cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.100516.v1
title: Deep VEGF up-regulation in atypical melanocytic lesions:Differential correlation with apoptosis in Spitz tumors and atypical melanocytic nevi

description: Background: The bases of the cell kinetics and microvessel profiles in cutaneous atypical melanocytic lesions (atypical melanocytic nevi, AMN, and Spitz tumors, ST) are poorly understood. No study has correlated cell kinetics, microvessel profile, and VEGF expression by topographic compartments in AMN and ST to date. Design: We selected low-grade AMN (93), high-grade AMN (31), ST (42), malignant melanomas (42, 15 radial growth phase MM-RGP and 27 vertical growth phase MM- VGP), and conventional melanocytic nevi (15 junctional, 20 compound), the latter two groups used as controls. Immunostaining for Ki-67 and VEGF, and in situ end labeling (ISEL) of DNA fragments (using Klenow fragment of DNA polymerase I) were scored by topographic compartments: junctional, superficial dermal (above 0.76 mm) and deep dermal (below 0.76 mm), screening the whole compartment in each case. Appropriate controls were run in each sample. CD-31-stained slides were used to estimate microvessel density. The results were statistically compared using analysis of variance and Student t- test, and considered significant if P&lt;0.05. Results: Superficial-to-deep gradient was maintained for Ki-67 in all lesions, but was significantly higher in MM. From junctional to deep dermal compartments, ST showed a progressive and statistically significant increase of ISEL indices (4.38%, 4.73%, 8.35%), which correlate directly with microvessel density (4.38, 4.39, 7.41 vessels/HPF). Dysplasia grading revealed an inverse correlation with apoptosis in AMN, but kept the superficial- deep gradient. VEGF expression by compartments appears in the Table. Junctional/ Superficial/ Deep Junctional Nevi/ 11.00/ --/ -- Compound Nevi/ 4.39/ 0.92/ 0.45 Spitz/ 29.04/ 34.85/ 42.82 LG-AMN/ 18.57/ 8.76/ 0.53 HG-AMN/ 16.74/ 7.20/ 5.56 MIS/ 5.52/ --/ -- MM-RGP/ 25.25/ 28.08/ 52.79<br>MM-VGP/ 39.65/ 55.21/ 43.83<br>Conclusion: Deep VEGF up-regulation characterizes the vascular reaction associated with high-grade AMN and inversely correlates with the apoptosis index. In contrast, VEGF expression in ST directly correlates with the microvessel density and apoptosis index and inversely with the proliferation index, suggesting that this distinctive blood vessel pattern is reactive to regressive cellular changes.
DOI: 10.6084/m9.figshare.100494
title: Alfalfa Cell Wall Proteomics Supplemental files

description: Supplemental data for: Verdonk JC, Hatfield RD and Sullivan ML (2012) Proteomic analysis of cell walls of two developmental stages of alfalfa stems. Front. Plant Sci. 3:279. doi: 10.3389/fpls.2012.00279 Update July 2015: The RAW files were replace with .mzXML files jul 2015. We are doing our best to include the RAW files as well.
DOI: 10.6084/m9.figshare.100443
title: Gaussian Job Archive for C14H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.100516.v2
title: Deep VEGF up-regulation in atypical melanocytic lesions: Differential correlation with apoptosis in Spitz tumors and atypical melanocytic nevi

