cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/105912
title: Meteorological Station data collected during research cruise SAV-10-33 using a RMYoung 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105911
title: Singlebeam Echosounder data collected during research cruise SAV-10-33 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105913
title: TSG (Thermosalinograph) data collected during research cruise SAV-10-33 using a SeaBird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105954
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SAV-10-41 using a RDI WM-300 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105958
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SAV-10-41 using a SeaBird SBE-25 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105953
title: Gyrocompass data collected during research cruise SAV-10-41 using a Yokogawa CMZ700B instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105956
title: Meteorological Station data collected during research cruise SAV-10-41 using a RMYoung 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105955
title: Singlebeam Echosounder data collected during research cruise SAV-10-41 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/105957
title: TSG (Thermosalinograph) data collected during research cruise SAV-10-41 using a SeaBird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.15131/shef.data.20393481
title: Living With Data: Qualitative data (focus groups, interviews)

description: <em>Living With Data </em>(https://livingwithdata.org/current-research) was a research project funded by The Nuffield Foundation. It aimed to understand people’s perceptions of how data about them is collected, analysed, shared and used, and how these processes could be improved. The term ‘data uses’ was used as a short and accessible way of talking to people about these processes. The Living With Data website includes a full description of the research aims and of the methods used, and links to all publications that resulted from the project. Links to the visualisations we used in our interviews and focus group research can be found here: https://livingwithdata.org/resources. We have consent to share our qualitative data with authorised researchers only. Please send your request to Professor Helen Kennedy (h.kennedy@sheffield.ac.uk) explaining why you are interested in accessing the data and your institutional/researcher affiliation.
DOI: 10.15131/shef.data.20393481.v2
title: Living With Data: Qualitative data (focus groups, interviews)

description: <em>Living With Data </em>(https://livingwithdata.org/current-research) was a research project funded by The Nuffield Foundation. It aimed to understand people’s perceptions of how data about them is collected, analysed, shared and used, and how these processes could be improved. The term ‘data uses’ was used as a short and accessible way of talking to people about these processes. The Living With Data website includes a full description of the research aims and of the methods used, and links to all publications that resulted from the project. Links to the visualisations we used in our interviews and focus group research can be found here: https://livingwithdata.org/resources. We have consent to share our qualitative data with authorised researchers only. Please send your request to Professor Helen Kennedy (h.kennedy@sheffield.ac.uk) explaining why you are interested in accessing the data and your institutional/researcher affiliation.
DOI: 10.15131/shef.data.20393481.v1
title: Living With Data: Qualitative data (focus groups, interviews)

description: <em>Living With Data </em>(https://livingwithdata.org/current-research) was a research project funded by The Nuffield Foundation. It aimed to understand people’s perceptions of how data about them is collected, analysed, shared and used, and how these processes could be improved. The term ‘data uses’ was used as a short and accessible way of talking to people about these processes. The Living With Data website includes a full description of the research aims and of the methods used, and links to all publications that resulted from the project. Links to the visualisations we used in our interviews and focus group research can be found here: https://livingwithdata.org/resources. We have consent to share our qualitative data with authorised researchers only. Please send your request to Professor Helen Kennedy (h.kennedy@sheffield.ac.uk) explaining why you are interested in accessing the data and your institutional/researcher affiliation.
DOI: 10.6069/qx9d-dj90
title: Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood Specimens

description: National screening programs use dried blood specimens to detect abnormal metabolism or aberrant protein function in infants shortly after birth, thus identifying disorders that are not clinically evident in the newborn period. Gut microbiota metabolites and immunological acute phase proteins are capable of revealing potential immune aberrations. Microbial metabolites interact with xenobiotic receptors (i.e., aryl hydrocarbon and pregnane-X) and maintain gastrointestinal tissue health, supported by acute-phase proteins, functioning as sensors of microbial immunomodulation and homeostasis. The delivery mode (vaginal or cesarean section) shapes the microbial colonization, which substantially modulates both the immune system's response and mucosal homeostasis. 
This study profiled microbial metabolites of the kynurenine and tryptophan pathway and acute phase proteins in 134 neonatal dried blood specimens. We newly established neonatal blood levels of the aryl hydrocarbon receptor microbial ligands (indole-3-aldehyde, indole-3-butyric acid, and indole-3-acetamide) on the second day of life. Furthermore, we observed divergent microbial metabolic profiles in neonates born vaginally or via cesarean section, hypothesizing potential microbial immunomodulatory influence. In summary, these findings suggest the supportive role of human gut microbiota in developing and maintaining immune system homeostasis.
DOI: 10.34740/kaggle/dsv/4021823
title: US counties COVID 19 dataset
DOI: 10.6084/m9.figshare.14893002
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2019/1

