bluuebunny/crossref_metadata_2025_split huggingface dataset:
Driving the expression of theSalmonella entericasv Typhimurium flagellum usingflhDCfromEscherichia coliresults in key regulatory and cellular differences
Authors: Albanna Ayman , Sim Martin , Hoskisson Paul A , Gillespie Colin , Rao Christopher V. , Aldridge Phillip 
Published: May 2018

ABSTRACTThe flagellar systems ofEscherichia coliandSalmonella entericaexhibit a significant level of genetic and functional synteny. Both systems are controlled by the flagellar specific master regulator FlhD4C2. Since the early days of genetic analyses of flagellar systems it has been known thatE. coli flhDCcan complement a ΔflhDCmutant inS. enterica. The genomic revolution has identified how genetic changes to transcription factors and / or DNA binding sites can impact the phenotypic outcome across related species. We were therefore interested in asking: using modern tools to interrogate flagellar gene expression and assembly, what would the impact be of replacing theflhDCcoding sequences inS. entericafor theE. coligenes at theflhDC S. enterciachromosomal locus? We show that even though all strains created are motile, flagellar gene expression is measurably lower whenflhDCECare present. These changes can be attributed to the impact of FlhD4C2DNA recognition and the protein-protein interactions required to generate a stable FlhD4C2complex. Furthermore, our data suggests that inE. colithe internal flagellar FliT regulatory feedback loop has a marked difference with respect to output of the flagellar systems. We argue due diligence is required in making assumptions based on heterologous expression of regulators and that even systems showing significant synteny may not behave in exactly the same manner.
Phosphatidylinositol 5 phosphate 4-kinase regulates plasma-membrane PIP3 turnover and insulin sensitivity in Drosophila
Authors: Sharma Sanjeev , Mathre Swarna , Visvanathan Sanjeev , Shinde Dhananjay , Raghu Padinjat 
Published: May 2018

AbstractPhosphatidylinositol-3,4,5-trisphosphate (PIP3) generation at the plasma membrane is a key event during activation of receptor tyrosine kinases such as the insulin receptor and is critical for normal growth and metabolism. The lipid kinases and phosphatases regulating PIP3 levels are described but mechanisms controlling their activity remain unclear. We report that in Drosophila, phosphatidylinositol 5 phosphate 4-kinase (PIP4K) function at the plasma membrane is required for normal PIP3 levels during insulin receptor activation. Depletion of PIP4K increases PIP3 levels and augments sensitivity to insulin through enhanced Class I phosphoinositide 3-kinase (PI3K) activity. Animals lacking PIP4K show enhanced insulin signalling dependent phenotypes in vivo and are resistant to the metabolic consequences of a high-sugar diet, highlighting the importance of PIP4K in normal metabolism and development. Thus, PIP4KS are key regulators of receptor tyrosine kinase signalling with implications for growth factor dependent processes including tumour growth, T-cell activation and metabolism.
Ethanol-Mediated Compaction and Crosslinking Enhance Mechanical Properties and Degradation Resistance While Maintaining Cytocompatibility of a Nucleus Pulposus Scaffold
Authors: Walters Joshua D. , Gill Sanjitpal S. , Mercuri Jeremy J. 
Published: May 2018

