bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the understanding of cytoneme-mediated morphogen gradients byin silicomodeling
Authors: Aguirre-Tamaral Adrián , Guerrero Isabel
Published: April 2021

Morphogen gradients are crucial for the development of organisms. The biochemical properties of many morphogens prevent their extracellular free diffusion, indicating the need of an active mechanism for transport. The involvement of filopodial structures (cytonemes) has been proposed for morphogen signaling. Here, we describe anin silicomodel based on the main general features of cytoneme-meditated gradient formation and its implementation into Cytomorph, an open software tool. We have tested the spatial and temporal adaptability of our model quantifying Hedgehog (Hh) gradient formation in twoDrosophilatissues. Cytomorph is able to reproduce the gradient and explain the different scaling between the two epithelia. After experimental validation, we studied the predicted impact of a range of features such as length, size, density, dynamics and contact behavior of cytonemes on Hh morphogen distribution. Our results illustrate Cytomorph as an adaptive tool to test different morphogens gradients and to generate hypotheses that are difficult to study experimentally.
Affordable and Effective Optokinetic Response Methods to Assess Visual Acuity and Contrast Sensitivity in Larval to Juvenile Zebrafish
Authors: Sánchez Alicia Gómez , Álvarez Yolanda , Colligris Basilio , Kennedy Breandán N.
Published: April 2021

Background

The optokinetic response (OKR) is an effective behavioural assay to investigate functional vision in zebrafish. The rapid and widespread use of gene editing, drug screening and environmental modulation technologies have resulted in a broader need for visual neuroscience researchers to access affordable and more sensitive OKR, contrast sensitivity (CS) and visual acuity (VA) assays. Here, we demonstrate how 2D- and 3D-printed, striped patterns or drums coupled with a motorised base and microscope provide a simple, cost-effective but efficient means to assay OKR, CS and VA in larval-juvenile zebrafish.

Results

In wild-type, 5 days post-fertilisation (dpf) zebrafish, the 2D or 3D drums printed with the standard OKR stimulus of 0.02 cycles per degree (cpd), 100% black-white contrast evoked equivalent responses of 24.2 or 21.8 saccades per minute, respectively. Furthermore, although the OKR number was significantly reduced compared to the 0.02 cpd drum (p<0.0001), the 2D and 3D drums evoked respectively equivalent responses with the 0.06 and 0.2 cpd drums. Notably, standard OKR responses varied with time of day; peak responses of 29.8 saccades per minute occurred in the early afternoon with significantly reduced responses occurring in the early morning or late afternoon, (18.5 and 18.4 saccades per minute, respectively). A customised series of 2D printed drums enabled analysis of visual acuity and contrast sensitivity in 5-21 dpf zebrafish. The saccadic frequency in visual acuity and contrast sensitivity assays, was inversely proportional to age, spatial frequency and contrast of the stimulus.

Conclusions

OKR, VA and CS of zebrafish larvae can be efficiently measured using 2D- or 3D-printed striped drums. For data consistency the luminance of the OKR light source, the time of day when the analysis performed, and the order of presentation of VA and CS drums must be considered. These simple methods allow effective and more sensitive analysis of functional vision in zebrafish.
RIF1 acts in DNA repair through phosphopeptide recognition of 53BP1
Authors: Setiaputra Dheva , Escribano-Diaz Cristina , Reinert Julia K. , Sadana Pooja , Zong Dali , Callen Elsa , Seebacher Jan , Nussenzweig Andre , Thomä Nicolas H. , Durocher Daniel
Published: April 2021

The chromatin-binding protein 53BP1 promotes DNA repair by orchestrating the recruitment of downstream effectors including PTIP, RIF1 and shieldin to DNA double-strand break sites. While how PTIP recognizes 53BP1 is known, the molecular details of RIF1 recruitment to DNA damage sites remains undefined. Here, we report that RIF1 is a phosphopeptide-binding protein that directly interacts with three phosphorylated 53BP1 epitopes. The RIF1-binding sites on 53BP1 share an essential LxL motif followed by two closely apposed phosphorylated residues. Simultaneous mutation of these sites on 53BP1 abrogates RIF1 accumulation into ionizing radiation-induced foci, but surprisingly only fully compromises 53BP1-dependent DNA repair when an alternative mode of shieldin recruitment to DNA damage sites is also disabled. Intriguingly, this alternative mode of recruitment still depends on RIF1 but does not require its interaction with 53BP1. RIF1 therefore employs phosphopeptide recognition to promote DNA repair but also modifies shieldin action independently of 53BP1 binding.
Refining the genomic location of SNP variation affecting Atlantic salmon maturation timing at a key large-effect locus
Authors: Sinclair-Waters Marion , Piavchenko Nikolai , Ruokolainen Annukka , Aykanat Tutku , Erkinaro Jaakko , Primmer Craig R.
Published: April 2021

Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes,vgll3andakap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, and thus enabling delineation of the influence of variation at these two genes on maturation timing. By rearing 5895 males to maturation age, of which 81% had recombinantvgll3/akap11allelic combinations, we found thatvgll3SNP variation was strongly associated with maturation timing, whereas there was little or no association betweenakap11SNP variation and maturation timing. These findings provide strong evidence supportingvgll3as the primary candidate gene in the chromosome 25 locus for influencing maturation timing. This will help guide future research for understanding the genetic processes controlling maturation timing. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.
The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis
Authors: Johnson Alexander , Dahhan Dana A , Gnyliukh Nataliia , Kaufmann Walter A , Zheden Vanessa , Costanzo Tommaso , Mahou Pierre , Hrtyan Mónika , Wang Jie , Aguilera-Servin Juan , van Damme Daniël , Beaurepaire Emmanuel , Loose Martin , Bednarek Sebastian Y , Friml Jiri
Published: April 2021

Clathrin-mediated endocytosis in plants is an essential process but the underlying mechanisms are poorly understood, not least because of the extreme intracellular turgor pressure acting against the formation of endocytic vesicles. In contrast to other models, plant endocytosis is independent of actin, indicating a mechanistically distinct solution. Here, by using biochemical and advanced microscopy approaches, we show that the plant-specific TPLATE complex acts outside of endocytic vesicles as a mediator of membrane bending. Cells with disrupted TPLATE fail to generate spherical vesicles, andin vitrobiophysical assays identified protein domains with membrane bending capability. These results redefine the role of the TPLATE complex as a key component of the evolutionarily distinct mechanism mediating membrane bending against high turgor pressure to drive endocytosis in plant cells.

One Sentence Summary

While plant CME is actin independent, we identify that the evolutionarily ancient octameric TPLATE complex mediates membrane bending against high turgor pressure in plant clathrin-mediated endocytosis.
Bacteroidalesspecies are a reservoir of phase-variable antibiotic resistance genes in the human gut microbiome
Authors: Yan Wei , Hall A. Brantley , Jiang Xiangfang
Published: April 2021

Phase-variable antibiotic resistance genes (ARGs) can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of phase-variable ARGs remains poorly understood. Here, we sought to assess the threat posed by phase-variable ARGs by systematically searching for phase-variable ARGs in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified phase-variable ARGs and categorized them into three classes based on the invertase regulating phase variation. In the human gut microbiome, phase-variable ARGs are commonly and exclusively distributed inBacteroidalesspecies. Through genomic analysis, we observed that phase-variable ARGs have convergently originated from ARG insertions into phase-variable capsule polysaccharide biosynthesis (CPS) loci at least three times. Moreover, all identified phase-variable ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of phase-variable ARGs. Overall, these findings reveal that phase-variable CPS loci inBacteroidalesspecies are an important hotspot for the emergence of clinically-relevant phase-variable ARGs.
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores
Authors: Fan Rui , Cui Qinghua
Published: April 2021

Gene functional enrichment analysis represents one of the most popular bioinformatics methods for annotating the pathways and function categories of a given gene list. Current algorithms for enrichment computation such as Fisher’s exact test and hypergeometric test totally depend on the category count numbers of the gene list and one gene set. In this case, whatever the genes are, they were treated equally. However, actually genes show different scores in their essentiality in a gene list and in a gene set. It is thus hypothesized that the essentiality scores could be important and should be considered in gene functional analysis. For this purpose, here we proposed WEAT (https://www.cuilab.cn/weat/), a weighted gene set enrichment algorithm and online tool by weighting genes using essentiality scores. We confirmed the usefulness of WEAT using two case studies, the functional analysis of one aging-related gene list and one gene list involved in Lung Squamous Cell Carcinoma (LUSC). Finally, we believe that the WEAT method and tool could provide more possibilities for further exploring the functions of given gene lists.
Autophagy modulation enhances enzyme replacement therapy response in Fabry disease
Authors: Abily-Donval Lénaig , Barbey Frédéric , Torre Stéphanie , Lesueur Céline , Chevrier Marc , Pereira Tony , Pilon Carine , Marret Stéphane , Tebani Abdellah , Bekri Soumeya
Published: April 2021

