Open Regions Research Articles

A multi-ancestry genome-wide association study identifies novel candidate loci in the RARB gene associated with hypertensive disorders of pregnancy

Genetic factors related to pregnancy-related traits are understudied, especially in ancestrally diverse cohorts. To assess maternal contributions to hypertensive disorders of pregnancy (HDP, we performed a multi-ancestry genome-wide association study (GWAS) of HDP in data from the North Carolina-based Personalized Environment and Genes Study (PEGS) cohort with validation in the UK Biobank (UKBB). The GWAS revealed two maternal loci associated with HDP at the genome-wide significance level. The lead independent variants were rs114954125 on chromosome 2 (near LRP1B; OR (95% CI): 2.96 (2.02,4.34); P=2.82 x 10-8) and rs61176331 on chromosome 3 (on RARB; OR (95% CI): 3.08 (2.12,4.48); P=3.52 x 10-9). We validated the associations near RARB with a meta-analysis of PEGS and the UK Biobank. We also identified cis-eQTLs in the candidate region associated with decreased RARB expression in macrophage cells exposed to Salmonella. Chromatin mapping in FUMA identified a significant interaction within chromosome 3's enhancer and open chromatin regions, with strong effects observed for RARB and H3P10 gene regulation in mesendoderm cells, mesenchymal stem cells, and trophoblast-like stem cells. We applied existing polygenic scores (PGS) for preeclampsia and gestational hypertension and found the scores were significantly associated with HDP in PEGS. The findings demonstrate the power of multi-ancestry studies for genetic discovery and highlight the relationship between immune response, regulation, and HDP and the utility of PGS for risk prediction.

Elevated EGR1 Binding at Enhancers in Excitatory Neurons Correlates with Neuronal Subtype-Specific Epigenetic Regulation.

Brain development and neuronal cell specification are accompanied with epigenetic changes to achieve diverse gene expression regulation. Interacting with cell-type specific epigenetic marks, transcription factors bind to different sets of cis-regulatory elements in different types of cells. Currently, it remains largely unclear how cell-type specific gene regulation is achieved for neurons. In this study, we generated epigenetic maps to perform comparative histone modification analysis between excitatory and inhibitory neurons. We found that neuronal cell-type specific histone modifications are enriched in super enhancer regions containing abundant EGR1 motifs. Further CUT&RUN data validated that more EGR1 binding sites can be detected in excitatory neurons and primarily located in enhancers. Integrative analysis revealed that EGR1 binding is strongly correlated with various epigenetic markers for open chromatin regions and associated with distinct gene pathways with neuronal subtype-specific functions. In inhibitory neurons, the majority of genomic regions hosting EGR1 binding sites become accessible at early embryonic stages. In contrast, the super enhancers in excitatory neurons hosting EGR1 binding sites gained their accessibility during postnatal stages. This study highlights the significance of transcription factor binding to enhancer regions, which may play a crucial role in establishing cell-type specific gene regulation in neurons.

Weakly nonlinear analysis of minimal models for Turing patterns

The simplest particle-based mass-action models for Turing instability – i.e. those with only two component species undergoing instantaneous interactions of at most two particles, with the smallest number of distinct interactions – fall into a surprisingly small number of classes of reaction schemes. In previous work we have computed this classification, with different schemes distinguished by the structure of the interactions. Within a given class the reaction stoichiometry and rates remain as parameters that determine the linear and nonlinear evolution of the system.Adopting the usual weakly nonlinear scalings and analysis reveals that, under suitable choices of reaction stoichiometry, and in nine of the 11 classes of minimal scheme exhibiting a spatially in-phase (“true activator-inhibitor”) Turing instability, stable patterns are indeed generated in open regions of parameter space via a generically supercritical bifurcation from the spatially uniform state. In three of these classes the instability is always supercritical while in six there is an open region in which it is subcritical. Intriguingly, however, in the remaining two classes of minimal scheme we require different weakly nonlinear scalings, since the coefficient in the usual cubic normal form unexpectedly vanishes identically. In these cases, a different set of asymptotic scalings is required.We present a complete analysis through deriving the normal form for these two cases also, which involves quintic terms. This fifth-order normal form also captures the behaviour along the boundaries between the supercritical and subcritical cases of the cubic normal form. The details of these calculations reveal the distinct roles played by reaction rate parameters as compared to stoichiometric parameters.We quantitatively validate our analysis via numerical simulations and confirm the two different scalings for the amplitude of predicted stable patterned states.

Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer.

Inter- and intra-tumor heterogeneity is considered a significant factor contributing to the development of endocrine resistance in breast cancer. Recent advances in single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) allow us to explore inter- and intra-tumor heterogeneity at single-cell resolution. However, such integrated single-cell analysis has not yet been demonstrated to characterize the transcriptome and chromatin accessibility in breast cancer endocrine resistance. In this study, we conducted an integrated analysis combining scRNA-seq and scATAC-seq on more than 80,000 breast tissue cells from two normal tissues (NTs), three primary tumors (PTs), and three tamoxifen-treated recurrent tumors (RTs). A variety of cell types among breast tumor tissues were identified, PT- and RT-specific cancer cell states (CSs) were defined, and a heterogeneity-guided core signature (HCS) was derived through such integrated analysis. Functional experiments were performed to validate the oncogenic role of BMP7, a key gene within the core signature. We observed a striking level of cell-to-cell heterogeneity among six tumor tissues and delineated the primary to recurrent tumor progression, underscoring the significance of these single-cell level tumor cell clusters classified from scRNA-seq data. We defined nine CSs, including five PT-specific, three RT-specific, and one PT-RT-shared CSs, and identified distinct open chromatin regions of CSs, as well as a HCS of 137 genes. In addition, we predicted specific transcription factors (TFs) associated with the core signature and novel biological/metabolism pathways that mediate the communications between CSs and the tumor microenvironment (TME). We finally demonstrated that BMP7 plays an oncogenic role in tamoxifen-resistant breast cancer cells through modulating MAPK signaling pathways. Our integrated single-cell analysis provides a comprehensive understanding of the tumor heterogeneity in tamoxifen resistance. We envision this integrated single-cell epigenomic and transcriptomic measure will become a powerful approach to unravel how epigenetic factors and the tumor microenvironment govern the development of tumor heterogeneity and to uncover potential therapeutic targets that circumvent heterogeneity-related failures.

The Contribution of Siliceous Plankton to Vertical Export Flux in the Eastern Mediterranean: A Comparative Study of the North Aegean, Cretan, and Ionian Seas

This study investigates the intricate dynamics of siliceous plankton species within the open marine regions of the Greek Seas, focusing on their seasonal and spatial variability. For this purpose, vertical export fluxes of diatoms (DtF), silicoflagellates (SF), and radiolaria (RF) were analyzed in three sediment trap time series obtained from the North Aegean, Cretan, and Ionian Seas. Special attention was given to diatom assemblages, resulting in the estimation of the DtF community structure and diversity for each studied site. Diatom flux values reached 353.9 × 103 valves m−2 day−1, 77.7 × 103 valves m−2 day−1, and 42.4 × 103 valves m−2 day−1 in the North Aegean, Ionian, and Cretan Seas, respectively. SF maxima were 1309.8 × 103 skeletons m−2 day−1 in the North Aegean Sea, 35.2 × 103 skeletons m−2 day−1 in the Ionian Sea, and 11.9 × 103 skeletons m−2 day−1 in the Cretan Sea (South Aegean Sea). RF values reached 13.9 × 103 radiolaria m−2 day−1, 11.9 × 103 radiolaria m−2 day−1, and 5.4 × 103 radiolaria m−2 day−1 in the North Aegean, Ionian, and Cretan Seas, respectively. The North Aegean Sea exhibited significantly higher mean total fluxes, particularly for diatoms, driven by the north-to-south oligotrophy gradient, which was influenced by riverine inflows and the nutrient-rich Black Sea water. In the Cretan and Ionian Seas, convective mixing and atmospheric deposition, especially during increased rainfall (precipitation) events, were identified as primary drivers for the increased siliceous plankton fluxes recorded in the late winter–spring months. Diatom communities were dominated by Naviculales and Fragilariales; the prevalence of the former in the North Aegean Sea is likely linked to the higher nutrient levels in its upper photic zone, as Naviculales includes species with a high affiliation to nutrient enrichment.

Influence of biofilm growth on permeability evolution in gravel layers of leachate collection system: A pore-scale analysis using Darcy-Brinkman-Stokes approach

Biofilm formation within the gravel layer of leachate collection systems (LCS) poses a significant challenge by reducing permeability, potentially leading to clogging. Understanding the impact of biofilm growth on the hydraulic performance of LCS is essential for optimizing gravel layer design. This study utilized the Navier-Stokes-Brinkman equations to develop a numerical model that describes fluid flow at the pore scale within both biofilm-covered and open pore regions of the LCS gravel layer. The model was validated using previous experimental and numerical results. A geometric model of a porous network composed of randomly packed spherical particles, reflecting actual particle sizes in LCS, was then established. This model was used to investigate the evolution of the flow field and changes in permeability under varying conditions of particle size, biofilm thickness, and permeability characteristics. The results showed that increasing biofilm thickness reduced channel cross-sectional area, elevated flow velocity, increased pressure drop, and caused an exponential decrease in permeability. The study also confirmed that the permeability and porosity of the biofilm significantly influenced the extent of permeability reduction in the LCS gravel layer. Additionally, smaller particle size combinations had a more pronounced effect on permeability reduction. These findings provide valuable insights at the pore scale, helping to predict the impact of biofilm growth on gravel layer permeability in LCS and offering essential guidance for future design and management strategies.

Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira

The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species.

A semi-automated method using object-based image analysis (OBIA) to detect and enumerate beluga whales in summer from very high-resolution (VHR) satellite imagery.

Very high-resolution (VHR) satellite imagery has proven to be useful for detection of large to medium cetaceans, such as odontocetes and offers some significant advantages over traditional detection methods. However, the significant time investment needed to manually read satellite imagery is currently a limiting factor to use this method across large open ocean regions. The objective of this study is to develop a semi-automated detection method using object-based image analysis to identify beluga whales (Delphinapterus leucas) in open water (summer) ocean conditions in the Arctic using panchromatic WorldView-3 satellite imagery and compare the detection time between human read and algorithm detected imagery. The false negative rate, false positive rate, and automated count deviation were used to assess the accuracy and reliability of various algorithms for reading training and test imagery. The best algorithm, which used spectral mean and texture variance attributes, detected no false positives and the false negative rate was low (<4%). This algorithm was able to accurately and reliably identify all the whales detected by experienced readers in the ice-free panchromatic image. The autodetection algorithm does have difficulty separately identifying whales that are perpendicular to one another, whales below the surface, and may use multiple segments to define a whale. As a result, for determining counts of whales, a reader should manually review the automated results. However, object-based image analysis offers a viable solution for processing large amounts of satellite imagery for detecting medium-sized beluga whales while eliminating all areas of the imagery which are whale-free. This algorithm could be adapted for detecting other cetaceans in ice-free water.

Critically ill patients will benefit from single isolated laminar-air-flow wards by improving the environmental microbial composition

BackgroundHospital-associated infection (HAI) is an important issue in intensive care units (ICUs). We still lack direct evidence on whether the ICU patients and/or the medical system can benefit from single isolated laminar-air-flow (LAF) wards.MethodsHigh-touched-surface (HTS) swabs from 5 sites in two kinds of wards with different ventilation systems were longitudinally collected for 16 S rRNA sequencing and Type IIB restriction site-associated DNA sequencing for Microbiome (2bRAD-M). Samples were collected for 3 months. The clinical data of patients admitted to different wards during the sampling time and the whole year were collected and compared.ResultsThe α-diversity of single wards with isolated LAF was significantly higher than open regions without LAF (p<0.01). β-diversity analysis showed differences between different wards and similarities among the same region. We also identified 3 genera attributed to the most difference between the two kinds of wards. 2bRAD-M analysis further revealed community divergence among different HTS sites. There was an overlap between HTS microbiome profiling and the clinically cultivated pathogens of patients with HAI. People in single wards had a better outcome than those in open regions (p<0.05), indicating that single wards had a protective effect for critically ill patients.ConclusionOverall, there was a prominent difference in the microbiome community between single wards and open regions. Single wards had more balanced communities which may lead to better outcomes for patients. For critically ill patients, single ward is recommended when arranging and constructing.

Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis.

Environmental exposure to dioxin has been linked to increased myocardial infarction. Smooth muscle cells (SMC) in the coronary vasculature play a critical role in atherosclerotic plaque remodeling due to their phenotypic plasticity, however, the detailed mechanism linking dioxin exposure to adverse SMC modulation is not well understood. Single-cell RNA and ATAC sequencing and histological analyses were performed on the aorta from mouse models of atherosclerosis exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or control. Primary human coronary artery SMC (HCASMC) treated in culture with TCDD were used to perform RNA-Seq, ATAC-Seq, and functional phenotypic assays. ChIP-Seq was performed with antibodies against Aryl-hydrocarbon receptor (AHR) and TCF21, two of known SMC modulating transcription factors. Modulated SMC were the most transcriptionally responsive cell type to dioxin in the atherosclerotic aorta. Dioxin accelerated disease phenotype by promoting a modulated SMC phenotype early, resulting in increased lesion size, migration of SMC, and macrophage recruitment to the lesion. We found C3 expressing modulated SMCs to be likely contributing to the increased macrophage recruitment and inflammation. Analysis of the RNA-Seq data from HCASMC treated with TCDD showed differential enrichment of biological pathways related to cell migration, localization, and inflammation. Furthermore, ATAC-Seq data showed a significant activation for pathways regulating vascular development, cell migration, inflammation, and apoptosis. With TCDD treatment, there was also enrichment of AHR ChIP-Seq peaks, while the TCF21 enrichment decreased significantly. The SMC-specific Ahr knockout resulted in increased oxidative stress in SMC, increased lesion size and macrophage content, and loss of SMC lineage cells in the lesion cap when exposed to TCDD, consistent with a more vulnerable plaque phenotype. Dioxin adversely remodels atherosclerotic plaque by accelerating the SMC- phenotypic modulation, and increasing inflammation and oxidative stress resulting in increased macrophage recruitment and lesion size. Dioxin may adversely affect the SMC phenotype and disease state by affecting the TCF21 occupancy in the open chromatin regions. Furthermore, we observed that SMC-specific deletion of Ahr in mice resulted in worsening of dioxin mediated SMC modulation and atherosclerosis, suggesting that Ahr in SMC confers protection against dioxin by promoting a stable plaque phenotype and reducing dioxin induced oxidative stress. Exposure to dioxin, an environmental pollutant present in tobacco smoke and air pollution, accelerates smooth muscle cell modulation, and atherosclerosis.Dioxin exposure leads to inflammatory smooth muscle cell phenotype characterized by complement pathway activation and increased macrophage recruitment to plaqueAryl-hydrocarbon receptor in SMC protects against oxidative stress, and promotes a stable plaque phenotype.

The distinct roles of NEIL1 and XPA in limiting aflatoxin B₁-induced mutagenesis in mice.

