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The evolutionary consequences of behavioural plasticity

TSSpredator-Web: A web-application for transcription start site prediction and exploration

Background With the rapid development of high-throughput RNA-seq technologies, the transcriptome of prokaryotes can now be studied in unprecedented detail. Transcription start site (TSS) identification provides critical insights into transcriptional regulation. Still, current command-line tools for the prediction of TSS remain challenging with respect to their usability and lack of integrated exploration features. Results We introduce TSS predator -W eb , an interactive web application that enhances the usability of the established yet unpublished tool, TSS predator . TSS predator -W eb facilitates TSS prediction from non-enriched and enriched RNA-seq data, classifies TSS relative to annotated genes, and allows users to explore results through dynamic visualizations and interactive tables. For the visualizations, we provide an UpSet plot summarizing the TSS distribution across experiments or classes, and a genome viewer that integrates transcriptomic and genomic data, which contextualizes the insights of the TSS predictions. To illustrate the usage of TSS predator -W eb , we provide a use case with Cappable-seq data from Escherichia coli . TSS predator -W eb is available on the TueVis visualization web-server at https://tsspredator-tuevis.cs.uni-tuebingen.de/ . Conclusions By combining user-friendly accessibility with interactive data exploration, TSS predator -W eb significantly facilitates genome-wide TSS analysis and interpretation in prokaryotes, empowering a broader range of researchers to generate biological insights from transcriptomic data.

Passenger perception of vehicle occupancy in public transport and factors that shape crowding estimations

Unravelling the role of redox active sites in nitrogen doped cerium oxide for associative ammonia decomposition

Abstract The catalytic decomposition of ammonia under mild conditions is a promising route for green hydrogen production. However, conventional dissociative ammonia decomposition pathways over metal sites are suffering from the Brønsted−Evans−Polanyi (BEP) constraint which establishes an inverse correlation between atomic N binding energy and the N-H bond dissociation energy. Herein, we report a ruthenium-supported nitrogen-doped cerium oxide (Ru/N-CeO 2 ) catalyst that breaks this limitation and exhibits significantly enhanced catalytic activity compared to its undoped counterpart. Furthermore, we reveal that N dopants can act as independent active sites, enabling an associative mechanism distinct from the conventional Ru-driven pathway. Comprehensive isotopic labelling experiments together with computational techniques elucidate the reaction mechanism over the N site and reveal a distinct correlation between the location of the active site and catalytic activity. The proximal N site exhibits the highest activity, challenging the conventional view that activity is dominated by metal–support interfacial sites. While N doping is a commonly used approach for surface modification, our findings show that it can also alter the reaction mechanism by introducing new active sites. These insights offer valuable guidance for the rational design of catalytic supports in ammonia decomposition and open new directions for catalytic systems limited by scaling relationships in heterogenous catalysis.

Plasma lipidomics, choline metabolites, and metabolic-associated steatotic liver disease (MASLD): A Coronary Artery Risk Development in Young Adults (CARDIA) study

Metabolic-associated steatotic liver disease (MASLD) is marked by accumulation of hepatic triacylglycerols (TAG), but many other lipids have been implicated. Choline metabolism has been shown to be related to MASLD, specifically through phosphatidylcholines (PC) role in hepatic TAG removal through very low density lipoproteins (VLDL). There are a lack of population-based studies with integrated data on lipidomics, choline metabolites, and MASLD. We tested associations between the plasma lipidome, choline metabolites, and MASLD using data from the Coronary Artery Risk Development in Young Adults (CARDIA) Study. The analytic sample included 1,039 participants with data on choline metabolite, lipidomic, and liver attenuation data [mean (SD) age: 45 (4); 57% female; 57% White race]. MASLD (n = 234) was defined as mean CT-derived liver attenuation < 51HU. Plasma lipidomics and choline metabolites were quantified from stored fasting plasma using liquid-chromatography and infusion-mass spectrometry. In logistic regression adjusted for sociodemographics, lifestyle, and clinical variables, total TAGs, diacylglycerols (DAG), and dihydroceramides (DCER) were positively, and lactosylceramides (LCER) were inversely, associated with MASLD. Species-level results revealed diverging MASLD associations for PCs, based on FA composition. In choline metabolite models, betaine was inversely associated with MASLD. A lipidomic risk score (LRS) derived from penalized regression of MASLD on lipid species was associated positively with choline, and inversely with betaine. We contribute population-based results to a growing literature relating lipidomics and MASLD. In our data, FA composition is biologically relevant to MASLD, particularly for PCs and TAGs. Our results link choline metabolites to both the plasma lipidome and to incident MASLD, furthering efforts in biomarker development and supporting mechanistic evidence using population-level data.

