cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.835779
title: Data and scripts used in Bayesian forecasting of coral bleaching in Abrolhos - Brazil

description: This repository contains numerical data on seawater parameters, reef monitoring field data, and Matlab scripts used for the construction of the conceptual model for short-term forecasting of coral bleaching in the Atlantic Ocean.
DOI: 10.15468/gg6cbg
title: Blütenspanner aus Vorarlberg, Austria occ., dem Fürstentum Liechtenstein und dem angrenzenden Graubünden (Lepidoptera, Geometridae, Eupitheciini) Zum Gedenken an den Vorarlberger Amateur-Entomologen Johann Battisti, 1898 - 1979

description: This dataset contains the digitized treatments in Plazi based on the original journal article Aistleitner, E. (2012): Blütenspanner aus Vorarlberg, Austria occ., dem Fürstentum Liechtenstein und dem angrenzenden Graubünden (Lepidoptera, Geometridae, Eupitheciini) Zum Gedenken an den Vorarlberger Amateur-Entomologen Johann Battisti, 1898 - 1979. Linzer biologische Beiträge 44 (2): 885-926, DOI: http://doi.org/10.5281/zenodo.4524580
DOI: 10.5281/zenodo.4521833
title: MODIS LST monthly daytime and nighttime low (0.05), median (0.50) and high (0.95) temperatures for year 2013 at 1-km

description: Layers include: Land Surface Temperature daytime low (0.05), median (0.50) and high (0.95) temperatures for the year 2013. Derived using the data.table package and quantile function in R. For more info about the MODIS LST product see: https://lpdaac.usgs.gov/dataset_discovery/modis/modis_products_table/mod11a2_v006. Antarctica is not included. To access and visualize maps use: OpenLandMap.org To download and compute with maps using Cloud-Optimized-GeoTIFF see <strong>this tutorial</strong>. If you discover a bug, artifact or inconsistency in the OpenLandMap maps, or if you have a question please use some of the following channels: Technical issues and questions about the code: https://gitlab.com/openlandmap/global-layers/-/issues General questions and comments: https://disqus.com/home/forums/landgis/ All files internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention: clm = theme: climate, lst = variable: land surface temperature, mod11a2.daytime = determination method: MOD11A2 product, day time values, d = median value / sd = standard deviation / u.95 = aggregation/statistics method: 95% probability upper quantile, 1km = spatial resolution / block support: 1 km, s0..0cm = vertical reference: land surface, 2000..2020 = time reference: from 2000 to 2020, v1.1 = version number: 1.1,
description: This work has received funding from the European Union's the Innovation and Networks Executive Agency (INEA) under Grant Agreement Connecting Europe Facility (CEF) Telecom project 2018-EU-IA-0095 (https://ec.europa.eu/inea/en/connecting-europe-facility/cef-telecom/2018-eu-ia-0095).
DOI: 10.5281/zenodo.4521832
title: MODIS LST monthly daytime and nighttime low (0.05), median (0.50) and high (0.95) temperatures for year 2013 at 1-km

