bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid quantitative electrochemical detection of SARS-CoV-2 antibodies in plasma and dried blood spot samples
Authors: Timilsina Sanjay S. , Durr Nolan , Jolly Pawan , Ingber Donald E.
Published: October 2022

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a highly contagious disease with several variants, continues to spread as part of the global pandemic. With the roll-out of vaccines and development of new therapeutics that may be targeted to distinct viral molecules, there is a need to screen populations for viral antigen-specific SARS-CoV-2 antibodies. Here, we describe a rapid, multiplexed, electrochemical (EC) platform with on-chip control that enables detection of SARS-CoV-2 antibodies in less than 10 min using 1.5 µL of a patient sample. The EC biosensor demonstrated 100% sensitivity and specificity, and an area under the receiver operating characteristic curve of 1, when evaluated using 93 clinical samples, including plasma and dried blood spot samples from 54 SARS-CoV-2 positive and 39 negative patients. This EC biosensor platform enables simple, cost-effective, sensitive, and rapid detection of anti-SARS-CoV-2 antibodies in complex clinical samples, which is convenient for monitoring host humoral responses to vaccination or viral infection in broad population testing, including applications in low-resource settings. We also demonstrate the feasibility of using dried blood spot samples that can be collected locally and transported to distant clinical laboratories at ambient temperature for detection of anti-SARS-CoV-2 antibodies which can be used for serological surveillance and demonstrate the utility of remote sampling.
High levels of serum cholesterol positively correlate with the risk of the development of vessel co-opting tumours in colorectal cancer liver metastases
Authors: Rada Miran , Krzywon Lucyna , Kapelanski-Lamoureux Audrey , Petrillo Stephanie , Reynolds Andrew R. , Lazaris Anthoula , Seidah Nabil , Metrakos Peter
Published: October 2022

Colorectal cancer liver metastatic (CRCLM) tumours present as two main histopathological growth patterns (HGPs) including desmoplastic HGP (DHGP) and replacement HGP (RHGP). The DHGP tumours obtain their blood supply by sprouting angiogenesis, whereas the RHGP tumours utilize an alternative vascularisation known as vessel co-option. In vessel co-option, the cancer cells hijack the mature sinusoidal vessels to obtain blood supply. Vessel co-option has been reported as an acquired mechanism of resistance to anti-angiogenic treatment in CRCLM. Here, we show the connection between the concentration of serum cholesterol and the development of vessel co-option in CRCLM. Our clinical data suggested that the elevation of serum cholesterol levels correlates with the risk of developing vessel co-opting tumours. Moreover, inhibition of the key modulators of cholesterol metabolism including HMGCR or PCSK9 attenuated the development of CRCLM tumours, as well as vessel co-option in vivo. Altogether, our data uncovered the importance of cholesterol in the development of vessel co-option tumours and demonstrated PCSK9 and HMGCR inhibitors as promising strategies to mitigate the development of vessel co-option tumours in CRCLM.
The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis
Authors: Zhao Ziyu , Vercellino Irene , Knoppová Jana , Sobotka Roman , Murray James W. , Nixon Peter J. , Sazanov Leonid A. , Komenda Josef
Published: October 2022

Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we have used cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the Mn4CaO5cluster that catalyzes water oxidation, thereby preventing the premature binding of Mn2+and Ca2+ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides new insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5cluster.
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)
Authors: Okeke Damasus C. , Lidman Jens , Matečko-Burmann Irena , Burmann Björn M.
Published: October 2022

In order to cope with the risk of stress-induced mutagenesis, cells in all kingdoms of life employ Y-family DNA polymerases to resolve resulting DNA lesions and thus maintaining the integrity of the genome. InEscherichia coli(E. coli) the DNA polymerase IV, or DinB, plays this crucial role in coping with these type of mutationsviathe so-called translesion DNA synthesis. Despite the availability of several high-resolution crystal structures important aspects of the functional repertoire of DinB remain elusive. In this study, we use advanced solution NMR spectroscopy methods in combination with biophysical characterization to elucidate the crucial role of the Thumb domain within DinB’s functional cycle. We find that the inherent dynamics of this domain guide the recognition of double-stranded (ds) DNA buried within the interior of the DinB domain arrangement and trigger allosteric signals through the DinB protein. Subsequently, we characterized the RNA polymerase interaction with DinB, revealing an extended outside surface of DinB and thus not mutually excluding the DNA interaction. Altogether the obtained results lead to a refined model of the functional repertoire of DinB within the translesion DNA synthesis pathway.
Diversity-oriented synthesis encoded by deoxyoligonucleotides
Authors: Hudson Liam , Mason Jeremy W. , Westphal Matthias V. , Richter Matthieu J. R. , Thielman Jonathan R. , Hua Bruce K. , Gerry Christopher J. , Xia Guoqin , Osswald Heather L. , Knapp John M. , Tan Zher Yin , Kokkonda Praveen , Tresco Ben I. C. , Liu Shuang , Reidenbach Andrew G. , Lim Katherine S. , Poirier Jennifer , Capece John , Bonazzi Simone , Gampe Christian M. , Smith Nichola J. , Bradner James E. , Coley Connor W. , Clemons Paul A. , Melillo Bruno , Hon C. Suk-Yee , Ottl Johannes , Dumelin Christoph E. , Schaefer Jonas V. , Faust Ann Marie E. , Berst Frédéric , Schreiber Stuart L. , Zécri Frédéric J. , Briner Karin
Published: October 2022

