bluuebunny/crossref_metadata_2025 huggingface dataset:
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery
Authors: Novella-Rausell Claudio , Grudniewska Magda , Peters Dorien J. M. , Mahfouz Ahmed
Published: July 2022

The cellular diversity and complexity of the kidney are on par with its physiological intricacy. Although our anatomical understanding of the different segments and their functions is supported by a plethora of research, the identification of distinct and rare cell populations and their markers remains elusive. Here, we leverage the large number of cells and nuclei profiles using single-cell (scRNA-seq) and single-nuclei (snRNA-seq) RNA-sequencing to build a comprehensive atlas of the adult mouse kidney. We created MKA (Mouse Kidney Atlas) by integrating 59 publicly available single-cell and single-nuclei transcriptomic datasets from eight independent studies. The atlas contains more than 140.000 cells and nuclei covering different single-cell technologies, age, and tissue sections. To harmonize annotations across datasets, we constructed a hierarchical model of the cell populations present in our atlas. Using this hierarchy, we trained a model to automatically identify cells in unannotated datasets and evaluated its performance against well-established methods and annotation references. Our learnt model is dynamic, allowing the incorporation of novel cell populations and refinement of known profiles as more datasets become available. Using MKA and the learned model of cellular hierarchies, we predicted previously missing cell annotations from several studies and characterized well-studied and rare cell populations. This allowed us to identify reproducible markers across studies for poorly understood cell types and transitional states.
PyGenePlexus: A Python package for gene discovery using network-based machine learning
Authors: Mancuso Christopher A , Liu Renming , Krishnan Arjun
Published: July 2022

PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest based on a molecular interaction network using supervised machine learning. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes.

Availability and Implementation

https://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus

Contact

arjun@msu.edu
“Rotating Frame Relaxation for Magic Angle Spinning Solid State NMR, A Promising Tool for Characterizing Biopolymer Motion”
Authors: Keeler Eric , McDermott Ann
Published: July 2022

Magic angle spinning NMR rotating frame relaxation measurements provide a powerful experimental strategy to probe biomolecules dynamics, as is illustrated by numerous recent applications. We discuss experimental strategies for this class of experiments, with a particular focus on systems where motion-driven modulation of the chemical shift interaction is the main mechanism for relaxation. We also explore and describe common strategies for interpreting the data sets and extracting motion timescale, activation energy, and angle or order parameters from rotating frame relaxation data. Using model free analysis, and numerical simulations, including time domain treatment, we explore conditions under which it is possible to obtain accurate and precise information about the timescales of motions. Overall, with rapid technical advances in solid state NMR, there is a bright future for this class of studies.
tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications
Authors: Holmes Andrew D. , Howard Jonathan M. , Chan Patricia P. , Lowe Todd M.
Published: July 2022

Recent high-throughput sequencing protocols have facilitated increased accuracy in measurements of transfer tRNAs (tRNAs) and tRNA-derived small RNAs (tDRs) from biological samples. However, commonly used RNA-seq analysis pipelines overlook special considerations given the unique features of tRNA metabolism. We present tRAX (tRNA Analysis of eXpression), a user-friendly analytic package for streamlined processing and graphic presentation of small-RNA sequencing data. Here, we apply it to both tRNAs and tDRs from mouse tissues to illustrate the extensive analysis and visualization features. Biologically compelling results demonstrate tRAX as an effective and accessible tool for in-depth characterization of tRNA and tDR transcriptomes.
Fast trimer statistics facilitate accurate decoding of large random DNA barcode sets even at large sequencing error rates
Authors: Press William H.
Published: July 2022

Predefined sets of short DNA sequences are commonly used as barcodes to identify individual biomolecules in pooled populations. Such use requires either sufficiently small DNA error rates, or else an error-correction methodology. Most existing DNA error-correcting codes (ECCs) correct only one or two errors per barcode in sets of typically ≲ 104 barcodes. We here consider the use of random barcodes of sufficient length that they remain accurately decodable even with ≳ 6 errors and even at 10% or 20% nucleotide error rates. We show that length 34 nt is sufficient even with ≳ 106 barcodes. The obvious objection to this scheme is that it requires comparing every read to every possible barcode by a slow Levenshtein or Needleman-Wunsch comparison. We show that several orders of magnitude speedup can be achieved by (i) a fast triage method that compares only trimer (three consecutive nucleotide) occurence statistics, precomputed in linear time for both reads and barcodes, and (ii) the massive parallelism available on today’s even commodity-grade GPUs. With 106 barcodes of length 34 and 10% DNA errors (substitutions and indels) we achieve in simulation 99.9% precision (decode accuracy) with 98.8% recall (read acceptance rate). Similarly high precision with somewhat smaller recall is achievable even with 20% DNA errors. The amortized computation cost on a commodity workstation with two GPUs (2022 capability and price) is estimated as between US$ 0.15 and US$ 0.60 per million decoded reads.
Gamma-interferon-inducible lysosomal thiol reductase maintains cardiac immuno-metabolic homeostasis in heart failure
Authors: Li Mark , Wang Jinxi , Qian Qingwen , Chen Biyi , Zhang Zeyuan , Barroso Elizabeth , Zhang Yuan , Hall Duane D. , Abel E. Dale , Song Long-Sheng , Yang Ling
Published: July 2022

