bluuebunny/crossref_metadata_2025 huggingface dataset:
The complex architecture of plant transgene insertions
Authors: Jupe Florian , Michael Todd P. , Rivkin Angeline C. , Zander Mark , Timothy Motley S. , Sandoval Justin P. , Keith Slotkin R. , Chen Huaming , Castagnon Rosa , Nery Joseph R. , Ecker Joseph R.
Published: March 2018

Over the last 35 years the soil bacterium Agrobacterium tumefaciens has been the workhorse tool for plant genome engineering. Replacement of native tumor-inducing (Ti) plasmid elements with customizable cassettes enabled insertion of a sequence of interest called Transfer DNA (T-DNA) into any plant genome. Although these T-DNA transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. To fill this gap, we analyzed transgenic Arabidopsis thaliana lines from three widely used collections (SALK, SAIL and WISC) with two single molecule technologies, optical genome mapping and nanopore sequencing. Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and for the first time the actual length of individual transgene insertions from 27 to 236 kilobases. De novo nanopore sequencing-based genome assemblies for two segregating lines resolved T-DNA structures up to 36 kb into the insertions and revealed large-scale T-DNA associated translocations and exchange of chromosome arm ends. The multiple internally rearranged nature of T-DNA arrays made full assembly impossible, even with long nanopore reads. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. This unprecedented nucleotide-level definition of T-DNA insertions enabled the mapping of epigenome data. We identify variable small RNA transgene targeting and DNA methylation. SALK_059379 T-DNA insertions were enriched for 24nt siRNAs and contained dense cytosine DNA methylation. Transgene silencing via the RNA-directed DNA methylation pathway was confirmed by in planta assays. In contrast, SAIL_232 T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. With the emergence of genome editing technologies that rely on Agrobacterium for gene delivery, this study provides new insights into the structural impact of engineering plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.
Continuous-trait probabilistic model for comparing multi-species functional genomic data
Authors: Yang Yang , Gu Quanquan , Zhang Yang , Sasaki Takayo , Crivello Julianna , O’Neill Rachel J. , Gilbert David M. , Ma Jian
Published: March 2018

A large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain underexplored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.
Meta-analysis challenges a textbook example of status signalling: evidence for publication bias
Authors: Sánchez-Tójar Alfredo , Nakagawa Shinichi , Sánchez-Fortún Moisès , Martin Dominic A. , Ramani Sukanya , Girndt Antje , Bókony Veronika , Kempenaers Bart , Liker András , Westneat David F. , Burke Terry , Schroeder Julia
Published: March 2018

The status signalling hypothesis aims to explain conspecific variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of house sparrows (Passer domesticus). We conducted a systematic review, and obtained raw data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, our meta-analysis did not support this prediction. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. First, the overall effect size of unpublished studies was zero, compared to the medium effect size detected in published studies. Second, the effect sizes of published studies decreased over time, and recently published effects were, on average, no longer distinguishable from zero. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook example in evolutionary and behavioural ecology, raise important concerns about the validity of the current scientific publishing culture, and should stimulate renewed interest in understanding within-species variation in ornamental traits.
In vivocloning of β 1-4 endoglucanase gene ofSerratia liquefaciensusing Muduction and itsin silicoanalysis
Authors: Sankar S. Gowri , Mary J. Asnet , Vennison S. John , Anand A. Alwin Prem
Published: March 2018

Cellulose is the major structural component in the plant cell wall. The bio-degradation of cellulose molecules is facilitated by cellulase. In the present study,in vivocloning of cellulase (β-1, 4 endoglucanase) gene from a cellulolytic bacteriumSerratia liquefaciensintoE. coliDH5α has been performed using mini-Mu phage transduction. The enzyme activity of cloned endoglucanase was 81.2U/mg at optimum temperature (40°C) and 80.2U/mg at optimum pH7, while the wildtype has 65.9U/mg and 64.9U/mg respectively. The conserved domain analysis shows thatS. liquefaciensendoglucanase belongs to GH8 family. The nucleotide sequence analysis of wildtype and cloned endoglucanase shows that mutations were found at residues 51(Lys - Asn), 203(Trp-Cys), 246(Thr-Iso), 260(Gly-Ala) and 288(Phe-Leu). The structural analysis shows the active site of wildtype endoglucanase is a narrow groove which lies parallel to the central axis, whereas cloned endoglucanase is broad and tilted to ∼70° from the central axis. The increased enzyme activity in the cloned endoglucanase is due to the structural modification conferred by changes in amino acid resulting in widening of the cleft in the active site.
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

Working 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

Klebsiella 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.

