cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/icpsr23660.v2
title: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 1994 [United States]
title: Version 2

description: The data contain records of defendants in criminal cases filed in United States District Court during fiscal year 1994. The data were constructed from the Administrative Office of the United States District Courts' (AOUSC) criminal file. Defendants in criminal cases may be either individuals or corporations. There is one record for each defendant in each case filed. Included in the records are data from court proceedings and offense codes for up to five offenses charged at the time the case was filed. (The most serious charge at termination may differ from the most serious charge at case filing, due to plea bargaining or action of the judge or jury.) In a case with multiple charges against the defendant, a "most serious" offense charge is determined by a hierarchy of offenses based on statutory maximum penalties associated with the charges. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF variables," that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 4.1-4.5 and 5.1-5.6. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 1994 [United States]
description: Criminal cases filed in United States District Court during fiscal year 1994.
DOI: 10.3886/icpsr23660
title: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 1994 [United States]
title: Archival Version

description: The data contain records of defendants in criminal cases filed in United States District Court during fiscal year 1994. The data were constructed from the Administrative Office of the United States District Courts' (AOUSC) criminal file. Defendants in criminal cases may be either individuals or corporations. There is one record for each defendant in each case filed. Included in the records are data from court proceedings and offense codes for up to five offenses charged at the time the case was filed. (The most serious charge at termination may differ from the most serious charge at case filing, due to plea bargaining or action of the judge or jury.) In a case with multiple charges against the defendant, a "most serious" offense charge is determined by a hierarchy of offenses based on statutory maximum penalties associated with the charges. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF variables," that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 4.1-4.5 and 5.1-5.6. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 1994 [United States]
description: Criminal cases filed in United States District Court during fiscal year 1994.
DOI: 10.3886/icpsr22300.v3
title: Federal Court Cases: Integrated Database, 2007
title: Version 3

description: The purpose of this data collection is to provide an official public record of the business of the federal courts. The data originate from district and appellate court offices throughout the United States. Information was obtained at two points in the life of a case: filing and termination. The termination data contain information on both filing and terminations, while the pending data contain only filing information.
description: Datasets: DS0: Study-Level Files DS1: Appellate Terminations Data with Docket Numbers Blanked DS2: Appellate Terminations Data with Docket Numbers Containing Original Values DS3: Civil Terminations Data with Docket Numbers, PLT and DEF Blanked DS4: Civil Terminations Data with Docket Numbers, PLT and DEF Containing Original Values DS5: Criminal Data with Docket Numbers Blanked DS6: Criminal Data with Docket Numbers Containing Original Values
description: All federal court cases in the United States in 2007. Smallest Geographic Unit: county
description: Starting with the year 2001, each year of data for Federal Court Cases is released by ICPSR as a separate study number. Federal Court Cases data for the years 1970-2000 can be found in FEDERAL COURT CASES: INTEGRATED DATA BASE, 1970-2000 (ICPSR 8429).
DOI: 10.5517/ccdc.csd.cc2b8wyg
title: CCDC 2153506: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2b8wzh
title: CCDC 2153507: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2b8x0k
title: CCDC 2153508: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2b8x1l
title: CCDC 2153509: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2b8x2m
title: CCDC 2153510: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2b8x3n
title: CCDC 2153511: Experimental Crystal Structure Determination

description: Related Article: Jing-yang Wang, Lei Mei, Yang Liu, Qiu-yan Jin, Kong-qiu Hu, Ji-pan Yu, Cai-shan Jiao, Meng Zhang, Wei-qun Shi|2023|ACS Omega|8|8894|doi:10.1021/acsomega.3c00640
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.cc2f71lb
title: CCDC 2241101: Experimental Crystal Structure Determination

description: Related Article: Kavyashree Kuppayya Gond, Mahagundappa Rachappa Maddani|2023|Org.Biomol.Chem.|21|2504|doi:10.1039/D2OB02134J
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: 10.3886/icpsr23081.v2
title: Federal Court Cases: Integrated Data Base Bankruptcy Petitions, 2006
title: Version 2

description: The purpose of this data collection is to provide an official public record of the business of the federal bankruptcy courts. The data include all petitions filed under the Bankruptcy Code in the United States Bankruptcy Courts on or after October 1, 2006, that were terminated in the 2006 fiscal year. For the bankruptcy data, the unit of analysis is a single case.
description: Datasets: DS1: Federal Court Cases: Integrated Data Base Bankruptcy Petitions, 2006
description: All federal Bankruptcy Court cases in the United States in 2006.
description: record abstracts
DOI: 10.3886/icpsr23081
title: Federal Court Cases: Integrated Data Base Bankruptcy Petitions, 2006
title: Archival Version

