bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential brain mechanisms of selection and maintenance of information during working memory
Authors: Quentin Romain , King Jean-Rémi , Sallard Etienne , Fishman Nathan , Thompson Ryan , Buch Ethan , Cohen Leonardo G 
Published: March 2018

AbstractWorking memory is our ability to select and temporarily hold information as needed for complex cognitive operations. The temporal dynamics of sustained and transient neural activity supporting the selection and holding of memory content is not known. To address this problem, we recorded magnetoencephalography (MEG) in healthy participants performing a retro-cue working memory task in which the selection rule and the memory content varied independently. Multivariate decoding and source analyses showed that selecting the memory content relies on prefrontal and parieto-occipital persistent oscillatory neural activity. By contrast, the memory content was reactivated in a distributed occipito-temporal posterior network, preceding the working memory decision and in a different format that during the visual encoding. These results identify a neural signature of content selection and characterize differentiated spatiotemporal constraints for subprocesses of working memory.
Emergence of carbapenem, beta-lactamase inhibitor and cefoxitin resistant lineages from a background of ESBL-producingKlebsiella pneumoniaeandK. quasipneumoniaehighlights different evolutionary mechanisms
Authors: Heinz Eva , Ejaz Hasan , Scott Josefin Bartholdson , Wang Nancy , Guanjaran Shruti , Pickard Derek , Wilksch Jonathan , Cao Hanwei , ul-Haq Ikram , Dougan Gordon , Strugnell Richard A 
Published: March 2018

AbstractKlebsiella pneumoniaeis recognised as a major threat to public health, with increasing emergence of multidrug-resistant lineages including strains resistant to all available antibiotics. We present an in-depth analysis of 178 extended-spectrum beta-lactamase (ESBL)-producingKlebsiellastrains, with a high background diversity and two dominant lineages, as well as several equally resistant lineages with less prevalence. Neither the overall resistance profile nor the virulence factors explain the prevalence of some lineages; we observe several putative hypervirulence factors across the population, including a reduced virulence plasmid, but this does not correlate with expansion of one or few highly virulent and resistant lineages. Phenotypic analysis of the profiles of resistance traits shows that the vast majority of the phenotypic resistance profiles can be explained by detailed genetic analyses. The main discrepancies are observed for beta-lactams combined with beta-lactamase inhibitors, where most, but not all, resistant strains carry a carbapenemase orampC. Complete genomes for six selected strains, including three of the 21 carbapenem-resistant ones, are reported, which give detailed insights into the early evolution of thebla-NDM-1enzyme, a carbapenemase that was first reported in 2009 and is now globally distributed. Whole-genome based high-resolution analyses of the dominant lineages suggests a very dynamic picture of gene transfer and selection, with phenotypic changes due to plasmid acquisition and chromosomal changes, and emphasize the need to monitor the bacteria at high resolution to understand the rise of high-risk clones, which cannot be explained by obvious differences in resistance profiles or virulence factors.ImportanceCarbapenem-resistant and extended-spectrum beta-lactamase (ESBL) carryingEnterobacteriaceaewere recently highlighted as critical priority fo the development of new treatments by the WHO.Klebsiella pneumoniaeis a member of theEnterobacteriaceaeand has seen a dramatic rise in clinical relevance due to its uncanny ability to accumulate multidrug-resistance plasmids. We present a detailed analysis of a set of ESBL-resistantK. pneumoniaeclinical isolates, and our high-resolution whole-genome sequence analyses highlight that acquisition of drug resistances is not a one-way street inK. pneumoniae, but a highly dynamic process of gain and loss, and that the most successful lineages in the clinic are not necessarily the most resistant or most virulent ones. Analysis of the virulence potential also shows that these strains harbour some, but not all, hallmarks of hypervirulent strains, emphasizing that it is not a clear distinction between hypervirulent and other strains, but equally in flux.
Acute alcohol administration dampens threat-related activation in the central extended amygdala
Authors: Hur Juyoen , Kaplan Claire M. , Smith Jason F. , Bradford Daniel E. , Fox Andrew S. , Curtin John J. , Shackman Alexander J. 
Published: March 2018

