cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.988671.v1
title: RP_pollen.xls

description: Data from:<br>Higuera, P. E., L. B. Brubaker, P. M. Anderson, F. S. Hu, and T. A. Brown. 2009.<br>Vegetation mediated the impacts of postglacial climate change on fire regimes<br>in the south-central Brooks Range, Alaska. Ecological Monographs 79:201-219. For each site, Code (CO), Ruppert (RP), Wild Tussock (WK), and Xindi (XI), there<br>are the six files: 1. xx_age_depth_data.txt – Depth (cm) and age (cal yr BP) from the published<br>age-depth model. 2. xx_age_depth_fig.pdf – Figure of the age-depth model, ¼ of Fig. 2 in Higuera<br>et al. (2009) 3. xx_charData.csv – Charcoal data in a CharAnalysis input file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 4. xx_charParams.csv – Parameter file CharAnalysis, with parameters as used in the<br>original publication. See https://sites.google.com/site/charanalysis/ for more details. 5. xx_charResults.csv – CharAnalysis results file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 6. xx_pollen.xls – Pollen counts for each sample. The tab “pollen_counts” and<br>“pollen_cm” contains raw the same data as in the tab “data” but in a raw format<br>used for plotting. Ages associated with each pollen sample have to be obtained<br>from the “xx_age_depth_data.txt” file, or from the appropriate column in the<br>“charData” file in the “xx_char.xls” file. Radiocarbon dates from each site are in the file “Higuera_et_al_2009_Table_B1”<br>in the folder titled “C14_dates” as published here:<br>http://www.esapubs.org/archive/mono/M079/007/ CONTACT:<br>Philip Higuera<br>phiguera@uidaho.edu<br>pehiguera@gmail.com Key words: Arctic, boreal forest, climate change, pollen analysis, tundra, shrub tundra,<br>paleoecology, Gates of the Arctic National Park Taxa: Alnus, Artemisia, Cyperaceae, Betula, Picea mariana, Picea glauca, Populus, Poaceae,<br>Salix, Sphagnum, Pediastrum
DOI: 10.6084/m9.figshare.988687.v1
title: Data, code, and figures from Dunnette et al. 2014

description: Data, code, and figures from Dunnette et al. 2014.
DOI: 10.6084/m9.figshare.988652.v2
title: Data from Higuera et al. 2009. Vegetation mediated the impacts of postglacial climate change on fire regimes in the south-central Brooks Range, Alaska. Ecological Monographs. 79: 201-219.

description: Data from:<br>Higuera, P. E., L. B. Brubaker, P. M. Anderson, F. S. Hu, and T. A. Brown. 2009.<br>Vegetation mediated the impacts of postglacial climate change on fire regimes<br>in the south-central Brooks Range, Alaska. Ecological Monographs 79:201-219. For each site, Code (CO), Ruppert (RP), Wild Tussock (WK), and Xindi (XI), there<br>are the six files: 1. xx_age_depth_data.txt – Depth (cm) and age (cal yr BP) from the published<br>age-depth model. 2. xx_age_depth_fig.pdf – Figure of the age-depth model, ¼ of Fig. 2 in Higuera<br>et al. (2009) 3. xx_charData.csv – Charcoal data in a CharAnalysis input file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 4. xx_charParams.csv – Parameter file CharAnalysis, with parameters as used in the<br>original publication. See https://sites.google.com/site/charanalysis/ for more details. 5. xx_charResults.csv – CharAnalysis results file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 6. xx_pollen.xls – Pollen counts for each sample. The tab “pollen_counts” and<br>“pollen_cm” contains raw the same data as in the tab “data” but in a raw format<br>used for plotting. Ages associated with each pollen sample have to be obtained<br>from the “xx_age_depth_data.txt” file, or from the appropriate column in the<br>“charData” file in the “xx_char.xls” file. Radiocarbon dates from each site are in the file “Higuera_et_al_2009_Table_B1”<br>in the folder titled “C14_dates” as published here:<br>http://www.esapubs.org/archive/mono/M079/007/ CONTACT:<br>Philip Higuera<br>phiguera@uidaho.edu<br>pehiguera@gmail.com Key words: Arctic, boreal forest, climate change, pollen analysis, tundra, shrub tundra,<br>paleoecology, Gates of the Arctic National Park Taxa: Alnus, Artemisia, Cyperaceae, Betula, Picea mariana, Picea glauca, Populus, Poaceae,<br>Salix, Sphagnum, Pediastrum
DOI: 10.6084/m9.figshare.988652.v1
title: Data from Higuera et al. 2009, Ecological Monographs

