bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of Arabidopsis ubiquitin ligase AtPUB46 enhances tolerance to drought and oxidative stress
Authors: Adler Guy , Mishra Amit Kumar , Maymon Tzofia , Raveh Dina , Bar-Zvi Dudy
Published: July 2018

The U-Box E3 ubiquitin ligase, AtPUB46, functions in the drought response: T-DNA insertion mutants of this single paralogous gene are hypersensitive to water- and oxidative stress (Adler et al. BMC Plant Biology 17:8, 2017). Here we analyze the phenotype of AtPUB46 overexpressing (OE) plants. AtPUB46-OE show increased tolerance to water stress and have smaller leaf blades and reduced stomatal pore area and stomatal index compared with wild type (WT). Despite this, the rate of water loss from detached rosettes is similar in AtPUB46-OE and WT plants. Germination of AtPUB46-OE seeds was less sensitive to salt than WT whereas seedling greening was more sensitive. We observed a complex response to oxidative stress applied by different agents: AtPUB46-OE plants were hypersensitive to H2O2 but hyposensitive to methyl viologen. AtPUB46-GFP fusion protein is cytoplasmic, however, in response to H2O2 a considerable proportion translocates to the nucleus. We conclude that the differential stress phenotype of the AtPUB46-OE does not result from its smaller leaf size but from a change in the activity of a stress pathway(s) regulated by a degradation substrate of the AtPUB46 E3 and also from a reduction in stomatal pore size and index.

Accession Numbers

Sequence data for this article can be found in: The Arabidopsis Information Resource database (http://www.arabidopsis.org) under accession numbers At5G18320 (PUB46).
Magnetic Polymer Models for Epigenomic Organisation and Phase Separation
Authors: Colì Davide , Michieletto Davide , Marenduzzo Davide , Orlandini Enzo
Published: July 2018

The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical (“epigenetic”) marks and threedimensional genome folding. Yet, the physical principles underlying the dynamical coupling between three-dimensional genomic organisation and one-dimensional epigenetic patterns remain elusive. To shed light on this issue, here we study by mean field theory and Brownian dynamics simulations a magnetic polymer model for chromosomes, where each monomer carries a dynamic epigenetic mark. At the single chromosome level, we show that a first order transition describes the unlimited spreading of epigenetic marks, a phenomenon that is often observed in vivo. At the level of the whole nucleus, experiments suggest chromosomes form micro-phase separated compartments with distinct epigenetic marks. We here discover that for a melt of magnetic polymers such a morphology is thermodynamically unstable, but can be stabilised by a nonequilibrium and ATP-mediated epigenetic switch between different monomer states.
Mutation of sequences flanking and separating transcription factor binding sites in a Drosophila enhancer significantly alter its output
Authors: Li Xiao-Yong , Eisen Michael B.
Published: July 2018

Here we explore how mutating different sequences in an enhancer that regulates patterned gene expression in Drosophila melanogaster embryos can affect its output. We used quantitative imaging to analyze the effects of a wide variety of mutations in the hunchback distal anterior enhancer. This enhancer has been shown to respond to the anterior morphogen Bicoid, but we found that mutations in only one of the five strong Bicoid sites in the enhancer has a significant effect on its binding. The pioneer factor Zelda, which binds to this enhancer and is the only other factor implicated in its activity besides Bicoid. However, we found that mutations of all its sites only has modest effect that is limited to reduction of its output in more posterior regions of the embryo, where Bicoid levels are low. In contrast to the modest effects of mutating known transcription factor binding sites, randomizing the sequences between Zelda and Bicoid sites significantly compromised enhancer activity. Finer mapping suggested that the sequences that determine activity are broadly distributed in the enhancer. Mutations in short sequences flanking Bicoid binding sites have stronger effects than mutations to Bicoid sites themselves, highlighting the complex and counterintuitive nature of the relationship between enhancer sequence and activity.
An amphipathic helix enables septins to sense micron-scale membrane curvature
Authors: Cannon Kevin S. , Woods Benjamin L. , Crutchley John M. , Gladfelter Amy S.
Published: July 2018

The geometry of cells is well described by membrane curvature. Septins are filament forming, GTP-binding proteins that assemble on positive, micrometer-scale curvatures. Here, we examine the molecular basis of curvature sensing by septins. We show that differences in affinity and the number of binding sites drive curvature-specific adsorption of septins. Moreover, we find septin assembly onto curved membranes is cooperative and show that geometry influences higher-order arrangement of septin filaments. Although septins must form polymers to stay associated with membranes, septin filaments do not have to span micrometers in length to sense curvature, as we find that single septin complexes have curvature-dependent association rates. We trace this ability to an amphipathic helix (AH) located on the C-terminus of Cdc12. The AH domain is necessary and sufficient for curvature sensing both in vitro and in vivo. These data show that curvature sensing by septins operates at much smaller length scales than the micrometer curvatures being detected.
An actuated neural probe architecture for reducing gliosis-induced recording degradation
Authors: Massey Travis L. , Kuo Leane S. , Fan Jiang Lan , Maharbiz Michel M.
Published: July 2018

