cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18226480
title: Gene syntax defines supercoiling-mediated transcriptional feedback

description: Data for "Gene syntax defines supercoiling-mediated transcriptional feedback"

This includes all of the data required to compile and build the figures.See the listed Github repository (archived through Zenodo) for code generation files. The link is listed in the published paper.

Zenodo deposit details

The zenodo deposit contains three files:



README.md (this file, also included in the data zip)

gene_syntax_supercoiling_data.7z (all of the data to make all paper figures)

plasmids.zip (plasmid sequences, in GenBank format for all plasmids)

software.zip (a snapshot of https://github.com/GallowayLabMIT/tangles_experimental, the related software to process this data)


For a higher compression ratio, the main data is compressed as a 7zip file instead of a zip file. Modern versions of Windows and MacOS are able to open this compressed file directly. If this doesn't work, the 7zip software is free and open-source and available at https://www.7-zip.org/

Data zip details

The data zip contains the following data:



Processed sequencing data in NGS_DATA/tangles_experimental, split by experiment type.

Plasmid metadata needed for plotting in projects

Flow data in instruments/data/attune and instruments/data/collaborators

Microscopy data in instruments/data/keyence

Antibody plate-reader data in instruments/data/plate_reader

qPCR data in instruments/qPCR

ddPCR data in instruments/Weiss.lab.ddPCR


Using this data

The Galloway lab uses a Python package called rushd to easily import datato make figures. If you want to reproduce figure plotting, the steps are:



Unzip this data deposit to any deposit.

Copy the full, absolute path to this folder, e.g. the folder containing   README.md



on Windows, this might look like C:\Users\username\Downloads\gene_syntax_supercoiling_data

on MacOS, this might be \home\username\Downloads\gene_syntax_supercoiling_data

on Linux, it might be \home\username\Downloads\gene_syntax_supercoiling_data



git clone or otherwise download the code for this paper to a folder.

Create a datadir.txt file with the path above, in the root of the code directory (e.g. at the same level of the README.md in the code repository). This should really be a single-line file containing only the path above!

Create a Python virtual environment using the requirements.txt file.

Run the Jupyter notebooks in the figures/ subdirectory.
DOI: 10.5281/zenodo.18226479
title: Gene syntax defines supercoiling-mediated transcriptional feedback

description: Data for "Gene syntax defines supercoiling-mediated transcriptional feedback"

This includes all of the data required to compile and build the figures.See the listed Github repository (archived through Zenodo) for code generation files. The link is listed in the published paper.

Zenodo deposit details

The zenodo deposit contains three files:



README.md (this file, also included in the data zip)

gene_syntax_supercoiling_data.7z (all of the data to make all paper figures)

plasmids.zip (plasmid sequences, in GenBank format for all plasmids)

software.zip (a snapshot of https://github.com/GallowayLabMIT/tangles_experimental, the related software to process this data)


For a higher compression ratio, the main data is compressed as a 7zip file instead of a zip file. Modern versions of Windows and MacOS are able to open this compressed file directly. If this doesn't work, the 7zip software is free and open-source and available at https://www.7-zip.org/

Data zip details

The data zip contains the following data:



Processed sequencing data in NGS_DATA/tangles_experimental, split by experiment type.

Plasmid metadata needed for plotting in projects

Flow data in instruments/data/attune and instruments/data/collaborators

Microscopy data in instruments/data/keyence

Antibody plate-reader data in instruments/data/plate_reader

qPCR data in instruments/qPCR

ddPCR data in instruments/Weiss.lab.ddPCR


Using this data

The Galloway lab uses a Python package called rushd to easily import datato make figures. If you want to reproduce figure plotting, the steps are:



Unzip this data deposit to any deposit.

Copy the full, absolute path to this folder, e.g. the folder containing   README.md



on Windows, this might look like C:\Users\username\Downloads\gene_syntax_supercoiling_data

on MacOS, this might be \home\username\Downloads\gene_syntax_supercoiling_data

on Linux, it might be \home\username\Downloads\gene_syntax_supercoiling_data



git clone or otherwise download the code for this paper to a folder.

Create a datadir.txt file with the path above, in the root of the code directory (e.g. at the same level of the README.md in the code repository). This should really be a single-line file containing only the path above!

Create a Python virtual environment using the requirements.txt file.

