bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in serum amyloid A, plasma high-density lipoprotein cholesterol and apolipoprotein A-I as useful biomarkers for Mycobacterium tuberculosis infection
Authors: Franco Fontes Cleuber , Silva Bidu Nadielle , Rodrigues Freitas Fatima , Maranhão Raul Cavalcante , Santos Monteiro Adriano de Souza , David Couto Ricardo , Martins Netto Eduardo
Published: June 2023

Introduction. In recent years, cholesterol has received interest in the study of infection due to evidence of a relationship between low plasma cholesterol levels and tuberculosis (TB).

Hypothesis/Gap Statement. Plasma lipid profiles of serum amyloid A (SAA), apolipoprotein A-I and high-density lipoprotein cholesterol (HDL-C) are biomarkers associated with symptomatic TB patients.

Objective. We aimed to evaluate plasma lipid profiles of apolipoprotein A-I, SAA and the size of HDL as biomarkers to diagnose symptomatic TB patients.

Methodology. Patients with TB symptoms attending the Instituto Brasileiro para a Investigação da Tuberculose/Fundação José Silveira (IBIT/FJS) between September 2015 and August 2016 for diagnosis of TB were studied. From 129 patients, 97 were classified as pulmonary TB and 32 as negative-bacilloscopy (non-TB group). Medical history, fasting serum and plasma were obtained. Total cholesterol (TC), HDL-C, apolipoprotein A-I and SAA were measured by enzymatic or immunochemical reaction assays. HDL size was measured by laser light-scattering.

Results. In TB patients, TC (147.0±37 vs. 168±44 mg dL−1), HDL-C (37±14 vs. 55±18 mg dL−1) and apolipoprotein A-I (102±41 vs. 156±47 mg dL−1) concentrations were lower (P<0.0001), while HDL particle size (10.16±1.02 vs. 9.62±0.67 nm) and SAA levels (280±36 vs. 19±8 mg L−1) were higher (P<0.0001). Using receiver-operating characteristic curve analysis for predicting TB, the cutoff values were <83.85 mg L−1 for SAA (sensitivity=96.88 %, specificity=78.43 %, P<0.0001), >44.50 mg dL−1 for HDL-C (sensitivity=75 %, specificity=72.16 %, P<0.001) and >118.5 mg dL−1 for apolipoprotein A-I (sensitivity=83.83 %, specificity=72.22 %, P<0.001).

Conclusion. SAA, HDL-C and apolipoprotein A-I are associated with TB infection and could be used as laboratory biomarkers, especially in patients who are negative for alcohol-acid-resistant bacilli.
EMBRACE: Explainable Multitask Burnout Prediction for Resident Physicians using Adaptive Deep Learning
Authors: Alam Saima , Alam Mohammad Arif Ul
Published: June 2023

Medical residency is associated with long working hours, demanding schedules, and high stress levels, which can lead to burnout among resident physicians. Although wearable and machine learning-based interventions can be useful in predicting potential burnout, existing models fail to clinically explain their predictions, thereby undermining the trustworthiness of the research findings and rendering the intervention apparently useless to residents. This paper develops, EMBRACE,ExplainableMultitaskBurnout pRediction usingAdaptivEdeep learning, that employs a novel framework for predicting burnout that is clinically explainable. At first, we develop, a wearable sensor based improved workplace activity and stress detection algorithm, using deep multi-task learning. Next, we present a novel Adaptive Multi-Task Learning (MTL) framework built on top of our activity and stress detection algorithm, to automatically detect burnout. Additionally, this model also completes the resident burnout survey automatically such a way that it can clinically estimate the same burnout level i.e., clinically explainable and trustworthy estimation. We evaluated the efficacy and explainability of EMBRACE using a real-time data collected from 28 resident physicians (2-7 days each) with appropriate IRB approval (IRB# 2021-017).
Unbiased estimation of the population-level motor module
Authors: Matsui Yusuke , Uno Kohei , Nojima Ippei
Published: June 2023

Motor module is a functional neurophysiological command for muscle coordination. In clinical settings, population-level characterization and comparison of motor modules are necessary to evaluate pathophysiological mechanisms and intervention effects. Previous studies have estimated individual motor modules and then compared them, but the validity of capturing the distribution of the latent population has not been fully understood. Our study aimed to address this issue by investigating the accuracy of estimating the population mean of motor modules. Through simulation experiments, we found that previous individual-based approach did not converge regardless of sample size and was vulnerable to noise. We developed an unbiased estimation algorithm using the framework of functional data analysis, which significantly improved estimation accuracy. Our findings highlight statistical challenges for motor module analysis and suggest the need for further research on new computational algorithms using large-scale clinical data.

