bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of a tattooed population and a possible role of tattoos as a risk factor for chronic diseases: Results from the LIFE-Adult-Study
Authors: Theune Loryn E. , Ghoreishi Narges , Müller-Graf Christine , Engel Christoph , Wirkner Kerstin , Baber Ronny , Laux Peter , Luch Andreas , Giulbudagian Michael 
Published: February 2025

AbstractTattoos and permanent make-up (PMU) gain increasing popularity among the general population. There are indications that pigments or their fragments may translocate within the body, however knowledge about possible systemic adverse effects related to tattoos is very limited. We investigated the prevalence of systemic chronic health effects including cardiologic diseases, cancer and liver toxicity and their relationship with the presence and characteristics of tattoos and PMU as part of the LIFE-Adult-study, a population-based cohort study. The control group without tattoos was from the same cohort and adjusted for confounders based on age, sex, smoking-status, body mass index, alcohol consumption and socioeconomic status. Of 4,248 participants, 7.4% (n=320) had either a tattoo (4.7%; n=199) or a permanent make-up (3.1%; n=135), or both (n=14). Thereof 5% (16/320) reported medical complications in relation to their tattoos or PMUs. Regarding systemic chronic health effects, increased odds ratios among the tattooed population were found for cardiologic diseases and liver toxicity. For non-melanoma skin cancer, results from the tattoo questionnaire gave no indication for any tumour development at the site of the tattoo. Our results demonstrate an increased risk for cardiologic and liver effects in participants bearing a tattoo. Strong differences in the observed effects between men and women point on the presence of a sex-specific bias. Even if no statistically robust conclusion can be drawn due to the small sample size, the results suggest that cardiologic outcomes and liver toxicity in tattooed individuals should be investigated further using prospective designs in larger cohorts.
Conspecific brood parasitism in the barn swallow (Hirundo rustica)
Authors: Jelínek Václav , Mari Lisandrina , Petrželková Adéla , Albrechtová Jana , Cepák Jaroslav , Kuhn Sylvia , Munclinger Pavel , Tomášek Oldřich , Šulc Michal , Albrecht Tomáš 
Published: February 2025

ABSTRACTConspecific brood parasitism (CBP) has been reported in many altricial avian species, yet its prevalence and underlying behavioural mechanisms remain poorly understood. We studied CBP in the barn swallow (Hirundo rustica), a species in which conspecific brood parasitism has been reported. We conducted parentage analysis on 1945 barn swallow broods involving 7816 offspring. Samples were collected over 12 breeding seasons at 5 colonies. Contrary to expectations, we identified only six cases of CBP (0.3 % of broods). By identifying all individuals involved, i.e. the parasitic females, the female hosts and the males that fathered the parasitic eggs, we determined that four cases of CBP resulted from either a failed nest takeover, the disappearance of a female partner or a disruption caused by researchers. Based on a review of the literature on CBP in seven other Hirundinidae, we conclude that there is only reliable evidence for CBP in cliff swallows (Petrochelidon pyrrhonata). Studies on other species either failed to identify the parasitic females or do not present sufficient evidence supporting the occurrence of CBP. Several studies relied on the appearance in the nest of two eggs within 24 hours to conclude that CBP occurred. However, based on the parentage analysis, we show that CBP only occurred in one out of 11 such cases in barn swallows. Our findings highlight that CBP is rare in our barn swallow populations, and have been likely overestimated in other studies. We emphasize the importance of frequent nest checks and rigorous genetic validation in CBP research. Overall, our results challenge existing assumptions about the prevalence of CBP and provide insights into the behavioural mechanisms that lead to CBP, with ecological and evolutionary implications.
Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules
Authors: Banerjee Pavel , Ray Sujay , Dai Liuhan , Sandford Erin , Chatterjee Tanmay , Mandal Shankar , Siddiqui Javed , Tewari Muneesh , Walter Nils G. 
Published: February 2025

AbstractEarly and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers—microRNAs (miRNAs), mutant DNAs, and proteins—remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.
Species-specific detection ofSchistosoma japonicumusing the ‘SNAILS’ DNA-based biosensor
Authors: Webb Alexander J. , Zhao Qin-Ping , Allan Fiona , Kelwick Richard J. R. , Emery Aidan M. , Freemont Paul S. 
Published: February 2025