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.14893041
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2019/2

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.14893002.v1
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2019/1

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.14893041.v1
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2019/2

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.14338883
title: Illumina reads analysis of Vibrio alfacsensis pSEA2-free strain LN95

description: Illumina reads of Vibrio alfacsensis pSEA2-free strain LN95 were used to confirm the loss of plasmid pSEA2 from strain 04Ya249. These reads were also used in search for the circular form of Tn6945, but it was not detected.<br><br>bam and bai files were posted in figshare to view mapping results in Tablet or IGV.<br><br># result of mapping to 04Ya249_submission.fas<br>LN95_04Ya249_mapped.sort.bam<br>LN95_04Ya249_mapped.sort.bam.bai<br><br># result of mapping to "att_seqs_04Ya249.fas"<br>LN95_atts_mapped.sort.bam<br>LN95_atts_mapped.sort.bam.bai<br>terminal commands, input files used for mapping and coverage analysis results were also posted. Illumina fastq files are available under SRA/DRA accession number DRA011762 .<br><br>The following two files are Sanger sequencing trace files of PCR-amplifed attTn from strain 04Ya249 genomic DNA.<br>attTn_type1_04Ta249-LN127-128-10_H10_016.ab1 <br>attTn_type2_04Ta249-LN127-128-9_G10_014.ab1<br>
DOI: 10.6084/m9.figshare.20371740
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2022

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.20371740.v2
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2022

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.20371740.v1
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2022

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.13332467
title: Complete genome of transconjugant TJ249

description: Complete genome sequence of transconjugant TJ249. <br>TJ249_pac.fasta.zip is read file from PacBio RSII. flye_assmbly.zip is flye output. <br>TJ249_flye_assembly_contig2.gb (IS and AMR genes derived from pSEA2) and TJ249_flye_assembly_contig1.gb (chromosome) are Genbank files for two circular contigs annotated by DFAST (https://dfast.ddbj.nig.ac.jp/).<br>fastq files are available from Sequence Read Archive accession number DRA013462.
DOI: 10.7284/103282
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise W0907A using a Hawaii UHDAS instrument system onboard the platform RV Wecoma

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103283
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise W0907A using a SeaBird SBE-911+ instrument system onboard the platform RV Wecoma

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103281
title: Singlebeam Echosounder data collected during research cruise W0907A using a Knudsen 3260 instrument system onboard the platform RV Wecoma

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.20422248
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2022

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.6084/m9.figshare.20422248.v1
title: Cartografia das narrativas dos casos de violência contra a mulher no Brasil em 2022

description: Através das coletas de publicações e suas posteriores análises, foi possível identificar as percepções dos usuários sobre a violência contra a mulher, quais os usuários influenciadores e a análise semântica a partir de redes de hashtags e palavras presentes nos tweets coletados. Além de aprofundar os estudos sobre violência contra a mulher, foi observado o impacto do uso de redes sociais digitais como território de compartilhamento de informações, experiências e relatos.
DOI: 10.26180/20422257
title: Data File: A Cluster-Randomised Controlled Trial of a Mental Health Literacy Program for Community Sport Leaders

description: Data set for paper: A Cluster-Randomised Controlled Trial of a Mental Health Literacy Program for Community Sport Leaders
DOI: 10.26180/20422257.v1
title: Data File: A Cluster-Randomised Controlled Trial of a Mental Health Literacy Program for Community Sport Leaders

description: Data set for paper: A Cluster-Randomised Controlled Trial of a Mental Health Literacy Program for Community Sport Leaders
DOI: 10.6084/m9.figshare.20422254
title: Tree and scripts used for biogeography and other downstream analysis

description: This tree was used to reconstruct the ancestral biogeography and estimate divergence times
DOI: 10.6084/m9.figshare.20422254.v1
title: Tree used for biogeography and other downstream analysis

description: This tree was used to reconstruct the ancestral biogeography and estimate divergence times
DOI: 10.34740/kaggle/dsv/4021889
title: Tales from the Pizza Guy
DOI: 10.6084/m9.figshare.20383014.v6
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.6084/m9.figshare.20383014.v7
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.6084/m9.figshare.20383014.v8
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.