cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc23ynqg
title: CCDC 1964926: Experimental Crystal Structure Determination

description: Related Article: Amit Mondal, Biswajit Bhattacharya, Susobhan Das, Surojit Bhunia, Rituparno Chowdhury, Somnath Dey, Malla Reddy Chilla|2020|Angew.Chem.,Int.Ed.|59|10971|doi:10.1002/anie.202001060
DOI: 10.5517/ccdc.csd.cc23ygh1
title: CCDC 1964733: Experimental Crystal Structure Determination

description: Related Article: Amit Mondal, Biswajit Bhattacharya, Susobhan Das, Surojit Bhunia, Rituparno Chowdhury, Somnath Dey, Malla Reddy Chilla|2020|Angew.Chem.,Int.Ed.|59|10971|doi:10.1002/anie.202001060
DOI: 10.5517/ccdc.csd.cc23yqng
title: CCDC 1964986: Experimental Crystal Structure Determination

description: Related Article: Amit Mondal, Biswajit Bhattacharya, Susobhan Das, Surojit Bhunia, Rituparno Chowdhury, Somnath Dey, Malla Reddy Chilla|2020|Angew.Chem.,Int.Ed.|59|10971|doi:10.1002/anie.202001060
DOI: 10.5281/zenodo.4472401
title: Sample Records. A systematic review in Circular Economy and Bioenergy addressed by Education and Communication

description: Sample Records. A systematic review in Circular Economy and Bioenergy addressed by Education and Communication
DOI: 10.6084/m9.figshare.14115575.v1
title: Data_normalized.csv

description: Relative peak abundances of metabolites detected by GC/EIMS
DOI: 10.6084/m9.figshare.14115575
title: Data_normalized.csv

description: Relative peak abundances of metabolites detected by GC/EIMS
DOI: 10.25678/00031q
title: Data for: The feedback between selection and demography shapes genomic diversity during coevolution

description: Species interactions and coevolution are integral to ecological communities, but we lack empirical information on when and how these interactions generate and purge genetic diversity. Using genomic time series data from host-virus experiments, we found that coevolution occurs through consecutive selective sweeps in both species, with temporal consistency across replicates. Sweeps were accompanied by phenotypic change (resistance or infectivity increases) and expansions in population size. In the host, population expansion enabled rapid generation of genetic diversity in accordance with neutral processes. Viral molecular evolution was, in contrast, confined to few genes, all putative targets of selection. This study demonstrates that molecular evolution during species interactions is shaped by both eco-evolutionary feedback dynamics and interspecific differences in how genetic diversity is generated and maintained.
DOI: 10.5281/zenodo.4562610
title: Electrophoresis Images of Acute Myeloid Leukemia Patients

description: The database consists of a set of 22 2DGE images obtained from the peripheral blood samples of 11 patients with acute myeloid leukemia. Of these, 11 images correspond to samples taken at the time of diagnosis, and the other 11 correspond to samples taken from the same patients after induction therapy (approximately 21–28 days after starting treatment). Images named with the suffix BEFORE refer to 2DGE images of samples taken at the time of diagnosis (before treatment), while images named with the suffix AFTER correspond to 2DGE images of samples taken after treatment. These 22 images are also made available with the preprocessing stage applied, to which the prefix PREPROC has been applied. Each image in the database is in tagged image file format (TIFF) format with a resolution of 300 dots per inch (DPI). In total, the database, which can be found in the Supplementary Materials, contains 44 images (22 raw 2DGE images and 22 pre-processed 2DGE images).
description: This research was funded by the Instituto Tecnologico Metropolitano ITM, grant number P17215. J.E.U. was recipient of the Jovenes Investigadores e Innovadores ITM 2020 program of the Instituto Tecnologico Metropolitano ITM of Medellin-Colombia.
DOI: 10.25345/c5vf7d
title: MassIVE MSV000086952 - High resolution mass spectrometry of Arctic ponds
title: This dataset contains high resolution mass spectrometry raw files from surface water collected from Arctic ponds.
DOI: 10.25810/fj1y-8c74.25
title: International Wire Services Coverage of Climate Change or Global Warming, 2004-2021 - January 2021

description:         The Media and Climate Change Observatory Data monitors 120 sources (across newspapers, radio and TV) in 54 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.25387/g3.13042784
title: Supplemental Material for Brose et al., 2020