description: The purpose of this data collection is to provide an official public record of the business of the federal bankruptcy courts. The data include all petitions filed under the Bankruptcy Code in the United States Bankruptcy Courts on or after October 1, 2006, that were terminated in the 2006 fiscal year. For the bankruptcy data, the unit of analysis is a single case.
description: Datasets: DS1: Federal Court Cases: Integrated Data Base Bankruptcy Petitions, 2006
description: All federal Bankruptcy Court cases in the United States in 2006.
description: record abstracts
DOI: 10.5281/zenodo.7753180
title: TUGMCL_BasicMilling

description: A data set collecting the design files, resulting G-code and 500Hz sensor data from four basic milling operations (face milling, end milling, plunge milling, slot milling). This is a preliminary version (0.1.0)
DOI: 10.5281/zenodo.7753181
title: TUGMCL_BasicMilling

description: A data set collecting the design files, resulting G-code and 500Hz sensor data from four basic milling operations (face milling, end milling, plunge milling, slot milling). This is a preliminary version (0.1.0)
DOI: 10.6069/d5q3-1j13
title: Global COVID-19 Estimates December 16, 2022 Release

description: This dataset contains estimates of deaths, vaccine coverage, hospital resource use, daily infections and testing, mask use, and social distancing due to COVID-19 for a number of countries and subnational areas. The projections for cumulative and daily deaths, infections, and social distancing each include three scenarios: The reference scenario is the forecast IHME deems most likely (for more on this scenario, please see the expanded summary in the Data Release Information Sheet under the "Files" tab of this record) The 80% mask use scenario assumes all locations reach 80% mask use within seven days The antiviral access scenario assumes globally distributed antivirals The model that produced these estimates incorporated data on observed COVID-19 deaths, hospitalizations, and cases, protective measures, mobility, and other factors.
DOI: 10.6084/m9.figshare.22320592
title: Transformed Counts

description: this dataset is used in a few analyses in the manuscript. It's name is transformed counts. It's a "tidy" dataset with ASV relative abundances.
DOI: 10.18112/openneuro.ds004100.v1.1.3
title: HUP iEEG Epilepsy Dataset
DOI: 10.6084/m9.figshare.22313563
title: 2019 GWAS Microbiome Experiment

description: RDS file containing data for the 2019 Switchgrass GWAS experiment. Contained in the file is a dataframe of counts, a dataframe of information about the samples, and a taxonomy dataframe for the ASVs
DOI: 10.6084/m9.figshare.22313563.v1
title: 2019 GWAS Microbiome Experiment

description: RDS file containing data for the 2019 Switchgrass GWAS experiment. Contained in the file is a dataframe of counts, a dataframe of information about the samples, and a taxonomy dataframe for the ASVs
DOI: 10.6084/m9.figshare.22320889
title: 0313_full.csv

description: 2017 Women's March Tweet Dataset, originally from Harvard Dataverse, modified by Ruyi Lu for UCLA DH120 final project, modifications done with R
DOI: 10.6084/m9.figshare.22320889.v1
title: 0313_full.csv

description: 2017 Women's March Tweet Dataset, originally from Harvard Dataverse, modified by Ruyi Lu for UCLA DH120 final project, modifications done with R
DOI: 10.6084/m9.figshare.3761562.v2533
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.3761562.v2534
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.10309062
title: Hotspots of PKS coding evidence within the Prymnesium parvum 12B1 v1.1 genome assembly

description: Input, intermediate, and results files for liftover of PKS hotspot analysis onto the P. parvum 12B1 v1.1 genome. 
See "Definition of PKS hotspots within the 12B1 genome" in the manuscript materials and methods for further details.
DOI: 10.5281/zenodo.10011738
title: InterProScan domain annotation on non-PKZILLA polypeptides

description: This is a .zip archive of the git repository and Nextflow workflow used for annotation of the non-PKZILLA protein domains (rest of proteome) 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.10023460 for analogous predictions but for all the PKZILLA proteins from Prymnesium parvum 12B1. 
Key files:

./run.sh entry script for running InterProScan
GFF3 file of InterProScan features, after post processing: './results/do_simple_nonparallel_scan:gff_nested_filter/filtered/ipr_merged.gff'
DOI: 10.5281/zenodo.10023425
title: Kallisto v0.50.0 expression quantification of day and night phase rRNA depletion RNA-Seq data from P. parvum strain 12B1

description: Kallisto v0.50.0 was used to quantify the following libraries: 
SRR23517916 (Night phase; https://trace.ncbi.nlm.nih.gov/Traces?run=SRR23517916) 
SRR23517917 (Day phase; https://trace.ncbi.nlm.nih.gov/Traces?run=SRR23517917)
Against this in silico predicted transcriptome: 12B1_v1.1.gff3__12B1_scaffolds_v1.1.fasta.mRNA.fa (seqkit sum: seqkit.v0.1_DLS_k0_559abfafd14eacd04de9c4d42af781a0) (Available from: https://doi.org/10.5281/zenodo.10023330)
SRR23517916 selected results: 
target_id length eff_length est_counts tpm 
PKZILLA-1 136088 135896 37629.1 0.713157 
PKZILLA-2 92413 92220.9 59960.9 1.67459 
PKZILLA-3 73850 73657.9 25959 0.907688
SRR23517917 selected results: 
target_id length eff_length est_counts tpm 
PKZILLA-1 136088 135895 66303.4 1.11135 
PKZILLA-2 92413 92220.3 98095.6 2.42293 
PKZILLA-3 73850 73657.3 1058 0.0327181
DOI: 10.5281/zenodo.10120639
title: Scripts, data, and analyses for extending flavoprotein (FLX) domains C-terminally to form extended FLX domains (eFLX) & performing structural predictions & alignments using AlphaFold2, RoseTTAFold, FoldSeek, and DALI

description: See associated manuscript for more details. 
To capture unannotated regions of the FLX domains for structural modeling, an extended flavin oxygenase domain (eFLX) was annotated by extending the C-terminus of the G3DSA:3.50.50.60 InterProScan FLX annotation to the N-terminus of the downstream annotation, using bedtools closest [1] and awk. Next, the annotation was expanded by 50 residues both upstream and downstream to account for potential inaccuracy in the domain annotations. The peptide FASTA representation of these eFLX domains were extracted, and subjected to 3D modelling using RoseTTAFold via the Robetta server [2], and AlphaFold2 (ColabFold v1.5.2-patch: AlphaFold2 using MMseqs2) using the ColabFold Google Collaboratory notebooks [3], [4]. After modeling, the rank 1 model and model 1 model from AlphaFold2 and RoseTTAFold, respectively, were used for structural similarity searches with FoldSeek via the FoldSeek server [5]. The DALI webserver was used for the structural similarity search to establish structural homology [6]. 
[1]        A. R. Quinlan and I. M. Hall, "BEDTools: a flexible suite of utilities for comparing genomic features," Bioinformatics, vol. 26, no. 6, pp. 841–842, Mar. 2010, doi: 10.1093/bioinformatics/btq033.
[2]        M. Baek et al., "Accurate prediction of protein structures and interactions using a three-track neural network," Science, Jul. 2021, doi: 10.1126/science.abj8754.
[3]        M. Mirdita, K. Schütze, Y. Moriwaki, L. Heo, S. Ovchinnikov, and M. Steinegger, "ColabFold: making protein folding accessible to all," Nat. Methods, vol. 19, no. 6, Art. no. 6, Jun. 2022, doi: 10.1038/s41592-022-01488-1.
[4]        J. Jumper et al., "Highly accurate protein structure prediction with AlphaFold," Nature, pp. 1–11, Jul. 2021, doi: 10.1038/s41586-021-03819-2.
[5]        M. van Kempen et al., "Fast and accurate protein structure search with Foldseek," Nat. Biotechnol., pp. 1–4, May 2023, doi: 10.1038/s41587-023-01773-0.
[6]        L. Holm, A. Laiho, P. Törönen, and M. Salgado, "DALI shines a light on remote homologs: One hundred discoveries," Protein Sci., vol. 32, no. 1, p. e4519, 2023, doi: 10.1002/pro.4519.
DOI: 10.25345/c5tx35h7k
title: MassIVE MSV000093895 - Comparative seed proteome profile reveals no alternation of major allergens of high yielding mung bean cultivars
title: Mung bean contains up to 25% of the protein, is one of the great sources of plant-based protein. Since many allergens also function as defense-related proteins, it is important to determine their abundance level in the high-yielding disease-resistant cultivars. In this study, for the first time, we compared the seed proteome of disease-resistant high-yielding mung bean cultivars developed by conventional breeding approach. Using label-free quantitative proteomic platform, we successfully identified and quantified a total of 1373 proteins. Comparative analysis between the high-yielding disease-resistant cultivar (MC5) and other three cultivars showed a total of 69 proteins were significantly altered in abundance and overlapped across the cultivars. Subsequent bioinformatic analysis of these altered proteins demonstrated that PDF1 (a defensin-like protein) exhibited high sequence similarity and epitope matching with the established peanut allergens (Ara h 12 and 13), indicating a potential mung bean allergen. Conversely, known mung bean allergen proteins such as Vig r 2, Vig r 4, LTP1, PR2, beta-Conglycinin, and Glycinin G4 showed no alternation in the MC5 compared to other cultivars. Taken together, our findings suggest that the known allergen profiles may not be impacted by the conventional plant breeding method to develop improved mung bean cultivars.
DOI: 10.5281/zenodo.10093616
title: Non-length-normalized graphical plots of the PKZILLA domains, modules, cDUFs, and exon extents

