bluuebunny/crossref_metadata_2025_split huggingface dataset:
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins
Authors: Ilnitskiy Ivan S , Zharikova Anastasia A , Mironov Andrey A 
Published: April 2022

Abstract
Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the evolutionary landscape of related proteins. Here, we present OrthoQuantum, a web server that allows for time-efficient analysis and visualization of phylogenetic profiles of any set of eukaryotic proteins. It is a simple-to-use tool capable of searching large input sets of proteins. Using data from open source databases of orthologous sequences in a wide range of taxonomic groups, it enables users to assess coupled evolutionary patterns and helps define lineage-specific innovations. The web interface allows to perform queries with gene names and UniProt identifiers in different phylogenetic clades and supplement presence with an additional BLAST search. The conservation patterns of proteins are coded as binary vectors, i.e., strings that encode the presence or absence of orthologous proteins in other genomes. These strings are used to calculate top-scoring correlation pairs needed for finding co-inherited proteins which are simultaneously present or simultaneously absent in specific lineages. Profiles are visualized in combination with phylogenetic trees in a JavaScript-based interface. The OrthoQuantum v1.0 web server is freely available at http://orthoq.bioinf.fbb.msu.ru along with documentation and tutorial.
Indole modulates cooperative protein–protein interactions in the flagellar motor
Authors: Gupta Rachit , Rhee Kathy Y , Beagle Sarah D , Chawla Ravi , Perdomo Nicolas , Lockless Steve W , Lele Pushkar P 
Published: April 2022

Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum's direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
Men’s Rights Activism and Anti-Feminist Resistance in Turkey and Norway
Authors: Eslen-Ziya Hande , Bjørnholt Margunn 
Published: April 2022

AbstractThis article, by addressing the growing anti-feminist activism and mobilization and its consequences for gender equality and women’s rights, sheds light on anti-feminist resistance in Turkey and Norway. Using the concept of counter movement, we study men’s rights mobilization in Turkey and Norway, two countries with different histories and realities of women’s rights and gender equality. We first compare how the respective men’s rights movements emerged in response to, or parallel with, the advances of women’s movements. Investigating mass media and social media content from the most prominent contemporary men’s rights groups in each country provides a qualitative comparative analysis of men’s rights mobilization. Men’s rights groups in Turkey and Norway share many of the same concerns, but while men’s rights activists in Turkey challenge gender equality and defend the traditional family, in Norway, men’s rights activism is a masculinist co-optation of the gender equality discourse.
Low-Dose Cadmium Potentiates Metabolic Reprogramming Following Early-Life Respiratory Syncytial Virus Infection
Authors: Jarrell Zachery R , Smith Matthew Ryan , Kim Ki-Hye , Lee Youri , Hu Xin , He Xiaojia , Orr Michael , Chen Yan , Kang Sang-Moo , Jones Dean P , Go Young-Mi 
Published: April 2022

Abstract
Respiratory syncytial virus (RSV) infection causes serious pulmonary disease and death in high-risk infants and elderly. Cadmium (Cd) is a toxic environmental metal contaminant and constantly exposed to humans. Limited information is available on Cd toxicity after early-life respiratory virus infection. In this study, we examined the effects of low-dose Cd exposure following early-life RSV infection on lung metabolism and inflammation using mouse and fibroblast culture models. C57BL/6J mice at 8 days old were exposed to RSV 2 times with a 4-week interval. A subset of RSV-infected mice was subsequently treated with Cd at a low dose in drinking water (RSV infection at infant age [RSVinf]+Cd) for 16 weeks. The results of inflammatory marker analysis showed that the levels of cytokines and chemokines were substantially higher in RSVinf+Cd group than other groups, implying that low-dose Cd following early-life RSV infection enhanced lung inflammation. Moreover, histopathology data showed that inflammatory cells and thickening of the alveolar walls as a profibrotic signature were evident in RSVinf+Cd. The metabolomics data revealed that RSVinf+Cd-caused metabolic disruption in histamine and histidine, vitamin D and urea cycle, and pyrimidine pathway accompanying with mechanistic target of rapamycin complex-1 activation. Taken together, our study demonstrates for the first time that cumulative Cd exposure following early-life RSV infection has a significant impact on subsequent inflammation and lung metabolism. Thus, early-life respiratory infection may reprogram metabolism and potentiate Cd toxicity, enhance inflammation, and cause fibrosis later in life.
The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies
Authors: Hoberecht Luke , Perampalam Pirunthan , Lun Aaron , Fortin Jean-Philippe 
Published: April 2022

