bluuebunny/crossref_metadata_2025 huggingface dataset:
Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae
Authors: Wells Heather L. , Loh Elizabeth , Nava Alessandra , Lee Mei Ho , Lee Jimmy , Sukor Jum R. A. , Navarrete-Macias Isamara , Liang Eliza , Firth Cadhla , Epstein Jonathan , Rostal Melinda , Zambrana-Torrelio Carlos , Murray Kris , Daszak Peter , Goldstein Tracey , Mazet Jonna A.K. , Lee Benhur , Hughes Tom , Durigon Edison , Anthony Simon J.
Published: October 2021

As part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxoviruses sequenced primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirus genomes sequenced from the Americas, including two sequences which are the first full-length bat morbillivirus genomes published to date. Our findings add to the vast number of viral sequences in public repositories that have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the paramyxovirus subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PASC), we describe a novel genus within this subfamily tentatively named Jeishaanvirus, which we propose should include as subgenera Jeilongvirus, Shaanvirus, and a novel South American subgenus Cadivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mojiang virus using the same demarcation criteria and show that members of the proposed subgenus Shaanvirus are paraphyletic. Importantly, this study underscores the critical importance of sequence length in PASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.
PyMVPD: A toolbox for multivariate pattern dependence
Authors: Fang Mengting , Poskanzer Craig , Anzellotti Stefano
Published: October 2021

Abstract

Cognitive tasks engage multiple brain regions. Studying how these regions interact is key to understand the neural bases of cognition. Standard approaches to model the interactions between brain regions rely on univariate statistical dependence. However, newly developed methods can capture multivariate dependence. Multivariate Pattern Dependence (MVPD) is a powerful and flexible approach that trains and tests multivariate models of the interactions between brain regions using independent data. In this article, we introduce PyMVPD: an open source toolbox for Multivariate Pattern Dependence. The toolbox includes pre-implemented linear regression models and artificial neural network models of the interactions between regions. It is designed to be easily customizable. We demonstrate example applications of PyMVPD using well-studied seed regions such as the fusiform face area (FFA) and the parahippocampal place area (PPA). Next, we compare the performance of different model architectures. Overall, artificial neural networks outperform linear regression. Importantly, the best performing architecture is region-dependent: MVPD subdivides cortex in distinct, contiguous regions whose interaction with FFA and PPA is best captured by different models.
Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine
Authors: Uehara Mika , Inoue Takashi , Kominato Minori , Hase Sumitaka , Sasaki Erika , Toyoda Atsushi , Sakakibara Yasubumi
Published: October 2021

Background

The intestinal microbiome is closely related to host health, and metatranscriptomic analysis can assess the functional activity of microbiomes by quantifying the bacterial gene expression level, which helps to elucidate the interaction between the microbiome and the environment. However, functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases and being unable to take full advantage of metatranscriptome to reveal the functional change among multiple environments.

Result

To close these gaps, we develop a novel method that integrates metagenome and metatranscriptome to analyze the functional activity of microbiomes between intestinal sites. This method reconstructs a reference metagenomic sequence across multiple intestinal sites, allowing the gene expression levels of microbiome including unknown bacterial genes to be compared between multiple sites. As a result of applying this method to metatranscriptomic analysis in the intestinal tract of common marmoset, the reconstructed metagenome covered most of the expressed genes and it revealed that the changes in bacterial gene expressions among the caecum, transverse colon, and faeces were more dynamic and sensitive to environmental shifts than its abundance. In typical, the coenzyme synthesis gene and antibacterial resistance gene were more highly expressed in the caecum and transverse colon than in faeces, while there was no significant change in abundance of these genes.

Conclusion

Our findings demonstrate that an analytical method that integrates metagenome and metatranscriptome in multiple intestinal sites captures functional changes in the microbiomes at the gene resolution level.
Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa
Authors: Bombin Andrei , Mosley Jonathan D. , Yan Shun , Bombin Sergei , Ferguson Jane F.
Published: October 2021

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host:microbiota interactions between clinical obesity classifications. We performed 16S rDNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-24.9), overweight (BMI 25-29.9), or obese (BMI ≥30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders includingFretibacterium, andTannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with host’s metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure, and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease.

