bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene expression signatures underlying inbreeding depression as revealed by whole-transcriptome analysis of selectively bred strains of the Pacific Oyster (Crassostrea gigas)
Authors: Shi Chenyu , Zhang Fuqiang , Li Qi , Liu Shikai
Published: May 2022

Exploring molecular mechanisms of inbreeding depression is significant for the conservation and sustainable use of the rare breed with a specific trait of high production value. In this work, we conducted whole-transcriptome analysis of two selectively bred Pacific oyster strains with one inbred strain showing significant growth depression. A total of 7980, 2677, and 28 differentially expressed protein-coding genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. The majority of DEGs and predicted target genes of DELs and DEMs were significantly enriched in biological process including immune response, cell proliferation, and apoptosis pathways. A set of genes with specific expression patterns as revealed by cluster profiling and enrichment analysis were identified, which may underlie inbreeding depression of the inbred strain. Furthermore, a competing endogenous RNA (ceRNA) network was constructed by integrative analysis of DEGs, DELs, and DEMs, supporting that ncRNAs, as regulators of gene expression, could be critical modulators in multiple subsystems involved in inbreeding depression.
Beneficial effects of cellular coinfection resolve inefficiency in influenza A virus transcription
Authors: Shartouny Jessica R. , Lee Chung-Young , Lowen Anice C.
Published: May 2022

For diverse viruses, cellular infection with single vs. multiple virions can yield distinct biological outcomes. We previously found that influenza A/guinea fowl/Hong Kong/WF10/99 (H9N2) virus (GFHK99) displays a particularly high reliance on multiple infection in mammalian cells. Here, we sought to uncover the viral processes underlying this phenotype. We found that the need for multiple infection maps amino acid 26K of the viral PA protein. PA 26K suppresses endonuclease activity and viral transcription, specifically within cells infected at low multiplicity. In the context of the higher functioning PA 26E, inhibition of PA using baloxavir acid augments reliance on multiple infection. Together, these data suggest a model in which sub-optimal activity of the GFHK99 endonuclease results in inefficient priming of viral transcription, an insufficiency which can be overcome with the introduction of additional viral templates to the cell. These findings offer rare mechanistic insight into the benefits of viral collective dispersal.

Graphical Abstract
Differential regulation of GUV mechanics via actin network architectures
Authors: Wubshet Nadab H. , Wu Bowei , Veerapaneni Shravan , Liu Allen P.
Published: May 2022

Actin networks polymerize and depolymerize to construct highly organized structures, thereby, endowing the mechanical phenotypes found in a cell. It is generally believed that the amount of filamentous actin and actin network architecture determine cytoplasmic viscosity and elasticity of the whole cell. However, the intrinsic complexity of a cell and numerous other endogenous cellular components make it difficult to study the differential role of distinct actin networks in regulating cell mechanics. Here, we model a cell by using giant unilamellar vesicles (GUVs) encapsulating actin filaments and networks assembled by various actin crosslinker proteins. Perturbation of these cytoskeletal vesicles using AC electric fields revealed that deformability depends on lumenal viscosity and actin network architecture. While actin-free vesicles exhibited large electromechanical deformations, deformations of GUVs encapsulating actin filaments were significantly dampened. The suppression of electrodeformation of actin-GUVs can be similarly recapitulated by using aqueous PEG 8000 solutions at different concentrations to modulate viscosity. Furthermore, alpha actinin-crosslinked actin networks resulted in decreased GUV deformability in comparison to actin filament-encapsulating GUVs, and membrane-associated actin networks through the formation of dendritic actin cortex greatly dampened electrodeformation of GUVs. These results highlight the organization of actin networks regulates the mechanics of GUVs and shed insights into the origin of differential deformability of cells.
Clinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens
Authors: Forde Brian M , Bergh Haakon , Cuddihy Thom , Hajkowicz Krispin , Hurst Trish , Playford E. Geoffrey , Henderson Belinda C. , Runnegar Naomi , Clark Julia , Jennison Amy V , Moss Susan , Hume Anna , Leroux Hugo , Beatson Scott A , Paterson David L , Harris Patrick NA
Published: May 2022

Background

Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting.

Materials/methods

We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MSLT) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams.

Results

Over four years (April 2017 to July 2021) 2,660 isolates were sequenced. This included MDR gram-negative bacilli (n=293 CPE, n=1309 ESBL), MRSA (n=620) and VRE (n=433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the three target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In one hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy.

Conclusions

Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.