Fabry disease is a lysosomal disease due to α-galactosidase A (a-GalA) deficiency. Since 2001, Enzyme replacement therapy (ERT) has been used as specific treatment of Fabry disease, with variable effects depending on patient gender and affected organs. In Fabry cells, the endososomal/lysosomal system is highly altered. Consequently, the exogenous enzyme may be mistargeted and trapped into intracellular vesicles instead of reaching the lysosomes. In this study, we aimed to investigate the mechanisms underlying the processing of the exogenous enzyme. We used Fabry cells (cultured fibroblasts and podocyte cell line) to study the enzyme internalization and its effects on the catabolism of the main a-Gal A substrate, globotriaosylceramide (Gb3), upon autophagy inhibition. The exogenous enzyme reaches the early endosome in a similar timeframe in Fabry and control cells, while its targeting to lysosomes is delayed in Fabry cells. Gb3 concentration is lowered upon therapeutic enzyme addition or wortmannin treatment with a synergetic effect. These findings illustrate the positive impact of autophagy inhibition on enzyme trafficking and processing, allowing the increase of functional enzyme rate within the lysosome. Given the high cost of ERT, a better understanding of the cellular fate of the exogenous enzyme may lead to improve its targeting to the lysosome.
Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms
Authors: Croxford Matthew , Elbaum Michael , Arigovindan Muthuvel , Kam Zvi , Agard David , Villa Elizabeth , Sedat John
Published: April 2021

Cryo-electron tomography (cryo-ET) allows for the high resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy regularized deconvolution (ER DC) to cryo-electron tomography data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied DC to severalin situcryo-ET data sets, and assess the results by Fourier analysis and subtomogram analysis (STA).
Interferon-γ-producing CD4+T cells drive monocyte activation in the bone marrow during experimentalLeishmania donovaniinfection
Authors: Romano Audrey , Brown Najmeeyah , Ashwin Helen , Doehl Johannes S.P. , Hamp Jonathan , Osman Mohamed , Dey Nidhi , Rani Gulab Fatima , Ferreira Tiago Rodrigues , Kaye Paul M.
Published: April 2021

Ly6Chiinflammatory monocytes develop in the bone marrow and migrate to the site of infection during inflammation. Upon recruitment, Ly6Chimonocytes can differentiate into dendritic cells or macrophages. According to the tissue environment they can also acquire different functions. Several studies have described pre-activation of Ly6Chimonocytes in the bone marrow during parasitic infection, but whether this process occurs during experimental visceral leishmaniasis and, if so, the mechanisms contributing to their activation are yet to be established. In wild type C57BL/6 (B6) mice infected withLeishmania donovani, the number of bone marrow Ly6Chimonocytes increased over time. Ly6Chimonocytes displayed a highly activated phenotype from 28 days to 5 months post infection (p.i), with >90% expressing MHCII and >20% expressing iNOS. In comparison, in B6.Rag2-/-mice <10% of bone marrow monocytes were MHCII+at day 28 p.i., an activation deficiency that was reversed by adoptive transfer of CD4+T cells. Depletion of CD4+T cells in B6 mice and the use of mixed bone marrow chimeras further indicated that monocyte activation was driven by IFN-γ produced by CD4+T cells. In B6.Il10-/-mice,L. donovaniinfection induced a faster but transient activation of bone marrow monocytes, which correlated with the magnitude of CD4+T cell production of IFN-γ and resolution of the infection. Under all of the above conditions, monocyte activation was associated with greater control of parasite load in the bone marrow. Through reinfection studies in B6.Il10-/-mice and drug (AmBisome) treatment of B6 mice, we also show the dependence of monocyte activation on parasite load. In summary, these data demonstrate that duringL. donovaniinfection, Ly6Chimonocytes are primed in the bone marrow in a process driven by CD4+T cells and whereby IFN-γ promotes and IL-10 limits monocyte activation and that the presence of parasites/parasite antigen plays a crucial role in maintaining bone marrow monocyte activation.
Neuronal Dystroglycan regulates postnatal development of CCK/cannabinoid receptor-1 interneurons
Authors: Miller Daniel S. , Wright Kevin M.
Published: April 2021