description: Layers include: Land Surface Temperature daytime low (0.05), median (0.50) and high (0.95) temperatures for the year 2013. Derived using the data.table package and quantile function in R. For more info about the MODIS LST product see: https://lpdaac.usgs.gov/dataset_discovery/modis/modis_products_table/mod11a2_v006. Antarctica is not included. To access and visualize maps use: OpenLandMap.org To download and compute with maps using Cloud-Optimized-GeoTIFF see <strong>this tutorial</strong>. If you discover a bug, artifact or inconsistency in the OpenLandMap maps, or if you have a question please use some of the following channels: Technical issues and questions about the code: https://gitlab.com/openlandmap/global-layers/-/issues General questions and comments: https://disqus.com/home/forums/landgis/ All files internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention: clm = theme: climate, lst = variable: land surface temperature, mod11a2.daytime = determination method: MOD11A2 product, day time values, d = median value / sd = standard deviation / u.95 = aggregation/statistics method: 95% probability upper quantile, 1km = spatial resolution / block support: 1 km, s0..0cm = vertical reference: land surface, 2000..2020 = time reference: from 2000 to 2020, v1.1 = version number: 1.1,
description: This work has received funding from the European Union's the Innovation and Networks Executive Agency (INEA) under Grant Agreement Connecting Europe Facility (CEF) Telecom project 2018-EU-IA-0095 (https://ec.europa.eu/inea/en/connecting-europe-facility/cef-telecom/2018-eu-ia-0095).
DOI: 10.15468/f7smab
title: Notizen zu einigen zentralasiatischen Goldwespen aus der Hedychridium roseum-Gruppe (Hymenoptera: Chrysididae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Arens, W. (2012): Notizen zu einigen zentralasiatischen Goldwespen aus der Hedychridium roseum-Gruppe (Hymenoptera: Chrysididae). Linzer biologische Beiträge 44 (2): 927-932, DOI: http://doi.org/10.5281/zenodo.4524603
DOI: 10.5281/zenodo.4524634
title: Data set from Lo Rito M, Raso I, Saracino A, Basile DP, Varrica A, Reali M, Carminati M, Frigiola A, Giamberti A. Primary Arterial Switch Operation for Late Presentation of Transposition of the Great Arteries With Intact Ventricular Septum. Semin Thorac Cardiovasc Surg. 2020 Nov 26:S1043-0679(20)30425-1. doi: 10.1053/j.semtcvs.2020.11.030. Epub ahead of print. PMID: 33249102.

description: Data set from the article Lo Rito M, Raso I, Saracino A, Basile DP, Varrica A, Reali M, Carminati M, Frigiola A, Giamberti A. Primary Arterial Switch Operation for Late Presentation of Transposition of the Great Arteries With Intact Ventricular Septum. Semin Thorac Cardiovasc Surg. 2020 Nov 26:S1043-0679(20)30425-1. doi: 10.1053/j.semtcvs.2020.11.030. Epub ahead of print. PMID: 33249102. This is the abstract: Transposition of the great arteries (TGA) with intact ventricular septum (IVS) are subject to neonatal arterial switch operation (ASO) to avoid deconditioning of the left ventricle (LV). Often an early repair is not feasible in developing countries where late referral is frequent. We aim to explore ASO outcomes in late TGA-IVS and compare "unfavorable candidates" (LV myocardial mass &lt;35gr/m<sup>2</sup> unfavorable geometry. banana-like LV shape) with other late TGA-IVS. Single-center retrospective study on late TGA-IVS who underwent primary ASO between 2015 and 2018. We divide patients into 2 groups: unfavorable candidates and favorable candidates TGA. We report categorical variables as number and percentage and continuous variables as median with interquartile range. Differences were assessed with Chi-squared or Fisher exact tests, Wilcoxon sign-rank, and Wilcoxon-rank sum tests. 45 TGA-IVS were referred with a median age of 35 days. Pre-operative echocardiography identified banana-like LV shape in 66.7%; unfavorable LV geometry in 47.6% and LV mass &lt;35gr/m<sup>2</sup> in 51%. Only 1 death occurred related to myocardial ischemia. Five patients (11%) required ECMO for LV dysfunction, with unfavorable candidates having a higher but not significant use (18.7% vs 6.9%, P = 0.33). At discharge, echocardiography demonstrated significant LV mass improvement compared to pre-operative (58.6 vs 33.8 gr/m<sup>2</sup>, P &lt; 0.0001) with no significant echocardiographic difference between unfavorable and favorable late-TGA. Primary ASO in late presenter TGA-IVS can be performed safely with low mortality having a low threshold to ECMO. Significantly unconditioned LV are amenable with primary ASO with good LV mass recovery.
DOI: 10.5281/zenodo.4524633
title: Data set from Lo Rito M, Raso I, Saracino A, Basile DP, Varrica A, Reali M, Carminati M, Frigiola A, Giamberti A. Primary Arterial Switch Operation for Late Presentation of Transposition of the Great Arteries With Intact Ventricular Septum. Semin Thorac Cardiovasc Surg. 2020 Nov 26:S1043-0679(20)30425-1. doi: 10.1053/j.semtcvs.2020.11.030. Epub ahead of print. PMID: 33249102.

