Summary Since 2017, GEO shares have fallen sharply from $30 to ~$8.50 per share, at one point below even the book value of $8.19 per share. President Biden recently signed an executive order that banned the renewal of Department of Justice contracts with private prisons, but the effect on GEO is way way less than the market thinks. The border crisis renders ICE dependent on GEO for capacity, making it near impossible for ICE to cut ties in the near future. With a market cap of just $1.02 Billion, GEO has the potential to increase 2-3x in the next 6-12 months. cropped image of african american prisoner reading book LightFieldStudios/iStock via Getty Images Thesis GEO Group (GEO) is a deeply mispriced provider of privately-owned prisons, falling from a price of $30+ in early 2017 to the current price of $8.50 per share. GEO has fallen primarily as a result of concerns about legislation regarding private prisons, a canceled dividend, the likely shift away from a REIT structure, and high levels of debt. These overblown concerns have created a pretty solid structural opportunity. kmosby1992@gmail.com password kmosby1992@gmail.com Subscribe Company overview GEO operates in several segments, such as GEO care, International services, and U.S. Secure Services. Source: Annual report 1 - U.S. Secure Services U.S. Secure services account for the majority of their revenue, 67%, and includes their correctional facilities and processing centers. Secure services manage 74,000 beds across 58 facilities as of the 2020 annual report. GEO transport is included in U.S. secure services, but we felt it warranted its own paragraph. GEO transport provides secure transportation services to government agencies. With 400 customized, U.S. Department of Transportation compliant vehicles, GEO transport drove more than 14 million miles in 2020. 2 - GEO Care GEO care is a series of programs designed to reintegrate inmates and troubled youth into society. They operate through reentry centers, non-residential reentry programs, and youth treatment programs. GEO care operates approximately 4-dozen reentry centers, which provide housing, employment assistance, rehabilitation, substance abuse counseling, and vocational and education programs to current and former inmates. Through their reentry segment, they operate more than 70 non-residential reentry programs that provide behavioral assessments, treatment, supervision, and education. GEO care made up 23% of total 2020 revenue. Geo monitoring is included in GEO care. Through a wholly-owned subsidiary, BI Inc., GEO offers monitoring technology for parolees, probationers, pretrial defendants, and individuals involved in the immigration process. As of the 2020 annual report, BI helps monitor ~155,000 individuals across all 50 states. 3 - International operations International operations made up only 10% of revenue in 2020, but it is showing signs of growth. GEO recently landed a 10-year contract with the United kingdom, which they expect to total $760 million in revenue over the course of the contract. They also landed an 8-year contract with the Scottish Prison Service, which grants an annualized revenue of $39 million and has a 4-year renewal period. Why is GEO Mispriced? While there are several reasons for the dramatic reduction in share price over the last 4 years, the main reason was the looming fear of legislation destroying privately owned prisons. To a degree, this fear materialized on January 26th, 2021, when President Biden signed an Executive Order ordering the Attorney General not to renew any Department of Justice contracts with "privately operated criminal detention facilities." At face value, this order seems as though it would have a devastating impact on GEO. However, only ~25% of total revenue is impacted in any form by this order. The executive order only concerns branches of the Department of Justice. Only 2 DOJ branches have business connections with GEO, the US Marshals (USMS), and the Bureau of Prisons (BOP). Source: Annual report It is imperative to note that Immigration and Customs Enforcement (ICE), is not a branch of the DOJ and is therefore unaffected by this order. Individual states, as well as other countries, are unaffected by this order Bureau of Prisons GEO currently holds several agreements with the BOP relating to operations of prisons across the country. As of year-end 2020, agreements involving the BOP accounted for 14% of total revenue. All revenue from the BOP will not disappear, as the executive order does not impact reentry facilities. In 2Q21, after the executive order was made, GEO renewed 5 BOP reentry contracts. GEO even scored a new contract with the BOP, regarding the construction and operation of a new facility in Tampa. United States Marshal Service The United States Marshal Service does not own o... Visit https://dataone.org/datasets/sha256%3A900514e651e0d2c774ad90f358c9db90884c2baf98c068f470b290b3c4b3103a for complete metadata about this dataset.