Background

The lysosome is a central player in maintaining immuno-metabolic homeostasis. However, mechanistic insights into the regulation of lysosome-dependent immuno-metabolism in the heart are lacking. Lysosomal reductase Gamma Interferon-Inducible Thiol Reductase (GILT) is the only identified lysosomal reductase that controls diverse sets of lysosomal enzymes and cargoes.

Methods

The role of cardiac GILT was assessed by generating a novel genetic mouse model and employing a multidisciplinary approach including surgical interventions, livein situhigh resolution microscopy, whole-tissue respirometry analysis, unbiased transcriptomic and metabolomic analyses, and various cell biology and biochemical assays.

Results

We found that expression and activity of GILT are reduced in hearts from humans and mice with heart failure (HF). Mice with cardiac specific loss of GILT develop late onset systolic HF at baseline. In the setting of nutrient-overload and experimental left ventricular pressure overload conditions, loss of GILT in cardiomyocytes accelerates the development of heart dysfunction. Transcriptomic and metabolic analyses further revealed that cardiac GILT deficiency alters adaptive immuno-metabolic signatures in the heart. Finally, at the cellular level, cardiac GILT deletion impaired mitochondrial respiration, which was in part due to NLR Family Pyrin Domain Containing 3 (NLRP3)-mediated elevation of mitochondrial oxidative stress.

Conclusions

Together, these findings identify a causal link between a lysosome-inflammation axis, mitochondrial function and heart failure. Elucidation of these mechanisms will identify novel therapeutic strategies for treating HF.
Efficient recovery of complete gut phage genomes by combined short- and long-sequencing
Authors: Chen Wei-Hua , Chen Jingchao , Sun Chuqing , Dong Yanqi , Jin Menglu , Lai Senying , Jia Longhao , Zhao Xueyang , Gao Na L , Liu Zhi , Bork Peer , Zhao Xing-Ming
Published: July 2022

Current metagenome-assembled human phage catalogs contained mostly fragmented genomes. Here, we developed a vigorous phage detection method involving phage enrichment and long-read sequencing and applied to 135 fecal samples. With ~10 times more efficient in obtaining complete genomes (~34%) than the Gut Virome Database, we identified the first megabasephage (~1.03Mb), and revealed the hidden diversity of the gut phageome including dozens of phages more prevalent than the crAssphages and Gubaphages.
Comparing the efficacy of data-driven denoising methods for a multi-echo fMRI acquisition at 7T
Authors: Beckers Abraham B. , Poser Benedikt A. , Keszthelyi Daniel
Published: July 2022

In functional magnetic resonance imaging (fMRI) of the brain the signal is dominated by (physiological) noise. Imaging at ultrahigh field strength is becoming increasingly popular as it offers increased spatial accuracy. The latter is of particular benefit in brainstem neuroimaging given the small cross-sectional area of most nuclei. Physiological noise scales with field strength in fMRI acquisitions, however. Although this problem is in part solved by decreasing voxel size, it is clear that adequate physiological denoising is of utmost importance in brainstem-focused fMRI experiments. Multi-echo sequences have been reported to facilitate highly effective denoising through TE-dependence of Blood Oxygen Level Dependent (BOLD) signals, in a denoising method referred to as multi-echo independent component analysis (ME-ICA). It has not been explored previously how ME-ICA compares to other data-driven denoising approaches at ultrahigh field strength. In the current study, we compared the efficacy of several denoising methods, including anatomical component based correction (aCompCor), Automatic Removal of Motion Artifacts (ICA-AROMA), ME-ICA, and a combination of ME-ICA and aCompCor. We assessed several data quality metrics, including temporal signal-to-noise ratio (tSNR), delta variation signal (DVARS) and spectral density of the global signal. Moreover, we looked at the ability of each method to uncouple the global signal and respiration. In line with previous reports at lower field strengths, we demonstrate that after applying ME-ICA, the data is best post-processed in order to remove spatially diffuse noise with a method such as aCompCor. Our findings indicate that ME-ICA combined with aCompCor and ICA-AROMA are highly effective denoising approaches for multi-echo data acquired at 7T. ME-ICA combined with aCompCor potentially preserves more signal-of-interest as compared to ICA-AROMA.

