cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1383212.v11
title: SERBP1 is a component of the Liver Receptor Homolog-1 transcriptional complex

description: Liver receptor homolog-1 (NR5A2) is an orphan nuclear receptor whose expression is essential for normal liver, intestine, and pancreas function. Nuclear receptors are ligand regulated transcription factors and NR5A2 has been shown to play a role in the transcriptional regulation of pathways involved in cancer. Elucidating the components of the NR5A2 transcriptional complex to better understand endogenous regulation of the receptor as well as its role in cancer remains a high priority. A sub-cellular enrichment strategy coupled with proteomic approaches was employed to identify putative NR5A2 coregulators. Nuclear fractionation protocol was essential for detection of NR5A2 peptides by MS, with most peptides being observed in the insoluble fraction (receptor bound to DNA). Duplicate data-dependent MS/MS runs using an inclusion/exclusion list improved the number of NR5A2 peptide identifications, including isoform-specific and fusion-specific peptides. Moreover, increased NR5A2 sequence coverage and a greater number of protein hits were observed with on-bead trypsin digestion of affinity captured protein. SERBP1 and ILF3 were identified as NR5A2 interacting partners. Both western blot and MS/MS analysis of endogenous receptor confirmed these binding partners are present in the NR5A2 transcriptional complex in established cell lines. Receptor knockdown by siRNA showed an increased in SERBP1 expression while ILF3 expression was unchanged. In contrast, receptor overexpression decreased only SERBP1 mRNA levels. Consistent with these data, in a promoter:reporter assay, binding of NR5A2 to the promoter region of SERBP1 resulted in a decrease in the expression level of the reporter gene, and subsequently, inhibiting transcription. In conclusion, using a sub-cellular enrichment strategy coupled with proteomic approaches, functionally relevant NR5A2 coregulators were identified. Given the receptor’s role in cancer progression, the study here elucidates additional transcriptional machinery involved in NR5A2 signaling and potentially provides new targets for therapeutics development.
DOI: 10.6084/m9.figshare.1381927.v1
title: attic

description: This is an experiment with FigShare's features
DOI: 10.6084/m9.figshare.1383212.v12
title: SERBP1 is a component of the Liver Receptor Homolog-1 transcriptional complex

description: Liver receptor homolog-1 (NR5A2) is an orphan nuclear receptor whose expression is essential for normal liver, intestine, and pancreas function. Nuclear receptors are ligand regulated transcription factors and NR5A2 has been shown to play a role in the transcriptional regulation of pathways involved in cancer. Elucidating the components of the NR5A2 transcriptional complex to better understand endogenous regulation of the receptor as well as its role in cancer remains a high priority. A sub-cellular enrichment strategy coupled with proteomic approaches was employed to identify putative NR5A2 coregulators. Nuclear fractionation protocol was essential for detection of NR5A2 peptides by MS, with most peptides being observed in the insoluble fraction (receptor bound to DNA). Duplicate data-dependent MS/MS runs using an inclusion/exclusion list improved the number of NR5A2 peptide identifications, including isoform-specific and fusion-specific peptides. Moreover, increased NR5A2 sequence coverage and a greater number of protein hits were observed with on-bead trypsin digestion of affinity captured protein. SERBP1 and ILF3 were identified as NR5A2 interacting partners. Both western blot and MS/MS analysis of endogenous receptor confirmed these binding partners are present in the NR5A2 transcriptional complex in established cell lines. Receptor knockdown by siRNA showed an increased in SERBP1 expression while ILF3 expression was unchanged. In contrast, receptor overexpression decreased only SERBP1 mRNA levels. Consistent with these data, in a promoter:reporter assay, binding of NR5A2 to the promoter region of SERBP1 resulted in a decrease in the expression level of the reporter gene, and subsequently, inhibiting transcription. In conclusion, using a sub-cellular enrichment strategy coupled with proteomic approaches, functionally relevant NR5A2 coregulators were identified. Given the receptor’s role in cancer progression, the study here elucidates additional transcriptional machinery involved in NR5A2 signaling and potentially provides new targets for therapeutics development.
DOI: 10.6084/m9.figshare.1383212.v14
title: SERBP1 is a component of the Liver Receptor Homolog-1 transcriptional complex

