cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.942382
title: Data Experiment 1

description: IVs are Orientation (Upright, Inverted), Target Name (Friend, Self, Unfamiliar) and Distractor Face (Friend, Self, Unfamiliar). All IVs are repeated-measures. The DV is reaction time (RT) for correct responses, measured in ms. Incorrect responses accounted for 5.2% of the data, and were removed prior to analysis (i.e. data presented here are for correct responses). For each participant, RT’s more than two standard deviations away from that participant’s mean were removed as outliers; these accounted for 10.3% of trials. Data presented here do not include these trials. Variables are labelled as follows: Orientation I = Inverted Up = Upright Target Name F = Friend S = Self U = Unfamiliar Distractor Face F = Friend S = Self U = Unfamiliar For example, the variable labelled “ISF” contains the average reaction time to respond a name when the Distractor Face was presented in an Inverted Orientation, when the Target Name to respond to was the participant’s own name, and when the Distractor Face was an image of a Friend.
DOI: 10.6084/m9.figshare.942376
title: Retrospective Risk-Taking Questionnaire

description: Retrospective questionnaire measures This questionnaire was created to retrospectively assess the sensation seeking, risk-taking, and impulsive behaviors in a longitudinal neuroimaging (MRI) cohort. As no behavioral markers of risk-taking were collected from participants concomitantly with the MRI data, we collected retrospective information of these behaviors using this written questionnaire. Participants were mailed this two-part questionnaire in 2013 to self-assess retrospectively their behaviors during adolescence. The first part of the questionnaire included three questions relating to the individual’s general recall of their own teenage behavior: i) How old were you when you engaged in the most risky behavior? ii) Compared to your peers, how much risky behavior did you engage in as a teenager? iii) Please describe the types of risky behaviors you engaged in as a teenager. Risky behavior was defined in the questionnaire as ‘behavior that is unsafe or might result in negative consequences.’ The second part of the questionnaire included adaptations of the following measures: Sensation-seeking Scale (SSS), Cognitive Appraisal of Risky Events (CARE) Questionnaire, Youth Risk Behavior Surveillance, Barratt Impulsiveness Scale (BIS), and Behavioral Inhibition System/Behavioral Approach System Scales.
DOI: 10.6084/m9.figshare.942390.v2
title: Bioclimate of Italy: application of the worldwide bioclimatic classification system

description: The worldwide bioclimatic classification system (WBCS) of Rivas-Martínez was applied to the Italian territory and surrounding areas between latitudes 35°47′–46°60′ N and longitudes 5°92′–21°39′ E. The ‘WorldClim’ precipitation and temperature dataset was used as the source data. Application of the WBCS in a geographic information system allowed the production of macrobioclimates, bioclimates, ombrotypes, continentality, compensated thermicity index and ombro-evaporal index maps at a scale of 1:5,500,000, and a map of thermotypes at a scale of 1:2,250,000. Moreover, the isobioclimates of Italy are identified and quantified in terms of areas. These maps are available here as raster datasets (1 km spatial resolution) and are useful for: (i) rapid bioclimatic diagnosis of the Italian territories; and (ii) vegetation–environment relationship modeling at the national scale.
DOI: 10.6084/m9.figshare.942390.v3
title: Bioclimate of Italy: application of the worldwide bioclimatic classification system

description: The worldwide bioclimatic classification system (WBCS) of Rivas-Martínez was applied to the Italian territory and surrounding areas between latitudes 35°47′–46°60′ N and longitudes 5°92′–21°39′ E. The ‘WorldClim’ precipitation and temperature dataset was used as the source data. Application of the WBCS in a geographic information system allowed the production of macrobioclimates, bioclimates, ombrotypes, continentality, compensated thermicity index and ombro-evaporal index maps at a scale of 1:5,500,000, and a map of thermotypes at a scale of 1:2,250,000. Moreover, the isobioclimates of Italy are identified and quantified in terms of areas. These maps are available here as raster datasets (1 km spatial resolution) and are useful for: (i) rapid bioclimatic diagnosis of the Italian territories; and (ii) vegetation–environment relationship modeling at the national scale.
DOI: 10.6084/m9.figshare.942347
title: Gaussian Job Archive for C8H12O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942346
title: Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

description: binary rawdata
DOI: 10.6084/m9.figshare.942347.v1
title: Gaussian Job Archive for C8H12O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942346.v1
title: Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

