cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17863/cam.69225
title: Research data supporting "Throttling Automatic Vectorization: When Less Is More"

description: This repository contains the code and data required to validate the results from the paper: "Throttling Automatic Vectorization: When Less Is More" Vasileios Porpodas and Timothy M. Jones 24th International Conference on Parallel Architectures and Compilation Techniques (PACT), 2015.
description: This record is licensed under a GPL version 3 licence.
description: 10.1109/PACT.2015.32
description: This work was supported by the EPSRC [grant number EP/K026399/1]
DOI: 10.17863/cam.69226
title: Supporting computer code for the paper 'Three-field block-preconditioners for models of coupled magma/mantle dynamics'

description: Included programs build on the FEniCS and PETSc libraries.
description: Supporting computer code for the paper: Rhebergen, S., Wells, G.N., Wathen, A.J. and Katz, R.F. Optimal three-field block-preconditioners for models of coupled magma/mantle dynamics, SIAM Journal on Scientific Computing.
DOI: 10.17863/cam.69227
title: Data record for article: Adaptive study of IL-2 dose frequency on regulatory T cells in type 1 diabetes (DILfrequency): a mechanistic, non-randomised, repeat dose,open label, response-adaptive study

description: Supporting data for a protocol paper "Adaptive study of IL-2 dose frequency on regulatory T cells in type 1 diabetes (DILfrequency): a mechanistic, non-randomised, repeat dose, open label, response-adaptive study", published in BMJ Open, repository URI - https://www.repository.cam.ac.uk/handle/1810/250599 . The data available is the pilot data shown in Figure 2, the clinical flow cytometry (FACS) assay used to ascertain the co-primary endpoints of the study. These endpoints are: the frequency of T regulatory cells (Tregs), CD25 expression on Tregs, and the frequency of autoreactive effector T lymphocytes (Teffs). As the data is indvidual-level human subject data, it cannot be hosted on an Open Data repository, but is instead available on completion of a licence at the authors' website - https://www-gene.cimr.cam.ac.uk/data/ . While the website should be checked for a more recent version, a representative licence (current at 30th September 2015) is available here.
description: This record is licensed under a JDRF/Wellcome Trust DIL Data Access Agreement licence.
description: This work was supported by the MRC [grant number G0800860], NIHR Cambridge Biomedical Research Centre, Wellcome Trust [grant number 091157, 100140], Sir Jules Thorn Award for Biomedical Research 2013 [grant number 13/JTA], and JDRF [grant number 9-2011-253].
DOI: 10.25345/c5223z
title: MassIVE MSV000087343 - GNPS -Aplysina cavernicola exo-metabolites
title: Project Title : Capture and concentration of Aplysina cavernicola exo-metabolites Morgane Mauduit
DOI: 10.34740/kaggle/dsv/2177571
title: Nepal ICU and Ventilators Occupancy for COVID
DOI: 10.6084/m9.figshare.12849059
title: <i>In silico</i> study on pH-based alanine scanning of Phylloseptin-2 helps determine potential mutant sites for futuristic therapeutic analogues

description: Analogues of Phylloseptins (PS), membranolytic antimicrobial peptides (AMPs), could replace antibiotics and combat growing multi-drug resistance in urinary tract infections. This study identifies potential mutant sites in a PS scaffold for generation of its analogues, using <i>in silico</i> alanine scanning mutagenesis. Initially, a PS scaffold from native peptides-PS1, PS2 and PS3, is identified using pH-based secondary structure (SS) profiles and conformational free energies after a 20 ns molecular dynamics (MD) simulation at 310 K. PS2 is identified as structurally stable scaffold. Further, alanine scanning is carried out for 17 amino acid residues, at varying pH for 10 ns MD simulation at 310 K to identify structurally and functionally significant and non-significant amino acids in PS2. H-bond occupancy and polar surface area are used as structural and functional parameters in the study. The statistical significance is determined using paired <i>t</i>-tests,using confidence interval of 90%. It was found that the amino acids viz., Leu (4), Val (16) and His (17), were structurally and functionally non-significant (<i>P</i> &gt; .1). Thus, the positions of these aforementioned amino acids in addition to amino acids viz., Ala (8) and Ala (11), can be used as potential mutant sites for generation of therapeutic analogues of PS2.
DOI: 10.6084/m9.figshare.12849059.v1
title: <i>In silico</i> study on pH-based alanine scanning of Phylloseptin-2 helps determine potential mutant sites for futuristic therapeutic analogues