We initiated a program of routine sequencing of multi-drug resistant organisms. A custom analysis pipeline was used to automate reporting by incorporating clinical meta-data with genomics to define clusters and support infection control interventions.
Automated and combined HIV, HBV, HCV, and syphilis testing among illegal gold miners in French Guiana using a standardized dried blood device
Authors: Pisoni Amandine , Reynaud Elisa , Douine Maylis , Hureau Louise , Cordellat Carmen Alcocer , Schaub Roxane , Poland Dennis , Monkel Richard , Lommen Joan , Yenkoyan Konstantin , Vreden Stephen , Nacher Mathieu , Tuaillon Edouard
Published: May 2022

Blood spotted onto filter paper can be easily collected outside healthcare facilities and shipped to a central laboratory for serological testing. However, dried blood testing generally requires manual processing for pre-analytical steps. In this study, we used a standardized blood collection device combined with an automated elution system to test illegal gold miners living in French Guiana for HIV, HBV, HCV and syphilis. We included 378 participants, 102 females and 266 males, in three illegal gold mining resting sites. Blood collected on the Ser-Col device (Labonovum) was eluted using an automated system (SCAUT Ser-Col automation, Blok System Supply) and an automated analyzer (Alinity i, Abbott). Ser-Col results were compared to both plasma results, considered the gold standard, and to DBS results, considered the reference sampling method using dried blood. In plasma samples, two participants (0.5%) tested positive for HIV, six (1.5%) tested positive for hepatitis B surface antigen (HBsAg), eight were weakly positive for anti-HCV antibodies but negative for HCV RNA, and 47 tested positive for treponemal antibodies (12.4%), including 20 females (19.6%) and 27 males (9.8%, p= 0.010179). We observed a full concordance of Ser-Col and DBS results for HIV diagnosis compared to plasma results. Ser-Col and DBS samples tested positive in five HBsAg carriers and negative for one participant with a low HBsAg level in plasma (0.5 IU/mL). All participants tested negative for HCV in Ser-Col and DBS samples, including the eight participants who tested low positive for HCV antibodies and HCV RNA negative in plasma. Among syphilis seropositive participants, 41 (87.2%) and 40 (85.1%) tested positive for treponemal antibodies in Ser-Col and DBS samples, respectively. The Ser-Col method allows automated dried blood testing of HIV, HBV, HCV and syphilis with performances comparable to DBS. Automated approaches to test capillary blood transported on dried blood devices may facilitate large-scale surveys and improve testing of populations living in remote areas.

Graphical abstract
Dauer quiescence as well as continuity of the life cycle after dauer-exit in Caenorhabditis elegans are dependent on the endoribonuclease activity of XRN-2
Authors: Chowdhury Tamoghna , Samajdar Aniruddha , Sardar Moumita , Chatterjee Saibal
Published: May 2022

Caenorhabditis elegans embarks on a quiescent dauer state upon exposure to unfavourable conditions and can sustain for a very long period without food, but it returns to continuous life cycle upon arrival of suitable conditions. Thus, dauer state plays a critical role in its adaptive fitness and survival. ATP-independent endoribonuclease activity of XRN-2 has been implicated in dauer microRNA metabolism, perturbation of which causes their collapse within a very short span of time. Here, we present a detailed comparative analyses of dauer transcriptomes from a conditional mutant strain for the endoribonuclease activity of XRN-2, maintained under control and experimental conditions. We observed that even a limited disruption of microRNA homeostasis in experimental dauers results in deregulation of a large number of mRNA targets. Our bioinformatic analyses, supported by morphological, physiological, and behavioral evidence further demonstrate critical changes in metabolism leading to a state unsupportive of dauer maintenance, alongside potential defects in multiple neuronal activities, which might have caused an overall disruption of dauer plasticity. We explore a possible role of this endoribonuclease activity towards the maintenance of chromatin architecture and transposon expression that in turn might affect the transcriptional program critically required for the maintenance of non-aging, long-lived dauers. Finally, we also demonstrate that perturbation of the endoribonuclease activity during the dauer state exerts drastic adverse effects on the continuity of life cycle after dauer-exit. They not only fail to recapitulate the wild type events of germline development and embryogenesis, but also present traits of very old worms and formation of ‘tumor-like’ structures in the proximal gonad.
The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency
Authors: Wahlen Sigrid , Matthijssens Filip , Van Loocke Wouter , Taveirne Sylvie , Kiekens Laura , Persyn Eva , van Ammel Els , De Vos Zenzi , De Munter Stijn , Matthys Patrick , Van Nieuwerburgh Filip , Taghon Tom , Vandekerckhove Bart , Van Vlierberghe Pieter , Leclercq Georges
Published: May 2022

