bluuebunny/crossref_metadata_2025_split huggingface dataset:
Warming and reduced rainfall alter fungal necromass decomposition rates and associated microbial community composition and functioning at a temperate-boreal forest ecotone
Authors: Cantoran Anahi , Maillard François , Bermudez Raimundo , Stefanski Artur , Reich Peter B. , Kennedy Peter G. 
Published: February 2025

ABSTRACTChanges in temperature and rainfall regimes will have significant yet potentially contrasting impacts on rates of soil organic matter (SOM) decomposition. To assess how a combined stress treatment of warming and drought impacts the decomposition of fungal necromass—a fast-cycling soil organic matter (SOM) pool—we incubatedHyaloscypha bicolornecromass under both ambient and altered conditions (air and soil warming +3.3°C and ∼40% reduced rainfall) at the B4Warmed experiment in Minnesota, USA. We conducted two multi-week incubations, one assessing mass loss and microbial community composition on decaying necromass after 1, 2, 7, and 14 weeks and the second characterizing the substrate utilization capacities of necromass- associated microbial communities after weeks 1 and 7. Warming and reduced rainfall significantly accelerated the initial rate of necromass decay by ∼20%, but overall mass loss was not different between treatments at the end of the 14-week incubation. The accelerated initial rate of decay paralleled shifts in microbial community composition and activity in the altered plots, demonstrating a higher metabolic capability to utilize C and N substrates early in decomposition but a lower capability later in decay. These findings highlight the dynamic, stage-dependent response of fungal necromass decomposition to altered climate regimes, underscoring the importance of considering both temporal dynamics and the functional capacity of microbial communities when assessing the impacts of climate change on soil carbon and nutrient cycling in forest ecosystems.
Experimental Evidence for Phosphorylation-Driven Allosteric Regulation of Alpha Synuclein Function
Authors: Dollar Ashlyn N. , Webb Ian K. 
Published: February 2025

ABSTRACTPhosphorylation of serine 129 (pS129) in the intrinsically disordered protein alpha synuclein has long been associated with neurodegenerative disease. In the past several years, the functional relevance of pS219 has been uncovered by electrophysiology, immunoprecipitation, and proteomics as intricately connected with neurotransmitter release and synaptic vesicle (SV) cycling. Unexpectedly, binding to SNARE complex proteins VAMP-2 and synapsin only occurs with phosphorylation-competent alpha synuclein. The VAMP-2 binding domain has been shown to be residues 96-110, which does not include the phosphorylated residue, hinting at allosteric regulation of alpha synuclein protein-protein interactions by pS129. Within this study, cross-linking, covalent labeling, and collision induced unfolding of alpha synuclein and pS129 – as well as an additional encountered form in the brain, oxidized-M1, M5, M116, M127 alpha synuclein – are studied utilizing tandem mass spectrometry. Collision induced unfolding of proteins gives a fingerprint of the structures’ relative compactness and stabilities of various conformations. Covalent labeling of proteins identifies solvent accessible residues and reveals the hydrophobicity (or hydrophilicity) of their microenvironment, while cross-linking of proteins maps the proximity of residue pairs. The combination of collision induced unfolding, covalent labeling, and cross-linking show unequivocally that phosphorylated-S129 alpha synuclein results in a more stable, more compact form. Our results provide evidence of an extensively folded amphipathic region that interacts strongly with the VAMP-2 binding domain. The phosphorylation-induced folding of the amphipathic region likely tunes other protein-protein interactions and interactions with SVs and membranes.
The pivotal role of a novel free fatty acid receptor GPR164 in the intestinal barrier function
Authors: Ikeda Takako , Masujima Yuki , Watanabe Keita , Nishida Akari , Yamano Mayu , Igarashi Miki , Sasaki Nobuo , Katoh Hironori , Kimura Ikuo 
Published: February 2025

