bluuebunny/crossref_metadata_2025 huggingface dataset:
in-silicaAnalysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA
Authors: Agarwal Ajay
Published: June 2020

The recent pandemic of COVID19 that has struck the world is yet to be battled by a potential cure. Countless lives have been claimed due to the existing pandemic and the societal normalcy has been damaged permanently. As a result, it becomes crucial for academic researchers in the field of bioinformatics to combat the existing pandemic. The study involved collecting the virulent strain sequence of SARS-nCoV19 for the country USA against human host through publically available bioinformatics databases. Usingin-silicaanalysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. The results of this study can provide further researchers better aspects and direction on developing vaccine and immune responses against COVID19. This work also aims at promoting the use of existing bioinformatics tools to faster streamline the pipeline of vaccine development.

The Situation of COVID19

A new infection respiratory disease was first observed in the month of December 2019, in Wuhan, situated in the Hubei province, China. Studies have indicated that the reason of this disease was the emergence of a genetically-novel coronavirus closely related to SARS-CoV. This coronavirus, now named as nCoV-19, is the reason behind the spread of this fatal respiratory disease, now named as COVID-19. The initial group of infections is supposedly linked with the Huanan seafood market, most likely due to animal contact. Eventually, human-to-human interaction occurred and resulted in the transmission of the virus to humans. [13].

Since then, nCoV-19 has been rapidly spreading within China and other parts of World. At the time of writing this article (mid-March 2020), COVID-19 has spread across 146 countries. A count of 164,837 cases have been confirmed of being diagnosed with COVID-19, and a total of 6470 deaths have occurred. The cumulative cases have been depicting a rising trend and the numbers are just increasing. WHO has declared COVID-19 to be a “global health emergency”. [14].

Current Scenario and Objectives

Currently, research is being conducted on a massive level to understand the immunology and genetic characteristics of the disease. However, no cure or vaccine of nCoV-19 has been developed at the time of writing this article.

Though, nCoV-19 and SARS-CoV are almost genetically similar, the respiratory syndrome caused by both of them, COVID-19 and SARS respectively, are completely different. Studies have indicated that –

“SARS was more deadly but much less infectious than COVID-19”.

-World Health Organization
Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity
Authors: Zhang Chengdong , Jin Xuanxuan , Chen Xianyang , Leng Qibin , Qiu Tianyi
Published: June 2020

The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is constantly changing with the places of transmission, but the reason remains to be revealed. Here, we presented the study that comprehensively analyzed the potential selective pressure of immune system restriction, which can drive mutations in circulating SARS-CoV-2 isolates. The results showed that the most common mutation sites of SARS-CoV-2 proteins were located on the non-structural protein ORF1ab and the structural protein Spike. Further analysis revealed mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 to escape cellular immunity under the long-term and large-scale community transmission. Meanwhile, the mutations on Spike protein may enhance the ability of SARS-CoV-2 to enter the host cells and escape the recognition of B-cell immunity. This study will increase the understanding of the evolutionary direction and warn about the potential immune escape ability of SARS-CoV-2, which may provide important guidance for the potential vaccine design.
The relationship between EEG and fMRI connectomes is reproducible across simultaneous EEG-fMRI studies from 1.5T to 7T
Authors: Wirsich Jonathan , Jorge João , Iannotti Giannarita , Shamshiri Elhum A , Grouiller Frédéric , Abreu Rodolfo , Lazeyras François , Giraud Anne-Lise , Gruetter Rolf , Sadaghiani Sepideh , Vulliémoz Serge
Published: June 2020

Both electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) are non-invasive methods that show complementary aspects of human brain activity. Despite measuring different proxies of brain activity, both the measured blood-oxygenation (fMRI) and neurophysiological recordings (EEG) are indirectly coupled. The electrophysiological and BOLD signal can map the underlying functional connectivity structure at the whole brain scale at different timescales. Previous work demonstrated a moderate but significant correlation between resting-state functional connectivity of both modalities, however there is a wide range of technical setups to measure simultaneous EEG-fMRI and the reliability of those measures between different setups remains unknown. This is true notably with respect to different magnetic field strengths (low and high field) and different spatial sampling of EEG (medium to high-density electrode coverage).

Here, we investigated the reproducibility of the bimodal EEG-fMRI functional connectome in the most comprehensive resting-state simultaneous EEG-fMRI dataset compiled to date including a total of 72 subjects from four different imaging centers. Data was acquired from 1.5T, 3T and 7T scanners with simultaneously recorded EEG using 64 or 256 electrodes. We demonstrate that the whole-brain monomodal connectivity reproducibly correlates across different datasets and that a moderate crossmodal correlation between EEG and fMRI connectivity of r≈0.3 can be reproducibly extracted in low- and high-field scanners. The crossmodal correlation was strongest in the EEG-β frequency band but exists across all frequency bands. Both homotopic and within intrinsic connectivity network (ICN) connections contributed the most to the crossmodal relationship.

