cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2009142
title: OTSCCsequencing

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (&lt;50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
DOI: 10.6084/m9.figshare.2009145
title: OTSCC.Sequencing Scripts & Code

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (&lt;50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
DOI: 10.6084/m9.figshare.2009205
title: Modelling a Sustainable City

description: We have tried to model a sustainable city based on population,energy mix,environment,food and Housing.Our main aim is to find how sustainable a city is based on different mix of the above listed parameters.
DOI: 10.6084/m9.figshare.2009205.v1
title: Modelling a Sustainable City

description: We have tried to model a sustainable city based on population,energy mix,environment,food and Housing.Our main aim is to find how sustainable a city is based on different mix of the above listed parameters.
DOI: 10.6084/m9.figshare.2009145.v1
title: OTSCC.Sequencing Scripts & Code

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (&lt;50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
DOI: 10.6084/m9.figshare.2009142.v2
title: OTSCCsequencing

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (&lt;50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
DOI: 10.6084/m9.figshare.2009217.v2
title: Proteomics_transcriptomics_LP

description: The study highlights the need to optimize tissue processing and analytical pipelines to 43 enable accurate integrated analysis of high throughput omics data; a sequential extraction of 44 RNA and protein entities and subsequent integrated analysis was identified to provide a 45 better representation of the molecular profile in terms concordant entities and pathways.
DOI: 10.6084/m9.figshare.2009232.v2
title: ChromatinAssortativity

description: Code associated to the paper using chromatin assortativity to integrate epigenomic datasets with 3D chromatin contact networks.
DOI: 10.6084/m9.figshare.2009139
title: Determinants of Desire for Children among HIV-Positive Women in the Afar Region, Ethiopia: Case Control Study

description: <b><i>Introduction:</i></b><i> </i>The desire for a child in Ethiopian society is normal. Among HIV positive women, due to the risk of MTCT, it is imperative to understand factors influencing women’s desire for children. This study aimed at assessing factors associated with desire for children among HIV-positive women in two selected hospitals of Afar Regional State, Ethiopia. <b><i>Methods:</i></b> A facility based case-control study was conducted among 157 cases (with a desire) and 157 controls of HIV positive individuals registered in the selected health facilities. The participants were selected by random sampling technique. Data were collected using face-to-face interview and was analyzed using logistic regression.
DOI: 10.6084/m9.figshare.2009217.v1
title: Strand.Anupama

description: The study highlights the need to optimize tissue processing and analytical pipelines to 43 enable accurate integrated analysis of high throughput omics data; a sequential extraction of 44 RNA and protein entities and subsequent integrated analysis was identified to provide a 45 better representation of the molecular profile in terms concordant entities and pathways.
DOI: 10.6084/m9.figshare.2009139.v1
title: Determinants of Desire for Children among HIV-Positive Women in the Afar Region, Ethiopia: Case Control Study

description: <b><i>Introduction:</i></b><i> </i>The desire for a child in Ethiopian society is normal. Among HIV positive women, due to the risk of MTCT, it is imperative to understand factors influencing women’s desire for children. This study aimed at assessing factors associated with desire for children among HIV-positive women in two selected hospitals of Afar Regional State, Ethiopia. <b><i>Methods:</i></b> A facility based case-control study was conducted among 157 cases (with a desire) and 157 controls of HIV positive individuals registered in the selected health facilities. The participants were selected by random sampling technique. Data were collected using face-to-face interview and was analyzed using logistic regression.
DOI: 10.6084/m9.figshare.2009142.v1
title: OTSCCsequencing

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (&lt;50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
DOI: 10.6084/m9.figshare.2009232.v3
title: ChromatinAssortativity

description: Code associated to the paper using chromatin assortativity to integrate epigenomic datasets with 3D chromatin contact networks.
DOI: 10.6084/m9.figshare.2009130
title: AZ2.0 Scripts & Code

description: Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. indica genome. The raw data described in this manuscript are submitted to the NCBI Short Read Archive under the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 (SRP013453).
DOI: 10.6084/m9.figshare.2009124
title: AZ1.0 Scripts and Code

description: Background: The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. Results: The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions: This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides
DOI: 10.6084/m9.figshare.2009130.v1
title: AZ2.0 Scripts & Code

description: Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. indica genome. The raw data described in this manuscript are submitted to the NCBI Short Read Archive under the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 (SRP013453).
DOI: 10.6084/m9.figshare.2009118
title: Le numérique: un outil complexe au service de la gériatrie. Pistes de recherche.

description: Devoir final du MOOC: numérique et recherche en sante et sciences du vivant.
DOI: 10.6084/m9.figshare.2009121
title: Cover Page

description: A list of the content included in this Figshare presentation
DOI: 10.6084/m9.figshare.2009232.v4
title: ChromatinAssortativity

description: Code associated to the paper: <br>Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativityVera PancaldiEnrique Carrillo-de-Santa-Pau, Biola Maria Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia and Daniel Rico<br><br><br>
DOI: 10.6084/m9.figshare.2009094
title: Images Used in Interface

description: These are the figures used in the interface. Two show the 3rd and 5th critical stages of the Edwards Aquifer J17 index well, while another is a map of the Edwards Aquifer. These figures are from the Aquiferium Project headed by Encompass Labs, the Edwards Aquifer Authority, and the University of Texas at Austin. <br>
DOI: 10.6084/m9.figshare.2009091
title: Versions of Edwards Aquifer Case Study Twine Interface