description: Data from:<br>Higuera, P. E., L. B. Brubaker, P. M. Anderson, F. S. Hu, and T. A. Brown. 2009.<br>Vegetation mediated the impacts of postglacial climate change on fire regimes<br>in the south-central Brooks Range, Alaska. Ecological Monographs 79:201-219. For each site, Code (CO), Ruppert (RP), Wild Tussock (WK), and Xindi (XI), there<br>are the six files: 1. xx_age_depth_data.txt – Depth (cm) and age (cal yr BP) from the published<br>age-depth model. 2. xx_age_depth_fig.pdf – Figure of the age-depth model, ¼ of Fig. 2 in Higuera<br>et al. (2009) 3. xx_charData.csv – Charcoal data in a CharAnalysis input file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 4. xx_charParams.csv – Parameter file CharAnalysis, with parameters as used in the<br>original publication. See https://sites.google.com/site/charanalysis/ for more details. 5. xx_charResults.csv – CharAnalysis results file. Units are in the<br>column headers: See https://sites.google.com/site/charanalysis/ for more details. 6. xx_pollen.xls – Pollen counts for each sample. The tab “pollen_counts” and<br>“pollen_cm” contains raw the same data as in the tab “data” but in a raw format<br>used for plotting. Ages associated with each pollen sample have to be obtained<br>from the “xx_age_depth_data.txt” file, or from the appropriate column in the<br>“charData” file in the “xx_char.xls” file. Radiocarbon dates from each site are in the file “Higuera_et_al_2009_Table_B1”<br>in the folder titled “C14_dates” as published here:<br>http://www.esapubs.org/archive/mono/M079/007/ CONTACT:<br>Philip Higuera<br>phiguera@uidaho.edu<br>pehiguera@gmail.com Key words: Arctic, boreal forest, climate change, pollen analysis, tundra, shrub tundra,<br>paleoecology, Gates of the Arctic National Park Taxa: Alnus, Artemisia, Cyperaceae, Betula, Picea mariana, Picea glauca, Populus, Poaceae,<br>Salix, Sphagnum, Pediastrum
DOI: 10.6084/m9.figshare.988624.v1
title: Slides and images for talks and posters

description: This file set contains slides and figures commonly used in talks or posters present by myself, colleagues, or others in the PaleoEcology and Fire Ecology Lab.
DOI: 10.6084/m9.figshare.988687.v2
title: Data, code, and figures from Dunnette et al. 2014

description: Data, code, and figures from Dunnette et al. 2014.
DOI: 10.6084/m9.figshare.988624.v2
title: Slides and images for talks and posters

description: This file set contains slides and figures commonly used in talks or posters present by myself, colleagues, or others in the PaleoEcology and Fire Ecology Lab.
DOI: 10.6084/m9.figshare.988687.v3
title: Data, code, and figures from Dunnette et al. 2014

description: README FILE FOR Higuera, P.E., and P. V. Dunnette. 2014. Data, code, and figures from Dunnette et al. 2014, New Phytologist. figshare. http://dx.doi.org/10.6084/m9.figshare.988687 =================== The archive includes the data and code needed to recreate the analyses in Dunnette et al. 2014: Dunnette, P. V., P. E. Higuera, K. K. McLauchlan, K. M. Derr, C. E. Briles, and M. H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist Accepted.
DOI: 10.6084/m9.figshare.988624.v3
title: Slides and images for talks and posters

description: This file set contains slides and figures commonly used in talks or posters present by myself, colleagues, or others in the PaleoEcology and Fire Ecology Lab.
DOI: 10.6084/m9.figshare.988687.v4
title: Data, code, and figures from Dunnette et al. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist.

