cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1092590.v1
title: InterProScan annotations of T. amboinensis genes

description: InterProScan was used to identify protein domains encoded by all T. amboinensis genes.
DOI: 10.6084/m9.figshare.1092592.v4
title: metaseq supplemental data (ChIP-seq BAMs, BG3 Su(Hw))

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092587
title: CDS sequences of T. amboinensis genes

description: Coding sequences of all T. amboinensis genes identified in the de novo transcriptome assembly.
DOI: 10.6084/m9.figshare.1092588
title: Protein sequences of T. amboinensis genes

description: Translated protein sequences of all T. amboinensis genes identified in the de novo transcriptome assembly.
DOI: 10.6084/m9.figshare.1092589
title: Gene ontology annotations of T. amboinensis genes

description: List of GO terms associated with every T. amboinensis genes.
DOI: 10.6084/m9.figshare.1092592.v3
title: metaseq supplemental data (ChIP-seq BAMs, BG3 Su(Hw))

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1093997.v14
title: Data (i.e., evidence) about evidence based medicine

description: <strong>At a glance</strong> <em>The numbers contained in this fileset speak for themselves: evidence based medicine is broken and in crisis.</em> <strong>Fileset contents</strong> <em><strong>- Raw data (versión 1):</strong></em> Excel archive: Raw data, interactive figures, and PubMed search terms <em><strong>- </strong><strong>Figure 1.</strong> </em> Unadjusted (Fig 1A) and adjusted (Fig 1B) PubMed publication trends (01/01/1992 to 30/06/2014). <em><strong>- </strong></em><em><strong>Figure 2</strong>.</em> Adjusted PubMed publication trends (07/01/2008 to 29/06/2014) <em><strong>- Figure 3</strong>.</em> Google search trends: Jan 2004 to Jun 2014 / 1-week periods<br>URL: http://www.google.com/trends/ <em><strong>- Supplementary Figures (S1-S6).</strong> PubMed publication</em> delay in the indexation processes does not explain the descending trends in the scientific output of evidence based medicine. <strong>Acknowledgments</strong> I would like to acknowledge the following persons for providing valuable concepts in data visualization and infographics: - Maria Fernanda Ramírez. Professor of graphic design. Universidad del Valle. Cali, Colombia. - Lorena Franco. Graphic design student. Universidad del Valle. Cali, Colombia. <strong>Related articles by this author (Jorge H. Ramírez)</strong> 1. Ramirez JH. Lack of transparency in clinical trials: a call for action. Colomb Med (Cali) 2013;44(4):243-6. URL: http://www.ncbi.nlm.nih.gov/pubmed/24892242 2. Ramirez JH. Re: Evidence based medicine is broken (17 June 2014) http://www.bmj.com/node/759181 3. Ramirez JH. Re: Global rules for global health: why we need an independent, impartial WHO (19 June 2014) http://www.bmj.com/node/759151 4. Ramirez JH. PubMed publication trends (1992 to 2014): evidence based medicine and clinical practice guidelines (04 July 2014) http://www.bmj.com/content/348/bmj.g3725/rr/759895 <strong> Recommended articles</strong> 1. Greenhalgh Trisha, Howick Jeremy,Maskrey Neal. Evidence based medicine: a movement in crisis? BMJ 2014;348:g3725 2. Spence Des. Evidence based medicine is broken BMJ 2014; 348:g22 3. Schünemann Holger J, Oxman Andrew D,Brozek Jan, Glasziou Paul, JaeschkeRoman, Vist Gunn E et al. Grading quality of evidence and strength of recommendations for diagnostic tests and strategies BMJ 2008; 336:1106 4. Lau Joseph, Ioannidis John P A, TerrinNorma, Schmid Christopher H, OlkinIngram. The case of the misleading funnel plot BMJ 2006; 333:597 5. Moynihan R, Henry D, Moons KGM (2014) Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much. PLoS Med 11(7): e1001655. doi:10.1371/journal.pmed.1001655 6. Katz D. A-holistic view of evidence based medicine<br>http://thehealthcareblog.com/blog/2014/05/02/a-holistic-view-of-evidence-based-medicine/
DOI: 10.6084/m9.figshare.1092588.v1
title: Protein sequences of T. amboinensis genes