Here we report a bio-statistical/informatics tool, ABioTrans, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data files deposited in the Gene Expression Omnibus or GEO database. Operated using any web browser application, ABioTrans provides easy options for multiple statistical distribution fitting, Pearson and Spearman rank correlations, PCA, k-means and hierarchical clustering, differential expression (DE) analysis, Shannon entropy and noise (square of coefficient of variation) analyses, as well as Gene ontology classifications.

We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants. FASTQ files and read counts data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) (GSE152128).

This dataset is associated with the following publication: Lee, F., I. Shah, Y.T. Soong, J. Xing, I.C. Ng, F. Tasnim, and H. Yu. Reproducibility and Robustness of High-Throughput S1500+ Transcriptomics on Primary Rat Hepatocytes for Chemical-Induced Hepatotoxicity Assessment. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 2: 282-295, (2021).

N/A

This dataset tracks annual reading and language arts proficiency from 2021 to 2022 for GEO Next Generation Academy School District vs. Indiana

This dataset tracks annual reading and language arts proficiency from 2021 to 2022 for Geo Next Generation High School vs. Louisiana and GEO Next Generation High School District

The dataset is created for use in the teaching of the undergraduate course BINF200 - Analysis of Biological Sequences and Structures, first used in Autumn 2023. The dataset contains (1) the processed, filtered and sample annotated sequenced reads in fasta format from Jayaraman et al (2019), repackaged in individual sample files and (2) a local database of variant surface glycoprotein (VSG) sequences in the Trypanosoma brucei reference strain TREU927. The original data are available in GEO dataset GSE114843. Further details about the original data are available at github.com/siddharthjayaraman/longread-application (archived at https://doi.org/10.5281/zenodo.10043245). The database of TREU927 VSG sequences is based on the (outdated) TREU927 genome v26. It is included for educational purposes and to reproduce results from the original publication. For research purposes always use the most recent genome version at tritrypdb.org. The code that was used to generate the present data as well as educational notebooks of downstream analyses are available at github.com/tmichoel/BINF200-bio-sequences-structures (archived at https://doi.org/10.5281/zenodo.10043222). Consider using Tree View to browse the files efficiently.

Geoscape G-NAF is the geocoded address database for Australian businesses and governments. It’s the trusted source of geocoded address data for Australia with over 50 million contributed addresses distilled into 15.4 million G-NAF addresses. It is built and maintained by Geoscape Australia using independently examined and validated government data.

From 22 August 2022, Geoscape Australia is making G-NAF available in an additional simplified table format. G-NAF Core makes accessing geocoded addresses easier by utilising less technical effort.

G-NAF Core will be updated on a quarterly basis along with G-NAF.

Further information about contributors to G-NAF is available here.

With more than 15 million Australian physical address record, G-NAF is one of the most ubiquitous and powerful spatial datasets. The records include geocodes, which are latitude and longitude map coordinates. G-NAF does not contain personal information or details relating to individuals.

Updated versions of G-NAF are published on a quarterly basis. Previous versions are available here

Users have the option to download datasets with feature coordinates referencing either GDA94 or GDA2020 datums.

Changes in the May 2025 release

• Nationally, the May 2025 update of G-NAF shows an overall increase of 47,194 addresses (0.30%). The total number of addresses in G-NAF now stands at 15,753,927 of which 14,909,770 or 94.64% are principal.

• At some locations, there are unit-numbered addresses that appear to be duplicate addresses. Geoscape is working to identify these locations and include these addresses as separate addresses in G-NAF. To facilitate this process, some secondary addresses have had the word RETAIL added to their building names. In the first instance, this process is being progressively rolled out to identified locations, but it is expected that the requirement for this will become ongoing.

• There is one new locality in G-NAF: Keswick Island, QLD.

