bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streptococcus mutans LiaSgene regulates its cross-kingdom interactions withCandida albicansto promote oral candidiasis
Authors: Cao Yanfan , Huang Shan , Du Jingyun , Wang Xiuqing , Gan Guowu , Chen Shuai , Huang Xiaojing 
Published: February 2025

AbstractCandida albicansandStreptococcus mutansare commonly associated with oral candidiasis and dental caries, respectively.C. albicansis frequently detected in the dental plaque of early childhood caries. The synergistic interaction betweenC. albicansandS. mutansin dental caries suggests that fungi enhance the production of acidic metabolites and contributes to the development of caries. However, the cross-kingdom interaction ofS. mutansin oral candidiasis and the pathways regulating hyphal formation remain unclear. TheliaSgene ofS. mutans593 plays a crucial role in maintaining membrane homeostasis. In comparison to theS. mutans593 and liaS-complementary strains, the liaS-strain significantly diminished the proliferation, biofilm formation, extracellular polysaccharide production, andC. albicanshyphal transformation of co-cultured microorganisms. The deletion ofliaSgene in the dual-species downregulated the expression of yeast-hyphal transformation related geneshwp1, ece1, als1, andals3inC. albicans, while also impacted the expression ofphr1andphr2. Additionally, liaS-inhibited glycolysis and pyruvate kinase activity inS. mutans, leading to a decreased in water-soluble and water-insoluble glucans production in biofilm. The significant downregulation of glucosyltransferase transcription relates genes expression in liaS-resulted in inhibition of the cross-kingdom interaction in the dual-species. In the murine oropharyngeal candidiasis model, dual-species infection with liaS-results in a reduction of fungal and hyphal invasion compared to the combinations ofC. albicansandS. mutans593. In conclusion,S. mutans/liaSplay a crucial role in the development of oral candidiasis suggests that it could be a targeted strategy for managing this condition.ImportanceCandidiasisinvolves the transition ofC. albicansinto hyphae and the fungi invasion of the oropharyngeal mucosa. The transformation of hyphal is influenced by a variety of internal and external environmental factors. Our research findings suggest that the deletion of theliaSgene leads to a reduction ingtfsgene expression, impacting glycolysis efficiency and effectively decreasing EPS production in the dual-species biofilm. Also, downregulation of the expression levels of yeast-hyphal transformation related genes to inhibiting the virulence function ofC. albicans. Our study demonstrates thatS. mutans593/liaSpromotes epithelial invasion ofC. albicansin mouse oropharyngeal candidiasis, offering a potential therapeutic approach for addressing cross-kingdom infections.
A bioinformatic workflow to facilitate the study of less-understood proteins: the case of SH2D2A
Authors: Gilmour Brian C. , Chan Hanna , Singh Sachin , Nyman Tuula A. , Lossius Andreas , Borowicz Paweł , Phuyal Santosh , Spurkland Anne 
Published: February 2025

AbstractAdaptor proteins are key regulators of immune signalling but are challenging to study due to redundant pathways that obscure clear functional “anchor” phenotypes. Making use of public single-cell RNA sequencing (scRNA-seq) datasets, we theorised that anchors could be identified by working in the reverse direction: starting from the transcriptomic level and working “bottom-up” to identify anchoring phenomena at the cell surface. We have produced a prototype workflow for this method using the case of the lymphocyte-enriched adaptor protein SH2D2A, whose function remains uncertain. Using our bottom-up analysis, we have identified a link between SH2D2A and T cell-T cell (T-T) synapses enriched for ITGB2. The functional implications of this link are currently being explored, but further application of this bioinformatic approach to less-understood proteins may prove useful in understanding the minutiae of immune cell signalling, with implications for immunotherapy.
Inactivated Zoonotic Influenza A(H5N8) Vaccine Induces Robust Antibody Responses Against Recent Highly Pathogenic Avian Influenza Clade 2.3.4.4b A(H5N1) Viruses
Authors: Liedes Oona , Ekström Nina , Haveri Anu , Solastie Anna , Vara Saimi , Rijnink Willemijn F. , Bestebroer Theo M. , Richard Mathilde , de Vries Rory D. , Lindh Erika , Ikonen Niina , Laaksonen Terhi , Holopainen Riikka , Kakkola Laura , Lappalainen Maija , Syrjänen Ritva K. , Julkunen Ilkka , Nohynek Hanna , Melin Merit 
Published: February 2025