NK cells are innate lymphocytes that eliminate virus-infected and cancer cells by cytotoxicity and cytokine secretion. In addition to circulating NK cells, distinct tissue-resident NK subsets have been identified in various organs. Although transcription factors regulating NK cell development and function have been extensively studied in mice, the role of RUNX2 in these processes has not been investigated, neither in mice nor in human. Here, by manipulating RUNX2 expression with either knockdown or overexpression in human hematopoietic stem cell-based NK cell differentiation cultures, combined with transcriptomic and ChIP-sequencing analyses, we established that RUNX2 drives the generation of NK cells, possibly through induction of IL-2Rβ expression in NK progenitor cells. Importantly, RUNX2 promotes tissue residency in human NK cells. Our findings have the potential to improve existing NK cell-based cancer therapies and can impact research fields beyond NK cell biology, since tissue-resident subsets have also been described in other lymphocyte subpopulations.
Relationships of Worldwide Onobrychis species: from seed & pod morphology and molecular perspective
Authors: Zarrabian Mohammad , Dehkordi Azam Nikbakht , Ehtemam Mohammad Hossein , Majidi Mohammad Mahdi
Published: May 2022

The present study aimed to investigate the phylogeny of 31 Onobrychis species with the help of seed and fruit macro & micro-morphological traits and ISSR molecular markers. The species were found to be highly variable in their seed and fruit morphological traits. Also, a new type of fruit (O. crista galli type), in addition to the three predefined types of fruit, was introduced. From molecular perspective, a set of 22 ISSR primers were shown to have a good efficiency for genetic discrimination among the species. Bayesian model based STRUCTURE analysis grouped the genotypes into 4 genetic clusters, and the high value of Fst calculated for these clusters indicated a high level of genetic differentiation among them. On the other hand, based on the Maximum Likelihood phylogenetic tree, our results are in agreement with the subgenus classification (Onobrychis and Sisyrosema), while contrary to Sisyrosema, the Onobrychis subgenus (the Lophobrychis and Onobrychis sections) appears not to be monophyletic. Furthermore, in contrast to the traditional taxonomic classification, species belonging to the Lophobrychis section do not form a coherent group, indicating that this section could be considered as a heterogeneous unit and perhaps could be merge into the Onobrychis section.

Highlight

This paper discusses a worldwide phylogenic analysis and population structures of Onobrychis genus. The results of this paper provide a comprehensive answer to complexity of subgenus and section discrimination.
Visualizing the Coordination of APE1 and DNA Polymerase β During Base Excision Repair
Authors: Fairlamb Max S. , Washington Todd M. , Freudenthal Bret D.
Published: May 2022

Base Excision Repair (BER) is carried out by a series of DNA repair proteins that function in a step-by-step process to identify, remove, and replace DNA damage. As DNA damage is processed during BER, the DNA transitions through various intermediate states, called BER intermediates, which if left exposed can develop into double-strand DNA breaks and trigger programmed cell death signaling. Previous studies have proposed that in order to minimize exposure of the BER intermediates, each protein may remain bound to its product prior to the next protein binding. Thus, a short-lived complex consisting of the BER intermediate, the incoming enzyme, and the outgoing enzyme may form between each step of the BER pathway. The transfer of BER intermediates between enzymes, known as BER coordination, has yet to be directly visualized and the mechanistic details of the process remain unclear. Here, we utilize single-molecule total internal reflection fluorescence (TIRF) microscopy to investigate the mechanism of BER coordination between apurinic/apyrimidinic endonuclease 1 (APE1) and DNA polymerase β (Pol β). When preformed complexes comprised of APE1 and the incised AP-site product were subsequently bound by Pol β, the Pol β enzyme dissociated shortly after binding in a majority of the observations. In the events where Pol β binding was followed by APE1 dissociation (i.e., DNA hand-off), Pol β had remained bound for a longer period of time to allow disassociation of APE1. Our results indicate that, in the absence of other BER factors, transfer of the BER intermediate from APE1 to Pol β during BER is dependent on the dissociation kinetics of APE1 and the duration that Pol β remains bound near the APE1-5’ nick complex. These findings provide insight into how APE1 and Pol β coordinate the transfer of DNA within the BER pathway.
Context-dependent effects explain divergent prognostic roles of Tregs in cancer
Authors: Amblard Elise , Soumelis Vassili
Published: May 2022