• The source data used for generating G-NAF STREET_LOCALITY_POINT data in New South Wales has an updated datum and changed from GDA94 to GDA2020. This has resulted in updates to the STREET_LOCALITY_POINT geometry for approximately 91,000 records, however, more than 95% of these have moved less than a metre.

• Geoscape has moved product descriptions, guides and reports online to https://docs.geoscape.com.au.

Further information on G-NAF, including FAQs on the data, is available here or through Geoscape Australia’s network of partners. They provide a range of commercial products based on G-NAF, including software solutions, consultancy and support.

Additional information: On 1 October 2020, PSMA Australia Limited began trading as Geoscape Australia.

License Information

Use of the G-NAF downloaded from data.gov.au is subject to the End User Licence Agreement (EULA)

The EULA terms are based on the Creative Commons Attribution 4.0 International license (CC BY 4.0). However, an important restriction relating to the use of the open G-NAF for the sending of mail has been added.

The open G-NAF data must not be used for the generation of an address or the compilation of an address for the sending of mail unless the user has verified that each address to be used for the sending of mail is capable of receiving mail by reference to a secondary source of information. Further information on this use restriction is available here.

End users must only use the data in ways that are consistent with the Australian Privacy Principles issued under the Privacy Act 1988 (Cth).

Users must also note the following attribution requirements:

Preferred attribution for the Licensed Material:

_G-NAF © Geoscape Australia licensed by the Commonwealth of Australia under the _Open Geo-coded National Address File (G-NAF) End User Licence Agreement.

Preferred attribution for Adapted Material:

Incorporates or developed using G-NAF © Geoscape Australia licensed by the Commonwealth of Australia under the Open Geo-coded National Address File (G-NAF) End User Licence Agreement.

What to Expect When You Download G-NAF

G-NAF is a complex and large dataset (approximately 5GB unpacked), consisting of multiple tables that will need to be joined prior to use. The dataset is primarily designed for application developers and large-scale spatial integration. Users are advised to read the technical documentation, including product change notices and the individual product descriptions before downloading and using the product. A quick reference guide on unpacking the G-NAF is also available.

This dataset is about books. It has 1 row and is filtered where the book is New ventures in geography. The map-reading book. It features 7 columns including author, publication date, language, and book publisher.

This dataset tracks annual reading and language arts proficiency from 2017 to 2022 for Geo International High School vs. Kentucky and Warren County School District

Context

Adapted from Wikipedia: OpenStreetMap (OSM) is a collaborative project to create a free editable map of the world. Created in 2004, it was inspired by the success of Wikipedia and more than two million registered users who can add data by manual survey, GPS devices, aerial photography, and other free sources.

To aid researchers, data scientists, and analysts in the effort to combat COVID-19, Google is making a hosted repository of public datasets including OpenStreetMap data, free to access. To facilitate the Kaggle community to access the BigQuery dataset, it is onboarded to Kaggle platform which allows querying it without a linked GCP account. Please note that due to the large size of the dataset, Kaggle applies a quota of 5 TB of data scanned per user per 30-days.

Content

This is the OpenStreetMap (OSM) planet-wide dataset loaded to BigQuery.

Tables: - history_* tables: full history of OSM objects. - planet_* tables: snapshot of current OSM objects as of Nov 2019.

The history_* and planet_* table groups are composed of node, way, relation, and changeset tables. These contain the primary OSM data types and an additional changeset corresponding to OSM edits for convenient access. These objects are encoded using the BigQuery GEOGRAPHY data type so that they can be operated upon with the built-in geography functions to perform geometry and feature selection, additional processing.

Resources

You can read more about OSM elements on the OSM Wiki. This dataset uses BigQuery GEOGRAPHY datatype which supports a set of functions that can be used to analyze geographical data, determine spatial relationships between geographical features, and construct or manipulate GEOGRAPHYs.