description: Background: The bases of the cell kinetics and microvessel profiles in cutaneous atypical melanocytic lesions (atypical melanocytic nevi, AMN, and Spitz tumors, ST) are poorly understood. No study has correlated cell kinetics, microvessel profile, and VEGF expression by topographic compartments in AMN and ST to date. Design: We selected low-grade AMN (93), high-grade AMN (31), ST (42), malignant melanomas (42, 15 radial growth phase MM-RGP and 27 vertical growth phase MM- VGP), and conventional melanocytic nevi (15 junctional, 20 compound), the latter two groups used as controls. Immunostaining for Ki-67 and VEGF, and in situ end labeling (ISEL) of DNA fragments (using Klenow fragment of DNA polymerase I) were scored by topographic compartments: junctional, superficial dermal (above 0.76 mm) and deep dermal (below 0.76 mm), screening the whole compartment in each case. Appropriate controls were run in each sample. CD-31-stained slides were used to estimate microvessel density. The results were statistically compared using analysis of variance and Student t- test, and considered significant if P&lt;0.05. Results: Superficial-to-deep gradient was maintained for Ki-67 in all lesions, but was significantly higher in MM. From junctional to deep dermal compartments, ST showed a progressive and statistically significant increase of ISEL indices (4.38%, 4.73%, 8.35%), which correlate directly with microvessel density (4.38, 4.39, 7.41 vessels/HPF). Dysplasia grading revealed an inverse correlation with apoptosis in AMN, but kept the superficial- deep gradient. VEGF expression by compartments appears in the Table. Junctional/ Superficial/ Deep Junctional Nevi/ 11.00/ --/ -- Compound Nevi/ 4.39/ 0.92/ 0.45 Spitz/ 29.04/ 34.85/ 42.82 LG-AMN/ 18.57/ 8.76/ 0.53 HG-AMN/ 16.74/ 7.20/ 5.56 MIS/ 5.52/ --/ -- MM-RGP/ 25.25/ 28.08/ 52.79<br>MM-VGP/ 39.65/ 55.21/ 43.83<br>Conclusion: Deep VEGF up-regulation characterizes the vascular reaction associated with high-grade AMN and inversely correlates with the apoptosis index. In contrast, VEGF expression in ST directly correlates with the microvessel density and apoptosis index and inversely with the proliferation index, suggesting that this distinctive blood vessel pattern is reactive to regressive cellular changes.
DOI: 10.6084/m9.figshare.100443.v1
title: Gaussian Job Archive for C14H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.100494.v1
title: RAW files

description: Supplemental data for: Verdonk JC, Hatfield RD and Sullivan ML (2012) Proteomic analysis of cell walls of two developmental stages of alfalfa stems. Front. Plant Sci. 3:279. doi: 10.3389/fpls.2012.00279
DOI: 10.6084/m9.figshare.100413
title: Simulated muons for the 5th MuSIC beam time

description: Plots characterising simulated muons in the detector of the 5th MuSIC beamline.
DOI: 10.6084/m9.figshare.100506.v1
title: Deep dermal up-regulation of HIF-1A is directly correlated with apoptosis in Spitz tumors

description: Background: The microvessel profile bases in cutaneous atypical melanocytic lesions (atypical melanocytic nevi, AMN, and Spitz tumors, ST) are poorly understood. No study has correlated microvessel profile and HIF-1 expression with cell kinetics by topographic compartments in AMN and ST to date. Design: We selected low-grade AMN (93), high-grade AMN (31), ST (42), malignant melanomas (42, 15 radial growth phase MM-RGP and 27 vertical growth phase MM- VGP), and conventional melanocytic nevi (15 junctional, 20 compound), the latter two groups used as controls. Immunostaining for Ki-67 and HIF-1, and in situ end labeling (ISEL) of DNA fragments (using Klenow fragment of DNA polymerase I) were scored by topographic compartments: junctional, superficial dermal (above 0.76 mm) and deep dermal (below 0.76 mm), screening the whole compartment in each case. Appropriate controls were run in each sample. CD-31-stained slides were used to estimate microvessel density. The results were statistically compared using analysis of variance and Student t- test, and considered significant if P&lt;0.05. Results: Superficial-to-deep gradient was maintained for Ki-67 in all lesions, but was significantly higher in MM. From junctional to deep dermal compartments, ST showed a progressive and statistically significant increase of ISEL indices (4.38%, 4.73%, 8.35%), and no correlation with microvessel density. Dysplasia grading revealed an inverse correlation with Ki67/ISEL index in AMN, but kept the superficial-deep gradient. HIF-1 expression by compartments appears in the Table. Junctional Superficial Deep Junctional Nevi/ 2.48/ --/ -- Compound Nevi/ 2.59/ 2.41/ 0 Spitz/ 16.32/ 15.09/ 14.12 LG-AMN/ 2.59/ 0.86/ 0 HG-AMN/ 3.42/ 0.55/ 0 MIS/ 0.76/ --/ --<br>MM-RGP/ 5.81/ 11.63/ --<br>MM-VGP/ 10.58/ 18.78/ 18.08<br>Conclusion: Deep dermal upregulation of HIF-1 characterizes Spitz tumor and vertical growth phase MM, with preservation of the superficial-deep gradient and direct correlation with apoptosis in Spitz tumors only. This over-expression represents an additional mechanism of neovascularization, which does not correlate directly with the vascular density level.
DOI: 10.6084/m9.figshare.100404
title: Results of the FRAPPE clustering analysis of the combined genome-wide SNP data from 5 different sources