IMPORTANCE

Obesity is a worldwide epidemic that is associated with a wide range of health issues. Microbiota were shown to influence metabolism and obesity development. Our study aimed to evaluate the interactions between obesity, salivary and fecal microbiota, and metabolite concentrations in healthy individuals. The oral bacterial community was more impacted by the obesity status of the host than fecal microbiota. Consistently for oral and fecal microbiota, the number of strong interactions between bacteria increased with the increase in the obesity status. Several predicted microbial metabolic pathways that were shown to be associated with metabolic health were uniquely enriched between obesity groups. In addition, these metabolic pathways were correlated with plasma and stool metabolites. Our results suggest that oral microbiota might better reflect the obesity status of the host than fecal microbiota, and that correlations between microbial taxa are altered during obesity.
Rates of primary production in groundwater rival those in oligotrophic marine systems
Authors: Overholt Will A. , Trumbore Susan , Xu Xiaomei , Bornemann Till L.V. , Probst Alexander J. , Krüger Markus , Herrmann Martina , Thamdrup Bo , Bristow Laura , Taubert Martin , Schwab Valérie F. , Hölzer Martin , Marz Manja , Küsel Kirsten
Published: October 2021

The terrestrial subsurface contains nearly all of Earth’s freshwater reserves1 and harbors upwards of 60% of our planet’s total prokaryotic biomass2,3. While genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the translocation of photosynthetically derived organic carbon4–6, corroborating measurements of carbon fixation in the subsurface are absent. Using a novel ultra-low level 14C-labeling technique, we show that in situ carbon fixation rates in a carbonate aquifer reached 10% of the median rates measured in oligotrophic marine surface waters, and were up to six-fold greater than those observed in lower euphotic zone waters where deep chlorophyll levels peak. Empirical carbon fixation rates were substantiated by both nitrification and anammox rate data. Metagenomic analyses revealed a remarkable abundance of putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria – the first representatives of this class expected to fix carbon via the Wood-Ljungdahl pathway. Based on these fixation rates, we extrapolate global primary production in carbonate groundwaters to be 0.11 Pg of carbon per year.
The role of cell geometry and cell-cell communication in gradient sensing
Authors: Fiorentino Jonathan , Scialdone Antonio
Published: October 2021

Cells can measure shallow gradients of external signals to initiate and accomplish a migration or a morphogenetic process. Recently, starting from mathematical models like the local-excitation global-inhibition (LEGI) model and with the support of empirical evidence, it has been proposed that cellular communication improves the measurement of an external gradient. However, the mathematical models that have been used have over-simplified geometries (e.g., they are uni-dimensional) or assumptions about cellular communication, which limit the possibility to analyze the gradient sensing ability of more complex cellular systems. Here, we generalize the existing models to study the effects on gradient sensing of cell number, geometry and of long-versus short-range cellular communication in 2D systems representing epithelial tissues. We find that increasing the cell number can be detrimental for gradient sensing when the communication is weak and limited to nearest neighbour cells, while it is beneficial when there is long-range communication. We also find that, with long-range communication, the gradient sensing ability improves for tissues with more disordered geometries; on the other hand, an ordered structure with mostly hexagonal cells is advantageous with nearest neighbour communication. Our results considerably extend the current models of gradient sensing by epithelial tissues, making a step further toward predicting the mechanism of communication and its putative mediator in many biological processes.

Author summary

Groups of cells collectively migrate in many biological processes, ranging from development to cancer metastasis. The migration is often driven by the gradient of a signaling molecule that can be shallow and noisy, raising the question of how cells can measure it reliably. Cellular communication has recently been suggested to play a key role in gradient sensing, and mathematical models with simplified cellular geometries have been developed to help interpret and design experiments. In this work, we generalize the existing mathematical models to investigate how short- and long-range cellular communication can increase gradient sensing in two-dimensional models of epithelial tissues. We analyze various cellular geometries and tissue size, and we identify the optimal setting that corresponds to different types of communication. Our findings will help pinpoint the communication mechanisms at work in a given tissue and the properties of the molecules that mediate the communication.
Guanosine-specific single-stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses
Authors: Kumakura Naoyoshi , Singkaravanit-Ogawa Suthitar , Gan Pamela , Tsushima Ayako , Ishihama Nobuaki , Watanabe Shunsuke , Seo Mitsunori , Iwasaki Shintaro , Narusaka Mari , Narusaka Yoshihiro , Takano Yoshitaka , Shirasu Ken
Published: October 2021