description: Analogues of Phylloseptins (PS), membranolytic antimicrobial peptides (AMPs), could replace antibiotics and combat growing multi-drug resistance in urinary tract infections. This study identifies potential mutant sites in a PS scaffold for generation of its analogues, using <i>in silico</i> alanine scanning mutagenesis. Initially, a PS scaffold from native peptides-PS1, PS2 and PS3, is identified using pH-based secondary structure (SS) profiles and conformational free energies after a 20 ns molecular dynamics (MD) simulation at 310 K. PS2 is identified as structurally stable scaffold. Further, alanine scanning is carried out for 17 amino acid residues, at varying pH for 10 ns MD simulation at 310 K to identify structurally and functionally significant and non-significant amino acids in PS2. H-bond occupancy and polar surface area are used as structural and functional parameters in the study. The statistical significance is determined using paired <i>t</i>-tests,using confidence interval of 90%. It was found that the amino acids viz., Leu (4), Val (16) and His (17), were structurally and functionally non-significant (<i>P</i> &gt; .1). Thus, the positions of these aforementioned amino acids in addition to amino acids viz., Ala (8) and Ala (11), can be used as potential mutant sites for generation of therapeutic analogues of PS2.
DOI: 10.6084/m9.figshare.12886990.v1
title: Computational and molecular dynamics simulation approach to analyze the impactof <i>XPD</i> gene mutation on protein stability and function

description: <i>XPD</i> acts as a functional helicase and aids in unwindingdouble helix around damaged DNA, leading to efficient DNA repair. Mutations of <i>XPD</i> give rise to DNA-repair deficiency diseasesand cancer proneness. In this study,cancer-causing missense mutation that could inactivate helicase function and hinderits binding with other complexes were analysed usingbioinformatics approach. Rigorous computational methodswere employed to understand the molecular pathogenic profile of mutation. The mutant model with the desired mutation was built with I-TASSER. GROMACS 5.0.1 was used to evaluate the effect of a mutation on protein stability and function. Of the 276 missense mutations, 64 were found to be disease-causing. Out of these 64, seven were of cancer-causing mutations. Among these, we evaluated K48R mutationin a computational simulated environment to determine its impact on protein stability and function since K48position was ascertained to be highly conserved and substitutionwith arginine could impair the <i>XPD</i> activity. Molecular Dynamic Simulation and Essential Dynamics analysis showed thatK48R mutation altered protein structural stabilityand produced conformational drift. Our predictions thus revealed that K48R mutation could impairthe <i>XPD</i>helicase activity and affectits ability to repair the damaged DNA, thus augmenting the risk for cancer.
DOI: 10.6084/m9.figshare.12886990
title: Computational and molecular dynamics simulation approach to analyze the impactof <i>XPD</i> gene mutation on protein stability and function

description: <i>XPD</i> acts as a functional helicase and aids in unwindingdouble helix around damaged DNA, leading to efficient DNA repair. Mutations of <i>XPD</i> give rise to DNA-repair deficiency diseasesand cancer proneness. In this study,cancer-causing missense mutation that could inactivate helicase function and hinderits binding with other complexes were analysed usingbioinformatics approach. Rigorous computational methodswere employed to understand the molecular pathogenic profile of mutation. The mutant model with the desired mutation was built with I-TASSER. GROMACS 5.0.1 was used to evaluate the effect of a mutation on protein stability and function. Of the 276 missense mutations, 64 were found to be disease-causing. Out of these 64, seven were of cancer-causing mutations. Among these, we evaluated K48R mutationin a computational simulated environment to determine its impact on protein stability and function since K48position was ascertained to be highly conserved and substitutionwith arginine could impair the <i>XPD</i> activity. Molecular Dynamic Simulation and Essential Dynamics analysis showed thatK48R mutation altered protein structural stabilityand produced conformational drift. Our predictions thus revealed that K48R mutation could impairthe <i>XPD</i>helicase activity and affectits ability to repair the damaged DNA, thus augmenting the risk for cancer.
DOI: 10.3886/e135023
title: Code and Data for: Report for 2020 by the AEA Data Editor

description: Code and some data to support figures and tables in the 2020 Report by the AEA Data Editor.
description: Manuscript verification requests received between Dec 1, 2019 and Nov 30, 2020 by the AEA Data Editor<br>.
DOI: 10.3886/e135023v1
title: Code and Data for: Report for 2020 by the AEA Data Editor