Run the Jupyter notebooks in the figures/ subdirectory.
DOI: 10.15468/dl.ukha6s
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma leorae"
 ]
}

 The dataset includes 88 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029844-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18701642
title: РАЗГРАНИЧЕНИЕ «ОРГАНИЗОВАННОЙ ГРУППЫ» И «ПРЕСТУПНОГО СООБЩЕСТВА» В УГОЛОВНОМ ПРАВЕ УЗБЕКИСТАНА И ДОКАЗЫВАНИЕ ИХ ПРИЗНАКОВ

description: Ushbu tezis O‘zbekiston Respublikasi jinoyat qonunchiligida sheriklikning ikki murakkab shakli — “uyushgan guruh” va “jinoiy hamjamiyat” — ni huquqiy mazmuni hamda ularning belgilarini sudda isbotlash masalalarini tahlil qiladi. Tadqiqot JKning 29–30-moddalari va 242-moddasi, JPKning dalillarni baholashga doir qoidalari, Oliy sud Plenumi tushuntirishlari, tezkor-qidiruv faoliyati natijalari va raqamli dalillar bilan ishlashdagi protsessual cheklovlar bilan uyg‘un holda yagona farqlash mezonlarini taklif etadi. Amaliy natija sifatida “minimal faktlar + minimal dalillar” matritsasi, 242-modda bo‘yicha tashkil etish/rəhbariyat/“faoliyatni ta’minlash” belgilarini tasdiqlash uchun chek‑list hamda dalillarni yo‘qotish (admissibility) xavflarini kamaytirishga qaratilgan tavsiyalar ishlab chiqiladi.
DOI: 10.5281/zenodo.18701641
title: РАЗГРАНИЧЕНИЕ «ОРГАНИЗОВАННОЙ ГРУППЫ» И «ПРЕСТУПНОГО СООБЩЕСТВА» В УГОЛОВНОМ ПРАВЕ УЗБЕКИСТАНА И ДОКАЗЫВАНИЕ ИХ ПРИЗНАКОВ

description: Ushbu tezis O‘zbekiston Respublikasi jinoyat qonunchiligida sheriklikning ikki murakkab shakli — “uyushgan guruh” va “jinoiy hamjamiyat” — ni huquqiy mazmuni hamda ularning belgilarini sudda isbotlash masalalarini tahlil qiladi. Tadqiqot JKning 29–30-moddalari va 242-moddasi, JPKning dalillarni baholashga doir qoidalari, Oliy sud Plenumi tushuntirishlari, tezkor-qidiruv faoliyati natijalari va raqamli dalillar bilan ishlashdagi protsessual cheklovlar bilan uyg‘un holda yagona farqlash mezonlarini taklif etadi. Amaliy natija sifatida “minimal faktlar + minimal dalillar” matritsasi, 242-modda bo‘yicha tashkil etish/rəhbariyat/“faoliyatni ta’minlash” belgilarini tasdiqlash uchun chek‑list hamda dalillarni yo‘qotish (admissibility) xavflarini kamaytirishga qaratilgan tavsiyalar ishlab chiqiladi.
DOI: 10.15468/dl.uyf2q8
title: Occurrence Download

description: A dataset listing the 47792 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-26 50,3 50,3 61,-26 61,-26 50))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2015-2025"
 ]
}

 The dataset's 47792 records were derived from 1340 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029831-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.xxe6xz54
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (38 records)
DOI: 10.15468/dl.pku94n
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma leorae"
 ]
}

 The dataset includes 88 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029846-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycesxa
title: Occurrence Download

description: A dataset containing 237 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pelseneeria Koehler & Vaney, 1908"
 ]
}

 The dataset includes 237 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051618-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p13qtbr7
title: Data to support evaluation of bioremediation of trichloroethene at Site K, Former Twin Cities Army Ammunition Plant, Arden Hills, Minnesota, 2020-2022

description: This metadata record consists of 16 tables containing data generated from laboratory experiments of trichloroethene (TCE) biodegradation and during field characterization and performance monitoring of a groundwater bioremediation pilot test conducted at Site K, Former Twin Cities Army Ammunition Plant, Arden Hills, Minnesota. The data was collected from December 2020 through December 2022. Laboratory experiment data include concentrations of volatile organic compounds (VOCs) and dissolved hydrocarbon gases including methane and ethene. Laboratory experiments were used to determine amendments for the groundwater bioremediation pilot test. Field data include concentrations of VOCs in soil core samples, information on wells used for the study, groundwater measurements of field parameters, and groundwater concentrations of VOCs, major and minor ions, nutrients, trace metals, dissolved organic carbon, dissolved hydrocarbon gases, and redox-sensitive species including sulfide, reduced manganese, ferrous iron, and methane. Microbial communities in samples and compound specific isotope analysis of groundwater samples were also assessed. Groundwater and soil data were collected for initial site characterization from December 2020 to June 2021 and from October 2021 to December 2022 to establish baseline conditions before addition of pilot test amendments, followed by approximately quarterly and monthly sampling events for performance monitoring of the pilot test. The data within these tables were used to assess natural and enhanced anaerobic biodegradation TCE and other VOCs and the potential to utilize bioremediation as a treatment method for the groundwater plume at Site K.
DOI: 10.15468/dl.jy3qhd
title: Occurrence Download

description: A dataset containing 1835 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adelphocoris vandalicus"
 ]
}

 The dataset includes 1835 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029847-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mbyf7
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iomys",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Brunei Darussalam, Cambodia, Indonesia, Lao People’s Democratic Republic, Myanmar, Malaysia, Philippines, Singapore, Thailand, Viet Nam, Timor-Leste, Chinese Taipei, China)",
 "Geometry POLYGON((90 -15, 90 35, 135 35, 135 -15, 90 -15))"
 ]
}