AbstractIntervertebral disc degeneration is a complex, cell-mediated process originating in the nucleus pulposus (NP) and is associated with extracellular matrix catabolism leading to disc height loss and impaired spine kinematics. Previously, we developed an acellular bovine NP (ABNP) for NP replacement that emulated human NP matrix composition and supported cell seeding; however, its mechanical properties were lower than those reported for human NP. To address this, we investigated ethanol-mediated compaction and crosslinking to enhance the ABNP’s dynamic mechanical properties and degradation resistance while maintaining its cytocompatibility. First, volumetric and mechanical effects of compaction only were confirmed by evaluating scaffolds after various immersion times in buffered 28% ethanol. It was found that compaction reached equilibrium at ∼30% compaction after 45 min, and dynamic mechanical properties significantly increased 2-6x after 120 min of submersion. This was incorporated into a crosslinking treatment, through which scaffolds were subjected to 120 min pre-compaction in buffered 28% ethanol prior to carbodiimide crosslinking. Their dynamic mechanical properties were evaluated before and after accelerated degradation by ADAMTS-5 or MMP-13. Cytocompatibility was determined by seeding stem cells onto scaffolds and evaluating viability through metabolic activity and fluorescent staining. Compacted and crosslinked scaffolds showed significant increases in DMA properties without detrimentally altering their cytocompatibility, and these mechanical gains were maintained following enzymatic exposure.
Inductive reasoning differs between taxonomic and thematic contexts: Electrophysiological evidence
Authors: Liu Fangfang , Han Jiahui , Zhang Lingcong , Li Fuhong 
Published: May 2018

AbstractInductive reasoning can be performed in different contexts, but it is unclear whether the neural mechanism of inductive reasoning performed in a thematic context (e.g., panda has x, so bamboo has x) is the same as that performed in a taxonomic context (e.g., panda has x, so bear has x). In the present study, participants were required to judge whether a conclusion was acceptable or not based on its premise, for which the taxonomic or thematic distances between premise and conclusion objects were either far or near. The ERP results indicated that the effect of reasoning context (taxonomic vs. thematic) was initially observed in the P2 component; while the distance effect (far vs. near) was observed in N400 and late components. Moreover, the distance effect on thematic-based inductive reasoning was found in the frontal and frontal-central brain regions, while the distance effect in taxonomic-based inductive reasoning conditions was found in the central-parietal and parietal regions. These results support the view that inductive reasoning is performed differently under different semantic contexts.
Evaluation of a guideline developed to reduce HIV-related stigma and discrimination in healthcare settings and establishing consensus
Authors: Feyissa Garumma Tolu , Lockwood Craig , Woldie Mirkuzie , Munn Zachary 
Published: May 2018

AbstractBackgroundDeveloping guidelines and policies is critical to address HIV-related stigma and discrimination (SAD) in healthcare settings. To this end, a multidisciplinary panel developed a guideline to reduce SAD. This project evaluated the appropriateness of implementing the guideline in the Ethiopian context.MethodsA consensus of the expert panel was established through a Delphi technique which was followed by a panel meeting. Initial tentative recommendations were distributed to experts through e-mails to be evaluated using the modified guideline implementability appraisal (GLIA) v.2.0 checklist.ResultsIn the first round of the Delphi survey, all (13) panel members evaluated the guideline. The overall score for the general domain of the modified GLIA checklist was 96.56%. The scores for individual recommendations ranged from 68.33% to 92.76%. Maximum and minimum scores were attained for measurability (97.71%) and flexibility (59.77%) domains respectively. Percentages mean score lower than 75% was obtained for flexibility and validity domains. Participants suggested that additional tools and training should be added to the guideline. In the second round of the survey, all the recommendations received endorsement with scores above 75%. Maximum and minimum scores were attained for measurability (100%) and flexibility (86.88%) domains respectively. During the panel meeting, issues of responsibility for implementing the guideline were discussed.ConclusionThe project evaluated implementability of a guideline developed to reduce HIV-related SAD in healthcare settings. The Delphi survey was followed by a half-day meeting that helped in further clarification of points.
Mutation load dynamics during environmentally-driven range shifts
Authors: Gilbert Kimberly J. , Peischl Stephan , Excoffier Laurent 
Published: May 2018