The development of functional neural circuits requires the precise formation of synaptic connections between diverse neuronal populations. The molecular pathways that allow GABAergic interneuron subtypes in the mammalian brain to recognize their postsynaptic partners remain largely unknown. The transmembrane glycoprotein Dystroglycan is localized to inhibitory synapses in pyramidal neurons, where it is required for the proper function of CCK+ interneurons. We show that deletion ofDystroglycanfrom pyramidal neurons selectively impairs CCK+ interneuron development during the first postnatal week. In the absence of postsynapticDystroglycan, presynaptic CCK+ interneurons fail to elaborate their axons and largely disappear from the cortex, hippocampus, amygdala, and olfactory bulb.Baxdeletion did not rescue CCK+ interneurons, suggesting that they are not eliminated by canonical apoptosis inDystroglycanmutants. Rather, we observed an increase in CCK+ interneuron innervation of the striatum, suggesting that the remaining CCK+ interneurons re-directed their axons to neighboring areas where Dystroglycan expression remained intact. Together these findings identify Dystroglycan as a critical regulator of CCK+ interneuron development.
Methylotroph Natural Product Identification by Inverse Stable Isotopic Labeling
Authors: Cummings Dale A. , Snelling Alice I. , Puri Aaron W.
Published: April 2021

Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically-enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a13C-carbon source and then identifying12C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate this method identifiesN-acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously identify five uncharacterized signals produced by a methylotroph, and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive13C-carbon sources.
Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
Authors: Shapiro Jason W. , Putonti Catherine
Published: April 2021

Background

A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools.

Methods

We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: 1) indels creating early stop codons and new start codons; 2) interruption by a selfish genetic element; and 3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees.

Results

We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g. T4), the Studiervirinae (e.g. T7), and the Pbunaviruses (e.g. PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single script for automated analysis and with utility functions and a walkthrough for researchers with specific use cases for each type of correction.
Particle Dynamics and Bioaerosol Viability of Aerosolized BCG Vaccine Using Jet and Vibrating Mesh Clinical Nebulizers
Authors: Redmann Rachel K. , Kaushal Deepak , Golden Nadia , Threeton Breeana , Killeen Stephanie Z. , Kuehl Philip J. , Roy Chad J.
Published: April 2021

Background

Bacillus Calmette–Guérin (BCG) is a vaccine used to protect against tuberculosis primarily in infants to stop early infection in areas of the world where the disease is endemic. Normally administered as a percutaneous injection, BCG is a live, significantly attenuated bacteria that is now being investigated for its potential within an inhalable vaccine formulation. This work investigates the feasibility and performance of four jet and ultrasonic nebulizers aerosolizing BCG and the resulting particle characteristics and residual viability of the bacteria post-aerosolization.

Methods

A jet nebulizer (Collison) outfitted either with a 3- or 6-jet head, was compared to two clinical nebulizers, the vibrating mesh Omron MicroAir and Aerogen Solo devices. Particle characteristics, including aerodynamic particle sizing, was performed on all devices within a common aerosol chamber configuration and comparable BCG innocula concentrations. Integrated aerosol samples were collected for each generator and assayed for bacterial viability using conventional microbiological technique.

Results and Conclusions

A batch lot of BCG (Danish) was grown to titer and used in all generator assessments. Aerosol particles within the respirable range were generated from all nebulizers at four different concentrations of BCG. The jet nebulizers produced a uniformly smaller particle size than the ultrasonic devices, although particle concentrations by mass were similar across all devices tested with the exception of the Aerogen Solo, which resulted in a very low concentration of BCG aerosols. The resulting measured viable BCG aerosol concentration fraction produced by each device approximated one another; however, a measurable decrease of efficiency and overall viability reduction in the jet nebulizer was observed in higher BCG inoculum starting concentrations, whereas the vibrating mesh nebulizer returned a remarkably stable viable aerosol fraction irrespective of inoculum concentration.
Redundancy between spectral and higher-order texture statistics for natural image segmentation
Authors: Herrera-Esposito Daniel , Gómez-Sena Leonel , Coen-Cagli Ruben
Published: April 2021

Visual texture, defined by local image statistics, provides important information to the human visual system for perceptual segmentation. Second-order or spectral statistics (equivalent to the Fourier power spectrum) are a well-studied segmentation cue. However, the role of higher-order statistics (HOS) in segmentation remains unclear, particularly for natural images. Recent experiments indicate that, in peripheral vision, the HOS of the widely adopted Portilla-Simoncelli texture model are a weak segmentation cue compared to spectral statistics, despite the fact that both are necessary to explain other perceptual phenomena and to support high-quality texture synthesis. Here we test whether this discrepancy reflects a property of natural image statistics. First, we observe that differences in spectral statistics across segments of natural images are redundant with differences in HOS. Second, using linear and nonlinear classifiers, we show that each set of statistics individually affords high performance in natural scenes and texture segmentation tasks, but combining spectral statistics and HOS produces relatively small improvements. Third, we find that HOS improve segmentation for a subset of images, although these images are difficult to identify. We also find that different subsets of HOS improve segmentation to a different extent, in agreement with previous physiological and perceptual work. These results show that the HOS add modestly to spectral statistics for natural image segmentation. We speculate that tuning to natural image statistics under resource constraints could explain the weak contribution of HOS to perceptual segmentation in human peripheral vision.
A Gene Encoding an Architectural RNA,hsrω, is a Host Genetic Modifier of Cancer Progression inDrosophila
Authors: Bajpai Anjali , Kundu Sushmita , Pandey Ravi Kant , Ateeq Bushra , Lakhotia Subhash C. , Sinha Pradip
Published: April 2021

