bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SARS-CoV-2 envelope (E) protein forms a calcium- and voltage-activated calcium channel
Authors: Antonides Lysbeth H. , Hurst Quenton W. , Ives Callum M. , Ramberg Kiefer , Ostrovitsa Nikitas , Scanlan Eoin , Caffrey Martin , Pitt Samantha J. , Zachariae Ulrich 
Published: October 2022

AbstractThe function of ion channels is essential in the infectious cycle of many viruses. To facilitate viral uptake, maturation and export, viruses must modify the ionic balance of their host cells, in particular of calcium ions (Ca2+). Viroporins encoded in the viral genome play a key part in altering the cell’s ionic homeostasis. In SARS-Coronavirus-2 (SARS-CoV-2) – the causative agent of Covid-19 – the envelope (E) protein is considered to form ion channels in ERGIC organellar membranes, whose function is closely linked to disease progression and lethality. Deletion, blockade, or loss-of-function mutation of coronaviral E proteins results in propagation-deficient or attenuated virus variants. The exact physiological function of the E protein, however, is not sufficiently understood. Since one of the key features of the ER is its function as a Ca2+storage compartment, we investigated the activity of E in the context of this cation. Molecular dynamics simulations and voltage-clamp electrophysiological measurements show that E exhibits ion channel activity that is regulated by increased luminal Ca2+concentration, membrane voltage, post-translational protein modification, and negatively charged ERGIC lipids. Particularly, calcium ions bind to a distinct region at the ER-luminal channel entrance, where they activate the channel and maintain the pore in an open state. Also, alongside monovalent ions, the E protein is highly permeable to Ca2+. Our results suggest that the physiological role of the E protein is the release of Ca2+from the ER, and that the distinct Ca2+activation site may serve as a promising target for channel blockers, potentially inhibiting the infectious cycle of coronaviruses.
Comparative genomics and phylogenomics ofCampylobacterunveil potential novel species and provide insights into niche segregation
Authors: Henaut-Jacobs Sarah , Passarelli-Araujo Hemanoel , Venancio Thiago M. 
Published: October 2022

AbstractCampylobacteris a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies onCampylobactergenerally focus on specific pathogenic species such asC. coliandC. jejuni. Currently, there are thousands of publicly availableCampylobactergenomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all availableCampylobactergenomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III ofC. coliis in fact a novel species (referred here asCampylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinctCampylobacterspecies. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics ofCampylobacterspecies with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that theCampylobactergenus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.
Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters
Authors: Diner Rachel E. , Zimmer-Faust Amy , Cooksey Emily , Allard Sarah , Kodera Sho M. , Kunselman Emily , Garodia Yash , Allen Andrew E. , Griffith John , Gilbert Jack A. 
Published: October 2022

AbstractOysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. For example, bacterial pathogens from both marine and terrestrial sources concentrate in oysters and can cause human illness when oysters are consumed raw. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to oyster hosts and the microbial ecology of pathogenic bacteria likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of fecal indicators,Vibrio parahaemolyticus, andVibrio vulnificus. Site-specific environmental conditions significantly influenced the composition and diversity of water microbial communities, which were linked to the highest concentrations of bothVibriospp. and fecal indicator bacteria. Oyster microbial communities, however, were less impacted by environmental variability and exhibited less variability in microbial community diversity and accumulation of target bacteria. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated potential pathogens in oysters, especiallyV. parahaemolyticus. This included an increase in cyanobacteria in both water and oyster digestive gland microbial communities, which could represent an environmental vector forVibriospp. transport and decreased relative abundance ofMycoplasmaand other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters.
The clock genePer1expression may exert diurnal control over hippocampal memory consolidation
Authors: Bellfy Lauren , Smies Chad W. , Bernhardt Alicia R. , Bodinayake Kasuni K. , Sebastian Aswathy , Stuart Emily M. , Wright Destiny S. , Lo Chen-Yu , Murakami Shoko , Boyd Hannah M. , von Abo Megan J. , Albert Istvan , Kwapis Janine L. 
Published: October 2022