Diversity-oriented synthesis (DOS)is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors, derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
A drug’s most potent target is not necessarily the source of its anti-cancer activity
Authors: Bhattacharjee Debanjan , Bakar Jaweria , Sausville Erin L. , Mendelson Brianna E. , Long Kaitlin , Smith Joan C. , Sheltzer Jason M.
Published: October 2022

The small-molecule drug ralimetinib was developed as an inhibitor of the kinase p38α, and it has advanced to phase 2 clinical trials in oncology. Here, we apply a multi-modal approach to demonstrate that ralimetinib’s anti-cancer activity occurs due to its ability to inhibit EGFR, rather than p38α. We find that cancer cell lines driven by EGFR mutations exhibit the greatest sensitivity to ralimetinib treatment, and ralimetinib phenocopies established EGFR inhibitors in pharmacogenomic profiling experiments. We further demonstrate that ralimetinib inhibits EGFR kinase activityin vitroandin cellulo, albeit at >30-fold higher concentrations than it inhibits p38α. Finally, while deletion of the gene encoding p38α has no effect on ralimetinib sensitivity, expression of the EGFR-T790M gatekeeper mutation confers resistance to ralimetinib treatment. These findings suggest that future clinical trials involving ralimetinib could incorporate EGFR mutation status as a biomarker to identify sensitive patients. Moreover, our results demonstrate that a compound’s anti-cancer effects should not necessarily be attributed to the protein that it inhibits most strongly, and instead, comprehensive cellular and genetic profiling is required to understand a drug’s mechanism-of-action.
Eleven key measures for monitoring general practice clinical activity during COVID-19 using federated analytics on 48 million adults’ primary care records through OpenSAFELY
Authors: Fisher Louis , Curtis Helen J. , Croker Richard , Wiedemann Milan , Speed Victoria , Wood Christopher , Brown Andrew , Hopcroft Lisa EM , Higgins Rose , Massey Jon , Inglesby Peter , Morton Caroline E. , Walker Alex J. , Morley Jessica , Mehrkar Amir , Bacon Seb , Hickman George , Macdonald Orla , Lewis Tom , Wood Marion , Myers Martin , Samuel Miriam , Conibere Robin , Baqir Wasim , Sood Harpreet , Drury Charles , Collison Kiren , Bates Chris , Evans David , Dillingham Iain , Ward Tom , Davy Simon , Smith Rebecca M. , Hulme William , Green Amelia , Parry John , Hester Frank , Harper Sam , Cockburn Jonathan , O’Hanlon Shaun , Eavis Alex , Jarvis Richard , Avramov Dima , Griffiths Paul , Fowles Aaron , Parkes Nasreen , MacKenna Brian , Goldacre Ben
Published: October 2022

Background

The COVID-19 pandemic has had a significant impact on delivery of NHS care. We have developed the OpenSAFELY Service Restoration Observatory (SRO) to describe this impact on primary care activity and monitor its recovery.

Objectives

To develop key measures of primary care activity and describe the trends in these measures throughout the COVID-19 pandemic.

Methods

With the approval of NHS England we developed an open source software framework for data management and analysis to describe trends and variation in clinical activity across primary care electronic health record (EHR) data on 48 million adults.

We developed SNOMED-CT codelists for key measures of primary care clinical activity selected by a expert clinical advisory group and conducted a population cohort-based study to describe trends and variation in these measures January 2019-December 2021, and pragmatically classified their level of recovery one year into the pandemic using the percentage change in the median practice level rate.

Results

We produced 11 measures reflective of clinical activity in general practice. A substantial drop in activity was observed in all measures at the outset of the COVID-19 pandemic. By April 2021, the median rate had recovered to within 15% of the median rate in April 2019 in six measures. The remaining measures showed a sustained drop, ranging from a 18.5% reduction in medication reviews to a 42.0% reduction in blood pressure monitoring. Three measures continued to show a sustained drop by December 2021.