Glial encapsulation of chronically implanted neural probes inhibits recording and stimulation, and this signal loss is a significant factor limiting the clinical viability of most neural implant topologies for decades-long implantation. We demonstrate a mechanical proof of concept for silicon shank-style neural probes intended to minimize gliosis near the recording sites. Compliant whiskers on the edges of the probe fold inward to minimize tissue damage during insertion. Once implanted to the target depth and retracted slightly, these whiskers splay outward. The splayed tips, on which recording sites could be patterned, extend beyond the typical 50-100 micron radius of a glial scar. The whiskers are micron-scale to minimize or avoid glial scarring. Electrically inactive devices with whiskers of varying widths and curvature were designed and monolithically fabricated from a five-micron silicon-on-insulator (SOI) wafer, and their mechanical functionality was demonstrated in a 0.6% agar brain phantom. Deflection was plotted versus deflection speed, and those that were most compliant actuated successfully. This probe requires no preparation for use beyond what is typical for a shank-style silicon probe.
Predicting subclinical psychotic-like experiences on a continuum using machine learning
Authors: Taylor Jeremy A , Larsen Kit Melissa , Dzafic Ilvana , Garrido Marta I
Published: July 2018

Previous studies applying machine learning methods to psychosis have primarily been concerned with the binary classification of chronic schizophrenia patients and healthy controls. The aim of this study was to use electroencephalographic (EEG) data and pattern recognition to predict subclinical psychotic-like experiences on a continuum between these two extremes in otherwise healthy people. We applied two different approaches to an auditory oddball regularity learning task obtained fromN= 73 participants:

A feature extraction and selection routine incorporating behavioural measures, event-related potential components and effective connectivity parameters;

Regularisation of spatiotemporal maps of event-related potentials.

Using the latter approach, optimal performance was achieved using the response to frequent, predictable sounds. Features within the P50 and P200 time windows had the greatest contribution toward lower Prodromal Questionnaire (PQ) scores and the N100 time window contributed most to higher PQ scores. As a proof-of-concept, these findings demonstrate that EEG data alone are predictive of individual psychotic-like experiences in healthy people. Our findings are in keeping with the mounting evidence for altered sensory responses in schizophrenia, as well as the notion that psychosis may exist on a continuum expanding into the non-clinical population.
Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci
Authors: Buckle Adam , Brackley Chris A , Boyle Shelagh , Marenduzzo Davide , Gilbert Nick
Published: July 2018

Chromatin folded into 3-D macromolecular structures is often analysed by 3C and FISH techniques, but frequently provide contradictory results. Instead, chromatin can be modelled as a simple polymer comprised of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), genomic disruptions (ATAC-seq) and structural anchors (CTCF) we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fibre varied along its length; combined with diffusing protein bridges and loop extrusion this model predicted the 3-D organisation of genomic loci at a population and single cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3-D and enable predictions of chromatin folding paths.
Responses of ground-dwelling spider assemblages to changes in vegetation from wet oligotrophic habitats of Western France
Authors: Lafage Denis , Djoudi El Aziz , Perrin Gwenhaël , Gallet Sébastien , Pétillon Julien
Published: July 2018

While many arthropod species are known to depend, directly or indirectly, on certain plant species or communities, it remains unclear to what extent vegetation shapes assemblages of other taxa, notably spiders. In this study, we tested whether the activity-density, composition, and diversity of ground-dwelling spiders were driven by changes in vegetation structure. Field sampling was conducted using pitfall traps in bogs, heathlands, and grasslands of Brittany (Western France) in 2013. A total of 8576 spider individuals were identified up to the species level (for a total of 141 species), as well as all plant species in more than 300 phytosociological relevés. A generalised linear model showed that spider activity–density was negatively influenced by mean vegetation height and mean Ellenberg value for moisture. Indices of diversity (α, β, and functional diversities) increased with increasing vegetation height and shrub cover (GLMs). Variables driving spider composition were mean vegetation height, dwarf shrub cover, and low shrub cover (results from a redundancy analysis). Spiders, some of the most abundant arthropod predators, are thus strongly influenced by vegetation structure, including ground-dwelling species. Although later successional states are usually seen as detrimental to local biodiversity in Europe, our results suggest that allowing controlled development of the shrub layer could have a positive impact on the diversity of ground-dwelling spiders.
Management performance mapping and the value of information for regional prioritization of management interventions
Authors: Buddenhagen C. E. , Piedra J. Andrade , Forbes G. A. , Kromann P. , Navarrete I. , Thomas-Sharma S. , Xing Y. , Choudhury R. A. , Andersen K. F. , Schulte-Geldermann E. , Garrett K. A.
Published: July 2018