ABSTRACTAlcohol abuse is common, imposes a staggering burden on public health, and is challenging to treat, underscoring the need to develop a deeper understanding of the underlying neurobiology. When administered acutely, ethyl alcohol reduces threat reactivity in humans and other animals, and there is growing evidence that threat-dampening and related negative reinforcement mechanisms support the etiology and recurrence of alcohol and other kinds of substance misuse. Converging lines of evidence motivate the hypothesis that these effects are mediated by the central extended amygdala (EAc)—including the central nucleus of the amygdala (Ce) and bed nucleus of the stria terminalis (BST)—but the relevance of this circuitry to acute alcohol effects in humans remains poorly understood. Using a single-blind, randomized-groups design, multiband imaging data were acquired from 49 social drinkers while they performed an fMRI-optimized emotional-faces/places paradigm after consuming alcohol or placebo. Relative to placebo, alcohol significantly dampened reactivity to threat-related emotional faces in the BST. To rigorously assess potential regional differences in activation, data were extracted from anatomically defined Ce and BST regions-of-interest. Analyses revealed a similar pattern of dampening across the two regions. In short, alcohol acutely dampens reactivity to threat-related faces in humans and it does so similarly across the two major divisions of the EAc. These observations provide a framework for understanding the translational relevance of addiction models derived from work in rodents, inform on-going debates about the functional organization of the EAc, and set the stage for bi-directional translational models aimed at developing improved treatment strategies for alcohol abuse and other addictions.
Clonal analysis reveals gradual recruitment of lateral root founder cells and a link between root initiation and cambium formation inArabidopsis thaliana
Authors: Dubrovsky Joseph G. 
Published: March 2018

AbstractThe pericycle gives rise to lateral roots (LRs) and lateral meristems (LMs; cambium and phellogen), however, a thorough clonal analysis of pericycle cell lineage has not been investigated. This study fills in this gap and addresses pericycle impact in LR and LM development.Heath-shock inducibleDS1transposition in35S-DS1-H2B:YFP; HS-Acseedlings results in production of YFP-labelled cell clones. These clones in pericycle cell derivatives were identified with a confocal microscopy and subjected to 3D reconstructions and analysis.Participation of pericycle founder cells (FC) in LR formation is more variable than previously considered. LR initiation was found most commonly involved the specification of just one FC in the longitudinal and one or two cells in transverse direction. After LR initiation, FCs continue to be recruited in both directions from pre-existing cells. Anticlinal divisions in the pericycle resulting in LMs start already in the young differentiation zone where only the protoxylem is differentiated.The clonal analysis demonstrated that pericycle cell activity related to LR formation is not separated in time and space from that related to LM formation and that LR FC recruitment is a gradual process. The analysis demonstrated that immediate pericycle progeny lack self-renewal capacity.
Adipose fin development and its relation to the evolutionary origins of median fins
Authors: Stewart Thomas A. , Ho Robert K. , Hale Melina E. 
Published: March 2018

AbstractThe dorsal, anal and caudal fins of vertebrates are proposed to have originated by the partitioning and transformation of the continuous median fin fold that is plesiomorphic to chordates. Evaluating this hypothesis has been challenging, because it is unclear how the median fin fold relates to the adult median fins of vertebrates. To understand how new median fins originate, here we study the development and diversity of adipose fins. Phylogenetic mapping shows that in all lineages except Characoidei (Characiformes) adipose fins develop from a domain of the larval median fin fold. To inform how the larva’s median fin fold contributes to the adipose fin, we studyCorydoras aeneus(Siluriformes). As the fin fold reduces around the prospective site of the adipose fin, a fin spine develops in the fold, growing both proximally and distally, and sensory innervation, which appears to originate from the recurrent ramus of the facial nerve and from dorsal rami of the spinal cord, develops in the adipose fin membrane. Collectively, these data show how a plesiomorphic median fin fold can serve as scaffolding for the evolution and development of novel, individuated median fins, consistent with the median fin fold hypothesis.
Protocadherin-mediated cell repulsion controls the central topography and efferent projections of the abducens nucleus
Authors: Asakawa Kazuhide , Kawakami Koichi 
Published: March 2018

SummaryCranial motor nuclei in the brainstem innervate diverse types of head and neck muscles. Failure in establishing these neuromuscular connections causes congenital cranial dysinnervation disorders (CCDDs) characterized by abnormal craniofacial movements. However, mechanisms that link cranial motor nuclei to target muscles are poorly understood at the molecular level. Here, we report that protocadherin-mediated repulsion mediates neuromuscular connection in the ocular motor system in zebrafish. We identify pools of abducens motor neurons that are topographically arranged according to soma size and convergently innervate a single muscle. Disruptions of Duane retraction syndrome-associated transcription factors reveal that these neurons require Mafba/MAFB, but not Sall4/SALL4, for differentiation. Furthermore, genetic perturbations of Pcdh17/Protocadherin-17 result in defective axon growth and soma clumping, thereby abolishing neuromuscular connectivity. Our results suggest that protocadherin-mediated repulsion forms the central topography and efferent projection pattern of the abducens nucleus following Mafba-dependent specification, and imply potential involvement of protocadherins in CCDD etiology.
LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data
Authors: Hughey Jacob J. 
Published: March 2018