AbstractGPR164 is a novel free fatty acid receptor, activated by both short-chain fatty acids and medium-chain fatty acids, and expressed throughout the gastrointestinal tract. Although GPR164 is reported to be involved in the release of gut hormones, the physiological functions of this receptor in the maintenance of intestinal homeostasis remain unclear. In this study, we explored the role of GPR164 in regulating intestinal barrier function using mice lackingGpr164gene (Gpr164-/-). A loss-of-function mutation inGPR164promoted cell proliferation and disrupted the intestinal barrier function in both Caco-2 cell line and mice. Genome-wide RNA-seq analysis revealed thatGPR164deletion caused aberrant wnt/β-catenin signaling, and the intraperitoneal injection of wnt/β-catenin inhibitor ameliorated a series of abnormalities ofGpr164-/-mice.Gpr164-/-mice also exhibited gut microbial dysbiosis and severe inflammation, indicating that deletion ofGpr164causes similar pathologies observed in patients with inflammation bowel disease (IBD). Thus, our findings uncover the pivotal role of GPR164 in the maintenance of intestinal barrier function, providing an attractive clinical target for IBD.
Highlighting the species diversity, pricing trends, and conservation concerns in a major ornamental fish hub
Authors: Ho Samuel CL , Chan Jeffery CF , Lee Wing Him , Sung Yik-Hei , Liew Jia Huan 
Published: February 2025

AbstractThe global ornamental fish trade presents significant challenges to conservation of biodiversity. Here we explore patterns in the freshwater ornamental fish market in Hong Kong, a major wildlife trading hub. Weekly surveys over three-months in the primary aquarium district documented 540 freshwater fish species from 73 families. We found that species occurrence in the market was largely price-driven, and minimum retail price was the strongest predictor of their frequency of occurrence. Along the occurrence-price gradient, we found that potentially undescribed species dominated the rare/expensive end of the market, potentially influenced by the anthropogenic allée effect. Alarmingly, 86 species (16%) were potentially undescribed, while 38% were either not evaluated or classified as Data Deficient by the IUCN. While common/cheaper species dominate the market, the substantial number of little-known species being sold is of conservation concern, underscoring the need for more extensive monitoring at the risk of losing them to unregulated exploitation.
Using aerial thermography to map terrestrial thermal environments in unprecedented detail
Authors: Alujević Karla , Garcia-Costoya Guillermo , Ratia Noa , Schmitz Emma , Godkin Russell S. , Gopal Akhila C. , Bujan Jelena , Logan Michael L. 
Published: February 2025

AbstractThe accurate quantification of thermal environments is crucial for predicting the impacts of climate change across ecosystems.Two major obstacles exist in mapping biologically relevant thermal landscapes: 1) overcoming the mismatch between the spatial resolution at which environmental data are typically collected and the scale at which a particular organism experiences thermal variation, and 2) quantifying thermal landscapes without substantial measurement gaps in time or space.We present a new method that integrates aerial thermography from uncrewed aerial vehicles with field-deployed operative temperature models to generate fine-scale, spatiotemporally complete maps of operative temperature.To ensure the accessibility of our method, we developed an R package, ‘throne’, which streamlines the necessary corrections to raw drone data and produces operative thermal landscapes for any day or time during which data loggers were deployed.Our method allows researchers to generate detailed and biologically relevant thermal landscapes for species of interest which should enhance our understanding of animal thermal ecology and improve our ability to forecast the responses of organisms to environmental change.
Artificial light at night intensifies effects of a parasitic flatworm on the water fleaDaphnia magna
Authors: Tüzün Nedim , Hölker Franz , De Meester Luc 
Published: February 2025

ABSTRACTArtificial light at night (ALAN) can strongly alter organismal traits, but its role in shaping species interactions remains poorly understood, especially so in aquatic ecosystems. By capitalizing on a recently discovered antagonistic interaction between a brood-parasitic flatworm andDaphnia magnawater fleas, we tested whether this interaction depends on exposure to ALAN. During a 19-day laboratory population growth experiment, we manipulated flatworm presence and nighttime light conditions in a full-factorial design. We confirmed the negative effects of flatworm predation onDaphniaabundance at the population level. Importantly, we showed that the flatworm-caused decrease inDaphniaabundance under ALAN (81%) was twice as strong compared to dark-night conditions (39%). Our findings are relevant for assessing the impact of ALAN on the development ofDaphniapopulations and thus top-down control of phytoplankton. Freshwater ecosystems in urbanized areas, where this parasitic interaction was first encountered, may be especially at risk, as these are typically exposed to high levels of stress factors, including light pollution.
Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation
Authors: Murcott Ben , Honig Floris , Halliwell Dominic Oliver , Tian Yuan , Robson James Lawrence , Manasterski Piotr , Pinnell Jennifer , Dix-Peek Thérèse , Uribe-Lewis Santiago , Ibrahim Ashraf EK , Sero Julia , Gurovich David , Nikolai Nikolas , Murrell Adele 
Published: February 2025