description: Translated protein sequences of all T. amboinensis genes identified in the de novo transcriptome assembly.
DOI: 10.6084/m9.figshare.1092589.v1
title: Gene ontology annotations of T. amboinensis genes

description: List of GO terms associated with every T. amboinensis genes.
DOI: 10.6084/m9.figshare.1092575
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092587.v1
title: CDS sequences of T. amboinensis genes

description: Coding sequences of all T. amboinensis genes identified in the de novo transcriptome assembly.
DOI: 10.6084/m9.figshare.1093997.v15
title: Data (i.e., evidence) about evidence based medicine

description: <strong>At a glance</strong> <em>The numbers contained in this fileset speak for themselves: evidence based medicine is broken and in crisis.</em> <strong>Fileset contents</strong> <em><strong>- Raw data (versión 1):</strong></em> Excel archive: Raw data, interactive figures, and PubMed search terms <em><strong>- </strong><strong>Figure 1.</strong> </em> Unadjusted (Fig 1A) and adjusted (Fig 1B) PubMed publication trends (01/01/1992 to 30/06/2014). <em><strong>- </strong></em><em><strong>Figure 2</strong>.</em> Adjusted PubMed publication trends (07/01/2008 to 29/06/2014) <em><strong>- Figure 3</strong>.</em> Google search trends: Jan 2004 to Jun 2014 / 1-week periods<br>URL: http://www.google.com/trends/ <em><strong>- Supplementary Figures (S1-S6).</strong> PubMed publication</em> delay in the indexation processes does not explain the descending trends in the scientific output of evidence based medicine. <strong>Acknowledgments</strong> I would like to acknowledge the following persons for providing valuable concepts in data visualization and infographics: - Maria Fernanda Ramírez. Professor of graphic design. Universidad del Valle. Cali, Colombia. - Lorena Franco. Graphic design student. Universidad del Valle. Cali, Colombia. <strong>Related articles by this author (Jorge H. Ramírez)</strong> 1. Ramirez JH. Lack of transparency in clinical trials: a call for action. Colomb Med (Cali) 2013;44(4):243-6. URL: http://www.ncbi.nlm.nih.gov/pubmed/24892242 2. Ramirez JH. Re: Evidence based medicine is broken (17 June 2014) http://www.bmj.com/node/759181 3. Ramirez JH. Re: Global rules for global health: why we need an independent, impartial WHO (19 June 2014) http://www.bmj.com/node/759151 4. Ramirez JH. PubMed publication trends (1992 to 2014): evidence based medicine and clinical practice guidelines (04 July 2014) http://www.bmj.com/content/348/bmj.g3725/rr/759895 <strong> Recommended articles</strong> 1. Greenhalgh Trisha, Howick Jeremy,Maskrey Neal. Evidence based medicine: a movement in crisis? BMJ 2014;348:g3725 2. Spence Des. Evidence based medicine is broken BMJ 2014; 348:g22 3. Schünemann Holger J, Oxman Andrew D,Brozek Jan, Glasziou Paul, JaeschkeRoman, Vist Gunn E et al. Grading quality of evidence and strength of recommendations for diagnostic tests and strategies BMJ 2008; 336:1106 4. Lau Joseph, Ioannidis John P A, TerrinNorma, Schmid Christopher H, OlkinIngram. The case of the misleading funnel plot BMJ 2006; 333:597 5. Moynihan R, Henry D, Moons KGM (2014) Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much. PLoS Med 11(7): e1001655. doi:10.1371/journal.pmed.1001655 6. Katz D. A-holistic view of evidence based medicine<br>http://thehealthcareblog.com/blog/2014/05/02/a-holistic-view-of-evidence-based-medicine/
DOI: 10.6084/m9.figshare.1093997.v16
title: Data (i.e., evidence) about evidence based medicine