Graphical Abstract
nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments
Authors: Proks Martin , Herrera Jose Alejandro Romero , Sedzinski Jakub , Brickman Joshua M.
Published: June 2023

Motivation

As a result of advancing single sequencing technology (scRNA-seq), it has become possible to study gene regulatory mechanism(s) and their influence on evolving cell states in time at the level of individual cells. Since 2009, numerous scRNA-seq protocols have been developed, each with its own advantages, disadvantages and library preparation complexities (Ziegenhain et al. 2017). However, the interpretation of data arising from these techniques often shares similar limitations, such as the lack of a standardized pre-processing workflow and consistent data reproducibility. Here we focus on the standardization of the plate based Massively Parallel RNA Single cell Sequencing (MARS-seq, Jaitin et al. 2014) pre-processing pipeline as described in MARS-seq2.0 (Keren-Shaul et al. 2019), which was developed at the Weizmann Institute of Science.

Results

To overcome the limitations mentioned above, we have taken the original MARS-seq2.0 pipeline and revised it to enable implementation using the nf-core framework (Ewels et al. 2020). By doing so, we have simplified pipeline execution enabling streamlined application, with increased transparency and scalability. Additionally, we have further improved the pipeline by implementing a custom workflow for RNA velocity estimation.

Availability and implementation

The pipeline is part of the nf-core bioinformatics community and is freely available athttps://github.com/nf-core/marsseqwith data analysis athttps://github.com/brickmanlab/proks-et-al-2023.
Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution
Authors: Nadalin F. , Marzi M.J. , Pirra Piscazzi M. , Fuentes P. , Procaccia S. , Climent M. , Bonetti P. , Rubolino C. , Giuliani B. , Papatheodorou I. , Marioni J.C. , Nicassio F.
Published: June 2023

Cancer is a highly heterogeneous disease, where phenotypically distinct subpopulations coexist and could be primed to different fates. Both genetic and epigenetic factors may drive cancer evolution, however little is known about whether and how such a process is pre-encoded in cancer clones. Using single-cell multi-omic lineage tracing and phenotypic assays, we investigate the predictive features of either tumour initiation or drug tolerance within the same cancer population. Clones primed to tumour initiationin vivodisplay two distinct transcriptional states at the baseline. Remarkably, these states share a distinctive DNA accessibility profile, highlighting an epigenetic basis for tumour initiation. The drug tolerant niche is also largely pre-encoded, but only partially overlaps the tumour-initiating one and evolves following two genetically and transcriptionally distinct trajectories. Our study highlights coexisting genetic, epigenetic and transcriptional determinants of cancer evolution, unravelling the molecular complexity of pre-encoded tumour phenotypes.
Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
Authors: Wei Jia , Stoesser Nicole , Matthews Philippa C. , Khera Tarnjit , Gethings Owen , Diamond Ian , Studley Ruth , Taylor Nick , Peto Tim E. A. , Walker A. Sarah , Pouwels Koen B. , Eyre David W. ,   COVID-19 Infection Survey team
Published: June 2023

SARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited, especially after widespread national testing stopped. We studied 245,895 adults ≥18y in the UK’s national COVID-19 Infection Survey with at least one infection (identified from positive swab tests done within the study, linked from national testing programmes, or self-reported by participants, up to their last study assessment). We quantified the risk of reinfection in multiple infection waves, including those driven by BA.1, BA.2, BA.4/5, and most recently BQ.1/CH.1.1/XBB.1.5 variants, in which most reinfections occurred. Reinfections had higher cycle threshold (Ct) values (lower viral load) and lower percentages self-reporting symptoms compared with first infections. Across multiple Omicron waves, protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year), but did not change or even slightly increased over time if this was with an even earlier variant (generally >1 year previously). Those 14-180 days after receiving their most recent vaccination had a lower risk of reinfection with all Omicron variants except BA.2 than those >180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30-45 years, and with either low or high Ct values in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; reinfection risk is likely driven as much by viral evolution as waning immunity.
Inflammatory Biomarkers and Physiomarkers of Late-Onset Sepsis and Necrotizing Enterocolitis in Premature Infants
Authors: Kumar Rupin , Kausch Sherry , Gummadi Angela K.S. , Fairchild Karen D. , Abhyankar Mayuresh , Petri William A. , Sullivan Brynne A.
Published: June 2023

Impact

Late-onset sepsis and necrotizing enterocolitis (NEC) in very low birth weight (VLBW, <1500g) premature infants can result in severe morbidity and mortality. Diagnosis is challenging due to overlap with non-infectious conditions, leading to a delayed or unnecessary antibiotic use.