description: binary rawdata
DOI: 10.6084/m9.figshare.942316
title: Analysing bone remodeling patterns after THA using patient specific FEM

description: Finite element analysis technique incorporates bone remodeling theories and it is extensively used in predicting bone remodeling patterns around the implant. However, a patient-specific finite element model would be more advantageous. Because, the influences of bone geometry, bone strength and gait patterns can be considered in a patient specific model. Therefore, this study leads to create accurate and more realistic algorithm to predict bone remodeling patterns for patients with total hip replacement using patient-specific finite element models. Patient-specific finite element models are being created for a number of patients and then the resulting bone remodeling patterns are being discussed.
DOI: 10.6084/m9.figshare.942326
title: Gaussian Job Archive for C4H10N2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942316.v1
title: Analysing bone remodeling patterns after THA using patient specific FEM

description: Finite element analysis technique incorporates bone remodeling theories and it is extensively used in predicting bone remodeling patterns around the implant. However, a patient-specific finite element model would be more advantageous. Because, the influences of bone geometry, bone strength and gait patterns can be considered in a patient specific model. Therefore, this study leads to create accurate and more realistic algorithm to predict bone remodeling patterns for patients with total hip replacement using patient-specific finite element models. Patient-specific finite element models are being created for a number of patients and then the resulting bone remodeling patterns are being discussed.
DOI: 10.6084/m9.figshare.942326.v1
title: Gaussian Job Archive for C4H10N2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942309
title: Investigating the role of structural remodelling in Atrial Fibrillation

description: ABI Research Forum 21 Feb 2014
DOI: 10.6084/m9.figshare.942305
title: Modelling Large Deformations of Ideally Incompressible Soft Tissues Using the Element-Free Galerkin Method

description: Large deformations of soft tissues are very challenging to be modelled using conventional mesh-based methods, such as Finite Element Method. Large distortion of mesh will lead to computational instability and failure. Hence we propose modelling large deformations of soft tissues using mesh less method.
DOI: 10.6084/m9.figshare.942309.v1
title: Investigating the role of structural remodelling in Atrial Fibrillation

description: ABI Research Forum 21 Feb 2014
DOI: 10.6084/m9.figshare.942294
title: Gaussian Job Archive for C4H6O4S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942294.v1
title: Gaussian Job Archive for C4H6O4S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.942299
title: Split Large Sequence File Script

description: Short script which can be used to split a large file of sequences into smaller files with a defined number of sequences or bases.
DOI: 10.6084/m9.figshare.942305.v1
title: Modelling Large Deformations of Ideally Incompressible Soft Tissues Using the Element-Free Galerkin Method

description: Large deformations of soft tissues are very challenging to be modelled using conventional mesh-based methods, such as Finite Element Method. Large distortion of mesh will lead to computational instability and failure. Hence we propose modelling large deformations of soft tissues using mesh less method.
DOI: 10.6084/m9.figshare.942299.v1
title: Split Large Sequence File Script

description: Short script which can be used to split a large file of sequences into smaller files with a defined number of sequences or bases.
DOI: 10.6084/m9.figshare.941095
title: UWO-VPC-2013.003-Camarasaur tooth rooted

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 145,325 vertices and 29,102 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941095.v1
title: UWO-VPC-2013.003-Camarasaur tooth rooted

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 145,325 vertices and 29,102 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941093
title: UWO-VPC-2013.001-Allosaur tooth rooted

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 72,989 vertices and 145,758 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941094
title: UWO-VPC-2013.004Camarasaur tooth shed

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 69,697 vertices and 139,213 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941092
title: UWO-VPC-2013.002-Allosaur tooth shed

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 34,702 vertices and 69,344 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941093.v1
title: UWO-VPC-2013.001-Allosaur tooth rooted

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 72,989 vertices and 145,758 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941075
title: Species Incidences for 16 ornithological sites

description: Full data from paper.
DOI: 10.6084/m9.figshare.941094.v1
title: UWO-VPC-2013.004Camarasaur tooth shed