Policymakers and donors often need to identify the locations and settings where technologies are most likely to have important effects, to increase the benefits from agricultural development or extension efforts. Higher quality information may help to target the high-payoff locations. The value of information (VOI) in this context is formalized by evaluating the results of decision making guided by a set of information compared to the results of acting without taking the information into account. We present a framework for management performance mapping that includes evaluating the VOI for decision making about geographic priorities in regional intervention strategies, in case studies of Andean and Kenyan potato seed systems. We illustrate use of Bayesian network models and recursive partitioning to characterize the relationship between seed health and yield responses and environmental and management predictors used in studies of seed degeneration. These analyses address the expected performance of an intervention based on geographic predictor variables. In the Andean example, positive selection of seed from asymptomatic plants was more effective at high altitudes in Ecuador. In the Kenyan example, there was the potential to target locations with higher technology adoption rates and with higher potato cropland connectivity, i.e., a likely more important role in regional epidemics. Targeting training to high performance areas would often provide more benefits than would random selection of target areas. We illustrate how assessing the VOI can help inform targeted development programs and support a culture of continuous improvement for interventions.
Link Your Sites (LYS.py): Coupling your PAML codeml results and homologous protein structures in PyMOL
Authors: Moreta Lys Sanz , da Fonseca Rute Andreia Rodrigues
Published: July 2018

The visualization of the molecular context of an amino acid mutation in a protein structure is crucial for the assessment of its functional impact and to understand its evolutionary implications. Currently, searches for fast evolving amino acid positions using codon substitution models like those implemented in PAML (Z. Yang, 2000) are done in almost complete proteomes, generating large numbers of candidate proteins that require individual structural analyses. Here I present a python wrapper script that integrates the output of PAML with the PyMOL visualization tool to automate the generation of protein structure models where positively selected sites are mapped along with the location of putative functional domains.
Ring nucleases deactivate Type III CRISPR ribonucleases by degrading cyclic oligoadenylate
Authors: Athukoralage Januka S , Rouillon Christophe , Graham Shirley , Grüschow Sabine , White Malcolm F
Published: July 2018

The CRISPR-Cas system provides adaptive immunity against mobile genetic elements in prokaryotes, utilising small CRISPR RNAs which direct effector complexes to degrade invading entities. Type III effector complexes were recently demonstrated to synthesise a novel second messenger, cyclic oligoadenylate (cOA), on binding target RNA. cOA in turn binds to and activates a range of downstream effector proteins including ribonucleases (Csm6/Csx1) and transcription factors via a CARF (CRISPR associated Rossman Fold) domain, inducing an antiviral state in the cell that is important for immunity. The mechanism of the “off-switch” that resets the system is not understood. Here, we report the identification of the nuclease that degrades these cOA ring molecules. The “Ring nuclease” is itself a CARF family protein with a metal independent mechanism, which cleaves cOA4 rings to generate linear di-adenylate species and switches off the antiviral state. The identification of Ring nucleases adds an important insight to the CRISPR-Cas system.
Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
Authors: Grobler Yolande , Yun Chi Y. , Kahler David J. , Bergman Casey M. , Lee Hangnoh , Oliver Brian , Lehmann Ruth
Published: July 2018

Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the insects ineffective as vectors. To utilize Wolbachia effectively as a tool against vector-borne viruses a better understanding of the host-Wolbachia relationship is needed. To investigate Wolbachia-insect interactions we used the Wolbachia/Drosophila model that provides a genetically tractable system for studying host-pathogen interactions. We coupled genome-wide RNAi screening with a novel high-throughput fluorescence in situ hybridization (FISH) assay to detect changes in Wolbachia levels in a Wolbachia-infected Drosophila cell line JW18. 1117 genes altered Wolbachia levels when knocked down by RNAi of which 329 genes increased and 788 genes decreased the level of Wolbachia. Validation of hits included in depth secondary screening using in vitro RNAi, Drosophila mutants, and Wolbachia-detection by DNA qPCR. A diverse set of host gene networks was identified to regulate Wolbachia levels and unexpectedly revealed that perturbations of host translation components such as the ribosome and translation initiation factors results in increased Wolbachia levels both in vitro using RNAi and in vivo using mutants and a chemical-based translation inhibition assay. This work provides evidence for Wolbachia-host translation interaction and strengthens our general understanding of the Wolbachia-host intracellular relationship.