description: Liver receptor homolog-1 (NR5A2) is an orphan nuclear receptor whose expression is essential for normal liver, intestine, and pancreas function. Nuclear receptors are ligand regulated transcription factors and NR5A2 has been shown to play a role in the transcriptional regulation of pathways involved in cancer. Elucidating the components of the NR5A2 transcriptional complex to better understand endogenous regulation of the receptor as well as its role in cancer remains a high priority. A sub-cellular enrichment strategy coupled with proteomic approaches was employed to identify putative NR5A2 coregulators. Nuclear fractionation protocol was essential for detection of NR5A2 peptides by MS, with most peptides being observed in the insoluble fraction (receptor bound to DNA). Duplicate data-dependent MS/MS runs using an inclusion/exclusion list improved the number of NR5A2 peptide identifications, including isoform-specific and fusion-specific peptides. Moreover, increased NR5A2 sequence coverage and a greater number of protein hits were observed with on-bead trypsin digestion of affinity captured protein. SERBP1 and ILF3 were identified as NR5A2 interacting partners. Both western blot and MS/MS analysis of endogenous receptor confirmed these binding partners are present in the NR5A2 transcriptional complex in established cell lines. Receptor knockdown by siRNA showed an increased in SERBP1 expression while ILF3 expression was unchanged. In contrast, receptor overexpression decreased only SERBP1 mRNA levels. Consistent with these data, in a promoter:reporter assay, binding of NR5A2 to the promoter region of SERBP1 resulted in a decrease in the expression level of the reporter gene, and subsequently, inhibiting transcription. In conclusion, using a sub-cellular enrichment strategy coupled with proteomic approaches, functionally relevant NR5A2 coregulators were identified. Given the receptor’s role in cancer progression, the study here elucidates additional transcriptional machinery involved in NR5A2 signaling and potentially provides new targets for therapeutics development.
DOI: 10.6084/m9.figshare.1383212.v13
title: -SERBP1 is a component of the Liver Receptor Homolog-1 transcriptional complex

description: Liver receptor homolog-1 (NR5A2) is an orphan nuclear receptor whose expression is essential for normal liver, intestine, and pancreas function. Nuclear receptors are ligand regulated transcription factors and NR5A2 has been shown to play a role in the transcriptional regulation of pathways involved in cancer. Elucidating the components of the NR5A2 transcriptional complex to better understand endogenous regulation of the receptor as well as its role in cancer remains a high priority. A sub-cellular enrichment strategy coupled with proteomic approaches was employed to identify putative NR5A2 coregulators. Nuclear fractionation protocol was essential for detection of NR5A2 peptides by MS, with most peptides being observed in the insoluble fraction (receptor bound to DNA). Duplicate data-dependent MS/MS runs using an inclusion/exclusion list improved the number of NR5A2 peptide identifications, including isoform-specific and fusion-specific peptides. Moreover, increased NR5A2 sequence coverage and a greater number of protein hits were observed with on-bead trypsin digestion of affinity captured protein. SERBP1 and ILF3 were identified as NR5A2 interacting partners. Both western blot and MS/MS analysis of endogenous receptor confirmed these binding partners are present in the NR5A2 transcriptional complex in established cell lines. Receptor knockdown by siRNA showed an increased in SERBP1 expression while ILF3 expression was unchanged. In contrast, receptor overexpression decreased only SERBP1 mRNA levels. Consistent with these data, in a promoter:reporter assay, binding of NR5A2 to the promoter region of SERBP1 resulted in a decrease in the expression level of the reporter gene, and subsequently, inhibiting transcription. In conclusion, using a sub-cellular enrichment strategy coupled with proteomic approaches, functionally relevant NR5A2 coregulators were identified. Given the receptor’s role in cancer progression, the study here elucidates additional transcriptional machinery involved in NR5A2 signaling and potentially provides new targets for therapeutics development.
DOI: 10.6084/m9.figshare.1381902
title: Cuke Particle Positions - 1998-2007 - Genetic sites

description: LTRANS V2 raw output: Longitude, Latitude, depth, boundary status, and release site. Directories are structured as G1998\152\1\ meaning treatmentyear\releaseday\bin\. Files are named para 1002.csv which contains all the positions (of that treatment, year, site, and release day) at the end of the first day.
DOI: 10.6084/m9.figshare.1381902.v1
title: Cuke Particle Positions - 1998-2007 - Genetic sites

description: LTRANS V2 raw output: Longitude, Latitude, depth, boundary status, and release site. Directories are structured as G1998\152\1\ meaning treatmentyear\releaseday\bin\. Files are named para 1002.csv which contains all the positions (of that treatment, year, site, and release day) at the end of the first day.
DOI: 10.6084/m9.figshare.1381890
title: The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

description: In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
DOI: 10.6084/m9.figshare.1381890.v1
title: The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

description: In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
DOI: 10.6084/m9.figshare.1381883
title: Gaussian Job Archive for C6H6Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381882
title: Data for: Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): evidence for rapid diversification and host shifts in spider wasps

description: Voucher ID and distribution for specimens sampled.
DOI: 10.6084/m9.figshare.1381883.v1
title: Gaussian Job Archive for C6H6Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381882.v1
title: Data for: Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): evidence for rapid diversification and host shifts in spider wasps

description: Voucher ID and distribution for specimens sampled.
DOI: 10.6084/m9.figshare.1381890.v2
title: The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

description: In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
DOI: 10.6084/m9.figshare.1381879
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381881
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381879.v1
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381880
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381890.v4
title: The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

description: In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
DOI: 10.6084/m9.figshare.1381880.v1
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381881.v1
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381878
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381890.v3
title: The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

