Accessibility Maps Research Articles

National-scale 1-km maps of hospital travel time and hospital accessibility in China

Ensuring equitable access to health services is crucial for public welfare and social equity, and is a key objective of the United Nations’ Sustainable Development Goals (SDGs). However, existing datasets often define hospital accessibility using travel time to hospitals in geographic dimension only, without considering the supply (hospital capacity) and demand (population distribution) dynamics. To overcome this limitation, we developed and validated a national-scale 1 km map of both hospital travel time and hospital accessibility in China. We used the Gaussian two-step floating catchment area (Ga2SFCA) model to calculate hospital accessibility, incorporating hospital capacity and service population. Various file types and statistical indicators are provided, making the dataset highly accessible for non-specialists. The dataset fills the gap in publicly available nationwide hospital accessibility data for China and can serve as a critical tool in optimizing resource allocation and developing targeted strategies to improve healthcare equity.

High-Resolution Genome-Wide Mapping of Chromatin Accessibility and Torsional Stress.

Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. Here, we introduce a high-resolution method based on the intercalator trimethylpsoralen (TMP) to address this challenge. We describe a method to establish the zero-torsion baseline while preserving the chromatin state of the genome. This approach enables both high-resolution mapping of accessibility and torsional stress in chromatin in the cell. Our analysis reveals transcription-generated torsional domains consistent with the twin-supercoiled-domain model of transcription and suggests a role for torsional stress in recruiting topoisomerases and in regulating 3D genome architecture via cohesin. This new method provides a potential path forward for using TMP to measure torsional stress in the genome without the confounding contribution of accessibility in chromatin.

Experience-Sharing to Support Inclusive Travel for Blind and Partially Sighted People

This research aimed to understand the challenges blind and partially sighted people experience in tourism and the travel information they need to plan their travel experiences effectively. To this end, we designed a mixed-methods study consisting of semi-structured interviews and co-design workshops, which were conducted to identify the needs of BPS people and the barriers experienced due to a lack of access to such information. The findings provide insights into the information-seeking process and highlight the role of experience sharing in cultivating a sense of agency, contribution, and interdependence. This study also contributes an accessible tourism ecosystem map based on our findings to highlight the different sources of travel information and their potential role in supporting inclusive travel for BPS people. The findings have implications for research and tourism service design and serve as a tool to motivate research on technologies to support inclusive leisure travel for BPS people and to inform the design of inclusive tourism services.

Single-cell transcriptome and chromatin accessibility mapping of upper lip and primary palate fusion.

Cleft lip and/or primary palate (CL/P) represent a prevalent congenital malformation, the aetiology of which is highly intricate. Although it is generally accepted that the condition arises from failed fusion between the upper lip and primary palate, the precise mechanism underlying this fusion process remains enigmatic. In this study, we utilized transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) to interrogate lambdoidal junction tissue derived from C57BL/6J mouse embryos at critical stages of embryogenesis (10.5, 11.5 and 12.5 embryonic days). We successfully identified distinct subgroups of mesenchymal and ectodermal cells involved in the fusion process and characterized their unique transcriptional profiles. Furthermore, we conducted cell differentiation trajectory analysis, revealing a dynamic repertoire of genes that are sequentially activated or repressed during pseudotime, facilitating the transition of relevant cell types. Additionally, we employed scATAC data to identify key genes associated with the fusion process and demonstrated differential chromatin accessibility across major cell types. Finally, we constructed a dynamic intercellular communication network and predicted upstream transcriptional regulators of critical genes involved in important signalling pathways. Our findings provide a valuable resource for future studies on upper lip and primary palate development, as well as congenital defects.

Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells.

