cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1512834.v242
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.1499289
title: etd_digital_diploma_disciplines

description: 国立国会図書館(NDL)が「国立国会図書館によるDOI付与」[1]のウェブページで公開している「学位論文に付与されたDOIのリスト(平成26年2月24日時点) tsv形式(zip): 67.3MB」[2]を用いて、「博士学位分野名」の集計を行ったデータ(タブ区切りテキスト)です。集計件数は140,904件です。<br>なお、空白文字と丸括弧に全半角が混在していたので、空白文字は除去、丸括弧は半角に統一する処理を施しています。 ※ もし、データ公開について問題等ございましたら、お手数ですが、jiro ***slis.tsukuba.ac.jp までご連絡ください(***を@に変換してください)。 [1] http://www.ndl.go.jp/jp/aboutus/dlib/cooperation/doi.html [2] http://dl.ndl.go.jp/files/etd_digital.zip
DOI: 10.6084/m9.figshare.1512834.v243
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.1499289.v2
title: etd_digital_diploma_disciplines

description: 国立国会図書館(NDL)が「国立国会図書館によるDOI付与」[1]のウェブページで公開している「学位論文に付与されたDOIのリスト(平成26年2月24日時点) tsv形式(zip): 67.3MB」[2]を用いて、「博士学位分野名」の集計を行ったデータ(タブ区切りテキスト)です。集計件数は140,904件です。<br>なお、空白文字と丸括弧に全半角が混在していたので、空白文字は除去、丸括弧は半角に統一する処理を施しています。 ※ もし、データ公開について問題等ございましたら、お手数ですが、jiro ***slis.tsukuba.ac.jp までご連絡ください(***を@に変換してください)。 [1] http://www.ndl.go.jp/jp/aboutus/dlib/cooperation/doi.html [2] http://dl.ndl.go.jp/files/etd_digital.zip
DOI: 10.6084/m9.figshare.1499289.v4
title: etd_digital_diploma_disciplines

description: 国立国会図書館(NDL)が「国立国会図書館によるDOI付与」[1]のウェブページで公開している「学位論文に付与されたDOIのリスト(平成26年2月24日時点) tsv形式(zip): 67.3MB」[2]を用いて、「博士学位分野名」の集計を行ったデータ(タブ区切りテキスト)です。集計件数は140,904件です。<br>なお、空白文字と丸括弧に全半角が混在していたので、空白文字は除去、丸括弧は半角に統一する処理を施しています。 ※ もし、データ公開について問題等ございましたら、お手数ですが、jiro ***slis.tsukuba.ac.jp までご連絡ください(***を@に変換してください)。 [1] http://www.ndl.go.jp/jp/aboutus/dlib/cooperation/doi.html [2] http://dl.ndl.go.jp/files/etd_digital.zip
DOI: 10.6084/m9.figshare.1512834.v244
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.1499289.v3
title: etd_digital_diploma_disciplines

description: 国立国会図書館(NDL)が「国立国会図書館によるDOI付与」[1]のウェブページで公開している「学位論文に付与されたDOIのリスト(平成26年2月24日時点) tsv形式(zip): 67.3MB」[2]を用いて、「博士学位分野名」の集計を行ったデータ(タブ区切りテキスト)です。集計件数は140,904件です。<br>なお、空白文字と丸括弧に全半角が混在していたので、空白文字は除去、丸括弧は半角に統一する処理を施しています。 ※ もし、データ公開について問題等ございましたら、お手数ですが、jiro ***slis.tsukuba.ac.jp までご連絡ください(***を@に変換してください)。 [1] http://www.ndl.go.jp/jp/aboutus/dlib/cooperation/doi.html [2] http://dl.ndl.go.jp/files/etd_digital.zip
DOI: 10.6084/m9.figshare.1512834.v245
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.1499273
title: Scattering of a plasmonic nanoantenna embedded in a silicon waveguide

description: Plasmonic antennas integrated on silicon devices have large and yet unexplored potential for controlling and routing light signals. Here, we present theoretical calculations of a hybrid silicon-metallic system in which a single gold nanoantenna embedded in a single-mode silicon waveguide acts as a resonance-driven filter. As a consequence of scattering and interference, when the resonance condition of the antenna is met, the transmission drops by 85% in the resonant frequency band. Firstly, we study analytically the interaction between the propagating mode and the antenna by including radiative corrections to the scattering process and the polarization of the waveguide walls. Secondly, we find the configuration of maximum interaction and numerically simulate a realistic nanoantenna in a silicon waveguide. The numerical calculations show a large suppression of transmission and three times more scattering than absorption, consequent with the analytical model. The system we propose can be easily fabricated by standard silicon and plasmonic lithographic methods, making it promising as real component in future optoelectronic circuits.
DOI: 10.6084/m9.figshare.1499273.v1
title: Scattering of a plasmonic nanoantenna embedded in a silicon waveguide

description: Plasmonic antennas integrated on silicon devices have large and yet unexplored potential for controlling and routing light signals. Here, we present theoretical calculations of a hybrid silicon-metallic system in which a single gold nanoantenna embedded in a single-mode silicon waveguide acts as a resonance-driven filter. As a consequence of scattering and interference, when the resonance condition of the antenna is met, the transmission drops by 85% in the resonant frequency band. Firstly, we study analytically the interaction between the propagating mode and the antenna by including radiative corrections to the scattering process and the polarization of the waveguide walls. Secondly, we find the configuration of maximum interaction and numerically simulate a realistic nanoantenna in a silicon waveguide. The numerical calculations show a large suppression of transmission and three times more scattering than absorption, consequent with the analytical model. The system we propose can be easily fabricated by standard silicon and plasmonic lithographic methods, making it promising as real component in future optoelectronic circuits.
DOI: 10.6084/m9.figshare.1499249
title: Analysis of the binding mode of laulimalide to microtubules: Establishing a laulimalide–tubulin pharmacophore