In a single-center cohort of VLBW infants, inflammatory biomarkers were elevated at the time of sepsis due to Gram-negative sepsis or NEC, but not other sepsis; compared to times without sepsis or NEC.

Physiomarkers of sepsis correlate with some biomarkers of sepsis, and combining their information could help in the early diagnosis of sepsis.

Background

Early diagnosis of late-onset sepsis (LOS) and necrotizing enterocolitis (NEC) in VLBW (<1500g) infants is challenging due to non-specific clinical signs. Inflammatory biomarkers increase in response to infection, but non-infectious conditions also cause inflammation in premature infants. Physiomarkers of sepsis exist in cardiorespiratory data and may be useful in combination with biomarkers for early diagnosis.

Objectives

To determine whether inflammatory biomarkers at LOS or NEC diagnosis differ from times without infection, and whether biomarkers correlate with a cardiorespiratory physiomarker score.

Methods

We collected remnant plasma samples and clinical data from VLBW infants. Sample collection occurred with blood draws for routine laboratory testing and blood draws for suspected sepsis. We analyzed 11 inflammatory biomarkers and a continuous cardiorespiratory monitoring (POWS) score. We compared biomarkers at gram-negative (GN) bacteremia or NEC, gram-positive (GP) bacteremia, negative blood cultures, and routine samples.

Results

We analyzed 188 samples in 54 VLBW infants. Biomarker levels varied widely, even at routine laboratory testing. Several biomarkers were increased at the time of GN LOS or NEC diagnosis compared with all other samples. POWS was higher in patients with LOS and correlated with five biomarkers. IL-6 had 78% specificity at 100% sensitivity to detect GN LOS or NEC and added information to POWS (AUC POWS = 0.610, POWS + IL-6 = 0.680).

Conclusion(s)

Inflammatory biomarkers discriminate sepsis due to GN bacteremia or NEC and correlate with cardiorespiratory physiomarkers. Baseline biomarkers did not differ from times of GP bacteremia diagnosis or negative blood cultures.
Perceived barriers and facilitators to geriatric trauma risk assessment: Instrument development and validation
Authors: Adeyemi Oluwaseun , Konda Sanjit , Grudzen Corita , DiMaggio Charles , Esper Garrett , Rogers Erin , Goldfeld Keith , Blecker Saul , Chodosh Joshua
Published: June 2023

Background

In the fast-paced and high-stress environment of the ED, conducting a thorough and efficient risk assessment is may be associated with various challenges such as time constraints and competing priorities. The aim of this study is to develop and validate a survey instrument that will comprehensively assesses emergency provider and nurses perceived barriers and facilitators to geriatric trauma risk assessment.

Methods

We designed two six-item survey that each assesses the barriers and facilitators to geriatric trauma risk assessment using the American College of Surgeons geriatric trauma management guidelines. Each item in the survey has a quantitative section, answered on a binary scale, and a qualitative open ended responses. Nine content experts performed content validation of the items in the scale and we computed Cohen’s Kappa, and item and scale content validity indices (CVIs).

Results

Most of the experts were male (56%), and non-Hispanic Whites (44%). A third of the content experts are MDs. Of the six items in the perceived barriers scale, five items were retained. The Cohen’s Kappa value across the five items ranged from 0.4 to 0.9 and the item and scale CVIs for the five items were 0.76 each. Of the six items in the perceived facilitators to geriatric trauma risk assessment, all six items were retained. The Cohen’s Kappa value across the six items was 1.00 and the item and scale CVIs for the six items were 1.00 each.

Conclusion

We presents an instrument that can assess the perceived barriers and facilitators to geriatric trauma risk assessment experienced by emergency providers and nurses.
A modular approach to handlein-vivodrift correction for high-density extracellular recordings
Authors: Garcia Samuel , Windolf Charlie , Boussard Julien , Dichter Benjamin , Buccino Alessio P. , Yger Pierre
Published: June 2023

High-density neural devices are now offering the possibility to record from neuronal populationsin-vivoat unprecedented scale. However, the mechanical drifts often observed in these recordings are currently a major issue for “spike sorting”, an essential analysis step to identify the activity of single neurons from extracellular signals. Although several strategies have been proposed to compensate for such drifts, the lack of proper benchmarks makes it hard to assess the quality and effectiveness of motion correction. In this paper, we present an exhaustive benchmark study to precisely and quantitatively evaluate the performance of several state-of-the-art motion correction algorithms introduced in literature. Using simulated recordings with induced drifts, we dissect the origins of the errors performed while applying motion-correction algorithm as a preprocessing step in the spike sorting pipeline. We show how important it is to properly estimate the positions of the neurons from extracellular traces in order to correctly estimate the probe motion, compare several interpolation procedures, and highlight what are the current limits for motion correction approaches.

Significance statement
Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming
Authors: Leles Suzana G. , Levine Naomi M.
Published: June 2023

Phytoplankton are responsible for half of all oxygen production and drive the ocean carbon cycle. Metabolic theory predicts that increasing global temperatures will cause phytoplankton to become more heterotrophic and smaller. Here we uncover the metabolic trade-offs between cellular space, energy, and stress management driving phytoplankton thermal acclimation and how these might be overcome through evolutionary adaptation. We show that the observed relationships between traits such as chlorophyll, lipid content, C:N and size can be predicted based on the metabolic demands of the cell, the thermal dependency of transporters, and changes in membrane lipids. We suggest that many of the observed relationships are not fixed physiological constraints but rather can be altered through adaptation. For example, the evolution of lipid metabolism can favor larger cells with higher lipid content to mitigate oxidative stress. These results have implications for rates of carbon sequestration and export in a warmer ocean.

Teaser

A tale of how photosynthetic microbes might defy current trends to become larger and grow faster in a warmer ocean.
Characterization of a uranium-tolerant green microalga of the genusCoelastrellawith high potential for the remediation of metal-polluted waters
Authors: Beaulier Camille , Dannay Marie , Devime Fabienne , Baggio Célia , Sakkout Nabila El , Raillon Camille , Courson Olivier , Bourguignon Jacques , Alban Claude , Ravanel Stéphane
Published: June 2023

Uranium (U) pollution of terrestrial and aquatic ecosystems poses a significant threat to the environment and human health because this radionuclide is chemotoxic. Characterization of organisms that tolerate and accumulate U is critical to decipher the mechanisms evolved to cope with the radionuclide and to propose new effective strategies for bioremediation of U-contaminated environments. Here, we isolated a unicellular green microalga of the genusCoelastrellafrom U-contaminated wastewater. We showed thatCoelastrellasp. PCV is much more tolerant to U thanChlamydomonas reinhardtiiandChlorella vulgaris.Coelastrellais able to accumulate U very rapidly, then gradually release it into the medium, behaving as an excluder to limit the toxic effects of U. The ability ofCoelastrellato accumulate U is remarkably high, with up to 600 mg U sorbed per g dry biomass.Coelastrellais able to grow and maintain high photosynthesis in natural metal-contaminated waters from a wetland near a reclaimed U mine. Over a single one-week growth cycle,Coelastrellais able to capture 25-55% of U from contaminated waters and demonstrates lipid droplet accumulation.Coelastrellasp. PCV is a very promising microalga for the remediation of polluted waters with valorization of algal biomass that accumulates lipids.

Graphical abstract
The catalytic-independent function of LSD1 modulates the epigenetic landscape of mouse embryonic stem cells
Authors: Malla Sandhya , Kumari Kanchan , Martinez-Gamero Carlos , García-Prieto Carlos A. , Stransky Stephanie , Caroli Jonatan , Álvarez-Errico Damiana , Saiki Paulina Avovome , Lai Weiyi , Lyu Cong , Gilthorpe Jonathan D. , Wang Hailin , Sidoli Simone , Mattevi Andrea , Mateus Andre , Esteller Manel , Roman Angel , Aguilo Francesca
Published: June 2023

Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di-methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for embryonic stem cell (ESC) self-renewal but is required for ESC growth and differentiation. Reexpression of a catalytically-dead LSD1 (LSD1MUT) recovers the proliferation capability of ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, a gain of H3K4me1 inLsd1knockout (KO) ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUTresults in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUTcontrol protein stability of UHRF1 and DNMT1 through interaction with the ubiquitin-specific peptidase 7 (USP7) and, consequently, inhibiting DNMT1 and UHRF1 ubiquitylation. Our studies elucidate for the first time a novel mechanism by which the scaffolding function of LSD1 controls DNA methylation in ESCs.
High genomic plasticity and unique features ofXanthomonas translucenspv.graminisrevealed through comparative analysis of complete genome sequences
Authors: Goettelmann Florian , Koebnik Ralf , Roman-Reyna Veronica , Studer Bruno , Kölliker Roland
Published: June 2023

Background

Xanthomonas translucenspv.graminis(Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.

Results

In this study, we produced high-quality, complete genome sequences of four strains ofXtg, complementing the recently obtained complete genome sequence of theXtgpathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found inXtgand corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation ofXtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes.

