bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Molecular Docking on the AlphaFold-Predicted Protein Structure Proteome: Identifying Target Protein Candidates for Puberulic Acid, a Suspected Lethal Nephrotoxin
Authors: Hayama Teppei , Sugawara Rin , Kamata Ryo , Sekijima Masakazu , Takeda Kazuki 
Published: February 2025

AbstractThis study presents a novelin silicoscreening method for identifying potential protein-ligand interactions within the complete structural proteome, as predicted by AlphaFold2, using puberulic acid as a test case. The methodology utilizes molecular docking simulations to predict interactions based on structural compatibility and binding affinity estimations. This approach highlights proteins, such as sodium/myo-inositol cotransporters, which exhibit theoretical high affinity for puberulic acid, suggesting possible competitive inhibition or mimetic interactions that could disrupt osmoregulation. It is important to clarify that these simulations provide a hypothetical framework for understanding potential interactions. The high docking scores do not directly translate to biological effects but serve as a basis for further experimental validation. This cautious interpretation acknowledges the inherent limitations of predictive modeling while maintaining confidence in the robustness of the computational process. Moreover, the exploratory nature of this study is supported by the fact that binding affinity predictions are not influenced by protein amino acid length or the predictive accuracy (pLDDT scores) provided by AlphaFold2. This independence from structural prediction metrics suggests that the docking results offer a reliable exploration of potential interactions across a wide array of proteins, making this approach a valuable asset in the fields of drug discovery and toxicological research. The ability to comprehensively identify candidate proteins with potential affinity to chemical compounds enhances the predictive capacity of toxicological assessments and supports the strategic development of safer pharmaceutical agents.
Lessons learned from applying eDNA surveying to diadromous fish detection across the north-east Atlantic region
Authors: Bhendarkar Mukesh , Claver Cristina , Mendibil Iñaki , Fraija-Fernández Natalia , Nachón David J. , Davison Phil I. , Bašić Tea , O’Leary Ciara , Roche William K , Azpiroz Iker , Acolas Marie-Laure , Lekuona Aitor , Ardaiz José , Diaz Estibaliz , Lambert Patrick , Lassalle Geraldine , Rodriguez-Ezpeleta Naiara 
Published: February 2025

AbstractRegular monitoring of diadromous fishes is critical to inform their management and conservation. Yet, thein-situdata collection these species is challenging due to their complex life cycle and low abundance. Focusing on the sea lamprey (Petromyzon marinus, Petromyzontidae) and the European shads (Alosa alosaandA. fallax, Clupeidae), emblematic diadromous fishes in the Northeast Atlantic region, this study leverages the use of water environmental DNA (eDNA) samples to monitor their distribution range. For that aim, we developed quantitative PCR (qPCR) and digital PCR (dPCR) assays and applied them to detect sea lamprey and European shad DNA in a network of 44 river basins across Spain, France, Ireland, and the UK. We found that qPCR efficiently detected presence/absence of shads, while the higher sensitivity of dPCR was essential for detecting the lower abundant and partly sessile behaving sea lamprey in the amount of water collected. Moreover, sea lamprey showed significantly lower eDNA copies per litre of water compared to shads, probably due to their larvae spending several years burrowed within soft sediments, reducing eDNA shedding into the water column. The integration of historical datasets with this snapshot wide-ranging study enhances our understanding of the distribution of sea lamprey and European shad in Atlantic rivers. Importantly, the lessons learned within this international collaboration are critical towards a prevailing framework for conservation of migratory fishes, highlighting the need of well-designed sampling strategies coupled with species-specific assays applied to eDNA samples to bust long-term monitoring efforts of diadromous species.
Advancements in Vaccine Development : A comprehensive design of a Multi-Epitopic Immunodominant Peptide Vaccine Targeting Kyasanur Forest Disease via Reverse Vaccinology
Authors: Pillai Sarika Baburajan , Jeyachandran Akshay , Pariyapurath Naseera Kannanthodi , Jagadibabu Sumitha , Rajaiah Paramasivan , Channappa Shivanandappa Kukkaler , Pachamuthu Rahul Gandhi , Premkumar Ananda Arona , Jagannathan Selvaraj 
Published: February 2025

