cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1512834.v253
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1499199
title: The Explorer Islamabad Issue 7

description: The Explorer Islmabad Issue 7
DOI: 10.6084/m9.figshare.1499204
title: Nelson rules failure analysis

description: An analysis of how often the nelson rules fail on different length sequences
DOI: 10.6084/m9.figshare.1499209.v2
title: University of Edinburgh APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Edinburgh during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1512834.v254
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1499199.v1
title: The Explorer Islamabad Issue 7

description: The Explorer Islmabad Issue 7
DOI: 10.6084/m9.figshare.1499209.v1
title: University of Edinburgh APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Edinburgh during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1499179
title: UCL APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by UCL during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1499179.v1
title: UCL APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by UCL during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1512834.v255
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1499204.v1
title: Nelson rules failure analysis

description: An analysis of how often the nelson rules fail on different length sequences
DOI: 10.6084/m9.figshare.1512834.v256
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1499145
title: 16S rRNA amplicon data from the paper : "The outer mucus layer hosts a distinct intestinal microbial niche"

description: The 16S rRNA gene segments spanning the variable V5 and V6 regions were amplified from DNA from mucus, contents, or mouse faecal samples using a multiplex approach with barcoded primers. The PCR amplified 16S V5-V6 amplicons were purified and prepared for sequencing on the Ion torrent PGM system according to the manufacturer’s instructions (Life Technologies). The FASTQ files provided correspond to the two microbial diversity status tested in the study: SPF (2 files) and sDMDMm2 defined flora (1 file). Each file corresponds to an Ion torrent chip.The corresponding mapping files (containing barcodes and sample metadata) are also provided in TXT format. These files can be used directly for analysis (eg. using the Qiime pipeline).
DOI: 10.6084/m9.figshare.1512834.v257
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1499204.v2
title: Nelson rules failure analysis

description: An analysis of how often the nelson rules fail on different length sequences
DOI: 10.6084/m9.figshare.1512834.v258
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1512834.v259
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1497978
title: Absence of vitamin K-dependent γ-carboxylation in human periostin extracted from fibrotic lung or secreted from a cell line engineered to optimize γ-carboxylation

description: Identifying the presence and absence of gamma-carboxylation of periostin and coagulation factor VII proteins
DOI: 10.6084/m9.figshare.1497988
title: Linguistic corpus of international nonproprietary names

description: Linguistic corpus of international nonproprietary names, comprising all INNs published to 2013, with analysis of character count, diachronic changes in formal properties, semantic analysis of taxonomy and instances of prohibited graphemes under WHO naming guidelines. The data was primarily used for a Master's thesis, and now being further developed in a PhD.
DOI: 10.6084/m9.figshare.1512834.v260
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1497961
title: Synbreed Biodiversity Panel Genotypes

description: <strong>Synbreed Diversity Panel Genotypes</strong> These data have been made available coupled with the publication of Beissinger, T., Gholami, M., Erbe, M., Weigend, S., Weigend, A., de Leon, N., Gianola, D., and Simianer, H., <em>Using the Varibility of Linkage Disequilibrium Between Populations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens</em>, Heredity, 2015. Please cite upon use. <strong>Synbreed – Synergistic Plant and Animal Breeding</strong> (Synbreed) was funded by the German Federal Ministry of Education and Research (BMBF) from 2009 -<br>2014 (Funding ID: 0315526) ; web address http://www.synbreed.tum.de/ ***<br>Samples were genotyped with 580K SNP Affymetrix Axiom® Genome-Wide Chicken Genotyping Array. <strong>Genotype_Matrix.Robj</strong><br>This file is a matrix of genotypes from 1,417 chickens encompassing 72 breeds, genotyped as part of the Synbreed Project. The file can be loaded into R with the load() command. Individuals are in rows and marker genotypes, coded 0, 1, and 2, are in columns. Row names are a breed index, so all rows named "1" are from breed 1, all rows named "2" are from breed 2, and so on. Column names are marker names. <strong>Genotype_Map.Robj</strong><br>This file is a map describing the 564,939 markers that were genotyped. The file can be loaded into R with the load() command. Each row describes a marker. The first column, named "SNP" provides the marker name. This column corresponds to the rows of the Genotype_Matrix.Robj file. The second column, named "Chr", is the chromosome. The third column, named "Pos", is the physical position of the marker.
DOI: 10.6084/m9.figshare.1497961.v1
title: Synbreed Biodiversity Panel Genotypes

