bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of theBorreliaceaePangenome Reveals a Conserved Genomic Archictecture Across Phylogenetic Scales
Authors: Lemieux Jacob E. 
Published: January 2024

AbstractThe FamilyBorreliaceaecontains arthropod-borne spirochetes that cause two widespread human diseases, Lyme disease (LD) and relapsing fever (RF). LD is a subacute, progressive illness with variable stage and tissue manifestations. RF is an acute febrile illness with prominent bacteremia that may recur and disseminate, particularly to the nervous system. Clinical heterogeneity is a hallmark of both diseases. While human clinical manifestations are influenced by a wide variety of factors, including immune status and host genetic susceptibility, there is evidence thatBorreliaceaemicrobial factors influence the clinical manifestations of human disease caused by this Family of spirochetes. Despite these associations, the spirochete genes that influence the severity and manifestations of human disease are, for the most part, unknown. Recent work has identified lineage-specific expansions of lipoproteome-rich accessory genome elements in virulent clones ofB. burgdorferi. Using publicly available genome assemblies, I show here that allBorreliaceaelineages for which sufficient sequence data is available harbor a similar pattern of strongly structured, lineage-specific expansions in their accessory genome, particularly among lipoproteins, and that this pattern holds across phylogenetic scales including genera, species, and genotypes. The relationships among pangenome elements suggest that infrequent episodes of marked genomic change followed by clonal expansion in geographically and enzootically structured populations may account for the unique lineage structure ofBorreliaceae. This analysis informs future genotype-phenotype studies amongBorreliaceaeand lays a foundation for studies of individual gene function guided by phylogenetic patterns of conservation, diversification, gain, and/or loss.
TDP-43 pathology links innate and adaptive immunity in amyotrophic lateral sclerosis
Authors: Evangelista Baggio A. , Ragusa Joey V. , Pellegrino Kyle , Wu Yija , Quiroga-Barber Ivana Yoseli , Cahalan Shannon R. , Arooji Omeed K. , Madren Jillann A. , Schroeter Sally , Cozzarin Joe , Xie Ling , Chen Xian , White Kristen K. , Ezzell J. Ashley , Iannone Marie A. , Cohen Sarah , Traub Rebecca E. , Li Xiaoyan , Bedlack Richard , Phanstiel Douglas H. , Meeker Rick , Stanley Natalie , Cohen Todd J. 
Published: January 2024

AbstractAmyotrophic lateral sclerosis is the most common fatal motor neuron disease. Approximately 90% of ALS patients exhibit pathology of the master RNA regulator, Transactive Response DNA Binding protein (TDP-43). Despite the prevalence TDP-43 pathology in ALS motor neurons, recent findings suggest immune dysfunction is a determinant of disease progression in patients. Whether TDP-43 pathology elicits disease-modifying immune responses in ALS remains underexplored. In this study, we demonstrate that TDP-43 pathology is internalized by antigen presenting cells, causes vesicle rupture, and leads to innate and adaptive immune cell activation. Using a multiplex imaging platform, we observed interactions between innate and adaptive immune cells near TDP-43 pathological lesions in ALS brain. We used a mass cytometry-based whole-blood stimulation assay to provide evidence that ALS patient peripheral immune cells exhibit responses to TDP-43 aggregates. Taken together, this study provides a novel link between TDP-43 pathology and ALS immune dysfunction, and further highlights the translational and diagnostic implications of monitoring and manipulating the ALS immune response.
Modeling Combination Chemo-Immunotherapy for Heterogeneous Tumors
Authors: Chen Shaoqing , Hu Zheng , Zhou Da 
Published: January 2024

AbstractHypermutable cancers create opportunities for the development of various immunotherapies, such as immune checkpoint blockade (ICB) therapy. However, emergent studies have revealed that many hypermutated tumors have poor prognosis due to heterogeneous tumor antigen landscapes, yet the underlying mechanisms remain poorly understood. To address this issue, we developed mathematical models to explore the impact of combining chemotherapy and ICB therapy on heterogeneous tumors. Our results uncover how chemotherapy reduces antigenic heterogeneity, creating improved immunological conditions within tumors, which, in turn, enhances the therapeutic effect when combined with ICB. Furthermore, our results show that the recovery of the immune system after chemotherapy is crucial for enhancing the response to chemo-ICB combination therapy.Author summaryThe challenge posed by intratumoral heterogeneity is gaining recognition in the field of cancer treatment. Despite the success of immune checkpoint blockade (ICB) therapies in enhancing overall survival across various cancer types, the complexity of therapeutic responses persists due to the heterogeneity of tumor antigens. In this study, we developed mathematical models to explore the evolutionary dynamics of tumors with both homogeneous and heterogeneous antigen landscapes. Our analysis reveals that tumors with heterogeneity exhibit resistance to ICB therapy, unlike their homogeneous counterparts which respond positively. Additionally, our models demonstrate that early treatment of heterogeneous tumors with chemotherapy leads to significant remission but also rapid recurrence. Notably, we identified a fascinating trade-off associated with chemotherapy—while suppressing the immune system, it creates a tumor immunological environment that becomes more conducive to ICB therapy. Finally, our modeling highlights the augmented response observed in tumors subjected to a chemo-ICB combination and shows the crucial role of immune recovery in the context of combination therapy.
Maturation and conformational switching of a de novo designed phase-separating polypeptide
Authors: Hilditch Alexander T. , Romanyuk Andrey , Hodgson Lorna R. , Mantell Judith , Neal Chris R. , Verkade Paul , Obexer Richard , Serpell Louise C. , McManus Jennifer J. , Woolfson Derek N. 
Published: January 2024