AbstractThe circadian system influences many different biological processes, including memory performance. While the suprachiasmatic nucleus (SCN) functions as the brain’s central pacemaker, satellite clocks have also been identified in other brain regions, such as the memory-relevant dorsal hippocampus. Although it is unclear how these satellite clocks contribute to brain function, one possibility is that they may serve to exert diurnal control over local processes. Within the hippocampus, for example, the local clock may contribute to time-of-day effects on memory. Here, we used the hippocampus-dependent Object Location Memory task to determine how memory is regulated across the day/night cycle in mice. First, we systematically determined which phase of memory (acquisition, consolidation, or retrieval) is modulated across the 24h day. We found that mice show better long-term memory performance during the day than at night, an effect that was specifically attributed to diurnal changes in memory consolidation, as neither memory acquisition nor memory retrieval fluctuated across the day/night cycle. Using RNA-sequencing we identified the circadian clock genePeriod1(Per1) as a key mechanism capable of supporting this diurnal fluctuation in memory consolidation, asPer1oscillates in tandem with memory performance. We then show that local knockdown ofPer1within the dorsal hippocampus has no effect on either the circadian rhythm or sleep behavior, although previous work has shown this manipulation impairs memory. Thus,Per1may independently function within the dorsal hippocampus to regulate memory in addition to its known role in regulating the circadian rhythm within the SCN.Per1may therefore exert local diurnal control over memory consolidation within the dorsal hippocampus.
Stochastic chain termination in bacterial pilus assembly
Authors: Giese Christoph , Puorger Chasper , Ignatov Oleksandr , Bečárová Zuzana , Weber Marco E. , Schärer Martin A. , Capitani Guido , Glockshuber Rudi 
Published: October 2022

SUMMARYAdhesive type 1 pili from uropathogenicEscherichia colistrains are filamentous, supramolecular protein complexes consisting of a short tip fibrillum and a long, helical rod formed by up to several thousand copies of the major pilus subunit FimA. Here, we reconstituted the entire type 1 pilus rod assembly reactionin vitro, using all constituent protein subunits in the presence of the assembly platform FimD, and identified the so-far uncharacterized subunit FimI as an irreversible assembly terminator. We provide a complete, quantitative model of pilus rod assembly kinetics based on the measured rate constants of FimD-catalyzed subunit incorporation. The model reliably predicts the length distribution of assembled pilus rods as a function of the ratio between FimI and the main pilus subunit FimA and is fully consistent with the length distribution of membrane-anchored pili assembledin vivo. The results show that the natural length distribution of adhesive pili formed via the chaperone-usher pathway results from a stochastic chain termination reaction.
An optimized messenger RNA vaccine candidate protects non-human primates from Zika virus infection
Authors: Bollman Brooke , Nunna Naveen , Bahl Kapil , Hsiao Chiaowen Joyce , Bennett Hamilton , Butler Scott , Foreman Bryant , Burgomaster Katherine E. , Aleshnick Maya , Kong Wing-Pui , Fisher Brian E. , Ruckwardt Tracy J. , Morabito Kaitlyn M. , Graham Barney S. , Dowd Kimberly A. , Pierson Theodore C. , Carfi Andrea 
Published: October 2022

AbstractZika virus (ZIKV), an arbovirus transmitted by mosquitoes, was identified as a cause of congenital disease during a major outbreak in the Americas in 2016. Vaccine design strategies relied on limited available isolate sequence information due to the rapid response necessary. The first-generation ZIKV mRNA vaccine, mRNA-1325, was initially generated and, as additional strain sequences became available, a second mRNA vaccine, mRNA-1893, was developed. Herein, we compared the immune responses following mRNA-1325 and mRNA-1893 vaccination and reported that mRNA-1893 generated comparable neutralizing antibody titers to mRNA-1325 at 1/20thof the dose and provided complete protection from ZIKV challenge in non-human primates. In depth characterization of these vaccines indicated that the observed immunologic differences could be attributed to a single amino acid residue difference that compromised mRNA-1325 virus-like particle formation.
Research on the relationship between industrial agglomeration and regional innovation from the dynamic perspective: evidence from China
Authors: Yang Boxu , Liu Xielin , Liu Wen 
Published: October 2022

Purpose
The purpose of this paper is to reveal the paradox between diversification and specialization from a dynamic perspective. More precisely, this paper will analyze the impact of diversification and specialization as well as their interaction on regional innovation in different development stages.

Design/methodology/approach
Based on the principles of new economic geography and innovation geography, data from 30 provinces from 2001 to 2017 was used to explore the relationship. Least squares regressions with fix effect were used to examine the hypotheses.

Findings
The results show that both diversification and specialization have a significant and positive impact on regional innovation. The interaction of diversification and specialization also significantly and positively impacts regional innovation. The effect of industrial agglomeration is heterogeneity under different development stages.

