Accessibility Maps Research Articles

Regulation of chromatin accessibility by hypoxia and HIF.

Reduced oxygen availability (hypoxia) can act as a signalling cue in physiological processes such as development, but also in pathological conditions such as cancer or ischaemic disease. As such, understanding how cells and organisms respond to hypoxia is of great importance. The family of transcription factors called Hypoxia Inducible Factors (HIFs) co-ordinate a transcriptional programme required for survival and adaptation to hypoxia. However, the effects of HIF on chromatin accessibility are currently unclear. Here, using genome wide mapping of chromatin accessibility via ATAC-seq, we find hypoxia induces loci specific changes in chromatin accessibility are enriched at a subset hypoxia transcriptionally responsive genes, agreeing with previous data using other models. We show for the first time that hypoxia inducible changes in chromatin accessibility across the genome are predominantly HIF dependent, rapidly reversible upon reoxygenation and partially mimicked by HIF-α stabilisation independent of molecular dioxygenase inhibition. This work demonstrates that HIF is central to chromatin accessibility alterations in hypoxia, and has implications for our understanding of gene expression regulation by hypoxia and HIF.

Accessible Maps in a Group of Classical or Quantum Channels

We study the problem of accessibility in a set of classical and quantum channels admitting a group structure. Group properties of the set of channels, and the structure of the closure of the analyzed group [Formula: see text] plays a pivotal role in this regard. The set of all convex combinations of the group elements contains a subset of channels that are accessible by a dynamical semigroup. We demonstrate that accessible channels are determined by probability vectors of weights of a convex combination of the group elements, which depend neither on the dimension of the space on which the channels act, nor on the specific representation of the group. Investigating geometric properties of the set [Formula: see text] of accessible maps we show that this set is nonconvex, but it enjoys the star-shape property with respect to the uniform mixture of all elements of the group. We demonstrate that the set [Formula: see text] covers a positive volume in the polytope of all convex combinations of the elements of the group.

Experience of using gene replacement therapy with Zolgensma® (onasemnogene abeparvovec) in real clinical practice in Russia

Objective: to analyze the safety and evaluate the effectiveness of therapy with onasemnogene abeparvovec in patients with spinal muscular atrophy in real clinical practice based on the experience of using the drug in the neuromuscular center of Research Clinical Pediatric Institute of Pirogov Russian National Research Medical University.Materials and methods. Patients with spinal muscular atrophy received therapy with onasemnogene abeparvovec based on the prescription of the drug according to vital indications by a council of physicians of Federal institutions (the availability of the drug was carried out within the framework of the MAP Program (global program of managed access MAP to AVXS-101 for eligible patients in countries, where it is not approved by regulatory authorities (NCT03955679), through funding from the charitable foundations, as well as through funding from the state fund “Circle of Kindness”. The drug tolerance was assessed and the analysis of side effects after drug administration was based on the criteria for adverse events (General criteria Adverse Event Terminology (CTCAE) v. 5.0) Patient motor function was assessed prior to treatment initiation and every 3–6 months after therapy using the Philadelphia Pediatric Hospital’s CHOP INTEND scale, total motor development based on Hammersmith Hospital Neurological Assessment Scale in Young Children, Part 2 (HINE-2), and the acquisition of new motor skills.Results. 41 children aged 5 to 47 months (weighing no more than 21 kg) received therapy with onasemnogene abeparvovec in the period from April 2020 to December 2021. Adverse events (hyperthermia, decreased appetite, nausea, vomiting) were registered in all patients with different degree of severity. Elevated levels of transaminases greater than 2 times the upper limit of the normal range were observed in 32 patients (78 %), thrombocytopenia in 9 patients (22 %). 15 patients (36 %) required a dose adjustment of corticosteroids.17 patients underwent assessment of motor scales after 6 months, 10 children were assessed after a year. The average improvement on the HINE-2 scale was 3.3 / 4.4 points, respectively. The average improvement on the CHOP INTEND Scale was 7.1 / 9.4 points after 6 / 12 months of therapy.Conclusion. The efficacy and safety of onasemnogene abeparvovec have been demonstrated in real clinical practice in the treatment of spinal muscular atrophy for children in different age groups with a body weight of no more than 21 kg.