description: <strong>At a glance</strong> <em>The numbers contained in this fileset speak for themselves: evidence based medicine is broken and in crisis.</em> <strong>Fileset contents</strong> <em><strong>- Raw data (versión 1):</strong></em> Excel archive: Raw data, interactive figures, and PubMed search terms <em><strong>- </strong><strong>Figure 1.</strong> </em> Unadjusted (Fig 1A) and adjusted (Fig 1B) PubMed publication trends (01/01/1992 to 30/06/2014). <em><strong>- </strong></em><em><strong>Figure 2</strong>.</em> Adjusted PubMed publication trends (07/01/2008 to 29/06/2014) <em><strong>- Figure 3</strong>.</em> Google search trends: Jan 2004 to Jun 2014 / 1-week periods<br>URL: http://www.google.com/trends/ <em><strong>- Supplementary Figures (S1-S6).</strong> PubMed publication</em> delay in the indexation processes does not explain the descending trends in the scientific output of evidence based medicine. <strong>Acknowledgments</strong> I would like to acknowledge the following persons for providing valuable concepts in data visualization and infographics: - Maria Fernanda Ramírez. Professor of graphic design. Universidad del Valle. Cali, Colombia. - Lorena Franco. Graphic design student. Universidad del Valle. Cali, Colombia. <strong>Related articles by this author (Jorge H. Ramírez)</strong> 1. Ramirez JH. Lack of transparency in clinical trials: a call for action. Colomb Med (Cali) 2013;44(4):243-6. URL: http://www.ncbi.nlm.nih.gov/pubmed/24892242 2. Ramirez JH. Re: Evidence based medicine is broken (17 June 2014) http://www.bmj.com/node/759181 3. Ramirez JH. Re: Global rules for global health: why we need an independent, impartial WHO (19 June 2014) http://www.bmj.com/node/759151 4. Ramirez JH. PubMed publication trends (1992 to 2014): evidence based medicine and clinical practice guidelines (04 July 2014) http://www.bmj.com/content/348/bmj.g3725/rr/759895 <strong> Recommended articles</strong> 1. Greenhalgh Trisha, Howick Jeremy,Maskrey Neal. Evidence based medicine: a movement in crisis? BMJ 2014;348:g3725 2. Spence Des. Evidence based medicine is broken BMJ 2014; 348:g22 3. Schünemann Holger J, Oxman Andrew D,Brozek Jan, Glasziou Paul, JaeschkeRoman, Vist Gunn E et al. Grading quality of evidence and strength of recommendations for diagnostic tests and strategies BMJ 2008; 336:1106 4. Lau Joseph, Ioannidis John P A, TerrinNorma, Schmid Christopher H, OlkinIngram. The case of the misleading funnel plot BMJ 2006; 333:597 5. Moynihan R, Henry D, Moons KGM (2014) Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much. PLoS Med 11(7): e1001655. doi:10.1371/journal.pmed.1001655 6. Katz D. A-holistic view of evidence based medicine<br>http://thehealthcareblog.com/blog/2014/05/02/a-holistic-view-of-evidence-based-medicine/
DOI: 10.6084/m9.figshare.1092575.v2
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://figshare.com/download/file/1577683.
DOI: 10.6084/m9.figshare.1093997.v17
title: Data (i.e., evidence) about evidence based medicine