Highlights

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ME-ICA and ICA-AROMA provide effective denoising for multi-echo 7T fMRI data

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High tSNR can be achieved in the brainstem with a multi-echo acquisition at 7T

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After ME-ICA, the data is best post-processed to correct for spatially diffuse noise
Genomic heterogeneity in pancreatic cancer organoids and its stability with culture
Authors: Usman Olalekan , Zhang Liting , Xie Gengqiang , Kocher Hemant M , Hwang Chang-il , Wang Yue Julia , Mallory Xian Fan , Irianto Jerome
Published: July 2022

The establishment of patient-derived pancreatic cancer organoid culture in recent years creates an exciting opportunity for researchers to perform a wide range of in vitro studies on a model that closely recapitulates the tumor. Among the outstanding questions in pancreatic cancer biology are the causes and consequences of genomic heterogeneity observed in the disease. However, to use pancreatic cancer organoids as a model to study genomic variations, we need to first understand the degree of genomic heterogeneity and its stability within organoids. Here, we used single-cell whole-genome sequencing to investigate the genomic heterogeneity of two independent pancreatic cancer organoids, as well as their genomic stability with extended culture. Clonal populations with similar copy number profiles were observed within the organoids, and the proportion of these clones was shifted with extended culture, suggesting the growth advantage of some clones. However, sub-clonal genomic heterogeneity was also observed within each clonal population, indicating the genomic instability of the pancreatic cancer cells themselves. Furthermore, our transcriptomic analysis also revealed a positive correlation between copy number alterations and gene expression regulation, suggesting the functionality of these copy number alterations.
Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations
Authors: Micheloni Manuel , Petrolli Lorenzo , Lattanzi Gianluca , Potestio Raffaello
Published: July 2022

Double-strand breaks (DSBs), i.e. the covalent cut of the DNA backbone over both strands, are a detrimental outcome of cell irradiation, bearing chromosomal aberrations and leading to cell apoptosis. In the early stages of the evolution of a DSB, the disruption of the residual interactions between the DNA moieties drives the fracture of the helical layout; in spite of its biological significance, the details of this process are still largely uncertain. Here, we address the mechanical rupture of DNA by DSBsviacoarse-grained molecular dynamics simulations: the setup involves a 3855-bp DNA filament and diverse DSB motifs, i.e. within a range of distances between strand breaks (or DSB distance). By employing a coarse-grained model of DNA, we access the molecular details and characteristic timescales of the rupturing process. A sequence-nonspecific, linear correlation is observed between the DSB distance and the internal energy contribution to the disruption of the residual (Watson-Crick and stacking) contacts between DNA moieties, which is seemingly driven by an abrupt, cooperative process. Moreover, we infer an exponential dependence of the characteristic rupture times on the DSB distances, which we associate to an Arrhenius law of thermally-activated processes. This work lays the foundations of a detailed, mechanistic assessment of DSBsin silico, as a benchmark to both numerical simulations and data from single molecule experiments.
UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells
Authors: Chen Chengyan , Shen Yanmin , Li Luqian , Ren Yaoxin , Wang Zhao-Qi , Li Tangliang
Published: July 2022

Nonsense-mediated mRNA decay (NMD) is a highly conserved regulatory mechanism of post-transcriptional gene expression in eukaryotic cells. NMD plays essential roles in mRNA quality and quantity control, and thus safeguards multiple biological processes including embryonic stem cell differentiation and organogenesis. UPF3A and UPF3B in vertebrate species, originated from a singleUPF3gene in yeast, are key factors in the NMD machinery. While UPF3B is a well-recognized weak NMD-promoting factor, whether UPF3A functions in promoting or suppressing NMD is under debate. In this study, we generated aUpf3aconditional knockout mouse strain, and established multiple lines of embryonic stem cells and somatic cells without UPF3A. Through extensive analysis on the expressions of 33 NMD targets, we found UPF3A neither represses NMD in mouse embryonic stem cells, somatic cells, nor in major organs including the liver, spleen, and thymus. Our study reinforces that UPF3A is dispensable for NMD when UPF3B is present. Furthermore, UPF3A may weakly and selectively promote NMD in certain murine organs.

Summary blurb

We generated a newUpf3ainducible knockout mouse model and showed that UPF3A does not repress expressions of NMD target genes in embryonic stem cells, somatic fibroblasts, as well as multiple tissues from adult mice.
Excessive fluid shear stress-mediated Klf4 leads to arteriovenous pathogenesis
Authors: Banerjee Kuheli , Lin Yanzhu , Gahn Johannes , Gupta Purnima , Graupera Mariona , Dobreva Gergana , Schwartz Martin , Ola Roxana
Published: July 2022

Background

Vascular networks form, remodel and mature under the influence of both fluid shear stress (FSS) and soluble factors. For example, FSS synergizes with Bone Morphogenic Protein 9 (BMP9) and BMP10 to promote and maintain vascular stability. Mutation of the BMP receptors ALK1, Endoglin or the downstream effector SMAD4 leads to Hereditary Hemorrhagic Telangiectasia (HHT), characterized by fragile and leaky arterial-venous malformations (AVMs). But how endothelial cells (EC) integrate FSS and BMP signals in normal vascular development and homeostasis, and how mutations give rise to malformations is not well understood.

