cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10028239
title: Prymnesium parvum 12B1 polyketide synthase (PKS) domain and module analysis

description: The .zip file contains source data and code for an analysis that determines the modular structure from the domain structure of type I modular polyketide synthases (PKSs) in the Prymnesium parvum strain 12B1 gene annotation. In brief, a regex is used against a string representation of the PKS domain structures to determine the module structure. Some manual modifications for calling modules were performed where they deviated. Resulting data is available in the .zip file as .bed, .FASTA, .xlsx files. See Manuscript for further details.
DOI: 10.5281/zenodo.10028177
title: PKZILLA candidate domains of unknown function (cDUFs) analysis

description: This dataset consisits of the source data, code, and derived data for an analysis of regions of the PKZILLA polypeptides that were not annotated by InterProScan, and thus are candidates to be domains of unknown function (cDUFs). See Manuscript for more details.
DOI: 10.5281/zenodo.10023459
title: InterProScan domain annotation of PKZILLA polypeptides

description: This is a .zip archive of the git repository and Nextflow workflow used for annotation of the PKZILLA protein domains using InterProScan. In brief, all possible InterProScan searches were performed via the latest InterProScan Docker container, with post-processing to remove certain redundant and overlapping PKS domain annotations. For further details, see archived files and code, and manuscript Materials and Methods.
The Nextflow ./work directory is not included to reduce complexity. Nextflow published results are available in ./results . 
See also: https://doi.org/10.5281/zenodo.10011739 , for analogous predictions but for all the non-PKZILLA annotated proteins from Prymnesium parvum 12B1. 
Key files:

./run.sh entry script for running InterProScan on PKZILLA-1,-2,-3
GFF3 file of InterProScan features, after post processing: './results/gff_nested_filter/filtered/ipr_merged.gff'
PDF of all features on PKZILLA-1, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-1.gff.dfv.svg.pdf'
PDF of all features on PKZILLA-2, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-2.gff.dfv.svg.pdf'
PDF of all features on PKZILLA-3, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-2.gff.dfv.svg.pdf'
./run2.sh entry script for performing a "beads on a string" figure generation, where representative domains are selected and length normalized.
PDF of selected diagnostic PKS domain features on PKZILLA-1 with normalized length: './results/beads_on_string:svg_2_pdf/1_PKZILLA-1.gff.dfv.svg_2_PKZILLA-1.gff.dfv.svg_3_PKZILLA-1.gff.dfv.svg_4_PKZILLA-1.gff.dfv.svg_5_PKZILLA-1.gff.dfv.svg_compose.svg.pdf'
PDF of selected diagnostic PKS domain features on PKZILLA-2 with normalized length: '/results/beads_on_string:svg_2_pdf/1_PKZILLA-2.gff.dfv.svg_2_PKZILLA-2.gff.dfv.svg_3_PKZILLA-2.gff.dfv.svg_4_PKZILLA-2.gff.dfv.svg_compose.svg.pdf'
PDF of selected diagnostic PKS domain features on PKZILLA-3 with normalized length: '/results/beads_on_string:svg_2_pdf/1_PKZILLA-3.gff.dfv.svg_2_PKZILLA-3.gff.dfv.svg_3_PKZILLA-3.gff.dfv.svg_compose.svg.pdf'
DOI: 10.5281/zenodo.10023440
title: SearchGUI proteomic search analysis for PKZILLAs in P. parvum 12B1

description: Exported .mzID (.mzIdentML) and .xlsx files for SearchGUI proteomic search engine analysis. See the "Materials and Methods" section of the linked pre-printed or peer-reviewed manuscript for full description.
The .mzID file is also uploaded via ProteomeXchange with identifier PXD044632. https://doi.org/10.6019/PXD044632
DOI: 10.5281/zenodo.10023359
title: Detailed mass spectrometry instrument method text description, used to produce proteomic data files for PKZILLA manuscript

