bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmentally Relevant Lead Exposure Alters Cell Morphology and Expression of Neural Hallmarks During SH-SY5Y Neuronal Differentiation
Authors: Morgan Rachel K. , Tapaswi Anagha , Polemi Katelyn M. , Miller Jenna L. , Sexton Jonathan , Bakulski Kelly M. , Svoboda Laurie K. , Dolinoy Dana C. , Colacino Justin A. 
Published: February 2025

AbstractLead (Pb) continues to be a public health burden, in the US and around the world, and yet the effects of historical and current exposure levels on neurogenesis are not fully understood. Here we examine the effects of a range of environmentally relevant Pb concentrations (0.16μM, 1.26μM, and 10μM Pb) relative to control on neural differentiation in the SH-SY5Y cell model. Pb exposure began on Day 5 and continued throughout differentiation at Day 18. We assessed morphological measures related to neurogenesis at several time points during this process, including the expression of proteins key in neural differentiation (β-tubulin III and GAP43), cell number and size, as well as the development of neurites. The bulk of detectable changes occurred with 10μM Pb exposure, most notably that of β-tubulin III and GAP43 expression. Effects with the 0.16μM and 1.26μM Pb exposure conditions increased as differentiation progressed, with significant reductions in cell and nuclear size as well as the number and length of neural projections by Day 18. Best benchmark concentration (BMC) analysis revealed many of these metrics to be susceptible to levels of Pb at or below historically relevant levels. This work highlights the disruption of neurite formation and protein expression as potential new mechanisms by which environmentally relevant Pb exposure impacts neurogenesis and morphology and perturb cognitive health throughout the life course.
AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network
Authors: Fadini Alisia , Li Minhuan , McCoy Airlie J. , Terwilliger Thomas C. , Read Randy J. , Hekstra Doeke , AlQuraishi Mohammed 
Published: February 2025

AbstractAdvances in machine learning have transformed structural biology, enabling swift and accurate prediction of protein structure from sequence. However, challenges persist in capturing sidechain packing, condition-dependent conformational dynamics, and biomolecular interactions, primarily due to scarcity of high-quality training data. Emerging techniques, including cryo-electron tomography (cryo-ET) and high-throughput crystallography, promise vast new sources of structural data, but translating raw experimental observations into mechanistically interpretable atomic models remains a key bottleneck. Here, we aim to address these challenges by improving the efficiency of structural analysis through combining experimental measurements with a landmark protein structure prediction method – AlphaFold2. We present an augmentation of AlphaFold2, ROCKET, that refines its predictions using cryo-EM, cryo-ET, and X-ray crystallography data, and demonstrate that this approach captures biologically important structural variation that AlphaFold2 does not. By performing structure optimization in the space of coevolutionary embeddings, rather than Cartesian coordinates, ROCKET automates difficult modeling tasks, such as flips of functional loops and domain rearrangements, that are beyond the scope of current state-of-the-art methods and, in some instances, even manual human modeling. The ability to efficiently sample these barrier-crossing rearrangements unlocks a new horizon for scalable and automated model building. Crucially, ROCKET does not require retraining of AlphaFold2 and is readily adaptable to multimers, ligand-cofolding, and other data modalities. Conversely, our differentiable crystallographic and cryo-EM target functions are capable of augmenting other structure prediction methods. ROCKET thus provides an extensible framework for the integration of experimental observables with biomolecular machine learning.
Knocking out histidine ammonia-lyase by using CRISPR-Cas9 abolishes histidine role in the bioenergetics and the life cycle ofTrypanosoma cruzi
Authors: de Freitas Nascimento Janaína , Barisón María Julia , Montanaro Gabriela Torres , Marchese Letícia , Oliveira Souza Rodolpho Ornitz , Silva Letícia Sophia , Guarnieri Alessandra Aparecida , Silber Ariel Mariano 
Published: February 2025

AbstractTrypanosoma cruzi,the causing agent of Chagas disease, is the only known trypanosomatid pathogenic to humans having a complete histidine to glutamate pathway, which involves a series of four enzymatic reactions that convert histidine into downstream metabolites, including urocanate, 4-imidazolone-5-propionate, N-formimino-L-glutamate and L-glutamate. Recent studies have highlighted the importance of this pathway in ATP production, redox balance, and the maintenance of cellular homeostasis inT. cruzi. In this work, we focus on the first step of the histidine degradation pathway, which is performed by the enzyme histidine ammonia lyase. Here we determined the kinetic and biochemical parameters of theT. cruzihistidine ammonia-lyase. By generating null mutants of this enzyme using CRISPR-Cas9 we observed that disruption of the first step of the histidine degradation pathway completely abolishes the capability of this parasite to metabolise histidine, compromising the use of this amino acid as an energy and carbon source. Additionally, we showed that the knockout of the histidine ammonia lyase affects metacyclogenesis when histidine is the only metabolizable source and diminishes trypomastigote infectionin vitro.
Mycobiome ofPinus pinastertrees naturally infected by the pinewood nematodeBursaphelenchus xylophilus
Authors: Vicente Cláudia S. L. , Varela Ana Rita , Vetrainno Anna , Espada Margarida , de Lurdes Inácio Maria 
Published: February 2025

