cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5442229
title: Datasets used in "Antibody interface prediction with 3D Zernike descriptors and SVM"

description: <b>Background:</b> In this work we present a novel method for antibody interface prediction from their experimentally-solved structures based on 3D Zernike Descriptors. Roto-translationally invariant descriptors are computed from circular patches of the antibody surface enriched with a chosen subset of physicochemical properties from the AAindex1 amino acid index set, and are used as samples for a binary classification problem. An SVM classifier is used to distinguish interface surface patches from non-interface ones. The proposed method was shown to outperform other antigen-binding interface prediction software.<b><br><br>seq_descriptors_4.5.tar.gz -</b> Contains the sequence descriptors generated from the antibody structures in the development/validation set which were used for feature selection with the Randomized Logistic Regression algorithm.<br><br><b>development_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the development/validation set; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files.<br><br><b>training_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the training set and the 3D Zernike Descriptors (rebalanced) for each antibody.<br><b><br>test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the antibody-antigen complexes in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><b>homology_modelled_test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the homology modelled antibody structures in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><br><br><br>
DOI: 10.6084/m9.figshare.5442289
title: Crop residue management : crop ans soil raw data (2010-2016)

description: Raw data from a field experiment on crop residue management in Gemblouw Agro-Bio Tech (ULg) experimental farm.<br>Latin square disposal of 4 contrasting treatments (CT-IN, CT-OUT, RT-IN, RT-OUT) where : <br>CT = conventional tillage (ploughing at 25cm)<br>RT = reduced tillage (at maximum 10 cm)<br>IN = incorporaiton of crop residues<br>OUT = exportation of crop residues<br>
DOI: 10.6084/m9.figshare.5442178
title: Data supporting Thompson et al. 2017 Individual and demographic consequences of mass eviction in cooperative banded mongooses. Animal Behaviour.

description: This data supports the following publication:<br>Faye J. Thompson, Harry H. Marshall, Emma I.K. Vitikainen, Andrew J. Young & Michael A. Cant (2017) Individual and demographic consequences of mass eviction in cooperative banded mongooses. <i>Animal Behaviour</i><i><br></i>Please read the "Read Me.txt" file for a full description of the data contained in each data set
DOI: 10.6084/m9.figshare.5442190
title: The ChIP-seq clean data of input sample

description: The ChIP-seq clean data of input sample<br>
DOI: 10.6084/m9.figshare.5442184
title: The ChIP-seq clean data of OX10

description: The ChIP-seq clean data of OX10
DOI: 10.6084/m9.figshare.5442178.v1
title: Data supporting Thompson et al. 2017 Individual and demographic consequences of mass eviction in cooperative banded mongooses. Animal Behaviour.

description: This data supports the following publication:<br>Faye J. Thompson, Harry H. Marshall, Emma I.K. Vitikainen, Andrew J. Young & Michael A. Cant (2017) Individual and demographic consequences of mass eviction in cooperative banded mongooses. <i>Animal Behaviour</i><i><br></i>Please read the "Read Me.txt" file for a full description of the data contained in each data set
DOI: 10.6084/m9.figshare.5442190.v2
title: The ChIP-seq clean data of input sample

description: The ChIP-seq clean data of input sample<br>
DOI: 10.6084/m9.figshare.5442229.v1
title: Training, validation and testing sample data used in "Antibody interface prediction with 3D Zernike descriptors and SVM"

description: This dataset contains the generated training, validation and testing samples used in the paper "Antibody interface prediction with 3D Zernike descriptors and SVM".<br>3D Zernike descriptors are used to represent protein surface shape, while Support-Vector Machine (SVM) is the binary classification technique employed to produce a model based on the training data which predicts the class labels of the test data given only the feature vectors of the test data.<br>Data are archived in the format .tar.xz, which can be extracted by common archive utilities. The archive contains a number of text files in the SVM light format. Each line records 1331 colon-separated pairs of numbers (the first one being a feature index - an integer ranging from 1 to 1331, the second a floating point number). <br>Background:In the related paper we present a novel method for antibody interface prediction from their experimentally-solved structures based on 3D Zernike Descriptors. Roto-translationally invariant descriptors are computed from circular patches of the antibody surface enriched with the physicochemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. A SVM classifier is used to distinguish interface surface patches from non-interface ones. By exploiting the spatial continuity of the antigen-binding regions, the Isolation Forest algorithm is used to discard false-positive patches isolated from the others. Each residue is assigned a score by the overlying predicted patches indicating its likelihood of belonging to the binding region: a residue is identified as belonging to the interface only if its score reaches a minimum threshold value. The proposed method was shown to outperform other state-of-the-art antigen-binding interface prediction software.
DOI: 10.6084/m9.figshare.5442166
title: The ChIP-seq clean data of OX7

description: The ChIP-seq clean data of OX7
DOI: 10.6084/m9.figshare.5442142
title: Interactive and Sculptural Printmaking in the Renaissance Catalogues A and B

description: European Single-Sheet Interactive Prints 1450-1700 Accompanying <i>Interactive and Sculptural Printmaking in the Renaissance </i>
DOI: 10.6084/m9.figshare.5442184.v1
title: peak-gene ox10

description: The candidate target genes of TsNAC1 in OX10 lines.
DOI: 10.6084/m9.figshare.5442190.v1
title: The ChIP-seq row data input

description: The ChIP-seq row data of input sample<br>
DOI: 10.6084/m9.figshare.5442229.v2
title: Datasets used in "Antibody interface prediction with 3D Zernike descriptors and SVM"

