Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Kidney failure, the decrease of kidney function below a threshold necessary to support life, is a major cause of morbidity and mortality. We performed a genome-wide association study (GWAS) of 406,504 individuals in the UK Biobank, identifying 430 loci affecting kidney function in middle-aged adults. To investigate the cell types affected by these loci, we integrated the GWAS with human kidney candidate cis-regulatory elements (cCREs) identified using single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq). Overall, 56% of kidney function heritability localized to kidney tubule epithelial cCREs and an additional 7% to kidney podocyte cCREs. Thus, most heritable differences in adult kidney function are a result of altered gene expression in these two cell types. Using enhancer assays, allele-specific scATAC-seq and machine learning, we found that many kidney function variants alter tubule epithelial cCRE chromatin accessibility and function. Using CRISPRi, we determined which genes some of these cCREs regulate, implicating NDRG1, CCNB1 and STC1 in human kidney function.

Current genomic deep learning models display decreased performance in cell type-specific accessible regions.

BACKGROUND: A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance genome-wide; however, cis regulatory elements (CREs), which play critical roles in gene regulation, make up only a small fraction of the genome. Furthermore, cell type-specific CREs contain a large proportion of complex disease heritability. RESULTS: We evaluate genomic deep learning models in chromatin accessibility regions with varying degrees of cell type specificity. We assess two modeling directions in the field: general purpose models trained across thousands of outputs (cell types and epigenetic marks) and models tailored to specific tissues and tasks. We find that the accuracy of genomic deep learning models, including two state-of-the-art general purpose models-Enformer and Sei-varies across the genome and is reduced in cell type-specific accessible regions. Using accessibility models trained on cell types from specific tissues, we find that increasing model capacity to learn cell type-specific regulatory syntax-through single-task learning or high capacity multi-task models-can improve performance in cell type-specific accessible regions. We also observe that improving reference sequence predictions does not consistently improve variant effect predictions, indicating that novel strategies are needed to improve performance on variants. CONCLUSIONS: Our results provide a new perspective on the performance of genomic deep learning models, showing that performance varies across the genome and is particularly reduced in cell type-specific accessible regions. We also identify strategies to maximize performance in cell type-specific accessible regions.

Water-Enhancing Gels Exhibiting Heat-Activated Formation of Silica Aerogels for Protection of Critical Infrastructure During Catastrophic Wildfire.

A promising strategy to address the pressing challenges with wildfire, particularly in the wildland-urban interface (WUI), involves developing new approaches for preventing and controlling wildfire within wildlands. Among sprayable fire-retardant materials, water-enhancing gels have emerged as exceptionally effective for protecting civil infrastructure. They possess favorable wetting and viscoelastic properties that reduce the likelihood of ignition, maintaining strong adherence to a wide array of surfaces after application. Although current water-enhancing hydrogels effectively maintain surface wetness by creating a barricade, they rapidly desiccate and lose efficacy under high heat and wind typical of wildfire conditions. To address this limitation, unique biomimetic hydrogel materials from sustainable cellulosic polymers crosslinked by colloidal silica particles are developed that exhibit ideal viscoelastic properties and facile manufacturing. Under heat activation, the hydrogel transitions into a highly porous and thermally insulative silica aerogel coating in situ, providing a robust protective layer against ignition of substrates, even when the hydrogel fire suppressant becomes completely desiccated. By confirming the mechanical properties, substrate adherence, and enhanced substrate protection against fire, these heat-activatable biomimetic hydrogels emerge as promising candidates for next-generation water-enhancing fire suppressants. These advancements have the potential to dramatically improve the ability to protect homes and critical infrastructure during wildfire.

A dual-targeted electrochemical aptasensor for neuroblastoma-related microRNAs detection.

Neuroblastoma (NB) is a significant pediatric cancer associated with high mortality rates, demanding innovative and appropriate approaches for its accurate detection. This paper described the design of a dual-target electrochemical aptasensor capable of simultaneously detecting neuroblastoma-associated microRNAs (miRNA-181 and miRNA-184) with exceptional sensitivity. Screen-printed carbon electrodes (SPCEs) were utilized with gold nanorods (AuNRs), and aptamers functionalized gold nanoparticles (AuNPs) to improve sensitivity, specificity, and portable detection ability. The detection method employed in this study includes differential pulse voltammetry (DPV) and cyclic voltammetry (CV). Our aptasensor exhibited remarkable limits of detections (LODs) of 5.10 aM for miRNA-181 and 9.39 aM for miRNA-184, respectively, along with a broad linear range spanning from 0.1 fM to 100 pM for both miRNAs. The practical significance of neuroblastoma diagnosis was shown through the validation of serum samples and comparison with quantitative polymerase chain reaction (qPCR). Our electrochemical aptasensor is user-friendly, easy to engineer, and offers a promising approach for accurately and selectively detecting important miRNA biomarkers in cancer screening and diagnosis, showing potential application in various clinical scenarios.