Conclusion

These results suggest a high adaptability ofXtg, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific toXtgwere identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation ofXtg.
A one-track model for spatiotemporal coordination ofBacillus subtilisseptal cell wall synthesis
Authors: Whitley Kevin D. , Grimshaw James , Roberts David M. , Karinou Eleni , Stansfeld Phillip J. , Holden Séamus
Published: June 2023

Bacterial cell division requires synthesis of a septal peptidoglycan (sPG) wall across the middle of the cell. This is accomplished by the divisome synthesis complex in coordination with numerous other division proteins—such as the essential tubulin homolog FtsZ—but the molecular mechanism of its spatiotemporal regulation remains unclear. Here, we investigate the dynamics of sPG synthesis in the model Gram-positive bacteriumBacillus subtilisusing live-cell single-molecule imaging of the divisome transpeptidase PBP2B. In contrast to previous models for division, we show that there is a single population of processively-moving PBP2B molecules whose motion is driven by peptidoglycan synthesis and is not associated with FtsZ treadmilling. However, although the motions of PBP2B and FtsZ are asynchronous, we demonstrate that processive PBP2B motion is partially dependent on FtsZ treadmilling. Additionally, we provide evidence that the divisome synthesis complex is multimeric. Our results support a new model for division inB. subtiliswhere a multimeric synthesis complex follows a single track dependent on sPG synthesis whose activity and dynamics are asynchronous with FtsZ treadmilling.
Post-Transplant Administration of G-CSF Impedes Engraftment of Gene Edited Human Hematopoietic Stem Cells by Exacerbating the p53-Mediated DNA Damage Response
Authors: Araki Daisuke , Chen Vicky , Redekar Neelam , Salisbury-Ruf Christi , Luo Yan , Liu Poching , Li Yuesheng , Smith Richard H. , Dagur Pradeep , Combs Christian , Larochelle Andre
Published: June 2023

Granulocyte colony stimulating factor (G-CSF) is commonly used as adjunct treatment to hasten recovery from neutropenia following chemotherapy and autologous transplantation of hematopoietic stem and progenitor cells (HSPCs) for malignant disorders. However, the utility of G-CSF administration afterex vivogene therapy procedures targeting human HSPCs has not been thoroughly evaluated. Here, we provide evidence that post-transplant administration of G-CSF impedes engraftment of CRISPR-Cas9 gene edited human HSPCs in xenograft models. G-CSF acts by exacerbating the p53-mediated DNA damage response triggered by Cas9- mediated DNA double-stranded breaks. Transient p53 inhibition in culture attenuates the negative impact of G-CSF on gene edited HSPC function. In contrast, post-transplant administration of G-CSF does not impair the repopulating properties of unmanipulated human HSPCs or HSPCs genetically engineered by transduction with lentiviral vectors. The potential for post-transplant G-CSF administration to aggravate HSPC toxicity associated with CRISPR-Cas9 gene editing should be considered in the design ofex vivoautologous HSPC gene editing clinical trials.

Graphical Abstract
Inflammatory macrophages prevent colonic goblet and enteroendocrine cell differentiation through Notch signaling
Authors: Atanga Roger , Romero Aaron S. , Hernandez Anthony Jimenez , Peralta-Herrera Eduardo , Merkley Seth D. , In Julie G. , Castillo Eliseo F.
Published: June 2023

Inflammatory macrophages in the intestine are a key pathogenic factor driving inflammatory bowel disease (IBD). Here, we report the role of inflammatory macrophage-mediated notch signaling on secretory lineage differentiation in the intestinal epithelium. Utilizing IL-10-deficient (Il10-/-) mice, a model of spontaneous colitis, we found an increase in Notch activity in the colonic epithelium as well as an increase in intestinal macrophages expressing Notch ligands, which are increased in macrophages upon inflammatory stimuli. Furthermore, a co-culture system of inflammatory macrophages and intestinal stem and proliferative cells during differentiation reduced goblet and enteroendocrine cells. This was recapitulated when utilizing a Notch agonist on human colonic organoids (colonoids). In summary, our findings indicate that inflammatory macrophages upregulate notch ligands that activate notch signaling in ISC via cell-cell interactions, which in turn inhibits secretory lineage differentiation in the gastrointestinal (GI) tract.
The evolutionary history of hepaciviruses
Authors: Li YQ , Ghafari M , Holbrook AJ , Boonen I , Amor N , Catalano S , Webster JP , Li YY , Li HT , Vergote V , Maes P , Chong YL , Laudisoit A , Baelo P , Ngoy S , Mbalitini SG , Gembu GC , Akawa P Musaba , Goüy de Bellocq J , Leirs H , Verheyen E , Pybus OG , Katzourakis A , Alagaili AN , Gryseels S , Li YC , Suchard MA , Bletsa M , Lemey P
Published: June 2023

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within theHepacivirusgenus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n =1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of theHepacivirusgenus.