This study confirms, using a considerably diverse range of recording setups, that simultaneous EEG-fMRI offers a consistent estimate of multimodal functional connectomes in healthy subjects that are dominantly linked through a functional core of ICNs across spanning across the different timescales measured by EEG and fMRI. This opens new avenues for estimating the dynamics of brain function and provides a better understanding of interactions between EEG and fMRI measures. This observed level of reproducibility also defines a baseline for the study of alterations of this coupling in pathological conditions and their role as potential clinical markers.
Nitrocellulose redox permanganometry: a simple method for reductive capacity assessment
Authors: Homolak J , Kodvanj I , Babic Perhoc A , Virag D , Knezovic A , Osmanovic Barilar J , Riederer P , Salkovic-Petrisic M
Published: June 2020

We propose a rapid, simple and robust method for measurement of reductive capacity of liquid and solid biological samples based on potassium permanganate reduction followed by trapping of manganese dioxide precipitate on a nitrocellulose membrane. Moreover, we discuss how nitrocellulose redox permanganometry (NRP) can be used for high-throughput analysis of biological samples and present HistoNRP, its modification used for detailed analysis of reductive capacity spatial distribution in tissue with preserved anatomical relations.
Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay
Authors: Hanson Quinlin M. , Wilson Kelli M. , Shen Min , Itkin Zina , Eastman Richard T. , Shinn Paul , Hall Matthew D.
Published: June 2020

The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike-ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure binding of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3,384 small molecule drugs and pre-clinical compounds was performed, yielding 25 high-quality, small-molecule hits that can be evaluated in cell-based models. This established AlphaLISA RBD-ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral-host interaction to further the development of interventions to address the global health pandemic.
Quantum dot probes for the quantitative study of drug transport by the MacAB TolC efflux pump in lipid scaffolds
Authors: Souabni Hager , dos Santos William Batista , Cece Quentin , Puvanendran Dhenesh , Picard Martin
Published: June 2020

ABC tripartite efflux pumps are macromolecular membrane protein machineries that expel a large variety of drugs and export virulence factors from Gram negative bacteria. Using a lipid scaffold mimicking the two-membrane environment of the transporter and designing spectroscopic conditions allowing the monitoring of both ATP hydrolysis and substrate transport in real time, we show that MacAB-TolC accommodates transport and energy consumption with high coupling efficiency.
In-situnon-lethal rapid test to accurately detect the presence of the nematode parasite,Anguillicoloides crassus, in European eel,Anguilla anguilla
Authors: De Noia M. , Poole R. , Kaufmann J. , Waters C. , Adams C. , McGinnity P. , Llewellyn M.
Published: June 2020

Anguillicoloides crassusis an invasive nematode parasite of the European eel,Anguilla anguilla, and one of the primary drivers of eel population collapse. The presence of the parasite has been shown to impact many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread ofA. crassus. However, until recently, accurate diagnosis of infection could only be achieved via terminal dissection. To supportA. anguillafisheries management in the context ofA. crassuswe developed a rapid non-lethal and non-invasive environmental DNA method to detect the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit at Glasgow University and in situ using Whatman qualitative filter paper No. 1 and a miniPCR DNA Discovery System™. Primers were specifically designed from the cytochrome oxidase mtDNA gene region. In situ extraction and amplification takes approx. 3h for up to 16 individuals with higher specificity and sensitivity compare to the laboratory Qiagen kit extraction. The local diagnostic procedure demonstrated Positive Predictive Values at 96% and Negative Predictive Values at 87%. Our method will be a powerful tool in the hands of fisheries managers to help protect this iconic but critically endangered species. It will allow a non-invasive monitoring of theA. crassusdispersion across the European waters.
ViR: a tool to account for intrasample variability in the detection of viral integrations
Authors: Pischedda Elisa , Crava Cristina , Carlassara Martina , Gasmi Leila , Bonizzoni Mariangela
Published: June 2020