Identification of Transit Service Gaps through Accessibility and Social Vulnerability Mapping in Miami-Dade County

Identification of Transit Service Gaps through Accessibility and Social Vulnerability Mapping in Miami-Dade County

Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq.

A hallmark feature of active cis-regulatory elements (CREs) in eukaryotes is their nucleosomal depletion and, accordingly, higher accessibility to enzymatic treatment. This property has been the basis of a number of sequencing-based assays for genome-wide identification and tracking the activity of CREs across different biological conditions, such as DNAse-seq, ATAC-seq , NOMeseq, and others. However, the fragmentation of DNA inherent to many of these assays and the limited read length of short-read sequencing platforms have so far not allowed the simultaneous measurement of the chromatin accessibility state of CREs located distally from each other. The combination of labeling accessible DNA with DNA modifications and nanopore sequencing has made it possible to develop such assays. Here, we provide a detailed protocol for carrying out the SMAC-seq assay (Single-Molecule long-read Accessible Chromatin mapping sequencing), in its m6A-SMAC-seq and m6A-CpG-GpC-SMAC-seq variants, together with methods for data processing and analysis, and discuss key experimental and analytical considerations for working with SMAC-seq datasets.

APPLICATION OF GEOGRAPHIC INFORMATION SYSTEM AND REMOTE SENSING IN GROUNWATER RECHARGE POTENTIAL OF ADO-EKITI, NIGERIA

The increasing demand for freshwater has been on the increase as a result of geometric population growth, erratic climate change and urbanization has necessitated more attention and reliance on groundwater resources most especially in Ado-Ekiti, Nigeria. This necessitates the urgent need for judicious management of available groundwater resources to meet the freshwater requirements in the studied area. Geographical Information System (GIS) and Remote Sensing (RS) techniques were used to map out the groundwater recharge potential of the studied area. Google Earth and Land Satellite (LANDSAT) 7 sensor of Enhanced Thematic Mapper Plus (ETM+), path 191 and row 55 were used to acquire the satellite imageries of Ado-Ekiti. Using high resolution imageries, a Digital Elevation Model (DEM) was developed with Surfer 8 and ArcGIS 10.0 softwares to identify areas with high, medium and low groundwater recharge zones in the studied area. The elevation, slope, land use/ land cover, drainage density, lineament density, lithology, flow direction, flow length and flow accumulation maps of the study area were generated by using the DEM. The groundwater recharge potential was obtained by overlaying all the thematic maps that affected the groundwater distribution. Each thematic map was weighted according to its effect on groundwater infiltration. The results showed that areas with high lineament density, long flow length, high flow accumulation, high drainage pattern, low slope (lowland region) and vegetation have high groundwater recharge potential, and areas with medium lineament density, flow length, flow accumulation, drainage density, slope and sparse vegetation, respectively have moderate groundwater recharge potential while areas with low lineament density, short flow length, low flow accumulation, low drainage density, high slope (highland region) and sparse vegetation have low groundwater recharge potential. Better information on groundwater recharge potential of the studied area was provided via easily read and accessible maps generated from remotely sensed data and ArcGIS 10.0 software. The results also revealed that geology survey should be carried out to validate the results.

Public transport accessibility: simulation of the usability of public transport in everyday situations

The article presents an innovative method of evaluating public transport accessibility. The evaluation is based on a simulation of the usability of public transport in real everyday situations. It measures the amount of time the residents of local communities need when they use public transport to reach various commonly used destinations at a specified time. The method’s main advantage is that it aims at reflecting everyday use of public transport. I demonstrate the use of the method by exploratory accessibility mapping, comparison of regions, and demonstration of the usability of partial indicators. Analysis results reveal the basic spatial patterns of public transport accessibility in Czechia: better accessibility in Moravia than Bohemia, good accessibility in the hinterland of large cities, and impaired accessibility in inner peripheries. Accessibility varies significantly depending on the time of day. The results also allow us to deduce how much of the population experience difficulties using public transport due to impaired accessibility.

