bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep mutationally scanned (DMS) CHIKV E3/E2 virus library maps viral amino acid preferences and predicts viral escape mutants of neutralizing CHIKV antibodies
Authors: Stumpf Megan M. , Brunetti Tonya , Davenport Bennett J. , McCarthy Mary K. , Morrison Thomas E. 
Published: December 2024

ABSTRACTAs outbreaks of chikungunya virus (CHIKV), a mosquito-borne alphavirus, continue to present public health challenges, additional research is needed to generate protective and safe vaccines and effective therapeutics. Prior research has established a role for antibodies in mediating protection against CHIKV infection, and the early appearance of CHIKV-specific IgG or IgG neutralizing antibodies protects against progression to chronic CHIKV disease in humans. However, the importance of epitope specificity for these protective antibodies and how skewed responses contribute to development of acute and chronic CHIKV-associated joint disease remains poorly understood. Here, we describe the deep mutational scanning of one of the dominant targets of neutralizing antibodies during CHIKV infection, the E3/E2 (also known as p62) glycoprotein complex, to simultaneously test thousands of p62 mutants against selective pressures of interest in a high throughput manner. Characterization of the virus library revealed achievement of high diversity while also selecting out non-functional virus variants. Furthermore, this study provides evidence that this virus library system can comprehensively map sites critical for the neutralization function of antibodies of both known and unknown p62 domain specificities.IMPORTANCEChikungunya virus (CHIKV) is a mosquito-borne alphavirus and re-emerging pathogen of global health concern that causes fever and debilitating acute and chronic joint pain. Prior studies established a critical role for antibodies in protection against CHIKV infection, however, the importance of different antibody epitopes engaged on the virus for these functions is poorly understood. Here, we describe the generation of a high-throughput, functional virus library capable of simultaneously identifying critical neutralization sites for multiple antibodies. We find that, through generation of the virus library, the plasticity of the viral glycoproteins tested varied by subdomains. Additionally, our study revealed new sites in the major CHIKV surface glycoprotein important for neutralization by previously proposed therapeutic monoclonal antibodies. Overall, this study describes a new tool that can be used to better understand antibody responses associated with distinct CHIKV infection outcomes and could contribute to the development of efficacious vaccines and antibody-based therapeutics.
Characterization ofSalmonella typhifrom Shallow Well Water in Sogomo, Eldoret, Kenya and its Antimicrobial Sensitivity toMoringa oleiferaSeed Extract
Authors: Joy Cheronoh , Rono Salinah , Emily Jelimo , Ramadhan Luvandale , Francis Kalule 
Published: December 2024

AbstractSalmonella typhiis a gram negative, rod-shaped bacterium that cause typhoid fever disease, a significant cause of human mortality especially in the developing countries. This illness occurs after ingestion ofSalmonella typhibacteria in contaminated water or food. This study aimed to isolate and identifySalmonella typhifrom shallow well waters and assess its sensitivity toMoringa oleiferaseed extract. Twelve wells were sampled randomly, and samples collected. 10mls of each sample were measured and put in twelve different sterile test tubes. Dilutions were done serially by diluting 1 ml of each sample in tubes having 9mls of distilled water. This was labelled 10-1 dilution. Further dilutions were done to dilution factor of 10-3. Inoculation was done inSalmonella Shigellaagar (SSA) and incubation done at 35 C for 24 hours. Re-inoculation was done in SSA by streaking to obtain pure isolates. These pure isolates were confirmed by biochemical tests (catalase, methyl red and Triple Sugar Iron tests). Anti-microbial sensitivity test was performed usingMoringa oleiferaseed extract and ofloxacin and norfloxacin drugs of antibiotic disc were used as positive and negative controls respectively. Poor method of human waste disposal, condition of sewage systems and inaccurate water treatment methods associate to well water contamination bySalmonella typhiand thus transmission. Results showed that 3 out of 12 water samples tested positive forSalmonella typhi. This gave a rate of 25% contamination of shallow wells in Sogomo by this bacterium. The bacterium was sensitive toMoringa oleiferaseed extract, with sensitivity increasing with higher extract concentrations. The results of the measurements of zones of inhibition were represented using graphs. The study highlights the need for public health education among the residents of Sogomo on proper sewage management, waste disposal and water treatment to prevent contamination.
An Atlas of Cellular Archetypes
Authors: Crowley George , Alon Uri , Quake Stephen R. 
Published: December 2024