Author summary

Insects such as mosquitos act as vectors to spread devastating human diseases such as Dengue, West Nile, and Zika. It is critical to develop control strategies to prevent the transmission of these diseases to human populations. A novel strategy takes advantage of an endosymbiotic bacterium Wolbachia pipientis. The presence of this bacterium in insect vectors prevents successful transmission of RNA viruses. The degree to which viruses are blocked by Wolbachia is dependent on the levels of the bacteria present in the host such that higher Wolbachia levels induce a stronger antiviral effect. In order to use Wolbachia as a tool against vector-borne virus transmission a better understanding of host influences on Wolbachia levels is needed. Here we performed a genome-wide RNAi screen in a model host system Drosophila melanogaster infected with Wolbachia to identify host systems that affect Wolbachia levels. We found that host translation can influence Wolbachia levels in the host.
Choline Transporter in α/β core neurons of Drosophila mushroom body non-canonically regulates pupal eclosion and maintains neuromuscular junction integrity
Authors: Hamid Runa , Hajirnis Nikhil , Kushwaha Shikha , Saleem Sadaf , Kumar Vimlesh , Mishra Rakesh K
Published: July 2018

Insect mushroom bodies (MB) have an ensemble of synaptic connections well-studied for their role in experience-dependent learning and several higher cognitive functions. MB requires neurotransmission for an efficient flow of information across synapses with the different flexibility to meet the demand of the dynamically changing environment of an insect. Neurotransmitter transporters coordinate appropriate changes for an efficient neurotransmission at the synapse. Till date, there is no transporter reported for any of the previously known neurotransmitters in the intrinsic neurons of MB. In this study, we report a highly enriched expression of Choline Transporter (ChT) in Drosophila MB. We demonstrate that knockdown of ChT in a sub-type of MB neurons called α/β core (α/βc) neurons leads to eclosion failure, peristaltic defect in larvae, and altered NMJ phenotype. These defects were neither observed on knockdown of proteins of the cholinergic locus in α/βc neurons nor by knockdown of ChT in cholinergic neurons. Thus, our study provides insights into non-canonical roles of ChT in MB.
Sibe: a computation tool to apply protein sequence statistics to folding and design
Authors: Cheung Ngaam J. , Yu Wookyung
Published: July 2018

Statistical analysis plays a significant role in both protein sequences and structures, expanding in recent years from the studies of co-evolution guided single-site mutations to protein folding in silico. Here we describe a computational tool, termed Sibe, with a particular focus on protein sequence analysis, folding and design. Since Sibe has various easy-interface modules, expressive architecture and extensible codes, it is powerful in statistically analyzing sequence data and building energetic potentials in boosting both protein folding and design. In this study, Sibe is used to capture positionally conserved couplings between pairwise amino acids and help rational protein design, in which the pairwise couplings are filtered according to the relative entropy computed from the positional conservations and grouped into several ‘blocks’. A human β2-adrenergic receptor (β2AR) was used to demonstrated that those ‘blocks’ could contribute rational design at functional residues. In addition, Sibe provides protein folding modules based on both the positionally conserved couplings and well-established statistical potentials. Sibe provides various easy to use command-line interfaces in C++ and/or Python. Sibe was developed for compatibility with the ‘big data’ era, and it primarily focuses on protein sequence analysis, in silico folding and design, but it is also applicable to extend for other modeling and predictions of experimental measurements.
Measurements of maize root plasticity under water stress in hydroponic chambers
Authors: Jubery Talukder Z. , Liu Sisi , Lubberstedt Thomas , Ganapathysubramanian Baskar , Attinger Daniel
Published: July 2018

1.

Under water stress, plants adjust root traits including depth of root system, root diameter, density of root per volume of soil, hydraulic conductance of root. In this experimental study, we present a method to quantify how hydraulic traits of maize roots adapt to drought. The experiments involve a microfluidic flow sensor and a custom-built pressure chamber, made of transparent plastic for visualization purposes. We measured how maize genotypes (PHB47 and PHZ51) grown for a week in deionized (DI) water and one day in hydroponic nutrients solution (called the irrigated condition) respond to one week of water stress. Conditions of water stress (called drought conditions) were created by mixing Polyethylene Glycol with the nutrients solution. Results show that under drought, the roots of both genotypes respond by approximately halving their global hydraulic conductance. This adjustment seems to be achieved mainly by reductions of the total surface area of the roots. Interestingly, the measured hydraulic conductivity of the roots grown under drought was significantly larger. In all, this study sheds light on how plants adapt to water stress in a hydroponic system, by decreasing root area and increasing root permeability.
Depletion of limiting rDNA structural complexes triggers chromosomal instability and replicative aging ofSaccharomyces cerevisiae
Authors: Fine Ryan D. , Maqani Nazif , Li Mingguang , Franck Elizabeth , Smith Jeffrey S.
Published: July 2018

