bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phylogenetic framework of the legume genusAeschynomenefor comparative genetic analysis of the Nod-dependent and Nod-independent symbioses
Authors: Brottier Laurent , Chaintreuil Clémence , Simion Paul , Scornavacca Céline , Rivallan Ronan , Mournet Pierre , Moulin Lionel , Lewis Gwilym P. , Fardoux Joël , Brown Spencer C. , Gomez-Pacheco Mario , Bourges Mickaël , Hervouet Catherine , Gueye Mathieu , Duponnois Robin , Ramanankierana Heriniaina , Randriambanona Herizo , Vandrot Hervé , Zabaleta Maria , DasGupta Maitrayee , D’Hont Angélique , Giraud Eric , Arrighi Jean-François 
Published: September 2018

SUMMARYSomeAeschynomenelegume species have the property of being nodulated by photosyntheticBradyrhizobiumlacking thenodABCgenes. Knowledge of this unique Nod (factor)-independent symbiosis has been gained from the modelA. eveniabut our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod-dependent process.To fill this gap, this study significantly broadened previous taxon sampling, including in allied genera, to construct a comprehensive phylogeny. This backbone tree was matched with data on chromosome number, genome size, low-copy nuclear genes and strengthened by nodulation tests and a comparison of the diploid species.The phylogeny delineated five main lineages that all contained diploid species while polyploid groups were clustered in a polytomy and were found to originate from a single paleo-allopolyploid event. In addition, new nodulation behaviours were revealed and Nod-dependent diploid species were shown to be tractable.The extended knowledge of the genetics and biology of the different lineages in the legume genusAeschynomeneprovides a solid research framework. Notably, it enabled the identification ofA. americanaandA. patulaas the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.
One drug multiple targets: An approach to predict drug efficacies on bacterial strains differing in membrane composition
Authors: Majumder Ayan , Biswal Malay Ranjan , Prakash Meher K. 
Published: September 2018

AbstractRational design methodologies such as quantitative structure activity relationships (QSAR) have conventionally focused on screening through several drugs for their activity against a single target, either a bacterial protein or membrane. Recent concerns in drug design such as the development of drug resistance by membrane adaptation, or the undesirable damage to gut microbiota require a paradigm shift in activity prediction. A complementary approach capable of predicting the activity of a single drug against diverse targets, the diversity arising from bacterial adaptation or a heterogeneous composition with other helpful or harmful bacteria, is needed. As a first predictive step towards this goal, we develop a quantitative model for the activity of daptomycin onStreptococcus aureusstrains with different membrane compositions, mainly varying in lysylation. The results of the predictions are good, and within the limits of the scarcely available data, hint at an interaction of daptomycin with the inner membrane. The complementary approach may in principle be extended to estimate the activity against gut bacterial membranes, when systematic data can be curated for training the model.
System-wide identification and prioritization of enzyme substrates by thermal analysis (SIESTA)
Authors: Saei Amir Ata , Beusch Christian M. , Sabatier Pierre , Wells Juan Astorga , Chernobrovkin Alexey , Rodin Sergey , Näreoja Katja , Thorsell Ann-Gerd , Karlberg Tobias , Cheng Qing , Lundström Susanna L. , Gaetani Massimiliano , Végvári Ákos , Arnér Elias S.J. , Schüler Herwig , Zubarev Roman A. 
Published: September 2018

AbstractDespite the immense importance of enzyme-substrate reactions, there is a lack of generic and unbiased tools for identifying and prioritizing substrate proteins which are modulated in the structural and functional levels through modification. Here we describe a high-throughput unbiased proteomic method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that enzymatic post-translational modification of substrate proteins might change their thermal stability. SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems in up to a depth of 7179 proteins. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, open new opportunities in investigating the effect of PTMs on signal transduction, and facilitate drug discovery.
Bundle-specific fornix reconstruction for dual-tracer PET-tractometry
Authors: Rheault Francois , Roy Maggie , Cunnane Stephen , Descoteaux Maxime 
Published: September 2018