ABSTRACTKyasanur Forest Disease (KFD), caused by the Kyasanur Forest Disease Virus (KFDV), is a tick-borne hemorrhagic fever virus first identified in Karnataka, South India, in 1957. The rising incidence of cases is alarming, particularly due to the potential spread of the disease to neighboring states. There presently exists no particular treatment, and the Chick embryo fibroblast (CEF) vaccine only provides temporary immunity and necessitates many doses, which results in poor immunisation rates among at-risk groups. This situation highlights the urgent need for a highly effective and user-friendly vaccine. Given that KFDV is classified as a BSL-4 pathogen, this study employs advanced immuno-informatics tools to design a safer vaccine construct. Promising results have identified the E protein of KFDV as an immunodominant target that can stimulate robust immune responses, including the production of neutralizing antibodies.The vaccine design utilized variousin silicotools to predict CTL, HTL and B-cell epitopes from the E protein, ensuring powerful immunological reactions. Quality attributes such as antigenicity, allergenicity, toxicity, and immunogenicity were assessed using specialized tools. A total of 16 epitopes (5 CTL, 3 HTL, and 8 B-cell) were identified, all exhibiting desirable properties like non-toxicity, non-allergenicity, high antigenic and immunogenic value. These epitopes were linked to form the PKFDVac-I vaccine, consisting of 279 amino acids with a MW of 29,162.32 Daltons. The constructed vaccine demonstrated stability and a robust immune response when docked with the TLR-4 receptor, indicating strong immunogenic potential. This multi-epitope peptide vaccine candidate developed via user-friendly and safer bio-informative tools represents a significant advancement in effective immunization strategies against KFDV infection, paving the way for future vaccine development efforts targeting other emerging infectious diseases. In conclusion, the integration of diverse epitopes into a cohesive vaccine prototype demonstrates a promising avenue for custom synthesis and application in immunization strategies. Further validation throughin vitroandin vivostudies is essential to authorize the effectiveness of the designed vaccine construct.
Anti-Parasitics with a Triple Threat: Targeting Parasite Enzymes, the Proton Motive Force, and Host Cell-Mediated Killing
Authors: Pandey Akanksha M. , Malwal Satish R. , Valladares-Delgado Mariana , Labrador-Fagúndez Liesangerli , Stella Bruno G. , Díaz-Pérez Luis José , Rey-Cibati André , Singh Davinder , Stampolaki Marianna , Hong Sangjin , Gennis Robert B. , Kolocouris Antonios , Benaim Gustavo , Oldfield Eric 
Published: February 2025

ABSTRACTWe investigated the effects of the tuberculosis drug candidate SQ109 (8a) and of its analog MeSQ109 (8b) againstLeishmania mexicanain promastigote and amastigote forms, as well as against host cell macrophages finding potent activity (1.7 nM) for MeSQ109 against the intracellular forms, as well as low toxicity (∼61 µM) to host cells, resulting in a selectivity index of ∼36,000. We then investigated the mechanism of action of MeSQ109 finding that it targeted parasite mitochondria, collapsing the proton motive force, as well as targeting acidocalcisomes, rapidly increasing the intracellular Ca2+concentration. Using anE. coliinverted membrane vesicle assay, we investigated the pH gradient collapse for SQ109 and 17 analogs finding that there was a significant correlation (on average R=0.67, p∼0.008) between pH gradient collapse and cell growth inhibition inTrypanosoma brucei, T. cruzi, L. donovaniandPlasmodium falciparum. We also investigated pH gradient collapse with other anti-leishmanial agents: azoles, antimonials, benzofurans, amphotericin B and miltefosine. The enhanced activity against intracellular trypanosomatids is seen withLeishmaniaspp. grown in macrophages but not withTrypanosoma cruziin epithelial cells and is proposed to be due in part to host-based killing, based on the recent observation that SQ109 is known to convert macrophages to a pro-inflammatory (M1) phenotype.
Targeted ubiquitination of NaV1.8 reduces sensory neuronal excitability
Authors: Tyagi Sidharth , Ghovanloo Mohammad-Reza , Alsaloum Matthew , Effraim Philip , Higerd-Rusli Grant P. , Dib-Hajj Fadia , Zhao Peng , Liu Shujun , Waxman Stephen G. , Dib-Hajj Sulayman D. 
Published: February 2025

