cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24388/k50002102
title: T. Koike, M. Kudo, I. Maeda, H. Yamada, Int. J. Chem. Kinet. 32 (2000), 1-16, Fig. 3, open symbols
DOI: 10.14457/kmutt.the.2010.348
title: บทเรียนคอมพิวเตอร์การสอน วิชาคอมพิวเตอร์และเทคโนโลยีสารสนเทศเบื้องต้น เรื่องคอมพิวเตอร์และอุปกรณ์ /
DOI: 10.5281/zenodo.838570
title: Mehra Data And Model For The English Regions

description: <strong>M</strong>ulti-dimensional <strong>E</strong>nvironment-<strong>H</strong>ealth <strong>R</strong>isk <strong>A</strong>nalysis (<strong>MEHRA</strong>) data and model for the English regions

This archive contains 4 objects in RDS (R Data Storage) format:


	<strong>Training </strong>and <strong>testing</strong> datasets - These have been assembled to carry out the experiments described in the paper 'Modelling air pollution, climate and health data using Bayesian Networks: a case study of the English regions' by Vitolo et al. (currently under review)
	<strong>BN model </strong>and <strong>DAG</strong> - These are the bayesian network and DAG resulting from the experiment described in the paper 'Modelling air pollution, climate and health data using Bayesian Networks: a case study of the English regions' by Vitolo et al. (currently under review)


The paper contains full details of the features, below is a short summary:


	Data were collected in England (United Kingdom) from 1981 to 2014.
	Mortality counts were obtained from the Office for National Statistics (ONS)
	The counts were standardized based on yearly regional population estimates obtained from the MYEDE dataset.
	Data from air quality monitoring stations were obtained from the UK Air Information Resource service hosted by the Department for Environment, Food & Rural Affairs (DEFRA).
	Weather variables derive from ECMWF ERA-Interim (global re-analysis dataset)
description: British Council Institutional Links Grant 172614334
description: {"references": ["Vitolo C., Russell A. and Tucker A. (2017). rdefra: Interact with the UK AIR Pollution Database from DEFRA. R package version 0.3.4 https://CRAN.R-project.org/package=rdefra, DOI: 10.5281/zenodo.838587.", "Vitolo C., Russell A. and Tucker A. (2016). rdefra: Interact with the {UK} {AIR} Pollution Database from {DEFRA}. The Journal of Open Source Software 1 (4), DOI: 10.21105/joss.00051.", "Vitolo C., Tucker A. and Russell A. (2016). kehra: An R package to collect, assemble and model air pollution, weather and health data. R package version 0.1.  https://CRAN.R-project.org/package=kehra, DOI: 10.5281/zenodo.55284.", "Vitolo C., Scutari M., Ghalaieny M., Tucker A. and Russell A. (2017). A multi-dimensional environment-health risk analysis system for the English regions. EGU General Assembly Conference Abstracts, 2017. http://meetingorganizer.copernicus.org/EGU2017/EGU2017-11880.pdf"]}
DOI: 10.3886/e100889v1
title: The Gun-Slave Hypothesis and the 18th Century British Slave Trade

description: The Gun-Slave Hypothesis is the long-standing idea that
European gunpowder technology played a key role in growing the transatlantic
slave trade. I combine annual data from the Transatlantic Slave Trade Database
and the Anglo-African Trade Statistics to estimate a Vector Error Correction Model
of the 18th century British slave trade that captures four versions
of the Gun-Slave Hypothesis: guns-for-slaves-in-exchange,
guns-for-slaves-in-production, slaves-for-guns-derived and the gun-slave cycle.
Three econometric results emerge. (1) Gunpowder imports and slave exports were
co-integrated in a long-run equilibrium relationship. (2) Positive deviations
from equilibrium gunpowder “produced” additional slave exports. This guns-for-slaves-in-production
result survives 17 placebo tests that replace gunpowder with non-lethal
commodities imports. It is also confirmed by an instrumental variables
estimation that uses excess capacity in the British gunpowder industry as an
instrument for gunpowder. (3) Additional slave exports attracted additional
gunpowder imports for 2-3 more years. Together these dynamics formed a
gun-slave cycle. Impulse-response functions generate large increases in slave
export in response to increases in gunpowder imports. I use these results to explain
the growth of slave exports along the Guinea Coast of Africa in the 18th
century.
DOI: 10.7910/dvn/cwyotq
title: Communist Ruling Elites Database (CRED): Yugoslavia Politburo/Presidium, 1940-1990