AbstractThe success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crispr-Verse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a comprehensive, user-friendly, and unified interface to add on- and off-target annotations via several alignment methods, rich gene and SNP annotations, and a dozen on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. We illustrate the general applicability of our tools by designing optimal gRNAs for three case studies: tiling CRISPRbe library for BRCA1 using the base editor BE4max, tiling RNA-targeting libraries for CD46 and CD55 using CasRx, and activation of MMP7 using CRISPRa. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project to facilitate its use by the CRISPR community (https://github.com/crisprVerse).
A Prospective Study to Improve Automated Blood Culture Diagnostics in Gram-Negative Sepsis by Implementing a “Diagnostic Stewardship Care-Bundle”
Authors: Gupta Ayush , Siddiqui Farha , Purwar Shashank , Saigal Saurabh , Sharma Jai Prakash , Kumar Sanjeev 
Published: April 2022

ABSTRACTObjectivesWe implemented a diagnostic stewardship care-bundle (DSB): “Sepsis-48” with the aim of evaluating its impact on changes in duration of key steps in automated blood culture diagnostics (aBCD), compliance to care-bundle and turnaround time (TAT).MethodsIn this prospective study, a care-bundle checklist for automated blood culture bottles (BCBs) received from adult intensive care units (AICUs) was implemented between July 2020-June 2021 (intervention period, P2) and compared with a retrospective, pre-intervention period (P1) between March-June 2020. Microbial identification in positive BCBs with gram-negatives (+nBCBs) was enabled by inoculating conventional biochemical tests directly (dID) and direct antimicrobial susceptibility testing (dAST) was done as per EUCAST RAST standard. Clinical reports were issued only if a RAST reportable gram-negative was identified in dID.ResultsWe observed significant reductions in the Loading time (LT) [63.5 (104.5-24.5) vs 32 (55-14) minutes, P<0.001] & time to dID+dAST performance (TTD) [186 (288.25-202.25) vs 115 (180-68) minutes, P=0.0018] in +nBCBs received from AICUs during P2. There was a significant increase in compliance to the bundle targets [LT≤45: 44% vs 66%, P=.006 and TTD≤120: 34% vs 51.7%, P=.03] during P2 (Table 2). Using dID+dAST method, provisional results could be read ∼13 hours earlier than those generated by VITEK®. Similar improvements were also noted for +nBCBs received from other locations.ConclusionsThe “diagnostic stewardship care-bundle” strategy to improve aBCD was successfully implemented leading to significant reductions in duration of targeted steps. Laboratories should implement “diagnostic stewardship care-bundles” as per their needs to improve microbiological diagnostics.
CaV3.1 T-type calcium channels regulate spatial memory processing in the dorsal subiculum
Authors: Joksimovic Srdjan M. , Ghodsi Seyed Mohammadreza , Heinsbroek Jasper A. , Orfila James E. , Busquet Nicolas , Tesic Vesna , Valdez Robert , Fine-Raquet Brier , Jevtovic-Todorovic Vesna , Raol Yogendra H. , Herson Paco S. , Todorovic Slobodan M. 
Published: April 2022

ABSTRACTThe dorsal subiculum (dSub) is one of the key structures responsible for the formation of hippocampal memory traces but the contribution of individual ionic currents to its cognitive function is not well studied. Although we recently reported that low-voltage-activated T-type calcium channels (T-channels) are crucial for the burst firing pattern regulation in the dSub pyramidal neurons, their potential role in learning and memory remains unclear. Here we used in vivo local field potential recordings and miniscope calcium imaging in freely behaving mice coupled with pharmacological and genetic tools to address this gap in knowledge. We show that the CaV3.1 isoform of T-channels is critically involved in controlling neuronal activity in the dSub in vivo. Altering burst firing pattern by inhibiting T-channel activity markedly affects calcium dynamics, synaptic plasticity, neuronal oscillations and phase-amplitude coupling in the dSub, thereby disrupting spatial learning. These results provide a crucial causative link between the CaV3.1 channels, burst firing activity of dSub neurons and memory processing, thus further supporting the notion that changes in neuronal excitability regulate memory trace formation. We posit that subicular CaV3.1 T-channels could be a promising novel drug target for cognitive disorders.
Caveolae couple mechanical stress to integrin recycling and activation
Authors: Lolo Fidel-Nicolás , Pavón Dácil M. , Grande-García Araceli , Elósegui-Artola Alberto , Segatori Valeria Inés , Sánchez-Perales Sara , Trepat Xavier , Roca-Cusachs Pere , del Pozo Miguel A. 
Published: April 2022