AbstractSingle cell RNA sequencing allows effective characterization of cell types and cell states. Cell types can be reliably identified as defined clusters via marker gene expression and differential expression analysis. However, once a cell type is identified, current analysis methods provide little information about the potential variety of functions within the cell type. Here, we apply a principled computational approach to understand the functional heterogeneity within a given cell type. It has been hypothesized that cells in competitive environments will conform to Pareto task optimality theory by organizing in low-dimensional polytopes in gene expression space, and that specialist phenotypes identified via Pareto Task Inference Analysis would be reproducible and general. We used the Tabula Sapiens atlas of single-cell RNA sequencing across cell types and tissues in the human body to test this hypothesis and discovered that most cell types are well-fit by this theory. Furthermore, we derived specialist phenotypes from this method, which were used to identify archetypes of cellular function that represent essential biological tasks. We compared the specialist phenotypes from common cell types shared across tissues and found consistent results. These phenotypes are derived from an unbiased approach and do not incorporate ideas from existing biological models or theories, and yet in many cases they recapitulate our understanding of the functions of major cell types. Taken together, these results suggest a principled approach to annotating the continuum of functions within each cell type.
Hyperballistic intercellular signaling through growth assisted positive feedback
Authors: Wang Meidi , González Louis , Saha Soutick , Josić Krešimir , Mugler Andrew , Bennett Matthew R. 
Published: December 2024

AbstractIntercellular signaling in bacteria is often mediated by small molecules secreted by cells. These small molecules disperse via diffusion which limits the speed and spatial extent of information transfer in spatially extended systems. Theory shows that a secondary signal and feedback circuits can speed up the flow of information and allow it to travel further. Here, we construct and test several synthetic circuits inEscherichia colito determine to what extent a secondary signal and feedback can improve signal propagation in bacterial systems. We find that positive feedback-regulated secondary signals propagate further and faster than diffusion-limited signals. Additionally, the speed at which the signal propagates can accelerate in time, provided the density of the cells within the system increases. These findings provide the foundation for creating fast, long-range signal propagation circuits in spatially extended bacterial systems.
Semi-Dirac Fermions in a Topological Metal
Authors: Shao Yinming , Moon Seongphill , Rudenko A. N. , Wang Jie , Herzog-Arbeitman Jonah , Ozerov Mykhaylo , Graf David , Sun Zhiyuan , Queiroz Raquel , Lee Seng Huat , Zhu Yanglin , Mao Zhiqiang , Katsnelson M. I. , Bernevig B. Andrei , Smirnov Dmitry , Millis Andrew J. , Basov D. N. 
Published: December 2024

Topological semimetals with massless Dirac and Weyl fermions represent the forefront of quantum materials research. In two dimensions, a peculiar class of fermions that are massless in one direction and massive in the perpendicular direction was predicted 16 years ago. These highly exotic quasiparticles—the semi-Dirac fermions—ignited intense theoretical and experimental interest but remain undetected. Using magneto-optical spectroscopy, we demonstrate the defining feature of semi-Dirac fermions—B2/3 scaling of Landau levels—in a prototypical nodal-line metal ZrSiS. In topological metals, including ZrSiS, nodal lines extend the band degeneracies from isolated points to lines, loops, or even chains in the momentum space. With calculations and theoretical modeling, we pinpoint the observed semi-Dirac spectrum to the crossing points of nodal lines in ZrSiS. Crossing nodal lines exhibit a continuum absorption spectrum but with singularities that scale as B2/3 at the crossing. Our work sheds light on the hidden quasiparticles emerging from the intricate topology of crossing nodal lines and highlights the potential to explore quantum geometry with linear optical responses.

Published by the American Physical Society
2024
Librarians’ perceptions and use of open access resources for economic sustainability in selected university libraries in Kwara State, Nigeria
Authors: Adeyemi Ismail Olatunji , Adeleke Quareebat Ayomide , Abdullahi Shamsudeen Aweda , Abdulazeez Robiat Gambari , Abdulazeez Monsuru Damilare , Abdulazeez Abubakar Folorunsho 
Published: December 2024

Purpose
Open access (OA) resources are free to access and help in research and teaching/learning, allowing libraries to manage resources more sustainably and effectively. Hence, this study aims to examine use of OA resources for economic sustainability among librarians in selected university libraries in Kwara State, Nigeria.

Design/methodology/approach
This study adopts descriptive survey research design. Using total enumeration sampling technique, a sample of 46 professional librarians were drawn from the selected universities. Questionnaire was used for data collection, and descriptive statistics was used for data analysis.

Findings
The findings show that most of the librarians had high level of awareness about OA resources. Results demonstrate that majority of the librarians used PubMed Central bi-weekly. Findings show that the librarians used OA resources to support academic research, enhance library’s collection without additional cost and facilitate information access for users with limited financial resources. Results indicate that most of the librarians perceived that OA resources impact library’s operational cost and goal of economic sustainability.

