cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3490244.v4
title: Quantitative proteomic profiling lung squamous carcinoma cells

description: Quantitative proteomic profiling the molecular signatures lung squamous carcinoma cells
DOI: 10.6084/m9.figshare.3490244.v5
title: Quantitative proteomic profiling lung squamous carcinoma cells

description: Quantitative proteomic profiling the molecular signatures lung squamous carcinoma cells
DOI: 10.6084/m9.figshare.3490244.v6
title: Quantitative proteomic profiling lung squamous carcinoma cells

description: Quantitative proteomic profiling the molecular signatures lung squamous carcinoma cells
DOI: 10.6084/m9.figshare.3490232
title: Final_filtered_SNPs.vcf

description: Final filtered SNP genotypes used for analysis in Puritz, J.B., Gold, J.R., and Portnoy, D.S. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.
DOI: 10.6084/m9.figshare.3490232.v2
title: Final_filtered_SNPs.vcf

description: Final filtered SNP genotypes used for analysis in Puritz, J.B., Gold, J.R., and Portnoy, D.S. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.
DOI: 10.6084/m9.figshare.3490232.v1
title: Final_filtered_SNPs.vcf

description: Final filtered SNP genotypes used for analysis in Puritz, J.B., Gold, J.R., and Portnoy, D.S. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.
DOI: 10.6084/m9.figshare.3490229
title: Final_Haps.gen

description: Final filtered RAD locus haplotypes used for analysis in Puritz, J.B., Gold, J.R., and Portnoy, D.S. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.
DOI: 10.6084/m9.figshare.3490226
title: TotalRawSNPs.vcf.gz

description: Total raw SNP and INDel calls for Puritz, J.B., Gold, J.R., and Portnoy, D.S. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.
DOI: 10.6084/m9.figshare.3490211
title: Dataset for practice session 1 in bioinformatics

description: Dataset for the practice in the data preprocessing and unsupervised learning in the introduction to bioinformatics course
DOI: 10.6084/m9.figshare.3490211.v1
title: New draft item

description: Dataset for the practice in the data preprocessing and unsupervised learning in the introduction to bioinformatics course
DOI: 10.6084/m9.figshare.3490211.v2
title: Dataset for practice session 1 in bioinformatics

description: Dataset for the practice in the data preprocessing and unsupervised learning in the introduction to bioinformatics course
DOI: 10.6084/m9.figshare.3490199
title: captions.docx

description: Dataset associated to the article "Transition between functional regimes in an integrate-and-fire network model of the thalamus", by Alessandro Barardi, Jordi Garcia-Ojalvo and Alberto Mazzoni.<br>
DOI: 10.6084/m9.figshare.3490199.v1
title: captions.docx

description: Dataset associated to the article "Transition between functional regimes in an integrate-and-fire network model of the thalamus", by Alessandro Barardi, Jordi Garcia-Ojalvo and Alberto Mazzoni.<br>
DOI: 10.6084/m9.figshare.3490187
title: Digitized version of Alwyn Gentry Transect data Sites table

description: This is a digitized version of the "Gentry Transect Coordinates" file (a non-OCR'd pdf located at http://www.mobot.org/mobot/research/gentry/gentry_coordinates.pdf). If using this file please refer to http://www.mobot.org/mobot/research/gentry/welcome.shtml for more information. There is no need to cite this digital version. Please cite the original.<br>
DOI: 10.6084/m9.figshare.3490187.v1
title: Digitized version of Alwyn Gentry Transect data Sites table

description: This is a digitized version of the "Gentry Transect Coordinates" file (a non-OCR'd pdf located at http://www.mobot.org/mobot/research/gentry/gentry_coordinates.pdf). If using this file please refer to http://www.mobot.org/mobot/research/gentry/welcome.shtml for more information. There is no need to cite this digital version. Please cite the original.<br>
DOI: 10.6084/m9.figshare.3490181
title: Experiment #4

description: Culture #4
DOI: 10.6084/m9.figshare.3490181.v1
title: New draft item

description: Culture #4
DOI: 10.6084/m9.figshare.3490175
title: Experiment #5

description: Culture #5
DOI: 10.6084/m9.figshare.3490175.v1
title: New draft item

description: Culture #5
DOI: 10.6084/m9.figshare.3490169
title: Experiment #6

description: Culture #6
DOI: 10.6084/m9.figshare.3490169.v1
title: New draft item