ABSTRACTCellular compartments formed by biomolecular condensation are a widespread feature of cell biology. These organelle-like assemblies compartmentalize macromolecules dynamically within the crowded intracellular environment. However, the intermolecular interactions that produce condensed droplets may also create arrested states and potentially pathological assemblies such as fibers, aggregates, and gels, through droplet maturation. Protein liquid-liquid phase separation is a metastable process, so maturation may be an intrinsic property of phase-separating proteins, where nucleation of different phases or states arise in supersaturated condensates. Here, we describe the formation of both phase-separated droplets and proteinaceous fibers driven by a de novo designed polypeptide. We characterize the formation of supramolecular fibers in vitro and in bacterial cells. We show that client proteins can be targeted to the fibers in cells using the droplet-forming construct. Finally, we explore the interplay between phase separation and fiber formation of the de novo polypeptide, showing that the droplets mature with a post-translational switch to largely β conformations, analogous to models of pathological phase separation.
Thermodynamic Characterization of LC3/GABARAP Ligands by Isothermal Titration Calorimetry
Authors: Dopfer Johannes , Schwalm Martin P. , Knapp Stefan , Rogov Vladimir V. 
Published: January 2024

AbstractIsothermal titration calorimetry (ITC) is a widely used technique for the characterization of protein-protein and protein-ligand interactions. It provides information on the stoichiometry, affinity, and the thermodynamic driving forces of interactions. This chapter exemplifies the use of ITC to investigate interactions between human autophagy modifiers (LC3/GABARAP proteins) and their interaction partners, the LIR motif containing sequences. The purpose of this report is to present a detailed protocol for the production of LC3/GABARAP-interacting LIR peptides usingE. coliexpression systems. In addition, we outline the design of ITC experiments using the LC3/GABARAP:peptide interactions as an example. Comprehensive troubleshooting notes are provided to facilitate the adaptation of these protocols to different ligand-receptor systems. The methodology outlined for studying protein-ligand interactions will help to avoid common errors and misinterpretations of experimental results.
What’s in a name (political risk)? A review of political risk and foreign investment decisions
Authors: DeGhetto Kaitlyn 
Published: January 2024

PurposeThere is an extensive research stream devoted to evaluating host country political risk as it relates to foreign investment decisions, and in today’s geopolitical climate, this type of risk is becoming increasingly salient to business leaders. Despite notable advancements related to understanding the importance of government-related risk, inconsistent conceptualizations and findings remain. Thus, the purpose of this paper is to offer a comprehensive overview of how host country political risk has been conceptualized, measured and studied in relation to multinational enterprises' (MNEs’) investment decisions. After reviewing the relevant literature, five major aspects of non-violent (government type, public corruption, leadership change) and violent (armed conflict, terrorism) political risk were identified. The organization and review of each aspect of political risk provide insights on fruitful directions for future research, which are discussed.Design/methodology/approachTo identify research articles on political risk and foreign investment, 13 leading management and international business journals were searched using relevant keywords (January 2000 to January 2023). Moreover, reviewing articles from these journals led to locating and reviewing additional relevant articles that the authors cited. Keyword searches were also conducted on Google Scholar and Web of Science in an effort to identify relevant articles outside of the 13 targeted journals.FindingsBoth violent and non-violent aspects of host country political risk have been studied in relation to MNEs' investment decisions. Specifically, five major aspects of host country political risk were identified (government type, public corruption, leadership change, armed conflict and terrorism). Although the general consensus is that risk related to the government often creates obstacles for MNEs, conceptualizations, measures and findings in prior research are not uniform.Originality/valueThis paper provides a comprehensive overview of host country political risk and foreign investment. In doing so, the aspects of political risk are identified, organized and overviewed.
Enterprise education in undergraduate business programmes advances students' negotiating competence and self-confidence
Authors: Enstroem Rickard , Benson Lyle 
Published: January 2024