description: README FILE -- UNDER DEVELOPMENT 4/11/2014 =================== Code needed to recreate the analyses in Dunnette et al. 2014: Dunnette, P. V., P. E. Higuera, K. K. McLauchlan, K. M. Derr, C. E. Briles, and M. H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist Accepted. The entire archive includes seven folders, with contents described below. Most data files are in .csv format, while some are in .xls format. The scripts to generate the figures for use in MATLAB software, and each script or function is fully commented, including dependencies. For some scripts, the statistics and curve fitting toolboxes are required; all other functions required are provided. =================== CH10_biogeochem CH10_biogeochemData.csv CH10_BSiData.csv CH10_LOI_data.csv =================== CH10_charcoal CH10_charData.csv CH10_charParams.csv CH10_charResults.csv Three files provide the raw input data, the parameters used, and the output data for charcoal analysis via the program CharAnalysis (see ‘Materials and Methods’ in main text). Missing values denoted by -9999 (*_charParams.csv) or NaN (*_charResults.csv). CH10_charData.csv includes the following raw data (by column): cmTop: top depth (cm) of the samplecmBot: bottom depth (cm) of the sampleageTop: estimated age at top of sample (cal. yr before CE 1950)ageBot: estimated age at bottom of sample (cal. yr before CE 1950)charVol: volume of sediment subsample from which charcoal was prepared (cm3)charCount: pieces of charcoal counted in the sample (#) Checksum values: CH10_charData.csv: 1202 rows (with headers), 6 columns Column 3 (ageTop (yr BP)):<br>Column 6 (charCount (#)): =================== CH10_chronology CH10_ageDepthData.csv Each file contains the output data from the program MCAgeDepth (Higuera et al. 2009, Ecological Monographs, 79:201–219), used to create Fig. 2 in the main text. Columns are as follows: Top depth of sample [cm]Calibrated age at sample top [cal yr BP]Upper 95% confidence intervals for data in column two.Lower 95% confidence intervals for data in column two.Sedimentation rate [cm/yr]Upper 95% confidence intervals for data in column five.Lower 95% confidence intervals for data in column five.Sample resolution [yr/sample]Upper 95% confidence intervals for data in column eight.Lower 95% confidence intervals for data in column eight. Missing values: none. Checksum values: CH10_AgeDepthData.csv: 1596 rows (with headers), 10 columns Column 1 (sampleCm): 642150.9<br>Column 2 (calAge): 4679522<br>Column 5 (sedAcc): 211.236<br>Column 8 (sampleRes): 6860.85
DOI: 10.6084/m9.figshare.988346.v1
title: Asymmetric epoxidation: a combined laboratory and molecular modelling experiment

description: The following transition states were located at the ωb97xd/6-311G(d,p) level<br>using a continuum solvent field corresponding to water using the Gaussian 09 program, revision D.01. They correspond to asymmetric epoxidation of an alkene using either the Shi Fructose catalyst or the Jacobsen Manganese oxidant.
DOI: 10.6084/m9.figshare.988687.v5
title: Data, code, and figures from Dunnette et al. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist.