Anger impacts face memory and face – object memory differently in children and adults

Abstract Angry facial expressions are quickly detected and trigger emotional and physiological responses. They are especially salient in threatening contexts and can alter attention and emotion recognition, particularly in individuals exposed to trauma or violence. These effects extend to memory, individuals with prior violence exposure showing impaired associative memory for angry faces. However, little is known about how angry faces and their context are encoded and retained in typically developing children and adults. In this study, thirty-eight 9- to 11-year-old children (22 girls) and thirty 18- to 30-year-old adults (15 female participants) learned face - object pairs that contained either neutral or angry faces. Memory was tested for faces, objects, and face - object associations. Adults outperformed children in face and associative memory, but not in object memory. Children remembered angry faces better than neutral ones, whereas adults showed no such difference. Angry faces impaired adults’ associative memory but had no effect on children’s associative memory. In both children and adults, memory for objects per se was not different for objects that had been learned with an angry vs. a neutral face. These findings suggest that angry expressions influence memory differently across age groups and memory modalities. In addition, the reduction in adults’ associative memory due to angry faces cannot be fully explained by attentional bias, as object memory remained unaffected. These findings have potential implications for clinical settings.

Strong interplay between polar and structural topologies

Prevalence of stunting and its determinants among children under five in 35 Sub-Saharan African countries (2011–2024): Insights from recent demographic health survey data using a generalized linear mixed-effects model with robust poisson regression

Background Despite efforts by initiatives like the World Bank’s ‘All Hands-on Deck’ and UNICEF’s programs to address stunting through multisectoral approaches, the burden of stunting remains alarmingly high in sub-Saharan Africa. This study utilized recent large-scale survey data from 35 SSA countries (2011–2024) to estimate the pooled prevalence of stunting and its determinants among children under 5 years of age. Key variables such as antenatal care visits, postnatal care, and maternal nutritional indicators, which previous studies did not account for, are incorporated into the analysis. Methods A secondary analysis was conducted using recent demographic and health survey data (2011–2024) from 35 sub-Saharan African (SSA) countries. A total weighted sample of 191,953 children under 5 years of age was included in the analysis. Descriptive and inferential analyses were performed using STATA 17. Forest plots were utilized to illustrate both pooled and country-specific stunting rates. Determinants of stunting were identified through a multilevel mixed-effects Poisson regression model with robust variance. The adjusted prevalence ratios and their 95% confidence intervals were used to assess the strength and statistical significance of associations. Result The pooled prevalence of stunting among children under 5 years of age in 35 sub-Saharan African countries was 29.89% (95% CI: 26.63, 33.14%), with the lowest level in Gabon (13.91%) and the highest in Burundi (55.80%). Being male children (aPR = 1.24, 95% CI: 1.21–1.26), being aged 12 months or older (aPR: ≥ 1.81, p < 0.01), insufficient antenatal care (ANC) visits (aPR: ≥ 1.17, p < 0.01), lack of postnatal visits(aPR = 1.03, 95% CI: 1.07, 1.05), children perceived as small or average at birth (aPR: ≥ 1.16, p < 0.01), mother without a higher education (aPR: ≥ 1.94, p < 0.01), living in a poor or average wealth household (aPR: ≥ 1.23, p < 0.01) were significant predictors of stunting. Conversely, maternal overweight (aPR = 0.81, 95% CI: 0.77–0.84) and obese mothers (aPR = 0.88, 95% CI: 0.85–0.90) were associated lower prevalence of stunting. Conclusion Study revealed significant country-level variations and rates exceeding 30% in 15 countries, signaling a major public health concern. The key individual, household and contextual factors associated with stunting in this study suggest the need for immediate actions expanding antenatal and postnatal care, promoting facility-based deliveries, enhancing maternal education, and media outreach. Long term strategies must tackle poverty, food systems, and equitable nutrition access, supported by governance and stability. A multisectoral approach integrating health, education, agriculture, WASH, and social protection ensures substantiable child growth, complemented by longitudinal research for policy coherence.

