cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5564334
title: Scripts to perform dynamic optimization of a model of invasive aspergillosis

description: Matlab scripts to perform optimization and analyses of a dynamic optimization model of invasive aspergillosis:<br> "Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis"<br> Jan Ewald, Flora Rivieccio, Lukáš Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta<br> https://doi.org/10.1101/2021.05.12.443764 File structure: --- Core optimization files ---<br> -- simulation.cpp --<br> Description of ODE model in 'C', used by solver to calculate the time course given the parameters, initial states and control variables -- simulation.mexa64 --<br> Compiled mex-File from simulation.cpp used as interface by MATLAB to 'C' files. -- optFun.m --<br> Definition of the objective function. Uses a control vector 'u' to calculate the, objective function value F, the time course of state variables 'x' and gradients used by the solver to determine the optimal control of 'u'. -- single_opt.m --<br> Function which performs an optimization run for a given parameter set and a randomized initial solution u0. Optimization can be conducted by SNOPT or in conjunction with IPOPT. Both solver are not provided here (proprietary). <br> --- Additional files ---<br> -- solve_with_ipopt.m --<br> Configuration file and interface to call the solver IPOPT. -- lognorm_mu.m --<br> Function to provide log-normal distributed samples given the standard deviation, reference value (mode of distribution) and number of samples which should be calculated. -- mice_param_alv.m --<br> Reference parameter set of the model for mice as host organism and cell numbers normalized per alveolus. -- parameter_model.m --<br> Definition of parameter container to handle interface to optFun-call by solvers which do not allow parameter in function call. --- Optimization Runs ---<br> -- rand_params.m --<br> Performs optimization runs for multiple randomized parameter sets and several scenarios to determine parameter sensitivity. -- doseresponse.m --<br> Performs optimization runs for a sequnce of initial conidial dosages to determine the dose response of the system. --- Scripts for post-analysis ---<br> -- rand_analysis.m --<br> Loads the data created by the optimization runs (rand_params.m) and performs parameter sensitivity analysis as well as produces plots for analysis related to parameter influence. -- doseanalysis.m --<br> Loads the data created by the optimization runs (doseresponse.m ) and produces dose response curves as well as additional plots and analyses. --- Optimization output files ---<br> -- rand_param_out/ --<br> Folder contains optimization results as MATLAB session-file for randomized parameters used for parameter sensitivity analysis. -- dose_out/ --<br> Folder contains optimization results as MATLAB session-file for dose response curve calculation.
DOI: 10.6084/m9.figshare.16792141.v1
title: Research report ‘Genetic factors of host glycogen metabolism and its relationship with the vaginal microbiome’

description: In this retrospective data analysis project we aim to answer the question whether single nucleotide polymorphisms in the TCF7L2 gene (rs7903146-T and rs7903146-T) associated with type 2 diabetes are linked with composition of the vaginal microbiome in a multi-ethnic cohort of premenopausal women. <b></b> We<b> </b>received data of 199 female participants of the HELIUS project and excluded 5 participants because of antibiotic use or diabetes status. The data consisted of vaginal microbiome (VMB) composition, genotypes for SNP rs7903146 and rs12255372, fasting blood glucose level, ethnicity, age and immigration status. We posted our research proposal online prior to data analysis.. We posted our research proposal online prior to data analysis. To answer the main research questions we classified the various VMB groups as either <i>Lactobacillus </i>dominant (<i>L.</i> <i>crispatus, L. iners </i>or other <i>Lactobacillus</i>)<i> </i>or low <i>Lactobacillus</i>. No difference was detected between the two vaginal microbiome groups and alleles at either SNP. Next we further specified <i>Lactobacillus</i>-dominant in either <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> and grouped all other VMB groups as ‘other’. Again, we saw no significant differences between <i>Lactobacillus </i>dominant microbiota and the type 2 diabetes risk alleles rs7903146-TT and rs12255732-TT. We conclude that there is no significant association between two known type 2 diabetes risk alleles and vaginal microbial composition.
DOI: 10.6084/m9.figshare.16792141
title: Research report ‘Genetic factors of host glycogen metabolism and its relationship with the vaginal microbiome’

