bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of EnvC and the phosphoenolpyruvate:sugar phosphotransferase system in resistance to MreB disruption
Authors: Sloan Ryan , Surber Jacob , Roy Emma , Hartig Ethan , Morgenstein Randy M. 
Published: July 2022

AbstractCell wall synthesis in bacteria is determine by two protein complexes: the elongasome and divisome. The elongasome is coordinated by the actin homolog MreB while the divisome is organized by the tubulin homolog FtsZ. While these two systems must coordinate with each other to ensure that elongation and division are coregulated, this cross talk has been understudied. Using the MreB depolymerizing agent, A22, we found that multiple gene deletions result in cells exhibiting increased sensitivity to MreB depolymerization. One of those genes encodes for EnvC, a part of the divisome that is responsible for splitting daughter cells after the completion of cytokinesis through the activation of specific amidases. Here we show this increased sensitivity to A22 works through two known amidase targets of EnvC: AmiA and AmiB. In addition, suppressor analysis revealed that mutations in the phosphoenolpyruvate:sugar phosphotransferase system (PTS) can suppress the effects of A22 in both wild-type and envC deletion cells. Together this work helps to link elongation, division, and metabolism.
ZER1 contributes to the carcinogenic activity of high-risk HPV E7 proteins
Authors: Nouel Joangela , White Elizabeth A. 
Published: July 2022

ABSTRACTHuman Papillomavirus (HPV) E7 proteins bind to host cell proteins to facilitate virus replication. Interactions between HPV E7 and host cell proteins can also drive cancer progression. We hypothesize that HPV E7-host protein interactions specific for high-risk E7 contribute to the carcinogenic activity of high-risk HPV. The cellular protein ZER1 interacts with the E7 protein from HPV16, the genotype most frequently associated with human cancers. The HPV16 E7-ZER1 interaction is unique among HPV E7 tested to date. Other E7 proteins, even from closely related HPV genotypes, do not bind ZER1, which is a substrate specificity factor for a CUL2-RING ubiquitin ligase. In the present study, we investigated the contribution of ZER1 to the carcinogenic activity of HPV16 E7. First, we mapped the ZER1 binding site to specific residues on the C-terminus of HPV16 E7. We showed that the mutant HPV16 E7 that cannot bind ZER1 is impaired in the ability to promote the growth of primary keratinocytes. We found that ZER1 and CUL2 contribute to but are not required for HPV16 E7 to degrade RB1. Cancer dependency data shows that ZER1 is an essential gene in most HPV-positive, but not HPV-negative, cancer cell lines. Depleting ZER1 impaired the growth of primary keratinocytes expressing HPV16 E7 or HPV18 E7 and of HPV16 and HPV18-positive cervical cancer cell lines. Taken together, our work demonstrates that ZER1 contributes to HPV-mediated carcinogenesis and is essential for the growth of HPV-positive cells.IMPORTANCEHPV16 is highly carcinogenic and is the most predominant HPV genotype associated with human cancers. The mechanisms that underlie differences between high-risk HPV genotypes are currently unknown, but many of these differences are likely attributable to the activities of the oncogenic HPV proteins, including E7. The HPV E7 oncoprotein is essential for HPV-mediated carcinogenesis. A large number of HPV E7 targets have been identified. However, it is unclear which of these many interactions contribute to the carcinogenic activity of HPV E7. Here, we characterized the interaction between HPV16 E7 and the host cell protein ZER1, testing whether this genotype-specific interaction could enable the enhanced carcinogenic activity of HPV16 E7. We found that ZER1 binding contributes to the growth promoting activity of HPV16 E7 and to the growth of HPV-positive cervical cancer cells. We propose that ZER1 makes an important contribution to HPV-mediated carcinogenesis.
Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
Authors: Simensen Vetle , Seif Yara , Almaas Eivind 
Published: July 2022