Conclusions

The COVID-19 pandemic was associated with a substantial change in primary care activity across the measures we developed, with recovery in most measures. We delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. We will continue to expand the set of key measures to be routinely monitored using our publicly available NHS OpenSAFELY SRO dashboards with near real-time data.
Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data
Authors: Kremer Cécile , Torneri Andrea , Libin Pieter J. K. , Meex Cécile , Hayette Marie-Pierre , Bontems Sébastien , Durkin Keith , Artesi Maria , Bours Vincent , Lemey Philippe , Darcis Gilles , Hens Niel , Meuris Christelle
Published: October 2022

Mathematical modeling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. In this study, we reconstructed outbreaks observed during a prospective study in a primary school and associated households in Liège (Belgium) during the academic year 2020-2021. In addition we performed a simulation study to investigate how the accuracy of estimated weekly positivity rates in a school depends on the proportion of a school that is sampled in a repetitive screening strategy. We found that transmission occurred mainly within the school environment and that observed positivity rates are a good approximation to the true positivity rate, especially in children. This study shows that it is worthwile to implement repetitive testing in school settings, which in addition to reducing infections can lead to a better understanding of the extent of transmission in schools during a pandemic and importation risk at the community level.
The ER tether VAPA is required for proper cell motility and anchors ER-PM contact sites to focal adhesions
Authors: Siegfried Hugo , Le Borgne Rémi , Durieu Catherine , De Azevedo Laplace Thaïs , Verraes Agathe , Daunas Lucien , Verbavatz Jean-Marc , Heuzé Mélina L.
Published: October 2022

Cell motility processes highly depend on the membrane distribution of Phosphoinositides (PInst), giving rise to cytoskeleton reshaping and membrane trafficking events. Membrane contact sites serve as platforms for lipid exchange and calcium fluxes between two organelles. Here, we show that VAPA, an ER membrane-resident contact site tether, plays a crucial role during cell motility. CaCo2 adenocarcinoma epithelial cells depleted for VAPA exhibit several collective and individual motility defects, disorganized actin cytoskeleton and altered protrusive activity. During migration, VAPA is required for the maintenance of PI(4,5)P2 levels at the plasma membrane, but not for PI(4)P homeostasis in the Golgi and endosomal compartments. Importantly, we show that VAPA regulates the dynamics of focal adhesions (FA) through its MSP domain, and is essential to stabilize and anchor ventral ER-PM contact sites to FA, thus mediating microtubule-dependent FA disassembly. To conclude, our results reveal unprecedented functions for VAPA-mediated membrane contact sites during cell motility and provides a dynamic picture of ER-PM contact sites connection with FA mediated by VAPA.
Centrosome amplification fine-tunes tubulin acetylation to differentially control intracellular organization
Authors: Monteiro Pedro , Yeon Bongwhan , Wallis Samuel S. , Godinho Susana A.
Published: October 2022

Intracellular organelle organisation is conserved in eukaryotic cells and is primarily achieved through active transport by motor proteins along the microtubule cytoskeleton. Microtubule posttranslational modifications (PTMs) contribute to microtubule diversity and differentially regulate motor-mediated transport. Here we show that centrosome amplification induces a global change in organelle positioning towards the cell periphery and facilitates nuclear migration through confined spaces. This reorganisation requires kinesin-1 and is analogous to loss of dynein. Cells with amplified centrosomes display increased levels of acetylated tubulin, a PTM known to enhance kinesin-1 mediated transport. Depletion of α-tubulin acetyltransferase 1 (αTAT1) to block tubulin acetylation, which has no impact on control cells, rescues the displacement of centrosomes, mitochondria and vimentin, but not Golgi or endosomes. Analyses of the distribution of acetylated microtubules indicates that the polarisation of modified microtubules, rather than levels alone, plays an important role in organelle positioning. We propose that tubulin acetylation differentially impacts kinesin-1-mediated organelle displacement, suggesting that each organelle must have its own sensing and response mechanisms to ensure fine-tuning of its distribution in cells.
Rates of global cellular translation and transcription during cell growth and the cell cycle in fission yeast
Authors: Basier Clovis , Nurse Paul
Published: October 2022