ABSTRACTFungi are important biological elements in the Pine wilt disease (PWD) complex. In the late stages of the disease, the pinewood nematode (PWN)Bursaphelenchus xylophilusfeeds on the fungal flora available in the pine tree for survival and multiplication. Previous studies have confirmed a close relation between the PWN and blue-stain fungi (Ophiostomatales), which are necrotrophic pathogens associated with bark beetles (Coleoptera: Scolytidae). The PWN is able to grow densely in the presence of these fungi, which results in a higher number of nematodes transferred to the insect-vectorMonochamusspp. To understand the spatial diversity and structure ofPinus pinastermycobiome, wood samples from PWN-infected and non-infected pine trees were collected in three locations of Continental mainland Portugal with different PWD records, during the maturation phase of the insect-vectorM. galloprovincialis(winter 2019-spring 2020). The PWN-mycobiome from the PWN-infectedP. pinasterwas also characterized. A total of 27 samples ofP. pinasterand 13 samples of PWN from PWN-infected trees were characterized using ITS2 amplicon sequencing. The diversity and structure of the fungal communities inP. pinastervaried with disease status suggesting that the PWN presence affects the endophytic fungal communities. For bothP. pinasterand PWN fungal communities, differences were also associated with locations (recent PWD loci Seia, and long-term PWN locus Companhia das Lezírias and Tróia). Ophiostomatales were mainly detected in PWN-infectedP. pinaster. This research contributes to increase the knowledge on the ecology of the fungal communities in PWD complex.
Engineering Plasmids with Synthetic Origins of Replication
Authors: Liu Baiyang , Peng Xiao , Bennett Matthew R. , Lakin Matthew R. , Chappell James 
Published: February 2025

AbstractPlasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, the reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity. Here we refactor the natural pMB1 origin and create plasmids with customizable copy numbers by tuning refactored components. We then create compatible origins that use synthetic RNA regulators to implement independent copy control. We further demonstrate that the synthetic origin of replication (SynORI) can be engineered modularly to respond to various signals, allowing for multiplexed copy-based reporting of environmental signals. Lastly, a library of 6 orthogonal SynORI plasmids is created and co-maintained in E. coli for a week. This work establishes the feasibility of creating plasmids with SynORI that can serve as a new biotechnology for synthetic biology.
Collaborative governance based on Triple Helix strategy for disaster risk reduction digitalization: experience from China
Authors: Gong Yixuan , Singh Ravi , Mi Jianing 
Published: February 2025

PurposeCollaborative effort plays an important role in urban disaster risk reduction. The paper aims to explore how Shenzhen, China, has applied the Triple Helix strategy, integrating the efforts of government, industry and academia, to promote disaster risk reduction digitalization.Design/methodology/approachIn-depth interviews were conducted with a purposive sample of 18 key informants (5–7 interviews per stakeholder group), specifically focusing on developing the Smart Emergency Management System. One of the co-authors conducted participatory observation in Shenzhen to gain valuable insights into the origins of the disaster risk reduction digitalization efforts in Shenzhen.FindingsThe disaster risk reduction digitalization in Shenzhen was initiated based on the Triple Helix model. Specifically, collaborative efforts among policy-driven government, profit-driven industry and research interest-driven academia were taken to establish a digital system. As the project was implemented, citizens became increasingly involved through a new platform established by the government. The participation of citizens feeds back into the development of the disaster risk reduction system. The most important functions of digital projects are data sharing and sector connecting.Research limitations/implicationsIn a country like China with a large land area, discussions at the local level involve different geographical environments, population characteristics and even local cultures. Therefore, researchers are encouraged to discuss more cases in different cultural backgrounds further.Originality/valueThis paper fulfills a case to establish disaster risk reduction digitalization based on the Triple Helix strategy, serving as a practical example for other cities aiming to improve their digital management capacities, not limited to disaster, but other developments.
Capital raising at Tata Motors: what to choose?
Authors: Ghalke Avinash , Mathews Sajit M. 
Published: February 2025

Learning outcomes
After completion of the case study, students will be able to understand various capital raising instruments and their impact on different stakeholders; analyse the financials of a company to select a fitting instrument; and communicate the company’s decision effectively, paying attention to language and style.

