bluuebunny/crossref_metadata_2025_split huggingface dataset:
Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols
Authors: Gürsoy Gamze , Emani Prashant , Brannon Charlotte M. , Jolanki Otto A. , Harmanci Arif , Strattan J. Seth , Miranker Andrew D. , Gerstein Mark 
Published: June 2018

AbstractThe generation of functional genomics datasets is surging, as they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). The intention of functional genomics experiments is not necessarily to study genetic variants, yet they pose privacy concerns due to their use of next-generation sequencing. Moreover, there is a great incentive to share raw reads for better analyses and general research reproducibility. Thus, we need new modes of sharing beyond traditional controlled-access models. Here, we develop a data-sanitization procedure allowing raw functional genomics reads to be shared while minimizing privacy leakage, thus enabling principled privacy-utility trade-offs. It works with traditional Illumina-based assays and newer technologies such as 10x single-cell RNA-sequencing. The procedure depends on quantifying the privacy leakage in reads by statistically linking study participants to known individuals. We carried out these linkages using data from highly accurate reference genomes and more realistic environmental samples.
Model-based assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-cell Immune Responses
Authors: Girel Simon , Arpin Christophe , Marvel Jacqueline , Gandrillon Olivier , Crauste Fabien 
Published: June 2018

AbstractActivation of naive CD8 T-cells can lead to the generation of multiple effector and memory subsets. Multiple parameters associated with activation conditions are involved in generating this diversity that is associated with heterogeneous molecular contents of activated cells. Naive cell polarisation upon antigenic stimulation and the asymmetric division that results are known to be a major source of heterogeneity and cell fate regulation. The consequences of stochastic uneven partitioning of molecular content upon subsequent divisions remain unclear. Here we aim at studying the impact of uneven partitioning on molecular-content heterogeneity and then on the immune response dynamics at the cellular level. To do so, we introduce a multiscale mathematical model of the CD8 T-cell immune response in the lymph node. In the model, cells are described as agents evolving and interacting in a 2D environment while a set of differential equations, embedded in each cell, models the regulation of intra and extracellular proteins involved in cell differentiation. Based on the analysis of in silico data at the single cell level, we show that immune response dynamics can be explained by the molecular-content heterogeneity generated by uneven partitioning at cell division. In particular, uneven partitioning acts as a regulator of cell differentiation and induces the emergence of two coexisting subpopulations of cells exhibiting antagonistic fates. We show that the degree of unevenness of molecular partitioning, along all cell divisions, affects the outcome of the immune response and can promote the generation of memory cells.
Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories
Authors: Bottaro Sandro , Bussi Giovanni , Pinamonti Giovanni , Reißer Sabine , Boomsma Wouter , Lindorff-Larsen Kresten 
Published: June 2018

AbstractRNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be non-trivial because it requires processing very high-dimensional data that are not easy to visualize and interpret.Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acids structures and molecular simulations. The software consists of a variety of analysis tools that allow the user to i) calculate distances between three-dimensional structures using different metrics, ii) back-calculate experimental data from three-dimensional structures, iii) perform cluster analysis and dimensionality reductions, iv) search three-dimensional motifs in PDB structures and trajectories and v) construct elastic network models (ENM) for nucleic acids and nucleic acids-protein complexes.In addition, Barnaba makes it possible to calculate torsion angles, pucker conformations and to detect base-pairing/base-stacking interactions. Barnaba produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations. The software is available as a command-line tool as well as a library, and supports a variety of 1le formats such as PDB, dcd and xtc 1les. Source code, documentation and examples are freely available athttps://github.com/srnas/barnabaunder GNU GPLv3 license.
Direct evidence for prediction signals in frontal cortex independent of prediction error
Authors: Dürschmid Stefan , Reichert Christoph , Hinrichs Hermann , Heinze Hans-Jochen , Kirsch Heidi E. , Knight Robert T. , Deouell Leon Y. 
Published: June 2018

AbstractPredictive coding (PC) has been suggested as one of the main mechanisms used by brains to interact with complex environments. PC theories posit top-down prediction signals, which are compared with actual outcomes, yielding in turn prediction-error signals, which are used, bottom-up, to modify the ensuing predictions. However, disentangling prediction from prediction-error signals has been challenging. Critically, while many studies found indirect evidence for predictive coding in the form of prediction-error signals, direct evidence for the prediction signal is mostly lacking. Here we provide clear evidence, obtained from intracranial cortical recordings in human surgical patients, that the human lateral prefrontal cortex generates prediction signals while anticipating an event. Patients listened to task-irrelevant sequences of repetitive tones including infrequent predictable or unpredictable pitch deviants. The amplitude of high frequency broadband (HFB) neural activity was decreased prior to the onset of expected relative to unexpected deviants in the frontal cortex only, and its amplitude was sensitive to the increasing likelihood of deviants following longer trains of standards in the unpredictable condition. Single trial HFB amplitudes predicted deviations and correlated with post-stimulus response to deviations. These results provide direct evidence for frontal cortex prediction signals independent of prediction-error signals.
Anti-α4β7 therapy targets lymphoid aggregates in the gastrointestinal tract of HIV-1 infected individuals
Authors: Uzzan Mathieu , Tokuyama Minami , Rosenstein Adam K. , Tomescu Costin , SahBandar Ivo N. , Ko Huaibin M. , Leyre Louise , Chokola Anupa , Kaplan-Lewis Emma , Rodriguez Gabriela , Seki Akihiro , Corley Michael J. , Aberg Judith , La Porte Annalena , Park Eun-young , Ueno Hideki , Oikonomou Ioannis , Doron Itai , Iliev Iliyan D. , Chen Benjamin K. , Lui Jennifer , Schacker Timothy W. , Furtado Glaucia C. , Lira Sergio A. , Colombel Jean-Frederic , Horowitz Amir , Lim Jean K. , Chomont Nicolas , Montaner Luis J. , Ndhlovu Lishomwa C. , Mehandru Saurabh 
Published: June 2018

ABSTRACTHerein, we present the first human study of anti-α4β7 therapy in a cohort of HIV-1 infected subjects with mild inflammatory bowel disease. α4β7+gut homing CD4+T cells are early viral targets and contribute to HIV-1 pathogenesis, likely by seeding the gastrointestinal (GI) tract with HIV. Although, simianized anti-α4β7 monoclonal antibodies (Mab) have shown promise in preventing or attenuating the disease course of SIV in Non-Human Primate studies, the mechanisms of drug action remain elusive and the impact on HIV-1 persistence remains unanswered. By sampling the immune inductive and effector sites of the GI tract, we have discovered that anti-α4β7 therapy led to a significant and unexpected attenuation of lymphoid aggregates, most notably in the terminal ileum. Given that lymphoid aggregates serve as important sanctuary sites for establishing and maintaining viral reservoirs, their attrition by anti-α4β7 therapy has important implications for HIV-1 therapeutics and eradication efforts, and defines a rational basis for the continued evaluation of anti-α4β7 therapy in HIV-1 infection.One Sentence SummaryAnti-α4β7 integrin therapy results in attrition of lymphoid aggregates within the gastrointestinal tract of HIV-1 infected individuals
Myosin driven Actin Filament Sliding is Responsible for Endoplasmic Reticulum and Golgi Movement
Authors: McKenna Joseph F , Webb Stephen E D , Kriechbaumer Verena , Hawes Chris 
Published: June 2018

AbstractThe plant secretory pathway is responsible for the production of the majority of proteins and carbohydrates consumed on the planet. The early secretory pathway is composed of Golgi bodies and the endoplasmic reticulum (ER) and is highly mobile in plants with rapid remodelling of the ER network. The dynamics of the ER and Golgi bodies is driven by the actin cytoskeleton and myosin motor proteins play a key role in this. However, exactly how myosin motor proteins drive remodelling in plants is currently a contentious issue. Here, using a combination of live cell microscopy and over-expression of non-functional myosins we demonstrate that myosin motor proteins drive actin filament sliding and subsequently the dynamics of the secretory pathway.SummaryIn plants, the actin cytoskeleton and myosins are fundamental for normal dynamics of the endomembrane system and cytoplasmic streaming. We demonstrate that this is in part due to myosin driven sliding of actin filaments within a bundle. This generates, at least in part, the motive force required for cell dynamicsin planta.
Neuronal Cells Confinement by Micropatterned Cluster-Assembled Dots with Mechanotransductive Nanotopography
Authors: Schulte Carsten , Lamanna Jacopo , Moro Andrea Stefano , Piazzoni Claudio , Borghi Francesca , Chighizola Matteo , Ortoleva Serena , Racchetti Gabriella , Lenardi Cristina , Podestà Alessandro , Malgaroli Antonio , Milani Paolo 
Published: June 2018

ABSTRACTThe in vitro fabrication of neural networks able to simulate brain circuits and to maintain their native connectivity is of strategic importance to gain a deep understanding of neural circuit physiology and brain natural computational algorithm(s). This would also enable a wide-range of applications including the development of efficient brain-on-chip devices or brain-computer interfaces. Chemical and mechanotransductive cues cooperate to promote proper development and functioning of neural networks. Since the 80’s, controlled growth of mammalian neuronal cells on micrometric patterned chemical cues with the development of synaptic connections and electrical activity has been reported, however the role of mechanotransductive signaling on the growth/organization of neural networks has not been investigated so far. Here we report the fabrication and characterization of patterned substrates for neuronal culture with a controlled structure both at the nano- and microscale suitable for the selective adhesion of neuronal cells. Nanostructured micrometric dots were patterned on passivated cell-repellent glass substrates by supersonic cluster beam deposition of zirconia nanoparticles through stencil masks. Cluster-assembled nanostructured zirconia surfaces are characterized by nanotopographical features that can direct the maturation of neural networks by mechanotransductive signaling. Our approach produces a controlled microscale pattern of adhesive areas with predetermined nanoscale morphology. We have validated these micropatterned substrates using a neuronal cell line (PC12 cells) and cultured hippocampal neurons. While cells have been uniformly plated on the substrates, they adhered only on the nanostructured zirconia regions, remaining effectively confined inside the nanostructured dots on which they were found to grow, move and differentiate.
Active fluctuations modulate gene expression in mouse oocytes
Authors: Almonacid Maria , El-Hayek Stephany , Othmani Alice , Queguiner Isabelle , Coulpier Fanny , Lemoine Sophie , Bastianelli Leila , Klein Christophe , Piolot Tristan , Mailly Philippe , Voituriez Raphaël , Genovesio Auguste , Verlhac Marie-Hélène 
Published: June 2018

AbstractIn mammals, the nucleus is central in oocytes, not defining the future embryo axis. Nucleus centring depends on an F-actin mediated pressure gradient. InFmn2−/−oocytes, lacking the F-actin nucleator Formin 2, the nucleus is off-centre and can be centred by re-expressing Formin 2. Here, we addressed the biological significance of nucleus positioning in mammalian oocytes. Using a dedicated computational 3D imaging approach, we observed nuclear architecture alterations in mouseFmn2−/−oocytes. RNA sequencing of control versusFmn2−/−oocytes detected 2285 mis-regulated genes. Rescue experiments showed that the process of nuclear positioning impacts nuclear architecture and gene expression. Using signal processing methods coupled to biophysical modelling allowing the extraction ofin vivomechanical properties of the nuclear envelope, we showed that F-actin-mediated activity promotes nuclear envelope shape fluctuations and chromatin motion. We thus propose a mechano-transduction model whereby nucleus positioning via microfilaments modulates oocyte transcriptome, essential for further embryo development.
Obesity and overweight issues could undermine Malaysia’s competitiveness
Authors: Hassan Hasliza , Sade Abu Bakar , Rahman Muhammad Sabbir 
Published: June 2018

PurposeThe Malaysian lifestyle has been undergoing changes over time. With better socio-economic conditions, Malaysians tend to consume more food today than they did previously. Excessive intakes of high calorie foods combined with little daily physical activity have led to increased numbers of overweight and obese people in the population. The purpose of this paper is to compare the incidence of overweight and obesity in the population in Malaysia with other Southeast Asian countries.Design/methodology/approachData for this research were based on secondary data of average weight, overweight and obese people for populations in the Southeast Asian countries. The analysis for this research focused on the population in Malaysia and compared it with populations from neighboring countries.FindingsThe population in Malaysia was ranked the second highest in the number of overweight and obese people in the Southeast Asian region. In addition, the rate of increase overweight and obese people in the population of Malaysia was found to be the highest in the region. Since the percentage of overweight and obese people had increased consistently from 2010 to 2014, there was a high possibility that the momentum would continue into the following few years.Originality/valueBeing overweight and obese was not desirable by the majority of people as it could lead to various health diseases and psychological problems. Unfortunately, the percentage of overweight and obese people in Malaysia seems to be increasing. Improved socio-economic conditions have increased the amount of food normally consumed by people. Although many people were found to be aware of the negative impact of being overweight and obese, the majority of them did not seem to take the initiative to reduce their body weight. This research is expected to create awareness of the alarming rate of increase in the number of overweight and obese people in Malaysia in order to encourage a healthier lifestyle.
Emotions and satisfaction at the hospital
Authors: Pinna Mariella , Del Chiappa Giacomo , Atzeni Marcello 
Published: June 2018