Plants activate immunity upon recognition of pathogen-associated molecular patterns. Although phytopathogens have evolved a set of effector proteins to counteract plant immunity, some effectors are perceived by hosts and induce immune responses. Here, we show that two secreted ribonuclease effectors, SRN1 and SRN2, encoded in a phytopathogenic fungus, Colletotrichum orbiculare, induce cell death in a signal peptide- and catalytic residue-dependent manner, when transiently expressed in Nicotiana benthamiana. The pervasive presence of SRN genes across Colletotrichum species suggested the conserved roles. Using a transient gene expression system in cucumber (Cucumis sativus), an original host of C. orbiculare, we show that SRN1 and SRN2 potentiate host pattern-triggered immunity. Consistent with this, C. orbiculare SRN1 and SRN2 deletion mutants exhibited increased virulence on the host. In vitro analysis revealed that SRN1 specifically cleaves single-stranded RNAs at guanosine, leaving a 3′-end phosphate. This activity has not been reported in plants. Importantly, the potentiation of C. sativus responses by SRN1 and SRN2 depends on the signal peptide and ribonuclease catalytic residues, suggesting that secreted SRNs cleave RNAs in apoplast and are detected by the host. We propose that the pathogen-derived apoplastic guanosine-specific single-stranded endoribonucleases lead to immunity potentiation in plants.
Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses
Authors: Lehmann Nathalie , Perrin Sandrine , Wallon Claire , Bauquet Xavier , Deshaies Vivien , Firmo Cyril , Du Runxin , Berthelier Charlotte , Hernandez Céline , Michaud Cédric , Thieffry Denis , Le Crom Stéphane , Thomas-Chollier Morgane , Jourdren Laurent
Published: October 2021

Abstract

Motivation

Core sequencing facilities produce huge amounts of sequencing data that need to be analysed with automated workflows to ensure reproducibility and traceability. Eoulsan is a versatile open-source workflow engine meeting the needs of core facilities, by automating the analysis of a large number of samples. Its core design separates the description of the workflow from the actual commands to be run. This originality simplifies its usage as the user does not need to handle code, while ensuring reproducibility. Eoulsan was initially developed for bulk RNA-seq data, but the transcriptomics applications have recently widened with the advent of long-read sequencing and single-cell technologies, calling for the development of new workflows.

Result

We present Eoulsan 2, a major update that (i) enhances the workflow manager itself, (ii) facilitates the development of new modules, and (iii) expands its applications to long reads RNA-seq (Oxford Nanopore Technologies) and scRNA-seq (Smart-seq2 and 10x Genomics). The workflow manager has been rewritten, with support for execution on a larger choice of computational infrastructure (workstations, Hadoop clusters, and various job schedulers for cluster usage). Eoulsan now facilitates the development of new modules, by reusing wrappers developed for the Galaxy platform, with support for container images (Docker or Singularity) packaging tools to execute. Finally, Eoulsan natively integrates novel modules for bulk RNA-seq, as well as others specifically designed for processing long read RNA-seq and scRNA-seq. Eoulsan 2 is distributed with ready-to-use workflows and companion tutorials.

Availability and implementation

Eoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL and CeCILL-C licenses at: http://outils.genomique.biologie.ens.fr/eoulsan/. The source code and sample workflows are available on GitHub: https://github.com/GenomicParisCentre/eoulsan. A GitHub repository for modules using the Galaxy tool XML syntax is further provided at: https://github.com/GenomicParisCentre/eoulsan-tools

Contact

eoulsan@bio.ens.psl.eu
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation
Authors: Lasri Ayoub , Shahrezaei Vahid , Sturrock Marc
Published: October 2021

Single cell RNA-sequencing (scRNA-seq) has very rapidly become the new workhorse of modern biology providing an unprecedented global view on cellular diversity and heterogeneity. In particular, the structure of gene-gene expression correlation contains information on the underlying gene regulatory networks. However, interpretation of scRNA-seq data is challenging due to specific experimental error and biases that are unique to this kind of data including drop-out (or technical zeros). To deal with this problem several methods for imputation of zeros for scRNA-seq have been developed. However, it is not clear how these processing steps affect inference of genetic networks from single cell data. Here, we introduce Biomodelling.jl, a tool for generation of synthetic scRNA-seq data using multiscale modelling of stochastic gene regulatory networks in growing and dividing cells. Our tool produces realistic transcription data with a known ground truth network topology that can be used to benchmark different approaches for gene regulatory network inference. Using this tool we investigate the impact of different imputation methods on the performance of several network inference algorithms. Biomodelling.jl provides a versatile and useful tool for future development and benchmarking of network inference approaches using scRNA-seq data.
Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation
Authors: Singh Anand P. , Wu Ping , Ryabichko Sergey , Raimundo João , Swan Michael , Wieschaus Eric , Gregor Thomas , Toettcher Jared E.
Published: October 2021