ABSTRACTGenome-scale metabolism can best be described as a highly interconnected network of biochemical reactions and metabolites. The flow of metabolites, i.e., flux, throughout these networks can be predicted and analyzed using approaches such as flux balance analysis (FBA). By knowing the network topology and employing only a few simple assumptions, FBA can efficiently predict metabolic functions at the genome scale as well as microbial phenotypes. The network topology is represented in the form of genome-scale metabolic models (GEMs), which provide a direct mapping between network structure and function via the enzyme-coding genes and corresponding metabolic capacity. Recently, the role of protein limitations in shaping metabolic phenotypes have been extensively studied following the reconstruction of enzyme-constrained GEMs. This framework has been shown to significantly improve the accuracy of predicting microbial phenotypes, and it has demonstrated that a global limitation in protein availability can prompt the ubiquitous metabolic strategy of overflow metabolism. Being one of the most abundant and differentially expressed proteome sectors, metabolic proteins constitute a major cellular demand on proteinogenic amino acids. However, little is known about the impact and sensitivity of amino acid availability with regards to genome-scale metabolism. Here, we explore these aspects by extending on the enzyme-constrained GEM framework by also accounting for the usage of amino acids in expressing the metabolic proteome. Including amino acids in an enzyme-constrained GEM of Saccharomyces cerevisiae, we demonstrate that the expanded model is capable of accurately reproducing experimental amino acid levels. We further show that the metabolic proteome exerts variable demands on amino acid supplies in a condition-dependent manner, suggesting that S. cerevisiae must have evolved to efficiently fine-tune the synthesis of amino acids for expressing its metabolic proteins in response to changes in the external environment. Finally, our results demonstrate how the metabolic network of S. cerevisiae is robust towards perturbations of individual amino acids, while simultaneously being highly sensitive when the relative amino acid availability is set to mimic a priori distributions of both yeast and non-yeast origins.
WITHDRAWN: Mitochondrial genome variation affects humoral and cell-mediated innate immune responses and infection outcomes
Authors: Salminen Tiina S. , Vesala Laura , Basikhina Yuliya , Kutzer Megan , Tuomela Tea , Lucas Ryan , Monteith Katy , Prakash Arun , Tietz Tilman , Vale Pedro F. 
Published: July 2022

Withdrawal StatementThe authors have withdrawn version 2 of this manuscript due to the erroneous revision with a related but different manuscript, which can now be found under doi: 10.1101/2024.03.28.587162. Note that version 1 of this preprint is correct and has now been published as doi: 10.1186/s12915-024-01858-5, which should be used for citation purposes. If you have any questions, please contact the corresponding author (Tiina S. Salminen,tiina.s.salminen@tuni.fi).
Monovalent and trivalent VSV-based COVID-19 vaccines elicit potent neutralizing antibodies and immunodominant CD8+ T cells against diverse SARS-CoV-2 variants
Authors: Parham Kate A. , Kim Gyoung Nyoun , Saeedian Nasrin , Ninkov Marina , Richer Connor G. , Li Yue , Wu Kunyu , Rashu Rasheduzzaman , Barr Stephen D. , Arts Eric J. , Haeryfar S.M. Mansour , Kang C. Yong , Troyer Ryan M. 
Published: July 2022

AbstractRecombinant vesicular stomatitis virus (rVSV) vaccines expressing Spike proteins of Wuhan, Beta and/or Delta variants of SARS-CoV-2 were generated and tested for induction of antibody and T cell immune responses in mice. rVSV-Wuhan and rVSV-Delta vaccines and a rVSV-Trivalent (mixed rVSV-Wuhan, -Beta, -Delta) vaccine elicited potent neutralizing antibodies (nAbs) against live SARS-CoV-2 Wuhan (USAWA1), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529) viruses. Prime-boost vaccination with rVSV-Beta was less effective in this capacity. Heterologous boosting of rVSV-Wuhan with rVSV-Delta induced strong nAb responses against Delta and Omicron viruses, with rVSV-Trivalent vaccine consistently effective in inducing nAbs against all the SARS-CoV-2 variants tested. All vaccines, including rVSV-Beta, elicited a spike-specific immunodominant CD8+ T cell response. Collectively, rVSV vaccines targeting SARS-CoV-2 variants of concern may be considered in the global fight against COVID-19.
Genomewide basis for nitrogen use efficiency in contrasting genotypes of rice
Authors: Sharma Narendra , Jaiswal Dinesh Kumar , Kumari Supriya , Dash Goutam Kumar , Panda Siddharth , Anandan Annamalai , Raghuram Nandula 
Published: July 2022

AbstractRice is an ideal crop with huge germplasm diversity and post-genomic resources for improvement of nitrogen (N) use efficiency (NUE). There is a paucity of comparative studies on rice genotypes contrasting for NUE, especially with urea, the predominant fertilizer in rice growing countries. In this study, low urea-responsive transcriptomes of contrasting rice genotypes namely Nidhi (low NUE) and Panvel1 (high NUE) were compared. They were based on whole plants grown for 21 days in pots containing nutrient-depleted soil fertilized with normal (15 mM) and low urea (1.5 mM) media. There were 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors and better photosynthesis, water use efficiency and post translational modifications. Many of their genes co-localized to NUE QTLs on chromosomes 1, 3 and 9. Field evaluation of the contrasting genotypes under different doses of urea revealed better performance of Panvel1 in different agronomic parameters including grain yield, transport/uptake efficiencies and NUE. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes from the same contrasting rice genotypes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and transcription factors among others contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.SummaryRice genotypes with contrasting urea use efficiency differ in the role of transporters, transcription factors, miRNAs, post-translational modifications, photosynthesis and water use efficiency
Research on the propagation and governance of public opinion information under the joint action of internal and external factors
Authors: Wang Jiakun , Li Yun 
Published: July 2022

