bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic
Authors: Mallon P.W.G. , Crispie F. , Gonzalez G. , Tinago W. , Garcia Leon A.A. , McCabe M. , de Barra E. , Yousif O. , Lambert J.S. , Walsh C.J. , Kenny J.G. , Feeney E. , Carr M. , Doran P. , Cotter P.D. 
Published: February 2021

AbstractBackgroundWhole-genome sequencing (WGS) of SARS-CoV-2 laboratory-confirmed cases can provide insights into viral transmission and genetic diversity at a population level. However, less is known about the impact of non-pharmaceutical interventions (NPIs), including ‘lockdowns’, on circulating SARS-CoV-2 lineages and variants of concern, the relative contribution of travel to re-emergence of pandemic waves within communities or how different lineages and variants contribute to disease severity.MethodsWe have conducted an analysis within a prospective, multicentre observational study of individuals attending four hospitals in the South-East of Ireland with COVID-19. Samples underwent WGS from which lineages and variants were assigned, lineage frequency was plotted over time and phylogenetic analysis was employed to determine the origin of variants detected post-lockdown. Univariate and multivariate analyses assessed relationships between viral lineage/variant and COVID-19 disease severity.ResultsWe analysed 225 genome sequences across two SARS-CoV-2 waves, 134 (59.6%) from wave 1 (March to June) and 91 (40.4%) from wave 2 (July to December), representing 15.2% of COVID-19 admissions to these hospitals during the sampling periods. Four variants (B.1.1.162, B1.1.70, B.1.1.267 and B.1.1) comprised 68% of variants detected during wave 1. Of these variants, only a single B.1.1.70 sequence was detected in wave 2, while the B.1.177 lineage emerged and contributed to 82.3% of lineages detected. Phylogenetic analysis suggested multiple introductions of wave 2 variants from outside Ireland. We found no consistent association between SARS-CoV-2 lineages and disease severity.ConclusionsThese data suggest elimination of common SARS-CoV-2 lineages from hospitalised cases associated with effective NPIs and that importation of new viral variants through travel was a significant contributor to the re-emergence of the pandemic in the second wave in Ireland. Our findings highlight the importance of genomic surveillance in identifying circulating viral genetic diversity and variants of concern and, also, modelling the disease burden of SARS-CoV-2.
Differential impact of plant secondary metabolites on the soil microbiota
Authors: Schütz Vadim , Frindte Katharina , Cui Jiaxin , Zhang Pengfan , Hacquard Stéphane , Schulze-Lefert Paul , Knief Claudia , Schulz Margot , Dörmann Peter 
Published: February 2021

AbstractPlant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16SrRNAgene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the composition of bacterial taxa on the phylum and genus levels. Alpha diversity was significantly altered by BOA or quercetin, but not by gramine. BOA treatment caused an increase in the relative abundances of only four genera, three of them belonging to the Actinobacteriota. Gramine or quercetin treatment resulted in the increase in relative abundance of 13 or 14 genera, respectively, most of them belonging to the Proteobacteria. The relative abundance of 22 genera was decreased after BOA treatment, 16 of which were also decreased by gramine or quercetin. Isolation and characterization of cultivable bacterial indicated an enrichment in specificArthrobacterorPseudomonasstrains. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a broad-spectrum inhibitory effect, with only few genera able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, benzoxazolinone or gramine biosynthesis which have evolved in different barley species, is accompanied with the association with distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.
Tankyrase-mediated ADP-ribosylation is a novel regulator of TNF-induced death
Authors: Liu Lin , Sandow Jarrod J. , Leslie Pedrioli Deena M. , Silke Natasha , Hu Zhaoqing , Morrish Emma , Chau Diep , Kratina Tobias , Kueh Andrew J. , Hottiger Michael O. , Webb Andrew I. , Lalaoui Najoua , Silke John 
Published: February 2021