Male autism spectrum disorder is linked to brain aromatase disruption by prenatal BPA in multimodal investigations and 10HDA ameliorates the related mouse phenotype.

Male sex, early life chemical exposure and the brain aromatase enzyme have been implicated in autism spectrum disorder (ASD). In the Barwon Infant Study birth cohort (n = 1074), higher prenatal maternal bisphenol A (BPA) levels are associated with higher ASD symptoms at age 2 and diagnosis at age 9 only in males with low aromatase genetic pathway activity scores. Higher prenatal BPA levels are predictive of higher cord blood methylation across the CYP19A1 brain promoter I.f region (P = 0.009) and aromatase gene methylation mediates (P = 0.01) the link between higher prenatal BPA and brain-derived neurotrophic factor methylation, with independent cohort replication. BPA suppressed aromatase expression in vitro and in vivo. Male mice exposed to mid-gestation BPA or with aromatase knockout have ASD-like behaviors with structural and functional brain changes. 10-hydroxy-2-decenoic acid (10HDA), an estrogenic fatty acid alleviated these features and reversed detrimental neurodevelopmental gene expression. Here we demonstrate that prenatal BPA exposure is associated with impaired brain aromatase function and ASD-related behaviors and brain abnormalities in males that may be reversible through postnatal 10HDA intervention.

Ruthenium speciation and distribution in the environment: A review.

The review focuses on speciation and migration of anthropogenic ruthenium (Ru) originated from nuclear industry releases and presents updated information regarding Ru in the environment. It provides analysis of the main pathways of Ru species distribution in the aqueous and terrestrial environment, starting from its natural occurrence, generation and release from anthropogenic sources, predominant speciation, and ending with bioaccumulation, which can be directly or indirectly related to human health. Literature sources belonging to the post-Chernobyl time frame were preferentially considered, in which Ru-103 and Ru-106 are the major fission isotopes studied due to their traceability in the environment and their relatively long half-lives.

Patterns and Risk Factors for Rehospitalizations Within the First 90 Days Following Discharge After Heart Transplantation.

BACKGROUND: Heart transplantation (HT) recipients are at risk for urgent rehospitalizations following discharge. However, data on prevalence, risk factors and clinical outcomes associated with post-HT rehospitalization are limited. METHODS: This study aims to describe patterns of urgent rehospitalizations in HT recipients at a cardiology reference center in Brazil. Rehospitalizations and deaths occurring within the first 90 days following hospital discharge were identified. Regression models were used to identify variables associated with urgent rehospitalizations. RESULTS: A total of 239 patients were included. Of those, 118 (49.4%) presented with a rehospitalization within 90 days following hospital discharge and 5 (2.01%) died. Most patients who were rehospitalized had one new hospital admission (86.0%). The main cause of urgent rehospitalization was infection (55.0%). In the multivariate analysis, elevated C-reactive protein at discharge and the occurrence of intracranial bleeding at index hospitalization were associated with an increased risk of readmission. Longer duration of index hospitalization and use of lower doses of azathioprine were associated with a lower risk of rehospitalization. CONCLUSION: Around half of HT recipients were rehospitalized within the first 90 days after hospital discharge. Understanding factors associated with post-HT rehospitalization may help the implementation of strategies to avoid patient morbidity and hospital costs.

Effects of environmental variability on phytoplankton structure, diversity and biomass at the Brazil-Malvinas Confluence (BMC).

The Brazil-Malvinas Confluence (BMC) is a significant biological frontier where distinct currents meet, fostering optimal conditions for phytoplankton development. In this study we tested the hypothesis that eddys promote an increase in phytoplankton biomass at the Brazil-Malvinas Confluence (BMC), altering species diversity. Phytoplankton were collected with Niskin bottles and nutrient concentrations assessed at two depths (Surface and Deep Chlorophyll Maximum Layer - DCML) in areas outside and under the influence of Cold-Core (CCE) and Warm-Core (WCE) Eddies. Environmental variables were determined in situ using a CTD profiler. Four regions were separated based on environmental variables and phytoplankton species, namely, the Brazil Current (BC), Malvinas Current (MC), CCE, and WCE. Species diversity was higher in the eddies. The conditions of the WCE were different from those of the CCE, with low temperature and salinity and high cell density values in the latter. The phylum Bacillariophyta was predominant in terms of species richness in all regions and was responsible for the higher cell density in the MC, while dinoflagellates were dominant in the BC and eddies. Therefore, eddy activity alters the structure, diversity and biomass of the phytoplankton community in the BMC.