description: Data set from the article Lo Rito M, Raso I, Saracino A, Basile DP, Varrica A, Reali M, Carminati M, Frigiola A, Giamberti A. Primary Arterial Switch Operation for Late Presentation of Transposition of the Great Arteries With Intact Ventricular Septum. Semin Thorac Cardiovasc Surg. 2020 Nov 26:S1043-0679(20)30425-1. doi: 10.1053/j.semtcvs.2020.11.030. Epub ahead of print. PMID: 33249102. This is the abstract: Transposition of the great arteries (TGA) with intact ventricular septum (IVS) are subject to neonatal arterial switch operation (ASO) to avoid deconditioning of the left ventricle (LV). Often an early repair is not feasible in developing countries where late referral is frequent. We aim to explore ASO outcomes in late TGA-IVS and compare "unfavorable candidates" (LV myocardial mass &lt;35gr/m<sup>2</sup> unfavorable geometry. banana-like LV shape) with other late TGA-IVS. Single-center retrospective study on late TGA-IVS who underwent primary ASO between 2015 and 2018. We divide patients into 2 groups: unfavorable candidates and favorable candidates TGA. We report categorical variables as number and percentage and continuous variables as median with interquartile range. Differences were assessed with Chi-squared or Fisher exact tests, Wilcoxon sign-rank, and Wilcoxon-rank sum tests. 45 TGA-IVS were referred with a median age of 35 days. Pre-operative echocardiography identified banana-like LV shape in 66.7%; unfavorable LV geometry in 47.6% and LV mass &lt;35gr/m<sup>2</sup> in 51%. Only 1 death occurred related to myocardial ischemia. Five patients (11%) required ECMO for LV dysfunction, with unfavorable candidates having a higher but not significant use (18.7% vs 6.9%, P = 0.33). At discharge, echocardiography demonstrated significant LV mass improvement compared to pre-operative (58.6 vs 33.8 gr/m<sup>2</sup>, P &lt; 0.0001) with no significant echocardiographic difference between unfavorable and favorable late-TGA. Primary ASO in late presenter TGA-IVS can be performed safely with low mortality having a low threshold to ECMO. Significantly unconditioned LV are amenable with primary ASO with good LV mass recovery.
DOI: 10.5517/ccdc.csd.cc23wnh5
title: CCDC 1962997: Experimental Crystal Structure Determination

description: Related Article: Zhejun Sun, Yuting Zhang, Huihao Zhou, Jun Xu, Qiong Gu|2021|Bioorg.Chem.|107|104537|doi:10.1016/j.bioorg.2020.104537
DOI: 10.5517/ccdc.csd.cc23wj2m
title: CCDC 1962860: Experimental Crystal Structure Determination

description: Related Article: Zhejun Sun, Yuting Zhang, Huihao Zhou, Jun Xu, Qiong Gu|2021|Bioorg.Chem.|107|104537|doi:10.1016/j.bioorg.2020.104537
DOI: 10.5281/zenodo.4436115
title: Annexes to the EFSA scientific report on Cumulative dietary risk assessment of chronic acetylcholinesterase inhibition by residues of pesticides