Practical implications
This study highlights the need for targeted training and resource development to enhance the effective use of OA resources. Meanwhile, the consistent usage of OA resources suggests the importance of the resources to librarians, aligning with previous studies on frequent use of established OA repositories.

Originality/value
This study provides evidence on the relevance and impact of OA resources use on economic sustainability, demonstrating the importance of OA resources in knowledge dissemination and fostering innovation.
The interpretation of China’s economic
modernization from the broad Marxist political economy
Authors: Xiang Guocheng , Liu Jingjing , Yang Yuxuan 
Published: December 2024

Purpose
The modernization of China’s economy is an integral part of
Chinese-style modernization. According to the principle of unifying
theoretical, historical and practical logic, theoretically explaining the
modernization of China’s economy is both a political necessity and a
higher scientific requirement.

Design/methodology/approach
Following this evolutionary line – from modes of production to the
general economic development mechanism and then to patterns of economic
operation and development – this paper employs the principal
contradiction analysis method to offer an interpretation of China’s
economic modernization from the broad Marxist political economy
perspective.

Findings
In economic terms, “get organized” primarily refers to the
development and mutual promotion of team-based and market-based division of
labor organizations, as discussed by Karl Marx. “Get
organized” (specifically the development of team-based division of
labor organizations) acts as the engine of China’s economic
modernization and serves as the historical logical starting point. Division
of labor is the theoretical logical starting point for interpreting
China’s economic modernization. The two of them are congruent,
achieving the unity of theoretical and historical logic at the starting
point. The development and mutual promotion of these “two types of
division of labor” inherently generate the general mechanism of
economic development first comprehensively discussed by Marx and Friedrich
Engels, which involves the division of labor development and market
expansion accumulating cyclically and reinforcing each other. This mechanism
drives both the high-speed and high-quality development of China’s
economic modernization.

Originality/value
The broad Marxist political economy paradigm facilitates explaining
China’s economic modernization theoretically, historically and
practically with unified logic. “Get organized” serves as both
the engine and the realization mechanism of this modernization, with the
Communist Party of China (CPC) consistently being the core force of this
organizational effort.
Solution of fractional Sturm–Liouville problems by generalized polynomials
Authors: Sadiq Shazia , Rehman Mujeeb ur 
Published: December 2024

PurposeIn this article, we present the numerical solution of fractional Sturm-Liouville problems by using generalized shifted Chebyshev polynomials.Design/methodology/approachWe combine right Caputo and left Riemann–Liouville fractional differential operators for the construction of fractional Sturm–Liouville operators. The proposed algorithm is developed using operational integration matrices of generalized shifted Chebyshev polynomials. We introduce a new bound on the coefficients of the shifted. Chebyshev polynomials subsequently employed to establish an upper bound for error in the approximation of a function by shifted Chebyshev polynomials.FindingsWe have solved fractional initial value problems, terminal value problems and Sturm–Liouville problems by plotting graphs and comparing the results. We have presented the comparison of approximated solutions with existing results and exact numerical solutions. The presented numerical problems with satisfactory results show the applicability of the proposed method to produce an approximate solution with accuracy.Originality/valueThe presented method has been applied to a specific class of fractional differential equations, which involve fractional derivatives of a function with respect to some other function. Keeping this in mind, we have modified the classical Chebyshev polynomials so that they involve the same function with respect to which fractional differentiation is performed. This modification is of great help to analyze the newly introduced polynomials from analytical and numerical point of view. We have compared our numerical results with some other numerical methods in the literature and obtained better results.
Life cycle assessment applied to facility management of exposed steel frames – case study
Authors: Matos Raquel , Rodrigues Hugo , Costa Aníbal Guimarães , Rodrigues Maria Fernanda , Lavy Sarel , Dixit Manish 
Published: December 2024

Purpose
Facility management (FM) plays an important role in the attainment of a sustainable built environment during the building operational stage since it is responsible for decisions that influence materials’ durability, waste, cost reduction and energy efficiency. However, the integration of the life cycle assessment (LCA) approach in FM presents some difficulties in obtaining complete inventories for building components, tracking material flows and defining system boundaries. This paper aims to establish the environmental impact comparison between maintenance actions and replacement interventions performed during the life cycle of a steel frame from a building facade.

Design/methodology/approach
For this purpose, the effects of different repair/maintenance actions and end-of-life scenarios were analysed using two tools: an LCA building information modelling-based tool and an LCA open-source tool.

Findings
The results showed that repairing and maintaining the steel structure is essential for the safety and preservation of the steel structure. However, steel maintenance and repair practices that involve fewer environmental impacts need to be explored.