AbstractChronic pain and addiction are a significant global health challenge. Voltage-gated sodium channel NaV1.8, a pivotal driver of pain signaling, is a clinically validated target for the development of novel, non-addictive pain therapeutics. Small molecule inhibitors against NaV1.8 have shown promise in acute pain indications, but large clinical effect sizes have not yet been demonstrated and efficacy in chronic pain indications are lacking.An alternative strategy to target NaV1.8 channels for analgesia is to reduce the number of channels that are present on nociceptor membranes. We generated a therapeutic heterobifunctional protein, named UbiquiNaV, that contains a NaV1.8-selective binding module and the catalytic subunit of the NEDD4 E3 Ubiquitin ligase. We show that UbiquiNav significantly reduces channel expression in the plasma membrane and reduces NaV1.8 currents in rodent sensory neurons. We demonstrate that UbiquiNaVis selective for NaV1.8 over other NaVisoforms and other components of the sensory neuronal electrogenisome. We then show that UbiquiNaVnormalizes the distribution of NaV1.8 protein to distal axons, and that UbiquiNaVnormalizes the neuronal hyperexcitability inin vitromodels of inflammatory and chemotherapy-induced neuropathic pain. Our results serve as a blueprint for the design of therapeutics that leverage the selective ubiquitination of NaV1.8 channels for analgesia.
Hexagonal modulation of theta rhythmic attentional sampling of visual space
Authors: Kienitz Ricardo , Martini Jan , Helfrich Randolph F. 
Published: February 2025

SummarySpatial attention improves visual perception by selecting behaviorally relevant sensory signals. Traditionally, attention has been conceptualized as a static spotlight, while recent evidence posited that attention operates as a moving spotlight that samples visual space sequentially in discrete snapshots that are clocked by theta rhythms (∼3-8 Hz). While theta rhythmic attentional sampling has mainly been observed in fronto-parietal and occipital areas, theta oscillations also hallmark entorhinal-hippocampal grid-cell networks, which encode physical space in hexagonal patterns that guide overt exploration and navigation. We hypothesized that visual attention might rely on the same underlying principles and sample visual space in a hexagonal, grid-like configuration. To test this hypothesis, twenty participants performed a cue-guided attention task that probed behavioral performance as a function of space and time. Reaction times were assessed as a function of spatial location and varying cue-target intervals, which revealed prominent, spatially-structured theta rhythms. Specifically, higher theta power was evident at spatial locations that were aligned to multiples of 60°, consistent with an underlying hexagonal organization. Participants that exhibited stronger hexagonal sampling relied less on the spatial cue to guide their attentional allocation. In sum, these findings suggest that covert visual attention relies on an underlying hexagonal grid-like structure known from the entorhinal-hippocampal system and highlight that theta rhythms reflect a common organizing principle for spatial cognition.Significance StatementAttention prioritizes sensory inputs to optimize behavior. But how does attention sample the environment in space and time? Here, we demonstrate that attentional sampling of visual space is not uniform, but preferentially explores locations that are oriented along a hexagonal pattern, reminiscent of the spatial configuration of entorhinal-hippocampal grid cells. Moreover, covert attentional sampling was clocked by theta oscillations (3-8 Hz). In sum, these findings provide evidence for a shared neural basis of underlying spatial attention and navigation and reveal that theta rhythms orchestrate sampling behaviors in space and time as a unifying principle underlying spatial cognition.
The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
Authors: Evangelista John Erol , Clarke Daniel J.B. , Xie Zhuorui , Olaiya Stephanie , Kim Heesu , Marino Giacomo B. , Byrd Anna , Srinivasan Shivaramakrishna , Srinivasan Sumana , Maurya Mano R. , Jenkins Sherry L. , Lutsky Andrew D. , Sasaya Lucas , Lachmann Alexander , Ahmed Nasheath , Diamant Ido , Sanchez Ethan , Ramachandran Srinivasan , Subramaniam Shankar , Ma’ayan Avi 
Published: February 2025

