bluuebunny/crossref_metadata_2025_split huggingface dataset:
S9BactDB: A database for S9 family of proteases in bacterial genomes
Authors: Nayak Soumya , Sowdhamini Ramanathan 
Published: January 2025

AbstractS9 family proteins are serine proteases, divided into four subfamilies, involved in several functions associated with cell signalling, defence response and development. However, the annotation, characterization and statistical information are lacking. This is compounded by the huge number of bacterial genomes available. Hence, we have performed computational searches for S9 family peptidases as a step towards organising, curating the sequences and classifying into subfamilies. We have analysed annotated S9 family sequences from ∼32000 bacterial genomes/proteomes. All the curated information are presented as S9BacDB database (http://caps.ncbs.res.in/S9BactDB), provided in a user friendly way. The database provides various features such as information on the assemblies used (assembly, BioProject and BioSample details of each strain), the annotated POPs and their statistical distribution, unique domain architectures and the associated sequences and curated phylogenetic analysis. In addition, it provides the unique motifs and the associated information for Prolyl OligoPeptidases (POP) subtypes. An ML model is also integrated that can classify recognised sequences into a S9 sub family category. In conclusion, S9BactDb is a comprehensive platform that provides meticulously curated data on statistical/bioinformatics analysis of all S9 family proteins originating from fully sequenced bacterial genomes in the RefSeq database.
Conservation of southern yellow-cheeked gibbons (Nomascus gabriellae) in the Anthropocene
Authors: Piskovska Pavla , Piskovsky Vit , Cheyne Susan 
Published: January 2025

AbstractThe endangered southern yellow-cheeked gibbons (Nomascus gabriellae) occupy a fragmented habitat in Vietnam and Cambodia, with declining populations due to hunting, habitat loss and climate change. This study integrates population viability modelling with expert surveys to offer comprehensive insights into the species’ current state and its future prospects in a human-shaped world. Our modelling confirms the current population decline and suggests that a reduction in habitat loss and hunting is necessary to save this unique species from extinction. While declining habitat poses a long-term extinction risk, the current hunting rates threaten the species’ survival on the timescale of several decades. Crucially, large populations in Phnom Prich and Keo Seima Wildlife Sanctuaries and Cat Tien, Chu Yang Sin and Bu Gia Map National Parks play a key role in the survival of this species, as does the connectivity of these habitats. The expert surveys confirm the priority of protecting large populations and provide specific conservation actions for the case of Cat Tien National Park that are based on systematic stakeholder mapping. Altogether, this work assesses the population viability of southern yellow-cheeked gibbons in the Anthropocene and suggests conservation strategies that incorporate both ecological and social aspects.Graphical AbstractHighlightsSouthern yellow-cheeked gibbons are at risk of extinction due to hunting, habitat loss and degra- dation.Habitat loss poses a long-term risk while hunting endangers southern yellow-cheeked gibbons on the timescale of the following few decades.Protecting large populations in Phnom Prich and Keo Seima Wildlife Sanctuaries and Cat Tien, Chu Yang Sin and Bu Gia Map National Parks plays a key role in saving southern yellow-cheeked gibbons from extinction.Specific conservation actions based on a systematic stakeholder mapping are identified for Cat Tien National Park.
Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance
Authors: Klope Matthew T. , Talukder Poulami , Blank Brian R. , Chelebieva Sevil , Chen Jun , Fontaine Shaun D. , Gonciarz Ryan L. , Jaishankar Priyadarshini , Lee Grace J. , Legac Jennifer , Mathur Vineet , Narayan Avani , Okitwi Martin , Orena Stephen , Settineri Nicholas S. , Tapia Juan , Taremwa Yoweri , Tumwebaze Patrick K. , Vinod Aswathy , Burrows Jeremy N. , Rosenthal Philip J. , Cooper Roland A. , Renslo Adam R. 
Published: January 2025