AbstractAs experiments to interrogate circadian rhythms increase in scale and complexity, methods to analyze the resulting data must keep pace. Although methods to detect rhythmicity in genome-scale data are well established, methods to detect changes in rhythmicity or in average expression between experimental conditions are often ad hoc. Here we present LimoRhyde (linear models for rhythmicity, design), a flexible approach for analyzing transcriptome data from circadian systems. Borrowing from cosinor regression, LimoRhyde decomposes circadian or zeitgeber time into multiple components, in order to fit a linear model to the expression of each gene. The linear model can accommodate any number of additional experimental variables, whether discrete or continuous, making it straightforward to detect differential rhythmicity and differential expression using state-of-the-art methods for analyzing microarray and RNA-seq data. In this approach, differential rhythmicity corresponds to a statistical interaction between an experimental variable and circadian time, whereas differential expression corresponds to the main effect of an experimental variable while accounting for circadian time. To demonstrate LimoRhyde’s versatility, we applied it to murine and human circadian transcriptome datasets acquired under various experimental designs. Our results show how LimoRhyde systematizes the analysis of such data, and suggest that LimoRhyde could become a valuable approach for assessing how circadian systems respond to genetic and environmental perturbations.
DNA crookedness regulates DNA mechanical properties at short length scales
Authors: Marín-González Alberto , Vilhena J. G. , Moreno-Herrero Fernando , Pérez Rubén 
Published: March 2018

ABSTRACTSequence-dependent DNA conformation and flexibility play a fundamental role in specificity of DNA-protein interactions. Here we quantify the DNA crookedness: a sequence-dependent deformation of DNA that consists on periodic bends of the base pair centers chain. Using molecular dynamics simulations, we found that DNA crookedness and its associated flexibility are bijective: unveiling a one-to-one relation between DNA structure and dynamics. This allowed us to build a predictive model to compute DNA stretching stiffness from solely its structure. Sequences with very little crookedness show extremely high stiffness and have been previously shown to form unstable nucleosomes and promote gene expression. Interestingly, the crookedness can be tailored by epigenetic modifications, known to affect gene expression. Our results rationalize the idea that the DNA sequence is not only a chemical code, but also a physical one that allows to finely regulate its mechanical properties and, possibly, its 3D arrangement inside the cell.
Mapping local and global liquid-liquid phase behavior in living cells using light-activated multivalent seeds
Authors: Bracha Dan , Walls Mackenzie T. , Wei Ming-Tzo , Zhu Lian , Kurian Martin , Toettcher Jared E. , Brangwynne Clifford P. 
Published: March 2018

SummaryRecent studies show that liquid-liquid phase separation plays a key role in the assembly of diverse intracellular structures. However, the biophysical principles by which phase separation can be precisely localized within subregions of the cell are still largely unclear, particularly for low-abundance proteins. Here we introduce a biomimetic optogenetic system, “Corelets”, and utilize its rapid and quantitative tunability to map the first full intracellular phase diagrams, which dictate whether phase separation occurs, and if so by nucleation and growth or spinodal decomposition. Surprisingly, both experiments and simulations show that while intracellular concentrations may be insufficient for global phase separation, sequestering protein ligands to slowly diffusing nucleation centers can move the cell into a different region of the phase diagram, resulting in localized phase separation. This diffusive capture mechanism liberates the cell from the constraints of global protein abundance and is likely exploited to pattern condensates associated with diverse biological processes.
Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity
Authors: Uren Webster Tamsyn M. , Consuegra Sofia , Hitchings Matthew , de Leaniz Carlos Garcia 
Published: March 2018

AbstractMicrobial communities have a crucial influence on host phenotype, and are of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and the skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, dietary differences are likely to be the major factor contributing to the large differences found in the gut microbiome between wild and captive fish. Our results highlight the scope of inter-population variation in the microbiome, and offer insights into the contributing deterministic factors.
A drug-tunable gene therapy for broad-spectrum protection against retinal degeneration
Authors: Santiago Clayton P. , Keuthan Casey J. , Boye Sanford L. , Boye Shannon E. , Imam Aisha A. , Ash John D. 
Published: March 2018