Accurate specification of female and male germ cells during embryonic development is critical for sexual reproduction. Primordial germ cells (PGCs) are the bipotential precursors of mature gametes that commit to an oogenic or spermatogenic fate in response to sex-determining cues from the fetal gonad. The critical processes required for PGCs to integrate and respond to signals from the somatic environment in gonads are not understood. In this study, we developed the first single-nucleus multiomics map of chromatin accessibility and gene expression during murine PGC development in both XX and XY embryos. Profiling of cell-type specific transcriptomes and regions of open chromatin from the same cell captured the molecular signatures and gene networks underlying PGC sex determination. Joint RNA and ATAC data for single PGCs resolved previously unreported PGC subpopulations and cataloged a multimodal reference atlas of differentiating PGC clusters. We discovered that regulatory element accessibility precedes gene expression during PGC development, suggesting that changes in chromatin accessibility may prime PGC lineage commitment prior to differentiation. Similarly, we found that sexual dimorphism in chromatin accessibility and gene expression increased temporally in PGCs. Combining single-nucleus sequencing data, we computationally mapped the cohort of transcription factors that regulate the expression of sexually dimorphic genes in PGCs. For example, the gene regulatory networks of XX PGCs are enriched for the transcription factors, TFAP2c, TCFL5, GATA2, MGA, NR6A1, TBX4, and ZFX. Sex-specific enrichment of the forkhead-box and POU6 families of transcription factors was also observed in XY PGCs. Finally, we determined the temporal expression patterns of WNT, BMP, and RA signaling during PGC sex determination, and our discovery analyses identified potentially new cell communication pathways between supporting cells and PGCs. Our results illustrate the diversity of factors involved in programming PGCs towards a sex-specific fate.

Variation of Soil Erosion Estimates when Using Different Maps of Arable Land of the Belgorod Region

Current medium- and small-scale estimates of soil erosion in Russia are very few. At the same time, a favorable situation has now developed for assessing the rates and volumes of soil erosion losses. Erosion models have been developed that are adapted to available digital elevation models, various farmland masks and climate databases have been created. The paper studies the accuracy of erosion estimates using various maps of arable land. Two maps are public (ESA WC, GLCLU), the third is the official Ministry of Agriculture (MA) of the Russian Federation, the fourth map is an author’s reference map of Alekseevsky district. It has been established that the map of the MA gives the most average arable land areas among the first three maps. Public access maps showed maximum and minimum estimates of arable land area. Comparison with the standard showed that the accuracy of the map of the MA does not exceed 90%, the remaining maps – 84 and 83%. The area of arable land in the Belgorod region varies slightly (from 1,445 to 1,586 thousand hectares); so the region is favorable for erosion modelling. Deviations from the average rates of soil erosion calculated using different maps of arable land in the region as a whole amounted to 7%, and in some areas reached 27%. Thus, today assessments of soil erosion at the regional level can be carried out with an error of at least 10–15% only as a result of the uncertainty in mapping the boundaries of arable land. In the Russia as a whole, data on the area of arable land varies significantly, from 80 to 132 million hectares. Consequently, the use of existing maps of arable land can lead to significant uncertainties in soil erosion estimates averaged at the level of districts and above.

Integrating Active and Passive Remote Sensing Data for Forest Age Estimation in Shangri-La City, China

The accurate mapping of age structure and access to spatially explicit information are essential to optimal planning and policy-making for forest ecosystems, including forest management and sustainable economic development. Specifically, surveying and mapping the age structure of forests is crucial for calculating the carbon sequestration capacity of forest ecosystems. However, spatial heterogeneity and limited accessibility make forest age mapping in mountainous areas challenging. Here, we present a new workflow using ICESat-2 LiDAR data integrated with multisource remote sensing imagery to estimate forest age in Shangri-La, China. Two methods—a climate-driven exponential model and a random forest algorithm—are compared to infer the age structure of the five dominant species in Shangri-La. The climate-driven model, with an R2 of 0.67 and an RMSE of 12.79 years, outperforms the random forest model. The derived wall-to-wall forest age map at 30 m resolution reveals that nearly all forests in Shangri-La are mature or overmature, especially among the high-elevation species Abies fabri (Mast.) Craib and Picea asperata Mast., compared with Pinus yunnanensis Franch., Quercus aquifolioides Rehd. and E.H. Wils. and Pinus densata Mast., where the age structure is more evenly distributed across different elevation ranges. Younger forests are frequently found around human settlements and along the Jinsha River valley, whereas older forests are located in remote and high-elevation areas that are less disturbed. The combined use of active and passive remote sensing data has resulted in substantial improvements in the spatial detail and accuracy of wall-to-wall age mapping, which is expected to be a cost-effective approach for supporting forest management and carbon accounting in this important ecological region. The method developed here can be scaled to other mountain areas both to understand the age patterns and structure of mountain forests and to provide critical information for forestation, reforestation and carbon accounting in surface-to-high mountain areas, which are increasingly crucial for climate mitigation.

Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes

Genome-wide association studies (GWAS) identified over fifty loci associated with lung cancer risk. However, underlying mechanisms and target genes are largely unknown, as most risk-associated variants might regulate gene expression in a context-specific manner. Here, we generate a barcode-shared transcriptome and chromatin accessibility map of 117,911 human lung cells from age/sex-matched ever- and never-smokers to profile context-specific gene regulation. Identified candidate cis-regulatory elements (cCREs) are largely cell type-specific, with 37% detected in one cell type. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs combined with transcription factor footprinting prioritize the variants for 68% of the GWAS loci. CCV-colocalization and trait relevance score indicate that epithelial and immune cell categories, including rare cell types, contribute to lung cancer susceptibility the most. A multi-level cCRE-gene linking system identifies candidate susceptibility genes from 57% of the loci, where most loci display cell-category-specific target genes, suggesting context-specific susceptibility gene function.

Empowering Vulnerable Regions through Accessible Disaster Mapping: Developing User-Friendly Platforms for Underdeveloped Regions and Non-Specialists

Empowering Vulnerable Regions through Accessible Disaster Mapping: Developing User-Friendly Platforms for Underdeveloped Regions and Non-Specialists

Empowering Disabled Voices: A Practical Guide for Methodological Shifts in Biology Education Research.

Biology education research provides important guidance for educators aiming to ensure access for disabled students. However, there is still work to be done in developing similar guidelines for research settings. By using critical frameworks that amplify the voices of people facing multiple forms of marginalization, there is potential to transform current biology education research practices. Many biology education researchers are still in the early stages of understanding critical disability frameworks, such as Disability Critical Race Studies (DisCrit), which consists of seven tenets designed to explore the intersecting experiences of ableism and racism. Our Research Methods Essay uses DisCrit as a model framework and pulls from other related critical disability frameworks to empower disabled voices in biology education research. Drawing from existing scholarship, we discuss how biology education researchers can design, conduct, and share research findings. Additionally, we highlight strategies that biology education scholars can use in their research to support access for participants. We propose the creation and sharing of Access and Equity Maps to help plan-and make public-the steps researchers take to foster access in their research. We close by discussing frequently asked questions researchers may encounter in taking on critical frameworks, such as DisCrit.

Mapping ignorance to uncover shortfalls in the knowledge on global Orthoptera distribution

Understanding the spatiotemporal distribution of species is fundamental for ecology, evolution and conservation. However, this and other aspects of biodiversity knowledge suffer from shortcomings and biases. Quantifying and mapping biodiversity knowledge shortfalls is therefore crucial to ascertain the current quality and completeness of biodiversity data, prioritize sites for (re)sampling, or plan conservation interventions. Here, we compile a comprehensive dataset of Orthoptera occurrences, and use it to create a global ‘ignorance map’ based on taxonomic, survey and temporal completeness, and on survey and temporal evenness of the inventories. We hypothesize that knowledge of Orthopteran biodiversity is relatively poorer in tropical regions compared to temperate regions, and in the south compared to the northern hemisphere. Due to biocultural factors, we expect regions in the tropics and the Global South to have lower levels of completeness and evenness in time and space for all the studied aspects of biodiversity information. Our findings show gaps in the knowledge of orthopteran distributions, which are characterized by low survey and temporal evenness in tropical regions, but also in many temperate regions (e.g., most of the countries in temperate Asia). The combination of multiple dimensions of biodiversity knowledge (taxonomic, spatial and temporal) reveals that biogeographic interpretations based on only one component can lead to an illusion of completeness. We believe that the novel framework used in our study can guide future research towards building more accessible maps of biogeographical ignorance for entire groups.

The Impact of Health Policy on Access to Healthcare: Utilizing Geographic Information Systems (GIS) for Detailed Access and Equity Mapping

Health policies are significant in relation to health equity and accessibility. Achieving equity in health care must understand the geographic distribution of health care and the impact of policy decisions on access Planners can use Geographic Information Systems (GIS) as an aid powerful to visualize and scrutinize these differences. The current study addresses some of the challenges of integrating multiple data sources, definitions of access and equity and the dynamic nature of health care processes. Furthermore, sophisticated analytical methods are needed to truly map all complex health care systems. Therefore this paper, describe a cross-sectional mental health treatment (C-SMHT) that uses a fuzzy inference system to assess justice and access to health care. Using ambiguous GIS data to address uncertainty and environmental variability, this approach provides a comprehensive picture of how policy change has shaped health disparities to improve. C-SMHT has many applications for policy makers as well as public health practitioners. This paper will provide a snapshot of mental health provider availability and utilization. Simulation studies to examine how the effectiveness of the C-SMHT approach can help to better identify underserved areas, better allocate resources, and deliver treatment were found to be good. A number of initiatives will be developed as part of this project to assess their impact on the availability of mental health services in defined areas or countries. In addition to providing recommendations to policy makers based on research findings, the simulation will also provide insights into how policies affect equity and access.

The public transport disadvantaged in a highly transit-oriented city: An analytical framework, key challenges and opportunities

This paper proposes a holistic framework to identify public transport disadvantaged areas in terms of the level of services (LOS), area-based accessibility, and facility-based accessibility by employing the General Transit Feed Specification (GTFS) dataset. The framework considers the spatial and temporal levels of transit services, the spatial separation by urban functional areas, the availability of facilities based on the cumulative opportunity method, and the minimum time cost based on dual accessibility. A case study is performed in Hong Kong. The results show that the main problem for rural residents using public transport services lies in walking to transit stops/piers instead of long waits at public transport stops or infrequent services. The map of area-based accessibility shows great variations by urban functional areas. Despite being a highly transit-dependent city, we find huge disparities of accessibility to public facilities within Hong Kong and people living in some rural areas have difficulties in accessing basic services such as education, health care and shopping through public transport. Theoretically, this study reinforces the significance of place-based transport disadvantage and its intricate relationship with urban form. Empirically, it provides practical recommendations for public transport planning. The findings can direct transit agencies to re-plan and deploy services such as introducing demand-responsive transit services to better address the needs of people living in transport disadvantaged areas.

Detailed mapping of chromatin accessibility and transcriptome of the healthy breast.

Detailed mapping of chromatin accessibility and transcriptome of the healthy breast.

Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry.

Single-nucleus analysis allows robust cell-type classification and helps to establish relationships between chromatin accessibility and cell-type-specific gene expression. Here, using samples from 92 women of several genetic ancestries, we developed a comprehensive chromatin accessibility and gene expression atlas of the breast tissue. Integrated analysis revealed ten distinct cell types, including three major epithelial subtypes (luminal hormone sensing, luminal adaptive secretory precursor (LASP) and basal-myoepithelial), two endothelial and adipocyte subtypes, fibroblasts, T cells, and macrophages. In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks. By integrating breast epithelial cell gene expression signatures with spatial transcriptomics, we identified gene expression and signaling differences between lobular and ductal epithelial cells and age-associated changes in signaling networks. LASP cells and fibroblasts showed genetic ancestry-dependent variability. An estrogen receptor-positive subpopulation of LASP cells with alveolar progenitor cell state was enriched in women of Indigenous American ancestry. Fibroblasts from breast tissues of women of African and European ancestry clustered differently, with accompanying gene expression differences. Collectively, these data provide a vital resource for further exploring genetic ancestry-dependent variability in healthy breast biology.

New Insights in the Computational pKb Determination of Primary Amines and Anilines.