Daily briefing: Genomes shake up the shark family tree

Epigenetic alterations in type 1 diabetes and their association with poor glycemic control: the SED1-EPI substudy

Abstract Type 1 diabetes (T1D) is an autoimmune disease characterized by β-cell destruction and insulin deficiency. Circulating microRNAs (miRNAs) are promising biomarkers for disease monitoring and complication risk assessment. This study aimed to describe the epigenetic profile in a multicenter Spanish T1D cohort and its association with clinical variables. We analyzed plasma samples from 125 participants (76 T1D, 49 controls) recruited across nine Spanish hospitals. Eight candidate miRNAs from a prior Asturias cohort study were quantified using RT-PCR. Associations with clinical and biochemical parameters were explored, and enrichment analysis was performed to investigate affected biological pathways. Of the miRNAs analyzed, only hsa-miR-200a-3p was significantly overexpressed in T1D versus controls ( p  = 0.035). In T1D patients, hsa-miR-200a-3p, hsa-miR-1-3p, and hsa-miR-340-5p showed positive correlations with HbA1c, while hsa-miR-224-5p correlated with body mass index (BMI). Poor glycemic control (HbA1c ≥ 7.5%) was associated with higher expression of hsa-miR-1-3p, hsa-miR-200a-3p, and hsa-miR-340-5p. No significant expression differences were found according to comorbidity or hypertension status. hsa-miR-200a-3p emerges as a potential biomarker for β-cell stress in long-standing T1D, while hsa-miR-1-3p and hsa-miR-340-5p may reflect glycemic control status and vascular risk. These findings support further evaluation of these miRNAs in larger, clinically diverse T1D cohorts.

Periplasmic gatekeeping of phage DNA entry by an rSAM enzyme matured effector with HxS repeats

Associations of cardiovascular risk factors with handgrip strength and gait speed among older males and females: A systematic review protocol

Introduction Cardiovascular risk factors (CRFs), such as hypertension, diabetes, dyslipidemia, and smoking are associated with several adverse health outcomes among older people, such as poor physical function. Handgrip strength and gait speed are key measures of physical function that indicate general health status among older people. Nevertheless, it is unclear which factors have the greatest impact on these measures in older adults. In addition, gender differences in cardiovascular disease risk are observed, with older women with a history of diabetes, obesity, and hypertension being more prone to cardiovascular events than older men. This may be related to different patterns of cardiovascular aging, which may impact the physical function of older men and women differently over time. This article aims to describe the protocol for a systematic review to identify which CRFs are associated with measures of physical function (handgrip strength and gait speed) and whether this association varies by sex. Methods and analysis A systematic search will be conducted in the PubMed, LILACS (Latin American and Caribbean Health Sciences Literature), Cochrane Library, Web of Science and Embase databases. The sorting and tracking of articles will be performed with the help of the Rayyan platform. Following the recommendations of the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P), the main reviewer will conduct the initial search and exclusion of duplicates, and two researchers will extract data from the selected articles independently and blindly, using an instrument built specifically for this research. Discrepancies will be solved by a third reviewer. Cross-sectional and/or longitudinal studies, involving community-dwelling older individuals and that have assessed the association between CRFs and measures of physical function (handgrip strength and/or gait speed) will be included. The methodological quality of the included studies will be assessed using the Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. PROSPERO registration number CRD420251167299.