Assessing cancer prognosis is a challenging task, given the heterogeneity of the disease. Multiple features (clinical, environmental, genetic) have been used for such assessments. The tumor immune microenvironment (TIME) is a key feature, and describing the impact of its many components on cancer prognosis is an active field of research. The complexity of the tumor microenvironment context makes it difficult to use the human TIME to assess prognosis, as demonstrated by the example of regulatory T cells (Tregs). The effect of Tregs on prognosis is ambiguous, with different studies considering them to be negative, positive or neutral. We focused on five different cancer types (breast, colorectal, gastric, lung and ovarian). We clarified the definition of Tregs and their utility for assessing cancer prognosis by taking the context into account via the following parameters: the Treg subset, the anatomical location of these cells, and the neighboring cells. With a meta-analysis on these three parameters, we were able to clarify the prognostic role of Tregs. We found that CD45RO+ Tregs had a reproducible negative effect on prognosis across cancer types, and we gained insight into the contributions of the anatomical location of Tregs and of their neighboring cells on their prognostic value. Our results suggest that Tregs play a similar prognostic role in all cancer types. We also established guidelines for improving the design of future studies addressing the pathophysiological role of Tregs in cancer.
Syntaxin Habc is required to open Unc18 to template SNARE assembly
Authors: Parra-Rivas Leonardo A. , Palfreyman Mark T. , Vu Thien N. , Jorgensen Erik M.
Published: May 2022

SNARE and Unc18 proteins form the core of the membrane fusion complex at synapses. The fusion machinery is evolutionarily ancient and mediates constitutive fusion in yeast. We demonstrate that the SNARE and Unc18 machinery in the nematode C. elegans can be replaced by yeast proteins and still carry out synaptic transmission. However, substitutions of individual components from yeast disrupts fusion. To understand the functional interactions within the core machinery we adopted an ‘interspecies complementation’ approach using yeast. Synaptic transmission could be restored in chimeras when two key interfaces were present: a novel Habc-Unc18 contact site and an Unc18-SNARE motif contact site. An open form of Unc18 could bypass the requirement for the Habc-Unc18 interface. Together, these data suggest that the Habc domain of syntaxin is required for Unc18 to adopt an open conformation; open Unc18 then templates SNARE complex formation.
Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript
Authors: Höllerer Simon , Jeschek Markus
Published: May 2022

Translation is a key determinant of gene expression and an important biotechnological engineering target. In bacteria, 5’-untranslated region (5’-UTR) and coding sequence (CDS) are well-known mRNA parts controlling translation and thus cellular protein levels. However, the complex interaction of 5’-UTR and CDS has so far only been studied for few sequences leading to non-generalisable and partly contradictory conclusions. Herein, we systematically assess the dynamic translation from over 1.2 million 5’-UTR-CDS pairs in Escherichia coli to investigate their collective effect using a new method for ultradeep sequence-function mapping. This allows us to disentangle and precisely quantify effects of known and hypothetical sequence determinants of translation. We find that 5’-UTR and CDS individually account for 53% and 20% of variance in translation, respectively, and show conclusively that, contrary to a common hypothesis, tRNA abundance does not explain expression changes between CDSs with different synonymous codons. Moreover, the obtained large-scale data clearly point to a base-pairing interaction between initiator tRNA and mRNA beyond the anticodon-codon interaction, an effect that is often masked for individual sequences and therefore inaccessible to low-throughput approaches. Our study highlights the indispensability of ultradeep sequence-function mapping to accurately determine the contribution of parts and phenomena involved in gene regulation.
High-density and scalable protein arrays for single-molecule proteomic studies
Authors: Aksel Tural , Qian Hongji , Hao Pengyu , Indermuhle Pierre F. , Inman Christina , Paul Shubhodeep , Chen Kevin , Seghers Ryan , Robinson Julia K. , De Garate Mercedes , Nortman Brittany , Tan Jiongyi , Hendricks Steven , Sankar Subra , Mallick Parag
Published: May 2022

Single-molecule proteomic studies are critically important for understanding the molecular origins of cellular phenotypes. However, no currently available technology can achieve both the single-molecule sensitivity and high dynamic range required to comprehensively analyze the complex mixtures of proteins in biological samples. One approach to achieve high sensitivity across a wide dynamic range would be to create a protein array that arranges billions of single molecules with regular spacing on a patterned surface. However, creating such a protein array has remained an unsolved challenge for the field. Here, we present a highly scalable method for fabricating dense single-molecule protein arrays using a specially designed DNA origami structure, protein click-conjugation, photolithography and surface functionalization. The origami-structure is enhanced via terminal deoxynucleotidyl transferase-extension, which generates brush-like projections, increasing the effective size of the origami from 88 nm to greater than 200 nm. These particles are large enough to enable super-Poisson deposition of individual protein molecules on a nano-patterned chip (>98% occupancy with only 1% of sites occupied with multiple protein molecules). This approach allowed for single-molecule protein display of 600 million protein molecules per microscope slide-sized chip with the potential to scale further with denser feature spacing. We hypothesize that this technology will ultimately enable the development of highly scalable proteomic analysis platforms that address the currently unmet need for protein measurements at single-molecule sensitivity across an exceptionally wide dynamic range of protein concentrations.
Role of theEGR2promoter antisense RNA in modulating chromatin accessibility and spatial genome organization
Authors: Martinez-Moreno Margot , Karambizi David , Hwang Hyeyeon , Fregoso Kristen , Chen Jia-Shu , Fajardo Eduardo , Fiser Andras , Tapinos Nikos
Published: May 2022