AbstractThe fitness of spatially expanding species has been shown to decrease over time and space, but specialist species tracking their changing environment and shifting their range accordingly have been little studied. We use individual-based simulations and analytical modeling to compare the impact of range expansions and range shifts on genetic diversity and fitness loss, as well as the ability to recover fitness after either a shift or expansion. We find that the speed of a shift has a strong impact on fitness evolution. Fastest shifts show the strongest fitness loss per generation, but intermediate shift speeds lead to the strongest fitness loss per geographic distance. Range shifting species lose fitness more slowly through time than expanding species, however, their fitness compared at equivalent geographic distances spread can be considerably lower. These counter-intuitive results arise from the combination of time over which selection acts and mutations enter the system. Range shifts also exhibit reduced fitness recovery after a geographic shift and may result in extinction, whereas range expansions can persist from the core of the species range. The complexity of range expansions and range shifts highlights the potential for severe consequences of environmental change on species survival.Author SummaryAs environments change through time across the globe, species must adapt or relocate to survive. Specialized species must track the specific moving environments to which they are adapted, as compared to generalists which can spread widely. During colonization of new habitat, individuals can accumulate deleterious alleles through repeated bottlenecks. We show through simulation and analytic modeling that the process by which these alleles accumulate changes depending upon the speed at which populations spread over a landscape. This is due to the increased efficacy of selection against deleterious variants at slow speeds of range shifts and decreased input of mutations at faster speeds of range shifts. Under some selective circumstances, shifting of a species range leads to extinction of the entire population. This suggests that the rate of environmental change across the globe will play a large role in the survival of specialist species as compared to more generalist species.
Analysis of the transcriptional logic governing differential spatial expression in Hh target genes
Authors: Cambón Manuel , Sánchez Óscar 
Published: May 2018

AbstractThis work provides theoretical tools to analyse the transcriptional effects of certain biochemical mechanisms (i.e. affinity and cooperativity) that have been proposed in previous literature to explain the differential spatial expression of Hedgehog target genes involved inDrosophiladevelopment. Specifically we have focused on the expression ofdecapentaplegicandpatched. The transcription of these genes is believed to be controlled by opposing gradients of the activator and repressor forms of the transcription factor Cubitus interruptus (Ci). This study is based on a thermodynamic approach, which provides expression rates for these genes. These expression rates are controlled by transcription factors which are competing and cooperating for common binding sites. We have made mathematical representations of the different expression rates which depend on multiple factors and variables. The expressions obtained with the model have been refined to produce simpler equivalent formulae which allow for their mathematical analysis. Thanks to this, we can evaluate the correlation between the different interactions involved in transcription and the biological features observed at tissular level. These mathematical models can be applied to other morphogenes to help understand the complex transcriptional logic of opposing activator and repressor gradients.Author summaryMorphogenic differentiation is a complex process that involves emission, reception and cellular response to different signals. It is well known that the same morphogenic signal can give rise to different cellular transcriptional responses that usually depend, among other factors, on transcription factors. In concordance with the activator threshold model, classically it has been distinguished between high and low threshold target genes in order to explain how cells receiving the same signal can activate different genes. However, in particular cases where the transcription is controlled by two opposing transcription factors, it has been tested that this logic is not valid. This motivates the necessity for describing new theoretical models in order to understand better these cellular responses. By a theoretical analysis we have deduced different versions of transcriptional logic that are significantly determined by how the opposing transcription factors cooperate between them in the transcription process. We have also tested these different scenarios focussing on the Drosophila Hh target genes, and we have reproduced similar conclusions to the ones obtained by other methodologies.
Estimating heterogeneous treatment effects by balancing heterogeneity and fitness
Authors: Zhang Weijia , Le Thuc , Liu Lin , Li Jiuyong 
Published: May 2018