Sir2 is a highly conserved NAD+-dependent histone deacetylase that functions in heterochromatin formation and promotes replicative lifespan (RLS) in the budding yeast,Saccharomyces cerevisiae. Within the yeast rDNA locus, Sir2 is required for efficient cohesin recruitment and maintaining stability of the tandem array. In addition to the previously reported depletion of Sir2 in replicatively aged cells, we discovered that subunits of the Sir2 containing complexes, SIR and RENT, were depleted. Several other rDNA structural protein complexes also exhibited age-related depletion, most notably the cohesin complex. We hypothesized that mitotic chromosome instability (CIN) due to cohesin depletion could be a driver of replicative aging. ChIP assays of the residual cohesin (Mcd1-13xMyc) in moderately aged cells showed strong depletion from the rDNA and initial redistribution to the point centromeres, which was then lost in older cells. Despite the shift in cohesin distribution, sister chromatid cohesion was partially attenuated in aged cells and the frequency of chromosome loss was increased. This age-induced CIN was exacerbated in strains lacking Sir2 and its paralog, Hst1, but suppressed in strains that stabilize the rDNA array due to deletion ofFOB1or through caloric restriction (CR). Furthermore, ectopic expression ofMCD1from a doxycycline-inducible promoter was sufficient to suppress rDNA instability in aged cells and to extend RLS. Taken together we conclude that age-induced depletion of cohesin and multiple other nucleolar chromatin factors destabilize the rDNA locus, which then results in general CIN and aneuploidy that shortens RLS.
Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during earlyDrosophila melanogasterembryogenesis
Authors: Li Xiao-Yong , Eisen Michael B.
Published: July 2018

The maternally deposited transcription factor Zelda binds to and is required for the activation of a large number of genes in earlyDrosophiladevelopment, and has been suggested to act as a pioneer factor. In this study, we investigated the temporal dynamics of Zelda binding along with the maternal patterning factors Dorsal and Caudal during early embryogenesis. We found in regions bound by Zelda and either Dorsal or Caudal, Zelda binding was detected, and reached maximum levels, earlier than Caudal and Dorsal, providing support of its role as a pioneer factor. We found that Dorsal and Caudal binding correlated strongly with Zelda binding at mitotic cycle 12, suggesting that Zelda is important for early binding by these factors and early onset of their target gene expression. At the same time, we show that among Dorsal target enhancers, the dorsal and ventral ectoderm enhancers are much more strongly associated with Zelda than mesoderm enhancers, revealing an additional function of Zelda in coordinating spatial activity of enhancers. We have also investigated the role of Zelda on chromatin structure. We found that in early embryos, before Dorsal and Caudal are bound at significant levels, Zelda binding is associated with histone acetylation and local histone depletion. These chromatin associated changes accompanied with increased local chromatin accessibility were also detected around Zelda peaks in coding sequences that do not appear to play a role in subsequent transcription factor binding. These findings suggest that Zelda binding itself can lead to chromatin structural changes. Finally, we found that Zelda motifs, both bound and unbound, tend to be associated with positioned nucleosomes, which we suggest may be important for the regulatory specificity of enhancers.
polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids
Authors: Clark Lindsay V. , Lipka Alexander E. , Sacks Erik J.
Published: July 2018

Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that requires a reference genome or uses priors that may be inappropriate for the population. Here we present several novel Bayesian algorithms that estimate genotype posterior probabilities, all of which are implemented in a new R package, polyRAD. Appropriate priors can be specified for mapping populations, populations in Hardy-Weinberg equilibrium, or structured populations, and in each case can be informed by genotypes at linked markers. The polyRAD software imports read depth from several existing pipelines, and outputs continuous or discrete numerical genotypes suitable for analyses such as genome-wide association and genomic prediction.
In-frame de novo mutation in BICD2 in two patients with muscular atrophy and arthrogryposis
Authors: Koboldt Daniel C. , Kastury Rama D. , Waldrop Megan A. , Kelly Benjamin J. , Mosher Theresa Mihalic , McLaughlin Heather , Corsmeier Don , Slaughter Jonathan L. , Flanigan Kevin M. , McBride Kim L. , Mehta Lakshmi , Wilson Richard K. , White Peter
Published: July 2018

