bluuebunny/crossref_metadata_2025 huggingface dataset:
Pronounced Genetic Separation Among Varieties of thePrimula cusickianaSpecies Complex, a Great Basin Endemic
Authors: Koontz Austin , Pearse William D. , Wolf Paul
Published: March 2021

Distinguishing between unique species and populations with strong genetic structure is a common challenge in population genetics, especially in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the relations between species complex members, and RADseq methods are commonly used to compare closely related species across thousands of genetic loci. Here we use RADseq to clarify the relations between geographically distinct but morphologically similar varieties of thePrimula cusickianaspecies complex, and to contextualize past findings of strong genetic structure among populations within varieties. Our genomic analyses demonstrate pronounced separation between isolated populations of this Great Basin endemic, indicating that the current varietal classification of complex members is inaccurate and emphasizing their conservation importance. We discuss how these results correspond to recent biogeographical models used to describe the distribution of other sky island taxa in western North America. Our findings also fit into a wider trend observed for alpinePrimulaspecies complexes, and we consider how heterostylous breeding systems may be contributing to frequent diversification via allopatric speciation in this genus.
Loss-of-function variants in the cardiac Kv11.1 channel as a genetic biomarker for SUDEP
Authors: Soh Ming S. , Bagnall Richard D. , Bennett Mark F. , Bleakley Lauren E. , Syazwan Erlina S. Mohamed , Phillips A. Marie , Chiam Mathew D.F. , McKenzie Chaseley E. , Hildebrand Michael , Crompton Douglas , Bahlo Melanie , Semsarian Christopher , Scheffer Ingrid E. , Berkovic Samuel F. , Reid Christopher A.
Published: March 2021

Objective

To compare the frequency and impact on channel function ofKCNH2variants in SUDEP patients with epilepsy controls comprising patients older than 50 years, a group with low SUDEP risk, and establish loss-of-functionKCNH2variants as predictive biomarkers of SUDEP risk.

Methods

We searched forKCNH2variants with a minor allele frequency of < 5%. Functional analysis inXenopus laevisoocytes was performed for allKCNH2variants identified.

Results

KCNH2variants were found in 11.1% (10/90) of SUDEP individuals compared to 6.0% (20/332) of epilepsy controls (p= 0.11). Loss-of-functionKCNH2variants, defined as causing > 20% reduction in maximal amplitude, were observed in 8.9% (8/90) SUDEP patients compared to 3.3% (11/332) epilepsy controls suggesting about three-fold enrichment (nominalp= 0.04).KCNH2variants that did not change channel function occurred at a similar frequency in SUDEP (2.2%; 2/90) and epilepsy control (2.7%; 9/332) cohorts (p> 0.99). RareKCNH2variants (< 1% allele frequency) associated with greater loss of function and an ∼11-fold enrichment in the SUDEP cohort (nominalp= 0.03).In silicotools were unable to predict the impact of a variant on function highlighting the need for electrophysiological analysis.

Conclusions

These data show that loss-of-functionKCNH2variants are enriched in SUDEP patients and suggest that cardiac mechanisms contribute to SUDEP risk. We propose that genetic screening in combination with functional analysis can identify loss-of-functionKCNH2variants that could act as biomarkers of an individual’s SUDEP risk.
In-vivo protein nitration and de-nitration facilitateVibrio choleraecell survival under anaerobic condition: Consequences of Nitrite induced protein nitration
Authors: Patra Sourav Kumar , Sinha Nilanjan , Chakraborty Subhamoy , Sengupta Ayantika , Roy Souvik , Ghosh Sanjay
Published: March 2021

Protein tyrosine nitration (PTN), a highly selective post translational modification, occurs in both prokaryotic and eukaryotic cells under nitrosative stress1. It is reported that the activities of many proteins are altered due to PTN2. PTN is found to be associated with many pathophysiological conditions like neurodegenerative and cardiac diseases etc.3. However, its physiological function is not yet clear. Like all other gut pathogensVibrio choleraealso faces nitrosative stress in the gut environment which makes its proteome more vulnerable to PTN. Here, we report for the first time in-vivo PTN inV. cholerae. We show that in-vivo protein nitration is nitrite dependent and nitration-denitration phenomenon actually facilitatesV. choleraecell survival in anaerobic or hypoxic condition. In our study, we found that the extent of in-vivo nitration is negatively correlated with the intracellular nitrite content and maximum nitration occurs during log phase ofV. cholerae. Most interestingly, a significant denitration was associated with increase in intracellular nitrate content during anaerobic incubation of aerobically grown late log phase cultures. In-vivo nitration could provide an avenue for toxic nitrite storage and nitrosative stress tolerance mechanism in many gut pathogens, whereas denitration could supply nitrate for cell survival in anaerobic nitrate deficient environment.
Insecticide resistance characteristic ofAnophelesvector species successfully controlled by deployment of pyrethroid and PBO long lasting insecticidal treated nets in Tanzania
Authors: Matowo Johnson , Weetman David , Pignatell Patricia , Wright Alexandra , Charlwood Jacques D , Kaaya Robert , Shirima Boniface , Moshi Oliva , Lukole Eliud , Mosha Jacklin , Manjurano Alphaxard , Mosha Franklin , Rowland Mark , Protopopoff Natacha
Published: March 2021

Long lasting insecticidal nets (LLINs) are a proven tool to reduce malaria transmission, but in Africa efficacy is being reduced by pyrethroid resistance in the major vectors. A cluster randomized trial in Muleba district, Tanzania demonstrated that permethrin LLINs co-treated with piperonyl butoxide (PBO), a synergist that can block pyrethroid-metabolizing enzymes in the mosquito, had much greater efficacy than pyrethroid-only nets. Insecticide resistance profiles and underlying mechanisms were investigated inAnopheles gambiaeandAn. funestusfrom Muleba during the trial. Diagnostic dose bioassays using permethrin, together with intensity assays, suggest pyrethroid resistance that is both strong and very common, but not extreme. Transcriptomic analysis found multiple P450 genes over expressed including CYP6M2, CYP6Z3, CYP6P3, CYP6P4, CYP6AA1 and CYP9K1 inAn. gambiaeand CYP6N1, CYP6M7, CYP6M1 and CYP6Z3 inAn. funestus. Indeed, very similar suites of P450 enzymes commonly associated with resistant populations elsewhere in Africa were detected as over expressed suggesting a convergence of mechanisms across Sub-Saharan African malaria vectors. The findings give insight into factors that may correlate with pyrethroid PBO LLIN success, broadly supporting model predictions, but revision to guidelines previously issued by the World Health Organization is warranted.
scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation
Authors: Heinen T. , Secchia S. , Reddington J. , Zhao B. , Furlong E.E.M. , Stegle O.
Published: March 2021

While the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies, using bulk sequencing, ignore much of this heterogeneity, reducing discovery and explanatory power. Single-cell approaches combined with F1 genetic designs provide a new opportunity to address this problem, however suitable computational methods to model these complex relationships are lacking.

Here, we developed scDALI, an analysis framework that integrates single-cell chromatin accessibility for unbiased cell state identification with allelic quantifications to assay genetic effects. scDALI builds on Gaussian process regression and can differentiate between homogeneous (pervasive) allelic imbalances and cell state-specific regulation. As a proof-of-principle, we applied scDALI to wholeDrosophilaembryos from F1 crosses, profiling sciATAC-seq at three embryonic stages. Even in these very complex samples, scDALI discovered hundreds of peaks with heterogeneous allelic imbalance, having effects in specific lineages and/or developmental stages. Our study provides a general strategy to identify the cellular context of allelic imbalance, a crucial step in linking genetic traits to cellular phenotypes.
Abi3 regulates microglial ramification and dynamic tissue surveillancein vivo
Authors: Simonazzi Elena , Jones Ruth E. , Chen Fangli , Ranson Adam , Stevenson-Hoare Joshua , Escott-Price Valentina , Sengpiel Frank , Morgan B. Paul , Taylor Philip R.
Published: March 2021

A rare coding variant of Abelson-interactor gene family member 3 (Abi3) is associated with increased risk of late-onset Alzheimer’s Disease (AD). Although Abi3 is recognised as a core microglial gene, its role in microglia is largely unknown. Here we demonstrate that Abi3 is crucial for normal microglial morphology, distribution, and homeostatic tissue surveillance activityin vivo.
Blunted Fas signaling favors RIPK1-driven neutrophil necroptosis in critically ill COVID-19 patients
Authors: Schweizer Tiziano A. , Shambat Srikanth Mairpady , Vulin Clément , Hoeller Sylvia , Acevedo Claudio , Huemer Markus , Gomez-Mejia Alejandro , Chang Chun-Chi , Baum Jeruscha , Hertegonne Sanne , Hitz Eva , Hofmaenner Daniel A. , Buehler Philipp K. , Moch Holger , Schuepbach Reto A. , Brugger Silvio D. , Zinkernagel Annelies S.
Published: March 2021

Critically ill COVID-19 patients are characterized by a severely dysregulated cytokine profile and elevated neutrophil counts, which are thought to contribute to disease severity. However, to date it remains unclear how neutrophils contribute to pathophysiology during COVID-19. Here, we assessed the impact of the dysregulated cytokine profile on the tightly regulated cell death program of neutrophils. We show that in a subpopulation of neutrophils, canonical apoptosis was skewed towards rapidly occurring necroptosis. This phenotype was characterized by abrogated caspase-8 activity and increased RIPK1 levels, favoring execution of necroptosis via the RIPK1-RIPK3-MLKL axis, as further confirmed in COVID-19 biopsies. Moreover, reduction of sFas-L levels in COVID-19 patients and hence decreased signaling to Fas directly increased RIPK1 levels and correlated with disease severity. Our results suggest an important role for Fas signaling in the regulation of cell death program ambiguity via the ripoptosome in neutrophils during COVID-19 and a potential therapeutic target to curb inflammation and thus influence disease severity and outcome.
Anti-fibrotic activity of an antimicrobial peptide in aDrosophilamodel
Authors: Khalili Dilan , Kalcher Christina , Baumgartner Stefan , Theopold Ulrich
Published: March 2021