description: These are the results structure analyses performed by FRAPPE, with default settings and K ranging from 2 to 16, on a combined dataset consisting in 3146 autosomal SNPs for 4025 individuals from 167 populations. For each analysis, each line corresponds to an individual. The first column is the population identifier, the second column is the individual identifier, the last columns are the proportions of the different ancestry classes determined by FRAPPE for the individual. The analyzed data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources.
DOI: 10.6084/m9.figshare.100413.v1
title: Simulated muons for the 5th MuSIC beam time

description: Plots characterising simulated muons in the detector of the 5th MuSIC beamline.
DOI: 10.6084/m9.figshare.100442
title: Exploratory analysis of combined genome-wide SNP data from 5 sources

description: These files are the raw results and figures corresponding to the study deposited un arXiv under the title "An exploratory analysis of combined genome-wide SNP data from several recent studies" and url http://arxiv.org/abs/1101.5519 These files are sub-structured in smaller file sets, the urls of which are given in the links section. It may be preferable to download these smaller file sets separately using these links, and uncompress the obtained archives in separate directories. The download of the present file set will result in an archive where all figures are in the same folder.
DOI: 10.6084/m9.figshare.100494.v2
title: Alfalfa Cell Wall Proteomics RAW files

description: Supplemental data for: Verdonk JC, Hatfield RD and Sullivan ML (2012) Proteomic analysis of cell walls of two developmental stages of alfalfa stems. Front. Plant Sci. 3:279. doi: 10.3389/fpls.2012.00279
DOI: 10.6084/m9.figshare.100343
title: all populations profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using all sampled populations. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.100298
title: west and south Eurasia profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the populations of west and south Eurasia. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.100343.v1
title: all populations profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using all sampled populations. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.100298.v1
title: west and south Eurasia profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the populations of west and south Eurasia. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.100494.v3
title: Alfalfa Cell Wall Proteomics Supplemental files

description: Supplemental data for: Verdonk JC, Hatfield RD and Sullivan ML (2012) Proteomic analysis of cell walls of two developmental stages of alfalfa stems. Front. Plant Sci. 3:279. doi: 10.3389/fpls.2012.00279
DOI: 10.6084/m9.figshare.99996
title: Austronesians profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the Austronesian populations of the sample. The Visaya Chabakano population is in a different colour because they speak a Spanish-based creole language, while the other populations speak Austronesian languages.
DOI: 10.6084/m9.figshare.100240.v1
title: Initial momentum distribution of decaying muons

description: The initial momentum distribution for muons that then decay between two counters. The muons are degraded with a variety of thickness aluminium plates (indicated by colour) then passed through two counters that sandwich a 0.5mm copper stopping target. Muons are selected in the upstream counter and their decay daughter electrons in the downstream counter. Simulation done using Geant4 with geometry based on the set up of the 5th MuSIC beam time.
DOI: 10.6084/m9.figshare.100241.v1
title: Simulated muon decay times with varying degraders

description: Simulated time differences between muon detetion and detection of their daughter electrons. The initial muons are modelled on the MuSIC beam and fired through a variety of different thickness degraders (indicated by the differing colours). Downstream of the degrader are two counters either side of a 0.5mm copper stopping target. Time differences are calculated between a parent muon in the upstream counter and daughter electrons in the downstream counter. Simulation implemented with Geant4 based upon the detector used during the 5th MuSIC beamtime at the RCNP in Osaka.
DOI: 10.6084/m9.figshare.99996.v1
title: Austronesians profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the Austronesian populations of the sample. The Visaya Chabakano population is in a different colour because they speak a Spanish-based creole language, while the other populations speak Austronesian languages.
DOI: 10.6084/m9.figshare.100239.v1
title: Muon momentum distribution at a copper stopping target