description: The detailed mass spectrometry method used to produce data files:P1A_techrep1_DG19854.raw , MD5: cb94e4c68dc8739f80e20986803b20c2 , SHA1: 289ab06f64b5262c95d08131fa8f4fcd9fef406aP1A_techrep2_DG19855.raw: MD5: 5cda6208209f49d6c324af1aef185952 , SHA1: b8e105d4f146a8bce0eae223f9e655d1168fc999P1A_techrep3_DG19856.raw: MD5: 9b6425a92cb8e66f9b5daef5ca83a06c , SHA1: e1cc14a880bade836389d6cd50a2807993534ad6
Produced proteomic data are available via ProteomeXchange with identifier PXD044632. See: https://doi.org/10.6019/PXD044632
Derived from: Filename: P1A_techrep1_DG19854.raw , MD5: cb94e4c68dc8739f80e20986803b20c2 , SHA1: 289ab06f64b5262c95d08131fa8f4fcd9fef406a
Per the Sample Information created via the Thermo Fisher Scientific FreeStyle 1.8 SP2 QF1 Mass spectrometry analysis software, the used instrument method name was "113_min_Standard_Sway3.meth"- P1A_techrep2_DG19855.raw: MD5: 5cda6208209f49d6c324af1aef185952 \, SHA1: b8e105d4f146a8bce0eae223f9e655d1168fc999- P1A_techrep3_DG19856.raw: MD5: 9b6425a92cb8e66f9b5daef5ca83a06c \, SHA1: e1cc14a880bade836389d6cd50a2807993534ad6 \,also appeared to use the same method as P1A_techrep1_DG19854.raw.
Method summary created via the Thermo Fisher Scientific FreeStyle 1.8 SP2 QF1 Mass spectrometry analysis software: Reports->Instrument Method :
Due to a seeming inability to select, copy paste, or print this Method Summary text to PDF, & have the text be maintained in an editable format (i.e. not rasterized to an image), the text was exported via screenshotting from the FreeStyle interface to PNG, followed by optical character using PDF OCR X Enterprise Editions (macOS; v3.0.35), and the text manually combined, lightly edited for OCR misrecognition, & attempted to match the indentation of the source documents using BBEdit (macOS; v14.6.6). There may be errors due to this manual transcription process.
DOI: 10.25345/c5q52fq28
title: MassIVE MSV000093896 - Urine proteome profile of emergency fire-induced smoke exposure firefighters identify potential carcinogenic effects: A pilot study
title: Firefighters are frequently exposed to a variety of chemicals formed from smoke, which pose a risk for numerous diseases, including cancer. Comparative urine proteome profiling could significantly improve our understanding of the early detection of potential cancer biomarkers. In this study, for the first time, the urine protein profiles of real-life smoke-exposed and non-exposed firefighters have been examined using a label-free proteomics platform. We identified and quantified a total of 1325 unique protein groups, of which 71 proteins showed differential expressions in abundance in response to smoke exposure (post) compared to the control (pre). Pathway analysis of these proteins showed proteins associated with epithelium development (RHCG, HEG1, ADAMTSL2) and Alzheimer's disease (SORL1) were significantly increased in abundance in response to smoke exposure samples. A cross-comparison analysis revealed seven proteins COL2A1, SDC4, RDX, POMC, APCS, ALDH1A1, and DDAH2 overlapped with the previously published urine cancer proteome datasets, suggesting potential risk of cancer. To the best of our knowledge, our findings demonstrated the potential therapeutic significance of the urine proteome in the development of non-invasive biomarkers in response to firefighters' exposure to fire smoke, which might be associated with cancer.
DOI: 10.17632/nycwc276b9.2
title: Refining the 8th edition TNM classification for EBV related nasopharyngeal carcinoma. Du et al.

