cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13071053
title: Additional file 1 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 1: Table S1. Overview of NGS experiments conducted in this study and data obtained from the literature. Ornithodoros moubata cell line names have been abbreviated by removal of “/CTVM” and Ornithodoros porcinus and Ornithodoros moubata have been abbreviated for convenience.
DOI: 10.6084/m9.figshare.13071059
title: Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 2: Table S2. ASFV-like transcripts detected in data from six Ornithodoros moubata cell lines and O.moubata ticks by mRNA-sequencing and data analysis from published sequences ASFV-like sequences from tick cell libraries lib01543-46 und lib01610-11 (total RNA) were identified using RIEMS. The resulting reads were blasted against the NCBI BLASTn database for confirmation and annotation. Ornithodoros moubata transcriptome data from a previous study42 was downloaded from GenBank, and ASFV-like sequences were identified by mapping the data against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences. The resulting reads and contigs were annotated after a BLASTn search against the entire BLASTn database. Sequencing data from the mRNA enriched OME21 library lib02965 was mapped against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences, and resulting contigs were blasted against the entire BLASTn database. Per sequence, only the hit with the lowest e-value is shown.
DOI: 10.6084/m9.figshare.13071059.v1
title: Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 2: Table S2. ASFV-like transcripts detected in data from six Ornithodoros moubata cell lines and O.moubata ticks by mRNA-sequencing and data analysis from published sequences ASFV-like sequences from tick cell libraries lib01543-46 und lib01610-11 (total RNA) were identified using RIEMS. The resulting reads were blasted against the NCBI BLASTn database for confirmation and annotation. Ornithodoros moubata transcriptome data from a previous study42 was downloaded from GenBank, and ASFV-like sequences were identified by mapping the data against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences. The resulting reads and contigs were annotated after a BLASTn search against the entire BLASTn database. Sequencing data from the mRNA enriched OME21 library lib02965 was mapped against a tailored database containing all known ASFV sequences and all previously obtained ASFV-like sequences, and resulting contigs were blasted against the entire BLASTn database. Per sequence, only the hit with the lowest e-value is shown.
DOI: 10.6084/m9.figshare.13071062.v1
title: Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 3: Table S3. BLASTn results of SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome. Shown are hits with the lowest e-value for viral, tick and mobile genetic element-related genes, as obtained by Blastn against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071038.v1
title: Additional file 15 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 15: Table S9. Results of small RNA sequencing and mapping against ASFV and ASFLI-elements. Small RNA was sequenced from Ornithodoros porcinus and Ornithodoros moubata nymphal stage ticks. After deduplication using BBMap, 22 nt siRNA and 28-29 nt piRNA fractions were extracted and mapped against ASFV and ASFLI-elements using Bowtie.
DOI: 10.6084/m9.figshare.13071071.v1
title: Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 6: Table S5. Results of tick and tick cell line screening for ASFLI-elements by qPCR. DNA from single ticks and every tick cell line (n=1) was extracted and analysed by qPCR for six ASFV-like genes as described in the ‘Material and methods’ section. All samples were tested with a qPCR control targeting a tick housekeeping gene to demonstrate successful DNA extraction and presence of tick DNA. Absence of ASFV in samples producing false positive results was proven by an OIE-listed qPCR.
DOI: 10.6084/m9.figshare.13071050.v1
title: Additional file 19 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 19: Table S12.Primer and probe sequences used in this study.
DOI: 10.6084/m9.figshare.13071065.v1
title: Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 4: Table S4. BLASTp results of all ORFs &gt;500 bp on SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome Shown are hits with the lowest e-value for viral-, tick and mobile genetic element-related proteins, as obtained by Blastp of ORFs &gt;500 bp against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071074.v1
title: Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071080
title: Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 9: Table S7. SPAdes-assembled contigs from deep sequencing data from libraries AGL001 and MPA001, as generated from museum-stored ticks. Data from libraries from museum-stored tick were mapped against ASFLI-element-containing databases of Ornithoidoros moubata (AGL001) and Ornithodoros porcinus (MPA001) using Bowtie2 (v.2.3.4.3) with default parameters. Subsequently, mapped reads were assembled using SPAdes and aligned to the corresponding ASFLI- element-contigs using MAFFT (v. 7.388) in Geneious.
DOI: 10.6084/m9.figshare.13071065
title: Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 4: Table S4. BLASTp results of all ORFs &gt;500 bp on SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome Shown are hits with the lowest e-value for viral-, tick and mobile genetic element-related proteins, as obtained by Blastp of ORFs &gt;500 bp against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071074
title: Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071062
title: Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 3: Table S3. BLASTn results of SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome. Shown are hits with the lowest e-value for viral, tick and mobile genetic element-related genes, as obtained by Blastn against the entire NCBI database.
DOI: 10.6084/m9.figshare.13071071
title: Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 6: Table S5. Results of tick and tick cell line screening for ASFLI-elements by qPCR. DNA from single ticks and every tick cell line (n=1) was extracted and analysed by qPCR for six ASFV-like genes as described in the ‘Material and methods’ section. All samples were tested with a qPCR control targeting a tick housekeeping gene to demonstrate successful DNA extraction and presence of tick DNA. Absence of ASFV in samples producing false positive results was proven by an OIE-listed qPCR.
DOI: 10.6084/m9.figshare.13071080.v1
title: Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