description: Laulimalide (LA) is a microtubule-stabilizing agent, currently in preclinical studies. However, studying the binding of this species and successfully synthesizing potent analogues have been challenging. The LA binding site is located between tubulin protofilaments, and therefore LA is in contact with two adjacent -tubulin units. Here, an improved model of the binding mode of LA in microtubules is presented, using the newly available crystal structure pose and an extended tubulin heterodimer complex, as well as molecular dynamics simulations. With this model, a series of LA analogues developed by Mooberry and coworkers are also analyzed in order to establish important pharmacophores in LA binding and cytotoxicity. In the side chain, – interactions are important contributors to LA binding, as are water-mediated hydrogen bonds. An intramolecular hydrogen bond is correlated with high cytotoxicity, and is dependent on macrocycle conformation. Therefore, while the epoxide and olefin groups in the macrocycle do not engage in specific interactions with the protein, they are essential contributions to an active macrocycle conformation, and therefore potency. Calculations reveal that a balance in binding affinity is important for LA activity, where the more potent compounds have larger interactions with the adjacent tubulin unit than the less-active analogs. Several modifications are suggested for the rational design of LA analogues that should not disrupt the active macrocycle conformation.
DOI: 10.6084/m9.figshare.1512834.v246
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.1499249.v1
title: Analysis of the binding mode of laulimalide to microtubules: Establishing a laulimalide–tubulin pharmacophore

description: Laulimalide (LA) is a microtubule-stabilizing agent, currently in preclinical studies. However, studying the binding of this species and successfully synthesizing potent analogues have been challenging. The LA binding site is located between tubulin protofilaments, and therefore LA is in contact with two adjacent -tubulin units. Here, an improved model of the binding mode of LA in microtubules is presented, using the newly available crystal structure pose and an extended tubulin heterodimer complex, as well as molecular dynamics simulations. With this model, a series of LA analogues developed by Mooberry and coworkers are also analyzed in order to establish important pharmacophores in LA binding and cytotoxicity. In the side chain, – interactions are important contributors to LA binding, as are water-mediated hydrogen bonds. An intramolecular hydrogen bond is correlated with high cytotoxicity, and is dependent on macrocycle conformation. Therefore, while the epoxide and olefin groups in the macrocycle do not engage in specific interactions with the protein, they are essential contributions to an active macrocycle conformation, and therefore potency. Calculations reveal that a balance in binding affinity is important for LA activity, where the more potent compounds have larger interactions with the adjacent tubulin unit than the less-active analogs. Several modifications are suggested for the rational design of LA analogues that should not disrupt the active macrocycle conformation.
DOI: 10.6084/m9.figshare.1512834.v247
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.1499248
title: Rodriguez-R Metagenomes

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1499248.v1
title: Rodriguez-R Metagenomes

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1499246
title: Mason et al Metagenomes, Metatranscriptomes, SAGs, and Yergeau metagenomes

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1512834.v248
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: 10.17632/dkx728tns4.12
title: Data for: Engineering geology of residual soil derived from mudstone in Zimbabwe

description: The soil properties and supplementary materials are provided.
DOI: 10.6084/m9.figshare.1499246.v1
title: Mason Data

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1512834.v249
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.1499239
title: Additional File 3

description: Additional File 3 in the anvi'o methods paper.
DOI: 10.6084/m9.figshare.1512834.v250
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.1499237
title: Additional File 1

description: Additional File 1 in the anvi'o methods paper.
DOI: 10.6084/m9.figshare.1499238
title: Additional File 2

description: Additional File 2 in the anvi'o methods paper.
DOI: 10.6084/m9.figshare.1499235
title: Mason et al SAGs

description: Anvi'o merged profile
DOI: 10.6084/m9.figshare.1499236
title: Sharon et al. metagenomes

description: Anvi'o merged profile
DOI: 10.6084/m9.figshare.1499238.v1
title: Additional File 2

description: Additional File 2 in the anvi'o methods paper.
DOI: 10.6084/m9.figshare.1499222
title: The Squeezed Limit of the Bispectrum for Multi-field Inflation

description: We calculate the squeezed limit of the bispectrum produced by inflation with multiple light fields. To achieve this we allow for different horizon exit times for each mode and calculate the intrinsic field-space three-point function in the squeezed limit using soft-limit techniques. We then use the delta N formalism from the time the last mode exits the horizon to calculate the bispectrum of the primordial curvature perturbation.
DOI: 10.6084/m9.figshare.1512834.v251
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.1499234
title: Overholt et al. cultivars

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1499222.v1
title: The Squeezed Limit of the Bispectrum for Multi-field Inflation

description: We calculate the squeezed limit of the bispectrum produced by inflation with multiple light fields. To achieve this we allow for different horizon exit times for each mode and calculate the intrinsic field-space three-point function in the squeezed limit using soft-limit techniques. We then use the delta N formalism from the time the last mode exits the horizon to calculate the bispectrum of the primordial curvature perturbation.
DOI: 10.6084/m9.figshare.1499234.v1
title: Overholt et al. cultivars

description: Anvi'o merged profile.
DOI: 10.6084/m9.figshare.1499235.v1
title: Mason et al SAGs

description: Anvi'o merged profile
DOI: 10.6084/m9.figshare.1499236.v2
title: Sharon et al. metagenomes

description: Anvi'o merged profile
DOI: 10.6084/m9.figshare.1512834.v252
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.1499236.v1
title: Sharon et al. metagenome

description: Anvi'o merged profile
DOI: 10.6084/m9.figshare.1499209
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/).