Fibrotic lesions accompany several pathological conditions including tumors. We show that expression of a dominant-active form of the Ras oncogene inDrosophilasalivary glands (SGs) leads to redistribution of components of the basement membrane (BM) and fibrotic lesions. Similar to several types of mammalian fibrosis, the disturbed BM attracts clot components including insect transglutaminase and phenoloxidase. SG epithelial cells show reduced apico-basal polarity accompanied by a loss of secretory activity. Both the fibrotic lesions and the reduced cell polarity are alleviated by ectopic expression of the antimicrobial peptide Drosomycin (Drs), which also restores secretory activity of the SGs. In addition to ECM components, both Drs and F-actin localize to fibrotic lesions.
Long-Term Imaging of Living Adult Zebrafish
Authors: Castranova Daniel , Samasa Bakary , Galanternik Marina Venero , Gore Aniket V. , Weinstein Brant M.
Published: March 2021

The zebrafish has become a widely used animal model due in large part to its accessibility to and usefulness for high-resolution optical imaging. Although zebrafish research has historically focused mostly on early development, in recent years the fish has increasingly been used to study regeneration, cancer metastasis, behavior, and other processes taking place in juvenile and adult animals. However, imaging of live adult zebrafish is extremely challenging, with survival of adult fish limited to a few tens of minutes using standard imaging methods developed for zebrafish embryos and larvae. Here, we describe a new method for imaging intubated adult zebrafish using a specially designed 3D printed chamber for long-term imaging of adult zebrafish on inverted microscope systems. We demonstrate the utility of this new system by nearly day-long observation of neutrophil recruitment to a wound area in living double-transgenic adult casper zebrafish with fluorescently labeled neutrophils and lymphatic vessels.
Influence of the TorD signal peptide chaperone on Tat-dependent protein translocation
Authors: Bageshwar Umesh K. , DattaGupta Antara , Musser Siegfried M.
Published: March 2021

The twin-arginine translocation (Tat) pathway transports folded proteins across energetic membranes. Numerous Tat substrates contain co-factors that are inserted before transport with the assistance of redox enzyme maturation proteins (REMPs), which bind to the signal peptide of precursor proteins. How signal peptides are transferred from a REMP to a binding site on the Tat receptor complex remains unknown. Since the signal peptide mediates both interactions, possibilities include: i) a coordinated hand-off mechanism; or ii) a diffusional search after REMP dissociation. We investigated the binding interaction between substrates containing the TorA signal peptide (spTorA) and its cognate REMP, TorD, and the effect of TorD on thein vitrotransport of such substrates. We found thatEscherichia coliTorD is predominantly a monomer at low micromolar concentrations (dimerizationKD> 50 µM), and this monomer binds reversibly to spTorA (KD≈ 1 µM). While TorD binds to membranes (KD≈ 100 nM), it has no apparent affinity for Tat translocons and it inhibits binding of a precursor substrate to the membrane. TorD has a minimal effect on substrate transport by the Tat system, being mildly inhibitory at high concentrations. These data are consistent with a model in which the REMP-bound signal peptide is shielded from recognition by the Tat translocon, and spontaneous dissociation of the REMP allows the substrate to engage the Tat machinery. Thus, the REMP does not assist with targeting to the Tat translocon, but rather temporarily shields the signal peptide.
Reduced neutralization of SARS-CoV-2 variants by convalescent plasma and hyperimmune intravenous immunoglobulins for treatment of COVID-19
Authors: Tang Juanjie , Lee Youri , Ravichandran Supriya , Grubbs Gabrielle , Huang Chang , Stauft Charles , Wang Tony , Golding Basil , Golding Hana , Khurana Surender
Published: March 2021

Hyperimmune immunoglobulin (hCoV-2IG) preparations generated from SARS-CoV-2 convalescent plasma (CP) are under evaluation in several clinical trials of hospitalized COVID-19 patients. Here we explored the antibody epitope repertoire, antibody binding and virus neutralizing capacity of six hCoV-2IG batches as well as nine convalescent plasma (CP) lots against SARS-CoV-2 and emerging variants of concern (VOC). The Gene-Fragment Phage display library spanning the SARS-CoV-2 spike demonstrated broad recognition of multiple antigenic sites spanning the entire spike including NTD, RBD, S1/S2 cleavage site, S2-fusion peptide and S2-heptad repeat regions. Antibody binding to the immunodominant epitopes was higher for hCoV-2IG than CP, with predominant binding to the fusion peptide. In the pseudovirus neutralization assay (PsVNA) and in the wild-type SARS-CoV-2 PRNT assay, hCoV-2IG lots showed higher titers against the WA-1 strain compared with CP. Neutralization of SARS-CoV-2 VOCs from around the globe were reduced to different levels by hCoV-2IG lots. The most significant loss of neutralizing activity was seen against the B.1.351 (9-fold) followed by P.1 (3.5-fold), with minimal loss of activity against the B.1.17 and B.1.429 (≤2-fold). Again, the CP showed more pronounced loss of cross-neutralization against the VOCs compared with hCoV-2IG. Significant reduction of hCoV-2IG binding was observed to the RBD-E484K followed by RBD-N501Y and minimal loss of binding to RBD-K417N compared with unmutated RBD. This study suggests that post-exposure treatment with hCoV-2IG is preferable to CP. In countries with co-circulating SARS-CoV-2 variants, identifying the infecting virus strain could inform optimal treatments, but would likely require administration of higher volumes or repeated infusions of hCOV-2IG or CP, in patients infected with the emerging SARS-CoV-2 variants.
Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics
Authors: Wu Yan , Lake Blue , Sos Brandon , Chen Song , Duong Thu E. , Yung Yun C. , Dong Weixiu , Limaye Siddarth , Chun Jerold , Zhang Kun
Published: March 2021