Importance

Carbapenem-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

Alcohol 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

The 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

The 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

Cranial 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.
Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits
Authors: Gilly Arthur , Suveges Daniel , Kuchenbaecker Karoline , Pollard Martin , Southam Lorraine , Hatzikotoulas Konstantinos , Farmaki Aliki-Eleni , Bjornland Thea , Waples Ryan , Appel Emil V. R. , Casalone Elisabetta , Melloni Giorgio , Kilian Britt , Rayner Nigel W. , Ntalla Ioanna , Kundu Kousik , Walter Klaudia , Danesh John , Butterworth Adam , Barroso Inês , Tsafantakis Emmanouil , Dedoussis George , Moltke Ida , Zeggini Eleftheria
Published: March 2018

The role of rare variants in complex traits remains uncharted. Here, we conduct deep whole genome sequencing of 1,457 individuals from an isolated population, and test for rare variant burdens across six cardiometabolic traits. We identify a role for rare regulatory variation, which has hitherto been missed. We find evidence of rare variant burdens overlapping with, and mostly independent of established common variant signals (ADIPOQ and adiponectin, P=4.2×10−8; APOC3 and triglyceride levels, P=1.58×10−26; GGT1 and gamma-glutamyltransferase, P=2.3×10−6; UGT1A9 and bilirubin, P=1.9×10−8), and identify replicating evidence for a burden associated with triglyceride levels in FAM189A (P=2.26×10−8), indicating a role for this gene in lipid metabolism.
LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data
Authors: Hughey Jacob J.
Published: March 2018

As 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

Sequence-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

Recent 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

Microbial 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.
Dynamics of sister chromatid resolution during cell cycle progression
Authors: Stanyte Rugile , Nuebler Johannes , Blaukopf Claudia , Hoefler Rudolf , Stocsits Roman , Peters Jan-Michael , Gerlich Daniel W.
Published: March 2018

Faithful genome transmission in dividing cells requires that the two copies of each chromosome’s DNA package into separate, but physically linked, sister chromatids. The linkage between sister chromatids is mediated by cohesin, yet where sister chromatids are linked and how they resolve during cell cycle progression has remained unclear. Here, we investigated sister chromatid organization in live human cells using dCas9-mEGFP labelling of endogenous genomic loci. We detected substantial sister locus separation during G2 phase, irrespective of the proximity to cohesin enrichment sites. Almost all sister loci separated within a few hours after their respective replication, and then rapidly equilibrated their average distances within dynamic chromatin polymers. Our findings explain why the topology of sister chromatid resolution in G2 largely reflects the DNA replication program. Further, these data suggest that cohesin enrichment sites are not persistent cohesive sites in human cells. Rather, cohesion might occur at variable genomic positions within the cell population.
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

Retinal 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.
Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
Authors: Molaro Antoine , Young Janet M. , Malik Harmit S.
Published: March 2018

Eukaryotic genomes must accomplish both compact packaging for genome stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin functions. Some histone variants are conserved across all eukaryotes, whereas others are lineage-specific. Here, we performed detailed phylogenomic analyses of “short H2A histone” variants found in mammalian genomes. We discovered a previously undescribed typically-sized H2A variant in monotremes and marsupials, H2A.R, which may represent the common ancestor of the short H2As. We also discovered a novel class of short H2A histone variants in eutherian mammals, H2A.Q. We show that short H2A variants arose on the X Chromosome in the common ancestor of all eutherian mammals and diverged into four evolutionarily distinct clades: H2A.B, H2A.L, H2A.P, and H2A.Q. However, the repertoires of short histone H2A variants vary extensively among eutherian mammals due to lineage-specific gains and losses. Finally, we show that all four short H2As are subject to accelerated rates of protein evolution relative to both canonical and other variant H2A proteins including H2A.R. Our analyses reveal that short H2As are a unique class of testis-restricted histone variants displaying an unprecedented evolutionary dynamism. Based on their X-Chromosomal localization, genetic turnover, and testis-specific expression, we hypothesize that short H2A variants may participate in genetic conflicts involving sex chromosomes during reproduction.
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

Purpose

The 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/approach

The 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.

Findings

Each 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 implications

These findings enable management and HR management to measure the quality of HR processes and help them to prioritise development actions.

Originality/value

The 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

Purpose

The 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/approach

The 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.