description: Additional file 9: Table S7. SPAdes-assembled contigs from deep sequencing data from libraries AGL001 and MPA001, as generated from museum-stored ticks. Data from libraries from museum-stored tick were mapped against ASFLI-element-containing databases of Ornithoidoros moubata (AGL001) and Ornithodoros porcinus (MPA001) using Bowtie2 (v.2.3.4.3) with default parameters. Subsequently, mapped reads were assembled using SPAdes and aligned to the corresponding ASFLI- element-contigs using MAFFT (v. 7.388) in Geneious.
DOI: 10.5281/zenodo.4074372
title: Grey literature strategies survey results and questionnaires: producers, users and collecting services

description: Survey results from three online surveys conducted in 2013 of research producing organisations,research users and collecting services involved in research for public policy and practice. Most respondents were from Australia. Questionnaires and SPSS versions also provided. Results have been published in various publications available in this collection.
DOI: 10.5281/zenodo.4074371
title: Grey literature strategies survey results and questionnaires: producers, users and collecting services

description: Survey results from three online surveys conducted in 2013 of research producing organisations,research users and collecting services involved in research for public policy and practice. Most respondents were from Australia. Questionnaires and SPSS versions also provided. Results have been published in various publications available in this collection.
DOI: 10.15468/2t4u32
title: Four new species of Trichoderma in the Harzianum clade from northern China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gu, Xin, Wang, Rui, Sun, Quan, Wu, Bing, Sun, Jing-Zu (2020): Four new species of Trichoderma in the Harzianum clade from northern China. MycoKeys 73: 109-132, DOI: http://dx.doi.org/10.3897/mycokeys.73.51424, URL: http://dx.doi.org/10.3897/mycokeys.73.51424
DOI: 10.15468/6dgmt8
title: Three new species of Conidiobolus sensu stricto from plant debris in eastern China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Nie, Yong, Cai, Yue, Gao, Yang, Yu, De-Shui, Wang, Zi-Min, Liu, Xiao-Yong, Huang, Bo (2020): Three new species of Conidiobolus sensu stricto from plant debris in eastern China. MycoKeys 73: 133-149, DOI: http://dx.doi.org/10.3897/mycokeys.73.56905, URL: http://dx.doi.org/10.3897/mycokeys.73.56905
DOI: 10.17632/b5yh42t3tj.1
title: Data for: Effects of light on the Ba/Ca ratios in coral skeletons

description: This file includes data in Table1, Fig.3, and Fig.4 in the manuscript, Effects of light on the Ba/Ca ratios in coral skeletons.
DOI: 10.17632/pyczkkttfx.1
title: Data for: An extensional collapse model for the Lhasa-Qiangtang orogen in central Tibet

description: These rock samples were collected from central Tibet,China. The geochronology and geochemical data are used in geological research.
DOI: 10.17632/t4rjd9hx52.1
title: Data for: Can liquid density-fluctuations near solid surface drive the motion of nanoscale droplets?

description: Data for: Can liquid density-fluctuations near solid surface drive the motion of nanoscale droplets?
DOI: 10.17632/z7yykjw9r7.1
title: Data for: Mercury and sulfur isotopic composition of sulfides from sediment-hosted lead-zinc deposits in Lanping basin, Southwestern China

description: This dataset includes for tables related to the submitted manuscript.
DOI: 10.17632/dhd5z8n6sv.1
title: Data for: Evolution of stony debris flows in laboratory experiments

description: Spread sheet provide full data sets Figure provide all outcomes of the experiments Videos show all runs
DOI: 10.5517/ccdc.csd.cc25yzw0
title: CCDC 2024823: Experimental Crystal Structure Determination

description: Related Article: Di Meng, Yangxi Xie, Qiupeng Peng, Jian Wang|2020|Org.Lett.|22|7635|doi:10.1021/acs.orglett.0c02832
DOI: 10.6084/m9.figshare.9768101.v8
title: Datasets, matrices and supplementary figure for QMaker

