cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8166200
title: Supplementary material 1 for Thesis Chapter 2 - An obligate aerobe hybridises hydrogen fermentation and carbon storage to adapt to hypoxia

description: Supplementary material for paired comparative metabolomics and proteomics on Mycobacterium smegmatis mc2155 during hypoxia, as part of chapter 2 for the thesis "Biochemistry and physiology of mycobacterial adaptations to energy starvation".


Description below is identical to that provided in 'Summary.docx'. 


Proteomics_analysis.xlsx


Includes raw and annotated data for comparative proteomics experiments for chapter 2.


The tab ‘Annotated comparisons’ contains fold change and p values for the comparisons for each protein from Mycobacterium smegmatis mc2155 derived from LFQ-Analyst. Functional annotations are derived from KEGG pathways and modules, which utilise the spreadsheets in ‘MSMEG gene annotation’ ‘Protein ids to KEGG pathway’ and ‘KEGG Pathway and Modules’ to link KEGG annotations to MSMEG_XXXX gene identifiers and MSMEG_XXXX to Uniprot ID. Output from LFQ-Analyst is provided in the ‘Full_dataset’, ‘Imputed_matrix’ and ‘Original_matrix’ tabs.


Data provided by the Monash Proteomics and Metabolomics Facility for upload into LFQ-analyst are provided as the ‘combined_protein.tsv’ and ‘LFQ-Analyst_experimental_design.txt’.


 


Metabolism_analysis.xlsx


Includes annotated data for comparative metabolomics experiments for chapter 2. Within the spreadsheet, TR refers to transition, ST refers to stationary phase and EXP refers to exponential phase. The tabs ‘TRvsEXP’, ‘STvsTR’ and ‘STvsEXP’ contain fold change and p values for each metabolite detected for each comparison. The remaining tabs categorise the metabolites based on KEGG database and IDEOM annotations. For broader categories (‘Lipid metabolism’,’ Carbohydrate metabolism’, ‘Cofactor metabolism’, ‘Nucleotide metabolism’, ‘Amino acid metabolism’ and ‘Peptides’ tabs), annotations were derived directly from filtering the ‘Map’ column of ‘Comparisons’ tab of the IDEOM worksheet (IDEOM_analysis.xlsb). Screenshots are pasted into each tab to show the filtering settings. The remaining tabs comprise narrower categories which were manually annotated with reference to KEGG pathways and maps, and also include rows corresponding to the proteomics data for these categories, so the proteomics and metabolomics data can be interpreted together. The ‘Proteomics’ tab contains the proteomics data referenced by these tabs, which is a copy of the ‘Annotated comparisons’ tab from the ‘Proteomics_analysis.xlsx’ file. A value of ‘N’ indicates the metabolite or protein (at least according to the name in the same row) was not found in these datasets.


The IDEOM worksheet (IDEOM_analysis.xlsb) was provided by the Monash Proteomics and Metabolomics Facility and was used for further analysis and for annotations. ‘Data_for_MA_no_normalization.csv’ was also provided by the Monash Proteomics and Metabolomics Facility for upload into Metaboanalyst (https://www.metaboanalyst.ca/).
DOI: 10.5281/zenodo.8188778
title: Supplementary material 2 for Thesis Chapter 2 - An obligate aerobe hybridises hydrogen fermentation and carbon storage to adapt to hypoxia

description: Supplementary material for cryo-EM tomography experiments. Cryo-EM Aerated Vs Anoxic.pptx contains representations from the best tomogram reconstructions. Anoxic_tomogram.mp4 and Aerated_tomogram.mp4 contain tomogram movies for one sample from each condition.
DOI: 10.5281/zenodo.8188779
title: Supplementary material 2 for Thesis Chapter 2 - An obligate aerobe hybridises hydrogen fermentation and carbon storage to adapt to hypoxia

description: Supplementary material for cryo-EM tomography experiments.


Cryo-EM Aerated Vs Anoxic.pptx contains representations from the best tomogram reconstructions.


Anoxic_tomogram.mp4 and Aerated_tomogram.mp4 contain tomogram movies for one sample from each condition.
DOI: 10.15468/dl.ufhdau
title: Occurrence Download

description: A dataset containing 351 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is one of (USA.5.9_1, USA.5.31_1, USA.5.2_1, USA.29.16_1, USA.29.1_1, USA.5.29_1, USA.29.4_1)",
 "TaxonKey is one of (Boechera rigidissima (Rollins) Al-Shehbaz, Boechera tiehmii (Rollins) Al-Shehbaz, Boechera tularensis Windham & Al-Shehbaz, Bruchia bolanderi Lesq., Draba asterophora var. asterophora, Draba asterophora var. macrocarpa C.L.Hitchc., Erigeron miser A.Gray, Eriogonum luteolum var. saltuarium Reveal, Helodium blandowii (F.Weber & D.Mohr) Warnst., Ivesia sericoleuca (Rydb.) Rydb., Lewisia kelloggii subsp. hutchisonii Dempster, Lewisia kelloggii subsp. kelloggii, Peltigera gowardii Lendemer & H.E.O'Brien, Meesia uliginosa Hedw., Lewisia longipetala (Piper) Clay, Orthotrichum praemorsum Venturi, Botrychium Sw., Eriogonum umbellatum var. torreyanum (A.Gray) M.E.Jones, Draba cruciata Payson, Hulsea brevifolia A.Gray, Dendrocollybia racemosa (Pers.) R.H.Petersen & Redhead)"
 ]
}

