cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6964805
title: Datasets and experiment data of long read alignment using partitioned reference indexes

description: Directories inside this zip file are,<br>--synthetic_reads This directory contains the datasets, scripts and the generated experimental data of the mapping evaluation based on synthetic reads. <br>--chromothriptic_read This directory contains the datasets, scripts and the generated experimental data of the mapping evaluation based on the ultra-long Nanopore chromothriptic read.<br>--nanopore_NA12878_reads This directory contains the scripts and the generated experimental data of the mapping evaluation based on the Nanopore NA12878 reads. The input read set is not included as it is publicly available from http://s3.amazonaws.com/nanopore-human-wgs/rel3-nanopore-wgs-84868110-FAF01132.fastq.gz<br>--indexing_memory_usage Contains the scripts (and their outputs) used to evaluate the peak memory usage of minimap2 with and without chromosome size balancing of the index.<br>--runtimeContains the scripts (and their outputs) used to measure the runtime of a single-idx vs n-part-idx-merged<br> <br><b>See the README.txt in the zip file for more information.</b><br><br>
DOI: 10.6084/m9.figshare.6964715
title: Negoro-Cartilage_processed data.xlsx

description: Focal and degenerative lesions of articular cartilage greatly reduce the patient’s quality of life. Various therapies including surgical treatment have been developed, but a definitive therapy is not yet known. Several cell therapy products have already been developed and are available in the market. In this study, we examined the clinical research trends related to cell therapy products in the cartilage repair field based on data obtained from the ClinicalTrial.gov website. Although this website does not provide comprehensive results of clinical trials, it offers information on prospective clinical trials, including work in progress, and thus allows for chronological analysis of the data. We selected 203 studies related to the field of cartilage regeneration from ClinicalTrial.gov. The results showed a shift in the clinical translational trend in utilized cells from cartilage- and bone marrow- to adipose tissue-based cells. Whereas the studies that used cartilage as the cell source included many Phase III trials, fewer studies using bone marrow and adipose tissue cells progressed to Phase III, suggesting that most clinical developments using the latter sources have not been successful so far. One product covered the entire period from the start of Phase I to the completion of Phase III, with a time to completion of more than 100 months. Translational trends in autologous chondrocyte implantation were also discussed. The use of ClinicalTrials.gov as the sole data source can yield a perspective view of the global clinical translational trends, which has been difficult to observe up to this point.
DOI: 10.6084/m9.figshare.6964640
title: objective NA=0.36.zmx

description: This is a Zemax design file of a objective with a NA of 0.36, it can be adopted in cold atom physics.
DOI: 10.6084/m9.figshare.6964604
title: Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

description: Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, <i>via</i> rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally ‘reset’ by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability.
DOI: 10.6084/m9.figshare.6964604.v1
title: Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

description: Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, <i>via</i> rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally ‘reset’ by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability.
DOI: 10.6084/m9.figshare.6964604.v2
title: Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

description: Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, <i>via</i> rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally ‘reset’ by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability.
DOI: 10.6084/m9.figshare.6964550
title: Supplementary data of article: The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae)

description: Supplementary_data_1: Gff3 files contained predicted gene set information by AUGUSTUS-3.2.2.Supplementary_data_2:The multi fasta file containing sequences the predicted genes based on the gff3 file indicates.<br>Supplementary_data_3:The multi fasta file containing traslated amino acid sequences of the predicted genes by AUGUSTUS-3.2.2.<br>Supplementary_data_4:Raw output results byBlast2GO version 5.1.12 of the predicted gene set.<br>Supplementary_data_5:Detailed results of RepeatMasker (version open-4.0.5 with Apis mellifera sequence library in Repbase 20160829 update version with RMBlastn version 2.2.27+)<br>Supplementary_data_6:All detailed results of orthologous search Toll and IMD pathway genes.<br>
DOI: 10.6084/m9.figshare.6964550.v1
title: Supplemental data