Practical implications
This paper verifies the positive role of diversification and specialization and their interaction in promoting regional innovation. The impact of industrial agglomeration on innovation is dynamic and changes with the regional development process. Emerging economies should make appropriate industrial agglomeration strategies according to their development stages.

Originality/value
This paper introduces diversification, specialization and their interaction into the research framework at the same time to analyze their impact on innovation performance which deepened the research of industrial agglomeration. Taking China as an example, this paper also examines the impact of industrial agglomeration on regional innovation in different development stages that expands the dynamic perspective of industrial agglomeration.
Examining the effect of interoperability factors on building information modelling (BIM) adoption in Malaysia
Authors: Ahmed Yunis Ali , Shehzad Hafiz Muhammad Faisal , Khurshid Muhammad Mahboob , Abbas Hassan Omayma Husain , Abdalla Samah Abdelsalam , Alrefai Nashat 
Published: October 2022

Purpose
Building information modelling (BIM) has transformed the traditional practices of the Architecture, Engineering and Construction (AEC) industry. BIM creates a collaborative digital representation of built environment data. Competitive advantage can be achieved with collaborative project delivery and rich information modelling. Despite the abundant benefits, BIM’s adoption in the AEC is susceptible to confrontation. A substantial impediment to BIM adoption often cited is data interoperability. Other facets of interoperability got limited attention. Other academic areas, including information systems, discuss the interoperability construct ahead of data interoperability. These interoperability factors have yet to be surveyed in the AEC industry. This study aims to investigate the effect of interoperability factors on BIM adoption and develop a comprehensive BIM adoption model.

Design/methodology/approach
The theoretical foundations of the proposed model are based on the European interoperability framework (EIF) and technology, organization, environment framework (TOE). Quantitative data collection from construction firms is gathered. The model has been thoroughly examined and validated using partial least squares structural equation modelling in SmartPLS software.

Findings
The study’s findings indicate that relative advantage, top management support, government support, organizational readiness and regulation support are determinants of BIM adoption. Financial constraints, complexity, lack of technical interoperability, semantic interoperability, organizational interoperability and uncertainty are barriers to BIM adoption. However, compatibility, competitive pressure and legal interoperability do not affect BIM adoption.

Practical implications
Finally, this study provides recommendations containing the essential technological, organizational, environmental and interoperability factors that AEC stakeholders can address to enhance BIM adoption.

Originality/value
To the best of the authors’ knowledge, this paper is one of the first studies to combine TOE and EIF in a single research model. This research provides empirical evidence for using the proposed model as a guide to promoting BIM adoption. As a result, the highlighted determinants can assist organizations in developing and executing successful policies that support BIM adoption in the AEC industry.
The business value of privacy-preserving technologies: the case of multiparty computation in the telecom industry
Authors: Ofe Hosea , Minnema Harm , de Reuver Mark 
Published: October 2022

PurposeThis paper aims to propose a framework for how privacy-preserving technologies (PETs) create business value for organizations. The framework was developed by examining the literature on privacy and information technology’s impact (symbolic and function). The authors evaluate the framework’s applicability using multiparty computation (MPC) as an instance of PETs, with expert interviews in the telecommunication industry.Design/methodology/approachIn an illustrative case of four telecommunication companies, the authors conducted semi-structured interviews with experts and used MPC as an instance of PET.FindingsThe evaluation of the framework indicates that PETs create business value for organizations: enhancing customer interactions, sales, personalized services, predicting market trends and collaboration among organizations. The findings show that business value of PETs is mainly driven by consumers and organizations willing to share data and collaborate.Research limitations/implicationsThis study was limited to the telecom sector and focused on MPC as an instance of PET. Further studies should be conducted to explore the benefits of other PETs and MPC. Future research could find out if this framework is also helpful for implementing other PETs or even other types of technology. The authors’ framework provides factors that future studies can use to quantify the impact of PETs. The authors hope that this framework provides an overarching reference for organizations considering the adoption of PETs.Practical implicationsThe authors’ findings inform managers in exploring the business value of PETs for organizations. This study also provides insights into which costs and risks to consider when implementing PETs.Originality/valueThis study is one of the few to propose a framework on how PETs create business value for organizations. Future research can use factors in the framework (e.g. customer interactions, sales, personalized services and market trend prediction) to conduct a quantitative study on PETs’ business value. Managers adopting PETs can use the framework to identify areas where PETs impact their organization.
Semiautomated process for generating knowledge graphs for marginalized community doctoral-recipients
Authors: Keshan Neha , Fontaine Kathleen , Hendler James A. 
Published: October 2022

Purpose
This paper aims to describe the “InDO: Institute Demographic Ontology” and demonstrates the InDO-based semiautomated process for both generating and extending a knowledge graph to provide a comprehensive resource for marginalized US graduate students. The knowledge graph currently consists of instances related to the semistructured National Science Foundation Survey of Earned Doctorates (NSF SED) 2019 analysis report data tables. These tables contain summary statistics of an institute’s doctoral recipients based on a variety of demographics. Incorporating institute Wikidata links ultimately produces a table of unique, clearly readable data.

