activities carried out on these applications are stored in the internal memory of the device. A comparative analysis of an existing mobile forensic tool was also performed to show the effectiveness of the methodology adopted.

Findings
Forensic artifacts were recovered from Allo application. Multimedia content such as images were also retrieved from the internal memory.

Research limitations/implications
As this study was conducted for forensic analysis, it assumed that the mobile device used already has USB debugging enabled on it, although this might not be the applicable in some of the cases. This work provides an optimal approach to acquiring artifacts with minimal use of third-party applications.

Practical implications
Most of the mobile devices contain messaging application such as Allo installed. A large amount of personal information can be obtained from the forensic analysis of these applications, which can be useful in any criminal investigation.

Originality/value
This is the first study which focuses on the Google Allo application. The proposed methodology was able to extract almost as much as the data obtained using earlier approaches, but with minimal third-party application usage.