bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of gliovascular functions of Aqp4 readthrough isoforms
Authors: Mueller Shayna M. , White Kelli McFarland , Fass Stuart B. , Chen Siyu , Shi Zhan , Ge Xia , Engelbach John A. , Gaines Seana H , Bice Annie R , Vasek Michael J. , Garbow Joel R. , Culver Joseph P. , Martinez-Lozada Zila , Cohen-Salmon Martine , Dougherty Joseph D. , Sapkota Darshan
Published: July 2023

Aquaporin-4 (AQP4) is a water channel protein that links astrocytic endfeet to the blood-brain barrier (BBB) and regulates water and potassium homeostasis in the brain, as well as the glymphatic clearance of waste products that would otherwise potentiate neurological diseases. Recently, translational readthrough was shown to generate a C-terminally extended variant of AQP4, known as AQP4x, that preferentially localizes around the BBB through interaction with the scaffolding protein α-syntrophin, and loss of AQP4x disrupts waste clearance from the brain. To investigate the function of AQP4x, we generated a novel mouse AQP4 line (AllX) to increase relative levels of the readthrough variant above the ∼15% of AQP4 in the brain of wildtype (WT) mice. We validated the line and assessed characteristics that are affected by the presence of AQP4x, including AQP4 and α-syntrophin localization, integrity of the BBB, and neurovascular coupling. We compared AllXHomand AllXHetmice to wildtype, and to previously characterized AQP4 NoXHetand NoXHommice, which cannot produce AQP4x. Increased dose of AQP4x enhanced perivascular localization of α- syntrophin and AQP4, while total protein expression of the two were unchanged. However, at 100% readthrough, AQP4x localization and formation of higher-order complexes was disrupted. Electron microscopy showed that overall blood vessel morphology was unchanged except for increased endothelial cell vesicles in NoXHommice, which may correspond to a leakier BBB or altered efflux that was identified in NoX mice using MRI. These data demonstrate that AQP4x plays a small but measurable role in maintaining BBB integrity as well as recruiting structural and functional support proteins to the blood vessel. This also establishes a new set of genetic tools for quantitatively modulating AQP4x levels.

Graphical Abstract
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Authors: Islam Md Zohorul , Zimmerman Sam , Weidanz Jon , Ordovas-Montanes Jose , Robben Michael , Luber Jacob M. , Kostic Aleksandar D
Published: July 2023

T cells primarily drive the autoimmune destruction of pancreatic beta cells in Type 1 diabetes (T1D). However, the profound yet uncharacterized diversity of the T cell populations in vivo has hindered obtaining a clear picture of the T cell changes that occur longitudinally during T1D onset. This study aimed to identify T cell clonal expansion and distinct transcriptomic signatures associated with T1D progression in Non-Obese Diabetic (NOD) mice. Here we profiled the transcriptome and T cell receptor (TCR) repertoire of T cells at single-cell resolution from longitudinally collected peripheral blood and pancreatic islets of NOD mice using single-cell RNA sequencing technology. Surprisingly, we detected a considerable high frequency of islet-matching T cell clones in the peripheral circulation and blood-matching T cell clones in the islets. Our analysis showed that transcriptional signatures of the T cells are associated with the matching status of the T cells, suggesting potential future applications as a marker for early prediction of diabetes onset using peripheral T cells. In addition, we discovered a high frequency of transcriptionally distinct double negative (DN) T cells that might arise from naïve and effector backgrounds through the loss of CD4 or CD8 in a yet unknown biological pathway. This study provides a single-cell level transcriptome and TCR repertoire atlas of T cells in NOD mice and opens the door for more research into the causes of type 1 diabetes and inflammatory autoimmune disease using mouse models.
Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing
Authors: Liu Fang , Patt Andrew , Chen Chloe , Huang Ruili , Xu Yanji , Mathé Ewy A. , Zhu Qian
Published: July 2023

Abstract

Drug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
Dopamine challenge reduces mental state attribution accuracy
Authors: Schuster Bianca A. , Sowden Sophie , Rybicki Alicia J. , Fraser Dagmar S. , Press Clare , Hickman Lydia , Holland Peter , Cook Jennifer L.
Published: July 2023

