cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7679948
title: Genome of Xenoturbella bocki

description: A denovo draft assembly of the genome of Pseudaphanostoma variabilis. <br>Assembled with Soapdenovo2. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .CDS2 and peptide2 files are predicitions of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads
DOI: 10.7284/130669
title: Meteorological Station data collected during research cruise AT40-01 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679930
title: The information of the differentially expressed genes (DEGs) between samples

description: The information of the differentially expressed genes (DEGs) between samples
DOI: 10.6084/m9.figshare.7679933
title: GeneExpression.rar

description: gene expression of three cultivars at three developing stages
DOI: 10.6084/m9.figshare.7679936
title: Transcriptome of Xenoturbella bocki from a single egg

description: A denovo assembly of the transcriptome of Xenoturbella bocki from a single egg.<br>Assembled with SoapTrans. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .nuc and .prot files are translations of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.6084/m9.figshare.7679915
title: Transcriptome of Symsagittifera roscoffensis embryo pool

description: A denovo assembly of the transcriptome of whole animals of of Pseudaphanostoma variabilis, 2 versions. <br>Assembled with SoapTrans. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.6084/m9.figshare.7679930.v1
title: The information of the differentially expressed genes (DEGs) between samples

description: The information of the differentially expressed genes (DEGs) between samples
DOI: 10.6084/m9.figshare.7679936.v1
title: Transcriptome of Xenoturbella bocki from a single egg

description: A denovo assembly of the transcriptome of Xenoturbella bocki from a single egg.<br>Assembled with SoapTrans. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .nuc and .prot files are translations of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.7284/130673
title: Multibeam Echosounder data collected during research cruise AT40-01 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679933.v1
title: GeneExpression.rar

description: gene expression of three cultivars at three developing stages
DOI: 10.6084/m9.figshare.7679885
title: Supplementary Material for: Unmet Medical Needs in Ulcerative Colitis: An Expert Group Consensus

description: <b><i>Background:</i></b> The authors aimed to conduct an extensive literature review and consensus meeting to identify unmet needs in ulcerative colitis (UC) and ways to overcome them. UC is a relapsing and remitting inflammatory bowel disease with varied, and changing, incidence rates worldwide. UC has an unpredictable disease course and is associated with a high health economic burden. During 2016 and 2017, a panel of experts was convened to identify, discuss and address areas of unmet need in UC. <b><i>Methods:</i></b> PubMed and Cochrane Library databases were searched for relevant articles describing studies performed in patients with UC. These findings were used to generate a set of statements relating to unmet needs in UC. Consensus on these statements was then sought from a panel of 9 expert gastroenterologists using a modified Delphi review process that consisted of anonymous surveys followed by live meetings. <b><i>Results:</i></b> In 2 literature reviews, over 5,000 unique records were identified and a total of 138 articles were fully reviewed. These were used to consider 26 areas of unmet need, which were explored in 2 face-to-face meetings, in which the statements were debated and amended, resulting in consensus on 30 final statements. The unmet needs identified were categorised into 7 areas: impact of UC on patients’ daily life; importance of early diagnosis and treatment; drawbacks of existing treatments; urgent need for new treatments; and disease-, practice- or patient-focused unmet needs. <b><i>Conclusions:</i></b> These expert group meetings found a number of areas of unmet needs in UC, which is an important first step in tackling them in the future. Future research and development should be focused in these areas for the management of patients with UC.
DOI: 10.6084/m9.figshare.7679915.v1
title: Transcriptome of Symsagittifera roscoffensis embryo pool

description: A denovo assembly of the transcriptome of whole animals of of Pseudaphanostoma variabilis, 2 versions. <br>Assembled with SoapTrans. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.6084/m9.figshare.7679882
title: Table S2

description: <b>Table S2. </b>Timings of puberty events and their associations with zBMI in girls
DOI: 10.6084/m9.figshare.7679933.v2
title: GeneExpression.rar

description: gene expression of three cultivars at three developing stages
DOI: 10.6084/m9.figshare.7679882.v1
title: Table S2

description: <b>Table S2. </b>Timings of puberty events and their associations with zBMI in girls
DOI: 10.7284/130674
title: Multibeam Echosounder data collected during research cruise AT40-01 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679852
title: Genome of Meara stichopi

description: denovo draft assembly of the genome of Meara stichopi. <br>Assembled with Soapdenovo2. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .CDS2 and peptide2 files are predicitions of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.25375/uct.7679843
title: Co-disposal Packing Protocols

description: Dataset to:<br>Mjonono, D., Harrison, S.T.L., Kotsiopoulos, A., (2019). Supplementing structural integrity of waste rock piles through improved packing protocols to aid acid rock drainage prevention strategies. Minerals Engineering 135, 13–20. <br><br>https://doi.org/10.1016/j.mineng.2019.02.029<br>
DOI: 10.6084/m9.figshare.7679852.v1
title: Genome of Meara stichopi