AbstractIn 2023, Finland faced an outbreak of highly pathogenic avian influenza caused by clade 2.3.4.4b A(H5N1) viruses, which spread from wild birds to fur farms. Vaccinations of individuals at-risk, such as fur and poultry farm workers, veterinarians, and laboratory workers, began in June 2024 using the MF59-adjuvanted inactivated (H5N8) vaccine manufactured by Seqirus (based on clade 2.3.4.4b A/Astrakhan/3212/2020). We investigated antibody responses following a two-dose vaccination regimen in 39 subjects. Vaccination induced comparable levels of functional antibodies both against the vaccine virus and two clade 2.3.4.4b viruses, either associated with outbreaks in fur animals in Finland or cattle in the United States. Upon two doses of the vaccine for previously unvaccinated people, the seroprotection rate against the vaccine virus was 83 % (95 % CI 70-97 %, titer ≥20) and 97 % (95 % CI 90-100 %, titer ≥40) using microneutralization or hemagglutinin inhibition assays, respectively. In a subset of previously H5-vaccinated individuals, the first dose already led to seroprotective titers, indicative of immunological recall. These data show that the vaccine is expected to confer cross-protection against currently circulating H5 clade 2.3.4.4b viruses.
State or personality trait: Determinants of boldness and shoal size preference in adult zebrafish
Authors: Singh Abhishek , Sharma Prabhat , Jain Mansha , Mahajan Pranati , Bajaj Jasmine , Gupta Vaidehi , Dingemanse Niels J. , Rajaraman Bittu Kaveri 
Published: February 2025

AbstractAnimals adjust their behavior in response to physiological states to optimize the trade-off between energy acquisition and survival. A key question in animal personality research is whether behavioral variation is driven by consistent physiological state differences or stable personality traits. This study evaluates boldness and shoal size discrimination in adult male zebrafish (Danio rerio) across three hunger states: same-day feeding (H0), 24-hour food deprivation (H1), and 48-hour food deprivation (H2). Behavioral assessments were conducted over two testing cycles, with each individual undergoing every test twice for each hunger state within each cycle. The assays comprised the Open Field Test (OFT), Emergence Test (ET), and Social Preference Test (SPT), with the SPT conducted under binary (4 vs. 2 fish) and ternary (4 vs. 2 vs. 1 fish) choice conditions. Hunger significantly reduced emergence latency, but did not affect exploratory behavior in the OFT. Hunger also enhanced preference for larger shoals above chance in the binary SPT during the second testing cycle, though this effect was absent in ternary choices. Testing cycle effects revealed habituation-driven increases in boldness in both the tests and a progressive shift toward larger shoal preferences in the binary SPT. Among all assays, only the OFT showed significant repeatability, making it a reliable measure of boldness. However, it did not show consistent individual differences in plasticity due to hunger. These results highlight the crucial role of labile physiological states, such as hunger and habituation, in driving behavioral variation and underscore the importance of designing studies that disentangle state-dependent behaviors from stable personality traits in animal personality research.
Neuromodulation of the endbulb of Held synapse in the cochlear nucleus
Authors: Groshkova Maria , Alvanos Theocharis , Qi Yumeng , Wang Fangfang , Wichmann Carolin , Hua Yunfeng , Moser Tobias 
Published: February 2025