Difficulties in reasoning about others’ mental states (i.e., mentalising / Theory of Mind) are highly prevalent among disorders featuring dopamine dysfunctions (e.g., Parkinson’s disease) and significantly affect individuals’ quality of life. However, due to multiple confounding factors inherent to existing patient studies, currently little is known about whether these socio-cognitive symptoms originate from aberrant dopamine signalling or from psychosocial changes unrelated to dopamine. The present study therefore investigated the role of dopamine in modulating mentalising in a sample of healthy volunteers. We used a double-blind, placebo-controlled procedure to test the effect of the D2 antagonist haloperidol on mental state attribution, using an adaptation of the Heider & Simmel (1944) animations task. On two separate days, once after receiving 2.5mg haloperidol and once after receiving placebo, 33 healthy adult participants viewed and labelled short videos of two triangles depicting mental state (e.g., surprising) and non-mental state (e.g., following) interactions. Using Bayesian mixed effects models we observed that haloperidol decreased accuracy in labelling both mental- and non-mental state animations. Our secondary analyses suggest that dopamine modulates inference from mental- and non-mental state animations via independent mechanisms, pointing towards two putative pathways underlying the dopaminergic modulation ofmentalstate attribution: Action representation and a shared mechanism supporting mentalising and emotion recognition. We conclude that dopamine is causally implicated in Theory of Mind. Our results have implications for the neurochemical basis of socio-cognitive difficulties in patients with dopamine dysfunctions and generate new hypotheses about the specific dopamine-mediated mechanisms underlying social cognition.
FiPhA: An Open-Source Platform for Fiber Photometry Analysis
Authors: Bridge Matthew F. , Wilson Leslie R. , Panda Sambit , Stevanovic Korey D. , Letsinger Ayland C. , McBride Sandra , Cushman Jesse D.
Published: July 2023

Significance

Fiber photometry is a widely used technique in modern behavioral neuroscience, employing genetically encoded fluorescent sensors to monitor neural activity and neurotransmitter release in awake-behaving animals, However, analyzing photometry data can be both laborious and time-consuming.

Aim

We propose the FiPhA (Fiber Photometry Analysis) app, which is a general-purpose fiber photometry analysis application. The goal is to develop a pipeline suitable for a wide range of photometry approaches, including spectrally resolved, camera-based, and lock-in demodulation.

Approach

FiPhA was developed using the R Shiny framework and offers interactive visualization, quality control, and batch processing functionalities in a user-friendly interface.

Results

This application simplifies and streamlines the analysis process, thereby reducing labor and time requirements. It offers interactive visualizations, event-triggered average processing, powerful tools for filtering behavioral events and quality control features.

Conclusions

FiPhA is a valuable tool for behavioral neuroscientists working with discrete, event-based fiber photometry data. It addresses the challenges associated with analyzing and investigating such data, offering a robust and user-friendly solution without the complexity of having to hand-design custom analysis pipelines. This application thus helps standardize an approach to fiber photometry analysis.
Fast Connectivity Gradient Approximation: Maintaining spatially fine-grained connectivity gradients while reducing computational costs
Authors: Nenning Karl-Heinz , Xu Ting , Tambini Arielle , Franco Alexandre R. , Margulies Daniel S. , Colcombe Stanley J. , Milham Michael P.
Published: July 2023

Brain connectome analysis suffers from the high dimensionality of connectivity data, often forcing a reduced representation of the brain at a lower spatial resolution or parcellation. However, maintaining high spatial resolution can both allow fine-grained topographical analysis and preserve subtle individual differences otherwise lost. This work presents a computationally efficient approach to estimate spatially fine-grained connectivity gradients and demonstrates its application in improving brain-behavior predictions.
Robust memory of face moral values is encoded in the human caudate tail: A simultaneous EEG-fMRI study
Authors: Ataei Ali , Amini Arash , Ghazizadeh Ali
Published: July 2023