TheEGR2promoter antisense RNA (AS-RNA) recruits chromatin remodeling complexes to inhibitEGR2transcription following peripheral nerve injury. Here we show that theEGR2-AS-RNA modulates chromatin accessibility and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters ofEGR2andC-JUNrespectively. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, theEGR2-AS-RNA induces changes in hierarchical TADs and increases transcription factor occupancy on an inter-TAD loop between a super-enhancer regulatory hub and the promoter ofmTOR. Our results show that theEGR2-AS-RNA may serve as regulator of chromatin remodeling and spatial genome organization in Schwann cells.
Chromosomal inversions can limit adaptation to new environments
Authors: Roesti Marius , Gilbert Kimberly J. , Samuk Kieran
Published: May 2022

Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But, what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may also provide one possible explanation for why inversions are often maintained as polymorphisms within species.
The swan genome and transcriptome: its not all black and white
Authors: Karawita Anjana C. , Cheng Yuanyuan , Chew Keng Yih , Challgula Arjun , Kraus Robert , Mueller Ralf C. , Tong Marcus Z. W. , Hulme Katina D. , Beielefeldt-Ohmann Helle , Steele Lauren E. , Wu Melanie , Sng Julian , Noye Ellesandra , Bruxner Timothy J. , Au Gough G. , Lowther Suzanne , Blommaert Julie , Suh Alexander , McCauley Alexander J. , Kaur Parwinder , Dudchenko Olga , Aiden Erez , Fedrigo Olivier , Formenti Giulio , Mountcastle Jacquelyn , Chow William , Martin Fergal J. , Ogeh Denye N. , Thiaud-Nissen Françoise , Howe Kerstin , Collins Joanna , Tracey Alan , Smith Jacqueline , Kuo Richard I. , Renfree Marilyn B. , Kimura Takashi , Sakoda Yoshihiro , McDougall Mathew , Spencer Hamish G. , Pyne Michael , Tolf Conny , Waldenström Jonas , Jarvis Erich D. , Baker Michelle L. , Burt David W. , Short Kirsty R.
Published: May 2022

The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.
Improving the RNA velocity approach using long-read single cell sequencing
Authors: Zhang Chen , Chen Weitian , Fang Yitong , Chen Zhichao , Xie Yeming , Chen Wenfang , Xie Zhe , Guo Mei , Wang Juan , Tan Chen , Wang Hongqi , Tang Chong
Published: May 2022

The concept of RNA velocity has been recently developed that allowed to look at the otherwise static single-cell RNA sequencing data in a dynamic way, which permitted inferences about cell fates. However, the more precise parameters, such as the number of exons/introns, can also be determined using long-read methods. Comparing the numbers of exons and introns allows including more genes for downstream velocity analysis and resolves the precise cell fate. The recently developed concept of “RNA velocity” concerns with dynamic changes in mRNA expression and complements single-cell RNA sequencing (scRNA-seq) data, which are static snapshots of a certain cell state taken at a given time point1. RNA velocity measures the change in mRNA abundance by differentiating the newly transcribed unspliced pre-mRNAs from mature spliced mRNAs. The rapidly developing long-read sequencing technology lends itself for RNA velocity analysis of scRNA-seq data, which was previously performed primarily using second-generation sequencing.
Communicating customer-CSR expectations on corporate websites: an analysis of the banking industry in the United Arab Emirates
Authors: Georgiadou Effrosyni
Published: May 2022

Purpose

The purpose of this paper is to explore customer–corporate social responsibility (-CSR) expectations communicated on the corporate websites of the banking sector in the United Arab Emirates (UAE) and identify patterns based on origin, ownership structure and compliance to Sharia law.

Design/methodology/approach

A quantitative content analysis of 28 bank corporate websites was conducted using Pérez and del Bosque's (2012) bank customers’ CSR scale which identifies five relevant dimensions of CSR: (1) customers, (2) investors, (3) employees, (4) community and (5) general interest groups, such as governments, regulatory bodies, NGOs and the media.