ABSTRACTTumor necrosis factor (TNF) is an inflammatory cytokine that, upon binding to its receptor TNFR1, can drive cytokine production, cell survival, or cell death and is a major component of an organism’s anti-pathogen repetoire1,2. TNF stimulation leads to the formation of two distinct signalling complexes, a well-defined membrane bound complex (complex 1), and a less well characterised cytosolic death inducing complex (complex 2). Using mass spectrometry, we identified the ADP-ribosyltransferase, tankyrase-1 (TNKS1/TNKS/ARTD5/PARP5a) as a novel native complex 2 component. Following a TNF-induced death stimulus TNKS1 is recruited to complex 2, resulting in complex 2 poly(ADP-ribosyl)ation (PARylation). Tankyrase inhibitors sensitise cells to TNF-induced death, which is correlated with increased complex 2 assembly. Tankyrase-mediated PARylation promotes recruitment of the E3 ligase RNF146 and RNF146 deficiency or proteasome inhibition results in increased levels of complex 2, suggesting that RNF146 causes proteasomal degradation of complex 2. Several viruses express ADP-ribose binding macrodomain proteins, and expression of the SARS-CoV-2 or VEEV macrodomain markedly sensitises cells to TNF-induced death. This suggests that ADP-ribosylation serves as yet another mechanism to detect pathogenic interference of TNF signalling and retaliate with an inflammatory cell death.
GABA administration limits viral replication and pneumonitis in a mouse model of COVID-19
Authors: Tian Jide , Middleton Blake , Kaufman Daniel L. 
Published: February 2021

AbstractDespite the availability of vaccines for COVID-19, serious illness and death induced by coronavirus infection will remain a global health burden because of vaccination hesitancy, possible virus mutations, and the appearance of novel coronaviruses. Accordingly, there is a need for new approaches to limit severe illness stemming from coronavirus infections. Cells of the immune system and lung epithelia express receptors for GABA (GABA-Rs), a widely used neurotransmitter within the CNS. GABA-R agonists have anti-inflammatory effects and can limit acute lung injury. We previously showed that GABA treatment effectively reduced disease severity and death rates in mice following infection with a coronavirus (MHV-1) which provides a potentially lethal model of COVID-19. Here, we report that GABA treatment also reduced viral load in the lungs, suggesting that GABA-Rs may provide a new druggable target to limit pulmonary coronavirus replication. Histopathological analysis revealed that GABA treatment reduced lung inflammatory infiltrates and damages. Since GABA is safe for human consumption, inexpensive, and available worldwide, it is a promising candidate to help treat COVID-19.
Intranasal type I interferon treatment is beneficial only when administered before clinical signs onset in the SARS-CoV-2 hamster model
Authors: Bessière Pierre , Wasniewski Marine , Picard-Meyer Evelyne , Servat Alexandre , Figueroa Thomas , Foret-Lucas Charlotte , Coggon Amelia , Lesellier Sandrine , Boué Frank , Cebron Nathan , Gausserès Blandine , Trumel Catherine , Foucras Gilles , Salguero Francisco J , Monchatre-Leroy Elodie , Volmer Romain 
Published: February 2021

AbstractImpaired type I interferons (IFNs) production or signaling have been associated with severe COVID-19, further promoting the evaluation of recombinant type I IFNs as therapeutics against SARS-CoV-2 infection. In the Syrian hamster model, we show that intranasal administration of IFN-α starting one day pre-infection or one day post-infection limited weight loss and decreased viral lung titers. By contrast, intranasal administration of IFN-α starting at the onset of symptoms three days post-infection had no impact on the clinical course of SARS-CoV-2 infection. Our results provide evidence that early type I IFN treatments are beneficial, while late interventions are ineffective, although not associated with signs of enhanced disease.One Sentence SummaryThe timing of type I interferon treatment is a critical determinant of its efficacy against SARS-CoV-2 infection.
Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis
Authors: Wang Nima , Wang Dalei 
Published: February 2021