Moral judgements about people based on their actions is a key component that guides social decision making. It is currently unknown how positive or negative moral judgments associated with a person’s face are processed and stored in the brain. Here, we investigate the long-term memory of moral values associated with human faces using simultaneous EEG-fMRI data acquisition. Results show that only a few exposures to morally charged stories of people, are enough to form long-term memories a day later for a relatively large number of new faces. Event related potentials (ERPs) showed a significant differentiation of remembered good vs bad faces over centerofrontal electrode sites (value ERP). EEG-informed fMRI analysis revealed a subcortical cluster centered on the left caudate tail (CDt) as a correlate of the face value ERP. Importantly neither this analysis nor a conventional whole brain analysis revealed any significant activation in cortical areas in particular the fusiform face area (FFA). Conversely an fMRI-informed EEG source localization using accurate subject-specific EEG head models also revealed activation in the caudate tail. Nevertheless, the detected caudate tail region was found to be functionally connected to the FFA, suggesting FFA to be the source of face-specific information to CDt. These results identify CDt as the main site for encoding the long-term value memories of faces in humans suggesting that moral value of faces activates the same subcortical basal ganglia circuitry involved in processing reward value memory for objects in primates.
miRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice
Authors: Lu Long , Chen Xinyu , Chen Jiaming , Zhang Zaoli , Zhang Zhen , Sun Yanyan , Wang Yuan , Xie Siwen , Ma Yinuo , Song Yuanyuan , Zeng Rensen
Published: July 2023

MicroRNAs (miRNAs) are small non-coding RNAs that play a vital role in plant responses to abiotic and biotic stress. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stress, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its targetSPLgenes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression ofmiPEP156eled to a reduction in the accumulation of reactive oxygen species (ROS) and Cd in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines and seedlings treated with exogenous miPEP156e. In contrast,miPEP156emutants displayed sensitivity to Cd stress due to the elevated accumulation of ROS and Cd. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter and ROS scavenging genes. Moreover, we identified five novel miPEPs involved in regulating Cd resistance through exogenous treatment of seedlings with synthetic corresponding miPEPs. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.
Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics
Authors: Ashwood Brennan , Jones Michael S. , Lee Yumin , Sachleben Joseph R. , Ferguson Andrew L. , Tokmakoff Andrei
Published: July 2023

Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base pairing to minimize the barrier height.
Structure and symmetries of the genetic codes for vertebrate, ascidian and yeast mitochondria
Authors: Kohli Rajeev
Published: July 2023

Genetic codes assign sixty-four codons to twenty amino acids. These assignments are known to follow certain rules. One question long considered but still unresolved is if these rules are derived from an underlying structure in genetic codes. Knowledge of such structure could facilitate better understanding of the biochemical, physico-chemical and evolutionary causes of the observed codon assignments. Our first finding reveals a coherent and symmetric structure in the genetic codes of vertebrate, ascidian, and yeast mitochondria. This structure is derived from a “simple” code that assigns all four codons with the same second nucleotide to a single amino acid if the first nucleotide is C or G, and assigns pairs of codons with the same second nucleotide to a single amino acid if the first nucleotide is A or U, and their third nucleotides are both purines (A and G) or both pyrimidines (U and C). The translation mechanism for the three mitochondria reflects this structure, one tRNA decoding each group of two or four codons into an amino acid. Our second finding is that the mycoplasma/spiroplasma and standard genetic codes are obtained by small sequential modifications of the vertebrate mitochondrial code and retain almost all its symmetries. We use group theory to characterize the symmetries of the simple and mitochondrial codes, and speculate on the implications of the structure for detecting translation errors and the evolution of the genetic code.
Seed size control via phloem end by callose deposition/degradation of β-1,3-glucanase
Authors: Liu Xiaoyan , Nakajima Kohdai P. , Wu Xiaoyan , Zhu Shaowei , Adhikari Prakash Babu , Okada Kentaro , Kurotani Ken-ichi , Ishida Takashi , Nakamura Masayoshi , Sato Yoshikatsu , Xie Liyang , Huang Chen , He Jiale , Sawa Shinichiro , Higashiyama Tetsuya , Notaguchi Michitaka , Kasahara Ryushiro D.
Published: July 2023

Seed formation is crucial for lives of plants as well as humans; however, the mechanisms governing seed size require further investigation. Here, we present a new mechanism to modify the seed size by the newly identified phloem end that support nutrient transport, at the chalazal end of the ovule, however, blocked by callose deposition. Callose is removed after central cell fertilization (open state), allowing nutrients to be transported to the seed. However, if fertilization fails, callose deposition persists (closed state), preventing the phloem end from transporting nutrients. β-1,3-glucanase genes, including putative plasmodesmata-associated proteins (AtBG_ppap), were identified as regulators of callose removal. TheAtbg_ppapmutant had the phloem end in the closed state and produced smaller seeds due to incomplete callose degradation. In contrast, theAtBG_ppapoverexpression line produced larger seeds than the wild type due to continuous callose degradation, indicating that the phloem end regulates substance flow via callose deposition/degradation.
Prevalence, determinants, and trends in the experience and perpetration of intimate partner violence among a cohort of gay, bisexual, and other men who have sex with men in Montréal, Toronto, and Vancouver, Canada (2017-2022)
Authors: Juwono Stephen , Anato Jorge Luis Flores , Kirschbaum Allison L. , Metheny Nicholas , Dvorakova Milada , Skakoon-Sparling Shayna , Moore David M. , Grace Daniel , Hart Trevor A. , Lambert Gilles , Lachowsky Nathan J. , Jollimore Jody , Cox Joseph , Maheu-Giroux Mathieu
Published: July 2023