Findings

The findings indicate that the most frequently communicated customer CSR expectations are general interest, customer- and community-oriented, with employee-related concerns being the least addressed. Global banks prioritize general concerns, regarding their legal and ethical responsibilities while domestic banks appear more customer-centric. None of the Islamic banks address their responsibility to the environment.

Originality/value

The paper contributes to the increasing number of studies conducted on CSR communication in emerging economies, and more specifically, to the dynamic yet underexplored market of the UAE. It provides scholars and practitioners with insights into the interplay of globalization, organizational characteristics and national influence on CSR communication through corporate websites, one of the most useful tools organizations can utilize to reach their customers and the wider public.
Corporate governance and financial reporting quality: a comparative study
Authors: Hasan Arshad , Aly Doaa , Hussainey Khaled
Published: May 2022

Purpose

This paper aims to investigate the impact of corporate governance on financial reporting quality (FRQ) in Pakistan and the UK.

Design/methodology/approach

In this paper, three accrual-based models are used to analyse FRQ for a sample of 1,550 firm-year observations, including 78 Pakistani firms and 77 UK firms, for the period 2009–2018.

Findings

The analysis shows that board size has a negative impact on FRQ while foreign ownership has a positive impact for Pakistani and UK firms. It also shows that board independence has a positive impact on FRQ of Pakistani firms, while board meetings frequency and audit committee independence have a negative impact. We make no such observation for UK firms. In addition, the analysis shows that board gender diversity and ownership concentration negatively affect FRQ of UK firms. This study makes no such observation for Pakistani firms.

Research limitations/implications

Due to the study’s focus on Pakistani and UK firms, the findings may not be generalizable to other developed and emerging economies.

Practical implications

The findings provide valuable insight to policymakers, regulators and investors by suggesting that the impact of board composition on FRQ of both Pakistani and UK firms is weak. The findings suggest that board size and foreign ownership are the attributes that require regulatory focus to increase FRQ. The negative impact of audit committee independence on FRQ induces rethinking among the policymakers in Pakistan and calls for fully independent audit committees.

Originality/value

To the best of the authors’ knowledge, this is the first research endeavour to compare the context of a developed and an emerging economy regarding the impact of corporate governance on FRQ. It also contributes to the governance literature by using three measures of FRQ and a comprehensive set of corporate governance attributes.
Characterizing the spaces of consumer value experience in value co-creation and value co-destruction
Authors: Sahhar Yasin , Loohuis Raymond
Published: May 2022

Purpose

This paper aims to explore how unreflective and reflective value experience emerges in value co-creation and co-destruction practices in a consumer context.

Design/methodology/approach

This paper presents a Heideggerian phenomenological heuristic consisting of three interrelated modes of engagement, which is used for interpretive sense-making in a dynamic and lively case context of amateur-level football (soccer) played on artificial grass. Based on a qualitative study using ethnographic techniques, this study examines the whats and the hows of value experience by individuals playing football at different qualities and in varying conditions across 25 Dutch football teams.

Findings

The findings reveal three interrelated yet distinct modalities of experience in value co-creation and co-destruction presented in a continuum of triplex spaces of unreflective and reflective value experience. The first is a joyful flow of unreflective value experience in emergent and undisrupted value co-creation practice with no potential for value co-destruction. Second, a semireflective value experience caused by interruptions in value co-creation has a higher potential for value co-destruction. Third, a fully reflective value experience through a completely interrupted value co-creation practice results in high-value co-destruction.

Research limitations/implications

This research contributes to the literature on the microfoundations of value experience and value creation by proposing a conceptual relationship between unreflective/reflective value experience and value co-creation and co-destruction mediated through interruptions in consumer usage situations.

Practical implications

This study’s novel perspective on this relationship offers practitioners a useful vantage point on understanding how enhanced value experience comes about in value co-creation practice and how this is linked to value co-destruction when interruptions occur. These insights help bolster alignment and prevent misalignment in resource integration and foster service strategies, designs and innovations to better influence consumer experience in journeys.

Originality/value

This study deploys an integral view of how consumer value experience manifests in value co-creation and co-destruction that offers conceptual, methodological and practical clarity.
A study of the virtual reality cybersickness impacts and improvement strategy towards the overall undergraduate students’ virtual learning experience
Authors: Mareta Sannia , Thenara Joseph Manuel , Rivero Rafael , Tan-Mullins May
Published: May 2022

Purpose

Virtual reality (VR) technologies have expanded their application domains towards education with pedagogical benefits including fully immersive learning environment and in-depth user engagement through scenario-based virtual simulations. Motion sickness (MS), however, has become one of the long-standing key challenges of the VR utilisation, even in gaming industries. Thus, this paper aims to present a preliminary study on understanding the VR MS, referred as cybersickness, in the teaching and learning (T&L) context at the University of Nottingham Ningbo China.