Lateral gene transfer (LT) from viruses to eukaryotic cells is a well-recognized phenomenon. Somatic integrations of viruses have been linked to persistent viral infection and genotoxic effects, including various types of cancer. As a consequence, several bioinformatic tools have been developed to identify viral sequences integrated into the human genome. Viral sequences that integrate into germline cells can be transmitted vertically, be maintained in host genomes and be co-opted for host functions. Endogenous viral elements (EVEs) have long been known, but the extent of their widespread occurrence has only been recently appreciated. Modern genomic sequencing analyses showed that eukaryotic genomes may harbor hundreds of EVEs, which derive not only from DNA viruses and retroviruses, but also from nonretroviral RNA viruses and are mostly enriched in repetitive regions of the genome. Despite being increasingly recognized as important players in different biological processes such as regulation of expression and immunity, the study of EVEs in non-model organisms has rarely gone beyond their characterization from annotated reference genomes because of the lack of computational methods suited to solve signals for EVEs in repetitive DNA. To fill this gap, we developed ViR, a pipeline which ameliorates the detection of integration sites by solving the dispersion of reads in genome assemblies that are rich of repetitive DNA. Using paired-end whole genome sequencing (WGS) data and a user-built database of viral genomes, ViR selects the best candidate couples of reads supporting an integration site by solving the dispersion of reads resulting from intrasample variability. We benchmarked ViR to work with sequencing data from both single and pooled DNA samples and show its applicability using WGS data of a non-model organism, the arboviral vectorAedes albopictus. Viral integrations predicted by ViR were molecularly validated supporting the accuracy of ViR results. Additionally, ViR can be readily adopted to detect any LT event providingad hocnon-host sequences to interrogate.
Impact of virus subtype and hostIFNL4genotype on large-scale RNA structure formation in the genome of hepatitis C virus
Authors: Simmonds P. , Cuypers L. , Irving W.L. , McLauchlan J. , Cooke G.S. , Barnes E. ,   STOP-HCV Consortium, Ansari M.A.
Published: June 2020

Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute associated with formation of large scale RNA structure in their genomic RNA. We developed novel methods to analyse and visualise genome-scale ordered RNA structure (GORS) predicted from the increasingly large datasets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localised exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally entirely distinct, even between subtypes 1a and 1b. Dynamic remodelling was further evident from comparison of HCV strains in different host genetic background. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in theIFNL4gene compared to the CC (non-expressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represents an important new element in RNA virus evolution and the adaptive interplay between virus and host.
Sexually Dimorphic DNA Damage Responses and Mutation Avoidance in the Mouse Germline
Authors: Bloom Jordana C. , Schimenti John C.
Published: June 2020

Germ cells specified during fetal development form the foundation of the mammalian germline. These primordial germ cells (PGCs) undergo rapid proliferation, yet the germline is highly refractory to mutation accumulation compared to somatic cells. Importantly, while the presence of endogenous or exogenous DNA damage has the potential to impact PGCs, there is little known about how these cells respond to stressors. To better understand the DNA damage response (DDR) in these cells, we exposed pregnant mice to ionizing radiation (IR) at specific gestational time points and assessed the DDR in PGCs. Our results show that PGCs prior to sex determination lack a G1 cell cycle checkpoint. Additionally, the response to IR-induced DNA damage differs between female and male PGCs post-sex determination. IR of female PGCs caused uncoupling of germ cell differentiation and meiotic initiation, while male PGCs exhibited repression of piRNA metabolism and transposon de-repression. We also used whole genome single-cell DNA sequencing to reveal that genetic rescue of DNA repair-deficient germ cells (Fancm-/-) leads to increased mutation incidence and biases. Importantly, our work uncovers novel insights into how PGCs exposed to DNA damage can become developmentally defective, leaving only those genetically fit cells to establish the adult germline.
An empirical test of the role of value certainty in decision making
Authors: Lee Douglas , Coricelli Giorgio
Published: June 2020

Most contemporary models of value-based decisions are built on value estimates that are typically self-reported by the decision maker. Such models have been successful in accounting for choice accuracy and response time, and more recently choice confidence. The fundamental driver of such models is choice difficulty, which is almost always defined as the absolute value difference between the subjective value ratings of the options in a choice set. Yet a decision maker is not necessarily able to provide a value estimate with the same degree of certainty for each option that he encounters. We propose that choice difficulty is determined not only by absolute value distance of choice options, but also by their value certainty. In this study, we first demonstrate the reliability of the concept of an option-specific value certainty using three different experimental measures. We then demonstrate the influence that value certainty has on choice, including accuracy (consistency), choice confidence, response time, and choice-induced preference change (i.e., the degree to which value estimates change from pre- to post-choice evaluation). We conclude with a suggestion of how popular contemporary models of choice (e.g., race model, drift-diffusion model) could be improved by including option-specific value certainty as one of their inputs.
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
Authors: Shrestha Utsab R. , Smith Jeremy C. , Petridis Loukas
Published: June 2020

Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy in the force fields and inadequate sampling. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD led to unbiased ensembles of unprecedented accuracy, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of variable sequence properties using two recently optimized force fields. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues).
Homologous chromosomes in asexual rotiferAdineta vagasuggest automixis
Authors: Simion Paul , Narayan Jitendra , Houtain Antoine , Derzelle Alessandro , Baudry Lyam , Nicolas Emilien , Cariou Marie , Guiglielmoni Nadège , Kozlowski Djampa KL , Gaudray Florence Rodriguez , Terwagne Matthieu , Virgo Julie , Noel Benjamin , Wincker Patrick , Danchin Etienne GJ , Marbouty Martial , Hallet Bernard , Koszul Romain , Limasset Antoine , Flot Jean-François , Van Doninck Karine
Published: June 2020

The several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloidA. vagavalidated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescentin situhybridization (FISH), we demonstrate that theA. vagagenome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure ofA. vagaand the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonalA. vagasuggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.
Quantitative mapping of mRNA 3’ ends inPseudomonas aeruginosareveals a pervasive role for premature 3’ end formation in response to azithromycin
Authors: Konikkat Salini , Scribner Michelle R. , Eutsey Rory , Hiller N. Luisa , Cooper Vaughn S. , McManus C. Joel
Published: June 2020

Pseudomonas aeruginosaproduces serious chronic infections in hospitalized patients and immunocompromised individuals, including patients with cystic fibrosis. The molecular mechanisms by whichP. aeruginosaresponds to antibiotics and other stresses to promote persistent infections may provide new avenues for therapeutic intervention. Azithromycin (AZM), an antibiotic frequently used in cystic fibrosis treatment, is thought to improve clinical outcomes through a number of mechanisms including impaired biofilm growth and quorum sensing (QS). The mechanisms underlying the transcriptional response to AZM remain unclear. Here, we interrogated theP. aeruginosatranscriptional response to AZM using a fast, cost-effective genome-wide approach to quantitate RNA 3’ ends (3pMap). We also identified hundreds ofP. aeruginosagenes with high incidence of premature 3’ end formation indicative of riboregulation in their transcript leaders using 3pMap. AZM treatment of planktonic and biofilm cultures alters the expression of hundreds of genes, including those involved in QS, biofilm formation, and virulence. Strikingly, most genes downregulated by AZM in biofilms had increased levels of intragenic 3’ ends indicating premature transcription termination, transcriptional pausing, or accumulation of stable intermediates resulting from the action of nucleases. Reciprocally, AZM reduced premature intragenic 3’ end termini in many upregulated genes. Most notably, reduced termination accompanied robust induction ofobgE, a GTPase involved in persister formation inP. aeruginosa. Our results support a model in which AZM-induced changes in 3’ end formation alter the expression of central regulators which in turn impairs the expression of QS, biofilm formation and stress response genes, while upregulating genes associated with persistence.
Genetic characterisation of a large antibiotic resistant environmental ST131E. coliplasmid using a long read hybrid assembly approach
Authors: James R.S. , Rangama S. , Clark V. , Wellington E.M.H.
Published: June 2020

Escherichia coliStrain Type 131 are a globally disseminated environmentalE. colithat has been linked to the capture and spread of plasmid mediatedblaCTX-Mtype extended spectrum beta-lactamase (ESBLs). Accurately identifying such resistance genes in their wider genetic context provides a greater understanding of the mechanisms of selection and persistence in the environment. In this study we use a novel DNA extraction and enrichment method in combination with a custom long-read scaffold hybrid-assembly and polishing pipe line to identify the genetic context of the plasmid borneblaCTX-Mgene previously identified in an ST131 environmentalE. coliisolate. This has allowed us to discern the complete structure of a ~100kb environmental plasmid and further resolve theblaCTX-Mvariant to the group 9blaCTX-M-27gene. The upstream IS26 insertion element associated with the global capture and dissemination ofblaCTX-M-15was also identified in proximity to blaCTX-M-27. Furthermore, the lack of conjugative machinery identified on this plasmid, in combination with a toxin-antitoxin and plasmid partitioning system, indicates a mechanism of vertical transmission to maintain persistence in a population.
Difference in somatosensory event-related potentials in the blind subjects leads to better performance in tactile P300 BCI
Authors: Grigoryan Rafael , Goranskaya Dariya , Demchinsky Andrey , Ryabova Ksenia , Kuleshov Denis , Kaplan Alexander
Published: June 2020

In this study, we have created an 8-command P300 tactile BCI with two stimuli types, running on a minimally modified consumer Braille display and tested it on 10 blind subjects and 10 sighted controls. Blind subjects have demonstrated 27% higher median accuracy than sighted controls (p< 0.05), proving that the blind subjects are not only able to use tactile BCI but also can achieve superior results in comparison with sighted subjects. Median accuracy in the blind group with the best stimuli type has reached 95%. The difference in event-related potentials between groups is located in frontocentral sites before 300 ms post-stimulus and corresponds with early cognitive ERP components. The blind subjects have higher amplitude and lower latency of ERPs. This result is consistent through experimental conditions with different tactile stimuli. The classification performance for the blind subjects is correlated with Braille reading speed. This enables a discussion about mechanisms of plastic changes during sensory compensation after vision loss and its dependence on personal perceptual experience.