The objective of the ESA TropForest project was to create a harmonised geo-database of ready-to-use satellite imagery to support 2010 global forest assessment performed by the Joint Research Centre (JRC) of the European Commission and by the Food and Agriculture Organization (FAO). Assessments for year 2010 were essential for building realistic deforestation benchmark rates at global to regional levels. To reach this objective, the project aimed to create a harmonised ortho-rectified/pre-processed imagery geo-database based on satellite data acquisitions (ALOS AVNIR-2, GEOSAT-1 SLIM6, KOMPSAT-2 MSC) performed during year 2009 and 2010, for the Tropical Latin America (excluding Mexico) and for the Tropical South and Southeast Asia (excluding China), resulting in 1971 sites located at 1° x 1° geographical lat/long intersections. The project finally delivered 1866 sites (94.7% of target) due to cloud coverages too high for missing sites. Spatial coverage: Check the spatial coverage of the collection on a map available on the Third Party Missions Dissemination Service.

This dataset is about books. It has 9 rows and is filtered where the book publisher is University of Reading Department of Geography. It features 7 columns including author, publication date, language, and book publisher.

Please note this dataset is the most recent version of the Administrative Boundaries (AB). For previous versions of the AB please go to this url: https://data.gov.au/dataset/ds-dga-b4ad5702-ea2b-4f04-833c-d0229bfd689e/details?q=previous

Geoscape Administrative Boundaries is Australia’s most comprehensive national collection of boundaries, including government, statistical and electoral boundaries. It is built and maintained by Geoscape Australia using authoritative government data. Further information about contributors to Administrative Boundaries is available here.

This dataset comprises seven Geoscape products:

• Localities
• Local Government Areas (LGAs)
• Wards
• Australian Bureau of Statistics (ABS) Boundaries
• Electoral Boundaries
• State Boundaries and
• Town Points

Updated versions of Administrative Boundaries are published on a quarterly basis.

Users have the option to download datasets with feature coordinates referencing either GDA94 or GDA2020 datums.

Notable changes in the May 2025 release

• Victorian Wards have seen almost half of the dataset change now reflecting the boundaries from the 2024 subdivision review. https://www.vec.vic.gov.au/electoral-boundaries/council-reviews/ subdivision-reviews.

  • There have been spatial changes (area) greater than 1 km2 to 66 wards in Victoria.

• One new locality ‘Kenwick Island’ has been added to the local Government area ‘Mackay Regional’ in Queensland.

  • There have been spatial changes(area) greater than 1 km2 to the local government areas 'Burke Shire' and 'Mount Isa City' in Queensland.

• There have been spatial changes(area) greater than 1 km2 to the localities ‘Nicholson’, ‘Lawn Hill’ and ‘Coral Sea’ in Queensland and ‘Calguna’, ‘Israelite Bay’ and ‘Balladonia’ in Western Australia.

• An update to the NT Commonwealth Electoral Boundaries has been applied to reflect the redistribution of the boundaries gazetted on 4 March 2025.

• Geoscape has become aware that the DATE_CREATED and DATE_RETIRED attributes in the commonwealth_electoral_polygon MapInfo TAB tables were incorrectly ordered and did not match the product data model. These attributes have been re-ordered to match the data model for the May 2025 release.

IMPORTANT NOTE: correction of issues with the 22 November 2022 release

• On 28 November 2022, the Administrative Boundaries dataset originally released on 22 November 2022 was amended and re-uploaded after Geoscape identified some issues with the original data for 'Electoral Boundaries'.
• As a result of the error, some shapefiles were published in 3D rather than 2D, which may affect some users when importing data into GIS applications.
• The error affected the Electoral Boundaries dataset, specifically the Commonwealth boundary data for Victoria and Western Australia, including 'All States'.
• Only the ESRI Shapefile formats were affected (both GDA94 and GDA2020). The MapInfo TAB format was not affected.
• Because the datasets are zipped into a single file, once the error was fixed by Geoscape all of Administrative Boundaries shapefiles had to be re-uploaded, rather than only the affected files.
• If you downloaded either of the two Administrative Boundary ESRI Shapefiles between 22 November and 28 November 2022 and plan to use the Electoral Boundary component, you are advised to download the revised version dated 28 November 2022. Apologies for any inconvenience.