Proliferating eukaryotic cells grow and undergo cycles of cell division. Growth is continuous whilst the cell cycle consists of discrete events. How the production of biomass is controlled as cells increase in size and proceed through the cell cycle is important for understanding the regulation of global cellular growth. This has been studied for decades but has not yielded consistent results. Previous studies investigating how cell size, the amount of DNA, and cell cycle events affect the global cellular production of proteins and RNA molecules have led to highly conflicting results, probably due to perturbations induced by the synchronisation methods used. To avoid these perturbations, we have developed a system to assay unperturbed exponentially growing populations of fission yeast cells. We generated thousands of single-cell measurements of cell size, of cell cycle stage, and of the levels of global cellular translation and transcription. This has allowed us to determine how cellular changes arising from progression through the cell cycle and cells growing in size affect global cellular translation and transcription. We show that translation scales with size, and additionally increases at late S-phase/early G2, then increases early in mitosis and decreases later in mitosis, suggesting that cell cycle controls are operative over global cellular translation. Transcription increases with both size and the amount of DNA, suggesting that the level of transcription of a cell may be the result of a dynamic equilibrium between the number of RNA polymerases associating and disassociating from DNA.
Decoding of YAP levels and dynamics by pluripotency factors
Authors: Meyer Kirstin , Lammers Nicholas C. , Bugaj Lukasz J. , Garcia Hernan G. , Weiner Orion D.
Published: October 2022

YAP is a transcriptional regulator that controls pluripotency, germ layer specification, and proliferation. Different subsets of YAP target genes are engaged in each physiological setting, but how YAP selectively regulates different effectors in different contexts is not known. Here we use optogenetics to investigate how the levels and dynamics of YAP activation control its pluripotency effectors Oct4 and Nanog. We observe different thresholds for repression of Oct4 and Nanog, enabling differential control of both genes through YAP levels. Pluripotency factors also decode YAP dynamics. Oct4 preferentially responds to oscillatory YAP inputs that mimic endogenous pulsatile YAP dynamics. Using single-cell live imaging of Oct4 transcription and computational-theoretical analysis of transcriptional regulation, we demonstrate that YAP dynamics are decoded by an adaptive change sensor that modulates Oct4 transcription burst frequency. Our results reveal how the levels and timing of YAP activation enable multiplexing of information transmission for key regulators of cellular differentiation and pluripotency.
Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover
Authors: Guzman Ulises H. , Aksnes Henriette , Ree Rasmus , Krogh Nicolai , Jakobsson Magnus E. , Jensen Lars J. , Arnesen Thomas , Olsen Jesper V.
Published: October 2022

Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ∼50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employed a multi-dimensional proteomics approach to analyzeSaccharomyces cerevisiaelacking NatA activity, which caused global proteome remodeling. Pulsed-SILAC experiments revealed that NatA-deficient strains consistently increased degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovered decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.

Teaser

A multidimensional proteomics approach reveals the effect of N-terminal acetylation onSaccharomyces cerevisiaecytosolic ribosomal proteins.
Targeted memory reactivation during sleep can induce forgetting of overlapping memories
Authors: Joensen Bárður H. , Harrington Marcus O. , Berens Sam C. , Cairney Scott A. , Gaskell M. Gareth , Horner Aidan J.
Published: October 2022

Memory reactivation during sleep can shape new memories into a long-term form. Reactivation of memories can be induced via the delivery of auditory cues during sleep. Although this targeted memory reactivation (TMR) approach can strengthen newly acquired memories, research has tended to focus on single associative memories. It is less clear how TMR affects retention for overlapping associative memories. This is critical, given that repeated retrieval of overlapping associations during wake can lead to forgetting, a phenomenon known as retrieval-induced forgetting (RIF). We asked whether a similar pattern of forgetting occurs when TMR is used to cue reactivation of overlapping pairwise associations during sleep. Participants learned overlapping pairs—learned separately, interleaved with other unrelated pairs. During sleep, we cued a subset of overlapping pairs using TMR. While TMR increased retention for the first encoded pairs, memory decreased for the second encoded pairs. This pattern of retention was only present for pairs not tested prior to sleep. The results suggest that TMR can lead to forgetting, an effect similar to RIF during wake. However, this effect did not extend to memories that had been strengthened via retrieval prior to sleep. We therefore provide evidence for a reactivation-induced forgetting effect during sleep.
Decreased associative processing and memory confidence in aphantasia
Authors: Wittmann Bianca C. , Şatırer Yılmaz
Published: October 2022

Visual imagery and mental reconstruction of scenes are considered core components of episodic memory retrieval. Individuals with absent visual imagery (aphantasia) score lower on tests of autobiographical memory, suggesting that aphantasia may be associated with differences in episodic and associative processing. In this online study, we tested aphantasic participants and controls on associative recognition and memory confidence for three types of associations encoded incidentally: associations between visual–visual and audio–visual stimulus pairs, associations between an object and its location on the screen, and intraitem associations. Aphantasic participants had a lower rate of high-confidence hits in all associative memory tests compared with controls. Performance on auditory–visual associations was correlated with individual differences in a measure of object imagery in the aphantasic group but not in controls. No overall group difference in memory performance was found, indicating that visual imagery selectively contributes to memory confidence. Analysis of the encoding task revealed that aphantasics made fewer associative links between the stimuli, suggesting a role for visual imagery in associative processing of visual and auditory input. These data enhance our understanding of visual imagery contributions to associative memory and further characterize the cognitive profile of aphantasia.
Differential Expression Analysis ofNothobranchius furzeriTransposable Elements from RNA-seq Data
Authors: Teefy Bryan , Malone Matthew , Benayoun Bérénice A.
Published: October 2022