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 69,697 vertices and 139,213 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941075.v1
title: Species Incidences for 16 ornithological sites

description: Full data from paper.
DOI: 10.6084/m9.figshare.941092.v1
title: UWO-VPC-2013.002-Allosaur tooth shed

description: Scanned with a Nextengine Desktop 3D Scanner and Scan Studio Pro (NextEngine) on high resolution settings. Model composed of 34,702 vertices and 69,344 faces. Saved as an *.stl file in MeshLab (v.1.3.2).
DOI: 10.6084/m9.figshare.941070
title: Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG)

description: Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by <i>in silico</i> experiments. Switches from the D-duplex (dimerization-competent) conformation to the I-duplex (initiation-competent) conformation and then to conformations with an open primer activation signal (PAS) structure have been examined for four fragments of U5 and primer binding site (PBS) region, the minimal fragment (nt 121–243), fragment 1 (nt 110–243), fragment 2 (nt 113–259), and extended fragment 2 (nt 109–261). Switches from the D-duplex conformation to the I-duplex conformation in the minimal fragment or fragment 1 and from the I-duplex conformation to conformations with exposed PAS motif in fragment 1 are similar in all MAL-like templates. A PAS exposure in fragment 2 and extended fragment 2 is supported by PBS stem extension which structure is affected by subtype-specific variations in CRF01_AE (the mutated motif <sup>116</sup>GUUAG<sup>120</sup>) and CRF02_AG (7-nt deletion downstream of the PBS motif and G/C/A insertion at the 3′ end of fragment 2). These switchable conformations contain the established structural elements essential for HIV-1 reverse transcription initiation as well as several elements that may also be relevant to initiation process, namely hairpins with GAAA apical loops and self-contained motifs of the duplicate insertion and the downstream palindromic sequence. Taken together, our findings suggest a role for the duplicate insertion of MAL-like templates in HIV-1 reverse transcription initiation process and possible mechanisms to realize this role.
DOI: 10.6084/m9.figshare.941070.v1
title: Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG)

description: Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by <i>in silico</i> experiments. Switches from the D-duplex (dimerization-competent) conformation to the I-duplex (initiation-competent) conformation and then to conformations with an open primer activation signal (PAS) structure have been examined for four fragments of U5 and primer binding site (PBS) region, the minimal fragment (nt 121–243), fragment 1 (nt 110–243), fragment 2 (nt 113–259), and extended fragment 2 (nt 109–261). Switches from the D-duplex conformation to the I-duplex conformation in the minimal fragment or fragment 1 and from the I-duplex conformation to conformations with exposed PAS motif in fragment 1 are similar in all MAL-like templates. A PAS exposure in fragment 2 and extended fragment 2 is supported by PBS stem extension which structure is affected by subtype-specific variations in CRF01_AE (the mutated motif <sup>116</sup>GUUAG<sup>120</sup>) and CRF02_AG (7-nt deletion downstream of the PBS motif and G/C/A insertion at the 3′ end of fragment 2). These switchable conformations contain the established structural elements essential for HIV-1 reverse transcription initiation as well as several elements that may also be relevant to initiation process, namely hairpins with GAAA apical loops and self-contained motifs of the duplicate insertion and the downstream palindromic sequence. Taken together, our findings suggest a role for the duplicate insertion of MAL-like templates in HIV-1 reverse transcription initiation process and possible mechanisms to realize this role.
DOI: 10.6084/m9.figshare.941070.v3
title: Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG)

description: Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by <i>in silico</i> experiments. Switches from the D-duplex (dimerization-competent) conformation to the I-duplex (initiation-competent) conformation and then to conformations with an open primer activation signal (PAS) structure have been examined for four fragments of U5 and primer binding site (PBS) region, the minimal fragment (nt 121–243), fragment 1 (nt 110–243), fragment 2 (nt 113–259), and extended fragment 2 (nt 109–261). Switches from the D-duplex conformation to the I-duplex conformation in the minimal fragment or fragment 1 and from the I-duplex conformation to conformations with exposed PAS motif in fragment 1 are similar in all MAL-like templates. A PAS exposure in fragment 2 and extended fragment 2 is supported by PBS stem extension which structure is affected by subtype-specific variations in CRF01_AE (the mutated motif <sup>116</sup>GUUAG<sup>120</sup>) and CRF02_AG (7-nt deletion downstream of the PBS motif and G/C/A insertion at the 3′ end of fragment 2). These switchable conformations contain the established structural elements essential for HIV-1 reverse transcription initiation as well as several elements that may also be relevant to initiation process, namely hairpins with GAAA apical loops and self-contained motifs of the duplicate insertion and the downstream palindromic sequence. Taken together, our findings suggest a role for the duplicate insertion of MAL-like templates in HIV-1 reverse transcription initiation process and possible mechanisms to realize this role.
DOI: 10.6084/m9.figshare.941070.v2
title: Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG)