PurposeUnder the new media environment, while enjoying the convenience brought by the propagation of public opinion information (referred to as public opinion), learning the evolution process of public opinion and strengthening the governance of the spreading of public opinion are of great significance to promoting economic development and maintaining social stability as well as effectively resisting the negative impact of its propagation.Design/methodology/approachThinking about the results of empirical research and bibliometric analysis, this paper focused on introducing key factors such as information content, social strengthening effects, etc., from both internal and external levels, dynamically designed public opinion spreading rules and netizens' state transition probability. Subsequently, simulation experiments were conducted to discuss the spreading law of public opinion in two types of online social networks and to identify the key factors which influencing its evolution process. Based on the experimental results, the governance strategies for the propagation of negative public opinion were proposed finally.FindingsThe results show that compared with other factors, the propagation of public opinion depends more on the attributes of the information content itself. For the propagation of negative public opinion, on the one hand, the regulators should adopt flexible guidance strategy to establish a public opinion supervision mechanism and autonomous system with universal participation. On the other hand, they still need to adopt rigid governance strategy, focusing on the governance timing and netizens with higher network status to forestall the wide-diffusion of public opinion.Practical implicationsThe research conclusions put forward the enlightenment for the governance of public opinion in management practice, and also provided decision-making reference for the regulators to reasonably respond to the propagation of public opinion.Originality/valueOur research proposed a research framework for the discussion of public opinion propagation process and had important practical guiding significance for the governance of public opinion propagation.
Using data mining technology to analyse the spatiotemporal public opinion of COVID-19 vaccine on social media
Authors: Li Tingting , Zeng Ziming , Sun Jingjing , Sun Shouqiang 
Published: July 2022

Purpose
The deployment of vaccines is the primary task in curbing the COVID-19 pandemic. The purpose of this paper is to understand the public’s opinions on vaccines and then design effective interventions to promote vaccination coverage.

Design/methodology/approach
This paper proposes a research framework based on the spatiotemporal perspective to analyse the public opinion evolution towards COVID-19 vaccine in China. The framework first obtains data through crawler tools. Then, with the help of data mining technologies, such as emotion computing and topic extraction, the evolution characteristics of discussion volume, emotions and topics are explored from spatiotemporal perspectives.

Findings
In the temporal perspective, the public emotion declines in the later stage, but overall emotion performance is positive and stabilizing. This decline in emotion is mainly associated with ambiguous information about the COVID-19 vaccine. The research progress of vaccines and the schedule of vaccination have driven the evolution of public discussion topics. In the spatial perspective, the public emotion tends to be positive in 31 regions, whereas local emotion increases and decreases in different stages. The dissemination of distinctive information and the local epidemic prevention and control status may be potential drivers of topic evolution in local regions.

Originality/value
The analysis results of media information can assist decision-makers to accurately grasp the subjective thoughts and emotional expressions of the public in terms of spatiotemporal perspective and provide decision support for macro-control response strategies and risk communication.
Drivers behind the accuracy of self-reported home valuations: evidence from an emerging economy
Authors: Tomal Mateusz 
Published: July 2022

PurposeThis paper aims to explore the drivers behind the accuracy of self-reported home valuations in the Warsaw (Poland) housing market.Design/methodology/approachIn order to achieve the research goal, firstly, unique data on subjective residential property values estimated by their owners were compared with market-justified ones. The latter was calculated using geographically weighted regression, which allowed for taking into account spatially heterogeneous buyers' housing preferences. An ordered logit model was then used to identify the factors influencing the probability of the occurrence of bias towards over or undervaluation.FindingsThe results of the study revealed that, on average, homeowners overvalued their properties by only 1.94%, and the fraction of interviewees estimating their properties accurately ranges from 20% to 68%, depending on the size of the margin of error adopted. The drivers of the valuation bias variation were the physical, locational and neighbourhood attributes of the property as well as the personal characteristics of the respondents, for which their age and employment situation played a key role.Originality/valueIn contrast to previous studies, this is the first to examine drivers behind the accuracy of self-reported home valuations in a Central and Eastern Europe country. In addition, this work is the first to consider heterogeneous housing preferences when calculating objective property values.
The emergence of e-learning and online-based training during the COVID-19 crisis: an exploratory investigation from Bangladesh
Authors: Shahriar Shamsul Huq Bin , Arafat Sayed , Islam Intijamul , Nur J. M. Ekram Hossain , Rahman Saifur , Khan Syful Islam , Alam M. Sayeed 
Published: July 2022