Further information on Administrative Boundaries, including FAQs on the data, is available here or through Geoscape Australia’s network of partners. They provide a range of commercial products based on Administrative Boundaries, including software solutions, consultancy and support.

Note: On 1 October 2020, PSMA Australia Limited began trading as Geoscape Australia.

The Australian Government has negotiated the release of Administrative Boundaries to the whole economy under an open CCBY 4.0 licence.

Users must only use the data in ways that are consistent with the Australian Privacy Principles issued under the Privacy Act 1988 (Cth).

Users must also note the following attribution requirements:

Preferred attribution for the Licensed Material:

Administrative Boundaries © Geoscape Australia licensed by the Commonwealth of Australia under Creative Commons Attribution 4.0 International license (CC BY 4.0).

Preferred attribution for Adapted Material:

Incorporates or developed using Administrative Boundaries © Geoscape Australia licensed by the Commonwealth of Australia under Creative Commons Attribution 4.0 International licence (CC BY 4.0).

What to Expect When You Download Administrative Boundaries

Administrative Boundaries is large dataset (around 1.5GB unpacked), made up of seven themes each containing multiple layers.

Users are advised to read the technical documentation including the product change notices and the individual product descriptions before downloading and using the product.

Please note this dataset is the most recent version of the Administrative Boundaries (AB). For previous versions of the AB please go to this url: https://data.gov.au/dataset/ds-dga-b4ad5702-ea2b-4f04-833c-d0229bfd689e/details?q=previous

License Information

Analysis of ‘COVID-19 Cases and Deaths Summarized by Geography’ provided by Analyst-2 (analyst-2.ai), based on source dataset retrieved from https://catalog.data.gov/dataset/d2e381bb-f395-4b40-979e-920a79a3db88 on 11 February 2022.

--- Dataset description provided by original source is as follows ---

Note: On January 22, 2022, system updates to improve the timeliness and accuracy of San Francisco COVID-19 cases and deaths data were implemented. You might see some fluctuations in historic data as a result of this change. Due to the changes, starting on January 22, 2022, the number of new cases reported daily will be higher than under the old system as cases that would have taken longer to process will be reported earlier.

Note: As of April 16, 2021, this dataset will update daily with a five-day data lag.

A. SUMMARY Medical provider confirmed COVID-19 cases and confirmed COVID-19 related deaths in San Francisco, CA aggregated by several different geographic areas and normalized by 2019 American Community Survey (ACS) 5-year estimates for population data to calculate rate per 10,000 residents.

Cases and deaths are both mapped to the residence of the individual, not to where they were infected or died. For example, if one was infected in San Francisco at work but lives in the East Bay, those are not counted as SF Cases or if one dies in Zuckerberg San Francisco General but is from another county, that is also not counted in this dataset.

Dataset is cumulative and covers cases going back to March 2nd, 2020 when testing began.

Geographic areas summarized are: 1. Analysis Neighborhoods 2. Census Tracts 3. Census Zip Code Tabulation Areas

B. HOW THE DATASET IS CREATED Addresses from medical data are geocoded by the San Francisco Department of Public Health (SFDPH). Those addresses are spatially joined to the geographic areas. Counts are generated based on the number of address points that match each geographic area. The 2019 ACS estimates for population provided by the Census are used to create a rate which is equal to ([count] / [acs_population]) * 10000) representing the number of cases per 10,000 residents.

C. UPDATE PROCESS Geographic analysis is scripted by SFDPH staff and synced to this dataset daily at 7:30 Pacific Time.

D. HOW TO USE THIS DATASET Privacy rules in effect To protect privacy, certain rules are in effect: 1. Case counts greater than 0 and less than 10 are dropped - these will be null (blank) values 2. Death counts greater than 0 and less than 10 are dropped - these will be null (blank) values 3. Cases and deaths dropped altogether for areas where acs_population < 1000

Rate suppression in effect where counts lower than 20 Rates are not calculated unless the case count is greater than or equal to 20. Rates are generally unstable at small numbers, so we avoid calculating them directly. We advise you to apply the same approach as this is best practice in epidemiology.