description: <strong>Synbreed Diversity Panel Genotypes</strong> These data have been made available coupled with the publication of Beissinger, T., Gholami, M., Erbe, M., Weigend, S., Weigend, A., de Leon, N., Gianola, D., and Simianer, H., <em>Using the Varibility of Linkage Disequilibrium Between Populations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens</em>, Heredity, 2015. Please cite upon use. <strong>Synbreed – Synergistic Plant and Animal Breeding</strong> (Synbreed) was funded by the German Federal Ministry of Education and Research (BMBF) from 2009 -<br>2014 (Funding ID: 0315526) ; web address http://www.synbreed.tum.de/ ***<br>Samples were genotyped with 580K SNP Affymetrix Axiom® Genome-Wide Chicken Genotyping Array. <strong>Genotype_Matrix.Robj</strong><br>This file is a matrix of genotypes from 1,417 chickens encompassing 72 breeds, genotyped as part of the Synbreed Project. The file can be loaded into R with the load() command. Individuals are in rows and marker genotypes, coded 0, 1, and 2, are in columns. Row names are a breed index, so all rows named "1" are from breed 1, all rows named "2" are from breed 2, and so on. Column names are marker names. <strong>Genotype_Map.Robj</strong><br>This file is a map describing the 564,939 markers that were genotyped. The file can be loaded into R with the load() command. Each row describes a marker. The first column, named "SNP" provides the marker name. This column corresponds to the rows of the Genotype_Matrix.Robj file. The second column, named "Chr", is the chromosome. The third column, named "Pos", is the physical position of the marker.
DOI: 10.6084/m9.figshare.1497988.v2
title: Linguistic corpus of international nonproprietary names

description: Linguistic corpus of international nonproprietary names, comprising all INNs published to 2013, with analysis of character count, diachronic changes in formal properties, semantic analysis of taxonomy and instances of prohibited graphemes under WHO naming guidelines. The data was primarily used for a Master's thesis, and now being further developed in a PhD.
DOI: 10.6084/m9.figshare.1512834.v261
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1497956
title: Spatio-Temporal Covariance and Cross-Covariance Functions of the Great Circle Distance on a Sphere

description: In this article, we propose stationary covariance functions for processes that evolve temporally over a sphere, as well as cross-covariance functions for multivariate random fields defined over a sphere. For such processes, the great circle distance is the natural metric that should be used to describe spatial dependence. Given the mathematical difficulties for the construction of covariance functions for processes defined over spheres cross time, approximations of the state of nature have been proposed in the literature by using the Euclidean (based on map projections) and the chordal distances. We present several methods of construction based on the great circle distance and provide closed-form expressions for both spatio-temporal and multivariate cases. A simulation study assesses the discrepancy between the great circle distance, chordal distance, and Euclidean distance based on a map projection both in terms of estimation and prediction in a space-time and a bivariate spatial setting, where the space is in this case the Earth. We revisit the analysis of Total Ozone Mapping Spectrometer (TOMS) data and investigate differences in terms of estimation and prediction between the aforementioned distance-based approaches. Both simulation and real data highlight sensible differences in terms of estimation of the spatial scale parameter. As far as prediction is concerned, the differences can be appreciated only when the interpoint distances are large, as demonstrated by an illustrative example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1497988.v1
title: Linguistic corpus of international nonproprietary names

description: Linguistic corpus of international nonproprietary names, comprising all INNs published to 2013, with analysis of character count, diachronic changes in formal properties, semantic analysis of taxonomy and instances of prohibited graphemes under WHO naming guidelines. The data was primarily used for a Master's thesis, and now being further developed in a PhD.
DOI: 10.6084/m9.figshare.1497978.v3
title: Absence of vitamin K-dependent y-carboxylation in human periostin extracted from fibrotic lung or secreted from a cell line engineered to optimize y- carboxylation

description: Identifying the presence and absence of gamma-carboxylation in periostin and coagulation factor VII proteins
DOI: 10.6084/m9.figshare.1512834.v262
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1497956.v1
title: Spatio-Temporal Covariance and Cross-Covariance Functions of the Great Circle Distance on a Sphere

description: In this article, we propose stationary covariance functions for processes that evolve temporally over a sphere, as well as cross-covariance functions for multivariate random fields defined over a sphere. For such processes, the great circle distance is the natural metric that should be used to describe spatial dependence. Given the mathematical difficulties for the construction of covariance functions for processes defined over spheres cross time, approximations of the state of nature have been proposed in the literature by using the Euclidean (based on map projections) and the chordal distances. We present several methods of construction based on the great circle distance and provide closed-form expressions for both spatio-temporal and multivariate cases. A simulation study assesses the discrepancy between the great circle distance, chordal distance, and Euclidean distance based on a map projection both in terms of estimation and prediction in a space-time and a bivariate spatial setting, where the space is in this case the Earth. We revisit the analysis of Total Ozone Mapping Spectrometer (TOMS) data and investigate differences in terms of estimation and prediction between the aforementioned distance-based approaches. Both simulation and real data highlight sensible differences in terms of estimation of the spatial scale parameter. As far as prediction is concerned, the differences can be appreciated only when the interpoint distances are large, as demonstrated by an illustrative example. Supplementary materials for this article are available online.