Human behaviors are at least partially driven by genomic regions that influence human-specific neurodevelopment. This includes genomic regions undergoing human specific sequence acceleration (Human Accelerated Regions or HARs) and regions showing human-specific enhancer activity (Human Gained Enhancers or HGEs) not present in other primates. However, prior studies on HAR/HGE activities involved mixtures of brain cell types and focused only on putative downstream target genes. Here, we directly measured cell type specific HAR/HGE activity in the developing fetal human brain using two independent single-cell chromatin accessibility datasets with matching single-cell gene expression data. Transcription factor (TF) motif analyses identified upstream TFs binding to HARs/HGEs and identified LHX2, a key regulator of forebrain development, as an active HGE regulator in neuronal progenitors. We integrated our TF motif analyses with published chromatin interaction maps to build detailed regulatory networks where TFs are linked to downstream genes via HARs/HGEs. Through these networks, we identified a potential regulatory role for NFIC in human neuronal progenitor networks via modulating the Notch signaling and cell adhesion pathways. Therefore, by using a single cell multi-omics approach, we were able to capture both the upstream and downstream regulatory context of HARs/HGEs, which may provide a more comprehensive picture of the roles HARs/HGEs play amongst diverse fetal cell types of the developing human brain.
Viscoelasticity and cell jamming state transition
Authors: Pajic-Lijakovic Ivana , Milivojevic Milan
Published: March 2021

Although collective cell migration (CCM) is a highly coordinated migratory mode, perturbations in the form of jamming state transitions and vice versa often occur even in 2D. These perturbations are involved in various biological processes, such as embryogenesis, wound healing and cancer invasion. CCM induces accumulation of cell residual stress which has a feedback impact to cell packing density. Density-mediated change of cell mobility influences the state of viscoelasticity of multicellular systems and on that base the jamming state transition. Although a good comprehension of how cells collectively migrate by following molecular rules has been generated, the impact of cellular rearrangements on cell viscoelasticity remains less understood. Thus, considering the density driven evolution of viscoelasticity caused by reduction of cell mobility could result in a powerful tool in order to address the contribution of cell jamming state transition in CCM and help to understand this important but still controversial topic. In addition, five viscoelastic states gained within three regimes: (1) convective regime, (2) conductive regime, and (3) damped-conductive regime was discussed based on the modeling consideration with special emphasis of jamming and unjamming states.
Talin mechanosensitivity is modulated by a direct interaction with cyclin-dependent kinase-1
Authors: Gough Rosemarie E. , Jones Matthew C. , Zacharchenko Thomas , Le Shimin , Yu Miao , Jacquemet Guillaume , Muench Ste P. , Yan Jie , Humphries Jonathan D. , Jørgensen Claus , Humphries Martin J. , Goult Benjamin T.
Published: March 2021

Talin is a mechanosensitive component of adhesion complexes that directly couples integrins to the actin cytoskeleton. In response to force, talin undergoes switch-like behaviour of its multiple rod domains that modulate interactions with its binding partners. Cyclin-dependent kinase-1 (CDK1) is a key regulator of the cell cycle, exerting its effects through synchronised phosphorylation of a large number of protein targets. CDK1 activity also maintains adhesion during interphase, and its inhibition is a prerequisite for the tightly choreographed changes in cell shape and adhesiveness that are required for successful completion of mitosis. Using a combination of biochemical, structural and cell biological approaches, we demonstrate a direct interaction between talin and CDK1 that occurs at sites of integrin-mediated adhesion. Mutagenesis demonstrated that CDK1 contains a functional talin-binding LD motif, and the binding site within talin was pinpointed to helical bundle R8 through the use of recombinant fragments. Talin also contains a consensus CDK1 phosphorylation motif centred on S1589; a site that was phosphorylated by CDK1in vitro. A phosphomimetic mutant of this site within talin lowered the binding affinity of KANK and weakened the mechanical response of the region, potentially altering downstream mechanotransduction pathways. The direct binding of the master cell cycle regulator, CDK1, to the primary integrin effector, talin, therefore provides a primordial solution for coupling the cell proliferation and cell adhesion machineries, and thereby enables microenvironmental control of cell division in multicellular organisms.

The direct binding of the master cell cycle regulator, CDK1, to the primary integrin effector, talin, provides a primordial solution for coupling the cell proliferation and cell adhesion machineries, and thereby enables microenvironmental control of cell division.
Exploring causal relationships between COVID-19 and cardiometabolic disorders: A bi-directional Mendelian randomization study
Authors: Xiang Yong , Chau Carlos Kwan-Long , Qiu Jinghong , Rao Shitao , So Hon-Cheong
Published: March 2021

Background

More than 100 million cases of COVID-19 have been reported worldwide. A number of risk factors for infection or severe infection have been identified, however observational studies were subject to confounding bias. In addition, there is still limited knowledge about the complications or medical consequences of the disease.