description: Code and some data to support figures and tables in the 2020 Report by the AEA Data Editor.
description: Manuscript verification requests received between Dec 1, 2019 and Nov 30, 2020 by the AEA Data Editor<br>.
DOI: 10.6084/m9.figshare.13730509
title: PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions

description: Mass transport under confinement is at the heart of all processes employing functionalised mesoporous silica materials, such as liquid chromatography, heterogeneous catalysis, and gas adsorption. Molecular simulation studies of mass transport in such settings require pore models that replicate the geometry, dimensions, and chemical structure of a surface-functionalised silica mesopore. We present a software tool that facilitates rapid model building of functionalised silica pores for systematic studies of confinement effects in various applications of relevant materials. The tool allows to choose the chemical structure and density of the ligands and to control the residual hydroxylation of the silica surface. Individual ligands can be placed at a user-defined position on the surface. Moreover, the tool supports an independent functionalisation of the interior and exterior pore surface. We explain each step of the pore generation, discuss the underlying assumptions and limitations, and introduce examples of generated cylindrical pore models for chromatography and catalysis.
DOI: 10.6084/m9.figshare.13730509.v1
title: PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions

description: Mass transport under confinement is at the heart of all processes employing functionalised mesoporous silica materials, such as liquid chromatography, heterogeneous catalysis, and gas adsorption. Molecular simulation studies of mass transport in such settings require pore models that replicate the geometry, dimensions, and chemical structure of a surface-functionalised silica mesopore. We present a software tool that facilitates rapid model building of functionalised silica pores for systematic studies of confinement effects in various applications of relevant materials. The tool allows to choose the chemical structure and density of the ligands and to control the residual hydroxylation of the silica surface. Individual ligands can be placed at a user-defined position on the surface. Moreover, the tool supports an independent functionalisation of the interior and exterior pore surface. We explain each step of the pore generation, discuss the underlying assumptions and limitations, and introduce examples of generated cylindrical pore models for chromatography and catalysis.
DOI: 10.6073/pasta/11d029504c292d7ded08fc542043212f
title: Hubbard Brook Experimental Forest: 15-minute Precipitation Standard Rain Gage Measurements, 2011 - present

description: Beginning in 2011, ten electronic weighing rain gauges were progressively implemented at the Hubbard Brook Experimental Forest to measure precipitation at 15-minute intervals. These data were gathered at the Hubbard Brook Experimental Forest in Thornton, NH, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.17632/pb8dk5vkgv.1
title: Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?

description: materials and methods as supplementary data to the review "Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?"
DOI: 10.5281/zenodo.4730482
title: Underwater noise from ships during 2014-2020

description: These data accompany the manuscript "Underwater noise from ships during 2014-2020" submitted for publication. These data consist of daily emissions of underwater noise emissions from global shipping, reported as noise energy in Joules, in three frequencies (63, 125 and 2000 Hz). The data is provided in zip compressed gridded binary netcdf3 data format using Climate & Forecast conventions.
DOI: 10.6084/m9.figshare.13894902.v1
title: Mechanical properties of MoS<sub>2</sub> nanotubes under tension: a molecular dynamics study

description: We investigate the tensile properties of MoS2 nanotubes by the implementation of a set of molecular dynamics runs, using a recently developed version of the Stillinger–Weber (SW) potential. The nanotubes considered are of the H and T polytypes, with zigzag and armchair chirality. We found that only nanotubes of diameter greater or equal than 30 Å are stable when modelled by the SW potential. Zigzag nanotubes have a larger elastic modulus than armchair nanotubes of the same polytype and diameter, and T nanotubes deform more easily than H nanotubes. We also found that elastic modulus, tensile strength, and point of rupture depend on diameter when the diameters are less than 60 Å. We investigate the role of defects on the mechanical response, finding that, while elastic modules is not appreciably affected by the presence of vacancies, tensile strength, and point of rupture value decrease significantly, in particular when the defect is a vacancy of a whole MoS2 unit. The presence of a defect also affects the nature of the rupture, with the fracture becoming brittle. Increasing the temperature makes Young's modulus and tensile strength decrease. The mechanical response of chiral nanotubes is also investigated.
DOI: 10.6084/m9.figshare.13894902
title: Mechanical properties of MoS<sub>2</sub> nanotubes under tension: a molecular dynamics study