description: Pfam_datasets.zip: Pfam training and test sets which were used with QMaker.<br>Matrices-normalized.zip: Eight output matrices for LG, Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>Figure S1_new.pdf: The performance of five matrices, i.e., Q.pfam, JTT, LG, WAG on five clade-specific datasets, i.e., Bird, Plant, Insect, Yeast Mammal.<br>Table S1 (Correlations).docx: Correlation values (1000x) between six new matrices and 20 existing matrices, upper half are correlations of frequencies, lower half are correlations of exchangeabilities.<br>sample_training_10alignments.zip, sample_training_10genes.zip: two small datasets and training scripts, one has 10 alignments (these alignments do not share species and are extracted from Pfam dataset, shoulf be trained with option -S), the other has 10 genes of a same species (extracting from Plant dataset, training with option -p). Each dataset will need ~30 mins training time on a 10-core machine.
DOI: 10.21227/jq88-dv24
title: Coronavirus (COVID-19) Geo-tagged Tweets Dataset

description: This dataset contains IDs and sentiment scores of the geo-tagged tweets related to the COVID-19 pandemic. The tweets are captured by an on-going project deployed at https://live.rlamsal.com.np. The model monitors the real-time Twitter feed for coronavirus-related tweets using 90+ different keywords and hashtags that are commonly used while referencing the pandemic. Complying with Twitter's content redistribution policy, only the tweet IDs are shared. You can re-construct the dataset by hydrating these IDs. The tweet IDs in this dataset belong to the tweets tweeted providing an exact location.-------------------------------------Recently added: Coronavirus (COVID-19) Tweets Sentiment Trend (Global)-------------------------------------Below is the quick overview of this dataset.— Dataset name: GeoCOV19Tweets Dataset— Number of tweets : 238,809 tweets— Coverage : Global— Language : English (EN)— Primary dataset : Coronavirus (COVID-19) Tweets Dataset (COV19Tweets Dataset)— Dataset updates : Everyday— Usage policy : As per Twitter's Developer Policy— Active keywords and hashtags: keywords.tsvPlease visit this page (primary dataset) for details regarding the collection date and time of each CSV file present in this dataset.
DOI: 10.6084/m9.figshare.13030430
title: Spike mutation D614G altersSARS-CoV-2 fitness and neutralization susceptibility

description: Raw data associated with Figures 1-4 and Extended Data Figures 2-4 and 7-9 of "Spike mutation D614G alters SARS-CoV-2 fitness".
DOI: 10.6084/m9.figshare.13030430.v1
title: Spike mutation D614G altersSARS-CoV-2 fitness and neutralization susceptibility

description: Raw data associated with Figures 1-4, S2, and S5-S7 of "Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility".
DOI: 10.6084/m9.figshare.13071812
title: Rakhine and Shark River mangrove degradation map

description: Raster file of mapped Rakhine and Shark River mangroves degradation following the methods of Lee et al., (in review), Estimating mangrove forest degradation extent using satellite data.<br> <br>
DOI: 10.6084/m9.figshare.13071812.v1
title: Rakhine and Shark River mangrove degradation map

description: Raster file of mapped Rakhine and Shark River mangroves degradation following the methods of Lee et al., (in review), Estimating mangrove forest degradation extent using satellite data.<br> <br>
DOI: 10.21227/n1ew-zw59
title: Gaussian Blobs of Varying numbers of samples, centers and features

description: The dataset has Gaussian Blobs of varying samples, centers and features. The number of samples ranges from 500 to 50,000. Similarly, the number of centers varies from 2 to 100, while the number of features varies from 2 to 2048. These different sets of Gaussian blobs can be used for testing clustering algorithms for their scalability and effectiveness.The filename of each gaussian blob inside compressed sets gives a sketch of the blob. For example, the file s50000_c50_f2048_X.csv contains 50,000 samples of data that have 2048 dimensions (features) with 50 centers. The blob files are organized based on their number of samples. For example, the compressed file "10,000 datapoints set.zip" contains a collection of Gaussian blobs with 10,000 samples of data with a varying number of centers and features. The documentation section has PDF documents that provide lists of files inside each compressed file.
DOI: 10.6084/m9.figshare.13071824
title: Supplementary Material for: Lipid-Producing Ciliochoroidal Melanoma with Expression of HMG-CoA Reductase

description: Uveal melanoma (UM) is the commonest primary intraocular malignancy in adults. There is limited published data on lipid production in UM. Here, we describe the clinical, histological, immunohistochemical, and molecular findings in a ciliochoroidal melanoma with lipid production and expression of the enzyme HMG-CoA reductase. This case highlights an unusual UM tumour phenotype with a high-risk molecular metastatic profile and discusses tumour lipogenesis and activation of the mevalonate pathway as a potential therapeutic target in managing lipidised ciliochoroidal UM.
DOI: 10.21227/x9zy-m436
title: Gaussian Blobs of Varying numbers of samples, centers and features