Findings

With 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 implications

This 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/value

This 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.
Customers’ quality demands as directions to the cold chicken supply chain management
Authors: Schiavo Gustavo , Korzenowski Andre Luis , Soares Batista Eduardo Roberto , Souza Davenilcio Luiz de , Scavarda Annibal
Published: March 2018

Purpose

The purpose of this paper is to analyze the perception of the cold chicken meat value in its supply chain and how to manage the influence of quality demands in this supply chain. It is based on the views that retails and restaurants have about the main quality aspects required to meet their end customers.

Design/methodology/approach

This paper surveyed 135 respondents from restaurants, butcheries, supermarkets, and convenience stores located in the Southern Brazilian metropolitan area. Principal component analysis followed by quality function deployment was performed to analyze the data.

Findings

The principal component analysis results in seven factors: product quality and flexibility of delivery; supply flexibility; responsiveness to market changes and product assortment; measurements of the inventory and competitiveness; product specificity; product availability and specificity cost; and delivery frequency. The comparative study on the steps of the process between restaurants and retailers shows that distribution, cutting and packaging are the key process steps in this chain.

Practical implications

The results show what process steps must be prioritized to comply with the customers’ quality requirements. Since the most important process steps are different for different customers, companies may elect what steps require more attention to satisfy the most profitable customer types.

Originality/value

Several studies are found in the literature that present a theoretical discussion on the quality demands of perishable products. The management of factors related to the process steps can help members of the supply chain in their decision-making processes. The contribution of this research is to identify, by an applied study, how the demanded quality aspects should be considered by the poultry industry to satisfy customers in different market segments.
Business process management – at the crossroads
Authors: Klun Monika , Trkman Peter
Published: March 2018

Purpose

Business process management (BPM) has attracted much focus throughout the years, yet there have been calls questioning the future of BPM. The purpose of this paper is to explore the current state of the field through a dynamic literature review and identify the main challenges for its future development.

Design/methodology/approach

A dynamic co-citation network analysis identifies the “evolution” of knowledge of BPM and the most influential works. The results present the developed BPM subthemes in the form of clusters.

Findings

The focus within the field has shifted from facilitating wide-ranging business performance improvements to creating introverted optimizations within a particular BPM subgroup. The BPM field has thus experienced strong fragmentation throughout the years and has accrued into self-fueling subareas of BPM research such as business process modeling and workflow management. Those subareas often neglect related disciplines in other management, process modeling and organizational improvement fields.

Research limitations/implications

The study is limited by the initial keyword choice of the authors. The subsequent co-citation analysis ameliorates the subjectivity since it produces a data set and contributions based on references.

Originality/value

A new combination of historical development and the state-of-the-art of the BPM field, by employing a co-citation and cluster analysis. This dynamic literature review presents the current state of the theoretical core and attempts to identify the crossroads that BPM has reached. The study can be replicated in the future to track the changes in the field.
New advanced concept of the flying capacitor asymmetric multilevel voltage source inverter
Authors: Jabberi Henda , Ben Ammar Faouzi
Published: March 2018

Purpose

To improve the voltage quality in AC adjustable high-power-speed-drive applications, the purpose of the paper is to provide a large number of output levels without increasing the number of commutation cells in the three-phase, n-cells flying capacitor voltage source asymmetric Multilevel Inverter (MI). The concept is based on the selection of different ratios between the breakdown voltages of two successive power devices. The new mathematical model is developed under various ratios, allows a thorough investigation of the harmonic distortions, flying capacitor energy storage, flying capacitor voltage balancing controllability and blocking voltage insulated gate bipolar transistor (IGBT) capability.

Design/methodology/approach

The asymmetrical design provides a large number of output levels without increasing the number of commutation cells. The important new analytical expression of capacitors voltage distribution is derived and extended to any ratio between the switch breakdown voltages of two successive power devices.

Findings

The detailed simulation study of the proposed concept has been carried out using MATLAB/Simulink. The power switches control of the three-phase three-cell MI is assured by new phase-shifted-multi-carrier pulse width modulation. The space vector representation is used to show the regular and irregular step output voltage in the complex plan (α,β).

Originality/value

In the paper, the n cells flying capacitor inverter, which typically operates in the (n + 1) levels mode, was extended to (n + 2), (n + 3) … until 2n levels with regular or irregular step output voltage. Consequently, the claimed advantages of the asymmetric MI are to improve power quality by reducing harmonic distortions and to reduce the requirement on capacitive energy storage in the circuit.
Frequency response analysis of periodically time varying circuits
Authors: Korotyeyev Igor
Published: March 2018

Purpose

The purpose of this paper is to introduce a method for the analysis of steady-state processes in periodically time varying circuits. The method is based on a new definition of frequency responses for periodic time-varying circuits.