Developmental patterning networks are regulated by multiple inputs and feedback connections that rapidly reshape gene expression, limiting the information that can be gained solely from slow genetic perturbations. Here we show that fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background can be combined to reveal quantitative regulatory dynamics from a complex genetic network in vivo. We engineer light-controlled variants of the Bicoid transcription factor and study their effects on downstream gap genes in embryos. Our results recapitulate known relationships, including rapid Bicoid-dependent expression of giant and hunchback and delayed repression of Krüppel. In contrast, we find that the posterior pattern of knirps exhibits a quick but inverted response to Bicoid perturbation, suggesting a previously unreported role for Bicoid in suppressing knirps expression. Acute modulation of transcription factor concentration while simultaneously recording output gene activity represents a powerful approach for studying how gene circuit elements are coupled to cell identification and complex body pattern formation in vivo.
Cold Atmospheric Plasma Differentially Affects Cell Renewal and Differentiation of Stem Cells and Apc-Deficient-Derived Tumor Cells in Intestinal Organoids
Authors: Hadefi Alia , Leprovots Morgane , Thulliez Max , Bastin Orianne , Lefort Anne , Libert Frédérick , Nonclercq Antoine , Delchambre Alain , Reniers François , Devière Jacques , Garcia Marie-Isabelle
Published: October 2021

Cold atmospheric plasma (CAP) treatment has been proposed as a potentially innovative therapeutic tool in the biomedical field, notably for cancer due to its proposed toxic selectivity on cancer cells versus healthy cells. In the present study, we addressed the relevance of three-dimensional organoid technology to investigate the biological effects of CAP on normal epithelial stem cells and tumor cells isolated from mouse small intestine. CAP treatment exerted dose-dependent cytotoxicity on normal organoids and induced major transcriptomic changes associated with global response to oxidative stress, fetal-like regeneration reprogramming and apoptosis-mediated cell death. Moreover, we explored the potential selectivity of CAP on tumor-like Apc-deficient versus normal organoids in the same genetic background. Unexpectedly, tumor organoids exhibited higher resistance to CAP treatment, correlating with higher antioxidant activity at baseline as compared to normal organoids. This pilot study suggests that the ex vivo culture system could be a relevant alternative model to further investigate translational medical applications of CAP technology.
DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci
Authors: Bader Aldo S. , Luessing Janna , Hawley Ben R , Skalka George L , Lu Wei-Ting , Lowndes Noel F , Bushell Martin
Published: October 2021

Proteins with RNA-binding activity are increasingly being implicated in DNA damage responses (DDR). Additionally, DNA:RNA-hybrids are rapidly generated around DNA double-strand breaks (DSBs), and are essential for effective repair. Here, using a meta-analysis of proteomic data, we identify novel DNA repair proteins and characterise a novel role for DDX17 in DNA repair. We found DDX17 to be required for both cell survival and DNA repair in response to numerous agents that induce DSBs. Analysis of DSB repair factor recruitment to damage sites suggested a role for DDX17 early in the DSB ubiquitin cascade. Genome-wide mapping of R-loops revealed that while DDX17 promotes the formation of DNA:RNA-hybrids around DSB sites, this role is specific to loci that are naturally deficient for DNA:RNA-hybrids. We propose that DDX17 facilitates DSB repair at loci that are inefficient at forming DNA:RNA-hybrids by catalysing the formation of DSB-induced hybrids, thereby allowing propagation of the damage response.
The HIV latency reversal agent HODHBt enhances NK Cell effector and memory-like functions by increasing IL-15 mediated-STAT activation
Authors: Macedo Amanda B. , Levinger Callie , Nguyen Bryan , Gupta Mampta , Cruz Conrad Russell Y. , Chiappinelli Katherine B. , Crandall Keith A. , Bosque Alberto
Published: October 2021

Elimination of latent HIV reservoirs is a critical endpoint to eradicate HIV. One therapeutic intervention against latent HIV is ‘shock and kill’. This strategy is based on the transcriptional activation of latent HIV with a Latency-Reversing Agent (LRA) with the consequent killing of the reactivated cell by either the cytopathic effect of HIV or the immune system. We have previously found that the small molecule 3-Hydroxy-1,2,3-benzotriazin-4(3H)-one (HODHBt) act as an LRA by increasing Signal Transducers and Activators of Transcription (STAT) activation mediated by IL-15 in cells isolated from aviremic participants. The IL-15 superagonist (N-803) is currently under clinical investigation to eliminate latent reservoirs. IL-15 and N-803 share similar mechanism of action by promoting the activation STATs and have shown some promise in pre-clinical models directed towards HIV eradication. In this work, we evaluated the ability of HODHBt to enhance IL-15 signaling in NK cells and the biological consequences associated with increased STAT activation in NK effector and memory-like functions. We showed that HODHBt increased IL-15-mediated STAT phosphorylation in NK cells, resulting in increased secretion of CXCL10 and IFN-γ and expression of cytotoxic proteins including Granzyme B, Granzyme A, Perforin, Granulysin, FASL and TRAIL. This increased cytotoxic profile results in an increase cytotoxicity against different tumor cell lines and HIV-infected cells. HODHBt also improved the generation of cytokine-induced memory-like NK cells. Overall, our data demonstrate that enhancing the magnitude of IL-15 signaling with HODHBt favors NK cell cytotoxicity and memory-like generation, and targeting this pathway could be further explored for HIV cure interventions.