description: Total muon momentum distribution at the copper stopping target in the MuSIC beam line. Muons are degraded with a variety of different thickness aluminium plates (indicated by colour) before passing through two counters that sandwich the copper stopping target at which this distribution is taken. Simulated using Geant4 based on the 5th MuSIC beam time.
DOI: 10.6084/m9.figshare.99986
title: Austro-Tai profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the Austronesian and Tai-Kadai populations of the sample. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.99962
title: Gaussian Job Archive for C12H11NO2S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99965
title: Sino-Hmong-Mien-Tai profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the Sino-Tibetan, Hmong-Mien and Tai-Kadai populations of the sample. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.99986.v1
title: Austro-Tai profile trees

description: The data consists in genome-wide SNPs that were obtained from 5 different sources, keeping the SNPs common to all 5 sources. The combined dataset consisted in 3146 autosomal SNPs for 4025 individuals from 167 populations. It was analyzed using FRAPPE, with default settings, and for K ranging from 2 to 16. For each value of K, the resulting ancestry profiles were averaged within each population, and a chi-squared distance between the average ancestry profiles were used to compute a distance tree using FastME. These trees were computed using the Austronesian and Tai-Kadai populations of the sample. The colour of a leaf is chosen according to the linguistic family of the corresponding population.
DOI: 10.6084/m9.figshare.99908
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99962.v1
title: Gaussian Job Archive for C12H11NO2S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99907
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99908.v1
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99987.v1
title: Statistical Analysis Plan - MATISSE RCT subgroup anlysis

description: Statistical Analysis Plan for a secondary analysis of the MATISSE randomised controlled trial (ISRCTN46150447), investigating baseline characteristics of participants as moderators of effectiveness.
DOI: 10.6084/m9.figshare.99907.v1
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99881
title: Gaussian Job Archive for C16H10N2O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99881.v1
title: Gaussian Job Archive for C16H10N2O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99888.v1
title: DOI-10.1002-path.1711980102 - 1711980102 J Pathol 198-56A.pdf

description: Introduction: Spitz tumors (ST) are poorly understood, their behavior can be unpredictable and their cell kineticis unknown. Methods: We selected ST (42), malignant melanomas (42, 15 radial growth phase MM-RGP and 27 vertical growth phase MM- VGP), and conventional melanocytic nevi (15 junctional, 20 compound), the latter two grou s used as controls. lmmunostainingfor Ki-67, p53, p21WAF1 and p27KIP1 was scored by topographic compartments (junctional, and dermal superficial and deep to 0.76 mm), screening the whole compartment in each case. CD-31-stained slides were used to estimate microvessel density. The results were statistically compared using analysis of variance and Student t-test, and consideredsignificantif P&lt;0.05. Results: Superficial-to-deep gradient was maintained for Ki-67 in all lesions, but significantly higher in MM. No differences in p53 immunoexpression were detected. ST revealed reverse pattern with significantly overexpressed p21WAF1 and p27KIP1 and increased microvessel density at the deep dermal compartment. Conclusions: The kinetic profile suggests an overall regression for ST and a dissociated and ineffective deep vascular proliferation to maintain the cell growth.
DOI: 10.6084/m9.figshare.99879
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99880
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99880.v1
title: Gaussian Job Archive for C12H12

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.99876
title: Student enjoyment and usefulness scores of role plays in a Medical Humanities module at KIST Medical College, Lalitpur, Nepal

description: Enjoyment and usefulness scores of role plays used during the medical humanities module (KIST Medical College, Nepal) according to gender and method of financing of medical education.<br>Gender: 1 = male, 2 = female<br>Method of financing: 1 = self-financing, 2 = scholarship Enjoyment and usefulness scores are scored between 1 (lowest) to 5 (highest).
DOI: 10.6084/m9.figshare.99878
title: Interactions: The Magic Word is "Neuroscience" (data)

description: This dataset consists of the raw data used for creating a frequency distribution of 100 words that appear in a sample of cognitive psychology article titles. All data were collected from the Altmetric database. The histogram appears in a blog post on the Altmetric blog.