Design/methodology/approach

A VR-based virtual classroom content was developed and tested for 60 undergraduate students having equal access to the same VR equipment. A two-step data collection, comprising qualitative and quantitative measures, was conducted for the participants. The aspects of how gender influences the cybersickness severity and how academic background affects the learning experience were investigated and analysed using analysis of variance F-test statistical approach.

Findings

The results demonstrated approximately 47% of the participants had experienced cybersickness, where 64% of them were females. With confidence level of 95% (a = 5%), the obtained p-value and F-statistical value for the respective gender and study discipline categories against the cybersickness symptoms confirmed the significance level between the two compared variables. Moreover, it is worth highlighting that the virtual movement speed, perspective angle and visual properties of the virtual environment were selected as the top three factors that caused the cybersickness.

Originality/value

The study is hoped to provide valuable pointers to current and future VR developers in minimising the cybersickness symptoms that would enable an effective T&L environment in higher education.
The workplace social performance of family firms: a configurational approach
Authors: Samara Georges , Parada María Jose , Fathallah Ramzi
Published: May 2022

Purpose

The purpose of this study is to explore the drivers for proactive workplace social performance in family firms through a configurational approach. Comparative research on family versus non-family firms and workplace social performance has produced mixed results. Consequently, several calls have been made to account for family business heterogeneity to understand better how family involvement in the business affects the workplace social performance. The authors respond to these calls by exploring the governance antecedents that can catalyze family firms’ workplace social performance.

Design/methodology/approach

Using qualitative comparative analysis, the authors analyze 131 family firms from the STEP survey data.

Findings

The authors find two governance configurations that lead to better family business workplace social performance. The first configuration is the combination of 100% family ownership, high family involvement in management and a mix of outside directors and family members on the board. The second configuration is the combination of less than 100% family ownership and low family involvement in management.

Originality/value

The study builds on and extends the nascent work suggesting the integration of agency and stewardship theories. The authors show that these two theoretical approaches are able to not only coexist, but that they can also be complementary in helping to understand the unique workplace social behaviors of family firms.
Is there a relationship between intensity of occupational therapy and functional outcomes in hospitalised older patients? A prospective cohort study
Authors: Marston Celia , Koye Digsu N. , Goonan Rose , Lim Kwang , Juj Genevieve , Klaic Marlena
Published: May 2022

Introduction

Delivering high‐intensity occupational therapy can improve functional outcomes for patients and reduce length of stay. However, there is little published evidence of this in the aged rehabilitation setting. This study aims to explore the association between intensity of occupational therapy interventions and functional outcomes in geriatric rehabilitation inpatients.

Methods

A prospective cohort study was conducted with adult inpatients admitted to a geriatric rehabilitation program. The intervention was the intensity of occupational therapy measured as high (≥30 minutes per day) versus low (<30 minutes per day). The primary outcome measured was change in functional performance, defined as a minimum of half a point improvement in the Katz Index of Activities of Daily Living (ADL) and/or the Lawton and Brody Scale of Instrumental ADL (IADL) at admission to rehabilitation, discharge and 3months post‐discharge.

Results

A total of 693 patients were included in the analysis. The mean age was 82.2 years (standard deviation [SD] = 7.9), 57% were females, and 64% had cognitive impairment. Patients (n = 210) who received greater than or equal to 30 minutes of occupational therapy daily were more likely to have clinically relevant functional improvements.; for both ADL (odds ratio [OR] = 1.87, 95% confidence interval [CI]: 1.24–2.83) and IADL (OR = 3.00, 95% CI: 1.96–4.61), after adjusting for age, sex, severity of function (ADL ≤ 2) at admission, frailty and cognitive impairment. Improvements in ADL and IADL were maintained for at least 3 months following discharge.

Conclusion

This study found that geriatric rehabilitation inpatients who received higher intensity of occupational therapy interventions were more likely to functionally improve than those who received lower intensity. Further research is required to determine if other factors, such as therapy type, influence functional outcomes.
Identifying violence against persons at a safety‐net hospital: Evidence from the first 6 months of implementation
Authors: Beauchamp Alaina M. , Kalra Anjali , Scroggins Heather , Pahl Brittany , Pitt Amanda , Skaliks Andrea , Jetelina Katelyn K.
Published: May 2022

Objective

To examine the prevalence and predictors of screening for violence against persons and victim service utilization within an integrated safety‐net health system.