AbstractSynapses vary greatly in synaptic strength and plasticity, even within the same circuitry or set of pre- and postsynaptic neurons. Neuromodulation is a candidate mechanism to explain some of this variability. Neuromodulators such as monoamines can differentially regulate presynaptic function as well as neuronal excitability. Variability is found also for the large calyceal synapses of the auditory pathway that are endowed with high synaptic vesicle (SV) release probability (Pvr) and large postsynaptic currents enabling reliable and temporally precise transmission of auditory information. Here we investigated whether the calyceal endbulb of Held synapse formed by auditory nerve fibers onto bushy cells (BCs) in the anteroventral cochlear nucleus (AVCN) is modulated by norepinephrine (NE) and serotonin (5-HT).Using electron microscopy (EM) of the cochlear nucleus we found evidence for putative monoaminergic varicosities in both ventral and dorsal divisions. Immunostaining for vesicular 5-HT and NE transporters revealed NE-containing and 5-HT-containing varicosities in the AVCN, juxtaposed to both endbulbs and BCs. Furthermore, we detected immunofluorescence for 5-HT1B, 5-HT4, 5-H7receptors (R) and α2C-adrenergic receptors (AR) in BCs. We used voltage-clamp recordings from mouse BCs in order to uncover potential presynaptic effects of neuromodulation, which revealed an increase in frequency of miniature excitatory postsynaptic currents (mEPSCs) upon application of NE but not 5-HT. Evoked synaptic transmission was unaffected by the application of either NE or 5-HT. Likewise, while studying the biophysical properties of the BCs, we did not observe effects of NE or 5-HT on low-voltage-activated K+(K+LVA) and hyperpolarization-activated mixed cation (HCN) channels during application. In summary, we report evidence for the presence of monoaminergic innervation in the cochlear nucleus and for subtle functional NE-neuromodulation at the endbulb of Held synapse.
Fiber optics in curved space-times
Authors: Mieling Thomas B. , Hudelist Mario 
Published: February 2025

Single-mode fibers are used in fiber-optic gyroscopes to measure the Sagnac effect and are planned to be used in forthcoming experiments on the gravitationally induced phase shift in single photons. However, current theoretical models of such experiments are limited to ray-optics approximations or, if based on wave optics, to a restricted class of fiber alignments. To overcome these shortcomings, this paper develops a comprehensive perturbative scheme to solve for electromagnetic modes, i.e., monochromatic solutions to Maxwell's equations, of arbitrarily bent step-index fibers in general stationary space-times. This leads to transport equations for the electromagnetic phase and polarization that include the gravitational redshift, the Sagnac effect, a generalization of Rytov's law to curved space, a gravitational Faraday effect in the form of shift-induced gyrotropy, as well as inverse spin Hall effects caused by fiber bending, gravitational acceleration, and space-time curvature.

Published by the American Physical Society
2025
Disequilibrium in plant distributions: Challenges and approaches for species distribution models
Authors: Sandel Brody , Merow Cory , Serra‐Diaz Josep M. , Svenning Jens‐Christian 
Published: February 2025

Abstract

Environmental conditions are dynamic, and plants respond to those dynamics on multiple time scales. Disequilibrium occurs when a response occurs more slowly than the driving environmental changes. We review evidence regarding disequilibrium in plant distributions, including their responses to paleoclimate changes, recent climate change and new species introductions. There is strong evidence that plant species distributions are often in some disequilibrium with their environmental conditions.

This disequilibrium poses a challenge when projecting future species distributions using species distribution models (SDMs). Classically, SDMs assume that the set of species occurrences is an unbiased sample of the suitable environmental conditions. However, a species in disequilibrium with the environment may have higher‐than‐expected occurrence probabilities (e.g. due to extinction debts) or lower‐than‐expected occurrence probabilities (e.g. due to dispersal limitation) in different areas. If unaccounted for, this will lead to biased estimates of the environmental suitability.

We review methods for avoiding such biases in SDMs, ranging from simple thinning of the occurrence dataset to complex dynamic and process‐based models. Such models require large data inputs, natural history knowledge and technical expertise, so implementing them can be challenging. Despite this, we advocate for their increased use, since process‐based models provide the best potential to account for biases in model training data and to then represent the dynamics of species occupancy as ranges shift.