Author summary

Sensory compensation following vision loss can be recognized as a unique model for neural plasticity. However, the magnitude of the effect and the specific tasks where it’s manifested is still a subject for debate. In this study, we have created a tactile brain-computer interface game to study how somatosensory processing is different between the blind and the sighted people. The participants were required to attend to tactile stimuli, and the correct stimulus was selected using realtime EEG classification. We have shown, for the first time, that the blind subjects are significantly better than the sighted in tactile brain-computer interface tasks. We have also found, that individual performance is correlated with Braille proficiency. This result links personal perceptual abilities in two different sensory tasks. EEG analysis revealed that differences in performance can be attributed to early cognitive processing steps. Along with practical considerations in brain-computer interface development, the results also add to the data on cognitive processing in the blind and enable the discussion on the importance of Braille education.
Cancer-specific associations of driver genes with immunotherapy outcome
Authors: Jun Tomi , Qing Tao , Dong Guanlan , Signaevski Maxim , Hopkins Julia F , Frampton Garrett M , Albacker Lee A , Cordon-Cardo Carlos , Samstein Robert , Pusztai Lajos , Huang Kuan-lin
Published: June 2020

Genomic features such as microsatellite instability (MSI) and tumor mutation burden (TMB) are predictive of immune checkpoint inhibitor (ICI) response. However, they do not account for the functional effects of specific driver gene mutations, which may alter the immune microenvironment and influence immunotherapy outcomes. By analyzing a multi-cancer cohort of 1,525 ICI-treated patients, we identified 12 driver genes in 6 cancer types associated with treatment outcomes, including genes involved in oncogenic signaling pathways (NOTCH, WNT, FGFR) and chromatin remodeling. Mutations ofPIK3CA, PBRM1, SMARCA4, andKMT2Dwere associated with worse outcomes across multiple cancer types. In comparison, genes showing cancer-specific associations—such asKEAP1, BRAF, and RNF43—harbored distinct variant types and variants, some of which were individually associated with outcomes. In colorectal cancer, a commonRNF43indel was a putative neoantigen associated with higher immune infiltration and favorable ICI outcomes. Finally, we showed that selected mutations were associated with PD-L1 status and could further stratify patient outcomes beyond MSI or TMB, highlighting their potential as biomarkers for immunotherapy.
Keen relationship between COVID_19 and food supply suggest some animal origin foods as excellent vehicle of SARS-Cov-2
Authors: Saeedi Nazli , Rafat Seyed Abbas
Published: June 2020

In recent months, nearly all countries tried to decrease human-to-human contact as the principal mode of transmission of SARS-CoV-2. However, other modes of transmission also need to be clarified in more depth, especially, the foodborne transmission. We assessed the effect of animal origin foods consumption on the pandemic of COVID-19. For this purpose, we studied the relationship among 20 food supply as independent variables, and the parameter of Total Cases as dependent variable. Here we show a relationship between a group of animal origin foods and total cases. Regression, Bayes, and Lasso results showed that eggs and fresh water fish have positive coefficient. So, among the transmission ways of COVID_19, the role of foodborne transmission should be more significant than previously thought. The possibility of animal origin foodborne transmission should be taken into more consideration. The perspective is to expand the surveillance of SARS-Cov-2 during the food production chain. In conclusion, the results of the present study indicate that one important vehicle for SARS-Cov-2 may be some of animal origin foods. It is recommended that virologists examine the possibility of freshwater fish and chicken‘s eggs being as excellent vehicles/preservatives for SARS-Cov-2.
Determinants of capital structure: evidence from Malaysian firms
Authors: Saif-Alyousfi Abdulazeez Y.H. , Md-Rus Rohani , Taufil-Mohd Kamarun Nisham , Mohd Taib Hasniza , Shahar Hanita Kadir
Published: June 2020

Purpose

The purpose of this paper is to examine the determinants of capital structure using a dataset of firms in Malaysia.

Design/methodology/approach

This paper carries out a panel data analysis of 8,270 observations from 827 listed non-financial firms on the Malaysia stock market over the period 2008–2017. To estimate the model and analyse the data collected from the DataStream and World Bank databases, the authors use static panel estimation techniques as well as two-step difference and system dynamic GMM estimator.