description: <i>Mitragyna speciosa</i> Korth., 1839 (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of <i>M. speciosa</i> ‘Rifat’ was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that Rifat is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of <i>M. speciosa</i> will facilitate an improved understanding of alkaloid biosynthesis and accelerate production of bioactive alkaloids in heterologous hosts.Figure S1 contains the scaffold mean read depth distributions in the final assembly. Figure S2 contains the frequency of gene counts in orthogroups between Rubiaceae species. Table S1 is a list of RNA-Seq, WGS, and 10X Chromium Libraries. Table S2 contains a list of chloroplast genomes used to identify sequences encoding the chloroplast genome in <i>Mitragyna speciosa. </i>Table S3 contains metrics of quality assessments based on alignment of whole genome shotgun sequencing to the final <i>Mitragyna speciosa</i> 'Rifat' assembly. Table S4 contains metrics of quality assessments based on alignment of RNA sequencing to the final <i>Mitragyna speciosa </i>'Rifat' assembly. Table S5 the Repeat Masker summary of results of elements in the <i>Mitragyna speciosa </i>genome. Table S6 contains the FPKM expression matrix of top five blast results of <i>Mitragyna speciosa</i> 'Rifat' working set of genes and<i> Catharanthus roseus</i>. Table S7 contains predicted biosynthetic clusters in <i>Mitragyna speciosa</i>.<br>
DOI: 10.25387/g3.13042784.v1
title: Supplemental Material for Brose et al., 2020

description: <i>Mitragyna speciosa</i> Korth., 1839 (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of <i>M. speciosa</i> ‘Rifat’ was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that Rifat is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of <i>M. speciosa</i> will facilitate an improved understanding of alkaloid biosynthesis and accelerate production of bioactive alkaloids in heterologous hosts.Figure S1 contains the scaffold mean read depth distributions in the final assembly. Figure S2 contains the frequency of gene counts in orthogroups between Rubiaceae species. Table S1 is a list of RNA-Seq, WGS, and 10X Chromium Libraries. Table S2 contains a list of chloroplast genomes used to identify sequences encoding the chloroplast genome in <i>Mitragyna speciosa. </i>Table S3 contains metrics of quality assessments based on alignment of whole genome shotgun sequencing to the final <i>Mitragyna speciosa</i> 'Rifat' assembly. Table S4 contains metrics of quality assessments based on alignment of RNA sequencing to the final <i>Mitragyna speciosa </i>'Rifat' assembly. Table S5 the Repeat Masker summary of results of elements in the <i>Mitragyna speciosa </i>genome. Table S6 contains the FPKM expression matrix of top five blast results of <i>Mitragyna speciosa</i> 'Rifat' working set of genes and<i> Catharanthus roseus</i>. Table S7 contains predicted biosynthetic clusters in <i>Mitragyna speciosa</i>.<br>
DOI: 10.21227/am2e-2r90
title: Test1

description: WIP.
DOI: 10.25678/00032r
title: Data for: A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination

description: Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P. sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).
DOI: 10.5281/zenodo.4562601
title: SCENE open data pilot

description: This data corresponds to the open data pilot described in Deliverable D6.7 of the SCENE project. https://scene-project.eu/
DOI: 10.5281/zenodo.4562600
title: SCENE open data pilot

description: This data corresponds to the open data pilot described in Deliverable D6.7 of the SCENE project. https://scene-project.eu/
DOI: 10.15468/tuku2t
title: The distributionof fourspeciesof thegenus Macrourus (Gadiformes: Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gon, Ofer, Miya, Tshoanelo, Mcmillan, Peter, Leslie, Robin (2021): The distributionof fourspeciesof thegenus Macrourus (Gadiformes: Macrouridae) from the Southern Ocean based on samples from the toothfish longline fishery. Zootaxa 4903 (1): 105-116, DOI: https://doi.org/10.11646/zootaxa.4903.1.6
DOI: 10.34943/34e3bfa3-87a4-4d84-aba6-2c9e14242ec8
title: Burrard Inlet Acoustic Doppler Current Profiler 600 kHz Deployed 2020-10-22

description: The RDI Workhorse Monitor ADCP 600 kHz (25605) was deployed on 2020-10-22 at Burrard Inlet. Burrard Inlet is a coastal fjord in southwestern British Columbia. This device is a Acoustic Doppler Current Profiler 600 kHz. Acoustic Doppler Current Profilers (ADCP) are hydroacoustic instruments, similar to sonars. ADCPs measure current speed and direction at multiple predetermined depths simultaneously. ADCPs use the Doppler effect of sound waves that are scattered by particles in seawater over a depth range. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 2.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.25387/g3.13645802
title: Supplemental Material for Boatwright et al., 2021