ABSTRACTOne gene could be transcribed to different RNA isoforms, and then produce various forms of protein sequences. This mechanism largely diversifies the cellular pool and allows natural selection to select from a wider range of substrates. Most of the deleterious changes should be either purged or only be observed in patients with deficiencies or diseases. In the cancer field, the “intra-gene” changes between tumor and normal tissues such as the alternative splicing, stop codon read-through, or protein domestication could not be captured by differential expression analyses. In this work, we collected public transcriptome and translatome data from ten patients with liver cancer, and performed genome-wide comparison on the stop codon read-through and protein domestication events. Both events could diversify the proteome without changing the genome sequence. Surprisingly, we found that compared to normal tissues, the tumor tissues globally have significantly higher occurrence of stop codon read-through events. Similarly, the translation signals of non-coding repetitive elements (protein domestication) are elevated in tumor samples. These read-through and domestication events show limited overlapping across the ten patients, suggesting the randomness of the occurrence. It also indicates that these tumor-specific read-through and domestication events should be deleterious, and should be purged by natural selection if they are not collected timely. Our work manifests the role of protein extension and domestication in liver cancer oncogenesis, and adds new aspects to the cancer field.
The Size-Weight Illusion is unimpaired in individuals with a history of congenital visual deprivation
Authors: Pant Rashi , Guerreiro Maria J. S. , Ley Pia , Bottari Davide , Shareef Idris , Kekunnaya Ramesh , Röder Brigitte 
Published: February 2021

AbstractVisual deprivation in childhood can lead to lifelong impairments in visual and multisensory processing. Here, the Size-Weight-Illusion was used to test whether visuo-haptic integration recovers after sight restoration. In Experiment 1, congenital (CC: 7 (3F), 8–35 years) and developmental cataract reversal individuals (DC: 9 (2F), 8–37 years), as well as congenitally blind (CB: 2 (1F), 33 and 44 years) and normally sighted individuals (SC: 10 (7F), 19-36 years) perceived larger objects as lighter than smaller objects of the same weight. In Experiment 2, CC (6 (1F), 17–44.7 years) and SC (7 (5F), 21-29 years) individuals performed identically when tested without haptic size cues. Together, this suggested that early visual experience is not necessary to perceive the Size-Weight-Illusion.
A developmental stage- and Kidins220/ARMS-dependent switch in astrocyte responsiveness to brain-derived neurotrophic factor
Authors: Jaudon Fanny , Albini Martina , Ferroni Stefano , Benfenati Fabio , Cesca Fabrizia 
Published: February 2021

ABSTRACTAstroglial cells are key to maintain nervous system homeostasis, as they are able to perceive a wide variety of extracellular signals and to transduce them into responses that may be protective or disruptive toward neighboring neurons through the activation of distinct signaling pathways. Neurotrophins are a family of growth factors known for their pleiotropic effects on neuronal survival, maturation and plasticity. In this work, we investigated: (i) the signaling competence of embryonic and postnatal primary cortical astrocytes exposed to brain-derived neurotrophic factor (BDNF); and (ii) the role of the scaffold protein Kinase D interacting substrate/ankyrin repeat-rich membrane spanning (Kidins220/ARMS), a transmembrane protein that mediates neurotrophin signaling in neurons, in the astrocyte response to BDNF. We found a shift from a kinase-based response in embryonic cells to a predominantly [Ca2+]i-based response in postnatal cultures associated with the decreased expression of the full-length BDNF receptor TrkB. We also found that Kidins220/ARMS contributes to the BDNF-activated intracellular signaling in astrocytes by potentiating both kinase and [Ca2+]ipathways. Finally, Kidins220/ARMS contributes to astrocytes’ homeostatic function by controlling the expression of the inwardly rectifying potassium channel (Kir) 4.1. Overall, our data contribute to the understanding of the complex role played by astrocytes within the central nervous system and identify Kidins220/ARMS as a novel actor in the increasing number of pathologies characterized by astrocytes’ dysfunctions.
Value co-creation and social media at bottom of pyramid (BOP)
Authors: Chatterjee Sheshadri , Nguyen Bang 
Published: February 2021

Purpose
The purpose of this study is to examine the value co-creation at bottom of the pyramid (BOP) using social media and to investigate how it is impacted by age, gender and peer influence.

Design/methodology/approach
A BOP approach provides sustainable profits by involving low-income producers and consumers by way of co-creating values. The focus of the BOP approach in the business environment in this study is to establish co-creation among the different stakeholders at the BOP level. With the help of a literature review and related theories, a conceptual model has been developed. The model has been tested statistically for validation using a survey by considering 314 usable respondents.

Findings
This study has focused on the impact of different issues such as age, gender and peer influence concerning the consumers at BOP segments involving in co-creation activities. The study finds that people at BOP segments emphasize more social media usage compared to the influence of peers in the context of co-creating values.

Research limitations/implications
Co-creation at BOP is a new approach. This study is unique research where it identifies the impact of gender, age and peer influence at the BOP level consumers for co-creation activities. The study also highlights the influence of social media on BOP consumers for co-creating values. The model so developed along with the findings of this study contribute to the overall body of knowledge in this area which has a wider theoretical and social implication.

Practical implications
The proposed model in this study can help organizations to understand the impact of age, gender, peer influence on value co-creation activities at BOP using social media. This study can help managers of the organizations involved in co-creation at BOP to formulate an appropriate strategy to get engaged with the customers at BOP. Finally, this study can motivate customers to value co-creating and engaging with organizations.

Originality/value
This study has primarily identified the impact of age, gender and peer influence for the consumers at BOP segments and is involved in different co-creation activities. The study has been mainly conducted in India, an emerging economy. None of such studies has been conducted in the emerging markets. Thus, this study claims to have possessed its uniqueness.
A novel approach for brain tumor detection by self-organizing map (SOM) using adaptive network based fuzzy inference system (ANFIS) for robotic systems
Authors: Baalamurugan K.M. , Singh Priyamvada , Ramalingam Vijay 
Published: February 2021

PurposeOne of the foremost research disciplines in medical image processing is to identify tumors, which is a challenging task practicing traditional methods. To overcome this, various research studies have been done effectively.Design/methodology/approachMedical image processing is evolving swiftly with modern technologies being developed every day. The advanced technologies improve medical fields in diagnosing diseases at the more advanced stages and serve to provide proper treatment.FindingsEither the mass growth or abnormal growth concerning the cells in the brain is called a brain tumor.Originality/valueThe brain tumor can be categorized into two significant varieties, non-cancerous and cancerous. The carcinogenic tumors or cancerous is termed as malignant and non-carcinogenic tumors are termed benign tumors. If the cells in the tumor are healthy then it is a benign tumor, whereas, the abnormal growth or the uncontrollable growth of the cell is indicated as malignant. To find the tumor the magnetic resonance imaging (MRI) is carried out which is a tiresome and monotonous task done by a radiologist. In-order to diagnosis the brain tumor at the initial stage effectively with improved accuracy, the computer-aided robotic research technology is incorporated. There are numerous segmentation procedures, which help in identifying tumor cells from MRI images. It is necessary to select a proper segmentation mechanism to detect brain tumors effectively that can be aided with robotic systems. This research paper focuses on self-organizing map (SOM) by applying the adaptive network-based fuzzy inference system (ANFIS). The execution measures are determined to employ the confusion matrix, accuracy, sensitivity, and furthermore, specificity. The results achieved conclusively explicate that the proposed model presents more reliable outcomes when compared to existing techniques.
Does religious perspective influence tax non-compliance? Evidence from Yemen
Authors: Al-Ttaffi Lutfi Hassen Ali , Abdul-Jabbar Hijattulah , Bin-Nashwan Saeed Awadh 
Published: February 2021