Findings

The results show that profitability, growth opportunity, tax-shield, liquidity and cash flow volatility have a negative and significant impact on debt measures. However, the effects of collateral, non-debt tax and earnings volatility on measures of debt are positive and significant. In addition, firm size, firm age, inflation rate and interest rate are important determinants of the present value of debt. The results also show a significant inverse U-shaped relationship between the firm's age and its capital structure. In general, the results support the proposition advocated by the pecking order and trade-off theories.

Practical implications

The results of this study necessitate formulation of various policy measures that can counter the effects of debt on firms.

Originality/value

The present study is among the earliest to use both the book and market value measures of capital structure. It also uses three proxies for each: total debt, long-term debt and short-term debt. It incorporates earning volatility and cash flow volatility as new independent variables in the model. These variables have not previously been used together with both book and market value measures of capital structure. The study also examines the non-monotonic relationship between firm's age and capital structure using a quadratic regression method. It applies both static panel techniques and dynamic GMM estimation techniques to analyse the data.
Capturing customer’s store loyalty through relationship benefits: moderating effect of retail innovation
Authors: Channa Nisar Ahmed , Bhutto Maqsood Hussain , Bhutto Musaira , Bhutto Niaz Ahmed , Tariq Beenish
Published: June 2020

Purpose

Research suggests that innovation plays a key role in creating a competitive edge and business survival in highly competitive industries like retail. Despite the importance of innovation in retail establishments, very limited efforts have been made so far to study how innovation influences consumer behavior in retail establishments. This paper aims to identify the impact of relationship benefits (i.e. confidence, social and special treatment benefits) on consumer’s loyalty with the retail store and examine the moderating effect of retailer innovation in these relationships.

Design/methodology/approach

To conduct this study, a sample comprised of 400 consumers of four retail sectors (i.e. household, electronics, textile and food) was chosen. The data were analyzed through partial least squares structural equation modeling (PLS-SEM) technique.

Findings

The findings of this research suggest a significant positive influence of confidence and special treatment benefits on consumer loyalty and that retail innovation moderates the link between relationship benefits and consumer loyalty.

Originality/value

This research contributes to the existing literature in the domain of retail customer loyalty by empirically testing the under-studied phenomenon of retail innovation with the help of contingency theory.
Causative effects of motivation to transfer learning among relational dyads: the test of a model
Authors: Matthews Brian , Daigle Jamie , Cooper Joy
Published: June 2020

Purpose

The purpose of this study is to validate multiplicative cycle that exists between the job readiness and satisfaction model explored by Matthewset al. (2018), the satisfaction and performance paradigmatic nuances analyzed by Judgeet al. (2001) and Gu and Chi (2009), in addition to the expectancy model theorized by Vroom (1964). The motivation to transfer learning serves as a conveyable variable transmitted within a learning continuum that sustains cyclical outputs.

Design/methodology/approach

An archetype to explore the connection between the three hypothesized theories is created through a neural network program. Exploring this connection develops deeper understandings of the derivatives of employee motivation as it pertains to its effect on readiness, satisfaction, performance and achievement dyads. A detailed analysis of the literature leads to the hypothesis that the motivation to transfer learning creates a multiplicative effect among hypothesized relationships.

Findings

The neural network program scaffolds the proposed general belief that positive effects of transfer motives cause a cyclical effect that continues to perpetuate among hypothesized dyads. Conversely, if this motivation decreases or ceases among one or more dyads, the cyclical effect will retract and, eventually stop.

Originality/value

Based on the neurologic outcome, one central theme emerged: managers must offer opportunities to acquire knowledge through assistive mechanisms (i.e. training) by providing external stability through controlled channels that activates the motivation to transfer learning into new opportunities. The transference of this knowledge produces reconstructive growth opportunities through continuous learning thus increasing performance.
Factors underlying the perceived importance of online student engagement strategies
Authors: Bolliger Doris U. , Martin Florence
Published: June 2020

Purpose

The purpose of this research study is to validate an instrument that measures the importance instructors and students place on online student engagement strategies.

Design/methodology/approach

The online student engagement strategies survey was completed by 160 faculty and 146 students. The data were analysed using descriptive statistics and an exploratory factor analysis. The factor structure was examined using a principal component analysis with an oblique rotation.

Findings

Results show that the Online Engagement Strategies Questionnaire has a valid and reliable structure. Based on the exploratory factor analysis, four engagement constructs emerged including peer engagement, multimodal engagement, instructor engagement, and self-directed engagement. Results and discussion assist in identifying key engagement strategies within this online student engagement framework.

