bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of 56K genomes identifies the relationship between antibiotic and metal resistance co-Occurrence and the spread of multidrug-resistant non-typhoidal Salmonella
Authors: Fenske Gavin J , Scaria Joy 
Published: June 2021

ABSTRACTSalmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-current genes were identified by constructing a co-occurrence matrix and group the genes using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic cooccurrence was isolated to one clade of S. enterica I 4,[5],12:i:.
Biochemical insight into novel Rab-GEF activity of the mammalian TRAPPIII complex
Authors: Harris Noah J , Jenkins Meredith L , Dalwadi Udit , Fleming Kaelin D , Nam Sung-Eun , Parsons Matthew AH , Yip Calvin K , Burke John E 
Published: June 2021

AbstractTransport Protein Particle complexes (TRAPP) are evolutionarily conserved regulators of membrane trafficking, with this mediated by their guanine nucleotide exchange factor (GEF) activity towards Rab GTPases. In metazoans evidence suggests that two different TRAPP complexes exist, TRAPPII and TRAPPIII. These two complexes share a common core of subunits, with complex specific subunits (TRAPPC9 and TRAPPC10 in TRAPPII and TRAPPC8, TRAPPC11, TRAPPC12, TRAPPC13 in TRAPPIII). TRAPPII and TRAPPIII have distinct specificity for GEF activity towards Rabs, with TRAPPIII acting on Rab1, and TRAPPII acting on Rab1 and Rab11. The molecular basis for how these complex specific subunits alter GEF activity towards Rab GTPases is unknown. Here we have used a combination of biochemical assays, hydrogen deuterium exchange mass spectrometry (HDX-MS) and electron microscopy to examine the regulation of TRAPPII and TRAPPIIII complexes in solution and on membranes. GEF assays revealed that the TRAPPIII has GEF activity against Rab1 and Rab43, with no detectable activity against the other 18 Rabs tested. The TRAPPIII complex had significant differences in protein dynamics at the Rab binding site compared to TRAPPII, potentially indicating an important role of accessory subunits in altering the active site of TRAPP complexes. Both the TRAPPII and TRAPPIII complexes had enhanced GEF activity on lipid membranes, with HDX-MS revealing numerous conformational changes that accompany membrane association. HDX-MS also identified a membrane binding site in TRAPPC8. Collectively, our results provide insight into the functions of TRAPP complexes and how they can achieve Rab specificity.
Modeling traumatic brain injury combined with hemorrhagic shock in rats: Neurological assessment and PET imaging with 18F-fluorodeoxyglucaric acid
Authors: Awwad Hibah O. , Hedrick Andria , Mdzinarishvili Alex , Houson Hailey , Standifer Kelly M. , Awasthi Vibhudutta 
Published: June 2021

ABSTRACTTraumatic brain injury (TBI) is a major cause of death and disability worldwide. Hemorrhagic shock (HS) aggravates tissue injury and complicates TBI recovery. We studied the combined insult of mild TBI and HS and investigated the impact of varying loss of blood volume on neurologic deficit and brain lesion volume. A novel positron emission tomography (PET) technique was employed to monitor tissue injury. Male Sprague Dawley rats received mTBI by controlled cortical impact (CCI) followed by withdrawal of 0%, 30-40%, 45%, or 50% of blood (mTBI, mTBI+HS≤40%, mTBI+HS45%, and mTBI+HS50%, respectively). Neurological deficit (mNSS= 5.6, 7.6, and 12.3) and mortality (2/12, 2/6, and 7/12) were worse in mTBI+HS≤40%, mTBI+HS45%, and mTBI+HS50%, respectively than in mTBI alone rats (no death; mNSS=3.3). Histologic lesion size increased 3.5-fold in mTBI+HS50% compared to mTBI alone and the infarct-avid PET agent 18F-fluorodeoxyglucaric acid (FGA) proportionately detected tissue necrosis in mTBI+HS50% rats. Based on these results, we conclude that HS aggravates mTBI-induced neurological deficits, tissue injury and mortality. PET/18F-FGA as an imaging marker can detect the extent of injury in a non-invasive manner.
Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data
Authors: McCalla Sunnie Grace , Siahpirani Alireza Fotuhi , Li Jiaxin , Pyne Saptarshi , Stone Matthew , Periyasamy Viswesh , Shin Junha , Roy Sushmita 
Published: June 2021