description: The dataset has Gaussian Blobs of varying samples, centers and features. The number of samples ranges from 500 to 50,000. Similarly, the number of centers varies from 2 to 100, while the number of features varies from 2 to 2048. These different sets of Gaussian blobs can be used for testing clustering algorithms for their scalability and effectiveness.The filename of each gaussian blob inside compressed sets gives a sketch of the blob. For example, the file s50000_c50_f2048_X.csv contains 50,000 samples of data that have 2048 dimensions (features) with 50 centers, and the s50000_c50_f2048_y.csv is the associated class data of the file s50000_c50_f2048_X.csv. The blob files are organized based on their number of samples. For example, the compressed file "10,000 datapoints set.zip" contains a collection of Gaussian blobs with 10,000 samples of data with a varying number of centers and features. The documentation section has PDF documents that provide lists of files inside each compressed file.
DOI: 10.21227/4pea-v635
title: Gaussian Blobs of Varying numbers of samples, centers and features

description: The dataset has Gaussian Blobs of varying samples, centers and features. The number of samples ranges from 500 to 50,000. Similarly, the number of centers varies from 2 to 100, while the number of features varies from 2 to 2048. These different sets of Gaussian blobs can be used for testing clustering algorithms for their scalability and effectiveness. There are two kinds of files inside the compressed sets. Files ending with "_X.csv" consist of datapoints, while the files ending with "_y.csv" represent respective class data.The filename of each gaussian blob inside compressed sets gives a sketch of the blob. For example, the file "s50000_c50_f2048_X.csv" contains 50,000 samples of data that have 2048 dimensions (features) with 50 centers, and the file "s50000_c50_f2048_y.csv" is the associated class data of the file "s50000_c50_f2048_X.csv". The blob files are organized based on their number of samples. For example, the compressed file "10,000 datapoints set.zip" contains a collection of Gaussian blobs with 10,000 samples of data with a varying number of centers and features. The documentation section has PDF documents that provide lists of files inside each compressed file.
DOI: 10.21227/vnk1-7p08
title: Gaussian Blobs of Varying numbers of samples, centers and features

description: The dataset has Gaussian Blobs of varying samples, centers and features. The number of samples ranges from 500 to 50,000. Similarly, the number of centers varies from 2 to 100, while the number of features varies from 2 to 2048. These different sets of Gaussian blobs can be used for testing clustering algorithms for their scalability and effectiveness. There are two kinds of files inside the compressed sets. Files ending with "_X.csv" consist of datapoints, while the files ending with "_y.csv" represent respective class data.The filename of each gaussian blob inside compressed sets gives a sketch of the blob. For example, the file "s50000_c50_f2048_X.csv" contains 50,000 samples of data that have 2048 dimensions (features) with 50 centers, and the file "s50000_c50_f2048_y.csv" is the associated class data of the file "s50000_c50_f2048_X.csv". The blob files are organized based on their number of samples. For example, the compressed file "10,000 datapoints set.zip" contains a collection of Gaussian blobs with 10,000 samples of data with a varying number of centers and features. The documentation section has PDF documents that provide lists of files inside each compressed file.
DOI: 10.6084/m9.figshare.7906757
title: Umbilical cord coiling index for the prediction of adverse pregnancy outcomes: a meta-analysis and sequential analysis

description: <b>Purpose:</b> To evaluate the potential association of abnormal cord coiling with adverse pregnancy outcomes. <b>Materials and methods:</b> We used the Medline (1966–2018), Scopus (2004–2018), Clinicaltrials.gov (2008–2018), Embase (1980–2018), Cochrane Central Register of Controlled Trials CENTRAL (1999–2018), and Google Scholar (2004–2018) databases. The date of last search was set on 31 May 2018. Language, country, or date restrictions were not applied during the literature research to prevent bias. All observational (both prospective and retrospective) studies that reported maternal and neonatal antenatal and perinatal outcomes based on the umbilical coiling index (UCI) status were considered as eligible for inclusion. Meta-analysis of the risk ratio (RR) and mean differences (MD) among hypocoiled/hypercoiled and normocoiled cases was performed with RevMan 5.3 software. Univariate metaregression and leave-one-out meta-analysis was performed with Open Meta-Analyst statistical software. Trial sequential analysis was performed with the trial sequential analysis (TSA) software. <b>Results:</b> Twenty four studies were finally included that involved 9553 pregnant women. Umbilical cord coiling was evaluated with the use of the umbilical coiling index (UCI). Values of the UCI below the 10th percentile were evaluated as hypocoiled and above the 90th percentile as hypercoiled. Hypocoiled cords were significantly associated with increased prevalence of preterm birth <b>Conclusions:</b> The findings of our meta-analysis underline the correlation of UCI abnormalities with antenatal and perinatal pathology. More studies are needed, however, to elucidate whether antenatal assessment of the UCI can be used as routine in clinical practice as well as its value in uncomplicated pregnancies.