Transposable elements (TEs) comprise large fractions of eukaryotic genomes, but their repetitive nature and high copy number makes bioinformatic analyses more complex. Here, we report three robust pipelines to analyze TE expression from RNA-seq data in a non-model organism, the African turquoise killifishNothobranchius furzeri. Our protocol can be run with either a genomic or transcriptomic reference depending on available computational resources, with options both for limited memory usage and for more computationally intensive analyses. Our protocol leverages both standard software for classical RNA-seq analysis pipelines as well as software specialized for TEs. This protocol uses input RNA-seq data from Illumina reads and can use data in either single-end or paired-end layout. Here, we show how to start from input RNA-seq data from aging killifish tissues using a publicly available data set from which we take single and paired reads, trim adapters, align and count trimmed reads, and perform differential expression analyses for TEs.
Immunohistochemical Staining of the Mosquito Ear
Authors: Andrés Marta , Bagi Judit , Albert Joerg T.
Published: October 2022

Immunohistochemistry has played a major role in improving our understanding of the anatomy and function of the nervous system. The use of fluorescent dyes that label different antigens reveals how biological tissues are built and how interactions between cells take place. Obtaining this information is particularly important in the case of the mosquito ear given its highly complex anatomy. This protocol describes an immunohistochemical technique to stain the mosquito ear. The first steps of the procedure include the embedding of the tissue in albumin-gelatin and its sectioning into thin slices to allow antibody penetration. The immunohistochemical procedure can be exploited to detect protein expression and localization by using antibodies specifically raised against the protein of interest or that recognize epitope tags fused to proteins using genome editing methods.
Acoustic Physiology in Mosquitoes
Authors: Su Matthew P. , Andrés Marta , Georgiades Marcos , Bagi Judit , Albert Joerg T.
Published: October 2022

The acoustic physiology of mosquitoes is perhaps the most complex within the entire insect class. Past research has uncovered several of its—sometimes stunningly unconventional—principles, but many mysteries remain. Their solution necessitates a concerted transdisciplinary effort to successfully link the neuroanatomical and biophysical properties of mosquito flagellar ears to the behavioral ecology of entire mosquito populations. Neuroanatomically, mosquito ears can rival those of humans in both complexity and sheer size. The approximately 16,000 auditory hair cells within the human organ of Corti, for example, are matched by the approximately 16,000 auditory neurons in the Johnston's organ of a maleAnophelesmosquito. Both human and mosquito ears receive very extensive efferent innervation, which modulates their function in ways that are as yet poorly understood. Different populations of neuronal and nonneuronal cell types divide the labor of the mosquito ear amongst themselves. Yet, what exactly this labor is, and how it is achieved, is at best vaguely known. For the majority of mosquitoes, biologically relevant sounds are inextricably linked to their flight tones. Either these flight tones are (directly) the sounds of interest or they contribute (indirectly) to the production of audible sound through a process called nonlinear distortion. Finally, male ears can generate tones themselves: The generation of an internal “phantom copy” of a female flight tone (orself-sustained oscillation) is believed to aid the male hearing process. Here, we introduce protocols that target the mosquitoes’ auditory neuroanatomy, electrophysiology, and behavior to help shed light on some of these issues.
CSR authenticity and micro-foundations of business: a systematic review
Authors: Hassan Yusuf , Pandey Jatin , Behl Abhishek , Pereira Vijay , Vaz Daicy
Published: October 2022

Purpose

The current market conditions are driving firms to plan, design and implement corporate social responsibility (CSR) policies that are true to the firms' real sense, i.e. authentic. Authenticity is an important aspect of micro-foundations of CSR in shaping the way social responsibility initiatives would impact the stakeholders including the customers, partners, current members of the organization and shareholders. This calls for a need to synthesize past research on CSR authenticity in order to propose directions for future research.

Design/methodology/approach

The current study synthesizes relevant literature on CSR authenticity using systematic literature review (SLR) approach. In total, 34 research works were identified and examined to seek insights on CSR authenticity.

Findings

Findings of the study identified various miro-, meso- and macro-level determinants of CSR authenticity and different set of outcomes having implications on business and society. The study also proposes a comprehensive definition of CSR authenticity which was somewhat missing in existing literature.