description: A retrospective cumulative risk assessment of dietary exposure to pesticide residues was conducted for chronic inhibition of acetylcholinesterase. The pesticides considered in this assessment were identified and characterised in a previous scientific report on the establishment of cumulative assessment groups of pesticides for their effects on the nervous system. The exposure assessments used monitoring data collected by Member States under their official pesticide monitoring programmes in 2016, 2017 and 2018, and individual food consumption data from 10 populations of consumers from different countries and from different age groups. Exposure estimates were obtained by means of a 2-dimensional probabilistic model, which was implemented in SAS® software. The characterisation of cumulative risk was supported by an uncertainty analysis based on expert knowledge elicitation. For each of the 10 populations, it is concluded with varying degrees of certainty that cumulative exposure to pesticides contributing to the chronic inhibition of acetylcholinesterase does not exceed the threshold for regulatory consideration established by risk managers. The input and output data for the exposure assessment are reported in the following annexes: Annex A – Input data for the exposure assessment of CAG-NCN Annex B – Output data for the Tier I exposure assessment of CAG-NCN Annex C – Output data for the Tier II exposure assessment of CAG-NCN The scientific report on the cumulative dietary risk assessment of chronic acetylcholinesterase inhibition by residues of pesticides can be found in the EFSA webpage: https://www.efsa.europa.eu/en/efsajournal/pub/6392
description: IT; en; xlsx; pesticides.MRL@efsa.europa.eu
DOI: 10.5281/zenodo.4436114
title: Annexes to the EFSA scientific report on Cumulative dietary risk assessment of chronic acetylcholinesterase inhibition by residues of pesticides

description: A retrospective cumulative risk assessment of dietary exposure to pesticide residues was conducted for chronic inhibition of acetylcholinesterase. The pesticides considered in this assessment were identified and characterised in a previous scientific report on the establishment of cumulative assessment groups of pesticides for their effects on the nervous system. The exposure assessments used monitoring data collected by Member States under their official pesticide monitoring programmes in 2016, 2017 and 2018, and individual food consumption data from 10 populations of consumers from different countries and from different age groups. Exposure estimates were obtained by means of a 2-dimensional probabilistic model, which was implemented in SAS® software. The characterisation of cumulative risk was supported by an uncertainty analysis based on expert knowledge elicitation. For each of the 10 populations, it is concluded with varying degrees of certainty that cumulative exposure to pesticides contributing to the chronic inhibition of acetylcholinesterase does not exceed the threshold for regulatory consideration established by risk managers. The input and output data for the exposure assessment are reported in the following annexes: Annex A – Input data for the exposure assessment of CAG-NCN Annex B – Output data for the Tier I exposure assessment of CAG-NCN Annex C – Output data for the Tier II exposure assessment of CAG-NCN The scientific report on the cumulative dietary risk assessment of chronic acetylcholinesterase inhibition by residues of pesticides can be found in the EFSA webpage: https://www.efsa.europa.eu/en/efsajournal/pub/6392
description: IT; en; xlsx; pesticides.MRL@efsa.europa.eu
DOI: 10.5281/zenodo.4470159
title: Mock communities for evaluating the performance of metagenomic classifiers

description: Set of 140 <em>in silico</em> microbial communities used to evaluate the performance of metagenomic classifiers. These mock communities have varying species diversity, intraspecific diversity, and genomic similarity to a standardized reference genome database. Each mock was simulated to a depth of 2.1 Gb using 2×150 bp paired-end reads with strain abundances following a log-normal distribution. Each mock community has the format ani&lt;<em>ani</em>&gt;_c&lt;<em>complexity</em>&gt;_st&lt;<em>strain_diversity</em>&gt;_r&lt;<em>replicate</em>&gt; where: <em>ani: </em>indicates the ANI between genomes in the mock and standardized reference database. This field is 95, 97, or 99 indicating ANI ranges of [95%, 97%), [97, 99%), and [99, 99.75%), respectively. Mock communities at 100% ANI are also provide as a baseline and were constructed from genomes within the standardized reference database. <em>complexity: </em>indicates the species diversity of the mock. This field is either LOW or HIGH indicating the mock is comprised of 100 +/- 25 or 500 +/- 100 species, respectively. <em>strain_diversity</em>: indicates the strain diversity within each species. This field is False or True indicating the mock is either comprised of a single strain (genome) from each species or up to 10 randomly selected strains (genomes) from each species. <em>replicate</em>: indicates the replicate number of the mock. Ten replicates were generated for each parameter combination. Mock communities were simulated under all combinations of these parameters, with the exception of mocks with HIGH species diversity and [95%, 97) ANI similarity as there were insufficient species with available genomes within this ANI range. <em>Note</em>: provided files contain both the low and high diversity mocks for the indicated parameters in the filename.
DOI: 10.5281/zenodo.4300920
title: MMGC: gene catalogues of the mouse and human microbiota