AbstractFor over two decades, artemisinin-based combination therapy (ACT) has been the standard of care for the treatment of uncomplicated falciparum malaria. However, artemisinin partial resistance (ART-R) is now prevalent in Southeast Asia and has emerged in eastern Africa, threatening ACT efficacy. Mechanistically, ART-R results from an endocytosis defect that limits concentrations of host-derived free heme in the parasite digestive vacuole, allowing early ring-stage parasites to survive exposure to the artemisinin component of ACT. The artemisinin-inspired 1,2,4-trioxolane artefenomel exhibits an extended pharmacokinetic exposure profile that predicts efficacy against ART-R parasites. Unfortunately, the development of artefenomel was halted recently after almost a decade of clinical trials. Herein, we describe the discovery of RLA-4735 and its single-enantiomer form RLA-5764, next-generation antimalarial trioxolanes that exhibit excellent in vitro potency againstPlasmodium falciparumand single-exposure efficacy in a murineP. bergheimodel, thus retaining many of the favorable pharmacokinetic and pharmacodynamic properties of artefenomel while markedly improving solubility and development potential. InP. falciparumsamples collected from patients in Uganda in 2019 and 2023, ex vivo ring-stage survival assays revealed the emergence of the ART-R phenotype over this timeframe, and furthermore demonstrated markedly superior activity of artefenomel and RLA-4735 as compared to dihydroartemisinin (the active metabolite of artemisinin components of ACTs) against ART-R parasites. Overall, our findings suggest a role for next-generation trioxolanes in addressing ART-R, and present a potent new, artefenomel-adjacent chemotype with good potential to deliver new development candidates.Summary SentenceKlope et. al. described the discovery and in vivo characterization of antimalarial endoperoxides effective against artemisinin-resistant parasites as potential development candidates for uncomplicated, blood-stage malaria.
Novel Single-Cell Multiomics Approach to Analyze Replication Timing and Gene Expression in Mouse Preimplantation Embryos
Authors: Shetty Anala V. , Steer Clifford J. , Low Walter C. 
Published: January 2025

AbstractAnalysis of a cell’s replication timing (RT) provides insight into how genes replicate, early or late, during the S-phase of the cell cycle. RT is cell-type specific, inheritable, and has been correlated to gene expression in normal and diseased states. However, most studies have been limited to somatic cells. Very little is known about RT control in early mouse embryos, and how it correlates with the start of transcription during zygote gene activation (ZGA), at the 2-cell stage. In this study, we developed a novel in-house single-cell multiomics approach to simultaneously analyze RT and gene expression in individual cells of the mouse 1-cell, 2-cell, and 4-cell embryos. We detected that RT was established at the 1-cell stage prior to ZGA. Surprisingly, we observed that the coordinated RT and gene expression control was different in early totipotent embryos, compared to previously published studies in somatic cells. Late replicating regions correlated with higher gene expression and open chromatin in the early developing embryos. Lastly, we performed an integrated pseudo time trajectory analysis combining RT and gene expression information per cell.
Network Pharmacognosy ofGalphimia glauca: Mapping the Molecular Landscape of a Traditional Mexican Medicinal Plant
Authors: Acosta María José Cambero , de Anda Jáuregui Guillermo 
Published: January 2025

AbstractThis study explores the pharmacological landscape ofGalphimia glauca, a traditional Mexican medicinal plant known for its sedative and anti-inflammatory effects. Using network pharmacognosy, we analyzed the interactions ofG. glauca’s bioactive compounds, Galphimines A-I, with human protein targets. SwissTargetPrediction identified 214 unique protein targets across the galphimines, revealing a core-periphery structure in a bipartite network where 41 targets are shared among all compounds. Further interaction analysis using STRING-DB generated a dense protein-protein interaction network comprising 1,386 connections. Centrality analysis highlighted proteins such as SRC, MTOR, and MAPK3 as key nodes involved in cell growth, proliferation, and immune regulation pathways, suggesting these as pivotal mediators ofG. glauca’s pharmacological effects. Community detection with the Walktrap algorithm further segmented the network into functionally relevant modules linked to cell survival, immune response, and inflammation, reflecting the therapeutic effects historically attributed toG. glauca. Our findings underscore the plant’s multi-target therapeutic potential and highlight the value of network-based approaches in understanding traditional medicine. This work lays the groundwork for further studies aimed at refining therapeutic strategies based onG. glauca’s bioactive compounds and suggests network pharmacognosy as a promising tool for assessing other traditional medicinal plants.
Green-synthesized silver and iron nanoparticles fromAlstonia booneiandTerminalia catappa asantimalarial agents in mice models
Authors: Abuh Ojomona O. , Surakat Olabanji A. , Azeez Luqmon A. , Rufia Akinlabi M. , Fasasi Kamilu A. , Adeleke Monsuru A. 
Published: January 2025

AbstractMalaria a major health scourge of high impact in sub-sahara, with a major control-drawback on issues of resistance of the parasite to antimalaria. Nanoparticles have been investigated for their capacity to effectively deliver antimalarial drugs to kill the parasites, avoid drug resistance evolution and maintain a low toxic side effects. This study investigated the antiplasmodial efficacies of two plant green-synthesized with AgNO3and FeSO4salts againstPlasmodium bergheiinfected mice using, an acute toxicity test (LD50) of theTerminalia-catappaAgNPs (TCA),Alstonia-booneiAgNPs (AA),Terminalia-catappaFeSO4(TCF) andAlstonia-booneiFeSO4(AF) in accordance with Lorke’s method. The LD50was above 5000 mg/kg of TCA and AA while 223.6 mg/kg in TCF and AF. Each nanoparticles exhibited high dose dependentP. bergheiinhibition which was 62.20 % and 75.6 % in the TCA 200 mg/kg AA 100 mg/kg, 61.5 % and 75.3 % in the TCF 300 mg/kg and AF 200 mg/kg and doses in the curative groups, 92. 4 % and 93.1 % for TCA 100 mg/kg, AA 100 mg/kg 94.1 in 100 mg/kg dose and AF had 92.1 % at 300 mg/kg doses in the prophylactic groups. The groups treated with orthodox drugs had low parasitemia while the negative control recorded high parasitemia. There was no significant difference (P ˃ 0.05) in the mean change of the dosage in the different nanoparticles. These findings revealed all nanoparticles possesses a dose-dependent curative and prophylactic antiplasmodial activity and calls for their development and standardization as effective and readily available antimalarial options.
Climate warming drives pulsed-resources and disease outbreak risk
Authors: Fay Rémi , Gamelon Marlène , Porphyre Thibaud 
Published: January 2025

AbstractClimate influences the risk of disease transmission and spread through its direct effects on the survival and reproduction of hosts and pathogens. However, the indirect influences of climate variation, as those mediated by food resources on host demography, are often neglected. Pulsed-resources produced by oak trees in temperate forests constitute important resources for seed consumers and strongly depend on temperatures. Using an individual-based model, we provide a theoretical exploration of the influence of climate warming on the dynamic of the African swine fever (ASF) in the seed consumer wild boar (Sus scrofa), considering both direct and indirect temperature effects. We show that climate warming directly decreases the persistence of the virus in the environment, but also increases the production of acorns with cascading effects on the seed consumer host species. Integrating these climatic effects suggests a decrease of ASF spread under future warmer conditions. Importantly, food-mediated indirect effects of climate may outweigh direct effects, reversing in some situations the predictions of epidemic dynamics under climate change. This shows that anticipating future epidemic risks requires a deep understanding of ecological systems, including all direct and indirect climatic effects.
Discovery of Isobavachin, a natural flavonoid, as an Apolipo-protein E4 (ApoE4) structure corrector for Alzheimer’s disease
Authors: Patil Sachin P. , Kuehn Bella , McCullough Christina , Bates Dean , Hazim Hadil , Diallo Mamadou , Francois Naomie 
Published: January 2025

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by extensive neurodegeneration and consequent severe memory loss. Apolipoprotein E4 (ApoE4) is the strongest genetic risk factor for AD, with its pathological effects linked to structural instability and altered interactions with lipids and other important disease proteins including amyloid beta (Aβ) and tau (τ). Therefore, correcting and stabilizing the ApoE4 structure has emerged as a promising therapeutic strategy for mitigating its detrimental effects. In this study, we investigated naturally occurring bioavailable flavonoids as ApoE4 stabilizers, focusing on their potential to modulate ApoE4 structure and function. Comprehensive investigation of a focused database using our integrated computational and experimental screening protocol led to the identification of Isobavachin as a potential corrector and stabilizer of ApoE4 structure. In addition, a few other bioavailable flavonoids with similar stabilizing properties were identified, albeit to a much lesser extent as compared to Isobavachin. The findings support the therapeutic potential of flavonoids as ApoE4 modulators and highlight Isobavachin as a lead candidate for further preclinical evaluation. These results provide new insights into the pharmacological targeting of ApoE4 and open avenues for the development of flavonoid-based, ApoE-directed therapies for AD.
Phage Mu Utilizes the Sliding Clamp for Late Gene Transcription
Authors: Ho Khang , Harshey Rasika M. 
Published: January 2025

AbstractMuC, along with core RNAP and σ70, is required for transcription of late genes of phage Mu. We observed that overexpression of MuC is lethal inE. coliand that host replication was over-initiating under these conditions. Suppressors of MuC lethality occurred in dnaA, diaA, and dnaX, genes involved in initiation of DNA replication. We hypothesized that lethality was likely due to increase in ATP-DnaA levels, which are normally kept in check by Hda-DnaN (β clamp). We noticed that MuC harbors a well-defined motif for interaction with the β clamp. We provide experimental support for this interaction and show that disrupting it through mutations in the clamp-binding motif on MuC, expressed from both plasmid and the phage genome, abrogated transcription from a MuC-dependent promoter as well as production of viable phage, respectively. Furthermore, we show that inactivation of β-clamp specifically inactivates C-dependent transcription but not σ70-dependent transcription. We conclude that MuC requires the b sliding clamp for transcribing late phage genes. To the best of our knowledge, this is the first demonstration of the involvement of the clamp, a processivity factor essential for DNA replication, for transcription byE. coliRNAP.
Studying
π+π−
photoproduction beyond Pomeron exchange
Authors: Bibrzycki Łukasz , Hammoud Nadine , Mathieu Vincent , Perry Robert J. , Akridge Alex , Fernández-Ramírez César , Montaña Gloria , Pilloni Alessandro , Rodas Arkaitz , Shastry Vanamali , Smith Wyatt A. , Winney Daniel , Szczepaniak Adam P. ,   Joint Physics Analysis Center
Published: January 2025

Forward photoproduction of π+π− pairs with invariant mass of the order of mρ∼770  MeV is traditionally attributed to Pomeron exchange. Based on a detailed analysis of the CEBAF Large Acceptance Spectrometer photoproduction data collected at photon energies below 4 GeV, it is shown from a study of the angular moments that the dynamics of two-pion photoproduction for |t|≳0.5  GeV2 cannot be explained by Pomeron exchange alone. This motivates the development of a new theoretical model of two-pion photoproduction which incorporates both two-pion and pion-nucleon resonant contributions. After fitting free parameters, the model provides an excellent description of the low moments of the angular distribution measured at CLAS and enables an assessment of the relative contributions of particular production mechanisms and an interpretation of the various features of the data in terms of these mechanisms.

Published by the American Physical Society
2025
Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off
Authors: Tabanera-Bravo Jorge , Godec Aljaž 
Published: January 2025

Adaptation refers to the ability to recover and maintain “normal” function on perturbations of internal or external conditions and is essential for sustaining life. Biological adaptation mechanisms are dissipative, i.e., they require a supply of energy such as the coupling to the hydrolysis of ATP. Via evolution the underlying biochemical machinery of living organisms evolved into highly optimized states. However, in the case of adaptation processes two quantities are optimized simultaneously, the adaptation speed or accuracy and the thermodynamic cost. In such cases one typically faces a trade-off, where improving one quantity implies worsening the other. The solution is no longer unique but rather a —the set of all physically attainable protocols along which no quantity can be improved without worsening another. Here we investigate Pareto fronts in adaptation-dissipation trade-offs for a cellular thermostat and a minimal ATP-driven receptor-ligand reaction network. We find convex sections of Pareto fronts to be interrupted by concave regions, implying the coexistence of distinct optimization mechanisms. We discuss the implications of such “compromise-optimal” solutions and argue that they may endow biological systems with a superior flexibility to evolve, resist, and adapt to different environments.

Published by the American Physical Society
2025
How does original equipment manufacturing brand disclosure affect purchase intention? The mediating role of brand competence and brand warmth
Authors: Ge Hong , Wang Wei , Wang Yuting , Tan Ran 
Published: January 2025

PurposeOriginal equipment manufacturers (OEMs) are increasingly discoursing well-known brands to support their own brands. This study explores how original equipment manufacturing (OEM) brand disclosure affects willingness to buy (WTB) by examining the mediation effect of perceived brand competence (PBC) and perceived brand warmth (PBW), as well as the moderating effects of product type and consumer self-esteem (CSE).Design/methodology/approachThis study builds on signal theory and the stereotype content model to theorize the mediating role of PBC and PBW between OEM brand disclosure and WTB. A 2×2 between-subjects experiment with 442 participants was conducted, employing ANOVA, seemingly unrelated regression and moderated mediation tests to examine the hypotheses.FindingsOEM brand disclosure is positively related to WTB through PBC and PBW. Specifically, PBC’s mediation effect on OEM brand disclosure is stronger than that of PBW. Additionally, the mediation effect of OEM brand disclosure on WTB via PBC is moderated by product type and CSE.Originality/valueThis study contributes to the existing brand self-disclosure and brand spillover literature by opening the black box of how OEM brand disclosure affects WTB and reveals the underlying mechanisms of PBC and PBW. It offers valuable insights for OEMs to leverage previous OEM brands to support their own brands by improving PBC and PBW and is more beneficial for consumers with high self-esteem and experience products.
Gender economic inclusion and sustainable development in Africa
Authors: Tchamyou Vanessa , Edoh Ofeh M. , Asongu Simplice 
Published: January 2025

PurposeThis study investigates how gender economic inclusion affects sustainable development in Africa.Design/methodology/approachThe study is focused on 42 African countries for the period 2000–2019. It argues that enhancing gender economic inclusion in all sectors of society promotes and sets a better pace for the attainment of sustainable development in Africa. The gender economic inclusion variable used is the number of females employed as a ratio of the working-age population. The study employs the generalized method of moments as the main analysis method alongside the ordinary least squares technique.FindingsThe results show that gender economic inclusion has a negative effect on sustainable development in Africa, but they reveal contradictions when income groups are taken into consideration. Specifically, the middle-income group in Africa experiences a positive effect of gender economic inclusion on sustainable development.Practical implicationsAs policy implications, this study recommends that policy makers in low-income countries in Africa do everything within their reach to have equitable gender-inclusive societies, that is, to narrow the gap between the already wealthy class of women and the poor. This could be done by having more women included in different economic sector activities, in order to create a more conducive atmosphere for sustainable development.Originality/valueThe study has complemented the existing literature by assessing the nexus between gender economic inclusion and sustainable development in Africa.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-06-2024-0498
Gamification affordances in self-health management: perspectives from achievement satisfaction and gamification exhaustion
Authors: Sun Jiayue , Gu Yadi , Gu Dongxiao , Su Kaixiang , Wang Xiaoyu , Liang Changyong , Yang Xuejie 
Published: January 2025

PurposeGamification has been widely applied in mobile fitness apps to motivate users to exercise continuously. Based on the affordances–psychological outcomes–behavioral outcomes framework, this study explores the roles of three specific gamification affordances (competition, visibility of achievement and interactivity) in self-health management (continuous use behavior and health behavior) from the perspectives of achievement satisfaction and gamification exhaustion.Design/methodology/approachWe test the research model using a structural equation model (SEM) with 505 self-reported data points. Furthermore, we apply fuzzy-set qualitative comparative analysis (fsQCA) to explore configurations of gamification affordances associated with self-health management behavior, reinforcing the SEM results.FindingsResults indicate that competition, visibility of achievement and interactivity can enhance achievement satisfaction, which further boosts self-health management behavior. However, competition and interactivity can also cause gamification exhaustion, which undermines self-health management behavior to some extent. Overall, the positive impacts of the three affordances outweigh the negative impacts.Practical implicationsThis study provides new insights for relevant practitioners on designing gamification affordances, aiding the sustainable development of mobile fitness apps and their long-term effects on self-health management. Visibility of achievement should be emphasized, and competition and interactivity should be thoughtfully designed to minimize their negative effects.Originality/valueThis study extends the affordances–psychological outcomes–behavioral outcomes framework and the literature on gamification and health management by applying both SEM and fsQCA methodologies to examine the relationship between specific gamification affordances and self-health management behavior.