Practical implications

The study provides strong theoretical and managerial implications. Particularly, the study provides directions for future research on the topic.

Originality/value

In this paper, a review of literature on CSR authenticity is currently missing.
Identities and the pursuit of legitimacy: A study of black women wine industry entrepreneurs
Authors: Ojediran Olufunmilola (Funmi) , Discua Cruz Allan , Anderson Alistair
Published: October 2022

Purpose

The aim of this study is to better understand how black women utilize capital to frame their entrepreneurial identities in order to become legitimate and thus challenge institutional norms. To achieve this, the study draws on perspectives on legitimacy, identity and capital and focuses on the well-established wine industry in South Africa.

Design/methodology/approach

Using in-depth qualitative data from semi-structured interviews, this study delves into the lived experiences of nine black women entrepreneurs and three stakeholders in the South African wine industry. Such a context is unique because of the aspects of exclusion and segregation of black women. The data were supplemented with associated secondary material and were analysed using the constant comparative technique.

Findings

This study reveals dissonance, that is, a misfit, between black women's social identities and their entrepreneurial self-identities in the South African wine industry; the study uncovers that specific capital forms allow framing their identity through heroical self-description, exploiting professionalism and enacting new roles to alter the perception of what is socially legitimate in the wine industry.

Originality/value

This study contributes to understanding by highlighting that black women entrepreneurs in the wine industry rebel against the expectation that they must fit into a predetermined role. The study highlights the relevance of legitimacy, identity and capital theoretical perspectives to study an underexplored context and unpack how black women challenge the barriers that affect their entrepreneurial identities in their quest to become legitimate. The value of this study revolves around revealing the underexplored connection between entrepreneurial identity and legitimacy through actions taken by black women entrepreneurs when reworking the role(s) tied to their social identities. The findings suggest the importance of capital, particularly cultural capital, in how black women entrepreneurs become legitimate in the wine industry. Avenues for further research are offered.
The role of Industry 4.0 technologies on performance measurement systems of supply chains during global pandemics: an interval-valued intuitionistic hesitant fuzzy approach
Authors: Amoozad Mahdiraji Hannan , Yaftiyan Fatemeh , Abbasi Kamardi Ali Asghar , Garza-Reyes Jose Arturo , Razavi Hajiagha Seyed Hossein
Published: October 2022

Purpose

This paper aims to investigate Supply Chain (SC) Performance Measurement Systems (PMSs) (SCPMSs) that are suitable and applicable to evaluate SC performance during unexpected events such as global pandemics. Furthermore, the contribution of Industry 4.0 Disruptive Technologies (IDTs) to implement SCPMSs during such Black Swan events is investigated in this study.

Design/methodology/approach

The research methodology is based upon a novel qualitative and quantitative mixed-method. A Systematic Literature Review (SLR) was initially employed to identify two complete lists of SCPMSs and IDTs. Then, a novel Interval-Valued Intuitionistic Hesitant-Fuzzy (IVIHF)-Delphi method was firstly developed in this paper to screen the extracted SCPMSs. Afterward, the Propriety, Economic, Acceptable, Resource, Legal (PEARL) indicator of the Hanlon method was innovatively applied to prioritize the identified IDTs for each finalized SCPMS.

Findings

Two high-score SCPMSs including the SC operations reference (SCOR) model and sustainable SCPMS were recommended to improve measuring the performance of the pharmaceutical SC of emerging economies such as Iran in which the societal, biological and economic issues were undeniable, particularly during unexpected events. Employing nine IDTs such as simulation, big data analytics, cloud technologies, etc., would facilitate implementing sustainable SCPMS from distinct perspectives.

Originality/value

This is one of the first papers to provide in-depth insights into determining the priority of contribution of IDTs in applying different SCPMSs during global pandemics. Proposing a novel multi-layer mixed-methodology involving SLR, IVIHF-Delphi, and the PEARL indicator of the Hanlon method is another originality offered by this paper.
On the inverse identification of wood elastic properties using a DIC-based FEMU approach
Authors: Henriques João , Xavier José , Andrade-Campos António
Published: October 2022

Purpose

This work aims to identify the linear elastic orthotropic material paramters of Pinus pinaster Ait. wood, using full-field measurements and an inverse identification strategy based on the finite element (FE) method updating technique.

Design/methodology/approach

Compression tests are carried out under uniaxial and quasi-static loading conditions on wood specimens oriented on the radial-tangential (RT) plane, with different grain orientations. Full-field displacements and strains are measured using digital image correlation (DIC), which are then used as a reference in the identification procedure. A FE model is implemented assuming plane stress conditions, where wood is modelled as an orthotropic homogeneous material. Based on the numerical results, a synthetic image reconstruction scheme is implemented to synthetically deform the reference experimental image, which is then processed by DIC and further compared to the experimental results.