AbstractThe neglected tropical disease schistosomiasis continues to be a global health concern, especially in low- and middle-income countries, with at least 250 million people infected worldwide and a further 779 million at risk of infection.Schistosoma japonicum, which is found in parts of South Asia, causes intestinal schistosomiasis in humans, as well as infecting up to forty other mammalian species. Therefore, novel diagnostics that can detectS. japonicumare desirable. In this study, we have further developed and refined the ‘SNAILS’ DNA-based biosensor technology for the detection of schistosomes and have applied this to the specific detection ofS. japonicum. Several new ‘SNAILS’ probe pairs were developed, and our optimised design successfully detected and differentiated between genomic DNA isolated from laboratory-derivedSchistosoma mansonicercariae andS. japonicumcercariae isolated from sites in the People’s Republic of China.
A Litmus Test for Confounding in Polygenic Scores
Authors: Smith Samuel Pattillo , Smith Olivia S. , Mostafavi Hakhamanesh , Peng Dandan , Berg Jeremy J. , Edge Michael D. , Harpak Arbel 
Published: February 2025

AbstractPolygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one’s genotype on their phenotype. However, because PGSs are constructed from population-level associations, they are influenced by factors other than direct genetic effects, including stratification, assortative mating, and dynastic effects (“SAD effects”). Our interpretation and application of PGSs may hinge on the relative impact of SAD effects, since they may often be environmentally or culturally mediated. We developed a method that estimates the proportion of variance in a PGS (in a given sample) that is driven by direct effects, SAD effects, and their covariance. We leverage a comparison of a PGS of interest based on a standard GWAS with a PGS based on a sibling GWAS—which is largely immune to SAD effects—to quantify the relative contribution of each type of effect to variance in the PGS of interest. Our method, Partitioning Genetic Scores Using Siblings (PGSUS, pron. “Pegasus”), breaks down variance components further by axes of genetic ancestry, allowing for a nuanced interpretation of SAD effects. In particular, PGSUS can detect stratification along major axes of ancestry as well as SAD variance that is “isotropic” with respect to axes of ancestry. Applying PGSUS, we found evidence of stratification in PGSs constructed using large meta-analyses of height and educational attainment as well as in a range of PGSs constructed using the UK Biobank. In some instances, a given PGS appears to be stratified along a major axis of ancestry in one prediction sample but not in another (for example, in comparisons of prediction in samples from different countries, or in ancient DNA vs. contemporary samples). Finally, we show that different approaches for adjustment for population structure in GWASs have distinct advantages with respect to mitigation of ancestry-axis-specific and isotropic SAD variance in PGS. Our study illustrates how family-based designs can be combined with standard population-based designs to guide the interpretation and application of genomic predictors.
Trends in gestational age at birth in the city of São Paulo, Brazil between 2012 and 2019
Authors: Lira Margarida Maria Tenório de Azevedo , de Freitas Marina , Bonilha Eliana de Aquino , Aly Célia Maria Castex , dos Santos Patrícia Carla , Niy Denise Yoshie , Diniz Carmen Simone Grilo 
Published: February 2025

AbstractStudies have shown that excessive obstetric interventions such as induced labor and caesarean sections have contributed to the shortening of the length of gestation, leading to a left shift in gestational age (GA) at birth. The aim of this study was to analyze trends in GA and the contribution of associated factors to changes in São Paulo city, Brazil during the period 2012-2019. We conducted an ecological time-series study of births in São Paulo using data from Brazil’s national live births information system (SINASC). We calculated the average annual percent change in the proportion of births by GA between 2012 and 2019 and between the first and second four-year periods of the time series by applying log transformation to the percentages, followed by Prais-Winsten regression. A total of 1,525,759 live births were analyzed. From 2015, there was an increase in the proportion of live births between 39 and 40 weeks from 2015 and a fall in the proportion of early term (37-38 weeks) and preterm (< 37 weeks) births throughout the study period. The average annual increase in the proportion of births at 39 and 40 weeks was 7.9% and 5.7%, respectively, while the proportion of births at other gestational ages showed a statistically significant reduction over the study period. These reductions were more pronounced in the first four-year period (2012-2015). The same trend was observed when the data were analyzed by type of delivery, type of service (public or private), maternal age, and maternal education level. The findings show that there was a right shift in the GA curve during the study period and a reduction in the proportion of preterm and early term births. These changes were more pronounced in births that occurred in private hospitals. These changes reflect public policies implemented to reduce obstetric interventions such as induced labor and caesarean section before labor, especially before 39 weeks of gestation.
A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity
Authors: Monzel Anna S. , Devine Jack , Kapri Darshana , Enriquez Jose Antonio , Trumpff Caroline , Picard Martin 
Published: February 2025