Author Summary

Several clinical trials targeting the HIV latent reservoir with LRAs have been completed. In spite of a lack of clinical benefit of these trials, they have been crucial to elucidate hurdles that ‘shock and kill’ strategies have to overcome to promote an effective reduction of the latent reservoir leading. These hurdles include low reactivation potential mediated by LRAs; the negative influence of some LRAs on the activity of Natural Killer and CD8T effector cells; an increased resistance to apoptosis of latently infected cells; and an exhausted immune system due to chronic inflammation. To that end, finding therapeutic strategies that can overcome some of these challenges could improve the outcome of ‘shock and kill’ strategies aimed towards HIV eradication. In here, we showed that the LRA HODHBt also improves IL-15 mediated NK effector and memory-like functions. As such, pharmacological enhancement of IL-15 mediated STAT activation can open new therapeutic venues towards an HIV cure.
The interaction effect of psychological capital on the relationship between self-driven personality and happiness at work in the present and post-COVID-19 era
Authors: Kawalya Charles , Kasekende Francis , Munene John C.
Published: October 2021

Purpose

The purpose of this paper is to examine how psychological capital (PsyCap) and self-driven personality fuse to affect happiness at work in the nursing profession in Uganda.

Design/methodology/approach

This paper adopts a cross-sectional descriptive and analytical design. The authors use structural equation modelling to test hypotheses. Using proportionate and simple random sampling procedures, a sample of 900 respondents was drawn from different hospitals in Uganda of which a response rate of 88.9% was obtained.

Findings

The magnitude effect of self-driven personality on happiness at work depends on PsyCap, implying that the assumption of non-additivity is met.

Research limitations/implications

Only a single research methodological approach was used, and future research through interviews could be undertaken to triangulate.

Practical implications

To boost happiness at the workplace, heads of hospitals should always endeavour to find a viable self-driven personality and PsyCap blend that can add value to nurses’ happiness in Uganda.

Social implications

It is essential for health human resource managers to understand, how self-driven personality and PsyCap foster happiness among nurses in Uganda.

Originality/value

This is one of the few studies that focus on testing the interactive effects of PsyCap on the relationship between self-driven personality and happiness at the workplace in Uganda’s health sector.
Emotion detection on webpages using biosensors integrated to a window-based dynamic control system
Authors: Isiaka Fatima , Abdulkarim Salihu Aish , Mwitondi Kassim , Adamu Zainab
Published: October 2021

Purpose

Detecting emotion on user experience of web applications and browsing is important in many ways. Web designers and developers find such approach quite useful in enhancing navigational features of webpages, and biomedical personnel regularly use computer simulations to monitor and control the behaviour of patients. On the other hand, law enforcement agents rely on human physiological functions to determine the likelihood of falsehood in interrogations. Quite often, online user experience is studied via tangible measures such as task completion time, surveys and comprehensive tests from which data attributes are generated. Prediction of users' emotion and behaviour in some of these cases depends mostly on task completion time and number of clicks per given time interval. However, such approaches are generally subjective and rely heavily on distributional assumptions making the results prone to recording errors.

Design/methodology/approach

The authors propose a novel method-a window dynamic control system that addresses the foregoing issues. Primary data were obtained from laboratory experiments during which forty-four volunteers had their synchronised physiological readings, skin conductance response (SCR), skin temperature (ST), eye movement behaviour and users’ activity attributes taken using biosensors. The window-based dynamic control system (PHYCOB I) is integrated to the biosensor which collects secondary data attributes from these synchronised physiological readings and uses them for two purposes. For both detection of optimal emotional responses and users' stress levels. The method's novelty derives from its ability to integrate physiological readings and eye movement records to identify hidden correlates on a webpage.

Findings

Results show that the control system detects basic emotions and outperforms other conventional models in terms of both accuracy and reliability, when subjected to model comparison that is, the average recoverable natural structures for the three models with respect to accuracy and reliability are more consistent within the window-based control system environment than with the conventional methods.