Findings

The results for both approaches were similar when both specimen configurations were used in a single run. However, when using the DIC-based FEMU approach with the on-axis configuration, the identified modulus of elasticity in the tangential direction and shear modulus are closer to the reference values.

Originality/value

This approach ensures a fair comparison between both sets of data since the full-field strain maps are obtained through the same filter and therefore have the same strain formulation, spatial resolution and data filtering. Firstly, the identification is performed using a single configuration, either the on-axis or the off-axis specimen. Secondly, the identification is carried out by merging data from both on-axis and off-axis configurations.
On the dynamic neural network toolbox design for identification, estimation and control
Authors: Chairez Isaac , Guarneros-Sandoval Israel Alejandro , Prud Vlad , Andrianova Olga , Ernest Sleptsov , Chertopolokhov Viktor , Bugriy Grigory , Mukhamedov Arthur
Published: October 2022

Purpose

There are common problems in the identification of uncertain nonlinear systems, nonparametric approximation, state estimation, and automatic control. Dynamic neural network (DNN) approximation can simplify the development of all the aforementioned problems in either continuous or discrete systems. A DNN is represented by a system of differential or recurrent equations defined in the space of vector activation functions with weights and offsets that are functionally associated with the input data.

Design/methodology/approach

This study describes the version of the toolbox, that can be used to identify the dynamics of the black box and restore the laws underlying the system using known inputs and outputs. Depending on the completeness of the information, the toolbox allows users to change the DNN structure to suit specific tasks.

Findings

The toolbox consists of three main components: user layer, network manager, and network instance. The user layer provides high-level control and monitoring of system performance. The network manager serves as an intermediary between the user layer and the network instance, and allows the user layer to start and stop learning, providing an interface to indirectly access the internal data of the DNN.

Research limitations/implications

Control capability is limited to adjusting a small number of numerical parameters and selecting functional parameters from a predefined list.

Originality/value

The key feature of the toolbox is the possibility of developing an algorithmic semi-automatic selection of activation function parameters based on optimization problem solutions.
Does publication history influence the integrity of the journals: studying publication timelines and their impact on journal metrics?
Authors: Shah Ubaid Ullah , Mushtaq Rabiya , Bhat Suhail Ahmad , Gul Sumeer
Published: October 2022

Purpose

The purpose of the study is to evaluate the relationship of Journal Publication Timeline (submission to first decision and submission to final decision) with various Journal Metrics (citing half-life, article influence score, the immediacy index, the acceptance rate, the impact factor (IF), five years IF, Eigenfactor and cited half-life) of top 600 journals retrieved from Journal Citation Report (JCR) 2020 under the tag, Elsevier Unified.

Design/methodology/approach

Top 600 journals in the decreasing order of the IFs under the tag, “Elsevier Unified” were retrieved from JCR 2020 of Clarivate Analytics. Information about “Journal Metrics” was ascertained using “Customized Service” of JCR, while information about the “Publication Timeline” of each journal was obtained using Elsevier's “Journal Insights Service.” It was found that only 177 journals provided the complete information regarding the “Publication Timeline” and hence considered for the study. Descriptive statistics and correlation analysis was conducted to test the different hypotheses.

Findings

It was found that submission to first decision has a significant relationship with the immediacy index, citing half-life and the acceptance rate. Submission to final decision has a significant relationship with Journal Impact Factor (JIF), the immediacy index, Eigenfactor, citing half-life and the acceptance rate.

Research limitations/implications

The study will provide the authors with sound and valuable information to support their selection of journals. Inferences in light of fluctuations in the scholarly communication process in terms of Publication Timelines and Journal Metrics can be deeply understood with the aid of the current study's findings. What considerations authors have to take before submitting their papers is the main implication of the study. Journal administrators can also benefit from the findings of the current study as it can help recruit and manage reviewers, which will ensure a successful publication timeline.

Originality/value

The study correlates Publication Timeline Indicators with Journal Metrics Indicators using secondary cross-sectional data. Though most previous studies only examine the relationship of the Publication Timeline with the Journal Impact Factor (JIF), there is very scarce literature that deciphers the influence of Publication Timeline indicators on different Journal Metrics indicators (including JIF).

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-02-2022-0108.
The effect of brand experiences and relational benefits on loyalty in the fast-food restaurants
Authors: Dandis Ala’ Omar , Wallace-Williams Donna Marie , Ni Arnt Kyawt , Wright Len Tiu , Abu Siam Yousef Ibrahim
Published: October 2022

Purpose

The aim of this study is to examine the role of relational benefits and brand experience measurements on willingness to pay more (WPM), effects of word of mouth (WOM) and repurchase intention (RI) in fast-food restaurants (FFR).