AbstractCells are subjected to multiple mechanical inputs throughout their lives. Their ability to detect these environmental cues is called mechanosensing, a process in which integrins play an important role. During cellular mechanosensing, plasma membrane (PM) tension is adjusted to mechanical stress through the buffering action of caveolae; however, little is known about the role of caveolae in early integrin mechanosensing regulation. Here, we show that Cav1KO fibroblasts increase adhesion to FN-coated beads when pulled with magnetic tweezers, as compared to wild type fibroblasts. This phenotype is Rho-independent and mainly derived from increased active β1-integrin content on the surface of Cav1KO fibroblasts. FRAP analysis and endocytosis/recycling assays revealed that active β1-integrin is mostly endocytosed through the CLIC/GEEC pathway and is more rapidly recycled to the PM in Cav1KO fibroblasts, in a Rab4-dependent manner. Moreover, the threshold for PM tension-driven β1-integrin activation is lower in Cav1KO MEFs than in wild type MEFs, through a mechanism dependent on talin activity. Our findings suggest that caveolae couple mechanical stress to integrin cycling and activation, thereby regulating the early steps of the cellular mechanosensing response.
Understanding the determinants of consumers' reverse exchange intention as an approach to e-waste recycling: a developing country perspective
Authors: Sabbir Md. Mahiuddin , Khan Tahsin Tabish , Das Amit , Akter Sharmin , Hossain Md. Alamgir 
Published: April 2022

PurposeEnd-of-life electronic products exchange (EEPE) program could be an effective approach to e-waste recycling that requires consumers' participation. Thus, it is highly recommended to study factors stirring consumer behavior with regard to EEPE programs, which is largely under-explored in the existing literature. Hence, grounding on the Theory of Planned Behavior (TPB) and Attitude-Behavior-Context (A-B-C) model, this study attempts to understand the determinants of consumers' EEPE intention by adding contextual and non-cognitive factors to the proposed research model.Design/methodology/approachEmploying a purposive sampling technique, respondents were drawn from university students and general consumers of electronic products in a developing country. Factor analysis, structural equation modeling (SEM) and SPSS PROCESS were used to analyze the collected data.FindingsEmpirical results confirm that subjective norm has the strongest positive impact on EEPE intention. Following this, attitude toward EEPE and perceived behavioral control play positive mediating roles in determining EEPE intention. Moreover, government initiatives moderate the unsolicited “attitude–intention gap”.Practical implicationsDrawing on this study's outcomes, the study urges to form comprehensive awareness-building campaigns, rules and regulations regarding proper e-waste management, promote “exchange offer” programs and educational programs to encourage EEPE.Originality/valueThis study makes two fresh contributions to the extant literature. First, by coupling the TPB and A-B-C theory, this study showed that both attitude (i.e. attitude toward EEPE) and context (i.e. government initiatives) are essential in eliciting individual-level post-consumption pro-environmental behavior (PEB) (i.e. EEPE). Second, government initiatives elucidate the attitude–intention gap in the reverse logistics context, especially in developing countries.
The impact of optimal parcel locker locations on costs and the environment
Authors: Peppel Marcel , Spinler Stefan 
Published: April 2022

PurposeLast-mile delivery is associated with a negative environmental impact and high costs. The purpose of this paper is to develop an approach to designing stationary parcel locker (SPL) networks while minimizing both CO2 equivalent (CO2e) emissions and costs during delivery and pick-up.Design/methodology/approachThis study uses a multinomial logit model to evaluate recipients' willingness to use SPLs based on their availability at home and travel distance. To determine optimal SPL locations, this study formulates a mixed-integer linear programming model.FindingsThe empirical study of different regional clusters reveals that optimal SPL locations can generate cost savings of up to 11.0%. SPLs have a positive impact on total CO2e emission savings in urban areas (i.e. up to 2.5%), but give rise to additional emissions (i.e. 4.6%) in less populated areas due to longer travel distances during the pick-up process.Originality/valueThis paper optimizes SPL locations and the ecological effect of SPLs by minimizing emissions and costs simultaneously. Furthermore, it extends existing discrete choice models by also including recipients' availability at home, increasing the accuracy of recipients' preferences. So far, the effect of SPLs has been studied for metropolitan areas only. A global logistics service provider shared a real dataset which allows us to study seven different regional clusters ranging from rural areas to large cities. Thus, this study contributes to the field of sustainable urban logistics.
What brings the state back in? An examination of contracting reversal
Authors: Hung Wan-Ju , Lu Jiahuan 
Published: April 2022