description: We investigate the tensile properties of MoS2 nanotubes by the implementation of a set of molecular dynamics runs, using a recently developed version of the Stillinger–Weber (SW) potential. The nanotubes considered are of the H and T polytypes, with zigzag and armchair chirality. We found that only nanotubes of diameter greater or equal than 30 Å are stable when modelled by the SW potential. Zigzag nanotubes have a larger elastic modulus than armchair nanotubes of the same polytype and diameter, and T nanotubes deform more easily than H nanotubes. We also found that elastic modulus, tensile strength, and point of rupture depend on diameter when the diameters are less than 60 Å. We investigate the role of defects on the mechanical response, finding that, while elastic modules is not appreciably affected by the presence of vacancies, tensile strength, and point of rupture value decrease significantly, in particular when the defect is a vacancy of a whole MoS2 unit. The presence of a defect also affects the nature of the rupture, with the fracture becoming brittle. Increasing the temperature makes Young's modulus and tensile strength decrease. The mechanical response of chiral nanotubes is also investigated.
DOI: 10.5281/zenodo.4716160
title: ECCC Mesonet-Smartphone Datasets

description: Contains the smartphone datasets (three months separately and all together), as well as the mesonet spreadsheets (both by time and by each station's ID)
DOI: 10.5281/zenodo.4716159
title: ECCC Mesonet-Smartphone Datasets

description: Contains the smartphone datasets (three months separately and all together), as well as the mesonet spreadsheets (both by time and by each station's ID)
DOI: 10.5281/zenodo.4730633
title: Soil Productivity Degradation in a Long-Term Eroded Olive Orchard under Semiarid Mediterranean Conditions

description: Olive groves are one of the most important agro-systems in the Mediterranean basin, and<br> the Andalusia region produces the highest quantity of olive oil in Europe. The aim of this work<br> was to evaluate the long-term (15 years) influence of two management practices in olive orchards—<br> conventional tillage (CT) and no tillage with bare soil and herbicide application (NT + H)—on<br> soil physical properties, infiltration capacity, erosion rates, and soil productivity. In addition, the<br> short-term (2 years) influence of no tillage with cover crop management (NT-CC) on these parameters<br> was also assessed. In the study area, CT and NT + H management practices showed unsustainable<br> erosion values, 9.82 and 13.88 Mg ha􀀀1 year􀀀1, respectively, while NT-CC inclusion decreased the<br> erosion rates (2.06 Mg ha􀀀1 year􀀀1). The implementation of NT-CC not only reduced erosion rates<br> but also caused a change in the trend of soil productivity loss observed under CT and NT + H. In<br> this sense, NT-CC showed a positive influence on soil quality. However, tillage removal led to a<br> significant reduction in the infiltration capacity of soils under NT + H and NT-CC, which will be a<br> serious handicap for water storage in an environment with continuous processes of water deficit.
DOI: 10.5281/zenodo.4730632
title: Soil Productivity Degradation in a Long-Term Eroded Olive Orchard under Semiarid Mediterranean Conditions

description: Olive groves are one of the most important agro-systems in the Mediterranean basin, and<br> the Andalusia region produces the highest quantity of olive oil in Europe. The aim of this work<br> was to evaluate the long-term (15 years) influence of two management practices in olive orchards—<br> conventional tillage (CT) and no tillage with bare soil and herbicide application (NT + H)—on<br> soil physical properties, infiltration capacity, erosion rates, and soil productivity. In addition, the<br> short-term (2 years) influence of no tillage with cover crop management (NT-CC) on these parameters<br> was also assessed. In the study area, CT and NT + H management practices showed unsustainable<br> erosion values, 9.82 and 13.88 Mg ha􀀀1 year􀀀1, respectively, while NT-CC inclusion decreased the<br> erosion rates (2.06 Mg ha􀀀1 year􀀀1). The implementation of NT-CC not only reduced erosion rates<br> but also caused a change in the trend of soil productivity loss observed under CT and NT + H. In<br> this sense, NT-CC showed a positive influence on soil quality. However, tillage removal led to a<br> significant reduction in the infiltration capacity of soils under NT + H and NT-CC, which will be a<br> serious handicap for water storage in an environment with continuous processes of water deficit.
DOI: 10.5281/zenodo.4730666
title: Soil Productivity Degradation in a Long-Term Eroded Olive Orchard under Semiarid Mediterranean Conditions