Dietary exposure to aflatoxin B₁ (AFB₁) is a risk factor for the development of hepatocellular carcinomas (HCCs). Following metabolic activation, AFB₁ reacts with guanines to form covalent DNA adducts, which induce high-frequency G > T transversions. The molecular signature associated with these mutational events aligns with the single base substitution signature 24 (SBS24) in the Catalog of Somatic Mutations in Cancer (COSMIC) database. Deficiencies in either base excision repair (BER) due to the absence of Nei-like DNA glycosylase 1 (NEIL1) or nucleotide excision repair (NER) due to the absence of xeroderma complementation group A protein (XPA) contribute to HCCs in murine models. In the current study, ultra-low error duplex sequencing was used to characterize mutational profiles in liver DNAs of NEIL1-deficient, XPA-deficient, and DNA repair-proficient mice following neonatal injection of 1 mg/kg AFB₁. Analyses of AFB₁-induced mutations showed high cosine similarity to SBS24, regardless of repair proficiency status. The absence of NEIL1 resulted in an approximately 30% increase in the frequency of mutations, with distribution suggesting preferential NEIL1-dependent repair of AFB₁ lesions in open chromatin regions. A trend of increased mutagenesis was also observed in the absence of XPA. Consistent with the role of XPA in transcription-coupled repair, mutational profiles in XPA-deficient mice showed disruption of the transcriptional bias in mutations associated with SBS24. Implications: Our findings define the roles of DNA repair pathways in AFB₁-induced mutagenesis and carcinogenesis in murine models, with these findings having implications in human health for those with BER and NER deficiencies.

Integrative analysis based on ATAC-seq and RNA-seq reveals a novel oncogene PRPF3 in hepatocellular carcinoma.

Assay of Transposase Accessible Chromatin Sequencing (ATAC-seq) is a high-throughput sequencing technique that detects open chromatin regions across the genome. These regions are critical in facilitating transcription factor binding and subsequent gene expression. Herein, we utilized ATAC-seq to identify key molecular targets regulating the development and progression of hepatocellular carcinoma (HCC) and elucidate the underlying mechanisms. We first compared chromatin accessibility profiles between HCC and normal tissues. Subsequently, RNA-seq data was employed to identify differentially expressed genes (DEGs). Integrating ATAC-seq and RNA-seq data allowed the identification of transcription factors and their putative target genes associated with differentially accessible regions (DARs). Finally, functional experiments were conducted to investigate the effects of the identified regulatory factors and corresponding targets on HCC cell proliferation and migration. Enrichment analysis of DARs between HCC and adjacent normal tissues revealed distinct signaling pathways and regulatory factors. Upregulated DARs in HCC were enriched in genes related to the MAPK and FoxO signaling pathways and associated with transcription factor families like ETS and AP-1. Conversely, downregulated DARs were associated with the TGF-β, cAMP, and p53 signaling pathways and the CTCF family. Integration of the datasets revealed a positive correlation between specific DARs and DEGs. Notably, PRPF3 emerged as a gene associated with DARs in HCC, and functional assays demonstrated its ability to promote HCC cell proliferation and migration. To the best of our knowledge, this is the first report highlighting the oncogenic role of PRPF3 in HCC. Furthermore, ZNF93 expression positively correlated with PRPF3, and ChIP-seq data indicated its potential role as a transcription factor regulating PRPF3 by binding to its promoter region. This study provides a comprehensive analysis of the epigenetic landscape in HCC, encompassing both chromatin accessibility and the transcriptome. Our findings reveal that ZNF93 promotes the proliferation and motility of HCC cells through transcriptional regulation of a novel oncogene, PRPF3.

Multi-winged Lorenz attractors due to bifurcations of a periodic orbit with multipliers (−1,i,−i)

Abstract We show that bifurcations of periodic orbits with multipliers ( − 1 , i , − i ) can lead to the birth of pseudohyperbolic (i.e. robustly chaotic) Lorenz-like attractors of three different types: one is a discrete analogue of the classical Lorenz attractor, and the other two are new. We call them two- and four-winged ‘Simó angels’. These three attractors exist in an orientation-reversing, three-dimensional, quadratic Hénon map. Our analysis is based on a numerical study of a normal form for this bifurcation, a three-dimensional system of differential equations with a Z4-symmetry. We investigate bifurcations in the normal form and describe those responsible for the emergence of the Lorenz attractor and the continuous-time version of the Simó angels. Both for the normal form and the 3D Hénon map, we have found open regions in the parameter space where the attractors are pseudohyperbolic, implying that for every parameter value from these regions every orbit in the attractor has positive top Lyapunov exponent.