description: In this retrospective data analysis project we aim to answer the question whether single nucleotide polymorphisms in the TCF7L2 gene (rs7903146-T and rs7903146-T) associated with type 2 diabetes are linked with composition of the vaginal microbiome in a multi-ethnic cohort of premenopausal women. <b></b> We<b> </b>received data of 199 female participants of the HELIUS project and excluded 5 participants because of antibiotic use or diabetes status. The data consisted of vaginal microbiome (VMB) composition, genotypes for SNP rs7903146 and rs12255372, fasting blood glucose level, ethnicity, age and immigration status. We posted our research proposal online prior to data analysis.. We posted our research proposal online prior to data analysis. To answer the main research questions we classified the various VMB groups as either <i>Lactobacillus </i>dominant (<i>L.</i> <i>crispatus, L. iners </i>or other <i>Lactobacillus</i>)<i> </i>or low <i>Lactobacillus</i>. No difference was detected between the two vaginal microbiome groups and alleles at either SNP. Next we further specified <i>Lactobacillus</i>-dominant in either <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> and grouped all other VMB groups as ‘other’. Again, we saw no significant differences between <i>Lactobacillus </i>dominant microbiota and the type 2 diabetes risk alleles rs7903146-TT and rs12255732-TT. We conclude that there is no significant association between two known type 2 diabetes risk alleles and vaginal microbial composition.
DOI: 10.5519/qd.yd40pnav
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (382 records)
DOI: 10.5281/zenodo.5564337
title: Reprinting of first-wave Gothic novels in the 19th century

description: An initial version of the data paper accompanying these datasets is published on my open notebook, <em>Price One Penny, new series</em>: https://popnewseries.hypotheses.org/574 The following datasets are available as separate tabs in a spreadsheet provided in OpenDocument Spreadsheet (.ods), an open standard file format that can be opened in OpenOffice, LibreOffice, Excel, Numbers, or Google Spreadsheets. <strong>Dataset A</strong> The final table of 13 collections, series, or publishers from the 19th century reprinting 29 first-wave Gothic novels grouped into categories. <strong>Dataset B</strong> A preliminary version of the previous table containing 48 publishers, collections, or series from the 19th century that have reprinted 35 novels that could have been construed as part of first-wave Gothic. <strong>Dataset C</strong> A different table of 12 “libraries” present in two catalogues for Milner & Co (four in the first, eight in the second) and reprinting 15 Gothic novels, forming a subset of the 35 novels in the previous dataset. All three datasets contain novels listed in rows and collection, publishers, or series listed in columns. If the novel in a given row was reprinted in the collection or series or by the publisher in a given column, the cell where they intersect will contain a date (the earliest reprint of that novel found in that collection or series or by that publisher), a volume number, some other information, or simply an "x". More information in the "Read me" tab of the spreadsheet.
DOI: 10.5281/zenodo.5564336
title: Reprinting of first-wave Gothic novels in the 19th century

description: An initial version of the data paper accompanying these datasets is published on my open notebook, <em>Price One Penny, new series</em>: https://popnewseries.hypotheses.org/574 The following datasets are available as separate tabs in a spreadsheet provided in OpenDocument Spreadsheet (.ods), an open standard file format that can be opened in OpenOffice, LibreOffice, Excel, Numbers, or Google Spreadsheets. <strong>Dataset A</strong> The final table of 13 collections, series, or publishers from the 19th century reprinting 29 first-wave Gothic novels grouped into categories. <strong>Dataset B</strong> A preliminary version of the previous table containing 48 publishers, collections, or series from the 19th century that have reprinted 35 novels that could have been construed as part of first-wave Gothic. <strong>Dataset C</strong> A different table of 12 “libraries” present in two catalogues for Milner & Co (four in the first, eight in the second) and reprinting 15 Gothic novels, forming a subset of the 35 novels in the previous dataset. All three datasets contain novels listed in rows and collection, publishers, or series listed in columns. If the novel in a given row was reprinted in the collection or series or by the publisher in a given column, the cell where they intersect will contain a date (the earliest reprint of that novel found in that collection or series or by that publisher), a volume number, some other information, or simply an "x". More information in the "Read me" tab of the spreadsheet.
DOI: 10.5063/f11v5ccr
title: The Belice River Basin: hilly lakes in 2018