Synthesis. Occurrence records for a species are often in disequilibrium with climate. SDMs trained on such data will produce biased estimates of a species' niche unless this disequilibrium is addressed in the modelling. A range of tools, spanning a wide gradient of complexity and realism, can resolve this bias.
On the Morphology of Toponyms: What Greek Inflectional Paradigms Can Teach us?
Authors: Marinis Michail I. 
Published: February 2025

AbstractThe research is a contribution to the investigation of the grammatical status of toponyms from the point of view of inflectional paradigmatic morphology. By examining data from Standard Modern Greek, as well as select data from its historical development, the analysis reveals that the inflectional morphology of toponyms shows significant differences not only from that of homonymous common nouns but also from certain categories of proper names, such as anthroponyms. Specifically, I conclude that (1) toponyms must have a tantum inflectional paradigm (either pluralia or singularia), and (2) they may present anti‐defective phenomena in their paradigm when they are compared with common nouns and other proper names. In the broader framework of Canonical Morphology, I introduce the term anti‐defectiveness to describe the second idiosyncratic property of toponyms: their capacity to circumvent the restrictions that lead to defective paradigms in other nouns of the same class.
The Adoption of Certification Policy for Gazelle Enterprises in China: A Bottom‐Up Approach
Authors: Wang Lei , Song Hui 
Published: February 2025

ABSTRACTAs a measure to cultivate innovative firms, a certification has been introduced and spread rapidly in many Chinese cities. We use data of Chinese prefecture‐level cities from 2008 to 2019 and investigate the causes of the adoption of the policy. Events such as term expirations (TEs) and cadres exchanges (CEs) are considered as potential internal causes, whereas pressure from peers and seniors is considered as potential external cause. A panel data model is used to analyze the causes of adoption. We find that, first, both TE and CE significantly promote adoption. Second, peer pressures significantly promote adoption but pressures from seniors do not. Third, TE significantly promotes adoption in northern China and CE significantly promotes adoption in southern China.
The gendered politics of the ‘local turn’ in peacebuilding: Acholi traditional justice and gender in post‐conflict Uganda
Authors: Fosu Richard , Gordon Eleanor 
Published: February 2025

AbstractTypically, advancing localised approaches to peacebuilding has evaded critical reflection on the power dynamics and harms that can arise. This paper considers the gender dynamics and gendered harms that can manifest themselves when adopting an uncritical approach to localisation in peacebuilding. To do so, it examines the use of mato oput (drinking the bitter root) in post‐conflict northern Uganda, as an example of a localised approach to post‐conflict transitional justice, to investigate these dynamics and harms. It draws from interviews and focus‐group discussions that were conducted in northern Uganda between 2020 and 2022 and engages with critical international relations scholarship on the ‘local turn’ in peacebuilding and the gendered nature of conflict and peace. The paper argues that in patriarchal societies, advancing localisation may entail a return to the traditional or customary order that reaffirms and reifies oppressive gender power relations and helps to consolidate gender inequalities, including unequal access to both security and justice.
Meditation Linked to Enhanced MRI Signal Intensity in the Pineal Gland and Reduced Predicted Brain Age
Authors: Plini Emanuele R. G. , Melnychuk Michael C. , Dockree Paul M. 
Published: February 2025