The Challenge of Predicting the Solar Wind Speed near Sunspot Minimum

By applying potential-field source-surface and potential-field current-sheet extrapolations to photospheric field maps from three different observatories, we predict the solar wind speed at Earth for several Carrington rotations during 2018–2021 and compare the results with in situ observations. The predicted speeds are taken to be inversely correlated with the rate of flux-tube expansion inside the source surface, located at a heliocentric distance of 2.5 R ⊙. The results often differ markedly from one observatory to another and are very sensitive to the latitudinal position of the ecliptic relative to the narrow belt of slow wind that surrounds the source-surface neutral line. Our main conclusions are that (1) the magnetograph measurements themselves are a major source of uncertainty in solar wind predictions; (2) these uncertainties are especially large near solar minimum, when Earth is located near the rapid transition between slow and fast wind that occurs on either side of the heliospheric current sheet; (3) comparison of the derived open field regions with observed coronal holes provides a strong, underutilized constraint on wind speed predictions; and (4) the observed polarity of the interplanetary magnetic field provides another important constraint on the location of the source region.

Hydroelastic responses of a multi-modular very large floating structure on a flexible bottom with lateral stress in a two-layer fluid

Based on the small-amplitude water wave theory, an analytical investigation is performed for the interaction between incident waves and a multi-modular very large floating structure (VLFS) in a two-layer fluid with a flexible seabed. A vertical porous flexible plate is fixed in the center of each floating plate to suppress the hydroelastic response. A key innovation is the modeling of both the VLFSs and the seabed as thin elastic plates with the lateral stress. The analytical expressions for dispersion relationships and vertical eigenfunctions are exactly derived in the water regions with a flexible seabed. The series solution of the velocity potential is obtained through the combination of inner product and the least squares approximation method. The study uniquely illustrates the impact of lateral stress and flexible seabeds on wave propagation, revealing that at low frequencies, waves in both open water and plate-covered regions with a flexible seabed exhibit the similar propagation characteristics. At higher frequencies, however, the propagation characteristics of the waves in the open water regions remain unaffected by the presence of a flexible seabed. The lateral stress has significant effects on the roots of dispersion relationships and the hydroelastic responses. The influences of other physical parameters of the fluid and structures are also displayed graphically. The results demonstrate that the increasing number of modules and extending the vertical plates effectively suppress hydroelastic responses and reduce wave transmission. The porous barriers can reduce the stress on the vertical plates and weaken the effect of barriers for suppressing hydroelastic response.

Placental methylation and pro-inflammatory protein levels in cord blood

IntroductionThe neonates’ inflammatory response may in part be shaped during development by the placental epigenome, but evidence is scarce. We investigated the association between placental DNA methylation and pro-inflammatory proteins in cord blood. MethodsA total of 249 mother-child dyads from the Harvard Epigenetic Birth Cohort were included in this study. Genome-wide methylation in placental DNA was assessed using the Illumina Human Methylation 450 Bead Chip array and verified by pyrosequencing. Cord blood inflammation markers assessed were interleukin-6, interleukin-8 and tumor necrosis factor α, intercellular adhesion molecule 1, serum amyloid A, and C-reactive protein. ResultsWe identified differential placental DNA methylation of three loci in the HIVEP3 gene shore region that were associated with TNFα protein levels in cord blood. TNFα levels were associated with mode of delivery, gestational age and birth order. Three other loci located in the open sea region of the BCL11B gene were associated with SAA protein levels in cord blood. SAA levels were associated with birthweight, gestational age, and infant sex. ConclusionsOur results suggest a potential role for HIVEP3 and BCL11B placental DNA methylation in the acute immune response of the neonate. These immune markers were correlated with several mother and child characteristics.