A note on Census ZIP Code Tabulation Areas (ZCTAs) ZIP Code Tabulation Areas are special boundaries created by the U.S. Census based on ZIP Codes developed by the USPS. They are not, however, the same thing. ZCTAs are areal representations of routes. Read how the Census develops ZCTAs on their website.

Row included for Citywide case counts, incidence rate, and deaths A single row is included that has the Citywide case counts and incidence rate. This can be used for comparisons. Citywide will capture all cases regardless of address quality. While some cases cannot be mapped to sub-areas like Census Tracts, ongoing data quality efforts result in improved mapping on a rolling bases.

--- Original source retains full ownership of the source dataset ---

By this short introduction using geospatial data in Python I combine three different types of data sources which can be implemented in one map. For this purpose I start with reading a .csv with random adresses in order to request geo coordinates from Google using its API and creating a new dataframe. I continue reading a zip folder into python with data from Natural Earth and geocode my first dataframe into a geo dataframe with the characteristics of geometry. It´s possible as well to construct a geodataframe manuelly by geopandas. Reading then geo spatial data from GeoJSON allows me to gain more exactly Polygons of the German districts for plotting them with previous geo dataframes into a unique map.

In a 2nd jupyter notebook I continued with Agglomerative and K-Means Clustering for the gdp per capita data by manipulating the Natural Earth data sheet.

In a following project I plan to start with SVM algorithms on these geo data.

view file "Using Geo Data in Python": https://bit.ly/2SN3oTl

view file "Agglomerative and Kmeans Clustering": https://bit.ly/2SN3D0H

Table of Contents

1. Main Description
2. File Descriptions
3. Linked Files
4. Installation and Instructions

1. Main Description

---------------------------

This is the Zenodo repository for the manuscript titled "A TCR β chain-directed antibody-fusion molecule that activates and expands subsets of T cells and promotes antitumor activity.". The code included in the file titled `marengo_code_for_paper_jan_2023.R` was used to generate the figures from the single-cell RNA sequencing data.

The following libraries are required for script execution:

• Seurat
• scReportoire
• ggplot2
• stringr
• dplyr
• ggridges
• ggrepel
• ComplexHeatmap

File Descriptions

---------------------------

• The code can be downloaded and opened in RStudios.
• The "marengo_code_for_paper_jan_2023.R" contains all the code needed to reproduce the figues in the paper
• The "Marengo_newID_March242023.rds" file is available at the following address: https://zenodo.org/badge/DOI/10.5281/zenodo.7566113.svg (Zenodo DOI: 10.5281/zenodo.7566113).
• The "all_res_deg_for_heat_updated_march2023.txt" file contains the unfiltered results from DGE anlaysis, also used to create the heatmap with DGE and volcano plots.
• The "genes_for_heatmap_fig5F.xlsx" contains the genes included in the heatmap in figure 5F.

Linked Files

---------------------

This repository contains code for the analysis of single cell RNA-seq dataset. The dataset contains raw FASTQ files, as well as, the aligned files that were deposited in GEO. The "Rdata" or "Rds" file was deposited in Zenodo. Provided below are descriptions of the linked datasets:

Gene Expression Omnibus (GEO) ID: GSE223311(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223311)

• Title: Gene expression profile at single cell level of CD4+ and CD8+ tumor infiltrating lymphocytes (TIL) originating from the EMT6 tumor model from mSTAR1302 treatment.
• Description: This submission contains the "matrix.mtx", "barcodes.tsv", and "genes.tsv" files for each replicate and condition, corresponding to the aligned files for single cell sequencing data.
• Submission type: Private. In order to gain access to the repository, you must use a reviewer token (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html).