We describe two unrelated patients, a 12-yr-old female and a 6-yr-old male, with congenital contractures and severe congenital muscular atrophy. Exome and genome sequencing of the probands and their unaffected parents revealed that they have the same de novo deletion in BICD2 (c.1636_1638delAAT). The variant, which has never been reported, results in an in-frame 3-bp deletion and is predicted to cause loss of an evolutionarily conserved asparagine residue at position 546 in the protein. Missense mutations in BICD2 cause autosomal dominant spinal muscular atrophy, lower-extremity predominant 2 (SMALED2), a disease characterized by muscle weakness and arthrogryposis of early onset and slow progression. The p.Asn546del clusters with four pathogenic missense variants in a region that likely binds molecular motor KIF5A. Protein modeling suggests that removing the highly conserved asparagine residue alters BICD2 protein structure. Our findings support a broader phenotypic spectrum of BICD2 mutations that may include severe manifestations such as cerebral atrophy, seizures, dysmorphic facial features, and profound muscular atrophy.
Food consumption among income classes and its response to changes in income distribution in rural China
Authors: Ren Yanjun , Zhang Yanjie , Loy Jens-Peter , Glauben Thomas
Published: July 2018

Purpose

Given the fact that the income disparity has become extremely severe in rural China, the purpose of this paper is to examine heterogeneity in food consumption among various income classes and to investigate the impact of changes in income distribution patterns on food demand in rural China.

Design/methodology/approach

In this study, the authors partition the households into five income classes according to the distribution of household per capita net income. Using household data drawn from the China Health and Nutrition Survey in 2011, a two-stage demand model is applied to estimate a food demand system for each of the income classes. After obtaining the estimated income elasticities of eight studied food groups for each income class, the authors then examine the responsiveness of food demand to the changes in income distribution by means of four scenarios with varying income distribution.

Findings

The empirical results indicate that substantial differences in food consumption exist across various income classes. Specifically, the lowest-income households are more sensitive to price and income changes for most studied food groups than the highest-income households are. In general, income responsiveness is higher for meats, aquatic products and dairy products. Based on estimated income elasticities, the projected food consumption under different income distribution patterns shows that changes in income distribution have significant influences on food consumption. In addition, the authors conclude that a more equal distribution of income would be associated with a higher demand for food in rural China.

Originality/value

This paper employs a two-stage demand model to estimate food demand in rural China by income classes. The results imply substantial differences in food demand for various income classes. Therefore, income distribution should be taken into account instead of an average estimation for the population as a whole when investigating food demand in rural China. Given the significant changes in income distribution in rural China, this study provides several important policy implications to alleviate income inequality and poverty, as well as to improve nutrition for lower-income classes.
Examining the inter-relationship among competitive market environments, green supply chain practices, and firm performance
Authors: Choi Seok-Beom , Min Hokey , Joo Hye-Young
Published: July 2018

Purpose

The purpose of this paper is to assess the impact of competitive market environments on the firm’s decision to adopt green supply chain management (GSCM) practices, while checking to see if the firm’s commitment to particular types of GSCM practices improves its performance.

Design/methodology/approach

To confirm a positive link between the firm’s GSCM practices to its performance, the authors collected the data from 322 Korean firms via questionnaire surveys and then analyzed these data using the structural equation model.

Findings

Among various types of GSCM practices, green purchasing has the greatest impact on both manufacturing and marketing performances. Also, internal environmental management positively influenced both manufacturing and marketing performances, whereas cooperation with customers and reverse logistics had no significant impact on the firm’s manufacturing and marketing performances.

Originality/value

To provide a practical advice for firms which are hesitant to embrace green supply chain practices due to skeptical views about their true managerial benefits, this paper discerned more effective GSCM practices from less effective GSCM practices. In so doing, this paper is one of the few studies which pinpointed what types of specific GSCM practices are most effective in enhancing firm performance.
The inverted U-shaped relationship between the network profile and the competitive advantage of supply chains
Authors: Swierczek Artur
Published: July 2018

Purpose

The purpose of this paper is twofold. First, the author aims to explore if there is a curvilinear relationship between the network rent, generated as a combination of the relational performance of two dyads and the network profile of the triadic supply chains. Second, the author seek to recognize the ideal network profile, consisting of the properties at the node and relationship level, that provides the highest network rents, and thus enables to increase the competitive advantage of supply chains.

Design/methodology/approach

The paper opted for an exploratory study using a survey of triads forming supply chains. In order to reveal the capability of yielding the network rent in the examined triads, multiple regression analysis with interaction effects was employed. Having confirmed the existence of supernormal profit, the author investigated the relationship between the network rent and the network index. Finally, a cluster analysis was conducted to compare the network profile in the group of triads generating higher network rents with the cluster yielding relatively lower network rents.

Findings

The obtained findings show that a combination of the relational performance of two dyads contributes to generating the network rent, and thus ensures a more favorable competitive position of supply chains. The results of the study also indicate that there is a significant curvilinear, inverted U-shaped relationship between the network profile and the competitive advantage of triadic supply chains. In addition, the following network properties appear to be particularly important for yielding higher network rents: network centrality, betweenness, network density and network size.