description: Olive groves are one of the most important agro-systems in the Mediterranean basin, and<br> the Andalusia region produces the highest quantity of olive oil in Europe. The aim of this work<br> was to evaluate the long-term (15 years) influence of two management practices in olive orchards—<br> conventional tillage (CT) and no tillage with bare soil and herbicide application (NT + H)—on<br> soil physical properties, infiltration capacity, erosion rates, and soil productivity. In addition, the<br> short-term (2 years) influence of no tillage with cover crop management (NT-CC) on these parameters<br> was also assessed. In the study area, CT and NT + H management practices showed unsustainable<br> erosion values, 9.82 and 13.88 Mg ha􀀀1 year􀀀1, respectively, while NT-CC inclusion decreased the<br> erosion rates (2.06 Mg ha􀀀1 year􀀀1). The implementation of NT-CC not only reduced erosion rates<br> but also caused a change in the trend of soil productivity loss observed under CT and NT + H. In<br> this sense, NT-CC showed a positive influence on soil quality. However, tillage removal led to a<br> significant reduction in the infiltration capacity of soils under NT + H and NT-CC, which will be a<br> serious handicap for water storage in an environment with continuous processes of water deficit.
DOI: 10.5281/zenodo.4730665
title: Soil Productivity Degradation in a Long-Term Eroded Olive Orchard under Semiarid Mediterranean Conditions

description: Olive groves are one of the most important agro-systems in the Mediterranean basin, and<br> the Andalusia region produces the highest quantity of olive oil in Europe. The aim of this work<br> was to evaluate the long-term (15 years) influence of two management practices in olive orchards—<br> conventional tillage (CT) and no tillage with bare soil and herbicide application (NT + H)—on<br> soil physical properties, infiltration capacity, erosion rates, and soil productivity. In addition, the<br> short-term (2 years) influence of no tillage with cover crop management (NT-CC) on these parameters<br> was also assessed. In the study area, CT and NT + H management practices showed unsustainable<br> erosion values, 9.82 and 13.88 Mg ha􀀀1 year􀀀1, respectively, while NT-CC inclusion decreased the<br> erosion rates (2.06 Mg ha􀀀1 year􀀀1). The implementation of NT-CC not only reduced erosion rates<br> but also caused a change in the trend of soil productivity loss observed under CT and NT + H. In<br> this sense, NT-CC showed a positive influence on soil quality. However, tillage removal led to a<br> significant reduction in the infiltration capacity of soils under NT + H and NT-CC, which will be a<br> serious handicap for water storage in an environment with continuous processes of water deficit.
DOI: 10.5519/qd.y872a8au
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (285 records)
DOI: 10.5281/zenodo.4730664
title: ENTSO-E Statistical Factsheet 2017 in Comma Separated Value (CSV) format

description: Inspired by the work of Matteo De Felice, & Ignacio Hidalgo Gonzaléz. (2019). ENTSO-E Statistical Factsheet 2018 in Comma Separated Value (CSV) format. http://doi.org/10.5281/zenodo.3461691 : The ENTSO-E Statistical Factsheet is unfortunately only available in a PDF file format. By, using Tabula and some manual correction work we have converted the net generation table into CSV files.
DOI: 10.5281/zenodo.4730663
title: ENTSO-E Statistical Factsheet 2017 in Comma Separated Value (CSV) format

description: Inspired by the work of Matteo De Felice, & Ignacio Hidalgo Gonzaléz. (2019). ENTSO-E Statistical Factsheet 2018 in Comma Separated Value (CSV) format. http://doi.org/10.5281/zenodo.3461691 : The ENTSO-E Statistical Factsheet is unfortunately only available in a PDF file format. By, using Tabula and some manual correction work we have converted the net generation table into CSV files.
DOI: 10.6084/m9.figshare.14519745
title: Paul2015_Paga.h5ad

description: Description
DOI: 10.6084/m9.figshare.14519745.v1
title: Paul2015_Paga.h5ad

description: Description
DOI: 10.5281/zenodo.4730674
title: Interfacial Ferroelectricity by van der Waals Sliding - SI

description: Interfacial Ferroelectricity by van der Waals Sliding - SI
DOI: 10.5281/zenodo.4730673
title: Interfacial Ferroelectricity by van der Waals Sliding - SI

description: Interfacial Ferroelectricity by van der Waals Sliding - SI