PurposeThis paper aims to enhance the understanding of tax non-compliance behaviour of owner-managers of small and medium enterprises (SMEs) in Yemen. Drawing on the behavioural perspective and not on the Shariaper se, this study investigated the perspectives of Muslims towards government’s right to impose tax, summarised in three categories: forbidden, permissible and permissible under certain conditions.Design/methodology/approachThis study was conducted using a self-administered survey to collect the required data from a sample of 500 SMEs in Yemen. Non-compliance is measured in terms of a single hypothetical tax scenario covering four types of tax situations. Yet, Muslims’ perspective towards the government’s right to impose tax was measured using the three perspectives stated above.FindingsAs the major finding, Muslims’ perspective towards taxation has a significant influence on their likely tax compliance behaviour. Specifically, the taxpayers who believed that tax is totally permissible (i.e. the government has the right to impose tax) were more compliant than those who believed that tax is totally forbidden. Furthermore, taxpayers’ non-compliance decisions are statistically related to tax rate and penalties.Practical implicationsThe findings could serve as a useful input for taxation policy and strategy in Yemen. It is recommended that government should stress the importance of paying tax as a citizen’s obligation and also emphasise the religious legality of taxation, as it is used for public purposes.Originality/valueThis study differs from the existing literature in that its empirical investigation scrutinises the effect of citizens’ perspectives towards taxation on their non-compliance behaviour within the Islamic religion itself, particularly, in a typical Muslim community such as Yemen. The study is pioneer in adopting the views of different scholars on the government’s right to collect taxes based on three religious views (forbidden, permissible and permissible under certain conditions), which were used for measurement.
Activity apprehension in experiential purchases
Authors: Miller Chadwick J. , Samper Adriana , Mandel Naomi , Brannon Daniel C. , Salas Jim , Troncoza Martha 
Published: February 2021

Purpose
The purpose of this paper is to examine how the number of activities within a multi-activity experience influences consumer preferences before and after consumption.

Design/methodology/approach
The hypotheses are tested using four experiments and a secondary data set from a river cruise firm that includes first-time river cruise purchases by consumers from this firm between January 2011 and December 2015 (n = 337,457).

Findings
Consumers prefer experiences with fewer (vs more) activities before consumption – a phenomenon, this paper calls “activity apprehension” – but prefer experiences with more (vs fewer) activities after consumption. A mediation analysis indicates that this phenomenon occurs because the highly perishable nature of activities makes consumers uncertain about their ability to use all the activities within the experience (usage uncertainty).

Practical implications
Evaluations of a multi-activity experience depend on both the number of activities and on whether the consumer is at the pre- or post-consumption stage of the customer journey. As such, firms looking to sell multi-activity experiences should design and promote these experiences in a way that minimizes activity apprehension.

Originality/value
This study is the first to demonstrate that consumer perceptions of an optimal experience depend on both the number of included activities and on the stage of the customer journey (i.e. pre- or post-purchase). It further contributes to the consumer experience literature by examining an unexplored activity characteristic, perishability, in shaping experiential purchase decisions. Finally, it demonstrates a new way in which experiential purchases differ from tangible product purchases.
Resource efficiency improvement: zero waste discharge planning in a pulp-and-paper firm under uncertainties
Authors: Jeng Shiou-Yun , Lin Chun-Wei , Tseng Ming-Lang , Jantarakolica Korbkul , Tan Raymond 
Published: February 2021

PurposeThis study develops an integrated zero waste discharge planning approach for improving resource efficiency in a pulp-and-paper manufacturing firm.Design/methodology/approachThe objectives of this study are to (1) identify the environmental, technical and social metrics in resource efficiency; (2) utilize fuzzy multi-objective programming and the hybrid particle swarm optimization algorithm to solve the fuzzy problem; and (3) develop an assessment for resource efficiency improvement in an industrial case study.FindingsThe findings demonstrate the superiority of hybrid particle swarm optimization algorithm in generating optimal results for a pulp-and-paper manufacturing firm.Practical implicationsThe findings demonstrate the superiority of hybrid particle swarm optimization algorithm in generating optimal results for a pulp-and-paper manufacturing firm.Originality/valueResource efficiency is a multi-objective problem in an uncertain environment. In particular, zero waste discharge planning involves minimizing the total cost and maximizing the waste material recovery rate, wastewater reuse, and waste heat recovery.