description: All study-level data, including training cohort, internal and external validation cohorts for M0 NPC patients as well as M1 NPC patietns are deposited in this dataset. Any additional information required to reanalyze the data reported in this paper is available after approval by the corresponding author and Sun Yat-sen University Cancer Center.
DOI: 10.6084/m9.figshare.25033967
title: EV charging and LMP forecasting data

description: Supplementary materials for paper "Price-Guided Battery Model with Reserve Purchasing for Aggregating Storage-like Devices"
DOI: 10.5281/zenodo.8231065
title: Datasets for Deep Imaging Inside Scattering Media Through Virtual Spatiotemporal Wavefront Shaping - Hyperspectral Reflection Matrices

description: There are two datasets of  hyperspectral reflection matrices (complex-valued):


> 'data_TiO2' is for 1 millimeter deep inside a dense TiO2 nanoparticle colloid;


> 'data_usaf' is for USAF target under 1-millimeter mouse brain tissue.


With these datasets, one can reconstruct high-resolution deep images using scattering matrix tomography (SMT). The SMT reconstruction code and more information can be found on GitHub.
DOI: 10.5281/zenodo.10531141
title: Datasets for Deep Imaging Inside Scattering Media Through Virtual Spatiotemporal Wavefront Shaping - Hyperspectral Reflection Matrices

description: There are two datasets of  hyperspectral reflection matrices (complex-valued):

> 'data_TiO2_Tb3' is for 1.5 millimeter deep inside a dense TiO2 nanoparticle colloid;

> 'data_usaf' is for USAF target under 1-millimeter mouse brain tissue.

With these datasets, one can reconstruct high-resolution deep images using scattering matrix tomography (SMT). The SMT reconstruction code and more information can be found on GitHub.
DOI: 10.5281/zenodo.8231064
title: Datasets for Deep Imaging Inside Scattering Media Through Virtual Spatiotemporal Wavefront Shaping - Hyperspectral Reflection Matrices

description: There are two datasets of  hyperspectral reflection matrices (complex-valued):

> 'data_TiO2_Tb3' is for 1.5 millimeter deep inside a dense TiO2 nanoparticle colloid;

> 'data_usaf' is for USAF target under 1-millimeter mouse brain tissue.

With these datasets, one can reconstruct high-resolution deep images using scattering matrix tomography (SMT). The SMT reconstruction code and more information can be found on GitHub.
DOI: 10.18739/a2gh9bb54
title: CESM2 Idealized Experiment Output: Summer atmospheric response to May snow cover loss over North American

description: This dataset contains output from a prescribed model experiment conducted to investigate the impact of snow cover loss over North America on summer atmospheric circulation. We utilized the National Center for Atmospheric Research’s Community Earth System Model version 2.2 to complete a 10-year control simulation. We then modified the land-surface restart files for May 1st of each year of the control period by reducing the snow cover over North America to zero. Using these modified files, we then completed a reduced snow simulation by rerunning three-month simulations from May through July for each of the ten years. This dataset contains both the 10-year control simulation as well as the May–July “no-snow” simulations for each year. 
 More details about the experimental setup and example output can be found in the following publication:
 Preece, J.R., Mote, T.L., Cohen, J. et al. Summer atmospheric circulation over Greenland in response to Arctic amplification and diminished spring snow cover. Nat Commun 14, 3759 (2023). https://doi.org/10.1038/s41467-023-39466-6
DOI: 10.5281/zenodo.10472479
title: Reproducibility of equatorial Kelvin waves in a superparameterized MIROC: data and codes

description: This dataset provides underlying data, processing scripts, and model coupling codes for two research articles:



Reproducibility of equatorial Kelvin waves in a superparameterized MIROC. Part I: Implementation and verification of blockwise-coupled SP-MIROC.

Reproducibility of equatorial Kelvin waves in a super-parameterized MIROC. Part II: Linear stability analysis of in-model Kelvin waves.


"model_data.zip" contains simulation results of SP-MIROC and sensitivity experiments described in the "Part I" article. It also includes post-processing scripts and parts of the SP-MIROC model that couple two components (SCALE-RM and MIROC6) consisting SP-MIROC.