APPLICATION OF GEOGRAPHIC INFORMATION SYSTEM AND REMOTE SENSING IN MAPPING SURFACE WATER IN EKITI CENTRAL SENATORIAL DISTRICT, NIGERIA

The demands on surface water for agricultural, industrial and domestic activities has been on the increase while the quality and quantity of freshwater supply is decreasing geometrically as a result of rapid population growth in Ekiti Central Senatorial District, Nigeria. The supply of surface water to every nock and crannies of the studied area must be met. To achieve this, the application of Geographic Information System (GIS) and remote sensing was used to map out surface water for effective and efficient water distribution at the required quantity and quality to the studied area. Surface water mapping provides accessible, accurate, readable and reliable information about the location, quantity, availability and distribution of surface water in Ekiti Central Senatorial District. The LANDSAT ETM+ was used to acquire the satellite imageries of surface water in the studied area. The surfer 8 and Arc GIS 10 softwares were used to generate the digital elevation model, flow direction, flow length, flow accumulation, land use and drainage maps of the studied area, respectively. The results revealed that the studied area has a steady flow of water which can be evenly distributed throughout the senatorial district. Water flows from the areas of high elevation to the areas of low elevation, while accumulates at the downstream of the water flow. Geographic Information Systems (GIS) and remote sensing technologies provides easily read and rapidly accessible maps that can be used to monitor the surface water to enhance water distribution for domestic, industrial and agricultural purposes and the system can also be used to manage water resources correctly and effectively.

Reducing the effects of the Ukraine war: analysis of increasing food imports from eco member states to azerbaijan

The paper analyzes the stabilization of the situation in Azerbaijan against the background of rising food prices on world markets as a result of the war in Ukraine. The authors studied the effects of the Ukrainian war on the world and Azerbaijani import markets. Opportunities to replace the import of Azerbaijan’s largest importers Russia and Ukraine by ECO member states were analyzed. It was also investigated the question of whether OIC member states can be considered as an alternative markets. Analysis and evaluations were conducted to find answers to these and other similar questions. As a result, using the tools of the International Trade Centers such as the Market Access Map, Export Potential Map, etc., three member states of the Economic Cooperation Organization (Turkey, Kazakhstan, and Pakistan) with high potential for strategic food products for Azerbaijan have been identified. The article concluded the following: the war in Ukraine still continues to destabilize the world market. The Azerbaijan state should find alternative sources in a very short time.

The "freight frame" model as a method of freight transport traffic urban organization

The paper justifies the use of the "freight frame" as a method of organizing the movement of freight vehicle in large metropolitan areas on the example of Samara city district. The study presents the characteristics of the "freight frame" of major European cities, Kazan and Moscow. A comparative analysis of approaches to the organization of the movement of freight vehicle on the basis of the "freight frame" of Russian cities and cities of foreign countries is carried out. Based on the use of the Yandex.Traffic service, an analysis of the congestion of the main transport highways of the city was carried out, a map of the transport accessibility of the city of Samara was compiled with the calculation of the transport accessibility indices of its districts. To analyze the load of freight transport in the Samara region and the city of Samara, the intensity and composition of the traffic of freight transport on the major streets of the city were calculated using the NETVISION Traffic software and hardware complex, differentiated by months and day time. The result of the analysis allowed to identify the most significant problems of traffic management. On the basis of the used methods of freight traffic analysis, the necessity of implementing the "freight frame" model in the city of Samara was justified. A set of sequential measures is proposed to ensure the step-by-step formation of the freight frame model.

School Location Analysis by Integrating the Accessibility, Natural and Biological Hazards to Support Equal Access to Education

This study proposes a new model for land suitability for educational facilities based on spatial product development to determine the optimal locations for achieving education targets in West Java, Indonesia. Single-aspect approaches, such as accessibility and spatial hazard analyses, have not been widely applied in suitability assessments on the location of educational facilities. Model development was performed based on analyses of the economic value of the land and on the integration of various parameters across three main aspects: accessibility, comfort, and a multi-natural/biohazard (disaster) risk index. Based on the maps of disaster hazards, higher flood-prone areas are found to be in gentle slopes and located in large cities. Higher risks of landslides are spread throughout the study area, while higher levels of earthquake risk are predominantly in the south, close to the active faults and megathrusts present. Presently, many schools are located in very high vulnerability zones (2057 elementary, 572 junior high, 157 senior high, and 313 vocational high schools). The comfort-level map revealed 13,459 schools located in areas with very low and low comfort levels, whereas only 2377 schools are in locations of high or very high comfort levels. Based on the school accessibility map, higher levels are located in the larger cities of West Java, whereas schools with lower accessibility are documented far from these urban areas. In particular, senior high school accessibility is predominant in areas of lower accessibility levels, as there are comparatively fewer facilities available in West Java. Overall, higher levels of suitability are spread throughout West Java. These distribution results revealed an expansion of the availability of schools by area: senior high schools, 303,973.1 ha; vocational high schools, 94,170.51 ha; and junior high schools, 12,981.78 ha. Changes in elementary schools (3936.69 ha) were insignificant, as the current number of elementary schools is relatively much higher. This study represents the first to attempt to integrate these four parameters—accessibility, multi natural hazard, biohazard, comfort index, and land value—to determine potential areas for new schools to achieve educational equity targets.