Purpose

Longitudinal data on the experience and perpetration of intimate partner violence (IPV) among gay, bisexual, and other men who have sex with men (GBM) is limited. We estimated the prevalence of past six-month (P6M) physical and/or sexual IPV (hereafter IPV) experience and perpetration, identified their determinants, and assessed temporal trends, including the impact of the COVID-19 pandemic.

Methods

We used data from the Engage Cohort Study (2017-2022) of GBM recruited using respondent-driven sampling in Montréal, Toronto, and Vancouver. Adjusted prevalence ratios (aPR) for determinants and self-reported P6M IPV were estimated using generalized estimating equations, accounting for attrition (inverse probability of censoring weights) and relevant covariates. Longitudinal trends of IPV were also assessed.

Results

Between 2017-2022, 1,455 partnered GBM (median age 32 years, 82% gay, and 71% white) had at least one follow-up visit. Baseline proportions were 31% for lifetime IPV experience and 17% for lifetime perpetration. During follow-up, P6M IPV experience was more common (6%, 95%CI: 5-7%) than perpetration (4%, 95%CI: 3-5%). Factors associated with P6M IPV experience include prior IPV experience (aPR=2.79, 95%CI: 1.83-4.27), less education (aPR=2.08, 95%CI: 1.14-3.79), and substance use (injection aPR=5.68, 95%CI: 2.92-11.54, non-injection aPR=1.70, 95%CI: 1.05-2.76). Similar factors were associated with IPV perpetration. IPV was stable over time; periods of COVID-19 restrictions were not associated with IPV changes in this cohort.

Conclusion

Prevalence of IPV was high among GBM. Determinants related to marginalization are associated with an increased risk of IPV. Interventions should address these determinants to reduce IPV and improve health.
Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice
Authors: Obr Martin , Percipalle Mathias , Chernikova Darya , Yang Huixin , Thader Andreas , Pinke Gergely , Porley Dario , Mansky Louis M , Dick Robert A , Schur Florian KM
Published: July 2023

Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembledin vitro, as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
The penetration of sunflower root tissues by the parasitic plantOrobanche cumanaWallr. is intracellular
Authors: Auriac MC , Griffiths C , Robin-Soriano A , Legendre A , Boniface MC , Muños S , Fournier J , Chabaud M
Published: July 2023

Parasitic plants cause yield losses for important crops. Among these,Orobanche cumanaWallr, sunflower broomrape, is one of the major pests for sunflower. Previous studies stated that in most cases, the haustorium, a specific parasitic plant organ, penetrates host roots intercellularly. However, host cellular mechanisms involved during the parasitic cells penetration remained poorly described.

We investigated sunflower root cellular behavior during haustorium penetration using various microscopy approaches including live cell imaging of inoculated transgenic fluorescent sunflower roots.

We showed that the haustorium ofO. cumanapenetrated living sunflower root tissues, as a result of the degradation of the host cell wall and the formation of a new host trans-cellular apoplastic compartment for haustorium accommodation. Moreover, broomrape induced cell divisions in outer root tissues at very early stages of the interaction, leading to localized hypertrophy at the site of broomrape attachments.

These findings are a change of paradigm in the research field of parasitic plants. They extend host root intracellular accommodation mechanisms initially shown for symbiotic and pathogenic biotrophic fungi to parasitic plants. It paves the way for future understanding and development of resistance to parasitic plants.