"linear_analyses.zip" contains codes for linear stability analyses of equatorial Kelvin waves. The background state is derived from the simulation results and observational data in model_data.zip.

"coupling_codes.zip" contains inter-model coupling codes in the GCM and CRM components of SP-MIROC.
DOI: 10.5281/zenodo.10472480
title: Reproducibility of equatorial Kelvin waves in a superparameterized MIROC: data and codes

description: This dataset provides underlying data and processing scripts for two research articles:



Reproducibility of equatorial Kelvin waves in a superparameterized MIROC. Part I: Implementation and verification of blockwise-coupled SP-MIROC.

Reproducibility of equatorial Kelvin waves in a super-parameterized MIROC. Part II: Linear stability analysis of in-model Kelvin waves.


"model_data.zip" contains simulation results of SP-MIROC and sensitivity experiments described in the "Part I" article. It also includes post-processing scripts and parts of the SP-MIROC model that couple two components (SCALE-RM and MIROC6) consisting SP-MIROC.

"linear_analyses.zip" contains codes for linear stability analyses of equatorial Kelvin waves. The background state is derived from the simulation results and observational data in model_data.zip.
DOI: 10.5281/zenodo.10537042
title: Reproducibility of equatorial Kelvin waves in a superparameterized MIROC: data and codes

description: This dataset provides underlying data, processing scripts, and model coupling codes for two research articles:



Reproducibility of equatorial Kelvin waves in a superparameterized MIROC. Part I: Implementation and verification of blockwise-coupled SP-MIROC.

Reproducibility of equatorial Kelvin waves in a super-parameterized MIROC. Part II: Linear stability analysis of in-model Kelvin waves.


"model_data.zip" contains simulation results of SP-MIROC and sensitivity experiments described in the "Part I" article. It also includes post-processing scripts and parts of the SP-MIROC model that couple two components (SCALE-RM and MIROC6) consisting SP-MIROC.

"linear_analyses.zip" contains codes for linear stability analyses of equatorial Kelvin waves. The background state is derived from the simulation results and observational data in model_data.zip.

"coupling_codes.zip" contains inter-model coupling codes in the GCM and CRM components of SP-MIROC.
DOI: 10.34740/kaggle/dsv/7438139
title: BBC News
DOI: 10.5517/ccdc.csd.cc2fvljf
title: CCDC 2259885: Experimental Crystal Structure Determination

description: Related Article: Ya-Fei Ma, Xiao-Li Liu, Xue-Ying Lu, Mei-Li Zhang, Yi-Xia Ren, Xiao-Gang Yang|2024|Spectrochim.Acta,Part A|309|123803|doi:10.1016/j.saa.2023.123803
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.cc2gm4bl
title: CCDC 2282509: Experimental Crystal Structure Determination

description: Related Article: Sudhakar Maddala, Kalidass Kollimalaian, Ankita Samal, Venkatakrishnan Parthasarathy|2024|Tetrahedron|151|133807|doi:10.1016/j.tet.2023.133807
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.cc2gm4fp
title: CCDC 2282512: Experimental Crystal Structure Determination

description: Related Article: Sudhakar Maddala, Kalidass Kollimalaian, Ankita Samal, Venkatakrishnan Parthasarathy|2024|Tetrahedron|151|133807|doi:10.1016/j.tet.2023.133807
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.cc2gwvmv
title: CCDC 2290888: Experimental Crystal Structure Determination

description: Related Article: Ziqin Peng, Pan Wang, Zhenhong Wei, Wenjing Guo, Haina Zhang, Hu Cai|2023|Inorg.Chem.|63|184|doi:10.1021/acs.inorgchem.3c02981
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.cc2gwwhr
title: CCDC 2290915: Experimental Crystal Structure Determination