Case overview/synopsis
This case study describes the funding choices available to Tata Motors Limited (TML), a major global automobile manufacturer based in India. Owing to a very high debt-to-equity ratio and very low debt service coverage ratio, the company urgently requires a fresh inflow of funds to bring its debt levels down and sustain growth. This financial state does not benefit the company in the short or the long run. TML has various options: Rights Issue, Qualified Institutional Placement, Preferential Allotment, Global Depository Shares and Follow-on Public Offering. Each mode has implications for individual stakeholders like the management, promoters, institutions with significant and minor stakes, and retail investors. The dilemma before TML is to choose the best capital-raising mode that suits the current requirements. This case study requires participants to choose an equity-raising mode that satisfies the stakeholders and communicate their decision tactfully to the general public.

Complexity/academic level
This case study is suitable for participants in a regular or executive MBA programme. It is designed to introduce the concepts of capital raising, the different instruments available for capital raising and the fundamentals of financial communication. This case study can be used in MBA courses like corporate finance, financial markets and business communication.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS1: Accounting and Finance.
Transition from emergency ICT-enabled education to blended education for future emergency preparedness and sustainability: a cross-sectional survey in Malaysia
Authors: Looi Kim Hoe 
Published: February 2025

PurposeThe COVID-19 pandemic has profoundly disrupted teaching and learning in higher education globally. The purposes of this study are to identify the demographics and contextual challenges of emergency ICT-enabled education related to the future preferred mode of education of instructors and suggest a transition from emergency ICT-enabled education to blended education for future emergency preparedness and sustainability.Design/methodology/approachThis quantitative, cross-sectional and correlational study administered an online survey using a structured questionnaire to collect data from 162 respondents during the closure of Malaysian higher education institutions due to the COVID-19 pandemic. Data were analysed using the Statistical Package for the Social Sciences.FindingsThis study found that 56% of the respondents preferred blended education in the future. Multiple discriminant analysis generated characteristic profiles of respondents who preferred conventional face-to-face education, online education and blended education in the future in terms of their demographic characteristics and salient contextual challenges.Research limitations/implicationsThis study is exploratory. The findings are not generalisable and the contextual challenges of emergency ICT-enabled education may evolve over time.Originality/valueThis study extends the existing literature by highlighting future preferred modes of education of instructors and suggests a resilience pedagogy of blended education for future emergency preparedness and sustainability.
Using a community of practice perspective to analyze MTE learning during lesson study
Authors: Appelgate Mollie , Dick Lara , Gupta Dittika , Soto Melissa Marie , Broderick Shawn 
Published: February 2025

PurposeThis research investigated how lesson study (LS) served as mathematics teacher educators’ (MTEs’) professional development. Using Wenger’s (1998) social theory of learning (STL) framework based on communities of practice (CoP), the authors demonstrate how MTEs’ learning evolved throughout the LS process.Design/methodology/approachThe four dimensions of Wenger’s (1998) STL (learning as belonging, learning as experience, learning as doing and learning as becoming) were used to systematically code MTEs’ written reflections across the phases of LS. A Pearson chi-squared test for association was run to determine significant relationships between phases of LS and the dimensions of MTE learning.FindingsMTEs’ learning varied across the phases of LS. Learning as belonging was significant in the initial planning and implementation cycle phases. Learning as experience was significant during the initial planning and final reflection phases. Learning as becoming was significant in the implementation cycle phase.Research limitations/implicationsThis study was limited to a group of five early-career MTEs who engaged in a modified LS process, which limits the scope of the findings.Practical implicationsUnderstanding how teachers learn through engagement in LS can provide insight into how to impact teacher learning.Originality/valueIt has been posited that one means of participant learning from LS is through the development of CoP. This paper explicitly considers the role of the evolving CoP by adopting Wenger’s (1998) STL as both theoretical grounding and an analytical approach to studying learning as members of a CoP engage in LS.
Coaching for secondary school adolescents: a systematic literature review
Authors: Celaya Iñaki , Cueto José Alejandro , Balaguer Alvaro , Ugarte Carolina 
Published: February 2025