Research limitations/implications

The paper is limited to using a window control system to detect emotions on webpages, while integrated to biosensors and eye-tracker.

Originality/value

The originality of the proposed model is its resistance to overfitting and its ability to automatically assess human emotion (stress levels) while dealing with specific web contents. The latter is particularly important in that it can be used to predict which contents of webpages cause stress-induced emotions to users when involved in online activities.
Effective hospital-wide lean implementation: top-down, bottom-up or through co-creative role modeling?
Authors: van Beers John C.A.M. , van Dun Desirée H. , Wilderom Celeste P.M.
Published: October 2021

Purpose

Lean implementations in hospitals tend to be lengthy or lack the desired results. In addressing the question, how can lean be implemented effectively in a hospital-wide setting, this paper aims to examine two opposing approaches.

Design/methodology/approach

The authors studied two Dutch university hospitals which engaged in different lean implementation approaches during the same four-year period: top-down vs bottom-up. Inductive qualitative analyses were made of 49 interviews; numerous documents; field notes; 13 frontline meeting observations; and objective hospital performance data. Longitudinally, the authors depict how the sequential events unfolded in both hospitals.

Findings

During the six implementation stages, the roles played by top, middle and frontline managers stood out. While the top managers of one hospital initiated the organization-wide implementation and then delegated it to others, the top managers of the other similar hospital merely tolerated the bottom-up lean activities. Eventually, only the hospital with the top-down approach achieved high organization-wide performance gains, but only in its fourth year after the top managers embraced lean in their own daily work practices and had started to co-create lean themselves. Then, the earlier developed lean infrastructure at the middle- and frontline ranks led to the desired hospital-wide lean implementation results.

Originality/value

Change-management insights, including basic tenets of social learning and goal-setting theory, are shown to advance the knowledge of effective lean implementation in hospitals. The authors found lean implementation “best-oiled” through role-modeling by top managers who use a phase-based process and engage in close cross-hierarchical or co-creative collaboration with middle and frontline managerial members.
Delivering on the promise: how are sustainability research institutes enabling interdisciplinary research?
Authors: Bolger Paul
Published: October 2021

Purpose

Despite the potential for research institutes to advance interdisciplinary research on university campuses, There have been few studies on how interdisciplinary research centres integrate multiple disciplines in practice, how they influence the collaborative behaviours of scientists and how they establish collaborative communities. This study aims to provide a deeper understanding of how interdisciplinary research is being enabled at research institutes and offers signposts for how research institutes can further embed interdisciplinarity within their units.

Design/methodology/approach

Within this study, 30 interviews were conducted with leadership and faculty within 4 sustainability research institutes in the USA exploring how research institutes support interdisciplinary research within their units. A thematic analysis on the interview data revealed themes on how research institutes are enabling interdisciplinary research within their organisations and universities.

Findings

The study highlights eight themes on how research institutes are, and can further, enable interdisciplinary research within their organisations and universities. Some of the themes are fully implemented within the research institutes, whilst others are more aspirational and highlight where institutes can create additional capability and capacity for interdisciplinary research within their units and universities.

Research limitations/implications

Whilst the study is limited to four major sustainability research institutes the findings will be applicable to all research centres and institutes attempting to create interdisciplinary research environments.

Practical implications

The study will be of particular interest to research institutes and university leadership who wish to cultivate a deeper culture of interdisciplinary research within their organisations.

Social implications

The advancement of inter- and transdisciplinary research within universities are seen by many academic institutions, expert groups and funding bodies as essential for solving wicked problems and grand challenges facing society. The findings of this paper will help universities increase their capacity for interdisciplinary research.

Originality/value

There are few comparable publications in terms of methodology, approach and focus on research institutes.
Hiding in plain sight: the emergence of modern dairy farms in India
Authors: Burkitbayeva Saule , Janssen Emma , Swinnen Johan
Published: October 2021

Purpose

This paper provides one of the first and most detailed accounts of the large modern dairy farms that are emerging in the dairy sector in India. Qualitative interviews are used to understand how these farms differ from their traditional smallholder counterparts and how well integrated they are into the value chains.

Design/methodology/approach

Snowball sampling was used to identify large farmers. In total, 49 in-depth interviews were conducted with large commercial modern farms in Punjab. A detailed description of the main characteristics of these modern dairy farms is provided. Data from previous studies conducted in Punjab is used to compare the new farms with traditional smallholder farms.

Findings

The modern dairy farms are much more advanced in their use of technology compared to their traditional counterparts. These large commercial modern farms are very well integrated into the value chains. They often, but not exclusively, sell milk to formal supply chains, sometimes on a contractual basis.