Methods

Here we performed bi-directional Mendelian randomization (MR) analysis to evaluate causal relationships between liability to COVID-19 (and severe/critical infection) and a wide range of around 30 cardiometabolic disorders (CMD) or traits. Genetic correlation (rg) was assessed by LD score regression(LDSC). The latest GWAS summary statistics from the COVID-19 Host Genetics Initiative was used, which comprised comparisons of general population controls with critically ill, hospitalized and any infected cases.

Results

Overall we observed evidence that liability to COVID-19 or severe infection may be causally associated with higher risks of type 2 diabetes mellitus(T2DM), chronic kidney disease(CKD), ischemic stroke (especially large artery stroke[LAS]) and heart failure(HF) when compared to the general population. On the other hand, our findings suggested that liability to atrial fibrillation (AF), stroke (especially LAS), obesity, diabetes (T1DM and T2DM), low insulin sensitivity and impaired renal function (low eGFR and diabetic kidney disease) may be causal risk factors for COVID-19 or severe disease. In genetic correlation analysis, T2DM, CAD, obesity, fasting insulin, CKD, gout, stroke and urate showed positive rg with critical or hospitalized infection. All above findings passed multiple testing correction at a false discovery rate (FDR)<0.05.

Conclusions

In summary, this study provides evidence for tentative bi-directional causal associations between liability to COVID-19 and severe disease and a number of CM disorders. Further replications and prospective studies are required to verify the findings.
N-myristoyltransferase inhibition is synthetic lethal in MYC-deregulated cancers
Authors: Lueg Gregor A. , Faronato Monica , Gorelik Andrii , Grocin Andrea Goya , Caamano-Gutierrez Eva , Falciani Francesco , Solari Roberto , Carr Robin , Bell Andrew S. , Bartlett Edward , Hutton Jennie A. , Llorian-Sopena Miriam , Chakravarty Probir , Brzezicha Bernadette , Janz Martin , Garnett Mathew J. , Calado Dinis P. , Tate Edward W.
Published: March 2021

HumanN-myristoyltransferases (NMTs) catalyze N-terminal protein myristoylation, a modification regulating membrane trafficking and interactions of >100 proteins. NMT is a promising target in cancer, but a mechanistic rationale for targeted therapy remains poorly defined. Here, large-scale cancer cell line screens against a panel of NMT inhibitors (NMTi) were combined with systems-level analyses to reveal that NMTi is synthetic lethal with deregulated MYC. Synthetic lethality is mediated by post-transcriptional failure in mitochondrial respiratory complex I protein synthesis concurrent with loss of myristoylation and degradation of complex I assembly factor NDUFAF4, followed by mitochondrial dysfunction specifically in MYC-deregulated cancer cells. NMTi eliminated MYC-deregulated tumors in vivo without overt toxicity, providing a new paradigm in which targeting a constitutive co-translational protein modification is synthetically lethal in MYC-deregulated cancers.

One-sentence summary

N-myristoyltransferase inhibition leads to post-transcriptional complex I failure and cell death in MYC-deregulated cancers
DrosophilaMale Accessory Gland Displays Developmental Ground Plan of a Primitive Prostate
Authors: Kumari Jaya , Sinha Pradip
Published: March 2021

Conservation of developmental genetic toolkits of functionally comparable organs from disparate phyla reveals their deep homology, which may help overcome the challenges of their confounding categorization as either homologous or analogous organs. A male accessory sexual organ in mammals, prostate, for instance, is anatomically disparate from its phylogenetically distant counterpart—the male accessory gland (MAG)—in insects likeDrosophila. By examining a select set of toolkit gene expression patterns, here we show thatDrosophilaMAG displays deep homology with the mammalian prostate. Like mammalian prostate, MAG morphogenesis is marked by recruitment of fibroblast growth factor receptor, FGFR, a tubulogenesis toolkit signaling pathway, starting early during its adepithelial genesis. Specialization of the individual domains of the developing MAG tube on the other hand is marked by expression of a posterior Hox gene transcription factor, Abd-B, while Hh-Dpp signaling marks its growth.DrosophilaMAG thus reveals developmental design of unitary bud-derived tube—a ground plan that appears to have been reiteratively co-opted during evolutionary diversification of male accessory sexual organs across distant phylogeny.
Food losses and waste quantification in supply chains: a systematic literature review
Authors: Kafa Nadine , Jaegler Anicia
Published: March 2021

Purpose

The purpose of this paper is to systematically review and critically examine food losses and waste quantification in supply chain, especially in studies that tackle all the supply chain activities in a real context.

Design/methodology/approach

This work employed a systematic literature review methodology on the extant literature focusing on peer-reviewed journal articles published from 2000 to 2019.

Findings

A systematic analysis of 117 articles reveals that downstream supply chains are studied to a greater extent than upstream supply chains, with an emphasis on consumer waste. The findings also highlight more than half of the articles focus on only one supply chain activity. In terms of the methodologies, surveys and modelling methods are the most used to measure food losses and wastes, adopt monetary, carbon emission and calorific metrics. This study highlights that while food losses and waste research remains a relevant field of study, it has yet to been fully explored.

Research limitations/implications

The main limit is the adoption of a systematic review method for food losses and waste quantification in supply chain.