description: Supplemental figures, tables and the CP-NAM VCF file. GBS were processed using Tassel version 5.2.52 (Bradbury et al.2007) following the GBS version 2 pipeline procedures (Glaubitz et al.2014). Tags were63aligned to the BTx623 version 3.1 annotated reference genome (McCormick et al. 2018), obtained from Phytozome (Goodstein et al. 2012), using BWA version 0.7.17 (Li and Durbin 2010). Beagle version 5.1 was used to impute missing genotype data in the variant call format (VCF) file resulting from the Tassel pipeline (Browning et al. 2018). The effects of SNPs were predicted using snpEff (Cingolani et al.2012).
DOI: 10.25387/g3.13645802.v1
title: Supplemental Material for Boatwright et al., 2021

description: Supplemental figures, tables and the CP-NAM VCF file. GBS were processed using Tassel version 5.2.52 (Bradbury et al.2007) following the GBS version 2 pipeline procedures (Glaubitz et al.2014). Tags were63aligned to the BTx623 version 3.1 annotated reference genome (McCormick et al. 2018), obtained from Phytozome (Goodstein et al. 2012), using BWA version 0.7.17 (Li and Durbin 2010). Beagle version 5.1 was used to impute missing genotype data in the variant call format (VCF) file resulting from the Tassel pipeline (Browning et al. 2018). The effects of SNPs were predicted using snpEff (Cingolani et al.2012).
DOI: 10.25678/00033s
title: Data for: A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

description: Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g. chromosome number and type or sex-related structural differences, to fine scale patterns e.g. recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. "Albock", a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. "Albock" and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of loci of interest, e.g. FST outliers, along the whitefish genome as well as assisting with the de novo assembly of a whitefish reference genome.
DOI: 10.25810/01kr-m051
title: Media and Climate Change Observatory Monthly Summary: “Take some comfort” that 64% now view climate change as an emergency - Issue 49, January 2021

description:         January 2021 saw media coverage of climate change or global warming around the world increase 7% from December 2020. However, January 2021 levels remain 28% lower than coverage a year earlier (January 2020). These trends were also consistent across monitoring of international wires services, where coverage increased 14% from the previous month but was still 39% lower than a year previous. Elsewhere, media coverage of climate change or global warming decreased across global radio (-9%) in January 2021 from the previous month of December, and was 15% lower than levels in January 2020. Figure 1 shows trends in newspaper media coverage at the global scale – organized into seven geographical regions around the world – from January 2004 through January 2021.
DOI: 10.15468/n9wmpd
title: Dendrothripoides moundi (Thysanoptera, Thripidae), a new species from Madagascar

description: This dataset contains the digitized treatments in Plazi based on the original journal article Goldarazena, Arturo, Matsumoto, Masami, Ranarilalatiana, Tolotra, Dianzinga, Niry T., Frago, Enric, Michel, Bruno (2020): Dendrothripoides moundi (Thysanoptera, Thripidae), a new species from Madagascar. Zootaxa 4877 (2): 396-400, DOI: https://doi.org/10.11646/zootaxa.4877.2.12
DOI: 10.25678/00034t
title: Data for: A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine whitefish radiation

description: Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. "Balchen" from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.
DOI: 10.17632/g9tpv4tpjw.1
title: Data for: 3D geometry of the Lanliao Fault revealed by seismic reflection profiles: Implications for earthquake clusters in the Dongpu Sag, North China

description: This file is the relocation data of earthquakes that occurred in the Dongpu Sag and its surroundings from January 2008 to November 2018, including each earthquake's longitude, latitude, focal depth, occurrence date, hour, minute, second, magnitude and residual error.
DOI: 10.15468/kf96zy
title: Four new species of Myrsidea (Phthiraptera: Amblycera: Menoponidae) from Chinese babblers (Passeriformes: Leiothrichidae, Paradoxornithidae, Timaliidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Lei, Lujia, Chu, Xingzhi, Dik, Bilal, Zou, Fasheng, Wang, Haitao, Gustafsson, Daniel R. (2020): Four new species of Myrsidea (Phthiraptera: Amblycera: Menoponidae) from Chinese babblers (Passeriformes: Leiothrichidae, Paradoxornithidae, Timaliidae). Zootaxa 4878 (1): 103-128, DOI: https://doi.org/10.11646/zootaxa.4878.1.4
DOI: 10.6084/m9.figshare.14115542
title: test