AbstractTractography is known to have problems reconstructing white matter bundles that are narrow, have high curvature, or go through partial volume voxels contaminated by CSF or gray matter. One such bundle is the fornix, the major output tract of the hippocampus, which is especially problematic with aging. Hippocampal atrophy and ventricular expansion make the fornix even harder (often impossible) to track with current state-of-the-art techniques. In this work, a bundle-specific tractography algorithm is proposed to fully reconstruct the fornix. By injecting shape, position, and orientation priors, fornix reconstruction is markedly is improved. We report an increase in spatial coverage and better reproducibility across test-retest. These improvements over classical tractography algorithms also enable tractometry of the fornix to be combined with dual-tracer positron emission tomography (PET) data in participants with mild cognitive impairment (MCI). MCI participants underwent a multi-modal brain imaging before and after a 6-month daily ketogenic supplement. We report, for the first time, significant diffusion measures and 18F-fluorodeoxyglucose (FDG) uptake differences in specific sub-sections of the fornix after the ketogenic supplement.
Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity
Authors: Chiang Austin W.T. , Li Shangzhong , Kellman Benjamin P. , Chattopadhyay Gouri , Zhang Yaqin , Kuo Chih-Chung , Gutierrez Jahir M. , Ghazi Faeazeh , Schmeisser Hana , Ménard Patrice , Bjørn Sara Petersen , Voldborg Bjørn G. , Rosenberg Amy S. , Puig Montserrat , Lewis Nathan E. 
Published: September 2018

AbstractViral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.
Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells
Authors: Delfarah Alireza , Parrish Sydney , Junge Jason A. , Yang Jesse , Seo Frances , Li Si , Mac John , Wang Pin , Fraser Scott E. , Graham Nicholas A. 
Published: September 2018

ABSTRACTCellular senescence is a mechanism by which cells permanently withdraw from the cell cycle in response to stresses including telomere shortening, DNA damage, or oncogenic signaling. Senescent cells contribute to both age-related degeneration and hyperplastic pathologies, including cancer. In culture, normal human epithelial cells enter senescence after a limited number of cell divisions, known as replicative senescence. Here, to investigate how metabolic pathways regulate replicative senescence, we used LC-MS–based metabolomics to analyze senescent primary human mammary epithelial cells (HMECs). We did not observe significant changes in glucose uptake or lactate secretion in senescent HMECs. However, analysis of intracellular metabolite pool sizes indicated that senescent cells exhibit depletion of metabolites from nucleotide synthesis pathways. Furthermore, stable isotope tracing with13C-labeled glucose or glutamine revealed a dramatic blockage of flux of these two metabolites into nucleotide synthesis pathways in senescent HMECs. To test whether cellular immortalization would reverse these observations, we expressed telomerase in HMECs. In addition to preventing senescence, telomerase expression maintained metabolic flux from glucose into nucleotide synthesis pathways. Finally, we investigated whether inhibition of nucleotide synthesis in proliferating HMECs is sufficient to induce senescence. In proliferating HMECs, both pharmacological and genetic inhibition of ribonucleotide reductase regulatory subunit M2 (RRM2), a rate-limiting enzyme in dNTP synthesis, induced premature senescence with concomitantly decreased metabolic flux from glucose into nucleotide synthesis. Taken together, our results suggest that nucleotide synthesis inhibition plays a causative role in the establishment of replicative senescence in HMECs.
Characterizing changes in glucocorticoid receptor internalization in the fear circuit in an animal model of post traumatic stress disorder
Authors: Moulton Emly , Chamness Marisa , Knox Dayan 
Published: September 2018

AbstractGlucocorticoid receptors (GRs) shuttle from the cytoplasm (cy) to the nucleus (nu) when bound with glucocorticoids (i.e. GR internalization) and alter transcriptional activity. GR activation within the fear circuit has been implicated in fear memory and post traumatic stress disorder (PTSD). However, no study to date has characterized GR internalization within the fear circuit during fear memory formation or examined how traumatic stress impacts this process. To address this, we assayed cy and nu GR levels at baseline and after auditory fear conditioning (FC) in the single prolonged stress (SPS) model of PTSD. Cy and nu GRs within the medial prefrontal cortex (mPFC), dorsal hippocampus (dHipp), ventral hippocampus (vHipp), and amygdala (AMY) were assayed using western blot. The distribution of GR in the cy and nu (at baseline and after FC) was varied across individual nodes of the fear circuit. At baseline, SPS enhanced cyGRs in the dHipp, but decreased cyGRs in the AMY. FC only enhanced GR internalization in the AMY and this effect was attenuated by SPS exposure. SPS also decreased cyGRs in the dHipp after FC. The results of this study suggests that GR internalization is varied across the fear circuit, which in turn suggests GR activation is selectively regulated within individual nodes of the fear circuit. The findings also suggest that changes in GR dynamics in the dHipp and AMY modulate the enhancing effect SPS has on fear memory persistence.
Microstimulation in a spiking neural network model of the midbrain superior colliculus
Authors: Kasap Bahadir , van Opstal A. John 
Published: September 2018

AbstractThe midbrain superior colliculus (SC) generates a rapid saccadic eye movement to a sensory stimulus by recruiting a population of cells in its topographically organized motor map. Supra-threshold electrical microstimulation in the SC reveals that the site of stimulation produces a normometric saccade vector with little effect of the stimulation parameters. Moreover, electrically evoked saccades (E-saccades) have kinematic properties that strongly resemble natural, visual-evoked saccades (V-saccades). These findings support models in which the saccade vector is determined by a center-of-gravity computation of activated neurons, while its trajectory and kinematics arise from downstream feedback circuits in the brainstem. Recent single-unit recordings, however, have indicated that the SC population also specifies instantaneous kinematics. These results support an alternative model, in which the desired saccade trajectory, including its kinematics, follows from instantaneous summation of movement effects of all SC spike trains. But how to reconcile this model with microstimulation results? Although it is thought that microstimulation activates a large population of SC neurons, the mechanism through which it arises is unknown. We developed a spiking neural network model of the SC, in which microstimulation directly activates a relatively small set of neurons around the electrode tip, which subsequently sets up a large population response through lateral synaptic interactions. We show that through this mechanism the population drives an E-saccade with near-normal kinematics that are largely independent of the stimulation parameters. Only at very low stimulus intensities the network recruits a population with low firing rates, resulting in abnormally slow saccades.Author SummaryThe midbrain Superior Colliculus (SC) contains a topographically organized map for rapid goal-directed gaze shifts, in which the location of the active population determines size and direction of the eye-movement vector, and the neural firing rates specify the eye-movement kinematics. Electrical microstimulation in this map produces eye movements that correspond to the site of stimulation with normal kinematics. We here explain how intrinsic lateral interactions within the SC network of spiking neurons sets up the population activity profile in response to local microstimulation to explain these results.
A collective modulatory basis for multisensory integration in C. elegans
Authors: Harris Gareth , Wu Taihong , Linfield Gaia , Choi Myung-Kyu , Liu He , Zhang Yun 
Published: September 2018

AbstractIn the natural environment, animals often encounter multiple sensory cues that are simultaneously present. The nervous system integrates the relevant sensory information to generate behavioral responses that have adaptive values. However, the signal transduction pathways and the molecules that regulate integrated behavioral response to multiple sensory cues are not well defined. Here, we characterize a collective modulatory basis for a behavioral decision in C. elegans when the animal is presented with an attractive food source together with a repulsive odorant. We show that distributed neuronal components in the worm nervous system and several neuromodulators orchestrate the decision-making process, suggesting that various states and contexts may modulate the multisensory integration. Among these modulators, we identify a new function of a conserved TGF-β pathway that regulates the integrated decision by inhibiting the signaling from a set of central neurons. Interestingly, we find that a common set of modulators, including the TGF-β pathway, regulate the integrated response to the pairing of different foods and repellents. Together, our results provide insights into the modulatory signals regulating multisensory integration and reveal potential mechanistic basis for the complex pathology underlying defects in multisensory processing shared by common neurological diseases.Author SummaryThe present study characterizes the modulation of a behavioral decision in C. elegans when the worm is presented with a food lawn that is paired with a repulsive smell. We show that multiple sensory neurons and interneurons play roles in making the decision. We also identify several modulatory molecules that are essential for the integrated decision when the animal faces a choice between the cues of opposing valence. We further show that many of these factors, which often represent different states and contexts, are common for behavioral decisions that integrate sensory information from different types of foods and repellents. Overall, our results reveal a collective molecular and cellular basis for integration of simultaneously present attractive and repulsive cues to fine-tune decision-making.
Peer networks in the school-to-work transition
Authors: Ruschoff Britta , Salmela-Aro Katariina , Kowalewski Thomas , Dijkstra Jan Kornelis , Veenstra René 
Published: September 2018

Purpose
The purpose of this paper is to investigate whether young people’s peer networks can be an asset in finding employment during the transition from school to work. It examines whether peer networks size and peers’ self-efficacy regarding their own job search are associated with job seekers’ career-relevant behaviors and outcomes, i.e., the number of applications completed and the number of job offers received.

Design/methodology/approach
Associations between job seekers’ peer networks and their job search behaviors and outcomes were investigated during their final year of vocational training. Sociometric measures were used to assess young people’s peer network size. Sociometric and self-report measures were used to establish the characteristics of the peers that comprise each job seekers’ network, resulting in the overall self-efficacy across each job seekers’ network.

Findings
The results show that peers’ efficacy beliefs are positively associated with young people’s engagement in job search activities (i.e. a greater number of applications completed) and indirectly associated with their job search outcomes (i.e. a greater number of job offers, which are mediated by the number of applications) that are independent of the peer network size.

Originality/value
The results underline that although peers might not provide instrumental support, encouraging interactions with (efficacious) peers may nonetheless be beneficial to young job seekers. Methodologically, the results demonstrate that the operationalization of self-efficacy as a network characteristic might provide us with valuable insights into the characteristics that turn social networks into beneficial social resources.
How psychologically entitled shoppers respond to service recovery apologies
Authors: Martin Brett , Strong Carolyn , O’Connor Peter 
Published: September 2018

Purpose
This paper aims to examine how a shopper’s level of psychological entitlement influences how consumers respond to different types of apology by a service provider.

Design/methodology/approach
Two experiments were performed. Study 1 tests the hypotheses that entitled shoppers prefer empathy apologies to norm violation apologies and that this effect is mediated by disgust and anger. Study 2 tests whether relative superiority apologies are more effective.

Findings
Study 1 shows that entitled shoppers prefer empathy apologies. Mediation analysis shows that entitled people feel disgust for norm violation apologies. Study 2 shows that entitled shoppers prefer relative superiority apologies. A standard apology results in negative perceptions of interactional justice, disgust and negative employee evaluations.

Research limitations/implications
Limitations include the scenario method. Implications include entitlement as a moderator of service recovery effectiveness, examining different types of apology and mediators which contribute to the marketing and entitlement literature.

Practical implications
The findings have implications for training employees in service recovery. Employees should not use a standard apology or an apology that treats entitled consumers as similar to other shoppers. Employees should express empathy or make them feel that they are a more valued customer than other store customers.

Originality/value
This research shows how entitlement moderates consumer responses to service recovery. The research answers calls to study different types of apology rather than studying a standard apology (vs no apology). The research is the first to relate entitlement to apologies and to show how disgust and justice perceptions underlie an entitled person’s judgments in service recovery.
The influence of acceptance and adoption drivers on smart home usage
Authors: Hubert Marco , Blut Markus , Brock Christian , Zhang Ruby Wenjiao , Koch Vincent , Riedl René 
Published: September 2018

PurposeThis study aims to develop a comprehensive adoption model that combines constructs from various theories and tests these theories against each other. The study combines a technology acceptance model, innovation diffusion theory and risk theory. It develops this model in a smart home applications context.Design/methodology/approachThe study is based on an online survey consisting of 409 participants, and the data are analyzed using structural equation modeling.FindingsEach theory provides unique insights into technology acceptance and numerous constructs are interrelated. Predictors from innovation diffusion and risk theory often display indirect effects through technology acceptance variables. The study identifies risk perception as a major inhibitor of use intention, mediated through perceived usefulness. Results reveal that the most important determinants of use intention are compatibility and usefulness of the application.Research limitations/implicationsStudies which do not examine different theories together may not be able to detect the indirect effects of some predictors and could falsely conclude that these predictors do no matter. The findings emphasize the crucial role of compatibility, perceived usefulness and various risk facets associated with smart homes.Originality/valueThis study broadens the understanding about the necessity of combining acceptance and adoption drivers from several theories to better understand the usage of complex technological systems such as smart home applications.
Career equality
Authors: Traavik Laura E.M. 
Published: September 2018

PurposeThe purpose of this study is to investigate inclusion, perceived opportunities and discrimination between men and women, across career levels, in a professional service firm in Norway.Design/methodology/approachA cross-sectional design with a survey was used. Employees across six different career levels in a large Norwegian professional service firm responded, resulting in a sample size of 912.FindingsMen report higher levels of inclusion and more opportunities and less discrimination in the work place than women do. Patterns of differences between men and women vary across career levels. At early mid-career, men and women have the largest differences in opportunities and inclusion experiences.Research limitations/implicationsA limitation with this study is the cross-sectional design and data collected from one company. This could limit the generalizability of the findings. Future research should include longitudinal designs. The empirical data demonstrate that men and women continue to have dissimilar experiences in the professional services, with women facing more career obstacles than men.Practical implicationsOrganizations can implement policies that foster inclusive environments and ensure career equality by providing development opportunities for both men and women. It is important that professional service firms recognize that at different career levels, perceptions of inclusiveness can vary.Originality/valueThis study provides empirical evidence that women continue to face different types of treatment in professional service firms, and offers suggestions for addressing these inequalities by introducing the concept of inclusiveness.