Etiology-specific incidence and mortality of diarrheal diseases in the African region: a systematic review and meta-analysis.

BACKGROUND: Diarrheal diseases substantially affect public health impact in low- and middle-income countries (LMIC), particularly in Africa, where previous studies have indicated a lack of comprehensive data. With a growing number of primary studies on enteric infections in Africa, this study aimed to estimate the incidence and mortality of diarrheal pathogens across all ages in Africa in the year 2020. We also explored different methodological assumptions to allow comparison with other approaches. METHODS: Through a systematic review and meta-analysis of data from African LMICs, we estimated the etiology proportions for diarrheal diseases and deaths. We combined the etiology proportions with incidence data collected from a population survey in Africa from 2020 and mortality data from the Global Health Observatory of WHO. RESULTS: We estimated 1,008 billion diarrhea cases (95% UI 447 million-1,4 billion) and 515,031 diarrhea deaths (95% UI 248,983-1,007,641) in the African region in 2020. In children under five, enteroaggregative E. coli (EAEC) (44,073 cases per 100,000 people, 95% UI 18,818 - 60,922) and G. lamblia (36,116 cases per 100,000 people, 95% UI 15,245 - 49,961) were the leading causes of illness. Enteroinvasive E. coli (EIEC) (155 deaths per 100,000 people, 95% UI 106.5-252.9) and rotavirus (61.5 deaths per 100,000 people, 95% UI 42.3-100.3) were the primary causes of deaths. For children over five and adults, Salmonella spp. caused the largest number of diarrheal cases in the population of children ≥ 5 and adults (122,090 cases per 100,000 people, 95% UI 51,833 - 168,822), while rotavirus (16.4 deaths per 100,000 people, 95% UI 4.2-36.7) and enteroaggregative E. coli (EAEC) (14.6 deaths per 100,000 people, 95% UI 3.9-32.9) causing the most deaths. Geographically, the highest incidence of diarrhea was in Eastern Africa for children under five (114,389 cases per 100,000 people, 95% UI 34,771 - 172,884) and Central Africa for children over five and adults (117,820 cases per 100,000 people, 95% UI 75,111-157,584). Diarrheal mortality was highest in Western Africa for both children below five and above (children < 5: 194.5 deaths per 100,000 people, 95% UI 120-325.4; children ≥ 5 and above: 33.5 deaths per 100,000 people, 95% UI 12.9-75.1). CONCLUSION: These findings provide new information on the incidence and mortality of sixteen pathogens and highlight the need for surveillance and control of diarrheal infectious diseases in Africa. The cause-specific estimates are crucial for prioritizing diarrheal disease prevention in the region.

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Kidney disease is highly heritable; however, the causal genetic variants, the cell types in which these variants function, and the molecular mechanisms underlying kidney disease remain largely unknown. To identify genetic loci affecting kidney function, we performed a GWAS using multiple kidney function biomarkers and identified 462 loci. To begin to investigate how these loci affect kidney function, we generated single-cell chromatin accessibility (scATAC-seq) maps of the human kidney and identified candidate cis-regulatory elements (cCREs) for kidney podocytes, tubule epithelial cells, and kidney endothelial, stromal, and immune cells. Kidney tubule epithelial cCREs explained 58% of kidney function SNP-heritability and kidney podocyte cCREs explained an additional 6.5% of SNP-heritability. In contrast, little kidney function heritability was explained by kidney endothelial, stromal, or immune cell-specific cCREs. Through functionally informed fine-mapping, we identified putative causal kidney function variants and their corresponding cCREs. Using kidney scATAC-seq data, we created a deep learning model (which we named ChromKid) to predict kidney cell type-specific chromatin accessibility from sequence. ChromKid and allele specific kidney scATAC-seq revealed that many fine-mapped kidney function variants locally change chromatin accessibility in tubule epithelial cells. Enhancer assays confirmed that fine-mapped kidney function variants alter tubule epithelial regulatory element function. To map the genes which these regulatory elements control, we used CRISPR interference (CRISPRi) to target these regulatory elements in tubule epithelial cells and assessed changes in gene expression. CRISPRi of enhancers harboring kidney function variants regulated NDRG1 and RBPMS expression. Thus, inherited differences in tubule epithelial NDRG1 and RBPMS expression may predispose to kidney disease in humans. We conclude that genetic variants affecting tubule epithelial regulatory element function account for most SNP-heritability of human kidney function. This work provides an experimental approach to identify the variants, regulatory elements, and genes involved in polygenic disease.