description: Culture #6
DOI: 10.6084/m9.figshare.3490142
title: Predicted secondary structure of Solemya velum symbiont 16S

description: Predictions of secondary structure of Solemya velum symbiont's 16s rRNA.
DOI: 10.6084/m9.figshare.3490142.v1
title: Predicted secondary structure of Solemya velum symbiont 16S

description: Predictions of secondary structure of Solemya velum symbiont's 16s rRNA.
DOI: 10.6084/m9.figshare.3490118
title: Supporting Information file.zip

description: Protective effects of bifidobacterium on intestinal barrier function in LPS-induced enterocyte barrier injury of Caco-2 monolayers and in a rat NEC model (the supporting information for the journal of Plos One).<br>
DOI: 10.6084/m9.figshare.3490118.v1
title: Supporting Information file.zip

description: Protective effects of bifidobacterium on intestinal barrier function in LPS-induced enterocyte barrier injury of Caco-2 monolayers and in a rat NEC model (the supporting information for the journal of Plos One).<br>
DOI: 10.6084/m9.figshare.3489980
title: Biological applications of pyrazoline-based half-sandwich ruthenium(III) coordination compounds

description: Biological applications of pyrazoline-based half-sandwich ruthenium(III) coordination compounds
DOI: 10.6084/m9.figshare.3489980.v1
title: Biological applications of pyrazoline-based half-sandwich ruthenium(III) coordination compounds

description: Biological applications of pyrazoline-based half-sandwich ruthenium(III) coordination compounds
DOI: 10.6084/m9.figshare.3489971
title: VALKYRIE site is now multilingual

description: This week we are going to begin publishing this site in more than one language. Thanks to the excellent contributions of Sylvain Durand, I created and configured a multilingual jekyll build (...)(excerpt)
DOI: 10.6084/m9.figshare.3489971.v1
title: VALKYRIE site is now multilingual

description: This week we are going to begin publishing this site in more than one language. Thanks to the excellent contributions of Sylvain Durand, I created and configured a multilingual jekyll build (...)(excerpt)
DOI: 10.6084/m9.figshare.3489968
title: Comments via Disqus in Project VALKYRIE's homepage

description: To configure Disqus comments in some Jekyll blog, I suggest using the universal code.Cooments can be moderated, answered, and curated on Disqus, and comment history will be shown in the page. All VALKYRIE readers are invated to opinate, suggest, or just comment and add his/her experience and ideas. All contributions are wellcome!(excerpt)
DOI: 10.6084/m9.figshare.3489968.v2
title: Comments via Disqus in Project VALKYRIE's homepage

description: To configure Disqus comments in some Jekyll blog, I suggest using the universal code.Cooments can be moderated, answered, and curated on Disqus, and comment history will be shown in the page. All VALKYRIE readers are invated to opinate, suggest, or just comment and add his/her experience and ideas. All contributions are wellcome!(excerpt)
DOI: 10.6084/m9.figshare.3489968.v1
title: Comments via Disqus

description: To configure Disqus comments in some Jekyll blog, I suggest using the universal code.Cooments can be moderated, answered, and curated on Disqus, and comment history will be shown in the page. All VALKYRIE readers are invated to opinate, suggest, or just comment and add his/her experience and ideas. All contributions are wellcome!(excerpt)
DOI: 10.6084/m9.figshare.3489965
title: Quaterly tweets - Project VALKYRIE

description: Integration between _Jekyll_ and Twitter through _jekyll-twitter-plugin_ created by _Robert Murray_. Unfortunately, Github does not permit this plugin, but this was bypassed serving the page locally and retrieving the html files - _voilà_!(excerpt)<br><br>
DOI: 10.6084/m9.figshare.3489965.v1
title: Quaterly tweets

description: Integration between _Jekyll_ and Twitter through _jekyll-twitter-plugin_ created by _Robert Murray_. Unfortunately, Github does not permit this plugin, but this was bypassed serving the page locally and retrieving the html files - _voilà_!
DOI: 10.6084/m9.figshare.3489965.v3
title: Quaterly tweets - Project VALKYRIE

description: Integration between _Jekyll_ and Twitter through _jekyll-twitter-plugin_ created by _Robert Murray_. Unfortunately, Github does not permit this plugin, but this was bypassed serving the page locally and retrieving the html files - _voilà_!(excerpt)<br><br>
DOI: 10.6084/m9.figshare.3489965.v2
title: Quaterly tweets