Sequence read archive (SRA) repository ID: SRX19088718 and SRX19088719

• Title: Gene expression profile at single cell level of CD4+ and CD8+ tumor infiltrating lymphocytes (TIL) originating from the EMT6 tumor model from mSTAR1302 treatment.
• Description: This submission contains the **raw sequencing** or `.fastq.gz` files, which are tab delimited text files.
• Submission type: Private. In order to gain access to the repository, you must use a reviewer token (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html).

Zenodo DOI: 10.5281/zenodo.7566113(https://zenodo.org/record/7566113#.ZCcmvC2cbrJ)

• Title: A TCR β chain-directed antibody-fusion molecule that activates and expands subsets of T cells and promotes antitumor activity.
• Description: This submission contains the "Rdata" or ".Rds" file, which is an R object file. This is a necessary file to use the code.
• Submission type: Restricted Acess. In order to gain access to the repository, you must contact the author.

Installation and Instructions

--------------------------------------

The code included in this submission requires several essential packages, as listed above. Please follow these instructions for installation:

> Ensure you have R version 4.1.2 or higher for compatibility.

> Although it is not essential, you can use R-Studios (Version 2022.12.0+353 (2022.12.0+353)) for accessing and executing the code.

1. Download the *"Rdata" or ".Rds" file from Zenodo (https://zenodo.org/record/7566113#.ZCcmvC2cbrJ) (Zenodo DOI: 10.5281/zenodo.7566113).

2. Open R-Studios (https://www.rstudio.com/tags/rstudio-ide/) or a similar integrated development environment (IDE) for R.

3. Set your working directory to where the following files are located:

• marengo_code_for_paper_jan_2023.R
• Install_Packages.R
• Marengo_newID_March242023.rds
• genes_for_heatmap_fig5F.xlsx
• all_res_deg_for_heat_updated_march2023.txt

You can use the following code to set the working directory in R:

> setwd(directory)

4. Open the file titled "Install_Packages.R" and execute it in R IDE. This script will attempt to install all the necessary pacakges, and its dependencies in order to set up an environment where the code in "marengo_code_for_paper_jan_2023.R" can be executed.

5. Once the "Install_Packages.R" script has been successfully executed, re-start R-Studios or your IDE of choice.

6. Open the file "marengo_code_for_paper_jan_2023.R" file in R-studios or your IDE of choice.

7. Execute commands in the file titled "marengo_code_for_paper_jan_2023.R" in R-Studios or your IDE of choice to generate the plots.

A. SUMMARY This dataset contains COVID-19 positive confirmed cases aggregated by several different geographic areas and by day. COVID-19 cases are mapped to the residence of the individual and shown on the date the positive test was collected. In addition, 2016-2020 American Community Survey (ACS) population estimates are included to calculate the cumulative rate per 10,000 residents.

Dataset covers cases going back to 3/2/2020 when testing began. This data may not be immediately available for recently reported cases and data will change to reflect as information becomes available. Data updated daily.

Geographic areas summarized are: 1. Analysis Neighborhoods 2. Census Tracts 3. Census Zip Code Tabulation Areas

B. HOW THE DATASET IS CREATED Addresses from the COVID-19 case data are geocoded by the San Francisco Department of Public Health (SFDPH). Those addresses are spatially joined to the geographic areas. Counts are generated based on the number of address points that match each geographic area for a given date.

The 2016-2020 American Community Survey (ACS) population estimates provided by the Census are used to create a cumulative rate which is equal to ([cumulative count up to that date] / [acs_population]) * 10000) representing the number of total cases per 10,000 residents (as of the specified date).

COVID-19 case data undergo quality assurance and other data verification processes and are continually updated to maximize completeness and accuracy of information. This means data may change for previous days as information is updated.

C. UPDATE PROCESS Geographic analysis is scripted by SFDPH staff and synced to this dataset daily at 05:00 Pacific Time.

D. HOW TO USE THIS DATASET San Francisco population estimates for geographic regions can be found in a view based on the San Francisco Population and Demographic Census dataset. These population estimates are from the 2016-2020 5-year American Community Survey (ACS).