Social implications
It also emphasises the crucial role of facility managers in promoting sustainability and supporting informed decision-making throughout the building’s life cycle, thereby aiding in the pursuit of sustainable development and the goal of decarbonisation by 2050.

Originality/value
This study reveals that maintenance processes in building management have a greater environmental impact compared to material replacement activities, especially concerning the steel structure within the case study building, as assessed using two LCA software tools. The findings provide valuable insights into the environmental impacts of maintenance and replacement phases and underscore the need for further investigation into more sustainable maintenance practices within facility management. Additionally, the study raises public awareness and engagement in environmental responsibility, contributing positively to the achievement of a sustainable built environment.
Even climate change is not fair: the impact of climate change on economic outcomes
Authors: Tawiah Vincent , Alessa Noha 
Published: December 2024

Purpose
From generation to generation, the poor and less developed have always borne the negative consequences of the extravagant lifestyles of the rich. The climate seems to perpetuate this injustice by punishing the good people with the consequences of the irresponsible acts of the wealthy. Therefore, this paper aims to establish the relationship between climate risk and carbon emissions. Then, this paper investigates the economic consequences of climate risk in both developed and developing countries.

Design/methodology/approach
This paper uses robust econometrics, including fixed effect and the two-step system generalised method of moments, on a large sample of 175 countries from 2008 to 2019.

Findings
Unsurprisingly, this paper found that climate risks are negatively associated with carbon emissions, indicating that countries with lower emissions are more exposed to frequent and severe climate-related disasters than those with higher emissions. Additionally, this paper discovered that climate risk has a negative impact on economic development, which is more pronounced in developing countries. The results are robust to alternative measurement and econometric modelling, including the system-generalized method of moments.

Originality/value
These findings suggest that developing countries, the least contributors to climate change, unfairly suffer from the environmentally irresponsible actions of high-emitting developed countries.
Implementation and impact of makerspaces in Indian academic libraries: a study of select three academic libraries of North India
Authors: Sharma Kailash Chand , Shrivastava Rishabh 
Published: December 2024

Purpose
This study aims to examine the current state of makerspaces in Indian academic libraries. The history of makerspace and its introduction in academic libraries have been elaborated and analysed. Makerspaces of three different academic libraries in Northern India have been compared in the study.

Design/methodology/approach
The data was collected using a well-structured interview schedule as well as complemented from the website of the institutions in the study. Field visits to the makerspaces were also conducted for understanding how users are working in makerspaces and the different benefits they gained from such working environments. The different tools and facilities provided by the makerspaces were also analysed and it was found that a versatile group of users can easily collaborate with the help of such interactive and lively environment.

Findings
It was found that tools like 3D printers enhanced the benefits and enriched creativity amongst non-tech savvy users too, by giving them a chance of using such tools. Interaction between different groups of people belonging to different fields and having varied experiences and expertise was also reported to be an important aspect of makerspaces. These places also were found to support the “Do it Yourself” culture among youngsters using the libraries. The study concludes that makerspaces are innovative ways in which libraries can encourage more and more users towards the libraries.

Originality/value
To the best of the authors’ knowledge, this study is one of the first studies on makerspaces in academic libraries in context of a growing economy like India. Makerspaces can be significantly useful for proper space management and utilisation of resources for academic libraries.
Personality expression is shaped by the early experienced social context in predatory mites
Authors: Chiara Violette 
Published: December 2024

AbstractResearch Highlights: Schausberger, P., & Nguyen, T. H. (2024). Early social isolation disrupts adult personality expression in group‐living mites. Journal of Animal Ecology. https://doi.org/10.1111/1365‐2656.14169. Personality traits in animals have been of great interest in the last decades. The number of studies demonstrating the existence of personality in a wide range of taxa is growing rapidly. Although the effect of early experience on later average values of behavioural traits is well documented, very few articles demonstrate the effects of those factors on personality expression itself. One factor in particular received very little, if not no, attention: social isolation. Although social isolation is known to have major impacts on later animal behaviour, it is still unknown whether it may favour or inhibit personality expression. In a recent study, Schausberger and Nguyen (2024) demonstrated that early‐life social isolation had strong effects on adults of the predatory mite Phytoseiulus persimilis. They show for the first time that early social isolation decreased the expression of personality in the activity of adults when tested in a social context. Interestingly, they observed the opposite effect when the same mites were tested alone: previously isolated mites were highly repeatable but group‐reared mites were not. Finally, they also show an indirect effect of early social isolation through mating: mating with a male who experienced social isolation increased the behavioural repeatability of females. This study not only reinforces the established understanding of personality but also paves the way for future research in the field.