description: Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by <i>in silico</i> experiments. Switches from the D-duplex (dimerization-competent) conformation to the I-duplex (initiation-competent) conformation and then to conformations with an open primer activation signal (PAS) structure have been examined for four fragments of U5 and primer binding site (PBS) region, the minimal fragment (nt 121–243), fragment 1 (nt 110–243), fragment 2 (nt 113–259), and extended fragment 2 (nt 109–261). Switches from the D-duplex conformation to the I-duplex conformation in the minimal fragment or fragment 1 and from the I-duplex conformation to conformations with exposed PAS motif in fragment 1 are similar in all MAL-like templates. A PAS exposure in fragment 2 and extended fragment 2 is supported by PBS stem extension which structure is affected by subtype-specific variations in CRF01_AE (the mutated motif <sup>116</sup>GUUAG<sup>120</sup>) and CRF02_AG (7-nt deletion downstream of the PBS motif and G/C/A insertion at the 3′ end of fragment 2). These switchable conformations contain the established structural elements essential for HIV-1 reverse transcription initiation as well as several elements that may also be relevant to initiation process, namely hairpins with GAAA apical loops and self-contained motifs of the duplicate insertion and the downstream palindromic sequence. Taken together, our findings suggest a role for the duplicate insertion of MAL-like templates in HIV-1 reverse transcription initiation process and possible mechanisms to realize this role.
DOI: 10.6084/m9.figshare.941063
title: Metadata for reef_resilience data file

description: For Zhang et al. PeerJ 2014
DOI: 10.6084/m9.figshare.941062
title: Coral richness, resistance, and recovery data

description: The core dataset for Zhang et al. 2014 PeerJ "Is coral richness related to community resistance to and recovery from disturbance?" https://peerj.com/articles/308/ See the related file "metadata_for_reefresilience_data" for more detail.
DOI: 10.6084/m9.figshare.941063.v1
title: Metadata for reef_resilience data file

description: For Zhang et al. PeerJ 2014
DOI: 10.6084/m9.figshare.940996
title: Runtime Configurability in PETSc

description: The ability to dynamically configure a deeply nested hierarchy of objects is a key feature in the design of PETSc. This allows the user to assemble an optimal solver tailored to problem characteristics without changing the application code, and also allows easy comparison among competing methods. We will demonstrate the efficacy of this approach for both linear and nonlinear systems. Moreover, we extend this paradigm to encompass residual evaluation and other key simulation operations.
DOI: 10.6084/m9.figshare.941061
title: Raw Data - “Biomineralization control related to population density under ocean acidification"

description: Raw data about the manuscript "“Biomineralization control related to population density under ocean acidification" submitted to Nature Climate Change.
DOI: 10.6084/m9.figshare.940993
title: Hydrogen diffusion around a Si(001)/Si(110) corner

description: Coordinate files and XYZ files for hydrogen diffusion around a corner on nanopillar on Si(001). Paper available at: http://arxiv.org/abs/1404.1769 Accepted in J. Phys.:Condens. Matter
DOI: 10.6084/m9.figshare.941062.v2
title: Coral richness, resistance, and recovery data

description: The core dataset for Zhang et al. 2014 PeerJ "Is coral richness related to community resistance to and recovery from disturbance?" https://peerj.com/articles/308/ See the related file "metadata_for_reefresilience_data" for more detail.
DOI: 10.6084/m9.figshare.940996.v1
title: Runtime Configurability in PETSc

description: The ability to dynamically configure a deeply nested hierarchy of objects is a key feature in the design of PETSc. This allows the user to assemble an optimal solver tailored to problem characteristics without changing the application code, and also allows easy comparison among competing methods. We will demonstrate the efficacy of this approach for both linear and nonlinear systems. Moreover, we extend this paradigm to encompass residual evaluation and other key simulation operations.
DOI: 10.6084/m9.figshare.941061.v1
title: Raw Data - “Biomineralization control related to population density under ocean acidification"

description: Raw data about the manuscript "“Biomineralization control related to population density under ocean acidification" submitted to Nature Climate Change.
DOI: 10.6084/m9.figshare.941062.v1
title: Coral richness, resistance, and recover data

description: The core dataset for Zhang et al. 2014 PeerJ "Is coral richness related to community resistance to and recovery from disturbance?" See the related file "metadata_for_reefresilience_data" for more detail.