AbstractBackgroundColorectal cancer (CRC) progression from adenoma to adenocarcinoma is associated with global reduction in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). DNA hypomethylation continues upon liver metastasis. Here we examine 5hmC changes upon progression to liver metastasis.Results5hmC is increased in metastatic liver tissue relative to the primary colon tumour and expression of TET2 and TET3 is negatively correlated with risk for metastasis in patients with CRC. Genes associated with increased 5-hydroxymethylcytosine show KEGG enrichment for adherens junctions, cytoskeleton and cell migration around a core cadherin (CDH2) network. Overall, the 5-hydroxymethylcyosine profile in the liver metastasis is similar to normal colon appearing to recover at many loci where it was originally present in normal colon and then spreading to adjacent sites. The underlying sequences at the recover and spread regions are enriched for SALL4, ZNF770, ZNF121 and PAX5 transcription factor binding sites. Finally, we show in a zebrafish migration assay using SW480 CRISPR-engineered TET knockout and rescue cells that reduced TET expression leads to a reduced migration frequency.ConclusionTogether these results suggest a biphasic trajectory for 5-hydroxymethyation dynamics that has bearing on potential therapeutic interventions aimed at manipulating 5-hydroxymethylcytosine levels.
Reconstructed Cell-Type Specific Rhythms in Human Brain link Alzheimer’s Pathology, Circadian Stress, and Ribosomal Disruption
Authors: Hollis Henry C. , Sharma Ashish , Sheehan Patrick W. , Maggi Leonard B. , Weber Jason D. , Hammarlund Jan A. , Bennet David A. , Menon Vilas , Musiek Erik S. , Anafi Ron C. 
Published: February 2025

SummaryAlzheimer’s disease (AD) disrupts behavioral circadian rhythms, but its effects on molecular rhythms in the human brain are poorly understood. Using single-nucleus RNA sequencing from post-mortem cortical samples, we informatically estimated the relative circadian phases of 409 persons with and without AD dementia. We then reconstructed circadian expression profiles across cell types. While core clock rhythms were preserved in AD, many cell-type specific circadian outputs were disrupted. Rhythms in ribosomal biogenesis and oxidative phosphorylation were dampened across cell types. Similar losses in ribosomal gene expression rhythms were observed in APP/PS1 mice, which showed further reductions in ribosomal protein expression and polysome-mediated translation after circadian desynchrony. Exploratory computational modeling reveals that altered translation may contribute to the increased circadian variability seen in AD patients. These findings reveal altered cell-type specific circadian output rhythms in the brains of AD affected patients, and highlight disrupted ribosomal rhythms as a feature of AD.
The economic strategies of superorganisms
Authors: Leahy Lily , Riskas Hannah L. , Halliwell Ben , Wright Ian J. , Carlesso Amelia G. , Sanders Nathan J. , Bishop Tom R. , Parr Catherine L. , Chown Steven L. , Andersen Alan N. , Gibb Heloise 
Published: February 2025