AbstractMitochondria are a diverse family of organelles that specialize to accomplish complimentary functions1–3. All mitochondria share general features, but not all mitochondria are created equal4.Here we develop a quantitative pipeline to define the degree of molecular specialization among different mitochondrial phenotypes – ormitotypes. By distilling hundreds of validated mitochondrial genes/proteins into 149 biologically interpretable MitoPathway scores (MitoCarta 3.05) the simple mitotyping pipeline allows investigators to quantify and interpret mitochondrial diversity and plasticity from transcriptomics or proteomics data across a variety of natural and experimental contexts. We show that mouse and human multi-organ mitotypes segregate along two main axes of mitochondrial specialization, contrasting anabolic (liver) and catabolic (brain) tissues. In cultured primary human fibroblasts exhibiting robust time-dependent and treatment-induced metabolic plasticity6–8, we demonstrate how the mitotype of a given cell type recalibrates i) over time in parallel with hallmarks of aging, and ii) in response to genetic, pharmacological, and metabolic perturbations. Investigators can now useMitotypeExplorer.organd the associated code to visualize, quantify and interpret the multivariate space of mitochondrial biology.
Extracellular vesicle production and membrane uptake promote repair and antibiotic tolerance inE. coli
Authors: Bos Julia , Abou Haydar Yasmina , Mayboroda Olena , Commere Pierre Henri , Mazel Didier 
Published: February 2025

AbstractBacterial extracellular vesicles (EVs) are nanosized lipid structures released in response to environmental stressors, such as phages and antibiotics. Despite their critical role in bacterial adaptability, the mechanisms by which EVs interact with membranes under stress remain poorly understood, due to challenges in visualizing these dynamic processes in live bacteria. Here, we use high-resolution fluorescence microscopy, flow cytometry, and cryo-electron microscopy to investigate EV production and uptake inEscherichia coliexposed to sub-minimum inhibitory concentration doses of polymyxin B (Pmb), a membrane-active antimicrobial peptide. Using fluorescently labeled Pmb and EVs, we track Pmb insertion and removal from membranes, EV production and uptake, and their effects on cell growth. Our findings demonstrate that EV production rapidly sequesters Pmb in the medium and facilitates its removal from bacterial membranes. For the first time, we demonstrated that EVs act as membrane plugs by adhering to or fusing with Pmb-damaged membranes. These dynamic processes work together to reduce the antibiotic load from the membranes, turn off the RcsA-mediated membrane stress response, and enable cells to resume growth. Although EVs do not provide resistance to Pmb, they enhance the survival and tolerance of bacterial populations. This study uncovers the dual role of EVs in Pmb sequestration and membrane repair, providing new insights into antibiotic tolerance mechanisms and paving the way for innovative approaches to combat antimicrobial resistance.
An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts
Authors: Dekker Joannes Adrianus Antonius , Hagan Richard , Collins Matthew , Hendy Jessica 
Published: February 2025

AbstractOrganic residues are a rich source of biomolecular information on ancient diets. In particular, foodcrusts, charred residues on ceramics, are commonly analysed for their lipid content and to a lesser extent protein in order to identify foods, culinary practices and material culture use in past populations. However, the composition of foodcrusts and the factors behind their formation are not well understood. Here we analyse proteomic data (available via ProteomeXchange with identifier PXD059930) from foodcrusts made using a series of mixtures of protein- (salmon flesh), lipid- (beef fat) and carbohydrate-rich (beetroot) foods to investigate the relationship between the biomolecular composition of the input and the recovered signal using conventional methods applied to archaeological material. Additionally, using 3D modelling we quantify the volume of foodcrust generated by different ingredient combinations The results highlight biases in the data obtained in the analyses of organic residues both in terms of identified resources reflecting the cooked foodstuffs, e.g. an overrepresentation of fish proteins, as well as with regards to the abundance of foodcrust, for example mixtures of only salmon and beef fat resulted in relatively small amounts of foodcrust, and suggest caution in interpreting the composition of residues formed from complex mixtures of foodstuffs.
Sequencing of a dairy isolate unlocksKluyveromyces marxianusas a host for lactose valorization
Authors: Thornbury Mackenzie , Knoops Adrien , Summerby-Murray Iain , Dhaliwal James , Johnson Sydney , Utomo Joseph Christian , Joshi Jaya , Narcross Lauren , Remondetto Gabriel , Pouliot Michel , Whiteway Malcolm , Martin Vincent J.J. 
Published: February 2025