AbstractEstimating heterogeneous treatment effects is an important problem in many medical and biological applications since treatments may have different effects on the prognoses of different patients. Recently, several recursive partitioning methods have been proposed to identify the subgroups that with different responds to a treatment, and they rely on a fitness criterion to minimize the error between the estimated treatment effects and the unobservable true effects. In this paper, we propose that a heterogeneity criterion, which maximizes the differences of treatment effects among the subgroups, also needs to be considered. Moreover, we show that better performances can be achieved when the fitness and the heterogeneous criteria are considered simultaneously. Selecting the optimal splitting points then becomes a multi-objective problem; however, a solution that achieves optimal in both aspects are often not available. To solve this problem, we propose a multi-objective splitting procedure to balance both criteria. The proposed procedure is computationally efficient and fits naturally into the existing recursive partitioning framework. Experimental results show that the proposed multi-objective approach performs consistently better than existing ones.Author summaryThe effects of a treatment are often not the same for different individuals with different gene expressions. Learning to predict the heterogeneous treatment effects from clinical and expression data is an important step towards personalized medical treatment. Existing computational methods are not ideal for the task because they do not address the interpretability of the model and do not consider the limited sample sizes in biological and medical applications. Our method addresses these issues and achieves superior performance in analyzing the treatment effects of radiotherapy on breast cancer patients.
Unbiased dynamic characterization of RNA-protein interactions by OOPS
Authors: Queiroz Rayner M. L. , Smith Tom , Villanueva Eneko , Monti Mie , Pizzinga Mariavittoria , Marti-Solano Maria , Mirea Dan-Mircea , Ramakrishna Manasa , Harvey Robert F. , Dezi Veronica , Degroeve Sven , Martens Lennart , Thomas Gavin H. , Willis Anne E. , Lilley Kathryn S. 
Published: May 2018

AbstractCurrent methods for the identification of RNA–protein interactions require a quantity and quality of sample that hinders their application, especially for dynamic biological systems or when sample material is limiting. Here, we present a new approach to enrich RNA-Binding Proteins (RBPs): Orthogonal Organic Phase Separation (OOPS), which is compatible with downstream proteomics and RNA sequencing. OOPS enables recovery of RBPs and free protein, or protein-bound RNA and free RNA, from a single sample in an unbiased manner. By applying OOPS to human cell lines, we extract the majority of known RBPs, and importantly identify additional novel RBPs, including those from previously under-represented cellular compartments. The high yield and unbiased nature of OOPS facilitates its application in both dynamic and inaccessible systems. Thus, we have identified changes in RNA-protein interactions in mammalian cells following nocodazole cell-cycle arrest, and defined the first bacterial RNA-interactome. Overall, OOPS provides an easy-to-use and flexible technique that opens new opportunities to characterize RNA-protein interactions and explore their dynamic behaviour.
Deep feature selection for Identification of Essential Proteins of Learning and Memory in Mouse Model of Down Syndrome
Authors: Abdeldayem Sara S. , Elhefnawi Mahmoud M. 
Published: May 2018

AbstractDown syndrome is a chromosomal abnormality related to intellectual disabilities that affects 0.1% of live births worldwide. It occurs when an individual has a full or partial extra copy of chromosome 21. This chromosome trisomy results in the overexpression of genes that is believed to be sufficient to interfere normal pathways and normal responses to stimulation, causing learning and memory deficiency. Therefore, by studying these proteins and the disturbance in pathways that are involved in learning and memory, we can consider drugs that would correct the observed perturbations, and therefore assist in enhancing the memory and learning. Here, from genes based on an earlier study that identified 77 proteins differentially expressed in normal and trisomic wild mice exposed to context fear conditioning (CFC), we provide a quantitative protein selection based on different feature selection techniques to select the most important proteins related to learning and memory. These techniques include Fisher score, Chi score, and correlation-based subset. In addition, a deep feature selection is utilized to extract high order proteins using deep neural networks. Three main experiments are carried out:studying the control mice’s response, studying the trisomy mice’s response, and studying the control-trisomy mice’s response. In each experiment, support vector machine classifier is used to assess these selected proteins ability to distinguish between learned and not-learned mice to the fear conditioning event. By applying the deep feature selection, fifteen proteins were selected in control mice, nine in trisomy mice, and seven in control-trisomy mice achieving distinguishing accuracies of 93%, 99%, 84% respectively compared to 74%, 78%, and 71% average accuracies of other selection methods. Some of these proteins have important biological function in learning such as CaNA, NUMb, and NOS.
An Event-related Potential Comparison of Facial Expression Processing between Cartoon and Real Faces
Authors: Zhao Jiayin , Wang Yifang , An Licong 
Published: May 2018