description: In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
DOI: 10.6084/m9.figshare.1381876
title: Table S2 Epidemiologic parameters for EVD and Marburg by Study

description: Epidemiologic parameters for EVD and Marburg by Study
DOI: 10.6084/m9.figshare.1381877
title: Table S3 Parameter estimates for the ongoing EVD outbreak in West Africa

description: Parameter estimates for the ongoing EVD outbreak in West Africa 2014-2015
DOI: 10.6084/m9.figshare.1381878.v1
title: Gaussian Job Archive for C25H34ClN3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1381874
title: Table S1 Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present

description: Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present
DOI: 10.6084/m9.figshare.1381875
title: Table S4 Risk factors for human to human transmission for infection with EVD

description: Risk factors for human to human transmission for infection with EVD
DOI: 10.6084/m9.figshare.1381875.v2
title: Table S4 Risk factors for human to human transmission for infection with EVD

description: Risk factors for human to human transmission for infection with EVD
DOI: 10.6084/m9.figshare.1381876.v2
title: Table S2 Epidemiologic parameters for EVD and Marburg by Study

description: Epidemiologic parameters for EVD and Marburg by Study
DOI: 10.6084/m9.figshare.1381877.v3
title: Table S3 Parameter estimates for the ongoing EVD outbreak in West Africa

description: Parameter estimates for the ongoing EVD outbreak in West Africa 2014-2015
DOI: 10.6084/m9.figshare.1381874.v2
title: Table S1 Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present

description: Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present
DOI: 10.6084/m9.figshare.1381876.v3
title: Table S2 Epidemiologic parameters for EVD and Marburg by Study

description: Epidemiologic parameters for EVD and Marburg by Study
DOI: 10.6084/m9.figshare.1381874.v1
title: Table S1 Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present

description: Human Outbreaks of Ebola Zaire, Ebola Sudan and Ebola Bundibugyo from 1976 to present
DOI: 10.6084/m9.figshare.1381875.v1
title: Table S4 Risk factors for human to human transmission for infection with EVD

description: Risk factors for human to human transmission for infection with EVD
DOI: 10.6084/m9.figshare.1381870
title: Fatiando a Terra: construindo uma base para ensino e pesquisa de geofísica

description: <strong>About </strong> This is a presentation I gave for the Department of Geophysics of the University of São Paulo. It's about my open-source project Fatiando a Terra (http://www.fatiando.org) and how I'm using for teaching geophysics and doing my own research on inverse problems. 'slides.pdf' is the presentation (made in Google Docs). The live demos were performed with some of the IPython notebooks in the 'notebooks' folder. You can view a static version of the notebooks on nbviewer (link below). The zip file 'iag-04-2015.zip' is an achive of the git repository: https://github.com/leouieda/iag-04-2015 <strong>Resumo </strong> O Fatiando a Terra (www.fatiando.org) é uma biblioteca feita na linguagem Python que tem como objetivo facilitar o trabalho de pesquisadores e professores na área geofísica. Os módulos da biblioteca foram planejados para facilitar a combinação de seus componentes de diversas formas. Por exemplo, o mesmo módulo de modelagem direta pode ser usado para produzir dados sintéticos, desenvolver um método de inversão ou como parte de uma interface gráfica interativa. Além disso, as funções da biblioteca podem ser combinadas com funções desenvolvidas pelo usuário e com as muitas bibliotecas científicas da linguagem Python. O módulo de problemas inversos automatiza grande parte da implementação de um novo método de inversão. O pesquisador implementa somente o cálculo de dados preditos e da matriz de sensibilidade, ambos reutilizando os diversos módulos de modelagem direta. Com essas duas funções, o usuário pode escolher livremente entre diversos métodos de optimização e regularização para executar sua inversão. Para o ensino de geofísica, a biblioteca pode ser combinada com a interatividade de outros programas, particularmente o IPython notebook (www.ipython.org). Conceitos difíceis de serem transmitidos em aula podem ser explorados pelos alunos de forma interativa, com botões, gráficos e animações. Por exemplo, para ensinar a reflexão e refração de ondas sísmicas, o professor pode utilizar simulações numéricas da propagação de ondas para produzir animações em tempo real. Outro exemplo é permitir aos alunos explorar como o campo geomagnético interage com um corpo geológico a diferentes latitudes para produzir uma anomalia magnética de campo total. Dessa forma, os alunos ganham experiência e intuição ao interagir com os resultados. A implementação de diversos métodos geofísicos em uma única biblioteca fornece a base necessária para a rápida criação de novas metodologias e material didático interativo. A maior parte da funcionalidade atual é para gravimetria e magnetometria, embora já exista um núcleo de sísmica e sismologia que está sendo desenvolvido. O projeto necessita de usuários e desenvolvedores para crescer e abranger os demais ramos da geofísica. O projeto é software livre e contribuições de qualquer forma são bem vindas.