Practical implications

The results suggest that supply chain managers should invest in acquiring more knowledge about food losses in the global network. Upstream supply chains should be more studied and integrated with the downstream supply chains. Using combined direct and indirect methods has the potential to deal with the contradictions of quantification, the lack of data and reduce losses over time and space.

Originality/value

Based on this review as the first one focusing exclusively on quantification of food losses and waste in supply chain context, the authors develop an aspiring research agenda that proposes opportunities for future research.

Headings

We analyse 117 studies addressing food losses and waste quantification.

Downstream food supply chains are more studied than upstream food supply chains.

Case studies of food supply chains in developed countries are more prolific.

The main metric to quantify food losses and waste is weight.
Factors limiting the adoption of hemp as an alternative sustainable material for green building delivery in Ghana
Authors: Agyekum Kofi , Adinyira Emmanuel , Oppon James Anthony
Published: March 2021

Purpose

The increased awareness of global environmental threats like climate change has created an upsurge of interest in low embodied carbon building materials for green building delivery. Though the literature advocates for the use of hemp-based building materials, there is no evidence of studies to explore its potential use in Ghana. Therefore, this study explores the potential factors that limit the adoption of hemp as an alternative sustainable material for green building delivery in Ghana.

Design/methodology/approach

A structured questionnaire was used to solicit the views of built environment professionals operating in construction, consulting and developer firms. The questions were developed through a comparative review of the related literature and complemented with a pilot review. Data were analysed via descriptive and inferential statistics.

Findings

On the average, the majority of the respondents showed a moderate level of awareness of hemp and its related uses in the construction industry. Also, certain key factors like the perceived association of hemp with marijuana, lack of expertise in the production of hemp-related building materials, farmers not getting the needed clearance for the cultivation of hemp, lack of legislation by the government in the legalisation of hemp and the inadequate knowledge of consumers on the benefits of hemp-based building materials were identified as potential limitations to the adoption of hemp as an alternative sustainable material for green building delivery.

Originality/value

The findings from this study provide insights into a less investigated area in sub-Saharan Africa and further provide new and additional information to the current state-of-the-art on the potential for the use of hemp in the building construction sector.
Do corporate financial flexibility, financial sector development and regulatory environment affect corporate investment decisions?
Authors: Mahmood Yasin , Rashid Abdul , Rizwan Muhammad Faisal
Published: March 2021

Purpose

This study aims to examine how corporate financial flexibility, financial sector development and the regulatory environment influence corporate investment decisions in an emerging economy after controlling for several macroeconomic factors.

Design/methodology/approach

The authors estimated random-effects models to empirically examine the impacts of corporate financial flexibility, banking sector development, equity market development, regulatory quality and corruption on corporate investment decisions. The empirical analysis is based on an unbalanced annual panel data set of a sample of 198 non-financial firms listed on the Pakistan Stock Exchange for the period 1992–2018.

Findings

The results show that financially flexible firms tend to invest more. The increased banking sector development, stock market development and better regulatory quality play a pivotal role for enabling firms to increase their investment ability. However, the results reveal that corruption acts as a barrier and reduces corporate investments during the examined period. The results suggest that unused borrowing capacity is a good source of financial flexibility. These results strongly support the pecking order theory, which explains why firms incline toward internal sources for financing their investments and why they prefer debt to equity when go for external financing.

Practical implications

The empirical findings of the study enable corporate managers to make better financing and investment decisions by understanding the significance of the attainment and maintenance of the corporate financial flexibility to enhance firm value. Furthermore, the findings enable corporate managers to examine and understand the role of banking sector development (BSD), equity market development (EMD), regulatory quality and the role of corruption in affecting corporate firms' investment ability, allowing them to make appropriate investment decisions, especially from an emerging economy perspective. The findings also help investors in making appropriate investment decisions while they are purchasing financial assets. Finally, the findings of the study have some implications for regulators as well. Specifically, the findings suggest that the authorities should implement economic and financial policies favoring banking sector as well as equity market development to enhance corporate investment.

Originality/value

The study significantly adds to the literature by examining the impact of financial flexibility, financial sector development and regulatory environment on corporate investment decisions. According to the authors' knowledge, the empirical evidence examining the impact of all of these factors on corporate investment is very scarce. Therefore, this study is an effort to fill the gap left in the literature.
The emergence and adoption of digitalization in the logistics and supply chain industry: an institutional perspective
Authors: Herold David M. , Ćwiklicki Marek , Pilch Kamila , Mikl Jasmin
Published: March 2021

Purpose

Despite increasing interest in digital services and products, the emergence of digitalization in the logistics and supply chain (L&SC) industry has received little attention, in particular from organizational theorists. In response, taking an institutionalist view, the authors argue that the emergence and adoption of digitalization is a socially constructed phenomenon.

Design/methodology/approach

This paper shows how actor-level frameshifts contribute to an emergence of an overarching “digitalization logic” in the L&SC industry at the field level. Building on a longitudinal analysis of field actors' frames and logics, the authors track the development of digitalization over the last 60 years in the L&SC sector.

Findings

The authors classify specific time periods by key field-configuring events, describe the relevant frameshifts in each time period and present a process that explains how and why digitalization has emerged, been adopted and manifested itself in the L&SC industry.