Originality/value

The study contributes to the theory by testing if the network rent can be yielded as a combination of the relational performance of two dyads in the triadic supply chains. The research also indicates that there is a curvilinear relationship between the network rent and the network profile of examined supply chains. Moreover, the study also addresses the link between the network profile, consisting of the multiple network properties simultaneously, in relation to the competitive advantage of supply chains.
An evaluation of supply chain integration across multi-tier supply chains of manufacturing-based SMEs in Malawi
Authors: Kanyoma Kizito Elijah , Agbola Frank Wogbe , Oloruntoba Richard
Published: July 2018

Purpose

The purpose of this paper is to explain the interrelationships in internal and external supply chain integration (SCI) across multiple tiers of manufacturing-based small and medium-sized enterprises (SMEs) in a developing country, Malawi.

Design/methodology/approach

Utilizing the resource-based view, resource-dependence and network theory perspectives, and drawing on a multiple embedded case-study approach, the research investigated the internal and external linkages within three-tier supplier, manufacturer and retailer SCs and described varying perspectives of SCI across supply chain positions.

Findings

Firms with strategic intra-firm resources were less committed to external integration, deploying their resources as a source of power to dominate and exploit their dependent partners. The SCI across multiple tiers was impaired by dependence but enhanced by interdependence strategies of firms. Although lack of trust, promotion of non-overlapping self-interests, corruption in sourcing processes and resource constraints negatively affected SCI, firm commitment to external integration promoted greater commitment among firms, thus having a positive effect on SCI.

Research limitations/implications

Further analysis of SCI of SME triads and a more systematic longitudinal analysis across other market segments should be explored to generalize the conclusions of this study.

Practical implications

The external influences on dyadic relationships go beyond the interactions of heterogeneous firms in the network to encompass interpersonal interactions across the network, where individuals may potentially prioritize personal connections and sabotage the interests of their firms.

Originality/value

The research explored the internal and external dimensions of SCI in multi-tier SCs of SMEs, and provided for the first time new evidence to show that firm commitment to engaging with partners complements the mechanisms of SCI within a developing country context. It highlights the need to develop trust, eliminate corruption, promote greater commitment of SC partners and encourage greater investment in firms’ resource capabilities to enhance SCI among SMEs.
Sub-administration: ideologies, myths and metaphors
Authors: Farmer David John
Published: July 2018

Purpose

The purpose of this paper is to recommend that public administration (PA) theory and practice should become more sensitive to its sub-administration, and to suggest how this can be done.

Design/methodology/approach

This conceptual paper maintains that this sub-administration includes those ideologies, myths and metaphors that contribute like an unconscious in shaping (and misshaping) governmental policy and administration. Descriptions of the nature of ideologies, myths and metaphors are given, along with some examples of those that are harmful – such as the ideologies of the American Business Model and neo-liberalism.

Findings

PA should seek to engage and oppose such ideologies, myths and metaphors that are problematic – both those constructed within and without of PA itself. It is recommended that, for such analytical purposes, PA should turn toward post-traditional PA, including the insights of post-modernism and epistemic pluralism.

Originality/value

The concept of sub-administration is of significant utility both for PA theorists and practitioners in strengthening public administrative performance. The author has offered such and/or similar recommendations in earlier publications, including in the International Journal of Organization Theory and Behavior, 19 (1), 90-102: 2016.
Neutrality as it never was: a short treatise on public administration theory
Authors: Miller Hugh T.
Published: July 2018

Purpose

Is public administration neutral? Scholarship does not interpret public administration as neutral, even though, on moral–ethical grounds, it frequently advises neutrality for practitioners. Five main schools of thought are surveyed. Neutrality and alternative expressions of it, such as nonpartisanship, expertise, impartiality or facilitation, are role prescriptions for practicing public administrators, and are typically offered as appropriate comportments in interacting with citizens and groups. At the same time, public administration is undeniably a political institution having political purposes and constitutive impacts. Indeed, the very existence of the administrative state is politically contestable. The paper aims to discuss these issues.

Design/methodology/approach

Critical reflection, political philosophy, political theory.

Findings

Scholars across the various schools of thought in public administration do not presuppose the presence of a neutral public administrator. However, there is sometimes an admonition to practitioners to behave as if they were politically neutral.

Practical implications

Advising practitioners that their practices are neutral masks the fact that public administration is an inherently political institution.

Originality/value

Neutral public administration is revealed as empty cant.
The public pursuit of closure: losses, fictions, and endings
Authors: Patterson Patricia
Published: July 2018

Purpose

This paper raises the possibility that closure is a myth, both in the sense of a narrative guiding a quest and in the sense of a social fiction. The paper aims to discuss this issue.

Design/methodology/approach

The paper examines parts played by public administration practice in quests with subtexts of death, love, and loss, and suggests that overlapping administrative and narrative fictions have their comforts and uses for grieving persons, for organizations, and for the social order.