SummaryEconomic principles can be applied to biological life to understand how resource allocation strategies maximise evolutionary fitness1. This approach has been applied in plants under the global slow-fast leaf economic spectrum which describes investment and return of carbon and nutrients in leaves1. Whether this applies to other taxa, indicating general principles, remains untested. We advance generality in economic theories of life by showing that a slow-fast spectrum captures the resource economics of a globally dominant group of superorganisms, the ants. Like plants, ants acquire resources through modular units, the workers. Here, we collect traits from ant workers of 123 species across large-scale environmental gradients. Ants trade-off investment in biomass, chemical elements (nitrogen, phosphorus), energy (metabolic rate) and worker number, against assimilation rates (resource revenue) and lifespan. This superorganism economic spectrum does not vary across environmental gradients, rather, both slow and fast strategies persist amongst co-occurring species. High phylogenetic conservatism suggests early lineages of ants diverged in their economic strategies and subsequently diversified, locking in fundamental templates of investment and resource return. The remarkable similarities in economic strategies employed by ants and plants for resource acquisition and use suggest that there may be common principles underlying the rules of life.
Non-sexual community transmission of mpox clade Ib in DR Congo
Authors: Bugeme Patrick Musole , Bugale Patrick Kazuba , Mukika Trust Faraja , O’Driscoll Megan , Perez-Saez Javier , Bugwaja Levi , Shangula Salomon Mashupe , Kasi Willy , Bengehya Justin , Ngai Stephanie , Carrion Martin Antonio Isidro , Jackson Jules , Katoto Patrick , Bahizire Esto , Mulopo-Mukanya Noella , Lessler Justin , Knee Jackie , Vetter Pauline , Lee Elizabeth C. , Mukadi-Bamuleka Daniel , Azman Andrew S , Malembaka Espoir Bwenge 
Published: February 2025

AbstractIntroductionIn September 2023, mpox clade Ib emerged in Kamituga, a mining zone in South Kivu, DR Congo, primarily through sexual transmission. This study investigates an mpox clade Ib outbreak in Uvira, an urban area 360 km from Kamituga, where the first case was reported in May 2024.MethodsFrom June to October 2024, clinical and household data from suspected mpox cases were collected at Uvira hospital and household investigations. Mpox laboratory confirmation was performed via PCR. We analyzed demographic, exposure, and clinical data to characterize putative transmission patterns, severity, and risk factors.ResultsAmong 973 suspected cases, 42.7% (415) had PCR results, with 77.6% (n=322) testing positive. The median age of suspected cases was 9 years (IQR: 3–20), with 63.7% under-15 (n=620) and 32.1% under-5 (n=312). Severe cases (≥100 lesions) were more frequent in children under 15 (25.6%, 142/554) than others (16.1%, 49/304; p<0.001). Acute malnutrition affected 12.2% (22/181) of children under-5. The case fatality ratio was 0.7% (7/973), rising to 4% (5/127) in infants under one year. Among HIV-tested individuals, 1.8% (6/329) were HIV-positive. Pregnant women accounted for 14.5% (19/131) of women aged 15-49 years. The vast majority reported exposures to other suspected mpox cases were in the household (67.9%), with limited sexual (6%) or healthcare-related occupational exposures (1.4%). Female sex workers represented 1.2% of cases. Animal exposures were predominantly domestic (97.4%, 38/39).ConclusionThis child-centered outbreak, driven by non-sexual transmission, underscores the need for pediatric vaccines, nutritional support, and household interventions. Adult-focused responses alone may be insufficient.
Treatment outcomes of tuberculosis among people living with HIV/AIDS: A comparative assessment of primary and tertiary healthcare centres in Nasarawa State, Nigeria
Authors: Aya Benjamin Mari , Salihu Ismail Ndalami , Ahmad Dalhatu Muhammad , Tyem Dinfa Dombin , Mari Ovye Stephen , Alu Namo David , Joseph Benjamin Nasara , Shuaib Faisal 
Published: February 2025