PurposeBusiness graduates’ enterprising capability augments their work readiness, transforming them into professionals capable of driving successful outcomes. At the core lie self-confidence and negotiating competence. However, embedding enterprise education and developing assessments to evidence learning is challenging. This study aims to offer a blueprint for establishing enterprise learning in the classroom and investigating the effectiveness of cultivating negotiating competence and self-confidence.Design/methodology/approachModelled on Kolb’s experiential learning cycle, students engage in in-class and real-life negotiations, assessing self-confidence using a scale founded in Bandura’s self-efficacy theory. Open-ended reflections are also submitted. Quantitative data is analysed through multiple linear regression, while quantitative and qualitative data triangulation substantiates enterprise learning in negotiating competence and self-confidence.FindingsStudents’ reflections show that low self-confidence poses an initial barrier in negotiations, overcome with successive engagements. Quantitative analysis uncovers response-shift biases, with female and male students overestimating initial self-confidence levels. The gender and difference score type interaction reveals a more pronounced bias among female students starting from a lower baseline than male students, implying a more substantial self-confidence improvement for female students. These findings challenge traditional assumptions about gender differences in negotiations and emphasize the need for nuanced perspectives.Originality/valueEnterprising capability is pivotal for business professionals. This study highlights the advancement of negotiating competence and self-confidence. It contributes uniquely to the development of enterprise education pedagogy. Focusing on nuanced gender differences challenges prevailing assumptions, providing a perspective to the discourse on negotiating competence and self-confidence in management training.
Livelihood vulnerability of Borana pastoralists to climate change and variability in Southern Ethiopia
Authors: Gatew Shetie , Guyo Nura 
Published: January 2024

Purpose
The purpose of this study results and recommendations will have a paramount significance for policymakers, policy advocates, development planners and practitioners who may be in need of such information for reconsideration, evaluation and inclusion into their respective development and humanitarian programming and operational strategies. Above all, the study result has further provided the local community with viable adaptation strategies to climate-induced changes in the study area.

Design/methodology/approach
This study was conducted to measure the livelihood vulnerability of Borana pastoralists to climate change and variability in southern Ethiopia. Pastoralists’ households were sampled using multistage sampling techniques. A total of 27 socio-economic and biophysical indicators were used to reflect vulnerability components: adaptive capacity, exposure and sensitivity. Principal component analysis was used to develop weights for indicators and to produce livelihood vulnerability index to classify households according to their level of vulnerability. Ordinal logistic regression was used to identify the determinants of vulnerability to climate-induced stresses.

Findings
The results showed that 24.4% of households were highly vulnerable, 60.3% were moderately vulnerable and 15.3% of households were less vulnerable to climate-induced stresses. Factor estimates of the logistic model further revealed that early warning information, bush encroachment, coping strategy, temperature, drought frequency, provision of humanitarian services and food shortage during the normal season of the year have a significant influence on vulnerability in the study area.

Social implications
The study’s results and recommendations will be of great significance to policymakers, development planners, and practitioners who require such information for reconsideration, evaluation, and inclusion in their respective development and humanitarian program and operational strategies. Most importantly, the study’s findings have provided the local community with practical adaptation strategies to climate-induced changes in the study area.

Originality/value
The study explored pastoralist perception of climate change and variability and measured the livelihood vulnerability of pastoralists’ households to climate change and variability and finally investigated viable adaptation and coping strategies in the study area.
Web-based visualization and rendering of aerial LiDAR point cloud for urban flood simulation
Authors: Saifi Sanjay , Anandakumar Ramiya M. 
Published: January 2024

Purpose
In an era overshadowed by the alarming consequences of climate change and the escalating peril of recurring floods for communities worldwide, the significance of proficient disaster risk management has reached unprecedented levels. The successful implementation of disaster risk management necessitates the ability to make informed decisions. To this end, the utilization of three-dimensional (3D) visualization and Web-based rendering offers decision-makers the opportunity to engage with interactive data representations. This study aims to focus on Thiruvananthapuram, India, where the analysis of flooding caused by the Karamana River aims to furnish valuable insights for facilitating well-informed decision-making in the realm of disaster management.

Design/methodology/approach
This work introduces a systematic procedure for evaluating the influence of flooding on 3D building models through the utilization of Web-based visualization and rendering techniques. To ensure precision, aerial light detection and ranging (LiDAR) data is used to generate accurate 3D building models in CityGML format, adhering to the standards set by the Open Geospatial Consortium. By using one-meter digital elevation models derived from LiDAR data, flood simulations are conducted to analyze flow patterns at different discharge levels. The integration of 3D building maps with geographic information system (GIS)-based vector maps and a flood risk map enables the assessment of the extent of inundation. To facilitate visualization and querying tasks, a Web-based graphical user interface (GUI) is developed.