Genetic variations among individuals within a population, or host genetics, determine disease susceptibility or resistance. Here we show that heterozygosity ofhsrω, a gene coding for a long noncoding architectural RNA (arcRNA), displays cancer susceptibility inDrosophila.Imaginal epithelia mutant for a null allele ofhsrω, hsrω66exhibits chronic stress, marked by loss of growth and proteostasis, besides cell death. Imaginal epithelia of larvae heterozygous forhsrω66also show cellular stress, but conditionally: for instance, upon heat shock. Somatic clones displaying loss of Lgl tumor suppressor in such stress-sensitive imaginal epithelia ofhsrω66heterozygotes develop into metastatic tumors, unlike those induced in wild type epithelia wherein these are eliminated by intrinsic tumor suppression. Further, cell-autonomous gain or loss ofhsrωinlglmutant clones, too, results in their tumor progression. Finally, we note a transcriptional increase in human sat III arcRNA, a functional analog ofDrosophila hsrω,in cancer cell lines. Loss of sat III decreases the viability of cancer cells under stress. Our findings suggest pervasive roles of arcRNA-coding genes as host genetic modifiers of cancer via their regulation of cell homeostasis.

Summary statement

Heterozygosity forhsrω,a gene coding for a long noncoding architectural RNA inDrosophila,induces hypersensitivity to physiological stress and promotes cancer progression in oncogenically targeted cells.
Iota-carrageenan prevents the replication of SARS-CoV-2 on an in vitro respiratory epithelium model
Authors: Varese Augusto , Ceballos Ana , Palacios Carlos , Figueroa Juan Manuel , Dugour Andrea Vanesa
Published: April 2021

There are, except for remdesivir, no approved antivirals for the treatment or prevention of SARS-CoV-2 infections. Iota-carrageenan formulated into a nasal spray has already been proven safe and effective in viral respiratory infections. We explored this antiviral activity in Calu-3, a human respiratory model cell line. A formula of iota-carrageenan and sodium chloride, as a nasal spray, already approved for human use, effectively inhibited SARS-CoV-2 infection in vitro, providing a more substantial reference for further clinical studies or developments.
Detailed total scattering analysis of disorder in ZIF-8
Authors: Metz Peter C. , Purdy Stephen C. , Ryder Matthew R. , Ganesan Arvind , Nair Sankar , Page Katharine
Published: April 2021

This work investigates the X-ray scattering signatures of disorder in the zeolitic imidazolate framework ZIF-8. Two layer disorder models are examined in reciprocal space and compared with conventional Rietveld analysis. Stacking faults along the [001] direction of the cubic lattice are in poor agreement with experimental powder diffraction data, consistent with previously reported density functional theory studies showing that these defects are energetically unfavorable compared with amorphization. Meanwhile, fluctuation of layer position along the [110] direction of the cubic lattice shows a significant agreement with experimental data. This result is interpreted analogously to an anisotropic strain mechanism, suggesting links between elastic anisotropy and crystallographic imperfections found in metal–organic framework materials. In direct space, it is demonstrated that models accounting for the static position disorder amongst the linker and metal sublattices are required to fit the experimental pair distribution function data.
Synchrotron radiation and X-ray free-electron lasers (X-FELs) explained to all users, active and potential
Authors: Hwu Yeukuang , Margaritondo Giorgio
Published: April 2021

Synchrotron radiation evolved over one-half century into a gigantic worldwide enterprise involving tens of thousands of researchers. Initially, almost all users were physicists. But now they belong to a variety of disciplines: chemistry, materials science, the life sciences, medical research, ecology, cultural heritage and others. This poses a challenge: explaining synchrotron sources without requiring a sophisticated background in theoretical physics. Here this challenge is met with an innovative approach that only involves elementary notions, commonly possessed by scientists of all domains.
Determinants of food safety behaviour among food vendors: the case of Nigeria
Authors: Madaki Mustapha Yakubu , Miroslava Bavorova
Published: April 2021

Purpose

To investigate the relationship between food safety knowledge, food safety attitudes, the accessibility of sanitation facilities, perceived economic and social constraints and food safety practices among food vendors of higher institutions of learning in Bauchi State, Nigeria.