description: README FILE -- UNDER DEVELOPMENT 4/11/2014 =================== Code needed to recreate the analyses in Dunnette et al. 2014: Dunnette, P. V., P. E. Higuera, K. K. McLauchlan, K. M. Derr, C. E. Briles, and M. H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist Accepted. The entire archive includes seven folders, with contents described below. Most data files are in .csv format, while some are in .xls format. The scripts to generate the figures for use in MATLAB software, and each script or function is fully commented, including dependencies. For some scripts, the statistics and curve fitting toolboxes are required; all other functions required are provided. =================== CH10_biogeochem CH10_biogeochemData.csv CH10_BSiData.csv CH10_LOI_data.csv =================== CH10_charcoal CH10_charData.csv CH10_charParams.csv CH10_charResults.csv Three files provide the raw input data, the parameters used, and the output data for charcoal analysis via the program CharAnalysis (see ‘Materials and Methods’ in main text). Missing values denoted by -9999 (*_charParams.csv) or NaN (*_charResults.csv). CH10_charData.csv includes the following raw data (by column): cmTop: top depth (cm) of the samplecmBot: bottom depth (cm) of the sampleageTop: estimated age at top of sample (cal. yr before CE 1950)ageBot: estimated age at bottom of sample (cal. yr before CE 1950)charVol: volume of sediment subsample from which charcoal was prepared (cm3)charCount: pieces of charcoal counted in the sample (#) Checksum values: CH10_charData.csv: 1202 rows (with headers), 6 columns Column 3 (ageTop (yr BP)):<br>Column 6 (charCount (#)): =================== CH10_chronology CH10_ageDepthData.csv Each file contains the output data from the program MCAgeDepth (Higuera et al. 2009, Ecological Monographs, 79:201–219), used to create Fig. 2 in the main text. Columns are as follows: Top depth of sample [cm]Calibrated age at sample top [cal yr BP]Upper 95% confidence intervals for data in column two.Lower 95% confidence intervals for data in column two.Sedimentation rate [cm/yr]Upper 95% confidence intervals for data in column five.Lower 95% confidence intervals for data in column five.Sample resolution [yr/sample]Upper 95% confidence intervals for data in column eight.Lower 95% confidence intervals for data in column eight. Missing values: none. Checksum values: CH10_AgeDepthData.csv: 1596 rows (with headers), 10 columns Column 1 (sampleCm): 642150.9<br>Column 2 (calAge): 4679522<br>Column 5 (sedAcc): 211.236<br>Column 8 (sampleRes): 6860.85
DOI: 10.6084/m9.figshare.988346.v3
title: Asymmetric epoxidation: a twinned laboratory and molecular modelling experiment

description: The coupling of a student experiment involving the preparation and use of a catalyst for the asymmetric epoxidation of an alkene with computational simulations of various properties of the resulting epoxide is set out in the form of a software toolbox from which students select appropriate components. At the core of these are the computational spectroscopic tools, whereby a measured spectrum can be interpreted in some detail using theoretical simulations. These include a range of modern chiroptical methods to accompany the increased use of such techniques in modern teaching laboratories. Computational experiments are captured in a Wiki-based electronic laboratory notebook, which features data-stamping, authenticated entries and inclusion of semantically intact data <em>via</em> interactive models rendered within the Wiki using JSmol and its referencing <em>via</em> a digital-object-identifier (DOI) to a digital data repository.
DOI: 10.6084/m9.figshare.988346.v2
title: Asymmetric epoxidation: a twinned laboratory and molecular modelling experiment

description: The coupling of a student experiment involving the preparation and use of a catalyst for the asymmetric epoxidation of an alkene with computational simulations of various properties of the resulting epoxide is set out in the form of a software toolbox from which students select appropriate components. At the core of these are the computational spectroscopic tools, whereby a measured spectrum can be interpreted in some detail using theoretical simulations. These include a range of modern chiroptical methods to accompany the increased use of such techniques in modern teaching laboratories. Computational experiments are captured in a Wiki-based electronic laboratory notebook, which features data-stamping, authenticated entries and inclusion of semantically intact data <em>via</em> interactive models rendered within the Wiki using JSmol and its referencing <em>via</em> a digital-object-identifier (DOI) to a digital data repository.
DOI: 10.6084/m9.figshare.988334.v1
title: Gaussian Job Archive for C58H118

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.988335.v1
title: Gaussian Job Archive for C58H118

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.988333.v1
title: Gaussian Job Archive for C58H118

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.988297
title: Debris-flow flume force measurements

description: This fileset includes (1) .zip file of all processed force data from the debris flow flume at the Richmond Field Station, UC Berkeley. 2007-2008. Files are named with identifier in YYMMDD format. (2) README file with more information. (3) Master table listing the file identifiers and run parameters (e.g. effective diameter, mean velocity). This work was supported by the STC program of the National Science Foundation via the National Center for Earth-surface dynamics under the agreement EAR-0120914.
DOI: 10.6084/m9.figshare.988297.v1
title: Debris-flow flume force measurements

description: This fileset includes (1) .zip file of all processed force data from the debris flow flume at the Richmond Field Station, UC Berkeley. 2007-2008. Files are named with identifier in YYMMDD format. (2) README file with more information. (3) Master table listing the file identifiers and run parameters (e.g. effective diameter, mean velocity). This work was supported by the STC program of the National Science Foundation via the National Center for Earth-surface dynamics under the agreement EAR-0120914.
DOI: 10.6084/m9.figshare.988268
title: Gaussian Job Archive for C58H118