Key message

Combination ofin vivoconfocal, large field and transmission electron microscopy approaches revealed how intimate the relationship between the parasitic plant broomrape (Orobanche cumanaWallr.) and its sunflower host (Helianthus annusL.) is at very early stages of their interaction.
The microbial metabolite Urolithin A reducesC. difficiletoxin expression and repairs toxin-induced epithelial damage
Authors: Ghosh Sweta , Erickson Daniel , Chua Michelle J , Collins James , Jala Venkatakrishna Rao
Published: July 2023

Clostridioides difficileis a gram-positive, anaerobic, spore-forming bacterium that is responsible for antibiotic-associated pseudomembranous colitis.Clostridioides difficileinfection (CDI) symptoms can range from diarrhea to life-threatening colon damage. Toxins produced byC. difficile(TcdA and TcdB) cause intestinal epithelial injury and lead to severe gut barrier dysfunction, stem cell damage, and impaired regeneration of the gut epithelium. Current treatment options for intestinal repair are limited. In this study, we demonstrate that treatment with the microbial metabolite urolithin A (UroA) attenuates CDI-induced adverse effects on the colon epithelium in a preclinical model of CDI-induced colitis. Moreover, our analysis suggests that UroA treatment protects againstC. difficile-induced inflammation, disruption of gut barrier integrity, and intestinal tight junction proteins in the colon of CDI mice. Importantly, UroA treatment significantly reduced the expression and release of toxins fromC. difficile, without inducing bacterial cell death. These results indicate the direct regulatory effects of UroA on bacterial gene regulation. Overall, our findings reveal a novel aspect of UroA activities, as it appears to act at both the bacterial and host levels to protect against CDI-induced colitis pathogenesis. This research sheds light on a promising avenue for the development of novel treatments forC. difficileinfection.

Importance

Therapy forC. difficileinfections includes the use of antibiotics, immunosuppressors, and fecal microbiota transplantation (FMT). However, these treatments have several drawbacks, including the loss of colonization resistance, promotion of autoimmune disorders, and the potential for unknown pathogens in donor samples. To date, the potential benefits of microbial metabolites in CDI-induced colitis have not been fully investigated. Here, we report for the first time that the microbial metabolite Urolithin A has the potential to block toxin production fromC. difficileand enhance gut barrier function to mitigate CDI-induced colitis.
LucFlow: A method to measure Luciferase reporter expression in single cells
Authors: Nooti Sunil , Naylor Madison , Long Trevor , Groll Braydon , Manu
Published: July 2023

Reporter assays, in which the expression of an inert protein is driven by gene regulatory elements such as promoters and enhancers, are a workhorse for investigating gene regulation. Techniques for measuring reporter gene expression vary from single-cell or single-molecule approaches having low throughput to bulk Luciferase assays that have high throughput. We developed a Luciferase Reporter Assay using Flow-Cytometry (LucFlow), which measures reporter expression in single cells immunostained for Luciferase. We optimized and tested LucFlow with a murine cell line that can be differentiated into neutrophils, into which promoter-reporter and enhancer-promoter-reporter constructs have been integrated in a site-specific manner. The single-cell measurements are comparable to bulk ones but we found that dead cells have no detectable Luciferase protein, so that bulk assays underestimate reporter expression. LucFlow is able to achieve a higher accuracy than bulk methods by excluding dead cells during flow cytometry. Prior to fixation and staining, the samples are spiked with stained cells that can be discriminated during flow cytometry and control for tube-to-tube variation in experimental conditions. Computing fold change relative to control cells allows LucFlow to achieve a high level of precision. LucFlow, therefore, enables the accurate and precise measurement of reporter expression in a high throughput manner.
Resolution enhancement with deblurring by pixel reassignment (DPR)
Authors: Zhao Bingying , Mertz Jerome
Published: July 2023

Improving the spatial resolution of a fluorescence microscope has been an ongoing challenge in the imaging community. To address this challenge, a variety of approaches have been taken, ranging from instrumentation development to image post-processing. An example of the latter is deconvolution, where images are numerically deblurred based on a knowledge of the microscope point spread function. However, deconvolution can easily lead to noise-amplification artifacts. Deblurring by post-processing can also lead to negativities or fail to conserve local linearity between sample and image. We describe here a simple image deblurring algorithm based on pixel reassignment that inherently avoids such artifacts and can be applied to general microscope modalities and fluorophore types. Our algorithm helps distinguish nearby fluorophores even when these are separated by distances smaller than the conventional resolution limit, helping facilitate, for example, the application of single-molecule localization microscopy in dense samples. We demonstrate the versatility and performance of our algorithm under a variety of imaging conditions.
Enterobacter Sp. SM3Exhibits Run-and-Tumble Motility
Authors: Johnson Silverio , Freedman Brian , Tang Jay X.
Published: July 2023