Findings

The paper confesses ambivalence about the actual existence of closure in historical rather than fictional time.

Originality/value

Using the metaphor of “closing the books,” the paper situates particular public reckonings with human loss in the context of justice-seeking and other public sector companions of “closure,” but resists the narrative closure of the authoritative answer and the happy ending.
Housing information modelling for BIM-embedded housing refurbishment
Authors: Kim Ki Pyung , Park Kenneth Sungho
Published: July 2018

Purpose

The purpose of this study is to identify building information modelling (BIM) input data sets within a BIM-embedded housing refurbishment process and enable construction professionals to use BIM as an information management platform for housing refurbishment projects.

Design/methodology/approach

A hypothetical case study using BIM tools for a housing refurbishment project is adopted to identify BIM input data sets to create a housing information model within a BIM system. Reliability of the research outcome is examined by conducting a comparative analysis between existing and simulated research outcomes.

Findings

This research identifies essential BIM input data sets during the early design phase. The importance of a well-integrated housing information model containing accurate as-built condition, cost and thermal performance information is essential to use BIM for housing refurbishment. BIM can be feasible for housing refurbishment when an information-enriched housing information model is constructed. Furthermore, the capability of BIM that can enable key project stakeholders to determine the most affordable refurbishment solution among various alternatives is identified as BIM can provide reliable cost estimations and thermal performance of refurbishment alternatives at the early design stage.

Research limitations/implications

The examined refurbishment processes and input data sets are confined to the early design phases as BIM use for housing refurbishment is limited.

Practical implications

This research will contribute to use BIM for housing refurbishment by providing essential BIM input data sets and BIM-embedded refurbishment processes.

Originality/value

This research reveals primary housing information data sets and BIM-embedded refurbishment processes at the early design phase.
Employment requirements in Swedish construction procurement – institutional perspectives
Authors: Troje Daniella , Kadefors Anna
Published: July 2018

Purpose

Today, social procurement and requirements to create employment for disadvantaged groups in particular, are increasingly used in the construction sector. The purpose of this paper is to explore the use of employment requirements and its organizational implications in Sweden, and to suggest a possible theoretical approach for studying this phenomenon in the future.

Design/methodology/approach

The paper is based on written sources describing influential Swedish cases where employment requirements have been used, as well as on interviews with central actors in industry and society.

Findings

Due to the increased use of employment requirements, the construction industry may currently be experiencing the initial stages of a process of institutional change. This implies that a traditional logic, where value is perceived as a function of the cost and quality of the physical product, is increasingly co-existing and competing with a logic where social value plays an important role.

Practical implications

An institutional perspective could enable a rich explication of processes, practices and roles, which might help individual practitioners and organizations to more purposefully work towards a more informed and effective use of employment requirements.

Originality/value

This study takes a first step towards increased theorization of the emergent practice of including employment requirements in construction procurement and its organizational implications. Thereby, research on this phenomenon may be more closely related to and informed by relevant developments in the wider academic community.
Factors driving contractors to implement energy management strategies in construction projects
Authors: Enshassi Adnan , Ayash Abed , Mohamed Sherif
Published: July 2018

Purpose

The purpose of this paper is to investigate the factors driving Palestinian construction contractors to implement energy management strategies during the execution of construction projects.

Design/methodology/approach

The study was conducted by administering a questionnaire that comprised 26 drivers for adopting energy management strategies. Data were collected from 67 contractors in the Gaza Strip. Factor analysis was adopted to explore the underlying relationships among the identified drivers.

Findings

Drivers were grouped into one of the four categories: economic and financial, institutional and legal, organisational and managerial and educational and informational. The results revealed that the majority of the respondents were of the view that economic and financial factors were the most important factors driving the adoption of energy management strategies by construction companies in the Gaza Strip. Of the economic and financial drivers, the cost savings derived from the adoption of energy management strategies was considered the most important item. Energy management education and training programmes are scarce in the Gaza Strip, and local contractors have no formal energy management education and training. The government needs to allocate sufficient funds for policy implementation and regulation enforcement.

Research limitations/implications

Difficulties in accessing energy management data are deemed as a limitation to this study, as the topic of energy management in the construction has received no or very little academic attention so far.

Practical implications

This study provides a valuable reference for studying ongoing research in the practice of energy management development in other industries and locations. The priority of the drivers for energy management will help the local contracting companies to focus on weak and strong points of the company for energy use development to remove these weak points and invest in strong points. This paper results can increase the encouragement for greater social responsibility of the contracting organisations towards energy use. Government and concerned organisations can get benefits from the identified factors in encouraging contractors to adopt energy management strategy in their projects.

Originality/value

This study is the first investigation of energy management aspects in a local construction industry, especially from contracting organisations.