Originality/value

The findings of the study provide insights about the evolution of a digitalization logic and thus advance the institutional view on digitalization in the L&SC industry.
Informational efficiency and governance in restricted share settings: boosting family business leaders' financing decisions
Authors: Dupuis Daniel , Bodolica Virginia , Spraggon Martin
Published: March 2021

Purpose

Volume-based liquidity ratios suffer from potential measurement bias due to share restriction and may misrepresent actual liquidity. To address this issue, the authors develop two modified metrics, the free-float liquidity and the alternative free-float illiquidity ratios. These measures are well suited to estimate liquidity in the presence of trading constraints, as can be found in closely held/state-owned entities, IPOs/SEOs with lockup restrictions, dual-class share structures and family-owned businesses.

Design/methodology/approach

The authors modify the turnover illiquidity ratio, where the number of outstanding shares is scaled by the public free float, and use natural log transformation to normalize free-float liquidity. Our dataset is composed of daily observations for US stocks included in the S&P 500 index over the 2015–2018 period. To test the validity of free-float (il)liquidity ratios, the authors perform a correlation analysis for various liquidity metrics. To examine their empirical efficiency, the authors employ pooled OLS regression models for family firms as a subsample of liquidity-constrained entities, relying on five different identifiers of family-owned businesses.

Findings

The authors’ empirical testing indicates that the proposed free-float (il)liquidity ratios compare favorably with other volume-based methods, such as Amihud's ratio, liquidity ratio and turnover ratio. For the subsample of family organizations as a restricted-share setting, the authors report significant coefficients for our free-float measures across all the family firm identifiers used. In particular, as free-float decreases with progressive family influence, the advanced ratios capture an increase (decrease) in perceived liquidity (illiquidity) that is absent in the other benchmarks.

Originality/value

This study allows the authors to inform the ongoing debate on the management and governance of publicly listed companies with various impediments to trade. Traditional measures understate illiquidity (overstate liquidity) as the fraction of free trading shares is limited by design or circumstances. The authors’ proposed free-float metrics offer informational gains for family leaders to aid in their financing decisions and for non-family outsiders to guide their investment choice. As a constrained free float inhibits price discovery processes, the authors discuss how restricted stock issuers may alleviate the attendant negative effects on governance and information opacity.
Investigation on reading behaviors and cognitive outcomes of Facebook health information
Authors: Syn Sue Yeon , Yoon JungWon
Published: March 2021

Purpose

This study aims to understand how college students' personal and health-related characteristics are related to their reading behaviors and cognitive outcomes of Facebook health information through eye tracking data and cognitive outcomes.

Design/methodology/approach

This study analyzed users' gaze movement data and results of recall and recognition tests to investigate users' reading patterns and their consequences with cognitive outcomes. The gaze movements are analyzed with eye tracking data including the average fixation count and time to first fixation.

Findings

The results of reading patterns show that Texts and Images are highly viewed and viewed immediately by participants when the posts were presented. There was no clear pattern with fixation counts to determine cognitive outcomes. However, the findings of study suggest that there is a clear pattern of reading Facebook posts with areas of interest (AOIs). Among five AOIs observed, participants viewed Images first and then Texts when a Facebook post is presented. On the other hand, they read Texts more carefully than Images. The findings of this study suggest that while images contribute to gaining users' attention, a clear and precise message needs to be delivered in text message to ensure readers' correct understanding and application of health information.

Originality/value

The user-centered evidence on reading behaviors and cognitive outcomes will make contributions to how health professionals and health organizations can make optimal use of Facebook for effective health information communication.

Peer review

The peer-review history for this article is available at: https://publons.com/publon/10.1108/OIR-05-2020-0177
Interactive effects of shading and disturbance on plant invasion in an arid shrubland: Assembly processes and CSR‐strategies
Authors: Escobedo Víctor M. , Rios Rodrigo S. , Gianoli Ernesto
Published: March 2021

Disturbance by small mammals and shrub canopies are ecological factors typical of arid ecosystems that may influence plant invasion through environmental and community changes. Whereas disturbance beneath shrub canopies may promote invasion by removing dominant species, disturbance in open areas may hinder plant invasion by increasing environmental harshness. However, we are unaware of studies explicitly addressing the interactive effects of disturbance by mammals and shading by shrubs on community assembly processes to understand plant invasion. In an arid shrubland, disturbance and shading were caused by the fossorial rodent Spalacopus cyanus and the shrub Flourensia thurifera, respectively. We used functional dispersion data (trait convergence vs. divergence) and Grime´s theory (competitive, stress‐tolerant and ruderal strategies, CSR) to gain insights into the underlying assembly processes.

We compared environmental conditions, richness and abundance of native and exotic species, as well as functional dispersion and prevalence of CSR‐strategies across four microsites (60 × 60 cm plots): undisturbed/open, undisturbed/shaded, disturbed/open and disturbed/shaded. We tested for functional differences between native and exotic species.

Species richness was similar among microsites for both native and exotic species. Shading ameliorated environmental conditions, promoted trait divergence and increased prevalence of C‐ and R‐strategies. Disturbance increased the abundance of exotic species and removed dominant species in shaded microsites. Exotic and native species were functionally different: exotics showed shorter life span, lower height, thinner stems and smaller leaves than natives.