The recent discovery of the peritrichous, swarm-competent bacteriumEnterobacter sp. SM3has offered a new opportunity to elucidate the role of swarming motility in the gut microbiome. Here we present first findings of the run-and-tumble behavior ofSM3in both a control solution of motility buffer and upon bulk exposure to the chemoattractants serine and aspartate, drawing a comparison with the well-studied behavior ofE. coli. It was found thatSM3runs with an average speed of approximately 30 µm/s for an average duration of 0.77 s. Tumble events occur for an average duration of 0.11 s with a 69◦average tumble angle. Both values are similar to that ofE. coli. When exposed to serine,SM3suppresses the frequency of tumble events, which in turn increases the average run duration. In addition, the average tumble angle was found to decrease in response to serine. However, when exposed to up to a millimolar concentration of aspartate,SM3does not demonstrate a notable change in run-and-tumble parameters. These results suggest that run-and-tumble is the characteristic swimming behavior ofSM3in its planktonic state. These findings serve as a benchmark in a quest to determine the connection among swimming, swarming, and the complex dynamics of the gut microbiome.

IMPORTANCE

Bacteria form the largest domain of living creatures on this planet. Our interactions with bacteria influence us in many ways, not the least of which being in regards to human health. A recently identified species of gut bacteria,Enterobacter sp. SM3, has been shown to reduce intestinal inflammation, suggesting that swarming could play a physiologically beneficial role. In this report, we study the motility of individualSM3bacteria This study is an essential step towards an overarching goal to understand the influence of bacterial motility on human health.
In silico designing of a multitope vaccine against Rhizopus microspores
Authors: Venkateswarulu T.C. , Shaik Asra Tasneem , Meduri Druthi Sri , Vajiha Vajiha , Dhusia Kalyani , Peele Abraham
Published: July 2023

Purpose

Mucorales has been described to be widely distributed during the most recent COVID-19 pandemic, with a greater frequency of disease in India, particularly among those with immune deficiencies. This study aims to use computational tools to develop a vaccine.

Design/methodology/approach

The authors investigated at Mucorales proteins that had previously been associated to virulence factors. Recent research suggests that a vaccine based on high-level cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B-cell lymphocyte (BCL) epitopes from diverse proteins might be developed. Furthermore, the vaccine assembly contains the targeted epitopes as well as PADRE peptides to induce an immune response. Computational approaches were used to analyze the immunological parameters used to build the suggested vaccine and validate its TLR-3 binding.

Findings

These studies show that the vaccination is capable of triggering a particular immune response. The authors offer a technique for developing and evaluating candidate vaccines using computational tools. To the best of their knowledge, this is the first immunoinformatic research of a prospective mucormycosis vaccine.

Originality/value

During this audit, a successful attempt was made to create a subunit MEV against black fungus. In the current study, MEV has been proposed as a suitable neutralizer candidate since it is immunogenic, secure, stable and interacts with human receptors. A stream study, on the other hand, is produced via a mixed vaccinosis approach. Following that, vaccinologists may perform more exploratory testing to evaluate whether the vaccine is effective.
COVID stress and depressive symptoms among high school students: a moderated mediation model of sleep quality and optimism
Authors: Nguyen Hung Thanh , Ho Thi Truc Quynh , Dau Minh Long
Published: July 2023

Purpose

This study aimed to investigate whether optimism buffers an indirect relationship between COVID stress and depressive symptoms via poor sleep quality among Vietnamese high school students.

Design/methodology/approach

Six hundred and eighty-five participants completed the Coronavirus Stress Measure, the Life Orientation Test-Revised, the Pittsburgh Sleep Quality Index and the Depression, Anxiety and Stress Scales. Process Macro 3.5 for SPSS (Model 4 and Model 14) was used to analyze the mediating effect and moderated mediation effect.

Findings

The results indicated that COVID stress was associated with an increase in depressive symptoms via the indirect pathway of poor sleep quality. Furthermore, optimism moderated the indirect relationship between COVID stress and depressive symptoms through poor sleep quality among Vietnamese students.

Originality/value

The study's findings may serve as a basis for the development of depression prevention interventions for students with high COVID stress in the COVID-19 pandemic.
The global market upsurge in web traffic and revenues during the epidemic: an exploratory research of e-learning companies
Authors: Bagdi Himanshu , Pothabathula Seshu Vardhan , Sharma Latika , Bulsara Hemantkumar P.
Published: July 2023

Purpose

The purpose of this paper is to understand the market for various e-learning platforms existing globally. The global pandemic transformed the traditional education sector into an e-learning industry and impacted the digital education sector proportionally. The wide impact on people to maintain a social distance shortened the space and enhanced student engagement with digital screens. The merchandise of electronic gadgets and e-learning platforms boosted global revenues ever before.