description: Related Article: Ziqin Peng, Pan Wang, Zhenhong Wei, Wenjing Guo, Haina Zhang, Hu Cai|2023|Inorg.Chem.|63|184|doi:10.1021/acs.inorgchem.3c02981
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.cc2gwwkt
title: CCDC 2290917: Experimental Crystal Structure Determination

description: Related Article: Ziqin Peng, Pan Wang, Zhenhong Wei, Wenjing Guo, Haina Zhang, Hu Cai|2023|Inorg.Chem.|63|184|doi:10.1021/acs.inorgchem.3c02981
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.cc2h4tfx
title: CCDC 2298539: Experimental Crystal Structure Determination

description: Related Article: Atie Shirvan, Hamid Golchoubian, Ehsan Rezaee|2024|Polyhedron|249|116812|doi:10.1016/j.poly.2023.116812
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.cc2hf1ss
title: CCDC 2306455: Experimental Crystal Structure Determination

description: Related Article: Yan Peng, Jonas Braun, Michael Schulze, Hagen Kaemmerer, Yannik F. Schneider, Christopher E. Anson, Wolfgang Wernsdorfer, Annie K. Powell|2024|Dalton Trans.|53|894|doi:10.1039/D3DT04141G
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.cc2hfvrk
title: CCDC 2307229: Experimental Crystal Structure Determination

description: Related Article: Samaneh Zarei, Mélina Motard, Samy Cecioni|2024|Org.Lett.|26|204|doi:10.1021/acs.orglett.3c03803
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.cc2hfvsl
title: CCDC 2307230: Experimental Crystal Structure Determination

description: Related Article: Samaneh Zarei, Mélina Motard, Samy Cecioni|2024|Org.Lett.|26|204|doi:10.1021/acs.orglett.3c03803
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: 10.5281/zenodo.10534966
title: Electrical stimulation in macaques' intralaminar thalamus for state-specific arousal regulation: network and transcriptional insights

description: In this research, we applied simultaneous EEG-fMRI and deep brain stimulation to the intralaminar thalamus in macaques under finely tuned propofol anesthesia. This approach led to the identification of an intralaminar-driven network responsible for rapid arousal during slow-wave oscillations.

ILN-DBS-GG.zip contains the preprocessed .nii functional MRI files for monkey M-G. ILN-DBS-JJ.zip contains the preprocessed .nii functional MRI files for monkey M-J.
DOI: 10.34740/kaggle/dsv/7438267
title: WallStreetBets 2022
DOI: 10.5517/ccdc.csd.cc2f7mmy
title: CCDC 2241660: Experimental Crystal Structure Determination

description: Related Article: Muntha Balaraju, Nagarjuna Kommu, Srinivas Vangara, Aswini K. Sahoo, Vikranth Thaltiri, Akhila K. Sahoo|2024|Chem.Commun.|60|827|doi:10.1039/D3CC05116A
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.cc2f7mq1
title: CCDC 2241663: Experimental Crystal Structure Determination

description: Related Article: Muntha Balaraju, Nagarjuna Kommu, Srinivas Vangara, Aswini K. Sahoo, Vikranth Thaltiri, Akhila K. Sahoo|2024|Chem.Commun.|60|827|doi:10.1039/D3CC05116A
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.cc2hgfm1
title: CCDC 2307783: Experimental Crystal Structure Determination

description: Related Article: Thi Mo Nguyen, Lucas Popek, David Matchavariani, Nicolas Blanchard, Vincent Bizet, Dominique Cahard|2024|Org.Lett.|26|365|doi:10.1021/acs.orglett.3c04043
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.cc2hgfn2
title: CCDC 2307784: Experimental Crystal Structure Determination

description: Related Article: Thi Mo Nguyen, Lucas Popek, David Matchavariani, Nicolas Blanchard, Vincent Bizet, Dominique Cahard|2024|Org.Lett.|26|365|doi:10.1021/acs.orglett.3c04043
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.