AbstractFaces play important roles in the social lives of humans. In addition to real faces, people also encounter numerous cartoon faces in daily life. These cartoon faces convey basic emotional states through facial expressions. Using a behavioral research methodology and event-related potentials (ERPs), we conducted a facial expression recognition experiment with 17 university students to compare the processing of cartoon faces with that of real faces. This study used face type (real vs. cartoon) and participant gender (male vs. female) as independent variables. Reaction time, recognition accuracy, and the amplitudes and latencies of emotion processing-related ERP components such as N170, vertex positive potential (VPP), and late positive potential (LPP) were used as dependent variables. The ERP results revealed that cartoon faces caused larger N170 and VPP amplitudes as well as a briefer N170 latency than did real faces; that real faces induced larger LPP amplitudes than did cartoon faces; and that angry faces induced larger LPP amplitudes than did happy faces. In addition, the results showed a significant difference in the brain regions associated with face processing as reflected in a right hemispheric advantage. The behavioral results showed that the reaction times for happy faces were shorter than those for angry faces; that females showed a higher facial expression recognition accuracy than did males; and that males showed a higher recognition accuracy for angry faces than happy faces. These results demonstrate differences in facial expression recognition and neurological processing between cartoon faces and real faces among adults. Cartoon faces showed a higher processing intensity and speed than real faces during the early processing stage. However, more attentional resources were allocated for real faces during the late processing stage.
Anti-corrosion performances of hybrid silane coatings on AZ31 alloy
Authors: Calabrese Luigi , Caprì Angela , Proverbio Edoardo 
Published: May 2018

Purpose
This paper aims to evaluate the efficacy of a zeolite-filled silane sol–gel coating as protective layer on pretreated AZ31 magnesium alloy substrates.

Design/methodology/approach
Anti-corrosion properties of a silane–zeolite composite coating, at various zeolite content, have been investigated on AZ31 magnesium substrates subjected to different surface pretreatment procedures before coating deposition. A short time etching by hydrofluoric acid (HF) and an anodic polarization in NaOH solution were used as surface pretreatments.

Findings
High hydrophobicity and good adhesion performances of coatings have been observed. Corrosion protection performance, during immersion in 3.5 per cent NaCl solution, was evaluated by means of electrochemical impedance spectroscopy tests. All coating formulations evidenced good barrier properties. Better durability properties have been shown by coating obtained on HF pretreated magnesium substrate and with a 60 per cent of zeolite content.

Originality/value
High electrochemical reactivity of magnesium alloys represents the mayor limit of its application in many different fields. In this concern, zeolite-based coatings are emerging as potentially effective environmentally friendly coating for metallic substrates. Despite aluminum and stainless steel substrates, in the literature, only expensive direct synthesis zeolite coating was investigated for its application on magnesium alloys protection. For this reason, this paper fulfills the need to assess the adhesion and anti-corrosion behavior of sol–gel silane–zeolite coating in magnesium alloy substrates.
Supply logistics integration in the Saudi food industry
Authors: Attia Ahmed 
Published: May 2018

PurposeThe purpose of this paper is to examine the effect of supply logistics integration (SLI) on inbound supply performance (ISP) and competitive performance (CP) in firms, in addition to examining the effect of ISP on CP.Design/methodology/approachTo demonstrate the effect of SLI on ISP and CP, different techniques such as factor analysis, correlation analysis, and structural equation modeling were used to verify the validity of the proposed conceptual model and to test the suggested hypotheses. This was accomplished by using data collected from 192 companies in the Saudi food industry (representing a response rate of 75.6 percent).FindingsAccording to the study’s findings, ISP is positively affected by SLI. Moreover, CP is directly affected by SLI and ISP.Research limitations/implicationsDue to the specific nature of the sample, the findings of the current research are applicable only to the food industry.Originality/valueThe current research introduced a conceptual model, which has been tested and verified in the Saudi food industry. The findings recommend that both SLI as well as ISP will contribute to improving the CP. In addition, SLI will improve the ISP.