description: The purpose of the dadatet is to test a semi-automatic procedure to enhance the segmentation phase of GEOBIA algorithms. Segmentation parameters were optimized by implementing a Python algorithm that minimizes an objective function, the root mean square of the over and under segmentation. The objective function can be optimized by assuming as reference either the areas or the perimeters of digitized ground truths.The proposed procedure was applied to map hilly lakes on high spatial resolution satellite images. The test area is a subset of the Belice River Basin (western Sicily, Italy). A great number of hilly lakes (or small reservoirs) for agricultural water supply are located in the basin.
DOI: 10.25345/c52p1d
title: MassIVE MSV000088218 - SELECTED_DEEP_SEA_SEDIMENT_FUNGI_CIGOM_20211012
title: As part of our investigations on the chemical diversity of organisms from unexplored marine habitats of Mexico, a series of 29 fungal strains isolated from deep-sea sediments (more than 600 m deep) from the Gulf of Mexico were investigated. The antimicrobial potential of their organic extracts from solid cultures grown under the OSMAC approach was assessed against a panel of ESKAPE bacteria and the yeast C. albicans. Chemical studies on the active scaled-up cultures and some small-scale cultures led to the isolation of benzochromenones from Alternaria sp. CIGOM4, benzodiazepines from P. echinulatum CONTIG4, a cytochalsin from Biatriospora sp. CIGOM2, and an imidazopyridoindole from Penicillium sp. CIGOM10. Molecular network analysis by GNPS combined with manual dereplication showed the enormous potential of these fungi to produce bioactive compounds.
DOI: 10.5063/f1x34vwc
title: The Belice River Basin: hilly lakes in 2018

description: The purpose of the dadatet is to test a semi-automatic procedure to enhance the segmentation phase of GEOBIA algorithms. Segmentation parameters were optimized by implementing a Python algorithm that minimizes an objective function, the root mean square of the over and under segmentation. The objective function can be optimized by assuming as reference either the areas or the perimeters of digitized ground truths.The proposed procedure was applied to map hilly lakes on high spatial resolution satellite images. The test area is a subset of the Belice River Basin (western Sicily, Italy). A great number of hilly lakes (or small reservoirs) for agricultural water supply are located in the basin.
DOI: 10.5281/zenodo.5564269
title: HCl measurement data using WMS in H2 and N2

description: In the article 'Trace level analysis of reactive ISO 14687 impurities in hydrogen fuel using laser-based spectroscopic detection methods' (https://doi.org/10.1016/j.ijhydene.2020.09.046) measurements of various reactive compounds are presented in hydrogen and nitrogen. The dataset contain data for HCl.
DOI: 10.5281/zenodo.5564268
title: HCl measurement data using WMS in H2 and N2

description: In the article 'Trace level analysis of reactive ISO 14687 impurities in hydrogen fuel using laser-based spectroscopic detection methods' (https://doi.org/10.1016/j.ijhydene.2020.09.046) measurements of various reactive compounds are presented in hydrogen and nitrogen. The dataset contain data for HCl.
DOI: 10.5281/zenodo.5564294
title: SNP genotype matrix for GWAS and Machine Learning analyses

description: <strong>SNP datasets used for GWAS and Machine Learning analyses</strong> All datasets come from the easyGWAS website: https://easygwas.ethz.ch/down/1/ <strong>=== Horton et al. 2012 ===</strong> <strong>1307 Arabidopsis genotypes x 214,057</strong> <strong>SNPs</strong> The file is called Horton2012.raw https://www.nature.com/articles/ng.1042 Preview of the first lines and columns: FID Chr1_657_T Chr1_3102_G Chr1_4648_A Chr1_4880_T Chr1_5975_G Chr1_6063_T Chr1_6449_C<br> 9381 2 2 2 0 0 0 0<br> 9380 0 0 0 0 0 0 2<br> 9378 2 2 2 0 0 0 0<br> 9371 2 2 2 0 0 0 0<br> 9367 0 0 0 2 0 0 0<br> 9363 2 2 2 0 0 0 0<br> 9356 0 2 2 0 0 0 0<br> 9355 2 2 2 0 0 0 0<br> 9354 2 2 2 0 0 0 0 ...etc... PLINK 1.9 was used to convert the .ped and .map file to a .raw format with: <pre><code class="language-bash">plink --file original_data/genotype --recodeA --tab</code></pre> Genotypes are encoded as 0, 1 or 2 with: <pre> SNP SNP_A --- ----- A A -&gt; 0 A C -&gt; 1 C C -&gt; 2 0 0 -&gt; NA </pre> Then only the Family ID was kept (same as individual ID) and other columns (Paternal ID, Maternal ID, Sex, Phenotype) were removed. The corresponding PLINK manual page used is here: https://zzz.bwh.harvard.edu/plink/dataman.shtml#recode
DOI: 10.6084/m9.figshare.16792594.v1
title: Reprinting of First Wave Gothic novels in the 19th century.ods