Results

Here we show that loss of Smad4 in murine ECs increases cells’ sensitivity to flow and the resulting AVMs are characterized by excessive elongation and polarity against the flow. Smad4 deletion also blocks the anti-proliferative response to high FSS, leading to loss of arterial identity. Our data show that loss of cell cycle arrest leads to loss of arterial identity, which is essential in AVM formation upon Smad4 depletion in ECs. Excessive flow-induced activation of KLF4-PI3K/AKT due to Cyclin dependent Kinase (CDK) activation mediates the aberrant morphological responses to flow triggering AVM formation.

Conclusions

Our results show that loss of polarization against the flow is not required for AVM formation upon EC Smad4 depletion. Instead, increased EC proliferation-mediated loss of arterial identity due to flow-induced PI3K/Akt/Cdks hyperactivation and Klf4 over-expression are the main events associated with AVM formation.
Dissecting peripheral protein-membrane interfaces
Authors: Tubiana Thibault , Sillitoe Ian , Orengo Christine , Reuter Nathalie
Published: July 2022

Peripheral membrane proteins (PMPs) include a wide variety of proteins that have in common to bind transiently to the chemically complex interfacial region of membranes through their interfacial binding site (IBS). In contrast to protein-protein or protein-DNA/RNA interfaces, peripheral protein-membrane interfaces are poorly characterized.

We collected a dataset of PMP domains representative of the variety of PMP functions: membrane-targeting domains (Annexin, C1, C2, discoidin C2, PH, PX), enzymes (PLA, PLC/D) and lipid-transfer proteins (START). The dataset contains 1328 experimental structures and 1194 AphaFold models. We mapped the amino acid composition and structural patterns of the IBS of each protein in this dataset, and evaluated which were more likely to be found at the IBS compared to the rest of the domains’ accessible surface.

In agreement with earlier work we find that about two thirds of the PMPs in the dataset have protruding hydrophobes (Leu, Ile, Phe, Tyr, Trp and Met) at their IBS. The three aromatic amino acids Trp, Tyr and Phe are a hallmark of PMPs IBS regardless of whether they protrude on loops or not. This is also the case for lysines but not arginines suggesting that, unlike for Arg-rich membrane-active peptides, the less membrane-disruptive lysine is preferred in PMPs. Another striking observation was the over-representation of glycines at the IBS of PMPs compared to the rest of their surface, possibly procuring IBS loops a much-needed flexibility to insert in-between membrane lipids. The analysis of the 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms. Besides revealing novel amino acids patterns at protein-membrane interfaces, our work contributes a new PMP dataset and an analysis pipeline that can be further built upon for future studies of PMPs properties, or for developing PMPs prediction tools using for example, machine learning approaches.
A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants
Authors: Chen Mingming , Kumakura Naoyoshi , Muller Ryan , Shichino Yuichi , Nishimoto Madoka , Mito Mari , Gan Pamela , Ingolia Nicholas T. , Shirasu Ken , Ito Takuhiro , Iwasaki Shintaro
Published: July 2022

Plants often generate secondary metabolites as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier of antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocalgates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a translation initiation factor (eIF). De novo transcriptome assembly revealed that the fungus belongs to Ophiocordyceps genus and its eIF4A, a molecular target of rocaglates, contains a amino acid substitution critical for rocaglate binding. Ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered Colletotrichum orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.
Odd skipped-related 1 controls the pro-regenerative response of Fibro-Adipogenic Progenitors
Authors: Kotsaris Georgios , Qazi Taimoor H. , Bucher Christian H. , Pöhle-Kronawitter Sophie , Ugorets Vladimir , Jarassier William , Börno Stefan , Timmermann Bernd , Giesecke-Thiel Claudia , Vallecillo-García Pedro , Economides Aris N. , Grand Fabien Le , Knaus Petra , Geissler Sven , Stricker Sigmar
Published: July 2022