Synthesis. Disturbance, by removing plant biomass, favoured exotic species in shaded microsites, where shrub canopy ameliorated environmental conditions and—by relaxing habitat filtering—promoted niche partitioning processes as well as C‐ and R‐strategies. We illustrate the value of linking trait‐based ecology approaches to micro‐environmental conditions, as it may provide insights into the underlying community processes when studying plant invasions at the local and microsite scales. Disturbed microsites beneath shrub canopies could be ‘hotspots’ where to concentrate efforts to manage plant invasions in arid ecosystems.
Examining omitted variable bias in anchoring premium estimates: Evidence based on assessed value
Authors: Zhou Tingyu , Clapp John M , Lu‐Andrews Ran
Published: March 2021

A new assessed value approach is proposed to control for the amount of persistent unobserved quality. The approach to a well‐established two‐stage framework developed by Genesove and Mayer (GM, 2001) is applied, who test the effect of an expected loss on final transaction prices in the housing market. It is shown that the assessed value model effectively mitigates the omitted variable bias and produces similar results as GM when the first‐stage residual is included. Importantly, the model does not rely on repeat sales and therefore provides a powerful new tool for estimating market value. Results are robust to alternative specifications, to controlling for loan‐to‐value ratios, to replacing final sale price with listing price, to alternative fixed effects, to subperiods, to different holding periods, to simulated quality, to excluding flippers, and to controlling improvements between sales.
Symptomatic features and prognosis of 932 hospitalized patients with coronavirus disease 2019 in Wuhan
Authors: Sun Liang Liang , Wang Jian , Wang Yu Sheng , Hu Ping Fang , Zhao Zheng Qing , Chen Wei , Ning Bei Fang , Yin Chuan , Hao Yu Shi , Wang Qiong , Wang Chen , Liu Ya Long , Chen Cheng , Yin Ji Zhong , Huang Hai , Xie Wei Fen
Published: March 2021

Objective

To discern the symptomatic features of coronavirus disease 2019 (COVID‐19) and to evaluate the severity and prognosis of the disease.

Methods

In this retrospective cohort study, 932 hospitalized patients with COVID‐19 in Wuhan were enrolled, including 52 severe and 880 non‐severe cases. All patients were followed up for 3 months after discharge. The symptomatic features and follow‐up data of the patients in both groups were analyzed and compared.

Results

Of the 932 patients, fever (60.0%), cough (50.8%) and fatigue (36.4%) were the most common symptoms. In total, 32.7% of the severe cases presented with gastrointestinal symptoms at disease onset, including anorexia, nausea, vomiting or diarrhea, which was significantly higher than that of the non‐severe group (P = 0.0015). The incidence of olfactory disturbance and dysgeusia was only 3.1% and 6.2%, respectively. After adjusting for age and sex, multivariate regression analysis showed that fever lasting for over 5 days (odds ratio [OR] 1.90, 95% confidence interval [CI] 1.00‐3.62, P = 0.0498), anorexia at onset (OR 2.61, 95% CI 1.26‐5.40, P = 0.0096), and modified Medical Research Council level above grade 2 when dyspnea occurred (OR 14.19, 95% CI 7.01‐28.71, P < 0.0001) were symptomatic risk factors for severe COVID‐19. During the follow‐up, cough (6.2%), dyspnea (7.2%), fatigue (1.8%), olfactory disturbance and dysgeusia (1.5%) were the significant remaining symptoms.

Conclusions

COVID‐19 causes clusters of symptoms with multiple systems involved. Certain symptomatic characteristics have predictive value for severe COVID‐19. Short‐term follow‐up data reveal that most patients have a good prognosis.
Eucalyptus species maintain secondary metabolite production under water stress conditions at the expense of growth
Authors: Manea Anthony , Tabassum Samiya , Leishman Michelle R.
Published: March 2021

Plants have evolved a vast array of secondary metabolites that help defend them against natural enemy attack. The production of these secondary metabolites is influenced by environmental factors, such as temperature, rainfall (soil water availability) and atmospheric [CO2], which may be altered under climate change. This study aimed to test how two of these environmental factors, namely soil water availability and [CO2], will affect secondary metabolite and biomass production in Eucalypts. To investigate this, we measured secondary metabolite and biomass production of three Eucalypt species (Eucalyptus grandis, E. moluccana, E. saligna) grown under ambient and elevated [CO2] (400 and 600 ppm, respectively) and water‐stressed and well‐watered conditions, in a fully factorial glasshouse experiment. The secondary metabolites measured were foliar phenolic concentration as well as terpene and green leaf volatile emissions. We found that water stress did not alter secondary metabolite production. Unsurprisingly, the water‐stressed plants maximised their water uptake potential by reducing shoot biomass but maintaining root biomass. The detrimental effects of water stress on shoot biomass production were not reduced under elevated [CO2] compared to ambient [CO2], despite all species experiencing significant reductions in stomatal conductance. Further, [CO2] as a single factor did not have a significant effect on species’ net carbon gain, with an increase in green leaf volatile emissions under elevated [CO2] being mitigated by a reduction in shoot biomass production. These results suggest that reductions in carbon gains due to water stress will affect the growth of Eucalypts rather than their chemical defence capabilities.