cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1383212.v4
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.1383129.v1
title: Gaussian Job Archive for Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383121
title: Neural Correlates of Human Echolocation of Path Direction during Walking

description: Echolocation can be used by blind and sighted humans to navigate their environment. The current study investigated the neural activity underlying processing of path direction during walking. Brain activity was measured with fMRI in three blind echolocation experts, and three blind and three sighted novices. During scanning, participants listened to binaural recordings that had been made prior to scanning while echolocation experts had echolocated during walking along a corridor which could continue to the left, right, or straight ahead. Participants also listened to control sounds that contained ambient sounds and clicks, but no echoes. The task was to decide if the corridor in the recording continued to the left, right, or straight ahead, or if they were listening to a control sound. All participants successfully dissociated echo from no echo sounds, however, echolocation experts were superior at direction detection. We found brain activations associated with processing of path direction (contrast: echo vs. no echo) in superior parietal lobule (SPL) and inferior frontal cortex in each group. In sighted novices, additional activation occurred in the inferior parietal lobule (IPL) and middle and superior frontal areas. Within the framework of the dorso-dorsal and ventro-dorsal pathway proposed by Rizzolatti and Matelli (2003), our results suggest that blind participants may automatically assign directional meaning to the echoes, while sighted participants may apply more conscious, high-level spatial processes. High similarity of SPL and IFC activations across all three groups, in combination with previous research, also suggest that all participants recruited a multimodal spatial processing system for action (here: locomotion).
DOI: 10.6084/m9.figshare.1383212.v5
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.1383121.v1
title: Neural Correlates of Human Echolocation of Path Direction during Walking

description: Echolocation can be used by blind and sighted humans to navigate their environment. The current study investigated the neural activity underlying processing of path direction during walking. Brain activity was measured with fMRI in three blind echolocation experts, and three blind and three sighted novices. During scanning, participants listened to binaural recordings that had been made prior to scanning while echolocation experts had echolocated during walking along a corridor which could continue to the left, right, or straight ahead. Participants also listened to control sounds that contained ambient sounds and clicks, but no echoes. The task was to decide if the corridor in the recording continued to the left, right, or straight ahead, or if they were listening to a control sound. All participants successfully dissociated echo from no echo sounds, however, echolocation experts were superior at direction detection. We found brain activations associated with processing of path direction (contrast: echo vs. no echo) in superior parietal lobule (SPL) and inferior frontal cortex in each group. In sighted novices, additional activation occurred in the inferior parietal lobule (IPL) and middle and superior frontal areas. Within the framework of the dorso-dorsal and ventro-dorsal pathway proposed by Rizzolatti and Matelli (2003), our results suggest that blind participants may automatically assign directional meaning to the echoes, while sighted participants may apply more conscious, high-level spatial processes. High similarity of SPL and IFC activations across all three groups, in combination with previous research, also suggest that all participants recruited a multimodal spatial processing system for action (here: locomotion).
DOI: 10.6084/m9.figshare.1383212.v6
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.v7
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.1383102
title: Gaussian Job Archive for Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383090
title: Virtual Viewing Time: The relationship between presence and sexual interest in androphilic and gynephilic men

description: <strong>Samle_ViVT.txt: </strong>variables necessary to describe the sample and to define the subject groups <strong>IPQ_ViVT.txt</strong>: all data of the Igroup Presence Questionnaire (IPQ) <strong>SSQ_ViVT.txt</strong>: all data of the Simulator Sickness Questionnaire (SSQ) <strong>RatingViewingTimeTurnArounds.txt</strong>: main data file with all reported dependent variables (sexual attraction rating, realism rating, viewing time, turn arounds)
DOI: 10.6084/m9.figshare.1383102.v1
title: Gaussian Job Archive for Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383080
title: Raw data for Kalathur et al., 2015 ‘The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach’

description: Data file 1. Legend: List of upregulated genes Data file 2. List of downregulated genes Data file 3. List of upregulated UPR genes with stress response elements in the promoter regions (-1000bp to +500bp) Data file 4. List of all the biological processes that are enriched in differentially regulated UPR genes Data file 5. List of all the pathways that are enriched among upregulated UPR genes Data file 6. List of components of UPR interactome shown in Figure 6 Data file 7. List of genes common between UPR and Apoptosis
DOI: 10.6084/m9.figshare.1383212.v8
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.1383042
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383080.v1
title: Raw data for Kalathur et al., 2015 ‘The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach’

description: Data file 1. Legend: List of upregulated genes Data file 2. List of downregulated genes Data file 3. List of upregulated UPR genes with stress response elements in the promoter regions (-1000bp to +500bp) Data file 4. List of all the biological processes that are enriched in differentially regulated UPR genes Data file 5. List of all the pathways that are enriched among upregulated UPR genes Data file 6. List of components of UPR interactome shown in Figure 6 Data file 7. List of genes common between UPR and Apoptosis
DOI: 10.6084/m9.figshare.1383040
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383042.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383040.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383212.v9
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.1383130.v6
title: GrainSizeTools script

description: <b>GrainSizeTools script</b> is a free open-source cross-platform script written in Python that provides a number of tools with the aim of characterizing the grain size and the actual distribution of grain sizes from thin sections. The script is suitable to use in paleopiezometry studies, using different 1D grain size measures, as well as to derive the actual 3D grain size distribution using two different methods. The script only requires the previous measurement of the grain sectional areas from a thin section. There is <b>no need</b> of previous knowledge of Python programming language to use the script and get the results. For advanced users, the script is organized in a modular way using Python functions, which facilitates to modify, reuse or extend the code if needed.
DOI: 10.6084/m9.figshare.1381927
title: attic

description: This is an experiment with FigShare's features
DOI: 10.6084/m9.figshare.1383212.v10
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.