Skeletal muscle regeneration requires the coordinated interplay of diverse tissue-resident- and infiltrating cells. Fibro-adipogenic progenitors (FAPs) are an interstitial cell population that provides a beneficial microenvironment for muscle stem cells (MuSCs) during muscle regeneration. Here we show that the transcription factor Osr1 is essential for FAPs to communicate with MuSCs and infiltrating macrophages, thus coordinating muscle regeneration. Conditional inactivation of Osr1 impaired muscle regeneration with reduced myofiber growth and formation of excessive fibrotic tissue with reduced stiffness. Osr1-deficient FAPs acquired a fibrogenic identity with altered matrix secretion and cytokine expression resulting in impaired MuSC viability, expansion and differentiation. Immune cell profiling suggested a novel role for Osr1-FAPs in macrophage polarization. In vitro analysis suggested that increased TGFβ signaling and altered matrix deposition by Osr1-deficient FAPs actively suppressed regenerative myogenesis. In conclusion, we show that Osr1 is central to FAP function orchestrating key regenerative events such as inflammation, matrix secretion and myogenesis.
Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes
Authors: Srivastava Akanksha , Kumar Arvind , Biswas Subhankar , Kumar Rajender , Srivastava Vaibhav , Rajaram Hema , Mishra Yogesh
Published: July 2022

High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma (γ)-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon γ-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by γ-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating γ-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of γ-radiation-responsive genes in cyanobacteria at large.

Highlights

γ-radiation alters PSII photophysiology and thylakoid proteome profile in Anabaena.

LexA modulates the cytosolic and thylakoid proteome of Anabaena under γ-radiation.

LexA functions as one of the regulators of radiation-responsive genes in Anabaena.
A quantitative rule to explain multi-spine plasticity
Authors: Chater T. E. , Eggl M. F. , Goda Y. , Tchumatchenko T.
Published: July 2022

Neurons receive thousands of inputs onto their dendritic arbour, where individual synapses undergo activitydependent changes in strength. The durable forms of synaptic strength change, long-term potentiation (LTP) and long-term depression (LTD) require calcium entry through N-methyl-D-aspartate receptors (NMDARs) that triggers downstream protein signalling cascades in the dendrite. Notably, changes in postsynaptic strengths associated with LTP and LTD are correlated to changes in spine head volume, referred to as structural LTP (sLTP) and structural LTD (sLTD). Intriguingly, LTP and LTD, including sLTP and sLTD, are not necessarily restricted to the active, targeted synapses (homosynapses), and the changes in synaptic strength can spread and affect the strengths of inactive or non-stimulated synapses (heterosynapses) on the same cell. Moreover, the plasticity outcome at both homo- and heterosynapses can depend on the number of stimulated sites when eliciting multi-spine plasticity. Precisely how neurons allocate resources for implementing the changes in strength at individual synapses depending on their proximity to input activity across space and time remains an open question. In order to gain insights into the elementary processes underlying multi-spine plasticity that engages both homosynaptic and heterosynaptic changes, we have combined experimental and mathematical modelling approaches. On the one hand, we used glutamate uncaging to precisely and systematically stimulate variable numbers of homosynapses sharing the same dendritic branch whilst monitoring tens of other heterosynapses on the same dendrite. Homosynaptic potentiation of clusters of dendritic spines leads to heterosynaptic changes that are dependent on NMDAR, CaMKII and calcineurin. On the other hand, inspired by the Ca2+levels hypothesis where different amounts of Ca2+lead to either growth or shrinkage of spines, we have built a model based on a dual-role Ca2+-dependent protein that induces sLTP or sLTD. Comparing our experimental results with model predictions, we find that(i)both collaboration and competition among spines for protein resources are key drivers of heterosynaptic plasticity and(ii)the temporal and spatial distance between simultaneously stimulated spines impact the resulting spine dynamics. Moreover, our model can reconcile disparate experimental reports of sLTP and sLTD at homo- and heterosynaptic spines. Our results provide a quantitative description of the heterosynaptic footprint over minutes and hours post-stimulation across tens of microns of dendritic space. This broadens our knowledge about the operation of non-linear dendritic summation rules and how they impact spiking decisions.
Exploring the “theory is king” thesis in accounting research: the case of actor-network theory
Authors: Lukka Kari , Modell Sven , Vinnari Eija
Published: July 2022

Purpose

This paper examines the influence of the normal science tradition, epitomized by the notion that “theory is king”, on contemporary accounting research and the epistemological tensions that may emerge as this idea is applied to particular ways of studying accounting. For illustrative purposes, the authors focus on research informed by actor-network theory (ANT) which can be seen as an “extreme case” in the sense that it is, in principle, difficult to reconcile with the normal science aspirations.

Design/methodology/approach

The paper offers an analysis based on a close reading of how accounting scholars, using ANT, theorize, and if they do engage in explicit theorizing, how they deal with the tensions that might emerge from the need to reconcile its epistemological underpinnings with those of the normal science tradition.

Findings

The findings of this paper show that the tensions between normal science thinking and the epistemological principles of ANT have, in a few cases, been avoided, as researchers stay relatively faithful to ANT and largely refrain from further theory development. However, in most cases, the tensions have ostensibly been ignored as researchers blend the epistemology of ANT and that of normal science without reflecting on the implications of doing so.