PurposeThis study aims to compare public and private hospitals based on both cognitive and affective components of patients’ satisfaction.Design/methodology/approachA survey of 770 Italian patients from public and private hospitals was conducted. Then, hierarchical and non-hierarchical cluster analyses and a series of chi-squared tests were run with the aim of segmenting patients’ emotional response.FindingsRespondents show different levels of satisfaction and a different emotional status based on the private or public nature of the service provider. The cluster analysis helped to identify two segments. Specifically, the cluster with the highest positive emotions is reported to have a higher level of satisfaction and a higher intention to return; this evidence is much stronger when a private service provider rather than a public one is considered. A series of chi-squared tests reveal that no significant differences exist among clusters based on socio-demographic characteristics.Research limitations/implicationsThis study uses a convenience sample and is highly context specific, and thus the authors are unable to make generalizations.Practical implicationsHospital managers should develop a customer-oriented approach, for example, by paying greater attention to patients’ emotions and experience, via conducting systematic surveys on patients’ emotions and improving the servicescape.Originality/valueThe main contribution of this study resides in simultaneously considering the role of cognitive and affective components on patients’ satisfaction and behavioural intention, and segmenting patients based on their emotional responses. Moreover, only few studies provide a comparison of public and private hospitals in Italy.
The good coach: implementation and sustainment factors that affect coaching as evidence-based intervention fidelity support
Authors: Gunderson Lara M. , Willging Cathleen E. , Trott Jaramillo Elise M. , Green Amy E. , Fettes Danielle L. , Hecht Debra B. , Aarons Gregory A. 
Published: June 2018

Purpose
Evidence-based interventions (EBIs) for human services unfold within complicated social and organizational circumstances and are influenced by the attitudes and behaviors of diverse stakeholders situated within these environments. Coaching is commonly regarded as an effective strategy to support service providers in delivering EBIs and attaining high levels of fidelity over time. The purpose of this paper is to address a lacuna in research examining the factors influencing coaching, an important EBI support component.

Design/methodology/approach
The authors use the Exploration, Preparation, Implementation, and Sustainment framework to consider inner- and outer-context factors that affect coaching over time. This case study of coaching draws from a larger qualitative data set from three iterative investigations of implementation and sustainment of a home visitation program, SafeCare®. SafeCare is an EBI designed to reduce child neglect.

Findings
The authors elaborate on six major categories of findings derived from an iterative data coding and analysis process: perceptions of “good” and “bad” coaches by system sustainment status; coach as peer; in-house coaching capacity; intervention developer requirements vs other outer-context needs; outer-context support; and inner-context support.

Practical implications
Coaching is considered a key component for effective implementation of EBIs in public-sector systems, yet is under-studied. Understanding inner- and outer-context factors illuminates the ways they affect the capacity of coaches to support service delivery.

Originality/value
This paper demonstrates that coaching can accomplish more than provision of EBI fidelity support. Stakeholders characterized coaches as operating as boundary spanners who link inner and outer contexts to enable EBI implementation and sustainment.
Effect of multilevel trust on effort-in-use and service co-design behaviour
Authors: Luk Sherriff T.K. , Liu Ben S.C. , Li Esther L.Y. 
Published: June 2018

Purpose
This paper aims to draw on the trust-commitment theory and the framework of service-dominant marketing logic to investigate the potential effect of trust at both brand and service personnel level on consumers’ value co-creation behaviour.

Design/methodology/approach
The study adopts a consumer perspective to investigate and interpret consumers’ value co-creation behaviour. The measurement scales were developed based on literature review and findings from focus group study. Survey interviews were undertaken in the USA and Hong Kong so as to test the potential moderator effect of country.

Findings
Effort-in-use and service co-design behaviour are two aspects of value cocreation behaviour. The findings provide theoretical expansion of the theory on value cocreation in two ways and suggest to discriminate the effect of consumer trust on and role in value cocreation behaviour at brand and service employee levels. Besides, the relationships among “trust in employee”, “trust in brand”, effort in use behaviour, service co-design behaviour, and customers’ perceived value actually could be moderated by country factor.

Research limitations/implications
The study only focuses on the behavioural dimension of value cocreation behaviour but provides a number of suggestions on how to expand the domain of the measurement scale for value co-creation behaviour, cultural influences and customer perceived value and identifies several potential moderators such as reputation of the service brand and type of service for future research.

Practical implications
The findings provide important insights to service marketers on how to adopt appropriate service strategy, service operation, marketing communications and service training to facilitate consumers’ value co-creation behaviour.

Originality/value
The present study represents the first attempt to investigate the potential impact of consumer trust at different levels on customers’ value cocreation behaviour. It explains the connections between trust as an antecedent to value cocreation under different country contexts, thereby adding new knowledge in both domains.