description: Jupyter notebooks and source files responsible for creating the non-length-normalized graphical plots of the PKZILLA domains, modules, cDUFs, and exon extents on the PKZILLA polypeptides.
DOI: 10.5281/zenodo.10028516
title: Tabular analysis of polyketide synthase domain active site residues for the PKZILLAs

description: In brief, the presence or absence of expected conserved enzyme active site residues within domains of the PKZILLAs, were matched to the polyketide ketosynthase (KS), acyl carrier protein (ACP), dehydratase (DH), ketoreductase (KR), flavin oxygenase (FLX), and enoyl (ER) domains, using either multiple sequence alignment liftover of active site location & residue as defined by InterProScan annotations, or, locations & residues defined as active site residues from literature sources.

./KS_ALL represents the scripts and source files used to generate the analyses. See run.sh , within.

Post_process_KS-ALL_analysis.ipynb represents the Jupyter notebook used to process the raw analyses into the presented tabular (.xlsx) form.

See Manuscript Materials and Methods for further details.

Summary of the active side residue results:

KS:All scored as active on the basis of catalytic cysteine. The below KS domains are scored as KS0, on the basis of variation of the histidine in the HGTGT motif:

PKZILLA-1__KS14 QGLGS

PKZILLA-1__KS19 QGLGS

PKZILLA-1__KS22 QGLGS

PKZILLA-1__KS25 QGLGS

PKZILLA-1__KS28 QGLGS

PKZILLA-1__KS31 GANGS

PKZILLA-1__KS34 QGLGS

PKZILLA-2__KS3 QGLGS

PKZILLA-2__KS6 QGLGS

PKZILLA-2__KS9 QGLGS

PKZILLA-2__KS11 QGLGS

PKZILLA-2__KS12 QGLGS

PKZILLA-3__KS6 AANGS

ACP:All scored as active (PPant prosthetic group attachment residue present)

DH:All scored as active, except possibly:PKZILLA-3__DH9

ER:Active site residues not defined in InterProScan or literature sources.

FLX:Active site residues not defined in InterProScan or literature sources.

KR:

KR domains come in two flavors: the canonical "full-length" contiguous domain, and the non-canonical split domain with two subdomains.KRs are 2 reciprocally similar subdomains - where the N-terminal subdomain "KRn" has a structural role, and the C-terminal subdomain "KRc" has the catalytic role.

Typically, the two KR subdomains are contiguous. 

However, it's precedendented (Porcine FAS) that these two KRn and KRc subdomains can become split with an ER in the middle. In the PKZILLAs, this can be observed for the KR-ER-KR in Module 28, it's actually KRn-ER-KRc. The first KRn-subdomain (KR26) is missing the catalytic residues (as are all of the KRn domains), while the second KRc-subdomain (KR27) has all of them. This split KR domain structure seems to be not that uncommon in the PKZILLAs, and the intervening domain is not limited to being an ER.

The KR.xlsx excel summarizes the status of the KRs, as active or inactive, and full-length (f), n-terminal subdomain (n), or c-terminal subdomain (c). The below KR domains are scored as inactive:

PKZILLA-1__KR26PKZILLA-1__KR29PKZILLA-1__KR31PKZILLA-2__KR6PKZILLA-2__KR11PKZILLA-2__KR20

Summary of the domain phylogenetics results:

Present in separate Zenodo item: https://doi.org/10.5281/zenodo.10152639