Design/methodology/approach

A digital data analytical tool retrieved the data for e-learning companies. While screening companies, the authors came up with more than 150 and later narrowed it to 71. Furthermore, revenues and market capitalisation data were collected from open-source websites of respective e-learning platforms at national and international stock exchanges. The data from the year 2018 to 2021 was used to predict the compound annual growth rate (CAGR) of the 2022–2027 market value of e-learning companies. The demographics of the statistical data were plotted using GraphPad Prism and Python Plotly. Also, the study attempted to underpin the association of annual revenue with market capitalisation for e-learning companies using Statistical Package for the Social Sciences (SPSS).

Findings

The financials of the e-learning platforms were compared from 2018 to 2021 based on the stock market exchange, which showed a gradual increase in revenues and influenced the market capitalisation by the 2022 financial year. Also, simultaneously validating the CAGR of 13.16%, the expected revenues from 2022 to 2027 were $830bn. The data plotted on the atlas choropleth exhibiting the e-learning users increased globally by 2022. The Web traffic data validated by the browsing gadget helped to validate the increase in revenues of the electronic gadget companies.

Originality/value

To the best of the authors’ knowledge, this is one of the pioneer studies postulating the study of e-learning demographics comparing the e-learning influence on the global digital market, Web user traffic and the education sector. The demographics of e-learning users by age, gender and gadget distribution validate the e-learning induction globally.
Conceptual model of predicting employee performance through the mediating role of employee engagement and empowerment
Authors: Al Zeer Imad , Ajouz Mousa , Salahat Mahmoud
Published: July 2023

Purpose

Considering the importance of employee performance in the changes in state higher education institutions, this study aims to conceptualize the mediating role of employee engagement and empowerment in predicting employee performance.

Design/methodology/approach

The study uses a quantitative survey method to collect data from staff members employed in higher education institutions and applies a partial least squares structural equation modeling to analyze the data. In addition, the study performs a systematic bibliometric analysis of contemporary literature on the factors influencing employee performance.

Findings

The study's results confirm employee engagement and empowerment's critical role in improving employee performance. Unexpectedly, the study also has found no supporting evidence of the relationship between work environment and employee performance. Further, the proposed model explains 51.6% of the variance in employee productivity.

Originality/value

Among the theoretical implications of this study are the importance of introducing new and theoretically sound mediators to explain how the relationship between a higher education institution's employee engagement and empowerment and its employees' performance unfolds.
Indian start-ups going public: return and volatility of stocks during bear and bull regimes
Authors: Das Khanindra Ch.
Published: July 2023

Purpose

Start-ups are successful in receiving valuation in billions of US dollars prior to initial public offering (IPO). However, to sustain higher valuation, the stocks need to perform consistently after the IPO. Short-run stock performance of India-based start-ups during the first year of IPO listing from March 2021 to March 2022 is analysed.

Design/methodology/approach

The paper deals with the new generation start-ups' stock performance in emerging market in terms of total and abnormal return generated in comparison to the market (NIFTY-200). Further, the volatility of returns during bear and bull regimes is analysed through a family of Markov-switching GARCH models using both normal and skewed distributions.

Findings

The results suggest that start-up stocks are more volatile during bear regime than in the bull run in market-based economies where price limit policy does not apply. Besides, the cumulative abnormal return over the market return was lower for majority of start-up IPO stocks.

Social implications

Though negative returns of the start-up stocks during the first year of IPO need not be surprising, higher volatility during bear regime is a matter of concern as it could severely impact retail investors and founders. The results hold implication for IPO regulation in emerging markets and for retail investors desirous of investing in start-up stocks.

Originality/value

Volatility of return is examined using a state-space model during the first year of the start-up IPO listing. The study contributes to the emerging market IPO literature by examining IPO performance in market-based economy. Previous IPO performance studies in emerging markets are predominantly based on ecosystems where start-ups are subjected to price limit policy, and it does not reflect the true nature of IPO performance across emerging markets.
Towards post-COVID-19 responsible academic air travel
Authors: Tseng Sherry Hsueh-Yu , Higham James , Lee Craig
Published: July 2023

Purpose

This study aims to shape the future of academic air travel practices by identifying the challenges between existing air travel-related policies and practicing responsible air travel.