description: Integration between _Jekyll_ and Twitter through _jekyll-twitter-plugin_ created by _Robert Murray_. Unfortunately, Github does not permit this plugin, but this was bypassed serving the page locally and retrieving the html files - _voilà_!(excerpt)<br><br>
DOI: 10.6084/m9.figshare.3489962
title: Beginning patient accrual (training) - Project VALKYRIE

description: This post shows a probable depiction of what we expect to be the enrollment of the first patient in VALKYRIE. This is a simulation, once the study still needs additional preparation and internal considerations. We show a possible problem that could happen during image review and its implications. We also discuss the best momment of letting information to be public.(excerpt)
DOI: 10.6084/m9.figshare.3489962.v2
title: Beginning patient accrual (training) - Project VALKYRIE

description: This post shows a probable depiction of what we expect to be the enrollment of the first patient in VALKYRIE. This is a simulation, once the study still needs additional preparation and internal considerations. We show a possible problem that could happen during image review and its implications. We also discuss the best momment of letting information to be public.(excerpt)
DOI: 10.6084/m9.figshare.3489962.v1
title: Beginning patient accrual (training)

description: This post shows a probable depiction of what we expect to be the enrollment of the first patient in VALKYRIE. This is a simulation, once the study still needs additional preparation and internal considerations. We show a possible problem that could happen during image review and its implications. We also discuss the best momment of letting information to be public.(excerpt)
DOI: 10.6084/m9.figshare.3489959
title: Retrospective survival analysis - differences between two versions of a dataset

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.(excerpt)
DOI: 10.6084/m9.figshare.3489959.v1
title: Retrospective analysis

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.
DOI: 10.6084/m9.figshare.3489959.v2
title: Retrospective analysis

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.(excerpt)
DOI: 10.6084/m9.figshare.3489959.v3
title: Retrospective analysis

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.(excerpt)
DOI: 10.6084/m9.figshare.3489959.v5
title: Retrospective survival analysis - differences between two versions of a dataset

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.(excerpt)
DOI: 10.6084/m9.figshare.3489959.v4
title: Retrospective survival analysis - differences between two versions of a dataset

description: Calculations shown here use data from patients diagnosed with DIPG between 2000-2013, with follow-up until 2014. Follow-up time of the patients in this database is a bit longer than that from the original data used to design VALKYRIE project, hence there are some numerical differences. This post illustrate how to present clinical research data in a transparent and fully reproducible way to an audience. Including individual patient data (de-identified) as well as the _script_ used to perform statistical analysis of data, this is an example of the possibilities of _open lab notebook_ and _open science_ paradigm. When the prospective trial data are collected, they will be equally published in the same format, becoming permanently available to analysis and criticism by interested third parties. I discussed the inspiration to this approach in this post in a personal blog.(excerpt)
DOI: 10.6084/m9.figshare.3489956
title: Historical control group in clinical trials - Project VALKYRIE

description: The historical control group consists of patients with DIPG, diagnosed between 2000 and 2013, _not_ treated with chemotherapy according to the HIT protocols (GPOH), adapted. Only patients who received radiation therapy at a dose of 40 Gy or higher were selected.(excerpt)<br>
DOI: 10.6084/m9.figshare.3489956.v1
title: Historical control group

description: The historical control group consists of patients with DIPG, diagnosed between 2000 and 2013, _not_ treated with chemotherapy according to the HIT protocols (GPOH), adapted. Only patients who received radiation therapy at a dose of 40 Gy or higher were selected.
DOI: 10.6084/m9.figshare.3489956.v2
title: Historical control group

description: The historical control group consists of patients with DIPG, diagnosed between 2000 and 2013, _not_ treated with chemotherapy according to the HIT protocols (GPOH), adapted. Only patients who received radiation therapy at a dose of 40 Gy or higher were selected.(excerpt)<br>
DOI: 10.6084/m9.figshare.3489956.v4
title: Historical control group in clinical trials - Project VALKYRIE

description: The historical control group consists of patients with DIPG, diagnosed between 2000 and 2013, _not_ treated with chemotherapy according to the HIT protocols (GPOH), adapted. Only patients who received radiation therapy at a dose of 40 Gy or higher were selected.(excerpt)<br>
DOI: 10.6084/m9.figshare.3489956.v3
title: Historical control group

description: The historical control group consists of patients with DIPG, diagnosed between 2000 and 2013, _not_ treated with chemotherapy according to the HIT protocols (GPOH), adapted. Only patients who received radiation therapy at a dose of 40 Gy or higher were selected.(excerpt)<br>
DOI: 10.6084/m9.figshare.3489953
title: The crew of Project VALKYRIE