description: denovo draft assembly of the genome of Meara stichopi. <br>Assembled with Soapdenovo2. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .CDS2 and peptide2 files are predicitions of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.7284/130668
title: Radiometer data collected during research cruise AT40-01 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679837
title: Transcriptome of Pseudaphanostoma variabilis

description: A denovo assembly of the transcriptome of whole animals of of Pseudaphanostoma variabilis. <br>Assembled with SoapTrans. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .nuc and .prot files are translations of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.25375/uct.7679843.v1
title: Co-disposal Packing Protocols

description: Dataset to:<br>Mjonono, D., Harrison, S.T.L., Kotsiopoulos, A., (2019). Supplementing structural integrity of waste rock piles through improved packing protocols to aid acid rock drainage prevention strategies. Minerals Engineering 135, 13–20. <br><br>https://doi.org/10.1016/j.mineng.2019.02.029<br>
DOI: 10.6084/m9.figshare.7679825
title: Genome of Pseudaphanostoma variabilis

description: A denovo draft assembly of the genome of Pseudaphanostoma variabilis. <br>Assembled with Soapdenovo2. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .CDS2 and peptide2 files are predicitions of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.7284/130671
title: Water Temperature data collected during research cruise AT40-01 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679825.v1
title: Genome of Pseudaphanostoma variabilis

description: A denovo draft assembly of the genome of Pseudaphanostoma variabilis. <br>Assembled with Soapdenovo2. Assembled sequence file is .scafSeq. <br>Sequence length cutoff used was 100bp. The .scaf.Statistics files contain statistics of the assembly. <br>The .CDS2 and peptide2 files are predicitions of coding nucleotides and peptides. <br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads.
DOI: 10.6084/m9.figshare.7679819
title: Proteogam02_Supplementary File 4_Transrate results.xlsx

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. Quality assessment of transcriptomes was done with Transrate v1.0.1 which generates standard metrics and remapping statistics.
DOI: 10.7284/130670
title: TSG (Thermosalinograph) data collected during research cruise AT40-01 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679801
title: Proteogam02_Supplementary File 3_Transcript annotation.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. For each sample the transcripts were annotated using the Trinotate annotation pipeline43. Swissprot database was used as main database and Amphipods proteins referenced on Uniref were used as custom database. Blastx and Blastp were used for the similarity search step with an e-value cutoff set at 1e-2. Blast results were then used for generate the annotation report with the same e-value cutoff.
DOI: 10.6084/m9.figshare.7679819.v2
title: Proteogam02_Supplementary File 4_Transrate results.xlsx

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. Quality assessment of transcriptomes was done with Transrate v1.0.1 which generates standard metrics and remapping statistics.
DOI: 10.7284/131011
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT41 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679801.v2
title: Proteogam02_Supplementary File 3_Transcript annotation.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. For each sample the transcripts were annotated using the Trinotate annotation pipeline43. Swissprot database was used as main database and Amphipods proteins referenced on Uniref were used as custom database. Blastx and Blastp were used for the similarity search step with an e-value cutoff set at 1e-2. Blast results were then used for generate the annotation report with the same e-value cutoff.
DOI: 10.6084/m9.figshare.7679801.v1
title: Proteogam02_Supplementary File 3_Transcript annotation.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. For each sample the transcripts were annotated using the Trinotate annotation pipeline43. Swissprot database was used as main database and Amphipods proteins referenced on Uniref were used as custom database. Blastx and Blastp were used for the similarity search step with an e-value cutoff set at 1e-2. Blast results were then used for generate the annotation report with the same e-value cutoff.
DOI: 10.7284/131021
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT41 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679780
title: Proteogam02_Supplementary File 2_Translated ORFs.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni and Echinogammarus marinus. Translations of coding sequence regions were produced for each transcriptome by Transdecoder from stop to stop codons, analysing only top strand with 500 top longest ORFs used for training, and retaining 600 base pair ORFs and only proteins with a minimum length of 50 amino acids. <br>
DOI: 10.7284/131019
title: Fluorometer data collected during research cruise AT41 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679780.v2
title: Proteogam02_Supplementary File 2_Translated ORFs.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni and Echinogammarus marinus. Translations of coding sequence regions were produced for each transcriptome by Transdecoder from stop to stop codons, analysing only top strand with 500 top longest ORFs used for training, and retaining 600 base pair ORFs and only proteins with a minimum length of 50 amino acids. <br>
DOI: 10.7284/131010
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT41 using a C&C C-Nav 3050 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/131014
title: Gravimeter data collected during research cruise AT41 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/131012
title: Meteorological Station data collected during research cruise AT41 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679726
title: Supplementary Material for: Risk Factors for Mortality in <b><i>Pneumocystis jirovecii</i></b> Pneumonia in Patients with Inflammatory Bowel Disease