description: Supplemental_data_1: Gff3 files contained predicted gene set information by AUGUSTUS-3.2.2.Supplemental_data_2:The multi fasta file containing sequences the predicted genes based on the gff3 file indicates.<br>Supplemental_data_3:The multi fasta file containing traslated amino acid sequences of the predicted genes by AUGUSTUS-3.2.2.<br>Supplemental_data_4:Raw output results byBlast2GO version 5.1.12 of the predicted gene set.<br>Supplemental_data_5:Detailed results of RepeatMasker (version open-4.0.5 with Apis mellifera sequence library in Repbase 20160829 update version with RMBlastn version 2.2.27+)<br>Supplemental_data_6:All detailed results of orthologous search Toll and IMD pathway genes.<br>
DOI: 10.6084/m9.figshare.6964550.v2
title: Supplementary data

description: Supplementary_data_1: Gff3 files contained predicted gene set information by AUGUSTUS-3.2.2.Supplementary_data_2:The multi fasta file containing sequences the predicted genes based on the gff3 file indicates.<br>Supplementary_data_3:The multi fasta file containing traslated amino acid sequences of the predicted genes by AUGUSTUS-3.2.2.<br>Supplementary_data_4:Raw output results byBlast2GO version 5.1.12 of the predicted gene set.<br>Supplementary_data_5:Detailed results of RepeatMasker (version open-4.0.5 with Apis mellifera sequence library in Repbase 20160829 update version with RMBlastn version 2.2.27+)<br>Supplementary_data_6:All detailed results of orthologous search Toll and IMD pathway genes.<br>
DOI: 10.6084/m9.figshare.6964550.v3
title: Supplementary data of article: The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae)

description: Supplementary_data_1: Gff3 files contained predicted gene set information by AUGUSTUS-3.2.2.Supplementary_data_2:The multi fasta file containing sequences the predicted genes based on the gff3 file indicates.<br>Supplementary_data_3:The multi fasta file containing traslated amino acid sequences of the predicted genes by AUGUSTUS-3.2.2.<br>Supplementary_data_4:Raw output results byBlast2GO version 5.1.12 of the predicted gene set.<br>Supplementary_data_5:Detailed results of RepeatMasker (version open-4.0.5 with Apis mellifera sequence library in Repbase 20160829 update version with RMBlastn version 2.2.27+)<br>Supplementary_data_6:All detailed results of orthologous search Toll and IMD pathway genes.<br>
DOI: 10.7284/113494
title: Fluorometer data collected during research cruise AE1025 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119083
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise TN319 using a Hawaii UHDAS instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121076
title: Anemometer data collected during research cruise TN319 using a RM Young 06206 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119085
title: Expendable Probe data collected during research cruise TN319 using a Sippican MK21 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119088
title: Gravimeter data collected during research cruise TN319 using a Bell BGM-3 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6964127
title: Additional file 3: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S2. List of 182 variants identified in 32 isolates (after excluding unrelated strains). (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6964133
title: Additional file 4: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S3. List of 81 mutations with predicted modification of protein sequences with COG annotation. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6964133.v1
title: Additional file 4: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S3. List of 81 mutations with predicted modification of protein sequences with COG annotation. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6964127.v1
title: Additional file 3: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S2. List of 182 variants identified in 32 isolates (after excluding unrelated strains). (XLSX 25 kb)
DOI: 10.7284/121244
title: Gyrocompass data collected during research cruise TN319 using a Sperry MK-37 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121075
title: Meteorological Station data collected during research cruise TN319 using a RM Young 26800 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121077
title: Radiometer data collected during research cruise TN319 using a Biospherical QSR-2150 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6964103
title: Additional file 1: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S1. Microbiological data and sequence metrics of S. aureus isolates included in the study. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6964109
title: Additional file 13: of Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor

description: Ovary activation scores. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6964103.v1
title: Additional file 1: of Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

description: Table S1. Microbiological data and sequence metrics of S. aureus isolates included in the study. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6964109.v1
title: Additional file 13: of Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor

description: Ovary activation scores. (XLSX 11 kb)
DOI: 10.7284/121078
title: Radiometer data collected during research cruise TN319 using a Eppley RAD instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121245
title: SSV (Sound Speed Velocimeter) data collected during research cruise TN319 using a AML SV&T instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119140
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise TN328 using a Hawaii UHDAS instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121112
title: Anemometer data collected during research cruise TN328 using a RM Young 06206 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119143
title: Expendable Probe data collected during research cruise TN328 using a Sippican MK21 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119146
title: Gravimeter data collected during research cruise TN328 using a Bell BGM-3 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6964070
title: Additional file 2: of Small area estimation of under-5 mortality in Bangladesh, Cameroon, Chad, Mozambique, Uganda, and Zambia using spatially misaligned data