Design/methodology/approach

Processes in inverter circuits are often described by differential equations with periodically variable coefficients and forcing functions. To obtain a steady-state periodic solution, the expansion of differential equations into a domain of two independent variables of time is made. To obtain differential equations with constant coefficients the Lyapunov transformation is applied. The two-dimensional Laplace transform is used to find a steady-state solution. The steady-state solution is obtained in the form of the double Fourier series. The transfer function and frequency responses for the inverter circuit are introduced.

Findings

A set of frequency characteristics are defined. An example of a boost inverter is considered, and a set of frequency responses for voltage and current are presented. These responses show a resonance that is missed if the averaged state-space method is used.

Originality/value

A new definition of frequency responses is presented. On the basis of frequency responses, a modulation strategy and filters can be chosen to improve currents and voltages.
Wideband DOA estimation based on incoherent signal subspace method
Authors: Ahmad Zeeshan , Song Yaoliang , Du Qiang
Published: March 2018

Purpose

Direction-of-arrival (DOA) estimation for wideband sources has attracted a growing interest in the recent decade because wideband sources are incorporated in many real-world applications such as communication systems, radar, sonar and acoustics. One way to estimate the DOAs of wideband signals is to decompose it into narrowband signals using discrete Fourier transform (DFT) and then apply well-established narrowband algorithms to each signal. Afterwards, results are averaged to yield the final DOAs. These techniques require scanning the full band of wideband sources, ultimately degrading the resolution and increasing complexity. This paper aims to propose a new DOA estimation methodology to solve these problems.

Design/methodology/approach

The new DOA estimation methodology is based on incoherent signal subspace method (ISSM). The proposed approach presents a criterion to select a single sub-band of the selected narrowband signals instead of scanning the whole signal spectrum. Then, the DOAs of wideband signals are estimated using the selected sub-band. Therefore, it is named as single sub-band (SSB)-ISSM.

Findings

The computational complexity of the proposed method is much lower than that of traditional DFT-based methods. The effectiveness and advantages of the proposed methodology are theoretically investigated, and computational complexity is also addressed.

Originality/value

To verify the theoretical analysis, computer simulations are implemented, and comparisons with other algorithms are made. The simulation results show that the proposed method achieves better performance and accurately estimates the DOAs of wideband sources.
Experimental evaluation of electric and magnetic properties of structural steel
Authors: Piccoli Phamella Reinert Tamanini , Cabral Sérgio Henrique Lopes , de Oliveira Luiz Fernando , Iaronka Odirlan , Harmel Diogo Fernando , Vieira João Paulo , Sapeli João Egídio
Published: March 2018

Purpose

This paper aims to present the proposition of a new experimental method for obtaining very crucial data of the structural steel that is used in the tank of oil filled power transformers, namely, the volumetric losses and the magnetic permeability, both in function of the density of magnetic flux. Although these data are not usually available, they are fundamental for helping the transformer designer in avoiding the occurrence of hot spots in the transformer tank. The adoption of a conventional Epstein frame has restrictions because of the incompatibility between it and the samples of the steel.

Design/methodology/approach

The basis of the proposition is the same as that of the Epstein frame, with significant attention paid to the additional losses in the winding that creates the magnetic flux to the samples in the core. These losses can be significant and are created by the harmonics of current along the windings and are summed to the ohmic losses. For separating these winding losses from the magnetic losses, each sample is made as being the core of a toroidal 1:1 transformer. Thus, two tests with two identic of these toroidal transformers are necessary.

Findings

The proposed methodology is simple, because it is very similar to the classical tests of transformers (no-load and short-circuit tests). The process of separation of losses requires only a numerical fitting of curves for adjusting the winding losses as a function of the current amplitude, and the obtained results are coherent with the expected behavior of the magnetic losses and the magnetic permeability of a structural steel.

Research limitations/implications

The method gives very approximate results in comparison to those obtained using the Epstein frame. The influences of the temperature and/or of the skin effect have not been evaluated.

Practical implications

Practical, real and thus confident data of structural steel, such as the magnetic permeability and the volumetric losses (hysteresis and Foucault), become available for the transformer designer to take actions for not only reducing the tank losses but also for avoiding the occurrence of hot spots through computer simulation.

Originality/value

The proposition is very new, as it allows to test steel samples with a size that does not fit to a usual Epstein frame. It takes into account the real influence of harmonic of currents in the losses along the winding of a classical Epstein frame, which has not been so far mentioned. It allows obtaining data of structural steel that had not been considered important until now.