AbstractSingle-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands of individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed to address this problem. Here, we present an expanded benchmarking study of eleven recent network inference methods on six published scRNA-seq datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that, while most methods have a modest recovery of experimentally derived interactions based on global metrics such as Area Under the Precision Recall curve, methods are able to capture targets of regulators that are relevant to the system under study. Among the top performing methods that use only expression were SCENIC, PIDC, MERLIN or Correlation. Addition of prior biological knowledge and the estimation of transcription factor activities resulted in the best overall performance with the Inferelator and MERLIN methods that use prior knowledge outperforming methods that use expression alone. We found little to no benefit from imputation for network inference, which is further dataset-dependent. Comparisons of inferred networks for comparable bulk conditions showed that the networks inferred from scRNA-seq datasets are often better or at par with the networks inferred from bulk datasets. Our analysis should be beneficial in selecting methods for network inference. At the same time, this highlights the need for improved methods and better gold standards for regulatory network inference from scRNAseq datasets.
Live whole-eye, ex vivo imaging and laser-induced micro injury of the corneal basal epithelium and visualization of resident macrophage responses
Authors: Gulka Sebastian M.D. , Litke Ana M. , Delaney Kerry. R. , Chow Robert L. 
Published: June 2021

AbstractPurposeIn this paper, we describe a novel live-imaging approach to visualize the short-term response of the mouse cornea to basal epithelial cell damage. Laser scanning confocal microscopy was used to induce precisely-defined, localized corneal basal epithelial cell damage and the live macrophage response to this damage was visualized and analyzed.MethodsLipophilic fluorescent dyes, SGC5 or FM 4-64, were injected into the anterior chamber of enucleated eyes and imaged live in whole-mount using confocal laser scanning microscopy. Laser-induced damage was performed by focusing onto a defined region of the corneal basal epithelium for a brief period using a high laser power setting and then returning to low laser power for imaging. Eyes from CX3CR1+/GFP mice were used to observe macrophage responses to laser damage in real-time.ResultsSGC5 or FM 4-64 dyes injected into the anterior chamber readily enter the cornea and are taken up by the stromal layer and labeled the outer membranes of corneal epithelial cells and remained stable when visualized using low laser power. Subjecting a defined region of the basal epithelium to high laser power for 1 minute or longer led to a rapid internalization of dye in the exposed basal epithelium cells and overall increase in cellular fluorescence. This change in fluorescence was also accompanied by cell swelling and contraction. Cellular internalization of the non-lipophilic, dye Alexa 647 hydrazide, indicated that membranes were compromised indicating that exposure to high power laser stimulation causes cellular damage to the basal epithelium. Visualization of corneal resident macrophages close to the site of laser-induced damage showed that within minutes, projecting macrophage filopodia extended towards the damaged region at a rate of 0.75µm/min for roughly 40 minutes.ConclusionWe have developed a novel approach to image the live cornea and its response to damage. Laser-scanning confocal microscopy can be utilized to induce localized damage to mouse corneal basal epithelium and elicit a macrophage morphological response. This approach represents a useful tool for studying corneal wound healing and cellular responses to damage using live whole-mount imaging.
Elevational changes in bacterial microbiota structure and diversity in an arthropod-disease vector
Authors: Aivelo Tuomas , Lemoine Mélissa , Tschirren Barbara 
Published: June 2021

AbstractEnvironmental conditions change rapidly along elevational gradients and have been found to affect community composition in macroscopic taxa, with lower diversity typically observed at higher elevations. In contrast, microbial community responses to elevation are still poorly understood. Specifically, the effects of elevation on vector-associated microbiota have not been studied to date, even though the within-vector microbial community is known to influence vector competence for a range of zoonotic pathogens. Here we characterize the structure and diversity of the bacterial microbiota in an important zoonotic disease vector, the sheep tick Ixodes ricinus, along replicated elevational gradient (630 - 1673 masl) in the Swiss Alps. 16S rRNA sequencing of the whole within-tick bacterial microbiota of questing nymphs and adults revealed a decrease in Faith’s phylogenetic microbial alpha diversity with increasing elevation, while beta diversity analyses revealed a lower variation in microbial community composition at higher elevations. We also found a higher microbial diversity later in the season and significant differences in microbial diversity among tick life stages and sexes, with lowest microbial alpha diversity observed in adult females. No associations between tick genetic diversity and bacterial diversity were observed. Our study demonstrates systematic changes in tick bacterial microbiota diversity along elevational gradients. The observed patterns mirror diversity changes along elevational gradients typically observed in macroscopic taxa, and they highlight the key role of environmental factors in shaping within-host microbial communities in ectotherms.
Benchmarking the practices of flexibility with maturity models and frameworks of organizational capabilities
Authors: Shukla Sanjai Kumar , Sushil  
Published: June 2021