Design/methodology/approach

A purposive sampling method was used to select 6 out of 13 public higher institutions of learning in the state and a random sampling method was used in selecting 181 food vendors from the list of 342 food vendors in the 6 institutions. Face-to-face survey interviews were carried out between June–September 2018 completing a structured questionnaire.

Findings

The result of the structural equation model revealed that food safety knowledge, food safety attitudes and economic and social control affected the food safety behaviour of the food vendors. Inaccessibility to sanitation facilities affected food safety behaviour negatively.

Practical implications

Appropriate measures to improve the food safety behaviour of food vendors in higher institutions of learning could include, for example, food safety training that could increase food safety knowledge and awareness, as well as improved access to sanitation facilities at vending sites.

Originality/value

There is no previous study that investigates the relationship between food safety knowledge, food safety attitudes, social and economic constraints, access to sanitation facilities and the food safety behaviour of food vendors in higher educational institutions in Nigeria.
Exploring the role of transaction costs in the intensity of organic food consumption in Brazil
Authors: Cechin Andrei , Medaets Jean Pierre Passos , Fornazier Armando , Zoghbi Ana Carolina Pereira
Published: April 2021

Purpose

Organic food has additional quality attributes compared to those found in conventional food, such as environmental responsibility and health benefits. Information about these attributes is scarce and complex, the assortment of organic foods is deficient and there are fewer places that sell this kind of food. These factors increase the uncertainty and the transaction costs (TCs) for potential organic fresh fruit and vegetable (FFV) consumers. This paper aims to show the influence of these costs on the intensity of organic FFV consumption, particularly among high-income consumers.

Design/methodology/approach

The empirical strategy was based on a survey, and data were collected by administering a structured online questionnaire among residents of the Brazilian Federal District. Organic food consumption was decomposed into three different intensity categories. Data analysis was based on two logistic models, a multinomial regression and an ordered regression, where perceived economic value and different dimensions of TCs were the main independent variables, and the intensity of organic food consumption was the dependent variable.

Findings

The results show that organic food consumers are not a homogeneous group, and that perceived economic value and the TCs associated with searching for marketplaces, inadequate product assortment and distrust in health benefits and in organic authenticity are important inhibitors of organic FFV consumption and help explain the intensity of consumption.

Originality/value

This study innovates, as it takes a post-purchase approach, examines different groups based on the intensity of their consumption of organic FFV and focuses on perceived economic value and TCs as important explanations of the intensity of organic FFV consumption.
Eating habits and consumer food shopping behaviour during COVID-19 virus pandemic: insights from Serbia
Authors: Marinković Veljko , Lazarević Jovana
Published: April 2021

Purpose

The COVID-19 virus pandemic has strongly influenced consumer behaviour worldwide. This paper aims to investigate how risk perceptions and precautions related to COVID-19 virus influence consumer eating habits and consequently, behaviour during shopping for food. Also, research tends to identify changes in consumer eating habits resulting from the current pandemic situation.

Design/methodology/approach

In total, 237 consumers from Serbia were online surveyed during November 2020. Starting from the methodology of the SOR model (Mehrabian and Russell, 1974), the questionnaire consists of seven-point Likert scale statements that measure risk perceptions and precautions as stimulus (S), eating habits as an organism (O) and food choice, precautions during shopping for food and food purchasing patterns as a response (S).

Findings

Research results confirm the difference in consumers' eating habits during and before a pandemic. Also, results indicate that perceived risk and precautions related to the COVID-19 virus have a statistically significant influence on consumers' eating habits which have changed during a pandemic, finally resulting in significant effects on consumers' food shopping behaviour.

Research limitations/implications

The main limitations of this study are observing only a few aspects related to COVID-19 virus pandemic and consumer food shopping behaviour, as well as measuring precautions, perceived risk and food shopping behaviour at one point in time besides the fact that pandemic situation constantly changes.

Originality/value

The study indicates that food manufacturers should pay attention to the consumers' eating habits and food shopping behaviour changes under the circumstances of COVID-19 virus pandemic. Identified changes can be used as opportunities to gain a competitive advantage on the market.
Drivers and barriers in the consumption of alternative staples. A systematic literature review and future research agenda
Authors: Shah Priya , Dhir Amandeep , Joshi Rohit , Tripathy Naliniprava
Published: April 2021

Purpose

Major cereal staples such as wheat, white rice and corn have a significant negative impact on the environment, a low nutritional profile and are associated with obesity. In comparison, alternative staples (such as rye, quinoa, buckwheat, etc.) are more environmentally sustainable and nutritious, yet are underused. There has been a recent surge in research into and awareness of alternative staples, but the current understanding of the different drivers of and barriers to their consumption remains fragmented.