Significance

Since the discovery of Hepatitis C virus, the search for animal virus homologues has gained significant traction, opening up new opportunities to study their origins and long-term evolutionary dynamics. Capitalizing on a large-scale screening of wild mammals, and genomic sequencing, we expand the novel rodent host range of hepaciviruses and document further virus diversity. We infer a significant influence of frequent cross-species transmission as well as some signal for virus-host co-divergence, and find comparative host and geographic structure. We also provide the first formal estimates of the timescale of hepaciviruses indicating an origin of about 22 million years ago. Our study offers new insights in hepacivirus evolutionary dynamics with broadly applicable methods that can support future research in virus evolution.
Technostress and information and communication technology usage among librarians in Nigerian universities
Authors: Olorunfemi Michael , Adekoya Clement Ola
Published: June 2023

Purpose

This paper aims to investigate technostress and information and communication technology (ICT) usage among librarians in Nigerian universities.

Design/methodology/approach

Descriptive survey research design was used for the study. Questionnaire was used for data collection. The data generated were analyzed using mean, frequency count and percentage.

Findings

A moderate extent of psychological, emotional and physical technostress was found among the librarians. The findings further revealed that technostress among the librarians could be reduced through organizational and technical support and the involvement of librarians in the ICT implementation process. The hypotheses tested revealed that there was a significant relationship between technostress and ICT usage among the librarians; female librarians exhibit a higher extent of technostress than male librarians, and there is no difference in the extent of ICT usage between male and female librarians in Nigerian universities.

Practical implications

Librarians cannot effectively use ICTs if they exhibit technostress.

Originality/value

The work is a creative attempt to know the difference in the extent of technostress and ICT usage among male and female librarians in Nigerian universities.
How do firms obtain benefits from quality awards: An empirical study of the winners of the China quality award
Authors: Li Xingxi , Wu Su , Liu Huiming
Published: June 2023

Purpose

Quality awards are widely considered symbols of successful quality management. The purpose of this paper is to empirically test the effects of the China Quality Award (CQA) on firms' performance. The study further explores how the benefits due to CQA are affected by contextual factors.

Design/methodology/approach

Using the data of CQA winners from 2001 to 2016, the event study method is applied to analyze the abnormal performance of winners. Furthermore, multiple regression models are proposed to evaluate the effects of contextual factors on the relationship between the award and profitability.

Findings

The findings show that CQA has positive impacts on profitability and fixed asset efficiency but not on labor productivity. Besides, state-owned firms and firms with high innovation intensity obtain more profitability benefits than others.

Originality/value

This is the first study to explain the relationship between quality awards and firm performance from a theoretical perspective, providing new insights into the quality management and performance literature. Furthermore, this study deepens the understanding of the relationship between quality awards and performance and reveals new implications. Some of the contextual factors examined, such as innovation intensity, are considered for the first time in quality award research.
A new quality measure for acceptance and payment with a QC/QA performance specification using Bayesian updating
Authors: Sullivan James L. , Novak David , Hernandez Eric , Van Den Berg Nick
Published: June 2023

Purpose

This paper introduces a novel quality measure, the percent-within-distribution, or PWD, for acceptance and payment in a quality control/quality assurance (QC/QA) performance specification (PS).

Design/methodology/approach

The new quality measure takes any sample size or distribution and uses a Bayesian updating process to re-estimate parameters of a design distribution as sample observations are fed through the algorithm. This methodology can be employed in a wide range of applications, but the authors demonstrate the use of the measure for a QC/QA PS with upper and lower bounds on 28-day compressive strength of in-place concrete for bridge decks.

Findings

The authors demonstrate the use of this new quality measure to illustrate how it addresses the shortcomings of the percent-within-limits (PWL), which is the current industry standard quality measure. The authors then use the PWD to develop initial pay factors through simulation regimes. The PWD is shown to function better than the PWL with realistic sample lots simulated to represent a variety of industry responses to a new QC/QA PS.

Originality/value

The analytical contribution of this work is the introduction of the new quality measure. However, the practical and managerial contributions of this work are of equal significance.
Leadership and communication: how to assess executive skills
Authors: Biggs Adam , Johnston Scott , Russell Dale
Published: June 2023

Purpose

Leadership assessment programs are intended to ensure that the organization retains or hires high-quality leadership. Among the many skills that must be included, executive communication is a cornerstone of effective leadership. However, there are many techniques to assessing executive communication that impose numerous advantages and disadvantages. The purpose of this study is to explore several techniques for evaluating executive communication skills in leadership assessment programs.