description: We produced protein cluster catalogues in order to establish the gene-level taxonomic overlap between the human and mouse microbiome. For gene-clustering, we concatenated 76,937,350 pre-clustered human predicted proteins for non-redundant, near-complete genomes of the UHGG with 45,598,646 mouse predicted protein-coding sequences from non-redundant, near-complete species of the MMGC, and performed protein clustering using the ‘linclust’ function from MMseqs285 v10-6d92c (-c 0.8 --cov-mode 1 --cluster-mode 2 --kmer-per-seq 80). Proteins were clustered at 100%, 90%, 80% and 50% sequence identity; clusters were considered shared if they contained genes from both human and mouse commensals. This archive includes two files for each sequence identity threshold: a representative protein sequence file (.fa) and a sequence membership file (.tsv).
DOI: 10.5281/zenodo.4300643
title: MMGC: custom Kraken2/Bracken database for analysing the mouse gut microbiome

description: Custom Kraken2/Bracken database built using the representative genomes for 1,021 microbial species from the mouse gut microbiota. Genomes include isolates and MAGs, but all are near-complete (&gt;90% completeness; &lt;5% contamination; maximum genome size ≤ 8 Mb; maximum contig count ≤ 500; N50 ≥ 10 kb; mean contig length ≥ 5 kb). This database achieved a mean read classification rate of 87.7% when benchmarked on 1,785 independent (i.e. non-contributory) mouse gut shotgun metagenome samples. An equivalent human database (UHGG) only attained classification rates of 36.6%. This database is a publicly available resource to facilitate more efficient/deeper analyses of mouse gut shotgun metagenomes. Find out more about the Mouse Microbial Genome Collection at our GitHub repository.
DOI: 10.5281/zenodo.4300919
title: MMGC: gene catalogues of the mouse and human microbiota

description: We produced protein cluster catalogues in order to establish the gene-level taxonomic overlap between the human and mouse microbiome. For gene-clustering, we concatenated 76,937,350 pre-clustered human predicted proteins for non-redundant, near-complete genomes of the UHGG with 45,598,646 mouse predicted protein-coding sequences from non-redundant, near-complete species of the MMGC, and performed protein clustering using the ‘linclust’ function from MMseqs285 v10-6d92c (-c 0.8 --cov-mode 1 --cluster-mode 2 --kmer-per-seq 80). Proteins were clustered at 100%, 90%, 80% and 50% sequence identity; clusters were considered shared if they contained genes from both human and mouse commensals. This archive includes two files for each sequence identity threshold: a representative protein sequence file (.fa) and a sequence membership file (.tsv).
DOI: 10.5281/zenodo.4470158
title: Mock communities for evaluating the performance of metagenomic classifiers