Findings
The efficiency of comprehensive 3D building maps in evaluating flood consequences in Thiruvananthapuram has been established by the research. By merging with GIS-based vector maps and a flood risk map, it becomes possible to scrutinize the extent of inundation and the affected structures. Furthermore, the Web-based GUI facilitates interactive data exploration, visualization and querying, thereby assisting in decision-making.

Originality/value
The study introduces an innovative approach that merges LiDAR data, 3D building mapping, flood simulation and Web-based visualization, which can be advantageous for decision-makers in disaster risk management and may have practical use in various regions and urban areas.
Intersectional entrepreneurship: the burden of contextual embeddedness beyond the business
Authors: Yamamura Sakura , Lassalle Paul 
Published: January 2024

PurposeThis paper aims to shed new light on the contextual embeddedness of intersectional entrepreneurs, i.e. entrepreneurs situated at the intersection of multiple marginalized diversity attributes, beyond simply business strategies and decisions. Taking an emic perspective on everyday practices as intersectional entrepreneurs, it uncovers neglected dimensions of the contextuality of intersectional discriminations.Design/methodology/approachThe study presents qualitative data analysis results of in-depth narrative interviews with six intersectional entrepreneurs, all LGBTIQA* entrepreneurs with further diversity dimensions. It provides an emic view of intersectional entrepreneurs, in their everyday lives and the contexts, in which they develop their businesses.FindingsIntersectional entrepreneurs face different burdens induced by social structures along the entrepreneurial process. While access to the niche market is more difficult and they lack community support, their realization of intersectional discrimination is crucial for the development of business strategies. Simultaneously, intersectional entrepreneurs use their specific diversity attributes to develop their business, yet this proximity of their identity and the business contents has severe consequences for their mental state. Intersectional entrepreneurs adjust to the balance of opportunity and vulnerability.Originality/valueAs intersectional entrepreneurs are barred from conventional institutional support and also have limited access to resources from their respective social networks, there is an urgency to provide specific support for such entrepreneurs.
Achieving professional qualifications using micro-credentials: a case of small packages and big challenges in higher education
Authors: Raj Rohit , Singh Arpit , Kumar Vimal , Verma Pratima 
Published: January 2024

PurposeThis study examined the factors impeding the implementation of micro-credentials and accepting it as a credible source of earning professional qualifications and certifications necessary for pursuing higher education or other career goals.Design/methodology/approachThe factors were identified by reflecting on the recent literature and Internet resources coupled with in-depth brainstorming with experts in the field of micro-credentials including educators, learners and employers. Two ranking methods, namely Preference Ranking for Organization Method for Enrichment Evaluation (PROMETHEE) and multi-objective optimization based on ratio analysis (MOORA), are used together to rank the major challenges.FindingsThe results of this study present that lack of clear definitions, ambiguous course descriptions, lack of accreditation and quality assurance, unclear remuneration policies, lack of coordination between learning hours and learning outcomes, the inadequate volume of learning, and lack of acceptance by individuals and organizations are the top-ranked and the most significant barriers in the implementation of micro-credentials.Research limitations/implicationsThe findings can be used by educational institutions, organizations and policymakers to better understand the issues and develop strategies to address them, making micro-credentials a more recognized form of education and qualifications.Originality/valueThe novelty of this study is to identify the primary factors influencing the implementation of micro-credentials from the educators', students' and employers' perspectives and to prioritize those using ranking methods such as PROMETHEE and MOORA.
Antecedents of internal reputation and its consequences on organizational outcomes: a systematic review
Authors: Lee Ling Hooi , Abdullah Zulhamri 
Published: January 2024

PurposeOrganizational reputation has come to the forefront amidst today’s increasingly competitive business environment. While the perspectives of external stakeholders continue to generate research attention among reputation scholars, perceptions of internal stakeholders like employees deserve similar or more focus due to their ability to sway external organizational reputation. Thoroughly understanding organizational variables that precede internal reputation perceptions among employees and the ensuing consequences enables effective reputation management measures. This study aims to develop a comprehensive framework that outlines the antecedents and consequences of the internal reputation concept.Design/methodology/approachThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 review protocol was applied. Around 24 journal articles were drawn from the Web of Science and Scopus databases and analyzed using qualitative content analysis.FindingsThe review revealed 31 constructs related to the internal reputation concept, which were categorized into seven main themes, and a comprehensive framework was developed. Future research recommendations include the need to expand the study’s parameters, adopt a different research method and target varied contexts to achieve a more exhaustive systematic literature review on internal reputation.Research limitations/implicationsThis study attempts to contribute to the understanding of the internal reputation concept, theories and reputation management practices through its findings.Originality/valueThis paper provides the first known systematic literature review of the internal reputation concept, which could provide practical guidance to professionals in internal reputation management and academic guidance for future research in internal reputation.