description: This dataset indicates the names of candidates and members of the winning coalition elite in Yugoslavia. These individuals comprised the Politburo/Presidium of the Communist Party of Yugoslavia (SKJ), and later League of Communists of Yugoslavia (SKJ), from 1940-90.
DOI: 10.5281/zenodo.838731
title: The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

description: This repository pertains to the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach.

For more information about how to reproduce this modeling, see the Sali lab website or the README file.
DOI: 10.5281/zenodo.838732
title: Modeling Of The Spindle Pole Body Core

description: This repository pertains to the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach.
DOI: 10.5281/zenodo.838791
title: The Molecular Architecture Of The Yeast Spindle Pole Body Core Determined By Bayesian Integrative Modeling

description: This repository pertains to the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach.

For more information about how to reproduce this modeling, see https://salilab.org/spb/ or the README file.
DOI: 10.5281/zenodo.838740
title: Proteomics_Analysis For Maier Et Al. 2017

description: This is an annotated proteomics data set used in the the paper "Impact of dietary resistant starch on the human gut microbiome, metaproteome and metabolome." mBio01343-17 

Proteomics analysis was lead by Lang Ho Lee. Colin J. Brislawn is the informatics point-of-contact.
DOI: 10.5281/zenodo.838741
title: Proteomics_Analysis For Maier Et Al. 2017

description: This is an annotated proteomics data set used in the the paper "Impact of dietary resistant starch on the human gut microbiome, metaproteome and metabolome." mBio01343-17 

Proteomics analysis was lead by Lang Ho Lee. Colin J. Brislawn is the informatics point-of-contact.
DOI: 10.5063/f1ns0rzx
title: Puerto Rico Bicknell's Thrush Surveys, 2015

description: A predictive model of the distribution of wintering habitat for Bicknell’s Thrush (Catharus bicknelli) (McFarland et al. 2013) indicated that a considerable extent of potentially suitable habitat for Bicknell's Thrush exists in the central highlands of Puerto Rico. This region has never been surveyed for the species. To test the predictions of the winter habitat model, and to better clarify the species’ distribution during the winter, we conducted surveys in areas throughout Puerto Rico identified as potentially suitable habitat.  

We conducted field surveys from January 2015 through March 2015. We visited 43 1-km2 cells that we selected from the winter habitat model using a generalized random tessellation stratified (GRTS) sampling approach. Within each cell, we surveyed a minimum of 3-5 points that were &gt;250 meters apart.  The location of points within each cell was determined systematically based on accessibility - all points were in forest adjacent to roads - and to ensure an even distribution of points across the cell.  Forest cover within a 50-m radius around each point was at least 50%. At each point, a single observer counducted 4 repeated surveys. Each survey lasted for 2.5 minutes, and repeated surveys were conducted in sequence, one after another.  A 1-minute playback of Bicknell’s Thrush vocalizations was broadcast before the second and fourth surveys; there was no delay the second and third surveys. Individuals of all species detected during each survey were registered.

References

McFarland KP, Rimmer CC, Goetz JE, Aubry Y, Wunderle JM Jr, Sutton A, Townsend JM, Sosa AL, Kirkconnell A. A winter distribution model for Bicknell's Thrush (Catharus bicknelli), a conservation tool for a threatened migratory songbird. PLoS One. 2013;8(1) e53986. doi:10.1371/journal.pone.0053986. PMID: 23326554; PMCID: PMC3541143.
DOI: 10.5281/zenodo.838806
title: Food Liking Electromyography (Fal1)

description: This dataset comprises born-open raw data collected during an experiment measuring facial emg during oral processing of foods. Raw data is in proprietary formats: Behavioural data is PST's Eprime 2 Professional (*.edat2) and Physiology data is Biopac's AcqKnowledge (*.ACQ). Text formatted raw data will be posted in a later version of the repository in a single archive once data collection is completed.
DOI: 10.5281/zenodo.838733
title: Gene Regulatory Networks For 38 Human Tissues

description: We reconstructed gene regulatory networks for 38 tissues from the Genotype-Tissue Expression project (GTEx), and used these networks to investigate gene expression and regulation across these tissues. In the RData file, we share the following objects:

- <strong>edges</strong>: an 19,476,492 by 3 data.frame including three columns: TF (the transcription factor's gene symbol), Gene (Ensembl ID), Prior (whether an edge is canonical (1) or non-canonical (0)).<br>
<br>
- <strong>exp</strong>: a 30,243 by 9,435 matrix including normalized expression data for each sample.<br>
<br>
- <strong>expTS</strong>: a 30,243 by 38 matrix including, for each gene and each tissue, information on whether the gene is expressed in a tissue-specific manner in that tissue (1) or not (0).<br>
<br>
- <strong>genes</strong>: a 30,243 by 4 data.frame that includes annotation information (Symbol) for Ensembl gene IDs (Name). This data.frame also includes information on whether genes are also transcription factors (AlsoTF), with options: no, yes/motif (TF with a known DNA-binding motif) yes/nomotif (TF without a known DNA-binding motif). In addition, the multiplicity of the gene (Multiplicity) is given.<br>
<br>
- <strong>net</strong>:  a 19,476,492 by 38 matrix that includes edge weights for each tissue. Edge order corresponds to edge order in the the object "edges".<br>
<br>
- <strong>netTS</strong>: a 19,476,492 by 38 matrix that includes information of whether edges are specific to a tissue (1) or not (0).<br>
<br>
- <strong>samples</strong>: a 9,435 by 2 data.frame that includes sample identifiers (matching the identifiers in "exp") and the tissue to which these samples belong.
description: This work was supported by grants from the US National institutes of Health, including grants from the National Heart, Lung, and Blood Institute (5P01HL105339, 5R01HL111759, 5P01HL114501, K25HL133599), the National Cancer Institute (5P50CA127003, 1R35CA197449, 1U01CA190234, 5P30CA006516, P50CA165962), the National Institute of Allergy and Infectious Disease (5R01AI099204), and the Charles A. King Trust Postdoctoral Research Fellowship Program, Bank of America, N.A., Co-Trustees and Sara Elizabeth O'Brien Trust, Bank of America, N.A., Trustee. Additional funding was provided through a grant from the NVIDIA foundation. This work was conducted under dbGaP approved protocol #9112 (accession phs000424.v6.p1).
DOI: 10.5281/zenodo.838734
title: Gene Regulatory Networks For 38 Human Tissues

description: We reconstructed gene regulatory networks for 38 tissues from the Genotype-Tissue Expression project (GTEx), and used these networks to investigate gene expression and regulation across these tissues. In the RData file, we share the following objects:

- <strong>edges</strong>: an 19,476,492 by 3 data.frame including three columns: TF (the transcription factor's gene symbol), Gene (Ensembl ID), Prior (whether an edge is canonical (1) or non-canonical (0)).<br>
<br>
- <strong>exp</strong>: a 30,243 by 9,435 matrix including normalized expression data for each sample.<br>
<br>
- <strong>expTS</strong>: a 30,243 by 38 matrix including, for each gene and each tissue, information on whether the gene is expressed in a tissue-specific manner in that tissue (1) or not (0).<br>
<br>
- <strong>genes</strong>: a 30,243 by 4 data.frame that includes annotation information (Symbol) for Ensembl gene IDs (Name). This data.frame also includes information on whether genes are also transcription factors (AlsoTF), with options: no, yes/motif (TF with a known DNA-binding motif) yes/nomotif (TF without a known DNA-binding motif). In addition, the multiplicity of the gene (Multiplicity) is given.<br>
<br>
- <strong>net</strong>:  a 19,476,492 by 38 matrix that includes edge weights for each tissue. Edge order corresponds to edge order in the the object "edges".<br>
<br>
- <strong>netTS</strong>: a 19,476,492 by 38 matrix that includes information of whether edges are specific to a tissue (1) or not (0).<br>
<br>
- <strong>samples</strong>: a 9,435 by 2 data.frame that includes sample identifiers (matching the identifiers in "exp") and the tissue to which these samples belong.
description: This work was supported by grants from the US National institutes of Health, including grants from the National Heart, Lung, and Blood Institute (5P01HL105339, 5R01HL111759, 5P01HL114501, K25HL133599), the National Cancer Institute (5P50CA127003, 1R35CA197449, 1U01CA190234, 5P30CA006516, P50CA165962), the National Institute of Allergy and Infectious Disease (5R01AI099204), and the Charles A. King Trust Postdoctoral Research Fellowship Program, Bank of America, N.A., Co-Trustees and Sara Elizabeth O'Brien Trust, Bank of America, N.A., Trustee. Additional funding was provided through a grant from the NVIDIA foundation. This work was conducted under dbGaP approved protocol #9112 (accession phs000424.v6.p1).
DOI: 10.5281/zenodo.838020
title: Hansard Speeches And Sentiment V2.4