Design/methodology/approach

The present study attempts to assimilate and incorporate the current knowledge on the drivers of and barriers to the consumption of alternative staples. Eighty-one empirical studies were curated and analysed according to stringent protocols in order to examine the existing research profile and themes arising from prior research in this domain.

Findings

The study presents a profile of the extensive existing literature examining the drivers of and barriers to the consumption of alternative staples. The thematic analysis of selected studies resulted in the identification of six drivers and seven barriers. The drivers are an awareness of health; awareness of environmental factors; recommendations; awareness of the brand, labels and source of origin; household structure and demographic attributes. The barriers are difficulty in preparation, lack of familiarity, lack of availability, lack of affordability, culture, product attributes and sensory attributes. The various research gaps and avenues for future research associated with the drivers and barriers identified are also presented.

Originality/value

The key outcomes of the study are the presentation of the research profile, the identification of various drivers and barriers, the recognition of gaps in the research and avenues for future research and, finally, the development of a theoretical framework entitled “Behavioral reasoning towards the consumption of alternative staples (BRCAS)”. The study offers various insights for nutritionists, marketers, policymakers and consumers by increasing awareness of alternative staples.
Farmland transfer and agricultural economic growth nexus in China: agricultural TFP intermediary effect perspective
Authors: Kuang Yuan-pei , Yang Jia-li , Abate Meseret-Chanie
Published: April 2021

Purpose

The multidimensional effects of farmland transfer in China have been profoundly unstudied. The purpose of this paper is to provide insights on the effects of the intermediary role of agricultural total factor productivity (TFP) of farmland transfer on agricultural economic growth in China.

Design/methodology/approach

Based on the agricultural data of 30 provinces in China over the period 2005–2018, this paper uses the intermediary effect model to test the relationship between farmland transfer, agricultural TFP and agricultural economic growth. This paper employed an intermediary effect test model to investigate the intermediary role of agricultural TFP in the influence of farmland transfer on agricultural economic growth.

Findings

The findings indicated that farmland transfer has a significant effect on promoting agricultural economic growth. There is a significant “inverted U-shaped” relationship between farmland transfer and agricultural TFP. The sample value of 84.3% of farmland transfers in China is still within the TFP promoting effect range. In addition, farmland transfer has an indirect impact on agricultural economic growth through the channel of agricultural TFP. Agricultural TFP plays a significant intermediary role, but the effect is relatively low

Originality/value

This paper is the first to provide fundamental evidence on the impact of farmland transfers on agricultural economic growth in China, driven by agricultural TFP as an intermediary factor. Agricultural TFP can reduce the involution effect of farmland transfer and promote an indirect effect on agricultural economic growth.
A community of practice for graduate students in health sciences
Authors: Wazni Liquaa , Gifford Wendy , Cantin Christina , Davies Barbara
Published: April 2021

Purpose

The aim of this study was to describe the experiences of graduate students who participated in the community of practice (CoP) and identify areas for improvement to support academic success.

Design/methodology/approach

In total, 19 graduate students engaged in a CoP to facilitate social interactions, knowledge sharing and learning within a culture of scholarship. A descriptive qualitative research study was conducted using semistructured interviews with eight participants who had attended the CoP meeting.

Findings

All participants were from the School of Nursing and perceived the CoP to be beneficial, particularly international students who had challenges in adapting to new academic and social environments. Areas for improvement include creating a group structure that enhances belonging and learning.

Originality/value

This is the first CoP that was implemented at the Faculty of Health Sciences at the authors’ university. It has been the authors’ experience that a CoP can benefit graduate students through networking, knowledge sharing, social support and learning. The finding of this research will be used to inform a new CoP to address the needs of graduate students. The authors will be adapting the CoP to the current context that includes a virtual platform during the COVID-19 pandemic and will include content specific for international students.
Exploring the affect heuristic in Iranian women entrepreneurs
Authors: Nouri Pouria
Published: April 2021

Purpose

Heuristics are fundamental components of the bounded rationality paradigm and influence entrepreneurs' decisions profusely. On the other hand, the affect heuristic is one of the most important heuristics. The body of knowledge on entrepreneurial heuristics is scattered on the whole and very superficial concerning women entrepreneurs, given that most studies have considered women and men entrepreneurs similar in showing heuristics. The dearth of research is more evident in the context of developing countries. Thus, to fill part of the existing research gaps, this study explores the affect heuristic in Iranian women entrepreneurs.