AbstractRetinal degenerations are a large cluster of diseases characterized by the irreversible loss of light-sensitive photoreceptors that impairs the vision of 9.1 million people in the US. An attractive treatment option is to use gene therapy to deliver broad-spectrum neuroprotective factors. However, this approach has had limited clinical translation because of the inability to control transgene expression. To address this problem, we generated an adeno-associated virus vector named RPF2 that was engineered to express domains of leukemia inhibitory factor fused to the destabilization domain of bacterial dihydrofolate reductase. Fusion proteins containing the destabilization domain are degraded in mammalian cells but can be stabilized with the binding of the drug trimethoprim. Our data show that expression levels of RPF2 are tightly regulated by the dose of trimethoprim, and can be reversed by trimethoprim withdrawal. We further show that stabilized RPF2 can protect photoreceptors and prevent blindness in treated mice.
Maturity assessment of HRM processes based on HR process survey tool: a case study
Authors: Zare Milad Shams , Tahmasebi Reza , Yazdani Hamidreza 
Published: March 2018

PurposeThe purpose of this paper is to assess the maturity of human resource management (HRM) processes of the Sazehgostar Co. based on human resource (HR) process survey tool (PST) and provide solutions for them.Design/methodology/approachThe HR PST was adopted as the reference model. Data were collected through interviews with HR experts and reviewing organisational documents. A scoring system (based on RADAR logic) is introduced to score the interviews and documents.FindingsEach element of HR PST consists of ten maturity levels. The results of the assessment showed that the overall average of the organisation’s HRM processes maturity is at level 2. The process of data management and HR systems with a score of five received the highest score, and the organisational capability development, talent management and rewards and recognition processes with a score of 1 received the lowest score.Practical implicationsThese findings enable management and HR management to measure the quality of HR processes and help them to prioritise development actions.Originality/valueThe existing literature does not present empirical research in the field of the maturity of HRM. Also, the analysis method used in this study will help organisations to perform self-assessment and determine the maturity of their processes.
Process architecture development using Riva and ARIS: comparative study
Authors: Tbaishat Dina 
Published: March 2018

Purpose
Business process modeling has been given great attention due to its crucial role in developing computer-based systems that support (and automate) organizational processes. In information systems, building the right process architecture is vital, since a poor division of organizational processes can lead to complex designs or incoherent structure. Moreover, process architecture acts as a “big picture” of what the organization does, and represents dynamic relationships between the existing processes, which, in turn, helps understand how the organization works (Ould, 2005). The paper aims to discuss these issues.

Design/methodology/approach
This paper discusses the derivation of a process architecture diagram (PAD) using the Riva method in detail, in contrast to the PAD developed using Architecture of Integrated Information Systems (ARIS). The information system selected as an example for this comparative study is in the context of academic libraries, embedding various yet generic library processes.

Findings
Organizational process architecture provides a basis for business management, based on specific framework supported by integrated tools and methods (Kozina, 2006). ARIS and Riva process architecture methods can be used to visualize and document organizational processes. Understanding the merits and weaknesses of each method is essential to identify possible areas of application.

Research limitations/implications
The processes selected were generic in most academic libraries not taking into consideration special personalized processes. These can be added though.

Practical implications
Both techniques are feasible and can be used to view and analyze library processes, allowing bridging the gap between theory and practice.

Originality/value
A number of process architecture methods are available, however, few studies focused on assessing these methods, and comparing some of them to find out how easy they are to be used in particular contexts, and whether they can be standardized.
Open innovation and firm performance: the role of organizational mechanisms
Authors: Oltra María J. , Flor M. Luisa , Alfaro José A. 
Published: March 2018

PurposeThe purpose of this paper is to examine the relationship between the use of open innovation (OI) practices and firm performance, and the role of organizational mechanisms (OMs) (formalization and decentralization) as moderator variables.Design/methodology/approachThe authors build a theoretical framework to define a set of hypotheses that are then verified in an empirical study. These theoretical propositions are tested by using the data gathered from a survey addressed to 244 firms in Spanish low- and medium-technology industries.FindingsWith regard to inbound practices, the practices oriented to cooperate with partners in a R&D context have a positive influence. The results show that outbound practices, either by direct generation of revenues from licensing payments or, more indirectly, through the indirect marketing and technical benefits that can stem from revealing have a positive effect on firm performance. Coupled practices, which are related to participation in clusters and innovation networks, have the highest impact on firm performance. In the industrial context examined, decentralization exerts a positive effect which enhances the effect of outbound practices meanwhile formalization reduces their positive effect.Practical implicationsThis study helps practitioners in low- and medium-technology firms to determine which OI practices are most beneficial to firm performance and how formalization and decentralization can influence the relationship between OI and firm performance.Originality/valueThis study helps determine the influence of OI practices in terms of inbound, outbound and coupled types through an analysis of low- and medium-technology firms. The OI literature is enriched by the types herein of the role of OMs, which includes an analysis of how formalization and decentralization moderate the influence of OI practices on firm performance.