ABSTRACTGrowing evidence demonstrates that meditation practice supports cognitive functions, including attention and interoceptive processing, and is associated with structural changes across cortical networks, including prefrontal regions and the insula. However, the extent of subcortical morphometric changes linked to meditation practice is less appreciated. A noteworthy candidate is the pineal gland, a key producer of melatonin, which regulates circadian rhythms that augment sleep‐wake patterns and may also provide neuroprotective benefits to offset cognitive decline. Increased melatonin levels, as well as increased fMRI BOLD signal in the pineal gland, have been observed in meditators versus controls. However, it is not known if long‐term meditators exhibit structural changes in the pineal gland linked to the lifetime duration of practice. In the current study, we performed voxel‐based morphometry (VBM) analysis to investigate: (1) whether long‐term meditators (LTMs) (n = 14) exhibited greater pineal gland MRI‐derived signal intensity compared to a control group (n = 969), (2) a potential association between the estimated lifetime hours of meditation (ELHOM) and pineal gland signal intensity, and (3) whether LTMs show greater grey matter (GM) maintenance (BrainPAD) that is associated with pineal gland signal intensity. The results revealed greater pineal gland signal intensity and lower BrainPAD scores (younger brain age) in LTMs compared to controls. Exploratory analysis revealed a positive association between ELHOM and greater signal intensity in the pineal gland but not with GM maintenance as measured by BrainPAD score. However, greater pineal signal intensity and lower BrainPAD scores were correlated in LTMs. The potential mechanisms by which meditation influences pineal gland function, hormonal metabolism, and GM maintenance are discussed – in particular, melatonin's roles in sleep, immune response, inflammation modulation, and stem cell and neural regeneration.
Autoinducer-2 signaling promotes intestinal colonization of
Aeromonas veronii
and induces cell apoptosis in loach (
Misgurnus anguillicaudatus
)
Authors: Li Yi , Han Shuo , Niu Wenfang , Gao Chao , Wang Yuqi , Qin Mengyuan , Han Jingjing , Xia Xiaohua , Wang Hailei 
Published: February 2025

ABSTRACT

Quorum sensing systems, particularly autoinducer-2 (AI-2) signaling, have significant effects on bacterial colonization and virulence. However, how they affect intestinal colonization by pathogens and subsequent host immune responses remains unclear. Here, we investigated the influence of AI-2 signaling on the intestinal colonization ability of
Aeromonas veronii
Z12 and the host’s immune response. We found that AI-2 signaling promoted the colonization of
A. veronii
to the intestine of loach (
Misgurnus anguillicaudatus
) and caused severe intestinal damage, while D-ribose, an AI-2 signaling inhibitor, effectively inhibited the colonization of
A. veronii
. Transcriptomic sequencing elucidated the molecular mechanism of this damage, revealing upregulation of p53 pathway genes associated with apoptosis. Furthermore, intestinal microbiota dysbiosis induced by
A. veronii
colonization was associated with host cell apoptosis, leading to nitrite accumulation, which increased intracellular reactive oxygen species (ROS) levels, which activated the p53 pathway, and induction of cell apoptosis. These findings provide insights into the interaction among bacterial quorum sensing, intestinal microbiota, and the host immune response, which highlight potential therapeutic targets for mitigating bacterial-induced intestinal damage.

IMPORTANCE

The intestinal colonization of pathogens regulated by autoinducer-2 (AI-2) signaling and its induced host response have not been fully characterized. Here, we revealed the effect of AI-2 on intestinal colonization of
Aeromonas veronii
and its induced cell apoptosis in loach. Our study demonstrated that the deficiency of AI-2 significantly reduced
A. veronii
colonization in the loach intestine and mitigated the tissue damage. Additionally,
A. veronii
colonization induced significant upregulation of p53 pathway genes and proteins, indicating a key role of AI-2 signaling in host responses. Understanding these mechanisms not only helps to elucidate the pathogenicity of
A. veronii
but also may provide broader insights into the pathogenic mechanisms of other pathogens, thus revealing general principles of pathogen–host interactions across different models. Furthermore, we found that
A. veronii
colonization led to intestinal microbiota dysbiosis, notably an increase in the abundance of
Hypomicrobium
sp., which was associated with nitrite accumulation, elevating reactive oxygen species levels, activating the p53 pathway, and inducing cell apoptosis. These findings provide important insights into the complex mechanisms of AI-2 signaling in bacterial–host interactions. Additionally, the regulatory role of AI-2 signaling may have potential clinical applications as an intervention strategy, offering new directions for developing treatments against intestinal infections.