ABSTRACTThe use of genetically modified non-conventional yeast provides significant potential for the bioeconomy by diversifying the tools available for the development of sustainable and novel products. In this study, we sequenced and annotated the genome ofKluyveromyces marxianusY-1190 to establish it as a platform for lactose valorization. The strain was chosen for rapid growth on lactose-rich dairy permeate, high transformation efficiency, and ease of culturing in bioreactors. Genomic sequencing revealed thatK. marxianusY-1190 possesses single nucleotide polymorphisms associated with efficient lactose metabolism. The strain is diploid with notable genomic heterogeneity, which appears to be critical for its robust growth and acid tolerance. To further exploit this platform strain, we developed protocols for gene and chromosome manipulation using CRISPR editing, constructed and validated a series of promoters compatible with MoClo vectors, and designed synthetically inducible promoters forK. marxianus. These tools enable precise control over gene expression, allowing for the tailored optimization of metabolic pathways and production processes. The synthetic promoters provide flexibility for dynamic expression tuning, while the CRISPR-based editing protocols facilitate targeted genetic modifications with high efficiency. Together, these advancements significantly enhance the genetic toolbox forK. marxianus, positioning it as a versatile platform for industrial biotechnology. These tools open new opportunities for the sustainable production of bio-based chemicals, fuels, and high-value products, leveraging lactose-rich feedstocks to contribute to a circular economy.
Repurposing of the RIPK1 selective benzo[1,4]oxazepin-4-one scaffold for the development of a type-III LIMK1/2 inhibitor
Authors: Mandel Sebastian , Hanke Thomas , Mathea Sebastian , Chatterjee Deep , Saraswati Hayuningbudi , Berger Benedict-Tilman , Schwalm Martin-Peter , Yamamoto Satoshi , Tawada Michiko , Takagi Terufumi , Röhm Sandra , Corrionero Ana , Alfonso Patricia , Baena Maria , Elson Lewis , Menge Amelie , Krämer Andreas , Pereira Raquel , Müller Susanne , Krause Daniela S. , Knapp Stefan 
Published: February 2025

AbstractBenzoxazepinones have been extensively studied as exclusively selective RIP kinase 1 inhibitors. This scaffold binds as a type-III inhibitor targeting the αC-out/DFG-out conformation. This inactive conformation results in a large expansion of the kinase back pocket, a conformation that has also been reported for LIM kinases. Scaffold hopping is common in the design of orthosteric kinase inhibitors, but has not been explored in the design of allosteric inhibitors, mainly due to the typically exclusive selectivity of type III inhibitors. Here, we hypothesized that the shared structural properties of LIMKs and RIPKs could lead to novel type III LIMK inhibitors using the benzoxazepinone scaffold. We report the discovery of a novel LIMK1/2 inhibitor that relies on this scaffold-based approach. The discovered compound10showed low nanomolar potency on LIMK1/2 and exceptional selectivity, as confirmed by a comprehensive selectivity panel with residual RIPK activity as the only off-target. The study provides one of the few examples for scaffold hopping for type-III inhibitors which are usually associated with exclusive target selectivity.Table of contents (TOC) graphics
Active zone maturation state controls synaptic output and release mode and is differentially regulated by neuronal activity
Authors: Akbergenova Yulia , Matthias Jessica , Littleton J. Troy 
Published: February 2025

AbstractSynapse formation requires the gradual accumulation of cytomatrix proteins and voltage-gated Ca2+channels (VDCCs) at presynaptic active zones (AZs) to support neurotransmitter release. To correlate AZ maturation with synaptic output, quantal imaging was performed at serially imaged time-stampedDrosophilasynapses. Evoked release strength correlated strongly with AZ age and accumulation of late AZ scaffolds, while immature sites lacking VDCC accumulation supported spontaneous release. To examine how neuronal activity regulates AZ maturation and protein accumulation, the effects of disruptions to SV fusion or action potential generation were analyzed. Decreasing neuronal activity reduced AZ seeding and caused hyperaccumulation of presynaptic material at existing AZs. Although enlarged AZs are also observed inrab3mutants, activity reduction acted through an independent mechanism that required postsynaptic glutamate receptor-dependent signaling. Together, these data indicate AZ maturation state sets distinct presynaptic release modes and output strength, with neuronal activity shaping both AZ number and size across development.
Mental exploration of future choices during immobility theta oscillations
Authors: Wang Mengni , Yuan Li , Leutgeb Stefan , Leutgeb Jill K. 
Published: February 2025

SUMMARYMental exploration enables flexible evaluation of potential future choices, guiding decision-making without requiring direct real-world iterations. Although the hippocampus is known to be active while imagining the future, the precise mechanisms that support mental exploration of future choices remain unclear. In the hippocampus, the theta rhythm (4-12 Hz) is prevalent during movement and supports memory coding during real-world exploration by organizing neuronal activity patterns into short virtual path segments (theta sequences) around the rat’s location. We observed these theta-related neural activity patterns during movement in a hippocampus-dependent working memory task and also, unexpectedly, theta oscillations and theta-related neural activity during immobility. Compared to standard theta sequences during movement, theta sequences during immobility differed in that they occurred at a shifted theta phase and preferentially represented remote locations, in particular the next choice in the working memory task. Coding for future locations was also observed during awake sharp wave ripple, but these short-lasting events occurred rarely and were biased toward frequently visited locations. Therefore, our findings suggest that recurring bouts of theta oscillations during immobility, which are also observed in primates and humans, support the cognitive demands of mental exploration in the hippocampal network and facilitate ongoing predictions of future choices.