Originality/value

The paper contributes to emerging debates on the role of the normal science tradition in contemporary accounting research, and also extends recent discussions on the role of theory in accounting research inspired by ANT. The paper proposes three reasons for the observed blending of epistemologies: unawareness of tensions, epistemological eclecticism and various political considerations.
Sociolinguistic repositories as asset: challenges and difficulties in Brazil
Authors: Meister Ko. Freitag Raquel
Published: July 2022

Purpose

This paper aims to provide a context for Brazilian Portuguese language documentation and its data collection to establish linguistic repositories from a sociolinguistic overview.

Design/methodology/approach

The main sociolinguistic projects that have generated collections of Brazilian Portuguese language data are presented.

Findings

The comparison with another situation of repositories (seed vaults) and with the accounting concept of assets is evocated to map the challenges to be overcome in proposing a standardized and professional language repository to host the collections of linguistic data arising from the reported projects and others, in the accordance with the principles of the open science movement.

Originality/value

Thinking about the sustainability of projects to build linguistic documentation repositories, partnerships with the information technology area, or even with private companies, could minimize problems of obsolescence and safeguarding of data, by promoting the circulation and automation of analysis through natural language processing algorithms. These planning actions may help to promote the longevity of the linguistic documentation repositories of Brazilian sociolinguistic research.
Intelligent personal assistant for personal computers using long short-term memory-based verbalizer
Authors: Swamidason Iwin Thanakumar Joseph , Tatiparthi Sravanthy , Velswamy Karunakaran , Velliangiri S.
Published: July 2022

Purpose

An intelligent personal assistant for personal computers (PCs) is a vital application for the current generation. The current computer personal assistant services checking frameworks are not proficient at removing significant data from PCs and long-range informal communication information.

Design/methodology/approach

The proposed verbalizers use long short-term memory to classify the user task and give proper guidelines to the users. The outcomes show that the proposed method determinedly handles heterogeneous information and improves precision. The main advantage of long short-term memory is that handle the long-term dependencies in the input data.

Findings

The proposed model gives the 22% mean absolute error. The proposed method reduces mean square error than support vector machine (SVM), convolutional neural network (CNN), multilayer perceptron (MLP) and K-nearest neighbors (KNN).

Originality/value

This paper fulfills the necessity of intelligent personal assistant for PCs using verbalizer.
The effects of spiritual expression at work during the COVID-19 crisis: evidence from a private hospital
Authors: Anzengruber Johanna
Published: July 2022

Purpose

This paper aims to explain the effects of spirituality at work on organizational commitment during the COVID-19 pandemic. In detail, it investigates whether the active part of spirituality at work, called spiritual expression, has a positive influence on organizational commitment in a hierarchically organized private hospital. In addition, it explores whether the sense of belonging at work mediates spiritual expressions and a person’s commitment toward the employer during times of severe crisis.

Design/methodology/approach

This study tests the hypotheses on a range of health-care personnel, including doctors, nurses, physicians, administrators, managers and cleaning staff. This study draws on quantitative data of more than one third of the employees of that private Austrian hospital (n= 96) and on insights from 12 qualitative interviews conducted over a period of four months during spring 2021.

Findings

This study finds strong evidence that spiritual expression at work is directly related to belonging and indirectly related to organizational commitment through belonging. This study extracts eight concurrent themes impacting the effectiveness of spirituality at work in the hospital.

Originality/value

This study provides insights on how to facilitate spiritual expression at work to increase flexibility and resilience in the health-care sector. All in all, spirituality at work is better understood as a “multi-authored” process, in which all participants, including the patients, co-create its meaning and implications.
Islamic equity funds and stock market: dynamic relation and market timing during the COVID-19 outbreak
Authors: Ben Khelifa Soumaya , Arsi Sonia
Published: July 2022

Purpose

This paper aims to explore the impact of the COVID-19 pandemic on the market timing skills of Islamic equity funds in Asia, Europe and North America.

Design/methodology/approach

The authors employed a two-step process. First, a Granger causality test is applied to test the bivariate relationship between Islamic fund indices and stock market ones by highlighting the impact of the COVID-19 pandemic. Second, the methodology of Treynor and Mazuy (1966) is deployed to account for the market timing abilities skills of Islamic fund managers during the pandemic period.

Findings

The investigation revealed mixed results. The European Islamic funds were positively impacted by the stock market as well as by the COVID-19 pandemic context. Additionally, compared to their Asian and North American peers, only European Islamic fund managers have the ability to time the market during the health crisis period.