 The dataset includes 351 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030872-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc1nys5k
title: CCDC 1547959: Experimental Crystal Structure Determination

description: Related Article: Jan Grrzegorz Malecki|2017|CSD Communication|||
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.cc1prqlr
title: CCDC 1571935: Experimental Crystal Structure Determination

description: Related Article: Fatemeh Niknam, Peyman Hamidizadeh, S. Masoud Nabavizadeh, Fatemeh Niroomand Hosseini, S. Jafar Hoseini, Peter C. Ford, Mahdi M. Abu-Omar|2019|Inorg.Chim.Acta|498|119133|doi:10.1016/j.ica.2019.119133
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.cc1pstgr
title: CCDC 1572985: Experimental Crystal Structure Determination

description: Related Article: R.J. Puddephatt, A. Abo-Amer, P.D. Boyle|2017|CSD Communication|||
description: Related Article: Anwar Abo-Amer, Paul D. Boyle, Richard J. Puddephatt|2018|Inorg.Chim.Acta|473|51|doi:10.1016/j.ica.2017.12.028
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.cc1psths
title: CCDC 1572986: Experimental Crystal Structure Determination

description: Related Article: R.J. Puddephatt, A. Abo-Amer, P.D. Boyle|2017|CSD Communication|||
description: Related Article: Anwar Abo-Amer, Paul D. Boyle, Richard J. Puddephatt|2018|Inorg.Chim.Acta|473|51|doi:10.1016/j.ica.2017.12.028
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.cc1pstjt
title: CCDC 1572987: Experimental Crystal Structure Determination

description: Related Article: R.J. Puddephatt, A. Abo-Amer, P.D. Boyle|2017|CSD Communication|||
description: Related Article: Anwar Abo-Amer, Paul D. Boyle, Richard J. Puddephatt|2018|Inorg.Chim.Acta|473|51|doi:10.1016/j.ica.2017.12.028
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.cc1pstkv
title: CCDC 1572988: Experimental Crystal Structure Determination

description: Related Article: R.J. Puddephatt, A. Abo-Amer, P.D. Boyle|2017|CSD Communication|||
description: Related Article: Anwar Abo-Amer, Paul D. Boyle, Richard J. Puddephatt|2018|Inorg.Chim.Acta|473|51|doi:10.1016/j.ica.2017.12.028
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.cc1psw1d
title: CCDC 1573034: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold|2017|CSD Communication|||
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.cc1pxlmt
title: CCDC 1576617: Experimental Crystal Structure Determination

description: Related Article: Jonathan Rourke, Guy Clarkson, Paul Shaw|2017|CSD Communication|||
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.cc1pxtw9
title: CCDC 1576842: Experimental Crystal Structure Determination

description: Related Article: Jonathan Rourke, Guy Clarkson, Paul Shaw|2017|CSD Communication|||
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.cc1pxtxb
title: CCDC 1576843: Experimental Crystal Structure Determination

description: Related Article: Jonathan Rourke, Guy Clarkson, Paul Shaw|2017|CSD Communication|||
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.cc1pz8pm
title: CCDC 1578231: Experimental Crystal Structure Determination

description: Related Article: Yan Guo, Yafeng He, Shengde Wu, Shuren Zhang, Dongfan Song, Zhenzhu Zhu, Zijian Guo, Xiaoyong Wang|2019|Inorg.Chem.|58|13150|doi:10.1021/acs.inorgchem.9b02033
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.cc1q6hxb
title: CCDC 1585182: Experimental Crystal Structure Determination

description: Related Article: S. Masoud Nabavizadeh, Fatemeh Niroomand Hosseini, Chan Park, Guang Wu, Mahdi M. Abu-Omar|2020|Dalton Trans.|49|2477|doi:10.1039/C9DT04261J
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.cc1qcpc4
title: CCDC 1590156: Experimental Crystal Structure Determination

description: Related Article: Weizu Zhuang|2017|CSD Communication|||
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.cc1z71mw
title: CCDC 1824028: Experimental Crystal Structure Determination