Design/methodology/approach

Employing an online questionnaire survey with a sample size of 503 respondents, the quantitative methodology included multiple regression and factor analysis to facilitate the analyses of data.

Findings

Relational benefits and their dimensions (confidence, special treatment and social benefits) found to positively impact WPM, WOM and RI. With reference to brand experiences, the current study found that behavioural and intellectual experiences have significant and positive effects on WPM, WOM and RI. Surprisingly, no positive significance was identified between sensory experiences and WPM, WOM and RI.

Practical implications

The findings show that relational benefits and brand experience dimensions play an essential role in improving brand loyalty.

Originality/value

The current study subscribes to the concept of relationship marketing theory, suggesting that loyalty to FFRs can be enhanced by offering customers relational benefits and augmenting their brand experiences.
Effects of biotic interactions on plant fecundity depend on spatial and functional structure of communities and time since disturbance
Authors: Walter Hanna E. , Pagel Jörn , Cooksley Huw , Neu Alexander , Schleuning Matthias , Schurr Frank M.
Published: October 2022

Biotic interactions in plant communities affect individual fitness and community dynamics. Interactions between plants vary in space, over time and with organisational complexity. Yet it is challenging to quantify temporal, spatial and functional determinants of different types of interactions between long‐lived perennial plant species and their effect on lifetime fecundity.

We studied how plant–plant, pollinator‐ and seed predator‐mediated interactions affect year‐to‐year variation in three fecundity components (cone production, seed set and seed survival) during post‐fire recovery. Age‐stratified data on the three fecundity components were collected in 19 even‐aged communities comprising 20 serotinous Protea shrub species in the South African Fynbos. We analyse data on these fecundity components with neighbourhood models to infer the sign and strength of interactions throughout post‐disturbance recovery, the neighbour plant traits that shape them and the spatial scale at which interactions take place. For each fecundity component, these models describe how neighbourhood effects change over time and with spatial distance between plants. We then predicted neighbourhood effects on individual fecundity components and cumulative reproductive output at different post‐fire stand ages for each focal plant.

Competitive effects on cone production and seed set increased with post‐fire stand age as biomass and floral resources for pollinators build up. In contrast, neighbourhood effects on seed survival were weak throughout post‐disturbance recovery. Plant–plant interactions were shaped by neighbour traits related to resource acquisition, whereas animal‐mediated interactions depended on neighbour traits related to resource availability for pollinators and seed predators. The spatial scale of the interactions increased from plant–plant over predator‐mediated to pollinator‐mediated interactions. The joint effect of these interactions on cumulative reproductive output caused the proportion of focal plants experiencing competition to increase with time since fire.

Synthesis. We show that temporal changes in biotic interactions throughout post‐disturbance recovery of perennial plant communities depend on functional traits and can be integrated into neighbourhood effects on lifetime fecundity. Studying the temporal, spatial and functional determinants of neighbourhood effects on lifetime fecundity is important for predicting not only individual plant fitness but also population and community dynamics in changing environments.
Stability of a dominant sponge‐symbiont in spite of antibiotic‐induced microbiome disturbance
Authors: Schmittmann Lara , Rahn Tanja , Busch Kathrin , Fraune Sebastian , Pita Lucía , Hentschel Ute
Published: October 2022

Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge‐model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge‐microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom‐made, sterile, flow‐through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic‐resistant bacteria, resulting in more complex, but less specific bacteria‐bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic‐induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria‐bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge‐symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host‐bacteria and bacteria‐bacteria interactions in the sponge holobiont.
Pandemic‐induced fear and government policy response as a measure of uncertainty in the foreign exchange market: Evidence from (a)symmetric wild bootstrap likelihood ratio test
Authors: Kathuria Khyati , Kumar Nand
Published: October 2022

The paper aims to examine the ability of a global fear index (GFI) based on the COVID‐19 pandemic and government policy responses as a measure of uncertainty in predicting eight Indian rupee‐based exchange rate return series: the Australian dollar, the Canadian dollar, the Swiss franc, the US dollar, the euro, the British pound sterling, the New Zealand dollar, and the Japanese yen. The predictability of the daily Indian rupee‐based exchange rate return series is tested using the recently developed wild bootstrap likelihood ratio test of Kim and Shamsuddin for the period 2 October 2020 to 8 March 2021. Both symmetric and asymmetric tests revealed GFI as an insignificant determinant of the Indian rupee‐based exchange rate return series. However, government policy responses are a significant determinant of the rupee–dollar exchange rate return series.