description: An initial version of the data paper accompanying these datasets is published on my open notebook, <em>Price One Penny, new series</em>: https://popnewseries.hypotheses.org/574The following datasets are available as separate tabs in a spreadsheet provided in OpenDocument Spreadsheet (.ods), an open standard file format that can be opened in OpenOffice, LibreOffice, Excel, Numbers, or Google Spreadsheets.Dataset AThe final table of 13 collections, series, or publishers from the 19th century reprinting 29 first-wave Gothic novels grouped into categories.Dataset BA preliminary version of the previous table containing 48 publishers, collections, or series from the 19th century that have reprinted 35 novels that could have been construed as part of first-wave Gothic.Dataset CA different table of 12 “libraries” present in two catalogues for Milner & Co (four in the first, eight in the second) and reprinting 15 Gothic novels, forming a subset of the 35 novels in the previous dataset.All three datasets contain novels listed in rows and collection, publishers, or series listed in columns. If the novel in a given row was reprinted in the collection or series or by the publisher in a given column, the cell where they intersect will contain a date (the earliest reprint of that novel found in that collection or series or by that publisher), a volume number, some other information, or simply an "x".More information in the "Read me" tab of the spreadsheet.
DOI: 10.6084/m9.figshare.16792594
title: Reprinting of First Wave Gothic novels in the 19th century.ods

description: An initial version of the data paper accompanying these datasets is published on my open notebook, <em>Price One Penny, new series</em>: https://popnewseries.hypotheses.org/574The following datasets are available as separate tabs in a spreadsheet provided in OpenDocument Spreadsheet (.ods), an open standard file format that can be opened in OpenOffice, LibreOffice, Excel, Numbers, or Google Spreadsheets.Dataset AThe final table of 13 collections, series, or publishers from the 19th century reprinting 29 first-wave Gothic novels grouped into categories.Dataset BA preliminary version of the previous table containing 48 publishers, collections, or series from the 19th century that have reprinted 35 novels that could have been construed as part of first-wave Gothic.Dataset CA different table of 12 “libraries” present in two catalogues for Milner & Co (four in the first, eight in the second) and reprinting 15 Gothic novels, forming a subset of the 35 novels in the previous dataset.All three datasets contain novels listed in rows and collection, publishers, or series listed in columns. If the novel in a given row was reprinted in the collection or series or by the publisher in a given column, the cell where they intersect will contain a date (the earliest reprint of that novel found in that collection or series or by that publisher), a volume number, some other information, or simply an "x".More information in the "Read me" tab of the spreadsheet.
DOI: 10.6084/m9.figshare.16791889
title: Raw for the journal publication: "Long-term responses of benthic invertebrates to rotenone treatment"

description: Raw data file from an investigation of the effects of rotenone treatment on the benthic invertebrates of the Fusta watercourse in Central Norway. The material was sampled with kick net in the period 2011-2016 from two lotic and three lentic sampling sites affected by rotenone, as well as the same number of sites/habitats from a neighboring control watercourse.
DOI: 10.6084/m9.figshare.16791889.v1
title: Raw for the journal publication: "Long-term responses of benthic invertebrates to rotenone treatment"

description: Raw data file from an investigation of the effects of rotenone treatment on the benthic invertebrates of the Fusta watercourse in Central Norway. The material was sampled with kick net in the period 2011-2016 from two lotic and three lentic sampling sites affected by rotenone, as well as the same number of sites/habitats from a neighboring control watercourse.
DOI: 10.15161/oar.it/74182
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.25919/q93x-nv37
title: Parkes observations for project P1080 semester 2021APRS_05

description: We propose continued timing observations of a new pulsar discovered with the MWA. Thanks to the interferometric advantages of the MWA and our recent GMRT follow-up, we have been able to determine the pulsar's position to ~5 arcseconds precision, which may help a faster convergence to its timing solution. This will help determine the pulsar's spin and astrometric parameters. The analysis of Parkes and GMRT data suggests that the pulsar is likely a steep-spectrum, low-luminosity object. Observations with the ultra-wide band low-frequency receiver will help further reinforce this, besides allowing us to explore the frequency dependence of its polarisation and a large variability that is seen at multiple frequency bands. Most importantly, these observations will ensure continued timing of the pulsar through the next semester when the MWA is unlikely to be available for regular observations.
DOI: 10.6084/m9.figshare.12280571
title: wicky-hauck-2020-BoundaryData.zip