A GIS and statistical based approach to assessing citizen awareness of the energy transition and climate change across algerian climatic zones

Butyrate extends health and lifespan in mice with mitochondrial deficiency

Abstract Mitochondrial diseases progressively lead to multisystemic failure with treatment options remaining extremely limited. Here, to investigate strategies that alleviate mitochondrial dysfunction, we first generate a ubiquitous and tamoxifen-inducible knockout mouse model of mitochondrial transcription factor A (TFAM), a nuclear-encoded protein involved in mitochondrial DNA (mtDNA) maintenance — Tfam fl/fl Ubc Cre-ERT2 (iTfamKO) mice. Systemic TFAM deficiency triggers mitochondrial decline in a myriad of tissues in adult mice. Consequently, iTfamKO mice manifest multiorgan dysfunction including lipodystrophy, sarcopenia, metabolic alterations, kidney failure, neurodegeneration, and locomotor dysregulation, which result in the premature death of these mice. Interestingly, iTfamKO mice display intestinal barrier disruption and gut dysbiosis, with diminished levels of microbiota-derived short-chain fatty acids (SCFAs), such as butyrate. Mice with a deficient proof-reading version of the mtDNA polymerase gamma (mtDNA-mutator mice) phenocopy the dysfunction of the intestinal barrier and bacterial dysbiosis with reduced levels of butyrate, suggesting that different mouse models of mitochondrial dysfunction share insufficient generation of butyrate. Transfer of microbiota from healthy control mice or administration of tributyrin, a butyrate precursor, delay multiple signs of multimorbidity, extending lifespan in iTfamKO mice. Mechanistically, butyrate supplementation recovers epigenetic histone acylation marks that are lost in the intestine of Tfam deficient mice. Overall, our findings highlight the relevance of preserving host-microbiota symbiosis in disorders related to mitochondrial dysfunction.

Implementing a novel PAM-4 modulation/demodulation scheme along with source and link protection in a high capacity data center architecture

Desirable data-center features include cost efficiency, high bandwidth, scalability, and protection against component failures. In this study, we propose an architecture that employs a small number of optical sources to transport data over a large number of links inside a data center. To further increase the bandwidth, two bits per symbol are transmitted by employing a novel technique for the generation and demodulation of pulse amplitude modulated (PAM) signals having a data rate of 100 Gbps. The proposed architecture provides protection against two major sources of breakdown, the laser source and the channel used for the transmission of signals. Furthermore, diversity gain can also be achieved by simultaneously transmitting the same optical signals through different channels inside the data center. The performance of the proposed architecture is observed in terms of bit error rate under different amplified spontaneous emission (ASE) noise powers.

Protective role of IRG1/itaconate in acute myocardial injury: association with NLRP3 inflammasome and oxidative stress

A hydro-topological strategy enables self-regulating biofilms for sustainable wastewater treatment

Abstract The moving bed biofilm reactor (MBBR) is a cornerstone technology in modern wastewater treatment, yet its performance is often hindered by carrier clogging, which significantly reduces overall treatment efficiency and undermines the technology’s environmental benefits. Here, we introduce a V-carrier hydro-topological design strategy that enables biofilm self-regulation, allowing simultaneous control of biofilm thickness and continuous hydraulic shear-induced self-cleaning. In a pure biofilm system treating real municipal wastewater for over 500 days, the V-carrier achieves stable and efficient nutrient removal even under low-temperature (9.1 °C) and high-loading conditions. Crucially, it achieves a 3.2-fold higher unit biomass nitrification rate with a biofilm biomass 44% lower than a conventional K3 carrier, demonstrating that treatment efficiency is decoupled from biomass quantity through optimal ecological niche design. This work establishes a paradigm for biofilm reactor design, transforming carriers from passive substrates into active regulators of microbial ecosystems, with profound implications for sustainable water infrastructure.