 The dataset includes 36 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029848-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18701225
title: Artifact of Input-Requirement-Aware Search-based Differential Testing of NumPy Implementations

description: This artifact includes:

1. The Docker image containing the ArrayDiff prototype.

2. The experimental data.
DOI: 10.60555/bvbr-k768
title: Plant Water Management
title: PWM

description: The primary objectives of the Plant Water Management (PWM) experiments were to:

a) Experimentally characterize and validate the use of passive capillary and  geometric control for plant watering in microgravity.
The research quantified the stability limits of capillary-driven flow under varying conditions, evaluated aeration and bubble management performance within root-zone analogs, and assessed start-up, shutdown, and drainage behaviors of the fluidic system on orbit and also correlated observed flow regimes and saturation levels with computational capillary flow models to improve predictive design tools for reduced-gravity systems.
b) Advance the PWM technology toward higher Technology Readiness Levels (TRL), demonstrating reliable, scalable configurations for integration into future space-based plant growth habitats.
The resulting data and models informed the design of next-generation, low-mass, low-power life-support and food-production systems for long-duration missions on the Moon, Mars, and beyond.
DOI: 10.60520/ieda/114342
title: A compiled experimental dataset of clinopyroxene-liquid pairs (2021-2025) for evaluating machine learning-based clinopyroxene thermobarometers

description: This data provides a curated compilation of 650 experimental clinopyroxene samples published between 2021 and 2025, designed as a benchmark for evaluating machine learning-based clinopyroxene thermobarometers. The data are organized into three key tables:

Table S1 contains the primary experimental data, including the major element compositions (12 oxides) of all 650 clinopyroxene samples, with pressure (P) and temperature (T) conditions. A subset of 214 samples also includes the corresponding co-existing melt compositions (13 oxides).

Table S2 provides calculated Mahalanobis distances for each sample, offering a quantitative metric to assess whether a sample’s composition falls within or outside the training domains of existing machine learning-based clinopyroxene thermobarometers, which is critical for evaluating model extrapolation reliability.

Table S3 presents a comparative analysis of pressure and temperature predictions generated by applying recent machine learning-based thermobarometers and a traditional thermobarometer pair to the compiled dataset, facilitating direct performance evaluation.

This structured data package is essential for rigorously testing the accuracy and applicability limits of published thermobarometers and serves as a foundational resource for developing and calibrating new thermobarometer.
DOI: 10.15468/dl.6n3c3c
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Petaurillus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Brunei Darussalam, Cambodia, Indonesia, Lao People’s Democratic Republic, Myanmar, Malaysia, Philippines, Singapore, Thailand, Viet Nam, Timor-Leste, Chinese Taipei, China)",
 "Geometry POLYGON((90 -15, 90 35, 135 35, 135 -15, 90 -15))"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029849-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.26s3xj
title: Occurrence Download

description: A dataset containing 38074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhithrogena",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 38074 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029851-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/seb-dgs-6nf
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x6f-4wb-0pr
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eah-tbk-tqd
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kcs-21m-99x
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2n0lny
title: CCDC 2443440: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0lpz
title: CCDC 2443441: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/jsk-z3x-sql
title: Amphibia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2n0lq0
title: CCDC 2443442: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0lr1
title: CCDC 2443443: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/1lt-tsl-9l4
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y0r-agk-d3h
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2n0ls2
title: CCDC 2443444: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0lv4
title: CCDC 2443446: Experimental Crystal Structure Determination

description: Related Article: Ren Zhou, Yuqi Jiang, Ruihao Huang, Dongmei Ran, Heyang Gao, Min Li, Weilong Ji, Minmin Xu, Yuanting Su|2025|Inorg.Chem.|64|15463|doi:10.1021/acs.inorgchem.5c01651
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/77a-efw-6wb
title: †Gublerina cuvillieri Kikoïne, 1948

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dga-6xf-4rw
title: Globorotalia Cushman, 1927

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2n5668
title: CCDC 2447859: Experimental Crystal Structure Determination

description: Related Article: Akito Nishiyama, Kanchana Chatchaipaiboon, Kotohiro Nomura|2025|Organometallics|44|1633|doi:10.1021/acs.organomet.5c00177
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/eps-qht-78v
title: Stomatorbina concentrica (Parker & Jones, 1864)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kgl-vwl-8y7
title: Planopulvinulina dispansa (Brady, 1884)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2n5679
title: CCDC 2447860: Experimental Crystal Structure Determination

description: Related Article: Akito Nishiyama, Kanchana Chatchaipaiboon, Kotohiro Nomura|2025|Organometallics|44|1633|doi:10.1021/acs.organomet.5c00177
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n568b
title: CCDC 2447861: Experimental Crystal Structure Determination

description: Related Article: Akito Nishiyama, Kanchana Chatchaipaiboon, Kotohiro Nomura|2025|Organometallics|44|1633|doi:10.1021/acs.organomet.5c00177
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/e4t-ane-pjy
title: Bulimina striata d'Orbigny in Guérin-Méneville, 1832

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.