PurposeOrganizational capabilities are crucial to achieve the objectives. A plethora of maturity models is available to guide organizational capabilities that create a perplexing situation about what stuff to improve and what to leave. Therefore, a unified maturity model addressing a wide range of capabilities is a necessity. This paper establishes that a flexibility maturity model is an unified model containing the operational, strategic and human capabilities.Design/methodology/approachThis paper does a comparative analysis/benchmarking studies of different maturity models/frameworks widely used in the information technology (IT) sector with respect to the flexibility maturity model to establish its comprehensiveness and application in the organization to handle multiple goals.FindingsThis study confirms that the flexibility maturity model has the crucial elements of all the maturity models. If the organizations use the flexibility maturity model, they can avoid the burden of complying with multiple ones and become objective-driven rather than compliance-driven.Research limitations/implicationsThe maturity models used in information technology sectors are used. This work will inspire other maturity models to adopt flexibility phenomena.Practical implicationsThe comparative analysis will give confidence in application of flexibility framework. The business environment and strategic options across organizations are inherently different that the flexibility maturity model well handles.Social implicationsA choice is put to an organization to see the comparison tables produced in this paper and choose the right framework according to the prevailing business situation.Originality/valueThis is the first study that makes a conclusion based on comparative benchmarking of existing maturity models.
Antecedents and consequences of Personal Financial Management Behavior: a systematic literature review and future research agenda
Authors: Goyal Kirti , Kumar Satish , Xiao Jing Jian 
Published: June 2021

PurposeThe purpose of this paper is to investigate the current state of research on Personal Financial Management Behavior (PFMB), with a prime focus on its antecedents and the consequences. By analyzing the research trends, methods, determinants and outcomes, the PFMB literature is synthesized, and agenda for future research is suggested. A framework is presented that portrays PFMB's antecedents and consequences and further specification of the mediation and moderation linkages.Design/methodology/approachThe review is based on 160 articles published during 1970–2020. It follows a systematic approach and presents the definitions and theories of PFMB, publication trends based on time, region, sample population, research designs, data collection and analysis techniques, along with antecedents and outcomes through content analysis.FindingsThe synthesis draws upon various factors affecting PFMB, such as demographics, socio-economic, psychological, social, cultural, financial experience, financial literacy (FL) and technological factors. The prominent outcomes of PFMB include financial satisfaction, relationship satisfaction, quality of life, financial success, happiness, financial vulnerability/resilience and financial well-being. The future research agenda sums up the recommendations in the form of research questions on variables and their linkages, followed by methodological advancements.Originality/valueThis paper covers the scholarly work done in this area in the past 51 years. To the best of authors' knowledge, this is the first attempt to offer a most comprehensive and collective scholarship of this subject. It further gives an extensive future research agenda.
Evidence-based training approach for higher education faculty: brief model of inclusion and training of the disabled
Authors: Zahid Gulnaz 
Published: June 2021

PurposeThis interventional study aims to test the effectiveness of thek training approach for higher education faculty members to facilitate students with disabilities (SwD) to promote inclusion in higher education by operationalising approaches on the basis of the social action model. It presents an evidence-based training model created on recognised theories and strategies in the field of disability.Design/methodology/approachThe study follows a single-case pre/post-test intervention design in which data were analysed quantitatively, followed by a thematic analysis of participants' feedback and trainer's reflections. Training sessions were aligned to the social action model, the perspective of reasonable accommodations and introduction to technological support for teaching-learning and policy issues. Eighty faculty members from different schools of a multi-disciplinary Pakistani university participated in these sessions. Data from only 63 faculty members were available for analyses.FindingsTeacher Perceptions of Facilitating Students with Disabilities (TP-FSD) scale served as a pre- and post-test measure. The quantitative assessment revealed knowledge and attitudinal gains after brief trainings. However, when findings were interpreted considering effect sizes and supported by qualitative findings, moderate effectiveness level was evident. Effectiveness can be interpreted by the internal and external validity checks and findings of multiple assessments.Practical implicationsThis study can be replicated by adapting the training approach and by considering its strengths and shortcomings mentioned in detail in the discussion section.Originality/valueThe study tested the effectiveness of brief faculty training to support SwD in a multi-disciplinary university having faculty with varied education and training experience.
Can the marketing innovation of purpose branding make brands meaningful and relevant?
Authors: Narayanan Sajith , Das Jyoti Ranjan 
Published: June 2021