PurposeIn recent years, there is a steady increase of studies documenting the emergence of “contracting back-in” in many countries around the world, that is, governments bringing previously contracted services back in-house and once again relying on public employees to deliver these services. Through a survey of the academic discourse on contracting back-in, this manuscript describes the phenomenon of contracting back-in and discusses its implications for “bringing the state back in”.Design/methodology/approachThe manuscript conducts a systematic review of existing literature on contracting back-in with a focus on the scope and rationale of contracting back-in.FindingsThe existing literature demonstrates that contracting back-in is often as common as contracting out and can be found in a variety of countries and across different service areas. Existing studies also suggest that contracting back-in is driven by a mix of managerial, political, and environmental factors. The rise of contracting back-in could imply a revival of the administrative state in public governance and a more dynamic, potentially more complicated, system of public service delivery.Originality/valueThe manuscript contributes to the special issue on “bringing the state back in” through the lens of government contracting. It adds a number of implications to the discussion on the emergence of the “new” administrative state and strategies to reinvent it.
An ensemble design of a cash crops-warehouse receipt system (WRS) based on blockchain smart contracts
Authors: Shao Deo , Kombe Cleverence , Saxena Stuti 
Published: April 2022

PurposeWarehouse receipt system (WRS) schemes aim to revitalize the market of cash crops, particularly those of the smallholder farmers. However, the existing government schemes for the smallholder farmers have not been much successful on account of issues related with transparency and trust deficit, thereby limiting farmers' access to credit for their farming activities as channeled via the formal financial institutions. Conceding that blockchain is an emerging technology, this study aims to theoretically posit the potential to optimize WRS in real time to bolster farmers' trust and privacy.Design/methodology/approachThe research bases itself on the design science research (DSR) approach. Using the DSR approach backed by the literature review and evolutionary prototyping, a blockchain-based WRS has been advanced in the study.FindingsThis study provides a design of a digital WRS, which serves as a proof of concept of blockchain technology (BCT) applications in improving transparency in the WRS in the agricultural sector. The findings from this study present the possibility of leveraging blockchain smart contracts to improve the linkages between the WRS stakeholders to promote trust and transparency that would eventually unlock the potentials of WRS schemes. Furthermore, the findings inform decision-makers and practitioners to prioritize the emerging technologies in revamping the classical WRS.Research limitations/implicationsThe study leaves research pointers for implementing BCT in agricultural supply chain and furthering the findings from the present study with an empirical agenda.Originality/valueWhilst research on the BCT applications across myriad sectors abounds, research on the BCT applications to address societal needs is conspicuously limited. Furthermore, research on the practical implementation of the BCT in real-world scenarios is few and far between. The present study seeks to plug these gaps by underlining the application and utility of blockchain in WRS. The study makes a significant contribution to the theory and practice of the agrarian supply chain management, specifically the WRS, by invoking design knowledge obtained through an iterative design process besides serving as an edifice for the integration of emerging technologies, notably BCT in the agricultural sector.
Intention of postgraduate students towards the online education system: application of extended technology acceptance model
Authors: Sinha Abhijit , Bag Sudin 
Published: April 2022

PurposeThe study is done to investigate the factors that affect the intention of higher education students towards online education. The research also focuses on the importance of students' stability and students' resilience on perceived usefulness and perceived easiness of use that frame the attitude towards the intention to use online education.Design/methodology/approachOnline survey method is employed using Google form link with a sample of 686 students of higher education. Excluding the outliers (univariate and multivariate), the final sample size (N = 679) considers the empirical results of the study. Partial least square structural equation modelling (PLS-SEM) is applied to unearth the relationship in the proposed research model of the study.FindingsThe empirical results indicate that perceived usefulness and perceived easiness of use have a direct impact on students' intention to use online education platform. Moreover, perceived usefulness and perceived easiness of use also have a positive influence on the students' attitude, which has a strong influence on students' intention to use online mode of education system. Also, students' stability and students' resilience have mixed impact on the level of perceived usefulness and perceived easiness of use that are the most useful determinants of attitude towards the intention to use online education.Research limitations/implicationsThe study counts on the technology acceptance model (TAM) where constructs like behavioural controllability, past exposure and perceived accordance are not considered for measuring the intention of students in adapting to online education.Originality/valueThis paper employs the extended model of technology acceptance with additional determinants, namely, students' stability and students' resilience, to investigate the intention to use the online form of education as an alternative to the offline mode.