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.988268.v1
title: Gaussian Job Archive for C58H118

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.987129
title: Unique Identifcation of research resources in studies in Reproducibility Project: Cancer Biology

description: Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/) aims to reproduce the key experiments from 50 landmark papers in cancer research. As a follow up to the previously published study, which showed a lack of indentifiability of research resources in the published biomedical literature (Vasilevsky, et al. 2014, PeerJ 1:e148), we analyzed 6 resource types reported in these papers to determine the identifiability of these resources. The resource types included antibodies, cell lines, constructs, knockdown reagents, model organisms and software. The results showed an average 85% of the resources were identifiable, and the ability to identify the resources varied amongst the resource types.
DOI: 10.6084/m9.figshare.987118
title: Cambridge APC payments for RCUK 2013-14

description: This Excel spreadsheet summarises data concerning the payment of Article Processing Charges for Open Access from the RCUK publication fund at the University of Cambridge for the year Apr 2013 to Mar 2014.
DOI: 10.6084/m9.figshare.987129.v1
title: Unique Identifcation of research resources in studies in Reproducibility Project: Cancer Biology

description: Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/) aims to reproduce the key experiments from 50 landmark papers in cancer research. As a follow up to the previously published study, which showed a lack of indentifiability of research resources in the published biomedical literature (Vasilevsky, et al. 2014, PeerJ 1:e148), we analyzed 6 resource types reported in these papers to determine the identifiability of these resources. The resource types included antibodies, cell lines, constructs, knockdown reagents, model organisms and software. The results showed an average 85% of the resources were identifiable, and the ability to identify the resources varied amongst the resource types.
DOI: 10.6084/m9.figshare.987118.v1
title: Cambridge APC payments for RCUK 2013-14

description: This Excel spreadsheet summarises data concerning the payment of Article Processing Charges for Open Access from the RCUK publication fund at the University of Cambridge for the year Apr 2013 to Mar 2014.
DOI: 10.6084/m9.figshare.987111
title: Agilent Barley Gene Expression Microarray Reannotation

description: An attempt was made to reannotate as many sequences as possible in the Agilent Barley Gene Expression Microarray, 4x44K, based on the UniProt plant protein collection and the Gramene rice genome annotation. After downloading the full sequences of the array oligos from the Core and EST sections of the NCBI Nucleotide Archive, the TIGR Plant Transcript Assembly and the DFCI Gene Indices collection, which were not provided with the array annotation, a search was made for possible homologs in the 2 February 2011 UniProt Knowledgebase Plant section and the Gramene rice genome assembly, version MSU6. A BLAST search was run with default parameters, the only modification being the use of the query sequence filtering for low complexity regions. After the BLAST search, the results were filtered, choosing the one with the best score, but requiring an e-value lower than 1e-30 and an overall fraction of iden- tical positions across the hit and query alignment of at least 50%. The description and GeneOntology (GO) associations were reannotated for all array oligos where a suitable homolog was found either in UniProt or in the Gramene database. The file contains the full sequence collection from which the array probes were derived, the Molecular function, Biological process and Cellular compartment Gene Ontology annotations in BiNGO (http://apps.cytoscape.org/apps/bingo) format and the annotation table with the UniProt and Gramene hits in a tab delimited file.
DOI: 10.6084/m9.figshare.988687.v15
title: Data, code, and figures from Dunnette et al. 2014, Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist In Press (doi: 10.1111/nph.12828)

description: SEE README.pdf OR README.md This archive includes data and scripts needed to reproduce the analyses in Dunnette et al. 2014; it includes 49 files and is 23 MB when downloaded as a .zip archive. After extracting the .zip archive, sort by file type. Most data files are in .csv format, while some are in .xls format. Scripts and functions are written for MATLAB software (*.m file type; www.mathworks.com), and each is file fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain<br>subalpine watershed. New Phytologist In Press doi: 10.1111/nph.12828