description: Full details are available at https://evanodell.com/projects/datasets/hansard-data

<strong>Summary</strong>

A public dataset of speeches in the Hansard, stored as a tibble class in RDS files, for the R programming language. The dataset provides information on every speech made in the House of Commons between the parliament returned from the 1979 general election and the parliamentary summer recess starting on 2017-07-20, with information on the speaking MP, their party, gender, birthdate, starting and finishing dates as an MP, and age at the time of the speech. The dataset also includes all speeches made from 1936 to the dissolution of parliament for the 1979 general election. The post-1979 election dataset is labelled hansard_senti_post_V24 and the pre-1979 election dataset is labelled hansard_senti_pre_V24.

The `hansard_senti_post_V24` dataset contains 2,169,348 speeches and 373,323,215 words. The `hansard_senti_pre_V24` dataset contains 2,977,461 speeches and 406,062,364 words. It is distributed under a Creative Commons 4.0 BY-SA licence.

<strong>Notes</strong>

The code and matching data used to generate this dataset is available on Github.

The data used to create this dataset was taken from the parlparse project operated by They Work For You and supported by mySociety.

The dataset is licensed under a Creative Commons Attribution 4.0 International License.

The code used to create this dataset is licensed under an MIT license.

Please contact me if you find any errors in the dataset. The integrity of the public Hansard record is questionable at times, and while I have improved it, the data is presented 'as is'.
description: This release is an update of previously released datasets. See full documentation for details.
DOI: 10.5281/zenodo.838800
title: Sequential Upload Test

description: A repository to test automated sequential uploading of new participants’ data.
DOI: 10.5281/zenodo.838801
title: Sequential Upload Test

description: A repository to test automated sequential uploading of new participants’ data.
DOI: 10.5281/zenodo.838148
title: Siddham Epigraphic Archive - Metadata and bibliography

description: This is an archived version of pre-publication metadata collected for the Siddham epigraphic corpus, and the bibliographic references cited in the metadata. The data listed here, along with the editions of epigraphic texts, will be made openly available through the online database at https://siddham.network/. Work-in-progress versions of collected metadata are archived here, and the publication versions will likewise be archived.

Latest version: 2019-01-30. This is the last offline version of the metadata and bibliography before ingestion into the database.

Archive versions: 2017-08-02, 2017-11-18.
DOI: 10.5281/zenodo.838149
title: Siddham Epigraphic Archive - Metadata And Bibliography

description: This is an archived version of pre-publication metadata collected for the Siddham epigraphic corpus, and the bibliographic references cited in the metadata. The data listed here, along with the editions of epigraphic texts, will be made openly available through the online database in the near future. Work-in-progress versions of collected metadata are archived here, and the publication versions will likewise be archived.
DOI: 10.15482/usda.adc/1373877
title: Feedstock Readiness Level (FSRL) evaluation: Millettia pinnata (pongamia), hydroprocessing (HEFA), Southeast, May 2017
DOI: 10.5281/zenodo.839011
title: Differential Gene Expression In Ipsc-Derived Macrophages After Ifng Stimulation And Salmonella Infection

description: We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = “LRT”) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details: http://www.biorxiv.org/content/early/2017/05/18/102392 .