Design/methodology/approach

With increasing concern over global warming, many institutions have implemented sustainability programmes to tackle carbon emissions and create sustainable practices. COVID-19 has resulted in many universities seizing the opportunity to maintain reduced levels of academic air travel emissions. However, the outdated travel-related policies have caused much scope for tension arising from the policy gap between pre-COVID university travel policies and academics' intentions to reduce their air travel emissions. This study interviewed academics at the University of Otago (New Zealand) to elicit detailed narratives of their perceptions of the university’s air travel-related policies, generating co-created and mutually informative insights.

Findings

The present programme of in-depth interviews with academic staff revealed that while most staff accept the need to reduce air travel emissions, they face challenges concerning career advancement, equity and equality issues. Universities will need to evolve their travel-related policies to address these challenges, enabling academics to adopt new practices that do not unreasonably disadvantage themselves, their disciplines or their institutions.

Originality/value

The findings contribute to the literature by highlighting the institutional policy challenges to responsible academic air travel and the need for the current policy gap to be resolved. The authors propose directions for a responsible academic air travel future that will require both top-down and bottom-up approaches involving academics and institutions.
Dark side of blockchain technology adoption in SMEs: an Indian perspective
Authors: O.N. Arunkumar , D. Divya , Kurian Jikku Susan
Published: July 2023

Purpose

The purpose of this paper is to understand the dark side of blockchain technology (BCT) adoption in small and mid-size enterprises. The focus of the authors is to decode the intricate relationship among the selected variables missing in the existing literature.

Design/methodology/approach

A focused group approach is initiated by the authors to identify the barriers. Total interpretive structural modeling, Matrice d'impacts croisés multiplication appliquée á un classment, that is, matrix multiplication applied to classification and decision-making trial and evaluation laboratory are used to analyze the complex relationships among identified barriers.

Findings

This study finds that implementation of BCT reduces maintenance cost by withdrawing manual effort, as BCT has better capability to quantify the internal status of the system (observability characteristic). The observability characteristic of BCT provides high compatibility to the system. This study also finds that the compatibility of BCT with the organization reduces implementation cost and facilitates project management. The findings of this study recommend analyzing maintenance cost and compatibility of BCT before implementing it. Small and mid-size enterprises can select complex BCT depending on the sophistication level of IT usage and IT project management capabilities.

Research limitations/implications

This study comes with various limitations, where the model developed by the authors may not be conclusive, as it is based exclusively on expert opinion. The samples collected may not help in validating the model statistically. Though the model has its limitations, it can still be considered as a nascent initiative for further investigation using structural equation modeling.

Originality/value

The outcomes of the theoretical and managerial contributions of the study can be categorized into three levels. This study can be used both by the industrialists and researchers to understand the barriers and the recovery methods thereafter. Suggestions that serve as future directives are also discussed by the authors.
The influence of open and closed innovation practices on economic performance: empirical evidence from Indian biotechnology industry
Authors: Hungund Sumukh , Gaur Jighyasu , Narayan Aishwarya
Published: July 2023

Purpose

The paper aims to examine the influence of closed and open innovation practices on economic performance. This papert also examines the mediating roles of innovation performance and firm performance. The study uses innovation theory based on knowledge management for theoretical support.

Design/methodology/approach

The methodology involves two steps. First, all the variables relevant to the adoption of innovative approaches and performance parameters are identified. Subsequently, primary data are gathered from decision-makers of 200 biotechnological firms and a structural equation modeling analysis is performed.

Findings

The study's results showed that the open innovation practice, such as interaction with large research and development (R&D) firms and customers, influences the performance parameters. The findings indicate that closed and open innovation practices positively impact performance measures like innovation, firm and economic performance. The results also indicate the mediating role of firm performance. However, the innovation performance was not found to mediate the relationship.

Originality/value

This examination gives experimental bits of knowledge from any confining influence innovation approaches in India. Analysts and specialists of firms can use the results of the current study to comprehend the effect of various innovation practices on different performance measures.
Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history
Authors: Zou Yang , Wei Zijie , Xiao Keyan , Wu Zhigang , Xu Xinwei
Published: July 2023

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high‐quality chromosome‐level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high‐depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage‐specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high‐altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.