Research limitations/implications

Despite its contribution to the Islamic finance literature, this study has some flaws. Indeed, the selected sample of three regions, namely Asia, Europe and North America, precludes extrapolating these conclusions. Other regions should be investigated to further our understanding of Islamic equity funds. Furthermore, due to data availability and accessibility, the study period was limited to a specific time of the COVID-19 pandemic. This shortcoming can be addressed through a multiwave investigation, especially since each region was exposed differently to the pandemic.

Practical implications

The paper provides scholars, portfolio managers and investors with insights regarding the investment dilemma during the COVID-19 pandemic period, especially for those wishing to hedge their pandemic risk exposure and/or diversify their portfolios. Equally, the depiction of potential market timing abilities of Islamic fund managers across the three regions would serve as a guide to identifying the most suitable internationally focused investment strategy.

Social implications

The paper provides scholars, portfolio managers and investors with insights regarding the investment dilemma during the COVID-19 pandemic period, especially for those wishing to hedge their pandemic risk exposure and/or diversify their portfolios. Equally, the depiction of potential market timing abilities of Islamic funds managers across the three regions would serve as a guide to identify the most suitable internationally focused investment strategy.

Originality/value

The originality of this investigation is that it is the first to examine Islamic equity fund managers and their skills to time the stock markets during the COVID-19 pandemic period in Asia, Europe and North America. The current paper extends the Islamic finance literature.
Subcontracting and enterprise development in India's informal manufacturing sector
Authors: Shekar K. Chandra , Nataraj Manikantha
Published: July 2022

Purpose

Subcontracting is a crucial cause behind the simultaneous existence of formal and informal entrepreneurship in India. This article aims to provide an over-time comparative analysis between the subcontracted and the non-subcontracted enterprises within the informal sector. Further, it also brings to fore the contribution of subcontracting towards ensuring sustainability of the informal enterprises.

Design/methodology/approach

By constructing a panel data from two rounds of NSS Unincorporated Enterprise Survey Data (2010 and 2015), and employing a PSM-DID method, considering labour productivity and net retained earnings as two critical indicators of growth and development of the informal sector firms, this study has made some broad claims regarding the differences in immediate and long run performances between the subcontracted and non-subcontracted informal sector enterprises in India.

Findings

This study finds that subcontracted enterprises have not only been performing at a much lower level than the non-subcontracted enterprises, they are also growing much slowly than their counterparts. However, it has been observed that for the establishments, who are capital abundant and also have a larger production capacity, subcontracting is showing the prospect for deriving sustainable gains.

Originality/value

This article contributes to the existing literature in the following two ways. Firstly, it provides an over-time comparative analysis between the subcontracted and the non-subcontracted enterprises within the informal sector. Secondly, it brings to fore the contribution of subcontracting towards ensuring sustainability of the informal enterprises.
Restoring the balance between humanity and nature through tourism entrepreneurship: a conceptual framework
Authors: Lupton Katie , Samy Christine
Published: July 2022

Purpose

For years, there has been an appalling crisis developing – that of the state of our planet. Humanity has become disconnected from nature, with devastating consequences. We are in an emergency state: a crisis of perception (HRH et al., 2010, p. 6). This paper puts forward a conceptual model for harmony restoration through tourism entrepreneurship.

Design/methodology/approach

In developing the proposed framework, the authors have adopted the seven core principles of Richard Dunne of the Harmony Project, inspired by HRH The Prince of Wales’s vision set out in his book “Harmony: A new way of looking at our world”. The authors propose that developing entrepreneurial tourism in respect of the harmony principles would enhance the industry and act as a platform to educate those that engage with it.

Findings

In this conceptual viewpoint paper, the authors draw upon the harmony principles to provide a cohesive framework for restoring harmony through entrepreneurship in tourism. The premise of our framework is that for the tourism industry to become more regenerative and transformative, it requires the continuing contributions of the entrepreneurs involved (De Lange and Dodds, 2017; Kirby, 2020).

Originality/value

The suggested framework builds on the work of David Kirby (2020) and epitomises a step toward harmony restoration through tourism and entrepreneurship, thus contributing to future research seeking to explore a novel and encircling approach to regeneration and tourism entrepreneurship. The paper provides a foundation for policy making to promote harmonious entrepreneurship practices in the tourism field.
Effects of equity, perceived organizational support and job satisfaction on organizational commitment in Macao's gaming industry
Authors: To Wai Ming , Huang Guihai
Published: July 2022

Purpose

This study explores the relationships between equity, perceived organizational support, job satisfaction, organizational commitment and counterproductive work behavior in Macao's gaming industry. Additionally, it investigates whether the Covid-19 outbreak has effects on employees' perceptions and behaviors.

Design/methodology/approach

Data were collected from two surveys using convenience sampling, one involving 260 casino employees in 2019 and another involving 250 employees in 2020 after the outbreak of Covid-19.