Originality/value

Most of the literature on the Indian dairy sector focuses on smallholders. However, understanding and acknowledging the emergence of modern dairy farms is very important in understanding the development of value chains not only in the dairy sector in India, but in domestic food sectors in developing countries in general. This qualitative data analysis is a necessary first step if more large-scale representative information is to be collected in the future.
The long and winding road of eHealth. The service ecosystem perspective
Authors: Sebastiani Roberta , Anzivino Alessia
Published: October 2021

Purpose

This paper aims to investigate the eHealth ecosystem’s evolution during the coronavirus disease 2019 (COVID-19) pandemic and its effects on the progression of care for patients with chronic cardiovascular disease.

Design/methodology/approach

To attain the aim of the study, this study chose to adopt a qualitative method that matches the complexity of the issue. The study was conducted in a real context through 44 face-to-face semi-structured interviews of key informants at different levels of the Italian eHealth service ecosystem, via Microsoft Teams. The interviews were carried out from June 2020 to January 2021. In this research, we adopted an abductive approach that enabled a process where the theoretical framework and the data analysis evolved at the same time.

Findings

The study results were used to develop a conceptual framework that considers the key factors enabling and constraining the evolutionary process of the eHealth service ecosystem. In particular, the drivers that emerged from the study were actor role empowerment, actor–network engagement and resource reconfiguration while the inhibitors were inter- and intra-actor misalignment, resource myopia and the platformisation gap. The findings also revealed the pivotal role of the meso level in the development of the eHealth service ecosystem, boosted by the COVID-19 pandemic.

Originality/value

By adopting a service ecosystem perspective, this paper contributes, at both a theoretical and a managerial level, to a better understanding of the dynamics related to the diffusion of eHealth. The study identifies the main issues that researchers, managers and policymakers should address to support the evolution of the eHealth service ecosystem, with particular regard to chronic cardiovascular disease.
Memoryscape: how managers can create lasting customer experiences
Authors: McColl Rod , Mattsson Jan , Charters Kathleen
Published: October 2021

Purpose

A detailed conceptualization of how service experiences are transformed into a memory and the circumstances surrounding a memorable experience is not available in the customer experience literature. This paper aims to address this gap using a multi-dimensional framework (memoryscape) to explain memory processes for service experiences.

Design/methodology/approach

The paper integrates psychology research, and particularly autobiographical memory, within customer experience management.

Findings

The paper proposes a comprehensive, multi-dimensional framework (memoryscape) of memory and highlights managerial implications.

Research limitations/implications

Marketers have yet to fully understand the role of memory in service experience consumption. In today’s service-dominant economy, understanding more about the memoryscape should be a managerial and research priority.

Practical implications

The authors present four managerial priorities for managing customer experience memories.

Originality/value

The authors assimilate theories and empirical research in psychology, particularly autobiographical memory, to propose an integrated conceptual framework of the service memory process (memoryscape), to provide insights for managers looking to create memorable customer experiences.
Territorial consumer behaviors on social media: a dark side of psychological ownership
Authors: Micu Petru Dorin , Ashley Christy
Published: October 2021

Purpose

The purpose of this paper is to investigate whether consumers experience territory infringements during interactions with other consumers on firm-managed social media pages and, if so, how consumers respond. In offline contexts, feelings of territoriality affect consumers’ responses to other people in ways that are detrimental to the firm. Less is known about the effects of territoriality in response to consumer-to-consumer interactions on social media. Firms need to understand the implications of these interactions as they encourage consumer engagement on firm-owned social media pages.

Design/methodology/approach

The current research examines whether territorial consumer behaviors occur in response to co-consumers on social media pages for a brand (Study 1) and a product (Study 2) using experimental studies.

Findings

The studies provide evidence that a perceived territory infringement by a co-consumer can provoke retaliation toward the co-consumer and reduce engagement on the firm-owned social media page. Psychological ownership toward the product or brand amplifies these effects.

Research limitations/implications

The findings were robust in the experimental scenarios that featured a brand and a product. However, future research should validate the results in a field study and include other brands and products.

Practical implications

The findings highlight conditions under which consumer-to-consumer interactions can decrease social media engagement on firm-owned social media pages.

Originality/value

The manuscript is the first to examine how territoriality and psychological ownership relate to negative consumer responses following consumer-to-consumer interactions on social media.
Empowering leadership and employees' work engagement: a social identity theory perspective
Authors: Arshad Muhammad , Qasim Neelam , Farooq Omer , Rice John
Published: October 2021

Purpose

This study aims to explore mediational mechanisms and conditions by which empowering leadership leads to positive outcomes at the employee level. Using social identity theory (SIT) as a foundation, the authors present an integrated moderated mediation model to explain the interactive effects of empowering leadership and leaders' prototypicality on employees' work engagement through the mediation of organizational identification (OI).

Design/methodology/approach

The research model was tested using multilevel nested data obtained from 634 employees working in 133 departments (teams) in the service sector of Pakistan.

Findings

The results reveal that empowering leadership influences work engagement through the mediation of OI. However, leader prototypicality has emerged as an important moderating condition for these relationships because, at a lower level of leader prototypicality, the positive effect of empowering leadership may diminish.

Practical implications

The results of this study suggest that organizations should promote empowering leadership to increase their employees' OI and work engagement. Furthermore, it is suggested that leader prototypicality is important along with empowering leadership to inculcate positive behavior among employees.

Originality/value

This is the first study of its nature, which used SIT to explain the indirect effect of empowering leadership on employees' work engagement via OI. Furthermore, the bounding condition of leader prototypicality is also studied for the first time in the context of the indirect relationship between empowering leadership and employees' work engagement via OI. The authors note that the novel unique findings of this study have the potential to open additional further avenues of research in the field of empowering leadership.
Characterization of the key aroma compounds in pork broth by sensory‐directed flavor analysis
Authors: Chang Yuan , Wang Shuqi , Chen Haitao , Zhang Ning , Sun Jie
Published: October 2021

The solvent‐assisted flavor evaporation, sensory evaluation, and partial least squares regression analysis were used to screen the relatively better flavor of pork broth among different stewing time (1, 2, 4, 6, and 8 h). A total of 48 volatile compounds were successfully characterized by gas chromatography‐mass spectrometry in the pork broth, which stewed for 4 h. The dominant volatiles were confirmed by aroma extract dilution analysis. Twenty‐seven odorants with flavor dilution factors between 2 and 1,024 were identified. Among them, odor activity values of 19 components were greater than or equal to 1. An aroma recombination test was performed, and a similar flavor (93.04 %) was simulated. Omission test further confirmed that 4‐hydroxy‐2,5‐dimethyl‐3(2H)‐furanone, hexanal, 1‐octen‐3‐ol, (E)‐2‐octenal, (E)‐2‐decenal, (E)‐2‐undecanal, (E, E)‐2,4‐decadienal, nonanoic acid, decanoic acid, 2‐heptanone, 3‐hydroxy‐2‐butanone, δ‐decanolactone, and 2‐acetylpyrrole were the key odorants of the aroma profile of pork broth.

Practical Application

Pork broth is popular in China, but lacks the study of its key aroma compounds, which restricts its industrial production. This study researched the optimum stewing time of pork broth and analyzed its key aroma compounds. Finally, the flavor profile can be obtained and understood. This study could provide a reference and further promote research on pork flavor.
Early experience with MR‐guided adaptive radiotherapy using a 1.5 T MR‐Linac: First 6 months of operation using adapt to shape workflow
Authors: de Leon Jeremiah , Crawford David , Moutrie Zoë , Alvares Stacy , Hogan Louise , Pagulayan Claire , Jelen Urszula , Loo Conrad , Aylward Jack D , Condon Kieran , Dunkerley Nicolle , Heinke Monique Y , Sampaio Sandy , Simon Kathy , Twentyman Tania , Jameson Michael G
Published: October 2021

Introduction

The magnetic resonance linear accelerator (MRL) offers improved soft tissue visualization to guide daily adaptive radiotherapy treatment. This manuscript aims to report initial experience using a 1.5 T MRL in the first 6 months of operation, including training, workflows, timings and dosimetric accuracy.

Methods

All staff received training in MRI safety and MRL workflows. Initial sites chosen for treatment were stereotactic and hypofractionated prostate, thoraco‐abdomino‐pelvic metastasis, prostate bed and bladder. The Adapt To Shape (ATS) workflow was chosen to be the focus of treatment as it is the most robust solution for daily adaptive radiotherapy. A workflow was created addressing patient suitability, simulation, planning, treatment and peer review. Treatment times were recorded breaking down into the various stages of treatment.

Results

A total of 37 patients were treated and 317 fractions delivered (of which 313 were delivered using an ATS workflow) in our initial 6 months. Average treatment times over the entire period were 50 and 38 min for stereotactic and non‐stereotactic treatments respectively. Average treatment times reduced each month. The average difference between reference planned and ionization chamber measured dose was 0.0 ± 1.4%.

Conclusion

The MRL was successfully established in an Australian setting. A focus on training and creating a detailed workflow from patient selection, review and treatment are paramount to establishing new treatment programmes.