PurposeThe extreme measures that have been taken by governments across the globe to minimize the spread of COVID-19 have had significant impacts on almost all the public sectors, especially on the economy and education. This study aims to address the approaches and prospective of online-based training and e-learning for employee learning and development during this COVID-19 crisis.Design/methodology/approachWith an emphasis on the qualitative approach and considering the complex COVID-19 emergency, required data were collected from in-depth interviews to interpret the experiences of the respondents.FindingsThe findings suggested that the digital learning ecosystem offered flexibility of time, place and pace, which provided essential convenience during the COVID-19 crisis. From the human resource (HR) perspective, the e-learning culture has enabled the organizations to quickly adopt the new normal, secure sustainable continuity of organizational development and ensure decent work and growth within and across organizations. The adoption of e-learning and flexible working conditions following the setback has enabled the organizations to quickly cope up with the new normal, causing a significant paradigm shift in the organizational culture and corporate sector of Bangladesh.Research limitations/implicationsThe study will assist the HR of any organization to contemplate e-learning systems as effective alternative training methods. Also, the study will be suggestive to traverse new dimensions and skillsets for the pedagogues.Originality/valueThis study offers new evidential scenarios regarding the emergence of effective e-learning initiatives and online-based learning programs for developing the workforce to be efficient and productive even in distressful and inconvenient COVID-19 situations.
Empirical evidence of practical considerations in local government tax portfolio composition: consequences of SPLOST taxes
Authors: Ambrosio Fabio 
Published: July 2022

PurposeThe purpose of this study is to explore and explain, through practical considerations, the ever-increasing presence of local option sales taxes and “special purpose” local option sales taxes (SPLOST) in the composition of the tax portfolio of local governments.Design/methodology/approachThis research is designed as a case study of county-level fiscal trends in Washington counties between 1990 and 2018. Data were collected for all 39 Washington counties for 29 years in three domains: revenue, crime and society. Observations were fitted to longitudinal models for tests of cointegration or trend, or to cross-sectional regression models for tests of predictive quality.FindingsThis study shows that the stated “special purpose” does not influence a county’s decision to impose a SPLOST. Furthermore, this study finds that indicators of educational attainment, income, poverty, unemployment and rural areas are the largest predictors of a county’s propensity to change the composition of its revenue portfolio in favor of the sales tax.Originality/valueTo the best of the author’s knowledge, this is the first study to explore whether indicators of a stated “special purpose” are statistically related to a county’s propensity to adopt a particular SPLOST. This study concludes that a county’s decision to adopt a SPLOST does not depend on the stated “special purpose.” In addition, it shows that urbanized counties with higher per capita income and education levels, but lower unemployment and poverty, can predictably import sales tax revenue from neighboring jurisdictions. This is a significant finding as it may explain why SPLOST is gaining popularity.
Co-patenting, co-ownership, and co-ideation as drivers for university business innovation: the case of public universities in Spain
Authors: Quero María José , Díaz-Méndez Montserrat , Ventura Rafael , Gummesson Evert 
Published: July 2022

PurposeThis paper explores whether, in the context of university–industry (U–I) collaboration, new innovation strategies can be developed through actors' interactions, the exchange of resources and the co-creation of value for and within the system. In the context of the U–I relationship, the innovation perspective can highlight the need to develop strategies that elicit new formulas of value co-creation, which then facilitate innovation as a result of actor collaboration.Design/methodology/approachA total of 45 public universities in Spain, representing 95% of the total, participated in qualitative research. Personal in-depth interviews with technology transfer officers (TTOs) were conducted by an external firm; in a second phase, two of the researchers conducted eight interviews with the directors of TTOs in those universities with higher rates of transfer.FindingsFindings reveal that enterprises with a technological focus are strengthening their relationships with universities and attempting to build a university business ecosystem by designing strategies for value co-creation such as co-ownership, co-patenting, and co-invention.Research limitations/implicationsThe empirical research is conducted in Spain, and results should be interpreted according to this context. Future research should examine new contexts (other countries) to improve the robustness of the data and enrich the results, thus enabling generalization of the management consequences.Originality/valueThe results provide a means to design strategies under a new collaborative and innovating logic. The theoretical framework contributes to theory, with implications for management.
The external cost of prostitution: Evidence from shutting down red light districts in the Netherlands
Authors: Giambona Erasmo , Ribas Rafael P. 
Published: July 2022

AbstractThis article examines the value of externalities created by the presence of sex workers in the city. Although a legal paid‐sex industry might contribute to the economy, it may also generate negative externalities. To identify the net impact of overt prostitution, we estimate changes in housing prices following the sudden closure of the two red light districts (RLDs) in the Dutch City of Utrecht. Our results show that the capitalization effect of RLDs is spatially heterogeneous. While some areas are unaffected, others are up to 12% more expensive if far from operating brothels. Interestingly, though, evidence also shows that RLDs increase local employment in a variety of sectors. All the aversion to living near RLDs is instead explained by petty crimes.