Design/methodology/approach
The authors use a customized semantic extract transform and loader (SETLr) script to ingest data from 2019 US doctoral-granting institute tables and preprocessed NSF SED Tables 1, 3, 4 and 9. The generated InDO knowledge graph is evaluated using two methods. First, the authors compare competency questions’ sparql results from both the semiautomatically and manually generated graphs. Second, the authors expand the questions to provide a better picture of an institute’s doctoral-recipient demographics within study fields.

Findings
With some preprocessing and restructuring of the NSF SED highly interlinked tables into a more parsable format, one can build the required knowledge graph using a semiautomated process.

Originality/value
The InDO knowledge graph allows the integration of US doctoral-granting institutes demographic data based on NSF SED data tables and presentation in machine-readable form using a new semiautomated methodology.
Preparation and tribological properties of SiO2/WO3 nanocomposite lubricant
Authors: Zhang Xiaomeng , Xiong Sang , Gao Feng , Du Jinyuan , Du Qin-Jian 
Published: October 2022

Purpose
WO3 particles were prepared by the sol-gel method. Tetraethyl silicate (TEOS) was used to obtain a SiO2-coated WO3 nanoparticle. Quantum chemical parameters of oleic acid, triethanolamine, glycerol and methyl pentane as dispersants were theoretically calculated. Tribological properties of SiO2/WO3 nanocomposite lubricant were carried out on an MRS-10A four-ball friction and wear tester.

Design/methodology/approach
The purpose of this study is to investigate the preparation and tribological properties of SiO2/WO3 nanocomposite lubricant.

Findings
The obtained SiO2-coated WO3 nanoparticle (nano-SiO2/WO3) with a particle size of about 70 nm. The calculated adsorption energy of triethanolamine on the surface of the steel ball is 554.6 eV, and triethanolamine is selected as the dispersant. The dispersion effect of SiO2/WO3 nanocomposite lubricant is good, which shows that triethanolamine oleate plays a good dispersion role in the preparation of lubricant, which is consistent with the calculation results of the adsorption capacity of dispersant. As a good auxiliary lubricant, SiO2 can improve the tribological properties and wear resistance of WO3.

Originality/value
Nanocomposite lubricants have been the focus of research in recent years, which could greatly reduce energy consumption. And the SiO2/WO3 exhibited excellent lubrication performance as a lubricant additive. The lubrication mechanism of SiO2/WO3 nanocomposite lubricant is the synergistic lubrication mechanism of friction film lubrication and antifriction bearing. This study could provide a certain reference for the practical application of nanocomposite lubricants.
Performance of small firms in a circular economy: configuring challenges and entrepreneurial orientation
Authors: Khan Eijaz Ahmed , Chowdhury Md. Maruf Hossan , Hossain Mohammad Alamgir , Mahmud A.K.M. Shakil , Baabdullah Abdullah M. , Dwivedi Yogesh K. 
Published: October 2022

PurposeSociety's concerns about environmental degradation have tightened competitive pressure and brought new challenges to small firms. Against this backdrop, this study develops a decision model to determine a suitable configuration for entrepreneurial orientation to help small firms manage circular economy challenges and improve their performance.Design/methodology/approachThis study used a multi-study and multi-method approach. Study 1, through qualitative in-depth interviews, identified a portfolio of circular economy challenges and entrepreneurial-orientation components. Study 2 applied the quality function deployment technique to determine the most important components of entrepreneurial orientation. Study 3 adopted a fuzzy set qualitative comparative analysis to determine the best configuration for challenges and components.FindingsThe findings reveal a set of challenges and identify the salient need to combine the negation of these challenges with the components of entrepreneurial orientation; this combination will improve the performance of small firms. The research extends the current knowledge of managing circular economy challenges and offers decision-makers insights into improving their resilience.Originality/valueThe use of the dynamic capability view, together with the multi-study and multi-method approach, may lead to an appropriate reconfiguration of entrepreneurial orientation, which, to date, has received limited empirical attention in the small-business-management discipline.