description: Related Article: Cristián Cuerva, José A. Campo, Mercedes Cano, Rainer Schmidt, Carlos Lodeiro|2018|J.Mater.Chem.C|6|9723|doi:10.1039/C8TC03308K
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: 10.34740/kaggle/dsv/8994346
title: BBC News
DOI: 10.5281/zenodo.12786419
title: The combined effect of climate change and building density on outdoor thermal comfort: a study in a southern middle sized Brazilian city)

description: The files present all outputs (hourly data by sidewalk orientation) of physiological temperature equivalent from the simulations carried out in the research "The combined effect of climate change and building density on outdoorthermal comfort: a study in a southern middle sized Brazilian city", classified according to the original ranges and Rosa's calibration.
DOI: 10.5281/zenodo.12786041
title: The combined effect of climate change and building density on outdoor thermal comfort: a study in a southern middle sized Brazilian city)

description: The files present all outputs (hourly data by sidewalk orientation) of physiological temperature equivalent from the simulations carried out in the research "The combined effect of climate change and building density on outdoorthermal comfort: a study in a southern middle sized Brazilian city", classified according to the original ranges and Rosa's calibration.
DOI: 10.5281/zenodo.12786042
title: PET outputs (research: The combined effect of climate change and building density on outdoor thermal comfort: a study in a southern middle sized Brazilian city)

description: The files present all outputs (hourly data by sidewalk orientation) of physiological temperature equivalent from the simulations carried out in the research "The combined effect of climate change and building density on outdoorthermal comfort: a study in a southern middle sized Brazilian city", classified according to the original ranges and Rosa's calibration.
DOI: 10.15468/dl.ayh8f5
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Lepidozia reptans (L.) Dumort."
 ]
}

 The dataset includes 24 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030873-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.23720982.v1
title: PDXNet Genetic Ancestry Reference Panel for SNPWeights

description: Novel reference panel for the genetic ancestry estimation program SNPWeights. This panel was created as part by researchers in the National Cancer Institute (NCI) supported PDX Development and Trial Centers Research Network (PDXNet).
DOI: 10.15468/dl.karafx
title: Occurrence Download

description: A dataset containing 47026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Prunus virginiana L."
 ]
}

 The dataset includes 47026 records from 461 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030874-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wjy4a
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Leptodontium brachyphyllum Broth. & Thér."
 ]
}

 The dataset includes 225 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030875-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pwcb3k
title: Occurrence Download

description: A dataset containing 509 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Malus spectabilis (Aiton) Borkh."
 ]
}

 The dataset includes 509 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030876-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4znyrn
title: Occurrence Download

description: A dataset containing 553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Leptodontium capituligerum Müll.Hal."
 ]
}

 The dataset includes 553 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030877-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xqqnf
title: Occurrence Download

description: A dataset containing 4458 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron simsii Planch."
 ]
}

 The dataset includes 4458 records from 188 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030878-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzc6uv
title: Occurrence Download

description: A dataset containing 192 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Leptodontium flexifolium (Dicks.) Hampe ex Lindb."
 ]
}

 The dataset includes 192 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030879-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dbnr7z
title: Occurrence Download

description: A dataset containing 2337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron prinophyllum (Small) Millais"
 ]
}

 The dataset includes 2337 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030880-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyapbm
title: Occurrence Download

description: A dataset containing 4122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron calendulaceum (Michx.) Torr."
 ]
}

 The dataset includes 4122 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030881-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bc52wv
title: Occurrence Download

description: A dataset containing 1080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Leptodontium longicaule Mitt."
 ]
}

 The dataset includes 1080 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030883-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vz3zta
title: Occurrence Download

description: A dataset containing 100220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hesperis matronalis L."
 ]
}

 The dataset includes 100220 records from 890 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030882-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/et2qqq
title: Executive Agreements Database, Statement Regarding the Agreement Between The United States and Laos Relating To Trade In Textiles and Textile Products, with Annexes, Signed At Washington September 15, 1994

description: KAV 4036

First signed 09/15/1994
Last signed 09/15/1994
Entry into force (supplemented by last signed) 09/15/1994

stamped 94-238

C06536135

cover memo
DOI: 10.5281/zenodo.10584715
title: Linked collectors and determiners for: A new species of African snake-eyed skink (Scincidae: Panaspis) from central and northern Namibia.

description: Natural history specimen data linked to collectors and determiners held within, "A new species of African snake-eyed skink (Scincidae: Panaspis) from central and northern Namibia". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/578c2892-8ead-46e7-9c46-de2968a3b3ba using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/578c2892-8ead-46e7-9c46-de2968a3b3ba. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10872676
title: Linked collectors and determiners for: A new species of African snake-eyed skink (Scincidae: Panaspis) from central and northern Namibia.

description: Natural history specimen data linked to collectors and determiners held within, "A new species of African snake-eyed skink (Scincidae: Panaspis) from central and northern Namibia". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/578c2892-8ead-46e7-9c46-de2968a3b3ba using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/578c2892-8ead-46e7-9c46-de2968a3b3ba. Formatted as a Frictionless Data package.