Application of Multichannel Access and Customer Journey Map in the Context of Innovative Business Projects

Application of Multichannel Access and Customer Journey Map in the Context of Innovative Business Projects

The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

ABSTRACT After myocardial infarction, the massive death of cardiomyocytes leads to cardiac fibroblast proliferation and myofibroblast differentiation, which contributes to the extracellular matrix remodelling of the infarcted myocardium. We recently found that myofibroblasts further differentiate into matrifibrocytes, a newly identified cardiac fibroblast differentiation state. Cardiac fibroblasts of different states have distinct gene expression profiles closely related to their functions. However, the mechanism responsible for the gene expression changes during these activation and differentiation events is still not clear. In this study, the gene expression profiling and genome-wide accessible chromatin mapping of mouse cardiac fibroblasts isolated from the uninjured myocardium and the infarct at multiple time points corresponding to different differentiation states were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and the distal area where the enhancers are located. A positive correlation was identified between the expression and promoter accessibility for many dynamically expressed genes, even though evidence showed that mechanisms independent of chromatin accessibility may also contribute to the gene expression changes in cardiac fibroblasts after MI. Moreover, motif enrichment analysis and gene regulatory network construction identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

Accessibility Mapping through Linking Land-Use Development Potentials and Planning for Cycling

The transport sector aims to address climate change by reducing emissions, and a key to achieving this goal is to increase uptake of sustainable modes such as walking, cycling, and public transport. Therefore, it is important to determine ways to achieve this goal and to build a portfolio of feasible reduction strategies. This study is based in Norway where the government has a clear policy objective to reduce growth in urban car traffic and assimilate future sustainable transport modes. Cycling has therefore gained importance in both policy discussions and programme implementation through providing dedicated infrastructure to increase its modal share. Ways to increase cycling can be plotted at both macro- and microlevels. At the micro-level, road design and improved conditions for cyclists can lead to an increase in cycling. At the macro-level, land-use planning can be one of the tools to promote cycling. We analyse the issue at a macro-level based on an Integrated Methodology for Land Use prognosis within Transportation Models (INMAP) which estimates the mutual eff ects of land-use plans and increased accessibility by e-bike. We assess the extent to which future growth areas, as earmarked by the strategic master plans of the cities of Oslo and Trondheim, coincide with the areas that have a high job accessibility by bicycle and e-bike. Analyses reveal that on the introduction of e-bikes in Oslo, accessibility to jobs in the city centre increases from 20,000–24,000 to over 28,000 jobs. For Trondheim, in terms of spatial expansion of accessibility for jobs, there is an extension of the catchment area from 6 km2 to 18 km2. Based on the findings, this study strongly recommends integrating the impact of e-bikes with land-use planning processes and decisions. Through active land-use management, municipalities and regional development authorities can take informed decisions to steer urban mobility in a more sustainable direction.

Water vulnerabilities mapping: a multi-criteria and multi-scale assessment in central Chile

Abstract One of the major challenges that populations have to face is vulnerability to water: lack of water, flooding, pollution, hazard sensitivity and coping capacity. Owing to economic, social and environmental inequalities, this paper focuses on water-related vulnerabilities in the Metropolitan Region of Santiago (RMS) in Chile. Our main objective is to understand, through mapping, the multiscalar logics of water vulnerability. This study is carried out at two scales: at the regional level (RMS), we proceed with open access municipal statistical data and maps, while at the local level, a more detailed analysis focusing on the Chacabuco Province is based on the same type of data but with either a higher spatial resolution (census districts) or a spatially more intensive data processing in order to take into account intra-municipal differences. In this way, we put into perspective the discourse developed in the Chilean media and by the inhabitants of Chacabuco Province regarding the province as an environmental ‘sacrifice zone’ for the RMS. The vulnerability maps are carried out at different scales in a simple and reproducible way by multi-criteria evaluation (MCE). The results confirm the hypothesis of a sacrifice zone and show that high-resolution data and adequate data processing give, on average, lower vulnerability scores than using only statistical data on the municipal level. The results provide a cartographic decision support for stakeholders. Limitations of the study are discussed and required further research is pointed out.

Mapping accessibility in Norway – a Method to Register and Survey the Status of Accessibility in urban areas and recreational areas

Abstract. The Norwegian mapping authority has developed a standard method for mapping accessibility mostly for people with limited or no walking abilities in urban and recreational areas. We choose an object-orientated approach where points, lines and polygons represents objects in the environment. All data are stored in a geospatial database, so they can be presented as web map and analysed using GIS software. By the end of 2020, more than 230 out of 356 municipalities are mapped using that method. The aim of this project is to establish a national standard for mapping of accessibility and to provide a geodatabase that shows the status of accessibility throughout Norway. The data provide a useful tool for national statistics, local planning authorities and private users. The results show that accessibility is still low and Norway still faces many challenges to meet the government’s goals for Universal Design.

Visualising public transport accessibility to inform urban planning policy in Hubli-Dharwad, India.

Rapid urbanisation in India is a key contributor to the overstressed public infrastructure. The urban public transport system is one of the important infrastructure systems. An effective public transportation network helps the city improve its accessibility, lower carbon footprint, and enhances economic growth and societal equity. India is a relatively poor country with limited public resources. Therefore, investing in an effective urban public transport system needs a tailored approach. Such an approach would entail using public transport to guide urban development. In this context, the first step would be to measure the accessibility levels of the existing public transport network and then use the accessibility mapping outputs to better inform the urban planning process. This study explores the Public Transport Accessibility Level (PTAL) tool that measures the accessibility of the public transport system and provides a spatial visualisation using Geographic Information System. PTAL is implemented taking Hubli-Dharwad as a case study for the base year (2020) superimposed with population and employment density, and future year (2031). The outcome of the research facilitates the city planning process by guiding transportation and land-use zoning integrations, direct public transport investments, demarcation of transit-oriented development zones, parking policies, and identifying locations of affordable and low-cost housing.

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

Common genetic polymorphisms associated with COVID-19 illness can be utilized for discovering molecular pathways and cell types driving disease pathogenesis. Given the importance of immune cells in the pathogenesis of COVID-19 illness, here we assessed the effects of COVID-19-risk variants on gene expression in a wide range of immune cell types. Transcriptome-wide association study and colocalization analysis revealed putative causal genes and the specific immune cell types where gene expression is most influenced by COVID-19-risk variants. Notable examples include OAS1 in non-classical monocytes, DTX1 in B cells, IL10RB in NK cells, CXCR6 in follicular helper T cells, CCR9 in regulatory T cells and ARL17A in TH2 cells. By analysis of transposase accessible chromatin and H3K27ac-based chromatin-interaction maps of immune cell types, we prioritized potentially functional COVID-19-risk variants. Our study highlights the potential of COVID-19 genetic risk variants to impact the function of diverse immune cell types and influence severe disease manifestations.

Design and Development of a Collaborative App with Accessibility Information about Tourist Sites

Introduction: Accessibility can help people with disabilities to participate actively in the society with equal access and equal opportunities. Accessible tourism enables people to become more included and enjoy tourism experiences. Technology has facilitated tourism for people with disabilities and a Geographic Information System (GIS) can provide the tourist guidance, navigable digital maps and enable the searching of places information. Purpose: The objective of this paper is to describe the development of a collaborative app with accessibility information in order to help people with disabilities planning and moving more independently. Method: To develop this work a research about GIS apps related to disabled people was carried out, a pilot project to validate the idea and the app development proposed. Results: The accessible places map was developed using free GIS technologies and is available for download in Google Play Store. Conclusions: The app will help people with disabilities to move more safely and comfortably, and the increase of public data in GIS by the civil engagement.

Equity of geographical access to public health facilities in Nepal

IntroductionGeographical accessibility is important against health equity, particularly for less developed countries as Nepal. It is important to identify the disparities in geographical accessibility to the three levels of public...