ABSTRACTThe NIH Common Fund Data Ecosystem (CFDE) program was established to facilitate data accessibility and interoperability across multiple Common Fund (CF) programs and promote collaborations and new discoveries by combining data from different CF programs. The CFDE Data Resource Center (DRC) was tasked with developing two web-based portals: an Information Portal to serve information about the CFDE, and a Data Portal to host harmonized metadata and processed data contributed by participating CF Data Coordination Centers (DCCs) and other sources. To achieve these goals, the CFDE DRC developed the CFDE Workbench, a web-based platform that hosts highly processed data, metadata, tools, use cases, and analyses developed by the CFDE. The Crosscut Metadata Model (C2M2) and several other processed data formats are hosted by the CFDE Workbench, including set libraries (XMTs), Knowledge Graph (KG) assertions, and attribute tables. These processed data formats make information derived from CF programs more findable, accessible, interoperable, and reusable (FAIR) and artificial intelligence (AI)-ready for cross-DCC knowledge discovery. In addition to these processed data formats, several other assets are served by the Workbench, including Extract Transform Load (ETL) pipelines, OpenAPI-documented and SmartAPI-registered Representational State Transfer (REST) Application Programming Interfaces (APIs), entity pages such as gene, drug, disease, or tissue landing pages, Playbook Workflow Builder (PWB) metanodes which are codified workflow steps involving DCC APIs, and chatbot specifications which are prompts helping chatbots to use DCC APIs to answer a wide range of user queries. Besides serving data, metadata, and code assets, the CFDE Workbench also has several tools that use these data, metadata, and code assets to enable cross-CF-program knowledge discovery use cases. Overall, the CFDE Workbench is a platform that consolidates efforts toward making CF programs funded resources harmonized, FAIR, and AI-ready. The CFDE Workbench website is available from:https://cfde.info/.
An integrated framework for aspect category-based sentiment analysis using adaptive feature selection and category-aware decision fusion strategies
Authors: Li Qingqing , Zeng Ziming , Sun Shouqiang , Li Tingting 
Published: February 2025

Purpose
Aspect category-based sentiment analysis (ACSA) has been widely used in consumer preference mining and marketing strategy formulation. However, existing studies ignore the variability in features and the intrinsic correlation among diverse aspect categories in ACSA tasks. To address these problems, this paper aims to propose a novel integrated framework.

Design/methodology/approach
The integrated framework consists of three modules: text feature extraction and fusion, adaptive feature selection and category-aware decision fusion. First, text features from global and local views are extracted and fused to comprehensively capture the potential information in the different dimensions of the review text. Then, an adaptive feature selection strategy is devised for each aspect category to determine the optimal feature set. Finally, considering the intrinsic associations between aspect categories, a category-aware decision fusion strategy is constructed to enhance the performance of ACSA tasks.

Findings
Comparative experimental results demonstrate that the integrated framework can effectively detect aspect categories and their corresponding sentiment polarities from review texts, achieving a macroaveraged F1 score (Fmacro) of 72.38% and a weighted F1 score (F1) of 79.39%, with absolute gains of 2.93% to 27.36% and 4.35% to 20.36%, respectively, compared to the baselines.

Originality/value
This framework can simultaneously detect aspect categories and corresponding sentiment polarities from review texts, thereby assisting e-commerce enterprises in gaining insights into consumer preferences, prioritizing product improvements, and adjusting marketing strategies.
Developing a framework for cloud computing adoption in academic libraries: an empirical investigation from university librarians
Authors: Nazir Shazia , Shahzad Khurram , Khan Shakeel Ahmad 
Published: February 2025

Purpose
This study aims to investigate the adoption of cloud computing by university libraries in Punjab province, Pakistan, identify the awareness of university librarians about the use of cloud computing in libraries, reveal the problems faced by university libraries in adopting cloud computing and develop a framework for cloud computing adoption in academic libraries.