Design/methodology/approach

This paper's data were gathered by conducting face-to-face interviews with 17 novice Iranian women entrepreneurs active in biotechnology, nanotechnology, advanced medicine, aerospace, textile and food sectors and analyzed through a thematic–narrative analysis.

Findings

According to the results, the main outcomes of the affect heuristic in Iranian women entrepreneurs are delaying the final decision (including an obsession with collecting too much information, overemphasizing the role of negative information and seeking external advice before making a decision), rash decisions (including evaluations based on satisfying decision strategies, too much enthusiasm about one's venture, as well as an optimistic assessment of different scenarios) and serious consideration of quitting (including too much disappointment and anger over discrimination).

Practical implications

Based on this paper's findings, novice women entrepreneurs should be heedful of their fear, which could not only delay their decisions but also paralyze their capability of decision-making. Furthermore, while under circumstances such as information overload and uncertainty, positive feelings like optimism and happiness could be very instrumental by enabling entrepreneurs to shorten the process of their decisions, women entrepreneurs should be very careful about the possible biases resulting from their positive affect.

Originality/value

This study is a pioneer in two respects. First, it explores women entrepreneurs' decision-making heuristics, which is often a neglected area of research. Second, coming to the conclusion that most of the research on women entrepreneurs has been conducted in the Western context, this paper focuses on the context of developing countries by targeting Iranian women entrepreneurs.
The impact modeling of project management function behaviors on construction labor productivity
Authors: Nguyen Luong Hai
Published: April 2021

Purpose

Construction labor productivity (LP) is the key element in forming the success of construction projects. Numerous studies on the topic of critical success factors (CSFs) within construction LP have been conducted, but the results have rarely emphasized developing factors related to managerial function behaviors (MFBs) and examining its relationship with construction LP, a key criterion for measuring construction effectiveness; these less researched topics were the aims of this study.

Design/methodology/approach

The empirical research studies were designed to develop managerial behavior's attributes based upon a literature adaptation and focus group studies (FGSs). Then, the causal relationships between MFBs and LP were examined by drawing on project-specific data collected from 195 completed construction projects in Vietnam, which was to the approach to an exploratory factor analysis (EFA) and Bayesian model averaging (BMA) technique.

Findings

The findings reveal that the MFBs' attributes were organized into a four-factor MFB framework: “cooperation emphasis (COOP),” “people orientation (PEOP),” “commitment emphasis (COMT)” and “leadership promotion (LEAD).” The findings reveal that COOP, PEOP and COMT have significant effects on LP.

Originality/value

The success of this approach is expected to broaden academic's horizons of factors affected LP and suggest a useful tool for supporting the project management professionals in enhancing construction LP and sustainability.
Leverage risks for supply chain robustness against corruption
Authors: Liu Xiaojing , Arthanari Tiru , Shi Yangyan
Published: April 2021

Purpose

This paper examines the establishment of supply chain robustness against corruption by utilizing risk interactions.

Design/methodology/approach

Based on empirical results from the New Zealand dairy industry, a system dynamics model is established to explore the underlying relationships among variables.

Findings

The results show that although certain supply chain risks seem unrelated to corruption, their mitigation would help mitigate the impact of corruption due to risk interactions; and mitigation of some of the risks is more effective in mitigating the impact of corruption. Leverage risks have been defined and identified in this research, which expands the extant knowledge in reducing the impact of corruption on supply chains.

Originality/value

The research illustrates how the impact of corruption can be studied in an integrated way with dairy supply chain SD analysis. It is a pioneering study to mitigate the impact of corruption on supply chains from supply chain robustness.
Food contamination, food safety and COVID-19 outbreak
Authors: Sim Saitin , Wiwanitkit Viroj
Published: April 2021

Purpose

COVID-19) is the present global problem. The potential for food borne transmission of COVID-19 becomes a present discussed public health issue. At present, there are many reports on the food contamination with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is no doubt that the viral contamination in food is possible. The authors summarize and discuss on food contamination, food safety and COVID-19 outbreak.

Design/methodology/approach

The authors give a commentary on the available data on food contamination during COVID-19 outbreak. Based on basic food safety principles, the authors build an argument on available recommendation regarding food safety during the COVID-19 outbreak.

Findings

It still lacks in many details of food safety during COVID-19 pandemic. Public health personnel usually refer to classical food safety principles for recommending general people about food safety, but it still lacks for updated specific data on COVID-19. The present commentary gives some few ideas and it is necessary to have further specific research on this specific issue.

Originality/value

This is an original commentary regarding the new contemporary problem on food contamination, food safety and COVID-19 outbreak.