Originality/value

The validated instrument fills a gap in the literature, and it has value to practitioners, researchers, administrators and policy makers because it has practical applications.
Applying the MOA (motivation-opportunity-ability) model for the evaluation of residents' participation in built heritage rehabilitation: the case of Constantine
Authors: Benedjma Iqbal , Mahimoud Aissa
Published: June 2020

Purpose

It has been widely recognised that the participation of residents is a significant issue in contemporary urban heritage conservation. However, studies confirm that the reasons behind residents' engagement are still difficult to assess, particularly in emerging countries. This paper aims to evaluate the factors that incite or prevent residents from participating in built heritage rehabilitation in the old city of Constantine, by applying the motivation-opportunity-ability (MOA) model.

Design/methodology/approach

A questionnaire-based survey was used to collect information from the residents. The collected data were then analysed using the structural equation model (SEM).

Findings

The findings show that the most significant factors affecting residents' participation were related to their motivations and abilities. Interestingly, factors related to the opportunities did not influence participation. Thus, autonomous rehabilitation according to the residents' motivation and abilities is more likely to be adopted.

Research limitations/implications

These findings are limited to the selected sample, and some variables have been eliminated through the SEM analysis.

Originality/value

However, as a first attempt to study residents' participation in built heritage rehabilitation in Constantine, the paper proposes a different perspective for assessing participation by considering its means and ends simultaneously. The paper also provides guidance to local decision-makers to improve the legal framework by implementing factors that encourage residents' involvement in sustainable heritage management.
New semi three-dimensional approach for simulation of Lamb wave clamp-on ultrasonic gas flowmeter
Authors: Mousavi Seyed Foad , Hashemabadi Seyed Hassan , Jamali Jalil
Published: June 2020

Purpose

The purpose of this study is to numerically simulate the Lamb wave propagation through a clamp-on ultrasonic gas flowmeter (UGF) in contact mode, using a new semi three-dimensional approach. Moreover, experimental and analytical modeling results for transit time difference method have been used to confirm the simulation results at different gas flow velocities from 0.3 to 2.4 m/s.

Design/methodology/approach

The new semi three-dimensional approach involves the simulation of the flow field of the gas in a three-dimensional model and subsequently the simulation of wave generation, propagation and reception in a two-dimensional (2D) model. Moreover, the analytical model assumes that the wave transitions occur in a 2D mode.

Findings

The new approach is a semi three-dimensional approach used in this work, has better accuracy than a complete 2D simulation while maintaining the computing time and costs approximately constant. It is faster and less expensive than a complete 3D simulation and more accurate than a complete 2D simulation. It was concluded that the new approach could be extended to simulate all types of ultrasonic gas and non-gas flowmeters, even under harsh conditions.

Originality/value

In this work, a new approach for the numerical simulation of all types of ultrasonic flowmeters is introduced. It was used for simulation of a Lamb wave ultrasonic flow meter in contact mode.
Out‐of‐hospital Circulatory Measures to Identify Patients With Serious Injury: A Systematic Review
Authors: Newgard Craig D. , Cheney Tamara P. , Chou Roger , Fu Rongwei , Daya Mohamud R. , O'Neil Maya E. , Wasson Ngoc , Hart Erica L. , Totten Annette M.
Published: June 2020

Objective

The objective was to systematically identify and summarize out‐of‐hospital measures of circulatory compromise as diagnostic predictors of serious injury, focusing on measures usable by emergency medical services to inform field triage decisions.

Methods

We searched Ovid MEDLINE, CINAHL, and the Cochrane databases from 1996 through August 2017 for published literature on individual circulatory measures in trauma. We reviewed reference lists of included articles for additional relevant citations. Measures of diagnostic accuracy included sensitivity, specificity, and area under the receiver operating characteristic curve (AUROC). Indicators of serious injury included resource need, serious anatomic injury, and mortality. We pooled estimates when data permitted.

Results

We identified 114 articles, reporting results of 111 studies. Measures included systolic blood pressure (sBP), heart rate (HR), shock index (SI), lactate, base deficit, and HR variability. Pooled out‐of‐hospital sensitivity estimates were sBP < 90 mm Hg = 19% (95% confidence interval [CI] = 12% to 29%), HR ≥ 110 beats/min = 28% (95% CI = 20% to 37%), SI > 0.9 = 37% (95% CI = 22% to 56%), and lactate > 2.0 mmol/L = 74% (95% CI = 48% to 90%). Pooled specificity estimates were sBP < 90 mm Hg = 95% (95% CI = 91% to 97%), HR ≥ 110 beats/min = 85% (95% CI = 74% to 91%), SI > 0.9 = 85% (95% CI = 72% to 92%), and lactate > 2.0 mmol/L = 62% (95% CI = 51% to 72%). Pooled AUROCs included sBP = 0.67 (95% CI = 0.58 to 0.75), HR = 0.67 (95% CI = 0.56 to 0.79), SI = 0.72 (95% CI = 0.66 to 0.77), and lactate = 0.77 (95% CI = 0.67 to 0.82). Strength of evidence was low to moderate.