description: Under-5 mortality estimates with uncertainty. (XLSX 796 kb)
DOI: 10.6084/m9.figshare.6964070.v1
title: Additional file 2: of Small area estimation of under-5 mortality in Bangladesh, Cameroon, Chad, Mozambique, Uganda, and Zambia using spatially misaligned data

description: Under-5 mortality estimates with uncertainty. (XLSX 796 kb)
DOI: 10.7284/121289
title: Gyrocompass data collected during research cruise TN328 using a Sperry MK-37 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121111
title: Meteorological Station data collected during research cruise TN328 using a RM Young 26800 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121113
title: Radiometer data collected during research cruise TN328 using a Biospherical QSR-2150 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119144
title: Singlebeam Echosounder data collected during research cruise TN328 using a Knudsen 320B/R instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5281/zenodo.4005949
title: SGB.Jul19

description: PhyloPhlAn metagenomic database "SGB.Jul19"
DOI: 10.7284/121290
title: SSV (Sound Speed Velocimeter) data collected during research cruise TN328 using a AML SV&T instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5281/zenodo.4005948
title: SGB.Jul19

description: PhyloPhlAn metagenomic database "SGB.Jul19"
DOI: 10.7284/137359
title: Gyrocompass data collected during research cruise TN348 using a Sperry NAVIGAT 3000 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/137360
title: Singlebeam Echosounder data collected during research cruise TN348 using a Knudsen 3260 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/137357
title: Gravimeter data collected during research cruise TN350 using a Bell BGM-3 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132938
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise TN354 using a Hawaii UHDAS instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132933
title: GNSS (Global Navigation Satellite System) data collected during research cruise TN354 using a C&C C-Nav 3050 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132944
title: Gyrocompass data collected during research cruise TN354 using a Sperry NAVIGAT 3000 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132934
title: Radiometer data collected during research cruise TN354 using a Biospherical QSR-2150 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6963983
title: Additional file 2: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

description: Figure S1. CRISPR-KO screening data quality assessment. (A) Average correlation between sgRNAs read-count replicates across cell lines. (B) Receiver operating characteristic (ROC) curve obtained from classifying fitness essential (FE) and non-essential genes based on the average logFC of their targeting sgRNAs. An example cell line OVCAR-8 is shown. (C) Area under the ROC (AUROC) curve obtained for cell lines from classifying FE and non-essential genes based on the average logFC of their targeting sgRNAs. (D) Recall for sets of a priori known essential genes from MSigDB and from literature when classifying FE and non-essential genes across cell lines (5% FDR). Each circle represents a cell line and coloured by tissue type. Box and whisker plots show median, inter-quartile ranges and 95% confidence intervals. (E) Genes ranked based on the average logFC of targeting sgRNAs for OVCAR-8 and enrichment of genes belonging to predefined sets of a priori known essential genes from MSigDB, at an FDR equal to 5% when classifying FE (second last column) and non-essential genes (last column). Blue numbers at the bottom indicate the classification true positive rate (recall). Figure S2. Assessment of copy number bias before and after CRISPRcleanR correction across cell lines. sgRNA logFC values before and after CRISPRcleanR for eight cell lines are shown classified based on copy number (amplified or deleted) and expression status. Copy number segments were identified using Genomics of Drug Sensitivity in Cancer (GDSC) and Cell Line Encyclopedia (CCLE) datasets. Box and whisker plots show median, inter-quartile ranges and 95% confidence intervals. Asterisks indicate significant associations between sgRNA LogFC values (Welchs t-test, p
DOI: 10.6084/m9.figshare.6963977
title: Additional file 1: of Population-level factors associated with maternal mortality in the United States, 1997â 2012

description: Technical Appendix. Contains a variable dictionary, results of our single predictor regression analyses, pairwise correlation of the variables listed in TableÂ 1, and results from our final model regression analysis. (TXT 19 kb)
DOI: 10.7284/132935
title: Radiometer data collected during research cruise TN354 using a Eppley RAD instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition