cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1348841
title: Grid convergence of PyGBe with a spherical molecule near spherical surface

description: Reproducibility package containing data, running script, plotting script and final plot of grid-convergence study for a spherical molecule near a charged surface.The running script invokes the open-source bioelectrostatics solver PyGBe with the given input data, computes the solvation plus surface energy and the error with respect to the analytical solution, and plots the final result of convergence. This result is part of the following publication:—<strong>"Poisson–Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code,"</strong> Christopher D. Cooper and Lorena A. Barba, Comput. Phys. Comm. (2016) doi:10.1016/j.cpc.2015.12.019 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348842.v2
title: Performance improvement of the PD-based bilateral teleoperators with time delay by introducing relative D-control

description: In a force-reflecting bilateral teleoperator with a time delay, teleoperator stability is a serious problem. We have studied a bilateral teleoperator system with a time delay. We obtained stable conditions using proportional derivative-based (PD-based) control law. In this paper, PD-based control law is further studied. First, we study a PD control law with relative damping gain and its stabilizing effect that previously has not been studied quantitatively. A stable condition is derived with this PD-based controller with relative damping gain. Next, teleoperator performance by the PD control law with relative damping is evaluated and compared to PD control laws with only grounded damping using transparency analysis with a hybrid matrix. We showed that, the performance of the PD-based controller can be improved by introducing relative damping gain into the controller. As a controller design example, numerical simulations and 1-DOF experiments were conducted. Finally, peg-in-hole experiments and performance evaluations in realistic multi-DOF environments were conducted to demonstrate performance improvements by introducing the relative damping. A controller design that guarantees both stability and performance was achieved by iterating stable gain setting and performance evaluation.
DOI: 10.6084/m9.figshare.1349230.v1
title: data for plos one

description: these are data using for spss analysis in the paper submited to plos one.
DOI: 10.6084/m9.figshare.1352064.v30
title: Biology lessons for schools using the fruit fly Drosophila

description: OVERVIEW: An overview of resources given here is listen under this link: https://droso4schools.wordpress.com/learning-resources/<br>RATIONALE: For more than 100 years the fruit fly <em>Drosophila</em> <em>melanogaster</em> has been at the forefront of biological research and thus provides highly refined conceptual understanding of biology. Accordingly, much of the core biology curriculum can be explained extremely well using flies, spiced up with exciting, simple and inexpensive experiments that are memorable, reflect contemporary research and provide students with clear comprehension. Here we provide readily tested school biology lessons in form of PowerPoint files which are supported by explanatory background information, risk assessments, lesson plans, instructions and any other additional information that may save teachers time and effort to set up these lessons in their own classes. Furthermore, we set up the droso4schools website (link below) which provides further support materials suitable for revision or homework tasks, or simply to enhance the learning experience. Further <em>Drosophila</em>-specific information and resources can be found under the second link given below. If you find our resources helpful for your teaching, please, help us by sending an informal email to Andreas.Prokop@manchester.ac.uk<br>
DOI: 10.6084/m9.figshare.1349230.v3
title: Neonatal isoflurane exposure induces neurocognitive impairment and abnormal hippocampal histone acetylation in mice

description: these are data using for spss analysis in the paper submited to plos one.
DOI: 10.6084/m9.figshare.1348840
title: LBW data

description: Risk factors for low birthweight
DOI: 10.6084/m9.figshare.1348842.v1
title: Performance improvement of the PD-based bilateral teleoperators with time delay by introducing relative D-control

description: In a force-reflecting bilateral teleoperator with a time delay, teleoperator stability is a serious problem. We have studied a bilateral teleoperator system with a time delay. We obtained stable conditions using proportional derivative-based (PD-based) control law. In this paper, PD-based control law is further studied. First, we study a PD control law with relative damping gain and its stabilizing effect that previously has not been studied quantitatively. A stable condition is derived with this PD-based controller with relative damping gain. Next, teleoperator performance by the PD control law with relative damping is evaluated and compared to PD control laws with only grounded damping using transparency analysis with a hybrid matrix. We showed that, the performance of the PD-based controller can be improved by introducing relative damping gain into the controller. As a controller design example, numerical simulations and 1-DOF experiments were conducted. Finally, peg-in-hole experiments and performance evaluations in realistic multi-DOF environments were conducted to demonstrate performance improvements by introducing the relative damping. A controller design that guarantees both stability and performance was achieved by iterating stable gain setting and performance evaluation.
DOI: 10.6084/m9.figshare.1348839
title: LBW SAS data

description: Risk factors for low birthweight, SAS version
DOI: 10.6084/m9.figshare.1349230.v2
title: data for plos one

description: these are data using for spss analysis in the paper submited to plos one.
DOI: 10.6084/m9.figshare.1348837
title: Echo state networks with Tikhonov regularization: optimization using integral gain

description: This study proposes feed-forward echo state networks (ESN) as an estimator, and couples it with second-order proportional-integral-derivative (PID) feedback extension to compensate for dead time in feedback systems. The system is tested for two-dimensional space motion patterns recognition and prediction using simulations, which allows control of noise input. Tikhonov regularization is employed for training readouts and second-order PID feedback minimizes prediction bias. Evaluation is done using mean squared error and the coupled system performs well compared to any of its standalone versions. The results suggest it is feasible to (1) ‘compress’ the memory capacity of the system, and (2) reduce the number optimization parameters, while maintaining the estimation performance and following the excitation property of the estimator. It is feasible to optimize the ESN using feedback gain although it plays a significant role in the proposed system because the improvement by bias correction is far greater than that of optimization; thus, simplifying the estimation to a feedback problem which is easily tuned using the Ziegler–Nichols method.
DOI: 10.6084/m9.figshare.1348841.v2
title: Grid convergence of PyGBe with a spherical molecule near spherical surface

description: This file bundle contains data, running script and final plot of grid-convergence study for a spherical molecule near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the solvation plus surface energy and the error with respect to the analytical solution, and plots the final result of convergence. This result is part of an upcoming paper. Publication information will be updated at the time of submission with the arXiv pre-print number, and at the time of publication with the final citation. PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348837.v2
title: Echo state networks with Tikhonov regularization: optimization using integral gain

description: This study proposes feed-forward echo state networks (ESN) as an estimator, and couples it with second-order proportional-integral-derivative (PID) feedback extension to compensate for dead time in feedback systems. The system is tested for two-dimensional space motion patterns recognition and prediction using simulations, which allows control of noise input. Tikhonov regularization is employed for training readouts and second-order PID feedback minimizes prediction bias. Evaluation is done using mean squared error and the coupled system performs well compared to any of its standalone versions. The results suggest it is feasible to (1) ‘compress’ the memory capacity of the system, and (2) reduce the number optimization parameters, while maintaining the estimation performance and following the excitation property of the estimator. It is feasible to optimize the ESN using feedback gain although it plays a significant role in the proposed system because the improvement by bias correction is far greater than that of optimization; thus, simplifying the estimation to a feedback problem which is easily tuned using the Ziegler–Nichols method.
DOI: 10.6084/m9.figshare.1348837.v1
title: Echo state networks with Tikhonov regularization: optimization using integral gain

description: This study proposes feed-forward echo state networks (ESN) as an estimator, and couples it with second-order proportional-integral-derivative (PID) feedback extension to compensate for dead time in feedback systems. The system is tested for two-dimensional space motion patterns recognition and prediction using simulations, which allows control of noise input. Tikhonov regularization is employed for training readouts and second-order PID feedback minimizes prediction bias. Evaluation is done using mean squared error and the coupled system performs well compared to any of its standalone versions. The results suggest it is feasible to (1) ‘compress’ the memory capacity of the system, and (2) reduce the number optimization parameters, while maintaining the estimation performance and following the excitation property of the estimator. It is feasible to optimize the ESN using feedback gain although it plays a significant role in the proposed system because the improvement by bias correction is far greater than that of optimization; thus, simplifying the estimation to a feedback problem which is easily tuned using the Ziegler–Nichols method.
DOI: 10.6084/m9.figshare.1348841.v3
title: Grid convergence of PyGBe with a spherical molecule near spherical surface

description: This file bundle contains data, running script and final plot of grid-convergence study for a spherical molecule near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the solvation plus surface energy and the error with respect to the analytical solution, and plots the final result of convergence. This result is part of an upcoming paper. Publication information will be updated at the time of publication with the final citation. The prreprint is: —<strong>"Probing protein orientation near charged surfaces with an implicit-solvent model and the PyGBe code,"</strong> Christopher D. Cooper, Lorena A. Barba; arXiv: 1503.08150 (submitted). PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348809
title: SASA-based hotspot prediction dataset S3

description: SASA-based hotspot prediction dataset S3
DOI: 10.6084/m9.figshare.1348804.v4
title: Protein orientation near a charged surface using PyGBe and protein G B1 D4

description: This file bundle contains data, running script and final plot of the protein-orientation study for protein G B1 D4' near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the orientation probability distribution and plots the final result. File set includes: —1 mesh, 2 bodies<br>—PQR file<br>—mesh-generation script for sensor surface<br>—input parameters and running script for mesher<br>—input file for PyGBe and running script<br>—CSV file of output (tilt, rotation, energy)<br>—Figure 11 of the paper and plotting script This result is part of an upcoming paper. Publication information will be updated at the time of submission with the arXiv pre-print number, and at the time of publication with the final citation. PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348802
title: Protein orientation near charged surface using PyGBe with immunoglobulin G

description: Reproducibility package containing data, running script and final plot of the protein-orientation study for immunoglobulin G near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the orientation probability distribution and plots the final result. The file set includes: —1 mesh, 2 bodies —PQR file —mesh-generation script for sensor surface —input parameters and running script for mesher —input file for PyGBe and running script —CSV file of output (tilt, rotation, energy) —Figure 11 of the paper and plotting script This result is part of the publication:—<b>"Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design,"</b> Christopher D. Cooper, Natalia C. Clementi, Lorena A. Barba; <i>J. Chem. Phys.</i>, Vol. 143: 124709 (2015) PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348800
title: Recent species in old Islands: the origin of introduced populations of Litoria aurea (Anura: Hylidae) in New Caledonia and Wallis

description: New Caledonia is a megadiverse tropical island in the southwest Pacific, however, inhabited by only one species of amphibian, <em>Litoria aurea</em> (Hylidae). We used both molecular (CO1 and ND4 gene sequencing) and morphometric data to explore its geographical origin and timing of colonisation. We tested whether this species arrived through transoceanic dispersal before human arrival in the island, or recently through anthropogenic introduction. We found a weak phylogeographical structure within this species, and lower haplotype diversity in New Zealand, New Caledonia and Wallis compared to Australia. No significant genetic differentiation was found between pairs of populations in New Caledonia and Wallis, or between pairs of population from these two islands. We observed a high level of morphometric differentiation between Australian and island populations, and a low level of morphometric differentiation between island populations. Our results support an Australian origin for insular frogs. The possibility of a trans-marine dispersal from Australia to New Caledonia and/or Wallis in-between the Eocene and the Pleistocene cannot be favoured, given the low level of genetic differentiation. Our results are consistent with a recent human introduction, most likely during European times. Our data support the historical absence of amphibians in the old island New Caledonia, and is consistent with the new biogeographical paradigm that this island was totally re-colonized after emergence in Eocene. More studies are necessary to explain the success of this frog in oceanic islands, where it is widespread and abundant, compared to Australia, where it is declining.
DOI: 10.6084/m9.figshare.1348803.v7
title: Grid convergence of PyGBe with protein G B1 D4

description: This file bundle contains data, running script and final plot of grid-convergence study for protein G B1 D4' near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the extrapolated value of solvation plus surface energy (with Richardson extrapolation), and plots the final result of convergence. This result is part of an upcoming paper. Publication information will be updated at the time of submission with the arXiv pre-print number, and at the time of publication with the final citation. PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods,"</em> Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers," Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>,<strong> 185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.1348800.v1
title: Recent species in old Islands: the origin of introduced populations of Litoria aurea (Anura: Hylidae) in New Caledonia and Wallis

description: New Caledonia is a megadiverse tropical island in the southwest Pacific, however, inhabited by only one species of amphibian, <em>Litoria aurea</em> (Hylidae). We used both molecular (CO1 and ND4 gene sequencing) and morphometric data to explore its geographical origin and timing of colonisation. We tested whether this species arrived through transoceanic dispersal before human arrival in the island, or recently through anthropogenic introduction. We found a weak phylogeographical structure within this species, and lower haplotype diversity in New Zealand, New Caledonia and Wallis compared to Australia. No significant genetic differentiation was found between pairs of populations in New Caledonia and Wallis, or between pairs of population from these two islands. We observed a high level of morphometric differentiation between Australian and island populations, and a low level of morphometric differentiation between island populations. Our results support an Australian origin for insular frogs. The possibility of a trans-marine dispersal from Australia to New Caledonia and/or Wallis in-between the Eocene and the Pleistocene cannot be favoured, given the low level of genetic differentiation. Our results are consistent with a recent human introduction, most likely during European times. Our data support the historical absence of amphibians in the old island New Caledonia, and is consistent with the new biogeographical paradigm that this island was totally re-colonized after emergence in Eocene. More studies are necessary to explain the success of this frog in oceanic islands, where it is widespread and abundant, compared to Australia, where it is declining.