Design/methodology/approach

Building upon case studies from novel commanding officer selection efforts in the military, the current study outlines three possible areas of executive communication for leadership assessment programs: panel-based interviews, guided discussion and executive writing.

Findings

Although each technique offers some advantages, the best technique depends upon the context. Panel-based interviews can provide excellent depth in evaluating candidates, whereas executive writing focuses more upon crafting a deliberate and clear message without the ability to clarify or use nonverbal cues. Selecting an appropriate technique depends greatly upon the workload imposed on the leadership assessment team and the number of candidates available.

Originality/value

Leadership selection programs are often done piecemeal or based on local experience. By building upon novel efforts in military commanding officer selection, the goal is to promulgate effective executive communication techniques that will enhance leadership selection through more effective communication across all levels of leadership positions.
Role of perceived COVID-19 disruption, personality traits and risk perception in determining the investment behavior of retail investors: a hybrid regression-neural network approach
Authors: Manzoor Arfat , Jan Andleebah , Shafi Mohammad , Ashraf Parry Mohammad , Mir Tawseef
Published: June 2023

Purpose

This study aims to assess the impact of personality traits, risk perception and perceived coronavirus disease 2019 (COVID-19) disruption on the investment behavior of individual investors in the Indian stock market.

Design/methodology/approach

This study adopts a survey approach. The sample comprises 315 active retail investors investing in the Indian stock exchange. Two-stage analysis technique regression and Artificial Neural Network (ANN) were used for data analysis. Study hypotheses were tested through regression and ANN was adopted to validate the regression results.

Findings

Two regression models were modeled to test the research hypotheses. Findings showed that risk perception and COVID-19 disruption have a significant positive and neuroticism has a significant negative impact on short-term investment decisions, while the role of conscientiousness in determining short-term investment decisions was not found significant. Results also showed a positive impact of neuroticism and conscientiousness and a negative impact of risk perception on long-term investment decisions. The role of COVID-19 disruption was found negative but insignificant in predicting long-term investment decisions.

Practical implications

This study has practical implications for many parties like retail investors, financial advisors and policymakers. This study will assist the investors to realize that they do not always take rational financial decisions. This study will suggest the financial advisors to use the knowledge of behavioral finance in making the advisors' advisory and wealth management decisions. This study will also assist the policymakers to outline behaviorally well-informed policy decisions to protect the interests of investors.

Originality/value

India is one of the fast-growing economies in the world. India has a vast population of active investors and determining investors' investment behavior adds novelty to this study as developed economies have remained the main focus of previous studies. The other novel feature of this study is that this study tries to assess the impact of COVID-19 disruption along with personality traits and risk perception on investment behavior. The other valuable factor of this study is the use of ANN to predict the relative importance of the exogenous variables.
The influence of gender and social attention to gender equality on applicant acceptance into venture development programs: competing perspectives
Authors: Reutzel Christopher R. , Belsito Carrie A. , Collins Jamie D.
Published: June 2023

Purpose

The purpose of this paper is to add to the small but growing body of research examining the influence of founder gender on new venture access to venture development programs.

Design/methodology/approach

Hypotheses were tested utilizing a sample of 482 nascent technology ventures which applied for admittance into a venture development organization headquartered in the southern region of the United States from March 2004 through February 2016.

Findings

Findings suggest that female-founded applicant ventures experience a higher likelihood of acceptance into venture development programs than male-founded applicant ventures. Results further suggest that social attention to gender equality reduces this effect for female-founded applicant ventures. Findings extend the understanding of the gendered nature of high-technology venturing and venture development organizations.

Research limitations/implications

The findings of this study may not generalize to new ventures operating in other contexts (e.g., non-U.S., low-tech, and other venture development programs). Additionally, this study's design and data limitations do not allow for the establishment of causality or address founder motivations to apply for acceptance into venture development programs.