description: These are the first through final versions of the Edwards Aquifer case study interface using the Twine program from Twinery.org, an open-source program that creates a choose-your-own-adventure type style of interface (i.e. game). They outline the initial setup, using the best case (BC), worst case (WC) and business-as-usual case (BAU) as scenarios. The last few versions incorporate the complete CSS code and pictures.
DOI: 10.6084/m9.figshare.2009121.v2
title: Cover Page

description: A list of the content included in this Figshare presentation
DOI: 10.6084/m9.figshare.2009094.v2
title: Images Used in Interface

description: These are the figures used in the interface. Two show the 3rd and 5th critical stages of the Edwards Aquifer J17 index well, while another is a map of the Edwards Aquifer. These figures are from the Aquiferium Project headed by Encompass Labs, the Edwards Aquifer Authority, and the University of Texas at Austin. <br>
DOI: 10.6084/m9.figshare.2009118.v1
title: Le numérique: un outil complexe au service de la gériatrie. Pistes de recherche.

description: Devoir final du MOOC: numérique et recherche en sante et sciences du vivant.
DOI: 10.6084/m9.figshare.2009070
title: "Variation of outdoor illumination as a function of solar elevation and light pollution" (Spitschan et al.) – Raw Data

description: <br><b>"Variation of outdoor illumination as a function of solar elevation and light pollution" (Spitschan <i>et al.</i>) – Raw Data</b>This is the raw data collected for the data base of outdoor illumination spectra described by Spitschan, Aguirre, Brainard & Sweeney (2016). The spectra provided here are raw, uncalibrated and unprocessed.Code to process these data is provided at https://github.com/spitschan/IlluminationSpectraDataset. MD5 (calibrationdata.tar.gz) = 92102c29bbc54f3d426d2d17f67ad526MD5 (dataraw.tar.gz) = 351c6d0c5dd44e748af483d035954504
DOI: 10.6084/m9.figshare.2009091.v1
title: Versions of Edwards Aquifer Case Study Twine Interface

description: These are the first through final versions of the Edwards Aquifer case study interface using the Twine program from Twinery.org, an open-source program that creates a choose-your-own-adventure type style of interface (i.e. game). They outline the initial setup, using the best case (BC), worst case (WC) and business-as-usual case (BAU) as scenarios. The last few versions incorporate the complete CSS code and pictures.
DOI: 10.6084/m9.figshare.2009232.v7
title: ChromatinAssortativity

description: Code associated to the paper: <br>Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativityVera PancaldiEnrique Carrillo-de-Santa-Pau, Biola Maria Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia and Daniel Rico<br><br><br>
DOI: 10.6084/m9.figshare.2009031
title: Insight Maker files

description: Wet Period Case–30 years of historical wet period on record (1974-2004)-including wettest years on record 1974-1983.–Represents the wet period case–Corresponds to wet cycle of AMO (Atlantic Mutidecadal Oscillation) Average (Status Quo) Case–Last 30 years of historical EAA data–Used the past to predict the future–Represents the status quo case–Includes the dry portion and wet portion of AMO cycle Dry Period Case– 25 years of historical dry period on record (1947-1973)-including drought of record (1947-1956)–Represents the dry period case–Future dry cycle includes dry cycle of AMO and overlay of IPCC climate change predictions
DOI: 10.6084/m9.figshare.2009232.v6
title: ChromatinAssortativity

description: Code associated to the paper: <br>Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativityVera PancaldiEnrique Carrillo-de-Santa-Pau, Biola Maria Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia and Daniel Rico<br><br><br>
DOI: 10.6084/m9.figshare.2009028
title: Mental Modeler files

description: These iterations of a concept map surrounding the idea of being sustainable with the Edwards Aquifer. The less specific mental modeler concept map is the final product showing how the most positive and negative factors can relate to one another in affecting the aquifer itself. This allowed the understanding of how to interrelate these factors on the respective programs of Insight Maker, Matlab, and Twine in creating our models.
DOI: 10.6084/m9.figshare.2009025
title: Edwards Aquifer data/regression analysis

description: The tables data were used to comparatively plot regressions between two factors affecting the Edwards Aquifer. Through these plots it can be observed which factors like well discharge and J-17 well levels can correlate with one another. The higher the R^2 value, the better and closer the fit is for the correlation between corresponding factors.
DOI: 10.6084/m9.figshare.2009031.v1
title: Insight Maker files

description: Wet Period Case–30 years of historical wet period on record (1974-2004)-including wettest years on record 1974-1983.–Represents the wet period case–Corresponds to wet cycle of AMO (Atlantic Mutidecadal Oscillation) Average (Status Quo) Case–Last 30 years of historical EAA data–Used the past to predict the future–Represents the status quo case–Includes the dry portion and wet portion of AMO cycle Dry Period Case– 25 years of historical dry period on record (1947-1973)-including drought of record (1947-1956)–Represents the dry period case–Future dry cycle includes dry cycle of AMO and overlay of IPCC climate change predictions
DOI: 10.6084/m9.figshare.2009016
title: MOOCSciNum-final_YoussefHlaoui.pdf

description: Exercice Final Mooc
DOI: 10.6084/m9.figshare.2009016.v1
title: MOOCSciNum-final_YoussefHlaoui.pdf

description: Exercice Final Mooc