description: <strong>At a glance</strong> <em>The numbers contained in this fileset speak for themselves: evidence based medicine is broken and in crisis.</em> <strong>Fileset contents</strong> <em><strong>- Raw data (versión 1):</strong></em> Excel archive: Raw data, interactive figures, and PubMed search terms <em><strong>- </strong><strong>Figure 1.</strong> </em> Unadjusted (Fig 1A) and adjusted (Fig 1B) PubMed publication trends (01/01/1992 to 30/06/2014). <em><strong>- </strong></em><em><strong>Figure 2</strong>.</em> Adjusted PubMed publication trends (07/01/2008 to 29/06/2014) <em><strong>- Figure 3</strong>.</em> Google search trends: Jan 2004 to Jun 2014 / 1-week periods<br>URL: http://www.google.com/trends/ <em><strong>- Supplementary Figures (S1-S6).</strong> PubMed publication</em> delay in the indexation processes does not explain the descending trends in the scientific output of evidence based medicine. <strong>Acknowledgments</strong> I would like to acknowledge the following persons for providing valuable concepts in data visualization and infographics: - Maria Fernanda Ramírez. Professor of graphic design. Universidad del Valle. Cali, Colombia. - Lorena Franco. Graphic design student. Universidad del Valle. Cali, Colombia. <strong>Related articles by this author (Jorge H. Ramírez)</strong> 1. Ramirez JH. Lack of transparency in clinical trials: a call for action. Colomb Med (Cali) 2013;44(4):243-6. URL: http://www.ncbi.nlm.nih.gov/pubmed/24892242 2. Ramirez JH. Re: Evidence based medicine is broken (17 June 2014) http://www.bmj.com/node/759181 3. Ramirez JH. Re: Global rules for global health: why we need an independent, impartial WHO (19 June 2014) http://www.bmj.com/node/759151 4. Ramirez JH. PubMed publication trends (1992 to 2014): evidence based medicine and clinical practice guidelines (04 July 2014) http://www.bmj.com/content/348/bmj.g3725/rr/759895 <strong> Recommended articles</strong> 1. Greenhalgh Trisha, Howick Jeremy,Maskrey Neal. Evidence based medicine: a movement in crisis? BMJ 2014;348:g3725 2. Spence Des. Evidence based medicine is broken BMJ 2014; 348:g22 3. Schünemann Holger J, Oxman Andrew D,Brozek Jan, Glasziou Paul, JaeschkeRoman, Vist Gunn E et al. Grading quality of evidence and strength of recommendations for diagnostic tests and strategies BMJ 2008; 336:1106 4. Lau Joseph, Ioannidis John P A, TerrinNorma, Schmid Christopher H, OlkinIngram. The case of the misleading funnel plot BMJ 2006; 333:597 5. Moynihan R, Henry D, Moons KGM (2014) Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much. PLoS Med 11(7): e1001655. doi:10.1371/journal.pmed.1001655 6. Katz D. A-holistic view of evidence based medicine<br>http://thehealthcareblog.com/blog/2014/05/02/a-holistic-view-of-evidence-based-medicine/
DOI: 10.6084/m9.figshare.1092575.v3
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092547
title: Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA

description: Antarctica is one of the harshest environments on the planet because of its extreme climatic conditions, with prolonged winters, freezing temperatures and lack of liquid water. While almost the entire continent (99.7%) is covered year round by snow and ice, some mountain peaks and coastal areas are ice-free and sustain life. Invertebrates dominate in this environment, but despite their obvious abundance, little is known of one major player, the rotifers. In this study, we examine the distribution and diversity of rotifers from across continental Antarctica using mitochondrial <i>c</i> oxidase subunit I DNA sequences, and compare to sequences extracted from specimens collected in limited locations in the Antarctic Peninsula (AP) and in Tierra del Fuego (TF) in South America. We identified rotifers of the Class Bdelloidea to be the most frequently sampled micro-organisms in soil and limno-terrestrial environments. From the Antarctic samples, 514 sequences were generated and 37 distinct lineages were identified (40 putative species based on the PTP model) within <i>Philodina</i>, <i>Adineta</i> and unidentified bdelloids (all currently considered endemic to Antarctica). Overall, we observed widespread ranges for some rotifers in continental Antarctica, many of them exceeding 2000 km. Only one bdelloid lineage (<i>Adineta</i> cf. <i>gracilis</i>) from continental Antarctica was also present in maritime Antarctica. No close similarities were found with worldwide locations, or amongst AP and TF. Our broad coverage across Antarctica shows unique lineages that may represent potential species surpassing what is presently known from morphology, even when conservative approaches are applied for species delimitation.
DOI: 10.6084/m9.figshare.1092575.v4
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092547.v2
title: Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA

description: Antarctica is one of the harshest environments on the planet because of its extreme climatic conditions, with prolonged winters, freezing temperatures and lack of liquid water. While almost the entire continent (99.7%) is covered year round by snow and ice, some mountain peaks and coastal areas are ice-free and sustain life. Invertebrates dominate in this environment, but despite their obvious abundance, little is known of one major player, the rotifers. In this study, we examine the distribution and diversity of rotifers from across continental Antarctica using mitochondrial <i>c</i> oxidase subunit I DNA sequences, and compare to sequences extracted from specimens collected in limited locations in the Antarctic Peninsula (AP) and in Tierra del Fuego (TF) in South America. We identified rotifers of the Class Bdelloidea to be the most frequently sampled micro-organisms in soil and limno-terrestrial environments. From the Antarctic samples, 514 sequences were generated and 37 distinct lineages were identified (40 putative species based on the PTP model) within <i>Philodina</i>, <i>Adineta</i> and unidentified bdelloids (all currently considered endemic to Antarctica). Overall, we observed widespread ranges for some rotifers in continental Antarctica, many of them exceeding 2000 km. Only one bdelloid lineage (<i>Adineta</i> cf. <i>gracilis</i>) from continental Antarctica was also present in maritime Antarctica. No close similarities were found with worldwide locations, or amongst AP and TF. Our broad coverage across Antarctica shows unique lineages that may represent potential species surpassing what is presently known from morphology, even when conservative approaches are applied for species delimitation.
DOI: 10.6084/m9.figshare.1092575.v6
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092575.v5
title: metaseq supplemental data (README file)

description: Supplementary data for the metaseq manuscript. This dataset is intended to be downloaded and unpacked automatically, along with the rest of the supplemental data files, using the <code>download-metaseq-supplemental.py</code> script found at http://files.figshare.com/1581826/download_metaseq_supplemental.py.
DOI: 10.6084/m9.figshare.1092545
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Data set of simulated outcomes

description: This data set is 2% of the total data, which was too large a file to upload. Full data available from andrew.phillips@ucl.ac.uk
DOI: 10.6084/m9.figshare.1092547.v1
title: Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA

description: Antarctica is one of the harshest environments on the planet because of its extreme climatic conditions, with prolonged winters, freezing temperatures and lack of liquid water. While almost the entire continent (99.7%) is covered year round by snow and ice, some mountain peaks and coastal areas are ice-free and sustain life. Invertebrates dominate in this environment, but despite their obvious abundance, little is known of one major player, the rotifers. In this study, we examine the distribution and diversity of rotifers from across continental Antarctica using mitochondrial <i>c</i> oxidase subunit I DNA sequences, and compare to sequences extracted from specimens collected in limited locations in the Antarctic Peninsula (AP) and in Tierra del Fuego (TF) in South America. We identified rotifers of the Class Bdelloidea to be the most frequently sampled micro-organisms in soil and limno-terrestrial environments. From the Antarctic samples, 514 sequences were generated and 37 distinct lineages were identified (40 putative species based on the PTP model) within <i>Philodina</i>, <i>Adineta</i> and unidentified bdelloids (all currently considered endemic to Antarctica). Overall, we observed widespread ranges for some rotifers in continental Antarctica, many of them exceeding 2000 km. Only one bdelloid lineage (<i>Adineta</i> cf. <i>gracilis</i>) from continental Antarctica was also present in maritime Antarctica. No close similarities were found with worldwide locations, or amongst AP and TF. Our broad coverage across Antarctica shows unique lineages that may represent potential species surpassing what is presently known from morphology, even when conservative approaches are applied for species delimitation.
DOI: 10.6084/m9.figshare.1092544
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Program

description: SAS program to read model output file.
DOI: 10.6084/m9.figshare.1092540
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting

description: Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting
DOI: 10.6084/m9.figshare.1092545.v2
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Data set of simulated outcomes

description: This data set is 2% of the total data, which was too large a file to upload. Full data available from andrew.phillips@ucl.ac.uk
DOI: 10.6084/m9.figshare.1092544.v2
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Program

description: SAS program to read model output file.
DOI: 10.6084/m9.figshare.1092540.v2
title: Potential future impact of a partially effective HIV vaccine in a southern African setting. Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting

description: Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting
DOI: 10.6084/m9.figshare.1092544.v1
title: Program

description: SAS program to read model output file.
DOI: 10.6084/m9.figshare.1092545.v1
title: Data set of simulated outcomes

description: This data set is 2% of the total data, which was too large a file to upload. Full data available from andrew.phillips@ucl.ac.uk