PurposeRecent research suggests that coaching in educational contexts plays a significant role in positive youth development. However, there is a scarcity of reviews investigating the impact of coaching on adolescents. Therefore, a systematic literature review was conducted to identify the coaching interventions developed in secondary schools, analyze how they propose the intervention process and what dimensions of positive youth development they improve.Design/methodology/approachThe systematic literature review method was applied to a sample of publications indexed in the Web of Science and Scopus databases, with no date restrictions, in English or Spanish, and applied to secondary school students.FindingsAbout 28 publications were included with precise information on the uses, areas of application and effects of coaching on students. About 45 dimensions were found, which were classified into five areas of positive youth development: personal, social, emotional, cognitive and moral. In all areas, there were dimensions with significant results due to the intervention, but this depended on the duration and type of application: individual, group or mixed. The dimensions most developed in the interventions were well-being, interpersonal relationships, conflict resolution, perceived competence and motivation.Originality/valueA positive youth development model was used to gain a better understanding of the coaching intervention improvements. Some recommendations are provided to improve the implementation of educational coaching interventions targeting coaches and educational professionals as well as for future systematic literature reviews.
Empowerment of women and its determinants in India: a state level analysis with NFHS-5 data
Authors: Mukhopadhyay Debabrata 
Published: February 2025

PurposeThis study examines the status of women’s empowerment and its socio-economic determinants based on living conditions across 22 Indian states and Union Territories by constructing a composite women empowerment index of six components including women participation in three household decisions(%) based on data from the National Family Health Survey(NFHS)-5, Phase I.Design/methodology/approachWe carry out a principal component analysis (PCA) for constructing a women empowerment index based on the above six indicators using a correlation matrix. Then we apply a static panel data approach to find out the role of socio-economic determinants such as per capita income (State level per capita GDP), years of schooling, the underage marriage of girls, the standard of living conditions such as access to safe drinking water, sanitization facility, use of iodized salt, etc.FindingsThe constructed composite index based on PCA determines one composite index for each time period, that is 2015–2016 and 2019–2020. The static panel regression is run for the composite index and six components of the index. The regression results considering eight socioeconomic and living conditions parameters demonstrate that the variables like the use of clean fuel cooking, the underage marriage of women, access to improved sanitation facility have an important impact in explaining variations in women empowerment over the years.Originality/valueThe major observations of this study in understanding the status and determinants of women empowerment across Indian states clearly show that women education is the key to improving women empowerment apart from several living condition variables.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-01-2023-0015
How do LGBTQ+ library catalog users talk about subject searching?
Authors: Moulaison-Sandy Heather , Dobreski Brian , Snow Karen 
Published: February 2025

PurposeSubject searching in the library catalog is a challenge for any user, but may be especially so for members of marginalized groups whose language diverges even further from established systems of subject headings. In this study, researchers employed the concept of code-switching to better understand the linguistic divide that members of the LGBTQ+ community face when formulating subject searches in the library catalog.Design/methodology/approachThrough a set of 15 interviews with adult library users identifying as LGBTQ+, researchers examined the difference between participants’ natural language when discussing books and their suggested search terms for these same items. Analysis of language switching was guided by a linguistic framework of semantic, syntactic and lexical elements.FindingsResults show that LGBTQ+ catalog users employ linguistic shifts when approaching the library catalog, particularly semantic shifts around terminology for genres and LGBTQ+ identities. Almost all participants were aware of their language switching to some extent, with many purposely employing it in an anticipatory attempt to match their perceptions of the catalog’s language.Social implicationsFor libraries looking to better support marginalized communities, this study offers insight into the linguistic perceptions and practices of these users and the disconnect they may face when searching for resources related to their identities. Pluralistic approaches to subject representation may offer one means of addressing this.Originality/valueThis study takes the novel approach of applying the concept of code-switching to better understand the needs and perceptions of library catalog users.
Adaptive practices as scaffolding in knowledge workers’ personal information management
Authors: Alon Lilach 
Published: February 2025

PurposeThis study aims to examine how knowledge workers navigate affective challenges in Personal Information Management (PIM), specifically anxiety, frustration, dependence and loss of control while managing complex, high-volume information. It explores the adaptive PIM practices they employ to mitigate these challenges.Design/methodology/approachUsing a qualitative phenomenological approach, 16 semi-structured interviews were conducted with knowledge workers. Thematic analysis was used to identify affective challenges and corresponding adaptive PIM practices.FindingsFindings of this study describe four key affective challenges: anxiety about information loss and system failure, frustration with information overload and inadequacies in PIM practices, dependence on digital systems and loss of control over fragmented information. To address these, participants adopted adaptive PIM practices, including backup routines, prioritization, decluttering, structured organization and redundant storage solutions. These practices functioned as scaffolding, reducing emotional strain and enhancing control over personal information spaces.Research limitations/implicationsThe study offers insights for designing PIM systems that address affective challenges, including automated backup prompts and decluttering tools and for workplace initiatives promoting PIM skill development to enhance productivity and well-being.Originality/valueThis study positions adaptive PIM practices as essential scaffolding that supports knowledge workers in managing the dual demands of functionality and emotional regulation within their information landscapes. By framing adaptive practices as scaffolding, the study contributes to a deeper understanding of how PIM skills and mastery address both the organizational and affective complexities faced by knowledge workers.