This dataset can be used to track the spread of COVID-19 throughout the city, in a variety of geographic areas. Note that the new cases column in the data represents the number of new cases confirmed in a certain area on the specified day, while the cumulative cases column is the cumulative total of cases in a certain area as of the specified date.

Privacy rules in effect To protect privacy, certain rules are in effect: 1. Any area with a cumulative case count less than 10 are dropped for all days the cumulative count was less than 10. These will be null values. 2. Once an area has a cumulative case count of 10 or greater, that area will have a new row of case data every day following. 3. Cases are dropped altogether for areas where acs_population < 1000 4. Deaths data are not included in this dataset for privacy reasons. The low COVID-19 death rate in San Francisco, along with other publicly available information on deaths, means that deaths data by geography and day is too granular and potentially risky. Read more in our privacy guidelines

Rate suppression in effect where counts lower than 20 Rates are not calculated unless the cumulative case count is greater than or equal to 20. Rates are generally unstable at small numbers, so we avoid calculating them directly. We advise you to apply the same approach as this is best practice in epidemiology.

A note on Census ZIP Code Tabulation Areas (ZCTAs) ZIP Code Tabulation Areas are special boundaries created by the U.S. Census based on ZIP Codes developed by the USPS. They are not, however, the same thing. ZCTAs are areal representations of routes. Read how the Census develops ZCTAs on their website.

Rows included for Citywide case counts Rows are included for the Citywide case counts and incidence rate every day. These Citywide rows can be used for comparisons. Citywide will capture all cases regardless of address quality. While some cases cannot be mapped to sub-areas like Census Tracts, ongoing data quality efforts result in improved mapping on a rolling bases.

Related dataset See the dataset of the most recent cumulative counts for all geographic areas here: https://data.sfgov.org/COVID-19/COVID-19-Cases-and-Deaths-Summarized-by-Geography/tpyr-dvnc

E. CHANGE LOG

• 9/11/2023 - data on COVID-19 cases by geography over time are no longer being updated. This data is currently through 9/6/2023 and will not include any new data after this date.
• 4/6/2023 - the State implemented system updates to improve the integrity of historical data.
• 2/21/2023 - system updates to improve reliability and accuracy of cases data were implemented.
• 1/31/2023 - updated “acs_population” column to reflect the 2020 Census Bureau American Community Survey (ACS) San Francisco Population estimates.
• 1/31/2023 - implemented system updates to streamline and improve our geo-coded data, resulting in small shifts in our case data by geography.
• 1/31/2023 - renamed column “last_updated_at” to “data_as_of”.
• 1/31/2023 - removed the “multipolygon” column. To access the multipolygon geometry column for each geography unit, refer to COVID-19 Cases and Deaths Summarized by Geography.
• 1/22/2022 - system updates to improve timeliness and accuracy of cases and deaths data were implemented.
• 4/16/2021 - dataset updated to refresh with a five-day data lag.

Each of 70 cell samples either at the control condition or treated with FDA-approved cancer drugs is sequenced by the single-ended random-primed mRNA-sequencing method with a read length of 100 base pairs, and a total of 70 raw sequence data files in the FASTQ format are generated. These sequence data files are then analyzed by a high-performance computational pipeline and ranked lists of gene signatures and biological processes related to drug-induced cardiotoxicity are generated for each drug. The raw sequence datasets and the analysis results have been carefully controlled for data quality, and they are made publicly available at the Gene Expression Omnibus (GEO) database repository of NIH. As such, this broad drug-stimulated transcriptomi dataset is valuable for the prediction of drug toxicities and their mitigations.

This dataset tracks annual reading and language arts proficiency from 2018 to 2022 for Geo Prep Mid-city Of Greater Baton Rouge vs. Louisiana and GEO Prep Mid-City Of Greater Baton Rouge School District