Findings

No significant difference was observed between mean scores from respondents in the first and second surveys on job equity, pay equity, perceived organizational support and job satisfaction (p > 0.05). However, significant changes were found in mean scores for three organizational commitment items (negative changes;p < 0.05) and three counterproductive work behavior items (positive changes;p < 0.05). Results of structural equation modeling indicated that job equity and pay equity affected perceived organizational support and job satisfaction while perceived organizational support impacted organizational commitment directly and indirectly through job satisfaction, all withR2values greater than 0.6. Organizational commitment negatively influenced counterproductive work behavior.

Research limitations/implications

The Covid-19 impact on casino employees' perceptions and behaviors was contingent upon the duration of pandemic.

Originality/value

The study is one of the first empirical studies to integrate social exchange theory and equity theory to organizational commitment in Macao's gaming industry. Job equity and pay equity were found to influence organizational commitment through perceived organizational support and job satisfaction. Additionally, the Covid-19 did not have significant effects on employees' equity, perceived organizational support and job satisfaction perceptions.
Health‐related quality of life in patients with neurofibromatosis 1 in Japan: A questionnaire survey using EQ‐5D‐5L
Authors: Yoshida Yuichi , Ehara Yuko , Koga Monji , Imafuku Shinichi
Published: July 2022

Neurofibromatosis 1 (NF1) is a genetic disorder characterized by various symptoms including dermatological, neurological, and osseous manifestations. These complications often cause cosmetic or functional disturbances, resulting in a significant impact on quality of life (QOL). However, there are limited data on QOL of individuals with NF1 in Japan. Therefore, we studied health‐related QOL in patients with NF1 compared with that in general populations and the association with severity grade using EQ‐5D. A cross‐sectional study was conducted for 73 adult NF1 patients (26 males and 47 females; mean age, 44.16 years). The EQ‐5D‐5L values and visual analog scale (VAS) in patients with NF1 were 0.738 ± 0.137 and 69.93 ± 19.14, respectively. Both scores were significantly lower in patients with NF1 than in healthy volunteers (p < 0.0001). The score for anxiety/depression was the highest among the five items of EQ‐5D. Although we investigated differences in the index value and VAS between stage 2 or less and stage 3 or higher, there was no difference in the scores between groups related to certification criteria for the public medical expenses subsidy system. EQ‐5D‐5L is a valuable assessment tool for health‐related QOL in patients with NF1, but it might not be sufficient for severity certification of NF1 in Japan. We would need the revision of the current certification based on the patients' demand in the future. Our findings might be useful for assessment of therapeutic effects and appropriate resource allocation in the care of patients with NF1.
Virtual reality as a spatial prompt in geography learning and teaching
Authors: Roelofsen Maartje , Carter‐White Richard
Published: July 2022

We examine the claim that virtual reality (VR) holds significant potential for pedagogical applications in geography. We do so with reference to results from a two‐year research‐teaching project embedded in a postgraduate course on “Heritage and Its Management.” We reflect on the implementation of a VR field trip to the Auschwitz‐Birkenau State Museum enabled by the high‐immersive Inside Auschwitz guided documentary, drawing on surveys and interviews held with students after their participation in the field trip. We found that VR technology may work as a (dis)inhibitor and provided users with a sense of social and temporal freedom to explore sites but in combination with a new set of spatial and perceptual constraints. The VR field trip generated curiosity about the “details” of the site, but we argue that learning with and through VR technology only became possible via active bodily adaptations and renewed understandings of bodily capacities and their inequalities. We conclude that VR works most effectively if conceived not as a journey into a self‐contained virtual realm but instead as a spatial prompt designed to provoke new questions for students already on the path to developing geographical understandings and imaginations related to specific sites.
Monocotyledon‐like Leaves from the Middle Jurassic of East Siberia (Russia)
Authors: FROLOV Andrey , ENUSHCHENKO Ilya
Published: July 2022

Leaf fragments of Herbifolia antiqua A. Frolov et Enushchenko gen. et sp. nov. from the Middle Jurassic (Aalenian) of the Irkutsk Coal Basin (Eastern Siberia, Russia) are reported. The following features are characteristic of H. antiqua gen. et sp. nov.: the presence of leaf sheaths, linear smooth‐edged leaves with parallel venation, anastomoses between the veins, anomocytic stomata, rhomb‐shaped ordinary epidermal cells. Such a combination of characters is widespread in modern monocotyledonous plants and is absent in fossil and modern cryptogam and gymnosperms. Due to the lack of evidence of an enclosed ovule in H. antiqua gen. et sp. nov., we attribute it to a typological angiosperm, based on its unique leaf structure characteristic of monocotyledons. The leaf epidermal structure of Herbifolia gen. nov. is most similar to those of modern Asparagales and Liliales.