Originality/value

This study adds to empirical findings regarding the influence of founder gender on new venture acceptance into venture development programs by developing and testing competing hypotheses. This study also extends extant research by examining the moderating effect of social attention to gender equality on the hypothesized relationships between founder gender and acceptance into venture development programs.
Director awards and board effectiveness
Authors: Baran Lindsay , Cheng Silu
Published: June 2023

We explore the impact of prestigious director awards on effectiveness in setting CEO compensation. Consistent with the positive announcement effect for firms with awardees, CEO compensation aligns more closely with shareholder interest and includes enhanced risk‐taking incentives for boards with awardees. The effect is most pronounced when the awardee is on the compensation committee or a committee chair, and results are robust to a 2SLS estimation using an instrumental variable based on connections to prior award winners. We find evidence that both additional prestigious board appointments and enhanced scrutiny of firms with awardees are channels for improvements in CEO compensation.
Patchiness caused by aphid herbivory and ozone events affects aphid's spread
Authors: Menendez Analia I. , Fernandez Sofia L. , Ghersa Claudio M.
Published: June 2023

Aphids exploit different patches that offer a favourable habitat during their life cycle. Continuous colonization of new patches is critical for the survival of these insect pests. We developed a mesocosm experimental system to study the effects of stress regimes on the colonization of plants by aphids. In the first experiment, we treated Eruca sativa Mill (arugula) plants with either low ozone (O3) (ambient air with no O3 added), elevated O3 (ambient air with O3 addition) or low O3 + Myzus persicae aphid feeding, with subsequent observation of natural aphid infestation over time. The second experiment consisted of aphid sources and differently treated aphid sinks. The aphid sources were also exposed to either low or high O3 levels. The colonization of the sinks was then monitored over time and distance from source. The infestation rate was increased if the patches had been recently exposed to aphid herbivory. On the contrary, aphids did not colonize patches that experienced a recent O3 episode. The patches of E. sativa plants without prior biotic or abiotic stress were colonized by aphids at the beginning of the experiment, but infestation was poor and most of the plants remained aphid‐free throughout the experiment. Aphids from control patches had a better chance of successfully disseminate on hosts with previous herbivory, and aphid spread from O3‐stressed plants was generally poor. Hence, the colonization risk for a generalist aphid plague will depend on the space–time arrangement between crop patches with different stress levels. Ozone contamination could have a negative effect on the spread infestation of aphids in annual crops, because of habitat fragmentation. Here, we present important information to understand how physiological traits of individuals can be scaled up to predict changes within populations in a scenario of climate change.
Recalcitrant cutaneous fungal infections—A growing problem
Authors: Koh Xuan Qi , Pan Jiun Yit
Published: June 2023

The incidence and prevalence of recalcitrant cutaneous fungal infections is on the rise. Terbinafine‐resistant Trichophyton has not only been widespread in India, but has also been reported in countries spread throughout the globe. Strains of yeasts such as Malassezia and Candida, which exist both as commensals and as pathogens to the human skin, have also been found to develop resistance to antifungals. Non‐dermatophyte moulds which can colonize and infect damaged nails are especially difficult to treat, not only due to resistance, but also because of poor drug penetration of hard keratin. Psychosocial factors such as the indiscriminate broad‐spectrum antifungal use in agriculture and in medicine, and poor adherence to hygienic measures to break the chain of infection contribute to the development of antifungal resistance. Such environments encourage fungi to develop various resistance mechanisms to withstand antifungal treatment. These include: (a) alteration of the drug target, (b) increasing efflux of drug/metabolites, (c) inactivation of drug, (d) bypass mechanisms or substitution of the pathway affected by the drug, (e) stress adaptation mechanisms and (f) biofilm formation. Understanding of such mechanisms and how they arise are crucial for development of new ways to prevent or overcome resistance. Novel antifungal treatments have recently been approved in the United States of America for treatment of vulvovaginal candidiasis. Ibrexafungerp (enfumafungin derivative) and oteseconazole (tetrazole) differ from their respective related drug classes of echinocandins and triazoles by having different structures, which lend these medicines advantage compared to traditional treatment by having a different binding site and more selectivity for fungi respectively. Other drugs designed to circumvent the known mechanisms of antifungal resistance are also at various phases of development. Concurrent measures at an institutional and individual level to address and limit inappropriate antifungal use to reduce development of antifungal resistance should be undertaken in a concerted effort to address this epidemic.
The effects of fire and stocking density on the unpalatable species Elytropappus rhinocerotis in Renosterveld vegetation in South Africa
Authors: Simons Megan , Samuels Igshaan , Morris Craig , Cupido Clement , Swarts Melvin , Knight Richard
Published: June 2023

Namaqualand Granite Renosterveld is a fire‐prone shrubland in South Africa and is dominated by Elytropappus rhinocerotis, an indigenous unpalatable shrub with encroaching properties. Using vegetation surveys, the study aimed to understand the effects of fire and grazing on the cover, density and plant species associations with E. rhinocerotis. Plant cover was unaffected by fire and grazing. Fire widened the range of densities of E. rhinocerotis, but grazing alone had no impact and thus cannot significantly promote E. rhinocerotis dominance. Stand density did not influence the species composition, which indicates that E. rhinocerotis neither competitively exclude nor actively facilitate other species.