We used the following commands in DESeq2:<br>
#Run DESeq2<br>
dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) <br>
dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)

#Extract differentially expressed genes in each condition<br>
ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) <br>
sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) <br>
ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))
DOI: 10.18430/m35upg
title: X-ray diffraction data for the crystal structure of LpxC from Pseudomonas aeruginosa in complex with PF-5081090 (5UPG)
DOI: 10.18430/m35v6d
title: X-ray diffraction data for the crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate (5V6D)
DOI: 10.18430/m35v77
title: X-ray diffraction data for the crystal structure of an uncharacterized protein from Neisseria gonorrhoeae (5V77)
DOI: 10.18430/m35v96
title: X-ray diffraction data for the crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine (5V96)
DOI: 10.18430/m35vbf
title: X-ray diffraction data for the crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis (5VBF)
DOI: 10.18430/m35vcp
title: X-ray diffraction data for the crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin (5VCP)
DOI: 10.18430/m35vct
title: X-ray diffraction data for the crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria (5VCT)
DOI: 10.18430/m35ve7
title: X-ray diffraction data for the crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP (5VE7)
DOI: 10.5281/zenodo.839010
title: Differential Gene Expression In Ipsc-Derived Macrophages After Ifng Stimulation And Salmonella Infection

description: We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = “LRT”) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details: http://www.biorxiv.org/content/early/2017/05/18/102392 .

We used the following commands in DESeq2:<br>
#Run DESeq2<br>
dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) <br>
dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)

#Extract differentially expressed genes in each condition<br>
ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) <br>
sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) <br>
ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))
DOI: 10.18430/m35vev
title: X-ray diffraction data for the crystal Structure of Phosphoribosylamine-glycine Ligase from Neisseria gonorrhoeae (5VEV)
DOI: 10.18430/m35vir
title: X-ray diffraction data for the crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abscessus in complex with NADP and compound FOL0091 (5VIR)
DOI: 10.18430/m35viu
title: X-ray diffraction data for the crystal Structure of Acetylornithine Aminotransferase from Elizabethkingia anophelis (5VIU)
DOI: 10.18430/m35vl1
title: X-ray diffraction data for the crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine (5VL1)
DOI: 10.18430/m35vm1
title: X-ray diffraction data for the crystal structure of a xyloylose kinase from Brucella ovis (5VM1)
DOI: 10.18430/m35vm8
title: X-ray diffraction data for the crystal structure of a Ribosomal RNA small subunit methyltransferase E from Neisseria gonorrhoeae bound to S-adenosyl methionine (5VM8)
DOI: 10.18430/m35vmb
title: X-ray diffraction data for the crystal structure of a glycine hydroxymethyltransferase from Acinetobacter baumannii (5VMB)
DOI: 10.18430/m35vmk
title: X-ray diffraction data for the crystal structure of a bifunctional GlmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1- phosphate N-acetyltransferase from Acinetobacter baumannii (5VMK)
DOI: 10.18430/m35vml
title: X-ray diffraction data for the crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b with bound NADP (5VML)
DOI: 10.17036/researchdata.aston.ac.uk.00000254
title: Stream segregation of concurrent speech and the verbal transformation effect: Influence of fundamental frequency
and lateralization cues
DOI: 10.18430/m35vmt
title: X-ray diffraction data for the crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD (5VMT)
DOI: 10.18430/m35vn2
title: X-ray diffraction data for the crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis in complex with NAD (5VN2)
DOI: 10.18430/m35vn4
title: X-ray diffraction data for the crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate (5VN4)
DOI: 10.18430/m35vn6
title: X-ray diffraction data for the crystal structure of Taurine dioxygenase from Burkholderia ambifaria (5VN6)
DOI: 10.18430/m35vnx
title: X-ray diffraction data for the crystal structure of an 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct (5VNX)
DOI: 10.18430/m35vog
title: X-ray diffraction data for the crystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp (5VOG)
DOI: 10.18430/m35vpq
title: X-ray diffraction data for the crystal structure of beta-lactamase from Burkholderia phymatum (5VPQ)
DOI: 10.18430/m35vpr
title: X-ray diffraction data for the crystal Structure of Cysteine desulfurase from Elizabethkingia anophelis with covalently bound pyridoxal phosphate (5VPR)