Study Setting

Emergency Department (ED) at Parkland Hospital—Dallas County's largest safety‐net provider of services for minority and underinsured and uninsured patients.

Study Design

Prospective, longitudinal study during the first 6 months of a universal violence against persons screener.

Data Collection

Health records were extracted for all patients with a visit to the ED between January and July, 2021. Modeling described the patient population across screening (screened vs. not screened) and, among those screened, the results (positive vs. negative), average time spent in the ED, and referral patterns for victim services.

Principal Findings

During the study period, 65,563 unique patients with 95,555 encounters occurred. Seventy‐one percent (n = 67,535) were screened for violence against persons and, of those, 2% screened positive (n = 1349). Of the patients who screened positive, 1178 (87%) were referred to and 806 (60%) received care at victim services. Implementing screening did not increase the length of stay at ED.

Conclusions

Systematic implementation of comprehensive violence screening at a safety‐net system can result in robust identification and timely referrals to victim services.
Meeting customer needs through ethical leadership and training: examining Australian bank employees
Authors: Halvorsen Beni , Bartram Timothy , Kia Narges , Cavanagh Jillian
Published: May 2022

We examine the process through which ethical leadership and ethical training contribute to the performance of employees through linking business ethics to customer orientation. Underpinned by social learning, we examine sequential mediation models of the process through which ethical climate, service climate and customer orientation mediate the relationships between ethical leadership and ethical training on employee performance. Utilising a sample of 187 employees from an Australian bank, we found support for our four hypotheses: ethical climate and customer orientation sequentially mediates the relationship between ethical leadership and employee performance; service climate and customer orientation sequentially mediates the relationship between ethical leadership and employee performance; service climate and customer orientation sequentially mediates the relationship between ethical training and employee performance; ethical climate and customer orientation sequentially mediates the relationship between ethics training and employee performance. Ethical leadership will have a stronger influence on improving employee performance relative to ethical training.
“An apple a day keeps the doctor away”: The potentials of apple bioactive constituents for chronic disease prevention
Authors: Oyenihi Ayodeji B. , Belay Zinash A. , Mditshwa Asanda , Caleb Oluwafemi J.
Published: May 2022

Apples are rich sources of selected micronutrients (e.g., iron, zinc, vitamins C and E) and polyphenols (e.g., procyanidins, phloridzin, 5′‐caffeoylquinic acid) that can help in mitigating micronutrient deficiencies (MNDs) and chronic diseases. This review provides an up‐to‐date overview of the significant bioactive compounds in apples together with their reported pharmacological actions against chronic diseases such as diabetes, cancer, and cardiovascular diseases. For consumers to fully gain these health benefits, it is important to ensure an all‐year‐round supply of highly nutritious and good‐quality apples. Therefore, after harvest, the physicochemical and nutritional quality attributes of apples are maintained by applying various postharvest treatments and hurdle techniques. The impact of these postharvest practices on the safety of apples during storage is also highlighted. This review emphasizes that advancements in postharvest management strategies that extend the storage life of apples should be optimized to better preserve the bioactive components crucial to daily dietary needs and this can help improve the overall health of consumers.
Health risk assessment using in vitro simulation in assessing bioavailability of cadmium in rice from main producing areas across China
Authors: Deng Ziyi , Yao Liyun , Fang Min , Wu Yongning , Gong Zhiyong
Published: May 2022

Rice is a recognized source of cadmium (Cd) exposure. In this study, a total of 102 rice samples were obtained from main producing rice regions of China, and the bioavailability of Cd in rice were assessed by using an in vitro digestion method combined with a Caco‐2 cell monolayer model. The results revealed that the average (range of) concentration of Cd in the rice samples was 0.2840 (0.0123–2.4710) mg/kg, and the average (range of) bioavailability of Cd in the rice samples was 23.94% (7.47–39.73%). We analyzed the recent rice consumption data and calculated the target hazard quotients (THQs) to evaluate the noncarcinogenic health risk of Cd in rice consumption for adults and children, respectively. We suggested that the most of investigated regions showed low risks of Cd in rice for general population, and the regions of Cd in rice near the limit deserves might be attracted more attention after taking bioavailability into account.

Practical Application

The cadmium content of rice itself will affect its corresponding bioavailability to a certain extent. By studying the in vitro bioavailability of cadmium rice with different pollution levels, it is helpful for the dose selection of animal experiments or toxicity tests, and finally, we may provide some references for the establishment of appropriate treatment scheme of rice Cd poisoning.