PurposePurpose branding is a concept that has gained momentum in recent years. It is a marketing innovation that has the potential to change why and how companies work. Still, academic research on purpose branding is scarce. This paper aims to increase awareness about purpose branding and showcase how it can be implemented successfully through account of Hindustan Unilever Limited (HUL).Design/methodology/approachThe study is based on qualitative research and case analysis of HUL by examining its published reports, its parent company’s trade publications, press articles and relevant studies in indexed journals.FindingsPurpose branding is a marketing innovation that delivers increased value to all stakeholders. The account of HUL reveals that purpose branding reaps economic rewards for the organization.Practical implicationsA study by Havas Media group involving 300,000 customers across 33 countries found that the customers would not care if 74% of brands in the world disappeared. In such a context, purpose branding provides a way to make the brand meaningful and play a worthy role in consumers’ lives. HUL’s brands that used this approach grew by 69% and accounted for 75% of its overall growth, showing how other organizations can imbibe it into their brands.Originality/valueDespite many trade publications on this trending topic, there is limited academic research on purpose branding. This paper focuses on understanding this concept and demonstrates its successful use by an organization.
Reliable introduction of critical assets: an explorative case study in railways
Authors: Moerman Jan-jaap , Braaksma Jan , van Dongen Leo 
Published: June 2021

PurposeAsset-intensive organizations rely heavily on physical assets that are often expensive, complex and have a significant impact on organizational performance. Past introductions of critical assets in various industries showed that despite many preparations in maintenance and operations, shortcomings were identified after deployment resulting in unreliable performance. The main purpose of this qualitative study is to explore the factors that determine how asset-intensive organizations can achieve reliable outcomes in critical asset introductions despite random failures as a result of increasing complexity and infant mortalities.Design/methodology/approachTo gain a detailed understanding of the issues and challenges of critical asset introductions, a case study in railways (rolling stock introductions) was conducted and analyzed using qualitative analysis.FindingsThe case showed that organizational factors were perceived as decisive factors for a reliable performance of the introduction, while the main focus of the introduction was on the asset and its technical systems. This suggests that more consideration toward organizational factors is needed. Therefore, a critical asset introduction framework was proposed based on 15 identified factors.Originality/valueReliable performance is often associated with technical systems only. This empirical study emphasizes the need for a more holistic perspective and the inclusion of organizational factors when introducing critical assets seeking reliable performance. This study demonstrated the application of the affinity diagramming technique in collectively analyzing the data adopting a multidisciplinary orientation.
Exploring the usability of the andragogical process model for learning for designing, delivering and evaluating a workplace communication partner training
Authors: Tessier Alexandra , Croteau Claire , Voyer Brigitte 
Published: June 2021

PurposeThis study aims to explore the usability of the andragogical process model for learning to develop, deliver and evaluate training to improve communication between adapted transport drivers and people living with communication disabilities and to identify the successes and limitations of the model in this context.Design/methodology/approachTwo aspects were considered to explore the usability of the andragogical process model for learning: a comparison between the elements of the model and the designing, delivering and evaluating processes of the training; and an appreciation evaluation.FindingsThe model was useful to systematically design, deliver and evaluate workplace training that was appreciated by the learners, even though most of the model’s elements were modified to meet the constraints of the trainer and the organization. Assessing the needs for learning, establishing a human climate conducive to learning and choosing appropriate training methods emerged as key elements that contributed to a successful appreciation of this training.Originality/valueThis study is one of the few that examines the possibility of a systematic application of the andragogical process model for learning to workplace training. Its results suggest that the model could be considered for application by non-professional trainers or external trainers from a workplace, but that organizational constraints must be considered when using it.