Conclusions

Out‐of‐hospital circulatory measures are associated with poor to fair discrimination for identifying trauma patients with serious injuries. Many seriously injured patients have normal circulatory measures (low sensitivity), but when present, the measures are highly specific for identifying patients with serious injuries.
Helping Friends or Influencing Foes: Electoral and Policy Effects of Campaign Finance Contributions
Authors: Schnakenberg Keith E. , Turner Ian R.
Published: June 2020

Campaign finance contributions may influence policy by affecting elections or influencing the choices of politicians once in office. To study the trade‐offs between these two paths to influence, we use a game in which contributions may affect electoral outcomes and signal policy‐relevant information to politicians. In the model, a campaign donor and two politicians each possess private information correlated with a policy‐relevant state of the world. The donor may allocate his or her budget to either an ally candidate who has relatively similar preferences or a moderate candidate whose preferences are relatively divergent from the donor's preferred policy. Contributions that increase the likelihood of the moderate being elected can signal good news about the donor's preferred policy and influence the moderate's policy choice. However, when the electoral effect of contributions is too small to demand sufficiently high costs to deter imitation by groups with negative information, this informational effect breaks down.
Neovascular glaucoma in patients with central retinal vein occlusion: A real‐life study in the anti‐VEGF era
Authors: Casselholm de Salles Manuel , Lindberg Charlotte , Epstein David
Published: June 2020

Purpose

To investigate the characteristics and treatment patterns of patients developing a neovascular event (NE) in the anterior chamber secondary to central retinal vein occlusion (CRVO) in an ordinary clinical setting.

Methods

In this retrospective real‐life study, data from 243 eyes presenting with CRVO during 2012–2013 were collected. Maximum follow‐up was 5 years. All patients that developed NE were included in the analysis.

Results

Of 243 eligible patients, 72 (30%) either presented with or developed NE during the follow‐up. In these 72 patients, 23 (32%) eyes already had evidence of NE at baseline. Twenty‐eight eyes (39%) developed NE after discontinuation of intravitreal therapy for macular oedema (ME). In this subgroup, the NE occurred 15.6 ± 13.8 months after the baseline visit and 4.1 ± 2.6 months after the last injection. Final best‐corrected visual acuity was 8.6 Early Treatment Diabetic Retinopathy Study (ETDRS) letters in the group of patients presenting with NE compared to 8.1 ETDRS letters in the group that developed NE later on. Of the patients presenting with intraocular pressure (IOP) below 30 mmHg, 3/29 (10%) needed subsequent cyclodiode laser therapy compared to 35/43 (81%) patients with a baseline IOP above 30 mmHg (p < 0.001).

Conclusions

In a clinical setting, many patients show evidence of NE already at the first visit. A substantial part of patients develops NE a long time after presentation, commonly a few months after discontinuation of intravitreal therapy for ME. The visual prognosis is similar for patients presenting with NE and patients developing NE during follow‐up. A high baseline IOP predicts the need for subsequent pressure‐lowering procedures.
Placental transfer of pesticides studied in human placental perfusion
Authors: Mathiesen Line , Mørck Thit Aarøe , Poulsen Marie Sønnegaard , Nielsen Jeanette Kolstrup Søgaard , Mose Tina , Long Manhai , Bonefeld‐Jørgensen Eva , Bossi Rossana , Knudsen Lisbeth E.
Published: June 2020

To investigate the transplacental transport of pesticides, the pyrethroid cypermethrin and the fungicide azoles, propiconazole and bitertanol were tested in the placental perfusion model. Cypermethrin, propiconazole and bitertanol were also tested in the BeWo cell transfer model. The pesticides were chosen with the selection criteria: use in Denmark, significant treated areas and knowledge on hormone‐disrupting effects. Propiconazole and bitertanol showed rapid transfer and adsorbance to the system in both placental perfusion and BeWo cell system, whereas cypermethrin had a slower transport across the placental cell layers in the two models. There was no difference between data of the single pesticides and their mixture in either placental perfusion or BeWo cell transfer model. Both the placental perfusion model and the BeWo cell model metabolized the pesticides and released metabolites into both foetal and maternal circulation. Using human exposure models, this study shows the potential exposure of the human foetus to pesticides cypermethrin, propiconazole and bitertanol and their metabolites.