description: Temperature boundary data, provided by PERMOS, gapfilled and used as boundary data in Wicky, J. & Hauck, C. (2020). Air Convection in the Active Layer of Alpine Rock Glaciers. Frontiers in Earth Sciences (2020).<br>
DOI: 10.6084/m9.figshare.12280571.v2
title: wicky-hauck-2020-BoundaryData.zip

description: Temperature boundary data, provided by PERMOS, gapfilled and used as boundary data in Wicky, J. & Hauck, C. (2020). Air Convection in the Active Layer of Alpine Rock Glaciers. Frontiers in Earth Sciences (2020).<br>
DOI: 10.6084/m9.figshare.12280571.v1
title: wicky-hauck-2020-BoundaryData.zip

description: Temperature boundary data, provided by PERMOS, gapfilled and used as boundary data in Wicky, J. & Hauck, C. (2020). Air Convection in the Active Layer of Alpine Rock Glaciers. Frontiers in Earth Sciences (in review).<br>
DOI: 10.5281/zenodo.5564420
title: Wikidata Dump Welding

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 35, <b>statement count</b>: 196, <b>triple count</b>: 2823
DOI: 10.5281/zenodo.5564419
title: Wikidata Dump Welding

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 35, <b>statement count</b>: 196, <b>triple count</b>: 2823
DOI: 10.5281/zenodo.5564422
title: Wikidata Dump Welding

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 35, <b>statement count</b>: 196, <b>triple count</b>: 2823
DOI: 10.5281/zenodo.5564421
title: Wikidata Dump Welding

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 35, <b>statement count</b>: 196, <b>triple count</b>: 2823
DOI: 10.6084/m9.figshare.14763528.v1
title: Trait data 2019 and 2020 experimental microclimate warming and light addition across Europe (FORMICA)

description: This dataset contains functional trait data (plant height and specific leaf area) measured on individuals in understorey plant communities subjected to experimental microclimate warming and lighting at three sites across Europe. Measurements were done in 2019 and 2020. The second tab of the excel contains metadata explaining the columns.
DOI: 10.6084/m9.figshare.14763501.v1
title: Cover data 2019 and 2020 experimental microclimate warming and light addition FORMICA

description: This dataset contains the covers measured in mesocosms subjected to experimental microclimate warming and light addition at three experimental sites across Europe in 2019 and 2020. Metadata explaining different columns is given on the second tab of the excel file.
DOI: 10.48370/ofd/c8yj5w/gslkf6
title: HMW_Primula_veris_L._H_8380.jpg

description: :unav
DOI: 10.48370/ofd/c8yj5w
title: Pierwiosnek lekarski (Primula veris L.), 8380

description: Herbarium
DOI: 10.48370/ofd/wwblqo/zdrg6f
title: HMW_Primula_veris_L._H_9021.jpg

description: :unav
DOI: 10.48370/ofd/wwblqo
title: Pierwiosnek lekarski (Primula veris L.), 9021

description: Herbarium
DOI: 10.48370/ofd/nqnyez/xryizv
title: HMW_Primula_veris_L._H_4564.jpg

description: :unav
DOI: 10.48370/ofd/nqnyez
title: Pierwiosnek lekarski (Primula veris L.), 4564

description: Herbarium
DOI: 10.48370/ofd/fs1phj/finpgd
title: HMW_Primula_veris_L._H_0632.jpg

description: :unav
DOI: 10.48370/ofd/fs1phj
title: Pierwiosnek lekarski (Primula veris L.), 632

description: Herbarium
DOI: 10.48370/ofd/g34miu/jjch11
title: HMW_Primula_veris_L._H_9325.jpg

description: :unav
DOI: 10.48370/ofd/g34miu
title: Pierwiosnek lekarski (Primula veris L.), 9325

description: Herbarium
DOI: 10.48370/ofd/n4m32s/1jheef
title: HMW_Primula_veris_L._H_3798.jpg

description: :unav
DOI: 10.48370/ofd/n4m32s
title: Pierwiosnek lekarski (Primula veris L.), 3798

description: Herbarium
DOI: 10.48370/ofd/mgoqy5/thfma7
title: HMW_Primula_veris_L._H_2388.jpg

description: :unav
DOI: 10.48370/ofd/mgoqy5
title: Pierwiosnek lekarski (Primula veris L.), 2388

description: Herbarium