Extensive research has already provided reliable methods for the in silico prediction of pKa, while a trustworthy strategy for pKb determination is still being sought. Indeed, the approaches previously exploited for computing pKa have shown their weakness in predicting pKb. In the light of the exceptional reliability demonstrated in the pKa calculation of a wide panel of organic acids, in this work, we exploited our "easy to use methodology", based on the direct approach, to predict the pKb of primary amines. Herein, CAM-B3LYP was compared to WB97XD and B3PW91, exploring the solvation model based on density (SMD) and the polarizable continuum model (PCM), in the presence of two explicit water molecules. Noteworthy, CAM-B3LYP and WB97XD returned completely different solvent accessible surfaces (SAS) and electron potential maps (EPM) for the bases and the conjugated acids, independently from the nature of the substituents. Once again, CAM-B3LYP/SMD/2H2O method confirmed its remarkable reliability, leading to a minimum average error (MAE) lower than 0.3. This outstanding result strengthens the trustworthiness of our method, already successfully applied to predict the pKa of different substituted phenols and carboxylic acids. Thus, our "easy-to-use" process can predict also the pKb of primary ammines and anilines, always ensuring consistent outputs.

Light-responsive transcription factors VvHYH and VvGATA24 mediate wax terpenoid biosynthesis in Vitis vinifera.

The cuticular wax that covers the surfaces of plants is the first barrier against environmental stresses and increasingly accumulates with light exposure. However, the molecular basis of light-responsive wax biosynthesis remains elusive. In grape (Vitis vinifera), light exposure resulted in higher wax terpenoid content and lower decay and abscission rates than controls kept in darkness. Assay for transposase-accessible chromatin with high-throughput sequencing and RNA-seq data were integrated to draw the chromatin accessibility and cis-elements regulatory map to identify the potential action sites. Terpenoid synthase 12 (VvTPS12) and 3-hydroxy-3-methylglutaryl-CoA reductase 2 (VvHMGR2) were identified as grape wax biosynthesis targets, while VvHYH and VvGATA24 were identified as terpenoid biosynthesis activators, as more abundant wax crystals and higher wax terpenoid content were observed in transiently overexpressed grape berries and Nicotiana benthamiana leaves. The interaction between VvHYH and the open chromatin of VvTPS12 was confirmed qualitatively using a dual luciferase assay and quantitatively using surface plasma resonance, with an equilibrium dissociation constant of 2.81 nm identified via the latter approach. Molecular docking simulation implied the structural nature of this interaction, indicating that 24 amino acid residues of VvHYH, including Arg106A, could bind to the VvTPS12 G-box cis-element. VvGATA24 directly bound to the open chromatin of VvHMGR2, with an equilibrium dissociation constant of 8.59 nm. Twelve amino acid residues of VvGATA24, including Pro218B, interacted with the VvHMGR2 GATA-box cis-element. Our work characterizes the mechanism underlying light-mediated wax terpenoid biosynthesis and provides gene targets for future molecular breeding.

Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq.

Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis.

CONTRIBUTION OF GIS IN HEALTH PLANNING, CASES OF ONCOLOGY IN ALGERIA

Geographic Information Systems (GIS) have become an essential tool in health planning, allowing for the analysis and visualization of spatial data to improve healthcare. In Algeria, the use of GIS in oncological care is still in its early stages, but has the potential to greatly enhance the planning and delivery of cancer services. This study aims to assess the contribution of GIS to health planning in the provision of oncological care in Algeria. Specifically, we will examine how Network analysis can be used to identify areas with high accessibility, map out healthcare facilities and resources, and optimize the allocation of resources to improve access to cancer treatment.A review of existing literature on the use of GIS in health planning and oncological care will be conducted, along with an analysis of cancer incidence data in Algeria. GIS software will be used to map out accessibility rates, healthcare facilities, and population distribution to identify areas in need of improved oncological services. The results of this study will provide valuable insights into how GIS can be utilized to enhance health planning in the provision of oncological care in Algeria. By identifying areas with high accessibility rates and mapping out healthcare resources, policymakers and healthcare providers can better allocate resources to improve access to cancer treatment and ultimately improve patient outcomes.

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.