AbstractOne of the Sustainable Development Goals for 2030 is to end the global TB epidemic. Translating this laudable target to reality requires strengthening collaborative tuberculosis/human Immunodeficiency Virus (TB/HIV) care at all levels to end TB in Nigeria. This study assessed the treatment outcomes of TB among people living with HIV (PLWH) and compared the treatment outcomes of TB between primary and tertiary healthcare facilities in Nasarawa State, Nigeria.This facility-based retrospective survey of TB patients living with HIV was conducted in two tertiary healthcare facilities and a primary healthcare centre (PHC). Records of eligible patients who completed treatment between January 2016 and December 2019 were abstracted using a data pro forma. Treatment outcomes were categorized as either successful or unsuccessful. Descriptive and inferential analyses were conducted, in addition to multivariate logistic regression.A total of 959 patients with a mean age of 33±14 years were evaluated; there were 847 adults (88.3%), and the proportion of females was 499 (52%). The proportion of patients who completed TB treatment was 26%; 20.5% were cured, while the mortality rate was 9.2%. The treatment success rate (TSR) was 46.5%; tertiary healthcare facilities had the highest unsuccessful treatment rates compared to the PHC. The TSR declined steadily from 68.8% in 2016 to 57.6% in 2019. Being treated at a tertiary healthcare facility (AOR=3.6, CI; 2.0-6.6) predicted successful treatment outcomes of TB among PLWH.TB’s overall TSR among PLWH was low. Within the outcome categories, the proportion of patients who completed treatment and those cured compared better with unfavourable outcomes. The rate of unsuccessful TB treatment is highest in tertiary healthcare facilities compared to PHC. However, being treated in the tertiary healthcare facility predicted successful treatment outcomes, while treatment failure, death, and loss to follow-up were highest in the tertiary healthcare facilities.
PEQI: A population dietary quality index for developed countries
Authors: Christopoulos Konstantinos , Christou Christina , Eleftheriou Konstantinos , Hassapis Christis 
Published: February 2025

AbstractBackgroundWhile there are numerous dietary quality indices for individuals, a lon-gitudinal population-level index is missing from the literature. This article presents a novel population-level dietary index, the Population Eating Quality Index (PEQI) that measures a country’s annual dietary quality.MethodsUsing data from the Food and Agriculture Organization and the Global Dietary Database, PEQI comprises of ten waste-adjusted food items for which weighted scores are assigned according to their effect on human health. Associations between the PEQI and health outcomes for a panel of developed countries were studied to further validate the instrument.ResultsThe index shows good predictive ability regarding life expectancy at birth and premature mortality for an average developed country.ConclusionsPEQI has multiple potential applications in the ecological study of health and nutrition as an exposure or even as an outcome.
The incubation periods of Monkeypox virus clade Ib
Authors: Perez-Saez Javier , Bugeme Patrick Musole , O’Driscoll Megan , Bugale Patrick Kazuba , Mukika Trust Faraja , Bugwaja Levi , Shangula Salomon Mashupe , Bengehya Justin , Ngai Stephanie , Carrion Martin Antonio Isidro , Jackson Jules , Mulopo-Mukanya Noella , Knee Jackie , Eckerle Isabella , Lee Elizabeth C. , Mukadi-Bamuleka Daniel , Lessler Justin , Azman Andrew S , Malembaka Espoir Bwenge 
Published: February 2025

AbstractBackgroundMonkeypox virus (MPXV) clade Ib, first detected in Democratic Republic of the Congo (DRC) in September 2023, spread internationally within months, prompting a WHO emergency declaration. Data on how this clade differs from others, including the incubation period which both shapes outbreak dynamics and informs epidemic response strategies, remain limited.MethodsWe use clinical, laboratory and reported exposure data from suspected and qPCR-confirmed mpox cases in Uvira, DRC to estimate the incubation period for MPXV clade 1b. We developed a Bayesian model to estimate incubation periods of various symptom onset definitions (rash, fever, any symptom), demographic factors and putative transmission route (sexual vs. non-sexual).ResultsAmong 92 PCR-confirmed cases, the median incubation period from exposure to rash was 18.6 days (95% CrI: 15.2-22.6). Five percent of cases are expected to develop a rash within 5.4 days (95% CrI; 3.4-7.6) and 95% within 37.6 days (95% CrI: 30.3-47.0). The incubation period differed by putative transmission route: sexual transmission had a shorter median (9.5 days, 95% CrI 3.7-16.4) than non-sexual transmission (18.9 days, 95% CrI: 15.3-23.0).ConclusionsIncubation periods for clade Ib are longer than previous estimates for other MPXV clades, but vary strongly by sexual vs. non-sexual exposures, the former closely aligning with observations from the predominantly sexually transmitted clade IIa global outbreak. These findings highlight the significant differences by transmission route – likely reflecting differences in infectious viral dose and suggest the need to revise global post-exposure monitoring recommendations.