description: People involved in this project (so far). Links to CVs.
DOI: 10.6084/m9.figshare.3489953.v2
title: The crew of Project VALKYRIE

description: People involved in this project (so far). Links to CVs.
DOI: 10.6084/m9.figshare.3489953.v1
title: The crew

description: People involved in this project (so far). Links to CVs.
DOI: 10.6084/m9.figshare.3489947
title: Estimate of the number of patients to enroll in a clinical trial - Project VALKYRIE

description: When we designed the Valkyrie trial several different considerations were made on how to calculate the number of patients to be recruited for the trial. In the end, the decision fell on the way as described in the project [methodology][meto] (translated from portuguese):<br> - #### 5.7.Sample size:<br> - The sample size does not depend on the initial question, which is not comparative. However, in order to ascertain secondary outcomes, it was necessary to calculate the expected number of patients to be recruited. Using data available from patients already treated in our hospital (as discussed above) as a pilot group, assuming a hazard ratio of 0.05 and choosing a statistical power of 80% and 0.5% alpha the minimum number of patients required in the experimental group (in a 1:2 design) is 16 patients. We expect to require 2 years to recruit this sample. The comparison group to be used will be the historic control group of patients treated at our institution between 2000 and 2013, with schemes other than HIT (number of patients 31, suitable for this experimental design). The powerSurvEpi package of R language was used to calculate the sample size (R Development Core Team, 2012).(excerpt)
DOI: 10.6084/m9.figshare.3489947.v2
title: Estimate of the number of patients to enroll in a clinical trial - Project VALKYRIE

description: When we designed the Valkyrie trial several different considerations were made on how to calculate the number of patients to be recruited for the trial. In the end, the decision fell on the way as described in the project [methodology][meto] (translated from portuguese):<br> - #### 5.7.Sample size:<br> - The sample size does not depend on the initial question, which is not comparative. However, in order to ascertain secondary outcomes, it was necessary to calculate the expected number of patients to be recruited. Using data available from patients already treated in our hospital (as discussed above) as a pilot group, assuming a hazard ratio of 0.05 and choosing a statistical power of 80% and 0.5% alpha the minimum number of patients required in the experimental group (in a 1:2 design) is 16 patients. We expect to require 2 years to recruit this sample. The comparison group to be used will be the historic control group of patients treated at our institution between 2000 and 2013, with schemes other than HIT (number of patients 31, suitable for this experimental design). The powerSurvEpi package of R language was used to calculate the sample size (R Development Core Team, 2012).(excerpt)
DOI: 10.6084/m9.figshare.3489947.v1
title: Estimate of the number of patients

description: When we designed the Valkyrie trial several different considerations were made on how to calculate the number of patients to be recruited for the trial. In the end, the decision fell on the way as described in the project [methodology][meto] (translated from portuguese):<br> - #### 5.7.Sample size:<br> - The sample size does not depend on the initial question, which is not comparative. However, in order to ascertain secondary outcomes, it was necessary to calculate the expected number of patients to be recruited. Using data available from patients already treated in our hospital (as discussed above) as a pilot group, assuming a hazard ratio of 0.05 and choosing a statistical power of 80% and 0.5% alpha the minimum number of patients required in the experimental group (in a 1:2 design) is 16 patients. We expect to require 2 years to recruit this sample. The comparison group to be used will be the historic control group of patients treated at our institution between 2000 and 2013, with schemes other than HIT (number of patients 31, suitable for this experimental design). The powerSurvEpi package of R language was used to calculate the sample size (R Development Core Team, 2012).(excerpt)
DOI: 10.6084/m9.figshare.3489944
title: Standard treatment for pediatric brainstem tumor patients

description: Children and adolescents with brainstem tumors have no standardized widely accepted treatment. In our hospital service, in the last 15 years, we treated 87 pediatric patients with brainstem tumors. Of those, 24 patients (28%) had focal tumors of the brainstem, which are usually benign, indolent and permit long-term survival if treated properly. In our department, 79% of these patients survived four years or more after their diagnosis, and most remain in follow-up clinic. In contrast, 63 patients (72%) were diagnosed with diffuse pontine tumors (DIPG). Among those patients, survival 2 years after diagnosis was only 6%, and no patients survived more than 4 years.(excerpt)