Recovering Bathymetry Using BP Neural Network Combined with Modified Gravity–Geologic Method: A Case Study in the South China Sea

The gravity–geologic method (GGM) is widely used for bathymetric predictions. However, the conventional GGM cannot be applied in regions without actual bathymetric data. The modified gravity–geologic method (MGGM) enhances the accuracy of bathymetric models by supplementing short-wavelength gravity anomalies with an a priori bathymetric model, but it overlooks the significance of actual bathymetric data in the prediction process. In this study, we used the BP neural network (BPNN), incorporating shipborne depth soundings and coastline data as zero-depth estimates combined with the MGGM to produce a bathymetric model (BPGGM_BAT) for the South China Sea (105°E–122°E, 0°N–26°N). The results indicate that the BPGGM_BAT model decreases the root-mean-square (RMS) of bathymetry differences from 154.33 m to approximately 140.43 m relative to multibeam depth data. Additionally, the RMS differences between the BPGGM_BAT model and multibeam depth data show further improvements of 19.63%, 20.10%, and 19.54% when compared with the recently released SRTM15_V2.6, GEBCO_2022, and topo_V27.1 models, respectively. The precision of the BPGGM_BAT model is comparable to that of the SDUST2023BCO model, as verified using multibeam depth data in open sea regions. The BPGGM_BAT model outperforms existing models with RMS differences of 8.54% to 32.66%, as verified using Electronic Navigational Chart (ENC) bathymetric data in the regions around the Zhongsha and Nansha Islands. A power density analysis suggests that the BPGGM_BAT model is superior to the MGGM_BAT model for predicting seafloor topography within wavelengths shorter than 15 km, and its performance is closely consistent with that of the topo_V27.1 and SDUST2023BCO models. Overall, this integrated method demonstrates significant potential for improving the accuracy of bathymetric predictions.

Study of Some Reproductive Traits in Mabuya multifasciata (Sauria: Scincidae) Regarding Sexual Dimorphism during 2013-2015

The Mabuya skink is a widely distributed species in India as well as in North East India and China (Zhaao and Adler, 1995; Ngnyen et al., 2009). In fact the species Mabuya multifasciata is commonly found in the open region of villages, secondary forests of different humid regions and in the region with variable temperatures (Ngnyen et al. 2009; Li et al. 2010). Many reptiles lay eggs while Mabuya gives birth to live young. This is a unique feature in case of lizards and skink as for example Mabuya multifasciata. We studied the size of the eggs and the nutrients and its effect on the reproductive cycle. The male reproductive cycle was also studied.

Correction: Gene expression and chromatin conformation of microglia in virally suppressed people with HIV.

"Despite ART, we detected occasional microglia containing cell-associated HIV RNA and HIV DNA integrated into open regions of the host's genome (∼0.005%)" should be corrected to: "Despite ART, we detected occasional microglia containing cell-associated HIV RNA and HIV DNA integrated into open regions of the host's genome (∼0.5%)."

Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare).

Plant responses to stress caused by high temperatures involve changes occurring at the molecular, metabolic, and physiological levels. Understanding the mechanisms by which plants recognize signals to activate this response is a prerequisite for identifying key genes and signaling pathways and for obtaining heat-tolerant plants. We demonstrated the first implementation of an assay for transposase-accessible chromatin to identify open chromatin regions (OCRs) in crown tissues of barley using three genotypes carrying different allelic forms of the sdw1 gene encoding gibberellin 20-oxidase subjected to elevated temperatures. In parallel, we performed gene expression analysis, which allowed us to relate changes in chromatin state to changes in transcriptional activity. The obtained data revealed that the hypersensitive chromatin regions within the genes were more repeatable than those outside the gene intervals. We observed that prolonged exposure to high temperatures increased chromatin accessibility. Genes with OCRs in their regulatory regions were involved in stress signaling and tolerance, including calcium-dependent protein kinase, mitogen-activated protein kinase (MAPK3), receptor-like cytoplasmic kinase (RLK), TIFY domain-containing transcriptional regulator, bZIP transcription factor, and regulatory protein NPR1. The effect of genotype on gene expression was not as pronounced as that of temperature. By combining results from the differential analysis of chromatin accessibility and expression profiles, we identified genes with high temperature-induced changes in chromatin accessibility associated with expression alterations. Importantly, our data revealed a relationship between the loss of chromatin accessibility in response to heat and the downregulation of genes related to gibberellin signaling.