description: <b>Background:</b> In this work we present a novel method for antibody interface prediction from their experimentally-solved structures based on 3D Zernike Descriptors. Roto-translationally invariant descriptors are computed from circular patches of the antibody surface enriched with a chosen subset of physicochemical properties from the AAindex1 amino acid index set, and are used as samples for a binary classification problem. An SVM classifier is used to distinguish interface surface patches from non-interface ones. The proposed method was shown to outperform other antigen-binding interface prediction software.<b><br><br>seq_descriptors_4.5.tar.gz -</b> Contains the sequence descriptors generated from the antibody structures in the development/validation set which were used for feature selection with the Randomized Logistic Regression algorithm.<br><br><b>development_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the development/validation set; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files.<br><br><b>training_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the training set and the 3D Zernike Descriptors (rebalanced) for each antibody.<br><b><br>test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the antibody-antigen complexes in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><b>test_set_non_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the antibody-antigen complexes in the test set of antibodies complexed with non-protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files.<br><br><b>homology_modelled_test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the homology modelled antibody structures in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><b>homology_modelled_test_set_non_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the homology modelled antibody structures in the test set of antibodies complexed with non-protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files.<br><br><br>
DOI: 10.6084/m9.figshare.5442142.v1
title: Interactive and Sculptural Printmaking in the Renaissance Catalogues A and B

description: European Single-Sheet Interactive Prints 1450-1700 Accompanying <i>Interactive and Sculptural Printmaking in the Renaissance </i>
DOI: 10.6084/m9.figshare.5442184.v2
title: peak-gene ox10

description: The candidate target genes of TsNAC1 in OX10 lines.
DOI: 10.6084/m9.figshare.5442166.v1
title: peak-gene

description: The target genes of TsNAC1 in OX7
DOI: 10.1184/r1/5441884
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160928152133_Experiment 2

description: subject 160928152133 nii files Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.Abstract:<br>Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.<br>
DOI: 10.1184/r1/5441878
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160928132100_Experiment 2

description: subject 160928132100 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included. <br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5441896
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Protocols

description: The protocols for the 8 functional runs (numbers reflect TRs). The "protocol by run" file describes for each participant, the correspondence between runs and protocols.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5441884.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160928152133_Experiment 2

description: subject 160928152133 nii files Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.Abstract:<br>Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.<br>
DOI: 10.6084/m9.figshare.5442166.v2
title: peak-gene ox7

description: The target genes of TsNAC1 in OX7
DOI: 10.1184/r1/5441878.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160928132100_Experiment 2

description: subject 160928132100 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included. <br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5441896.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Protocols

description: The protocols for the 8 functional runs (numbers reflect TRs). The "protocol by run" file describes for each participant, the correspondence between runs and protocols.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.6084/m9.figshare.5441875
title: Geochemical and isotopic evidences from groundwater and surface water for understanding of natural contamination in chronic kidney disease of unknown etiology (CKDu) endemic zones in Sri Lanka

description: Chronic kidney disease of unknown etiology (CKDu) is the main health issue in the dry zone of Sri Lanka. Despite many studies carried out, causative factors have not been identified yet clearly. According to the multidisciplinary researches carried out so far, potable water is considered as the main causative factor for CKDu. Hence, the present study was carried out with combined isotopic and chemical methods to understand possible relationships between groundwater; the main drinking water source, and CKDu in four endemic areas in the dry zone. Different water sources were evaluated isotopically (<sup>2</sup>H, <sup>3</sup>H and <sup>18</sup>O) and chemically from 2013 to 2015. Results revealed that prevalence of CKDu is significantly low with the groundwater replenished by surface water inputs. It is significantly high with the groundwater stagnated as well as groundwater recharged from regional flow paths. Thus, the origin, recharge mechanism and flow pattern of groundwater, as well as geological conditions which would be responsible for natural contamination of groundwater appear as the main causative factors for CKDu. Therefore, detailed investigations should be made in order to identify the element(s) in groundwater contributing to CKDu. The study recommends providing drinking water to the affected zones using water sources associated with surface waters.
DOI: 10.6084/m9.figshare.5442184.v5
title: The ChIP-seq clean data of OX10

description: The ChIP-seq clean data of OX10
DOI: 10.1184/r1/5441872
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160928111622_Experiment 2

description: subject 160928132100 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included. <br>
DOI: 10.6084/m9.figshare.5441875.v1
title: Geochemical and isotopic evidences from groundwater and surface water for understanding of natural contamination in chronic kidney disease of unknown etiology (CKDu) endemic zones in Sri Lanka

description: Chronic kidney disease of unknown etiology (CKDu) is the main health issue in the dry zone of Sri Lanka. Despite many studies carried out, causative factors have not been identified yet clearly. According to the multidisciplinary researches carried out so far, potable water is considered as the main causative factor for CKDu. Hence, the present study was carried out with combined isotopic and chemical methods to understand possible relationships between groundwater; the main drinking water source, and CKDu in four endemic areas in the dry zone. Different water sources were evaluated isotopically (<sup>2</sup>H, <sup>3</sup>H and <sup>18</sup>O) and chemically from 2013 to 2015. Results revealed that prevalence of CKDu is significantly low with the groundwater replenished by surface water inputs. It is significantly high with the groundwater stagnated as well as groundwater recharged from regional flow paths. Thus, the origin, recharge mechanism and flow pattern of groundwater, as well as geological conditions which would be responsible for natural contamination of groundwater appear as the main causative factors for CKDu. Therefore, detailed investigations should be made in order to identify the element(s) in groundwater contributing to CKDu. The study recommends providing drinking water to the affected zones using water sources associated with surface waters.
DOI: 10.6084/m9.figshare.5442166.v3
title: peak-gene ox7

description: The target genes of TsNAC1 in OX7
DOI: 10.6084/m9.figshare.5442184.v4
title: The ChIP-seq row data OX10

description: The ChIP-seq row data of ox10 lines