Design/methodology/approach
This study used a quantitative research method by using a questionnaire as an instrument to address the study’s objectives. A total of 65 university libraries of Punjab Province were the population of the study. A purposive sampling technique was used. The SPSS software was used for the analysis of data.

Findings
The study found that the majority of university libraries in the Punjab province have the necessary information and communication technology (ICT) infrastructure. Among the three cloud computing models (SaaS, PaaS and IaaS), Software as a Service (SaaS) was the most widely adopted model in university libraries. The study identified various cloud-based services provided by university libraries. Librarians showed limited awareness of cloud service providers, with the majority only being aware of Amazon Web Services. Librarians acknowledged various challenges in adopting cloud-based library services, including poor internet connectivity, high subscription and renewal costs, data security and privacy concerns.

Originality/value
This study has provided a framework based on empirical findings of the study to efficiently adopt cloud-based library services in academic libraries.
How to shape individual innovation competencies? Proposing a tool for the corporate environment
Authors: Bittencourt Bruno Anicet , Scholz Junior Henrique , Faccin Kadigia , Genari Denise 
Published: February 2025

Purpose
In recent years, there have been many discoveries in terms of identifying and measuring innovation competencies (ICs) but not regarding the process of shaping such ICs. This study aims to understand how ICs are shaped in a corporate environment and thereby broaden the existing knowledge on IC development in the business context

Design/methodology/approach
The authors conduct a qualitative study using the design science research methodology. This methodology makes it possible to find solutions instead of merely explaining the research problem and generates a greater impact through artifact creation.

Findings
This study proposes the use of the innovation competencies development cycle, a tool that develops employee ICs and comprises a diagnostic stage and six fundamental stages. The diagnosis stage is intended to analyze whether the environment in which the tool will be applied has the required foundation to guarantee its effective functioning and obtain the expected results. The other six stages are designed mainly using the innovation pedagogy approach, the individual IC behaviors and the experimental learning.

Research limitations/implications
The study’s limitations include the application of the tool to a single sector and company size. In addition, the sample of participating employees was reduced.

Practical implications
This study has practical implications in the field of management, as it delivers a tool that can be applied to business companies. This tool aims to help managers shape innovation skills in their employees.

Social implications
This study contributes with a real proposal for a tool to shape innovation competencies. This study will help employees and organizations become more innovative.

Originality/value
The IC theme has been previously examined only within the academic and not the corporate environment, a gap addressed by this study. Therefore, this study adopts the perspective of developing ICs by not only measuring but also identifying and classifying this group of competencies.
Assessment of sustainability consciousness among pre-service teachers in China under the “Double Carbon” goal
Authors: Gong Qian , Liu Jian , Chen Xi , He Yongjie , Sun Xiaomin , Tan Zhiyao , Su Xiaojie 
Published: February 2025

Purpose
This study aims to identify the level of sustainability consciousness among preservice teachers in China under the “Double Carbon” goal.

Design/methodology/approach
A sustainability consciousness questionnaire was distributed to 2,795 preservice teachers aged 17–26 years old from first-year undergraduate to third-year postgraduate students through an online questionnaire tool. The mean, standard deviation and correlation of their sustainability knowingness, attitude and behavior were analyzed using SPSS software.

Findings
First, preservice teachers scored high in sustainability knowingness, attitude and behavior. Second, across different household types, disciplines and university levels (double first-class and nondouble first-class), preservice teachers’ sustainability consciousness scores were comparable to each other. Finally, a negative correlation was found between sustainability knowingness and attitude as well as knowingness and behavior. However, the authors observed a positive correlation between sustainability attitude and behavior. Overall, the level of sustainability consciousness among Chinese preservice teachers is high and no significant differences exist between the sustainability consciousness of preservice teachers with different household types, in different disciplines and at different levels of universities. Influenced by the contextual differences of the relevant concepts in the questionnaire, there is a certain degree of structural differences in the preservice teachers’ level of sustainability consciousness across the dimensions.

Originality/value
This study contributes to the literature by investigating the current status of sustainability consciousness level among preservice teachers in China under the “Double Carbon” goal. The findings of this study provide universities and relevant departments with recommendations for education for sustainable development policies.