description: Set of 140 <em>in silico</em> microbial communities used to evaluate the performance of metagenomic classifiers. These mock communities have varying species diversity, intraspecific diversity, and genomic similarity to a standardized reference genome database. Each mock was simulated to a depth of 2.1 Gb using 2×150 bp paired-end reads with strain abundances following a log-normal distribution. Each mock community has the format ani&lt;<em>ani</em>&gt;_c&lt;<em>complexity</em>&gt;_st&lt;<em>strain_diversity</em>&gt;_r&lt;<em>replicate</em>&gt; where: <em>ani: </em>indicates the ANI between genomes in the mock and standardized reference database. This field is 95, 97, or 99 indicating ANI ranges of [95%, 97%), [97, 99%), and [99, 99.75%), respectively. Mock communities at 100% ANI are also provide as a baseline and were constructed from genomes within the standardized reference database. <em>complexity: </em>indicates the species diversity of the mock. This field is either LOW or HIGH indicating the mock is comprised of 100 +/- 25 or 500 +/- 100 species, respectively. <em>strain_diversity</em>: indicates the strain diversity within each species. This field is False or True indicating the mock is either comprised of a single strain (genome) from each species or up to 10 randomly selected strains (genomes) from each species. <em>replicate</em>: indicates the replicate number of the mock. Ten replicates were generated for each parameter combination. Mock communities were simulated under all combinations of these parameters, with the exception of mocks with HIGH species diversity and [95%, 97) ANI similarity as there were insufficient species with available genomes within this ANI range. <em>Note</em>: provided files contain both the low and high diversity mocks for the indicated parameters in the filename.
DOI: 10.5281/zenodo.4116249
title: Virus+ Sequence Masked Mouse Reference Genome (GRCm38)

description: A version of the mouse genome (GRCm38) masked for all possible viral sequences. See Virus+ Masked Human Genome for a masked human reference database. The following commands were used to generate the additional virus sequence masked reference database: <strong>1) Download all RefSeq and Neighbor nucleotide records:</strong> https://www.ncbi.nlm.nih.gov/nuccore/?term=Viruses[Organism]%20NOT%20cellular%20organisms[ORGN]%20NOT%20wgs[PROP]%20NOT%20gbdiv%20syn[prop]%20AND%20(srcdb_refseq[PROP]%20OR%20nuccore%20genome%20samespecies[Filter]) <strong>2) Shred the downloaded viral genomes using shred.sh from the bbtools package</strong> shred.sh in=refseq_virus_reformated.fasta out=virus_shred.fasta.gz length=85 minlength=75 overlap=30 <strong>3) Map shredded virus sequence to the GRCm38</strong><strong> genome using bbmap.sh from the bbtools package</strong> bbmap.sh ref=GRCm38.fa.gz in=virus_shred.fasta.gz outm=map_mouse_all_viruses.sam minid=0.90 <strong>4) Mask virus sequenced mapped regions from the GRCm38 genome using bbmask.sh from the bbtools package</strong> bbmask.sh in=GRCm38.fa.gz out=GRCm38_virus_masked.fasta.gz sam=map_mouse_all_viruses.sam <strong>5) Remove all N's to further reduce file size using seqkit</strong><br> seqkit -is replace -p "n" -r "" GRCm38_virus_masked.fasta.gz &gt; mouse_virus_masked.fasta_Ns_removed.gz <strong>Additional References:</strong> bbtools seqkit NCBI Virus Genome RefSeq
DOI: 10.5281/zenodo.4300642
title: MMGC: custom Kraken2/Bracken database for analysing the mouse gut microbiome

description: Custom Kraken2/Bracken database built using the representative genomes for 1,021 microbial species from the mouse gut microbiota. Genomes include isolates and MAGs, but all are near-complete (&gt;90% completeness; &lt;5% contamination; maximum genome size ≤ 8 Mb; maximum contig count ≤ 500; N50 ≥ 10 kb; mean contig length ≥ 5 kb). This database achieved a mean read classification rate of 87.7% when benchmarked on 1,785 independent (i.e. non-contributory) mouse gut shotgun metagenome samples. An equivalent human database (UHGG) only attained classification rates of 36.6%. This database is a publicly available resource to facilitate more efficient/deeper analyses of mouse gut shotgun metagenomes. Find out more about the Mouse Microbial Genome Collection at our GitHub repository.