Raw imaging data for Tsue, Kania, et al (2024), "Oligonucleotide-mediated proximity-interactome mapping (O-MAP): A unified method for RNA-targeted microenvironment-mapping in situ."

With the forecast increase in air traffic demand over the next decades, it is imperative to develop tools to provide traffic flow managers with the information required to support decision making. In particular, decision-support tools for traffic flow management should aid in limiting controller workload and complexity, while supporting increases in air traffic throughput. While many decision-support tools exist for short-term traffic planning, few have addressed the strategic needs for medium- and long-term planning for time horizons greater than 30 minutes. This paper seeks to address this gap through the introduction of 3D aircraft proximity maps that evaluate the future probability of presence of at least one or two aircraft at any given point of the airspace. Three types of proximity maps are presented: presence maps that indicate the local density of traffic; conflict maps that determine locations and probabilities of potential conflicts; and outliers maps that evaluate the probability of conflict due to aircraft not belonging to dominant traffic patterns. These maps provide traffic flow managers with information relating to the complexity and difficulty of managing an airspace. The intended purpose of the maps is to anticipate how aircraft flows will interact, and how outliers impact the dominant traffic flow for a given time period. This formulation is able to predict which "critical" regions may be subject to conflicts between aircraft, thereby requiring careful monitoring. These probabilities are computed using a generative aircraft flow model. Time-varying flow characteristics, such as geometrical configuration, speed, and probability density function of aircraft spatial distribution within the flow, are determined from archived Enhanced Traffic Management System data, using a tailored clustering algorithm. Aircraft not belonging to flows are identified as outliers.

https://upload.wikimedia.org/wikipedia/commons/7/79/VEGFR2_bound_to_axitinib.gif" alt="image">

Introduction

This dataset is a replication of the dataset described in the paper Generative Modeling for Protein Structures by Namrata Anand and Po-Ssu Huang. The data is used to train a Generative Adversarial Network with the capability of creating protein structures.

Content

The data is stored in a hdf5 file and is structured in the following manner:

{
 "test_16": "16x16 numpy arrays",
 "train_16": "16x16 numpy arrays",
 "test_64": "64x64 numpy arrays",
 "train_64": "64x64 numpy arrays",
 "test_128": "128x128 numpy arrays"
 "train_128": "128x128 numpy arrays"
}

and contains the following number of numpy arrays:

test_16: 69,713

train_16: 1,820,586

test_64: 11,835

train_64: 331,006

test_128: 3,276

train_128: 98,748

Quickstart

Running the following will yeild ```python3 import h5py import matplotlib.pyplot as plt

dataset = h5py.File('dataset.hdf5', 'r') test_64 = dataset['test_64']

plt.imshow(test_64[1], cmap='viridis') plt.colorbar() plt.show() ``` https://i.imgur.com/lb2bOzo.png" alt="image">

Acknowledgements

@incollection{NIPS2018_7978,
title = {Generative modeling for protein structures},
author = {Anand, Namrata and Huang, Possu},
booktitle = {Advances in Neural Information Processing Systems 31},
editor = {S. Bengio and H. Wallach and H. Larochelle and K. Grauman and N. Cesa-Bianchi and R. Garnett},
pages = {7494--7505},
year = {2018},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/7978-generative-modeling-for-protein-structures.pdf}

https://cdn.rcsb.org/rcsb-pdb/v2/common/images/rcsb_logo.png" alt="image"> H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

The Digital Geologic Map of Cape Cod National Seashore and Vicinity, Massachusetts is composed of GIS data layers complete with ArcMap 9.3 layer (.LYR) files, two ancillary GIS tables, a Map PDF document with ancillary map text, figures and tables, a FGDC metadata record and a 9.3 ArcMap (.MXD) Document that displays the digital map in 9.3 ArcGIS. The data were completed as a component of the Geologic Resources Inventory (GRI) program, a National Park Service (NPS) Inventory and Monitoring (I&M) funded program that is administered by the NPS Geologic Resources Division (GRD). Source geologic maps and data used to complete this GRI digital dataset were provided by the following: U.S. Geological Survey. Detailed information concerning the sources used and their contribution the GRI product are listed in the Source Citation sections(s) of this metadata record (caco_metadata.txt; available at http://nrdata.nps.gov/caco/nrdata/geology/gis/caco_metadata.xml). All GIS and ancillary tables were produced as per the NPS GRI Geology-GIS Geodatabase Data Model v. 2.1. (available at: http://science.nature.nps.gov/im/inventory/geology/GeologyGISDataModel.cfm). The GIS data is available as a 9.3 personal geodatabase (caco_geology.mdb), and as shapefile (.SHP) and DBASEIV (.DBF) table files. The GIS data projection is NAD83, UTM Zone 19N. That data is within the area of interest of Cape Cod National Seashore.