Understanding effectiveness of a low-cost food package for ensuring food security during the COVID-19 at the household level: Difference-in-differences analyses of a quasi-experimental trial in Bangladesh

Introduction The emergence of COVID-19 pandemic compelled to undertake a ‘lockdown or shutdown’ approach to control the spread of the virus. People from resource-limited settings experienced food insecurity due to lack of supply and access to adequate food during lockdown. Therefore, we developed a low-cost food package and assessed its effectiveness to improve household food insecurity during the COVID-19 pandemic. Method A food package was developed with low-cost, culturally acceptable foods. Each food basket, designed to support a family of four adults and/or one child for 15 days costs 23 USD. A community-based quasi-experimental intervention study was conducted to evaluate the effectiveness of the food package. A total of 245 participants were enrolled in the intervention group, and 244 participants in the control group. A community-based census was carried out to identify vulnerable households and were randomly assigned to the intervention or control groups. Data was collected to assess changes in food insecurity status using the Household Food Insecurity Access Scale, as well as dietary diversity, food frequency, morbidity, and nutritional outcomes. Results Statistically significant changes (p < 0.05) in food insecurity status were observed in the intervention group before, during, and after the intervention. The proportion of food-insecure households decreased from 45.31% to 7.80%, while the proportion of food-secure households increased from 8.60% to 31.02% after one month of intervention. The Difference-in-Differences (DID) models estimated a 13.10 percentage point improvement in proportions of food-secure households and a 16.20 percentage point reduction in food-insecure households, both of which were statistically significant (p < 0.05). Conclusion A low-cost food intervention improved the food security status of vulnerable families during COVID-19 lockdown. This finding suggests that government and other aid agencies can adopt the developed food package to ameliorate household food insecurity in adverse situations.

A novel dual-dimensional contrastive self-supervised learning-based framework for rolling bearing remaining useful life prediction

Abstract Accurate bearing remaining useful life (RUL) can effectively ensure the safe operation of equipment and enhance production efficiency. Despite the widespread application of deep learning-based prediction methods, most rely on supervised learning to directly map input signals to output RUL. However, this often ignores crucial representational properties like smoothness and monotonicity, leading to disorganized and uninterpretable representations that significantly degrade performance. To enhance representation, this paper proposes a novel dual-dimensional contrastive self-supervised learning-based framework named DCSSL for RUL prediction of rolling bearings. It is carried out in two consecutive stages. In the first stage, a strategy combining random cropping and timestamp masking for constructing positive pairs for contrastive learning is proposed. The dual-dimensional contrastive loss function that combines temporal-level and instance-level is devised to enable the model to learn state representations in unlabeled vibration data and mine rolling bearing degradation trends. Then, in the second stage, RUL prediction of labeled vibration data is achieved by fine-tuning the newly constructed prediction head. Experimental validation of DCSSL on a large number of RUL prediction tasks demonstrates its superior performance over other state-of-the-art methods.

Shared genetic and neuroimmune architecture links type 1 diabetes with neurocognitive traits

Abstract Type 1 diabetes, particularly with childhood onset, is associated with altered neurocognitive traits, yet the underlying biological mechanisms are unclear. Here, we integrate genome-wide association results with single-cell epigenomic profiles and show that type 1 diabetes heritability is enriched in accessible chromatin of human brain-resident cells, most notably microglia, across neurodevelopment into adulthood. Bonferroni-corrected cross-trait genetic correlation analyses reveal negative correlations of type 1 diabetes with intelligence, executive function, and bipolar disorder, and a positive correlation with myasthenia gravis. Conjunctional false discovery rate analysis identifies pleiotropic loci jointly influencing type 1 diabetes and neurocognitive traits, including the 17q21.31 neurogenomic hub. Mendelian randomization further demonstrates protective effects of educational attainment, intelligence, Alzheimer’s disease, and bipolar disorder on type 1 diabetes risk, whereas liability to multiple sclerosis and myasthenia gravis increases type 1 diabetes risk. In the reverse direction, liability to type 1 diabetes is associated with increased risk of myasthenia gravis. We identify several gene expression regulatory variants in brain and immune cells that jointly influence type 1 diabetes and neurocognitive traits, some of which show concordant differential expression in disease-affected versus control tissue. Together, these findings highlight pleiotropic genetic and neuroimmune mechanisms that link type 1 diabetes with cognition and neuropsychiatric disease risk.