description: <b><i>Background:</i></b> <i>Pneumocystis jirovecii</i> pneumonia (PJP) is highly fatal once infection is established. In this study, we investigated the risk of PJP mortality in patients with inflammatory bowel disease (IBD). <b><i>Methods:</i></b> We conducted a retrospective observational study of case data from IBD patients who developed PJP, compiled from 17 collaborating institutions. Parameters such as age, sex, medications used, and blood test results were analyzed to identify risk factors for mortality. <b><i>Results:</i></b> The mortality rate among the 28 IBD patients who developed PJP was 17.9%. A low serum albumin level at the start of IBD treatment was identified as a risk factor for mortality and showed the following association with probability of death (<i>P</i>): <i>P</i> = 1/[1 + exp(–5.5 + 2.4 × Alb). The probability of death exceeded 0.5 when serum albumin was 2.2 g/dL or lower. <b><i>Conclusion:</i></b> Patients with IBD who develop PJP have a high mortality rate and often cannot continue treatment with medication alone. Therefore, it is necessary to pay attention to albumin levels at the start of immunosuppressive therapy when creating a treatment plan.
DOI: 10.7284/131016
title: Meteorological Station data collected during research cruise AT41 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679726.v1
title: Supplementary Material for: Risk Factors for Mortality in <b><i>Pneumocystis jirovecii</i></b> Pneumonia in Patients with Inflammatory Bowel Disease

description: <b><i>Background:</i></b> <i>Pneumocystis jirovecii</i> pneumonia (PJP) is highly fatal once infection is established. In this study, we investigated the risk of PJP mortality in patients with inflammatory bowel disease (IBD). <b><i>Methods:</i></b> We conducted a retrospective observational study of case data from IBD patients who developed PJP, compiled from 17 collaborating institutions. Parameters such as age, sex, medications used, and blood test results were analyzed to identify risk factors for mortality. <b><i>Results:</i></b> The mortality rate among the 28 IBD patients who developed PJP was 17.9%. A low serum albumin level at the start of IBD treatment was identified as a risk factor for mortality and showed the following association with probability of death (<i>P</i>): <i>P</i> = 1/[1 + exp(–5.5 + 2.4 × Alb). The probability of death exceeded 0.5 when serum albumin was 2.2 g/dL or lower. <b><i>Conclusion:</i></b> Patients with IBD who develop PJP have a high mortality rate and often cannot continue treatment with medication alone. Therefore, it is necessary to pay attention to albumin levels at the start of immunosuppressive therapy when creating a treatment plan.
DOI: 10.6084/m9.figshare.7679720
title: Proteogam02_Supplementary File 1_QC.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. Control quality of reads was performed by FastQC version V0.11.2.
DOI: 10.7284/131020
title: Multibeam Echosounder data collected during research cruise AT41 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679720.v1
title: Proteogam02_Supplementary File 1_QC.zip

description: We sequenced the transcriptomes of a male individual and a female individual for seven different taxonomical groups: <i>Gammarus fossarum A, G. fossarum B, G. fossarum C</i>, <i>Gammarus wautieri</i>, <i>Gammarus pulex</i>, <i>Echinogammarus berilloni</i> and <i>Echinogammarus marinus</i>. Control quality of reads was performed by FastQC version V0.11.2.
DOI: 10.7284/131022
title: Multibeam Echosounder data collected during research cruise AT41 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679687
title: High quality genome map of Sousa chinensis annotation file

description: The annotation result for Sousa chinensis genome
DOI: 10.7284/131015
title: Radiometer data collected during research cruise AT41 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679660
title: Class corpora per project

description: The data includes a collection of corpora of Java classes for object-oriented software projects.
DOI: 10.7284/131013
title: Singlebeam Echosounder data collected during research cruise AT41 using a Knudsen 3260 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.21253/dmu.7679690.v1
title: D1.1 Case studies

description: The SHERPA consortium looked at ten case studies that would give a broad overview of the many<br>ethical issues faced in current use and implementation of smart information systems (artificial<br>intelligence and Big Data). Smart information systems (SIS) offer businesses, governments,<br>customers, and society as a whole, great potential and opportunity to increase profits, automate<br>tedious jobs, improve services, and create advancements in knowledge and innovation. However,<br>there are also many potential issues and concerns raised with emerging technologies. SIS are having<br>a profound ability to shape and change the way we interact with the world and it is important to<br>identify ethical issues being faced in different social domains.<br>
DOI: 10.7284/131018
title: Water Temperature data collected during research cruise AT41 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.21253/dmu.7679690.v2
title: D1.1 Case studies

description: The SHERPA consortium looked at ten case studies that would give a broad overview of the many<br>ethical issues faced in current use and implementation of smart information systems (artificial<br>intelligence and Big Data). Smart information systems (SIS) offer businesses, governments,<br>customers, and society as a whole, great potential and opportunity to increase profits, automate<br>tedious jobs, improve services, and create advancements in knowledge and innovation. However,<br>there are also many potential issues and concerns raised with emerging technologies. SIS are having<br>a profound ability to shape and change the way we interact with the world and it is important to<br>identify ethical issues being faced in different social domains.<br>
DOI: 10.6084/m9.figshare.7679660.v2
title: Class corpora per project

description: The data includes a collection of corpora of Java classes for object-oriented software projects.
DOI: 10.6084/m9.figshare.7679660.v1
title: Class corpora per project

description: The data includes a collection of corpora of Java classes for object-oriented software projects.