Scale reduction from source to target maps inevitably leads to conflicts of map symbols in cartography and geographic information systems (GIS). Displacement is one of the most important map generalization operators and it can be used to resolve the problems that arise from conflict among two or more map objects. In this paper, we propose a combined approach based on constraint Delaunay triangulation (CDT) skeleton and improved elastic beam algorithm for automated building displacement. In this approach, map data sets are first partitioned. Then the displacement operation is conducted in each partition as a cyclic and iterative process of conflict detection and resolution. In the iteration, the skeleton of the gap spaces is extracted using CDT. It then serves as an enhanced data model to detect conflicts and construct the proximity graph. Then, the proximity graph is adjusted using local grouping information. Under the action of forces derived from the detected conflicts, the proximity graph is deformed using the improved elastic beam algorithm. In this way, buildings are displaced to find an optimal compromise between related cartographic constraints. To validate this approach, two topographic map data sets (i.e., urban and suburban areas) were tested. The results were reasonable with respect to each constraint when the density of the map was not extremely high. In summary, the improvements include (1) an automated parameter-setting method for elastic beams, (2) explicit enforcement regarding the positional accuracy constraint, added by introducing drag forces, (3) preservation of local building groups through displacement over an adjusted proximity graph, and (4) an iterative strategy that is more likely to resolve the proximity conflicts than the one used in the existing elastic beam algorithm.

This EnviroAtlas dataset shows the approximate walking distance from a park entrance at any given location within the EnviroAtlas community boundary. The zones are estimated in 1/4 km intervals up to 1km then in 1km intervals up to 5km. Park entrances were included in this analysis if they were within 5km of the community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

JOBS PROXIMITY INDEXSummaryThe jobs proximity index quantifies the accessibility of a given residential neighborhood as a function of its distance to all job locations within a CBSA, with larger employment centers weighted more heavily. Specifically, a gravity model is used, where the accessibility (Ai) of a given residential block- group is a summary description of the distance to all job locations, with the distance from any single job location positively weighted by the size of employment (job opportunities) at that location and inversely weighted by the labor supply (competition) to that location. More formally, the model has the following specification: Where i indexes a given residential block-group, and j indexes all n block groups within a CBSA. Distance, d, is measured as “as the crow flies” between block-groups i and j, with distances less than 1 mile set equal to 1. E represents the number of jobs in block-group j, and L is the number of workers in block-group j. The Longitudinal Employer-Household Dynamics (LEHD) has missing jobs data in all of Puerto Rico and a concentration of missing records in Massachusetts. InterpretationValues are percentile ranked with values ranging from 0 to 100. The higher the index value, the better the access to employment opportunities for residents in a neighborhood. Data Source: ACS 2017 - 2021 5 year summary data. Longitudinal Employer-Household Dynamics (LEHD) data, 2017. Related AFFH-T Local Government, PHA and State Tables/Maps: Table 12; Map 8. To learn more about the Jobs Proximity Index visit: https://www.hud.gov/program_offices/fair_housing_equal_opp/affh ; https://www.hud.gov/sites/dfiles/FHEO/documents/AFFH-T-Data-Documentation-AFFHT0006-July-2020.pdf, for questions about the spatial attribution of this dataset, please reach out to us at GISHelpdesk@hud.gov. Date of Coverage: 2017 - 2021 ACSDate Updated: 10/2023

Over the last year, Statistics Canada (StatCan) and Canada Mortgage and Housing Corporation (CMHC) have collaborated on the implementation of a set of proximity measures to services and amenities. CMHC funded this collaboration to generate data and analytical work in support of the National Housing Strategy. The result of this collaboration is the first nation-wide Proximity Measures Database (PMD). This database is now available as an early release to meet urgent information needs of departments and other stakeholders across Canada who are dealing with the COVID-19 crisis. The current situation involving COVID-19 emphasizes the importance of having timely and accessible information available to the public at all levels of government. Proximity measures developed for this project are relevant to the current situation by providing a wealth of information (at the granular level) in terms of proximity to health facilities, pharmacies and other essential services/amenities that can be used to make rapid informed decisions at different geographical levels. WARNING: This map contains detailed data which makes it heavy to load. To improve loading time, please uncheck the "Proximity measures" group from legend at loading, then load only the desired thematic.

This EnviroAtlas dataset shows the approximate walking distance from a park entrance at any given location within the EnviroAtlas community boundary. The zones are estimated in 1/4 km intervals up to 1km then in 1km intervals up to 5km. Park entrances were included in this analysis if they were within 5km of the community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

In any given 1-square meter point in this EnviroAtlas dataset, the value shown gives the percentage of impervious surface within 1 square kilometer centered over the given point. Water is shown as '-99999' in this dataset to distinguish it from land areas with low impervious. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Connecticut and Vicinity State Boundary data are intended for geographic display of state boundaries at statewide and regional levels. Use it to map and label states on a map. These data are derived from Northeastern United States Political Boundary Master layer. This information should be displayed and analyzed at scales appropriate for 1:24,000-scale data. The State of Connecticut, Department of Environmental Protection (CTDEP) assembled this regional data layer using data from other states in order to create a single, seamless representation of political boundaries within the vicinity of Connecticut that could be easily incorporated into mapping applications as background information. More accurate and up-to-date information may be available from individual State government Geographic Information System (GIS) offices. Not intended for maps printed at map scales greater or more detailed than 1:24,000 scale (1 inch = 2,000 feet.)

Additional file 1: Figure S1. Pearson correlation coefficients between the gene co-expression matrix and three different matrices based on spatial positioning of genes: the CGP map (blue bars), the raw gene proximity map (green bars), and the normalized gene proximity map (yellow bars) for each of the 23 chromosomes for 10 ENCODE cell lines. Figure S2. (A) ROC curve for the gene compartment classification using leading eigenvectors of the CGP matrix for GM12878 and K562 cell lines. The horizontal axis is the false positive rate (1 − specificity) and the vertical axis is the true positive rate (sensitivity). The red dot indicates the optimal operating point. Components of the top 50 leading eigenvectors were used as features for the classification model. (B) Effect of the number of eigenvectors used in the gene compartment label classifier. The horizontal axis represents the number of eigenvectors in the CGP matrix used for model construction, ranged from 1 to 50. The vertical axis is the average AUROC of the resultant model over the 10-fold cross validation. The red circles and blue squares (almost completely coincide) represent the GM12878 and K562 cell lines respectively. Using the first leading eigenvector alone does not yield a good classification result. By additionally incorporating the second and third eigenvectors, the AUROC witnesses a dramatic increase (from 0.57 to 0.70). On the other hand, using more than 10 eigenvectors does not provide a substantial performance improvement any more. Figure S3. Objective function based on the empirical gene expression profile and randomized profiles, computed using the raw gene proximity map. The histogram for randomized profiles is normalized to have zero mean. A main difference between the plots generated from the CGP and the raw gene proximity map is that for cell lines RPMI-7951, SJCRH30 and SK-N-DZ, the value of the gene proximity map-based objective function generated from the empirical expression profile is mixed with the values generated from randomized profiles. Figure S4. Change in relative spatial positioning of chromosomes between cell lines GM12878 and K562. The layout of this network is in the same way as Figure 6 in the main text, but the inter-chromosomal proximity matrix here was computed using the gene proximity map instead of the corrected proximity measure. As compared to Figure 6, the connections between chromosomes 3 and 10, and between chromosomes 9 and 22, are no longer easily identified. Table S1. Top 20 inter-chromosomal gene interactions in cell lines GM12878 and K562 respectively. These pairs of genes were selected based on the fact that they are located on different chromosomes and have the largest values in the corresponding CGP map.

Feature layer generated from running the Find Existing Locations solutions for 25_percent_obesity_rate.Expression 25_percent_obesity_rate within a distance of 1 Miles from Map Notes (Areas)

Connecticut and Vicinity County Boundary data are intended for geographic display of state and county boundaries at statewide and regional levels. Use it to map and label counties on a map. These data are derived from Northeastern United States Political Boundary Master layer. This information should be displayed and analyzed at scales appropriate for 1:24,000-scale data. The State of Connecticut, Department of Environmental Protection (CTDEP) assembled this regional data layer using data from other states in order to create a single, seamless representation of political boundaries within the vicinity of Connecticut that could be easily incorporated into mapping applications as background information. More accurate and up-to-date information may be available from individual State government Geographic Information System (GIS) offices. Not intended for maps printed at map scales greater or more detailed than 1:24,000 scale (1 inch = 2,000 feet.)

This service provides distances to known electricity transmission substations. The distances are represented as a regular grid (raster) surface or as isolines. The values represent the minimum distance, to the nearest transmission substations. The proximity values are calculated over Australian land mass, and include inland water bodies. Topography of the terrain and curvature of the earth were not taken into consideration in any calculations i.e. actual traversal distances will be greater than those calculated

In any given 1-square meter point in this EnviroAtlas dataset, the value shown gives the percentage of impervious surface within 1 square kilometer centered over the given point. Water is shown as '-99999' in this dataset to distinguish it from land areas with low impervious. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

In any given 1-square meter point in this EnviroAtlas dataset, the value shown gives the percentage of impervious surface within 1 square kilometer centered over the given point. Water is shown as '-99999' in this dataset to distinguish it from land areas with low impervious. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Protein-Protein, Genetic, and Chemical Interactions for Go CD (2021):A proximity-dependent biotinylation map of a human cell. curated by BioGRID (https://thebiogrid.org); ABSTRACT: Compartmentalization is a defining characteristic of eukaryotic cells, and partitions distinct biochemical processes into discrete subcellular locations. Microscopy1 and biochemical fractionation coupled with mass spectrometry2-4 have defined the proteomes of a variety of different organelles, but many intracellular compartments have remained refractory to such approaches. Proximity-dependent biotinylation techniques such as BioID provide an alternative approach to define the composition of cellular compartments in living cells5-7. Here we present a BioID-based map of a human cell on the basis of 192 subcellular markers, and define the intracellular locations of 4,145 unique proteins in HEK293 cells. Our localization predictions exceed the specificity of previous approaches, and enabled the discovery of proteins at the interface between the mitochondrial outer membrane and the endoplasmic reticulum that are crucial for mitochondrial homeostasis. On the basis of this dataset, we created humancellmap.org as a community resource that provides online tools for localization analysis of user BioID data, and demonstrate how this resource can be used to understand BioID results better.

Vicinity map of the project area

The Digital Geologic Map of Kenai Fjords National Park and vicinity, Alaska is composed of GIS data layers complete with ArcMap 9.3 layer (.LYR) files, three ancillary GIS tables, a Map PDF document with ancillary map text, figures and tables, a FGDC metadata record and a 9.3 ArcMap (.MXD) Document that displays the digital map in 9.3 ArcGIS. The data were completed as a component of the Geologic Resources Inventory (GRI) program, a National Park Service (NPS) Inventory and Monitoring (I&M) funded program that is administered by the NPS Geologic Resources Division (GRD). Source geologic maps and digital data used to complete this GRI digital dataset were provided by the following: U.S. Geological Survey (Alaska Science Center). Detailed information concerning the sources used and their contribution the GRI product are listed in the Source Citation sections(s) of this metadata record (kefj_metadata.txt; available at http://nrdata.nps.gov/kefj/nrdata/geology/gis/kefj_metadata.xml). All GIS and ancillary tables were produced as per the NPS GRI Geology-GIS Geodatabase Data Model v. 2.1. (available at: http://science.nature.nps.gov/im/inventory/geology/GeologyGISDataModel.cfm). The GIS data is available as a 9.3 personal geodatabase (kefj_geology.mdb), and as shapefile (.SHP) and DBASEIV (.DBF) table files. The GIS data projection is NAD83 Alaska Albers. The data is within the area of interest of Kenai Fjords National Park.