description: test
DOI: 10.6084/m9.figshare.14115542.v1
title: test

description: test
DOI: 10.6084/m9.figshare.14115713.v1
title: Data and Code used in "A new approach for evaluation of the economic impact of decentralized electrification projects"

description: data (inputs) and code to reproduce each step of "A new approach for evaluation of the economic impact of decentralized electrification projects"
DOI: 10.6084/m9.figshare.14115713
title: Data and Code used in "A new approach for evaluation of the economic impact of decentralized electrification projects"

description: data (inputs) and code to reproduce each step of "A new approach for evaluation of the economic impact of decentralized electrification projects"
DOI: 10.15468/cgyzpm
title: Two new species of Fauveliopsidae (Annelida, Sedentaria) from submarine caves and deep sea, Japan

description: This dataset contains the digitized treatments in Plazi based on the original journal article Jimi, Naoto, Fujimoto, Shinta, Ogawa, Akito, Fujita, Yoshihisa, Shigenobu, Yuya, Imura, Satoshi (2020): Two new species of Fauveliopsidae (Annelida, Sedentaria) from submarine caves and deep sea, Japan. Zootaxa 4878 (2): 385-391, DOI: https://doi.org/10.11646/zootaxa.4878.2.11
DOI: 10.25810/jgyv-zg57.34
title: New Zealand Newspaper Coverage of Climate Change or Global Warming, 2000-2021 - January 2021

description:         The Media and Climate Change Observatory Data monitors 120 sources (across newspapers, radio and TV) in 54 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.5281/zenodo.3541624
title: Zebrafish Pathway Metabolite MetFrag Local CSV (Beta)

description: This is a local CSV file of Zebrafish metabolites extracted from wikipathways and KEGG for MetFrag (https://msbi.ipb-halle.de/MetFrag/) and literature (currently DOI: 10.1371/journal.pone.0213661). All metabolites associated with wikipathways entries were extracted by Egon Willighagen using the following query: http://sparql.wikipathways.org/sparql?default-graph-uri=&query=PREFIX+gpml%3A++++%3Chttp%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml%23%3E%0D%0APREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0D%0APREFIX+dc%3A++++++%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0D%0APREFIX+rdf%3A+++++%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E+%0D%0A%0D%0Aselect+distinct+%3Fmetabolite+%28str%28%3FtitleLit%29+as+%3Ftitle%29+where+%7B%0D%0A++%3Fmetabolite+a+wp%3AMetabolite+%3B%0D%0A++++dcterms%3AisPartOf+%3Fpw+.%0D%0A++%3Fpw+dc%3Atitle+%3FtitleLit+%3B%0D%0A++++wp%3AorganismName+%22Danio+rerio%22%5E%5Exsd%3Astring+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on Open pathway data from the KEGG Zebrafish pathway (https://www.genome.jp/kegg-bin/show_pathway?dre01100) was extracted by Marek Ostaszewski. The resulting identifiers were mapped to chemical structures using the Chemical Translation Service (https://cts.fiehnlab.ucdavis.edu/batch), the CompTox Chemistry Dashboard batch search (https://comptox.epa.gov/dashboard/dsstoxdb/batch_search) and individual resources (KEGG, ChEBI, HMDB) where applicable. Conversions between structural formats were performed using Open Babel (http://openbabel.org/wiki/Main_Page). 13 Nov update: DOI: 10.1371/journal.pone.0213661 was added and mapped up using PubChem services (https://pubchem.ncbi.nlm.nih.gov/); PubChem CIDs and two additional columns "annothits" and "annothitcnt" from the PubChem download files were added. This file is a <strong>BETA </strong>version to start a collection of Zebrafish metabolites for identification using MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. TODO: to add PubChem "Zebrafish" query: https://pubchem.ncbi.nlm.nih.gov/#query=zebrafish&tab=pathway&selected_id_type=cid
description: Beta version - (semi-)automated extraction and mapping only, no experimental verification
DOI: 10.5517/ccdc.csd.cc23g0k5
title: CCDC 1949886: Experimental Crystal Structure Determination

description: Related Article: Taotao Hao, Yongsheng Yang, Wenting Liang, Chunying Fan, Xin Wang, Wanhua Wu, Xiaochuan Chen, Haiyan Fu, Hua Chen, Cheng Yang|2021|Chemical Science|12|2614|doi:10.1039/D0SC05213B