cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.979429.v6
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979215.v1
title: wykorzystanie oceny zdrowia finansowego autorstwa K.Bartodziej, K. Fabiszewskiej, M.Hołowińskiej, M.Pięciak

description: recenzja projektu f
DOI: 10.6084/m9.figshare.979238.v2
title: Experiments on tsunami waves

description: Data used for figures in manuscript entitled: <em>Generation of surface waves by an underwater moving bottom: Experiments and application to tsunami modelling</em> Description of files: <strong>Fig. 2 </strong><br>(a) quiver20.dat, <br>(b) quiver200.dat, <br>(c) quiver500.dat<br><strong>Fig. 3:</strong> <br>(main) DeltaE_experiment.dat, <br>(main) DeltaE_theory.dat; <br>(inset) DeltaE_inset_experiment.dat,<br>(inset) DeltaE_inset_theory.dat<br><strong>Fig. 4:<br></strong>(main)<br>(a) eta-t_20ms_theory_exp.dat,<br>(a) eta-t_20ms_experimental_exp.dat;<br>(b) eta-t_20ms_theory_sin.dat,<br>(b) eta-t_20ms_experimental_exp.dat,<br>(c) eta-t_200ms_theory_exp.dat,<br>(c) eta-t_200ms_experimental_exp.dat;<br>(d) eta-t_200ms_theory_sin.dat,<br>(d) eta-t_200ms_experimental_exp.dat,
DOI: 10.6084/m9.figshare.979238.v3
title: Experiments on tsunami waves

description: Data used for figures in manuscript entitled: <em>Generation of surface waves by an underwater moving bottom: Experiments and application to tsunami modelling</em>
DOI: 10.6084/m9.figshare.979429.v7
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979238.v5
title: Experiments on tsunami waves

description: Data used for figures in manuscript entitled: <br><em>Generation of surface waves by an underwater moving bottom: Experiments and application to tsunami modelling</em> <strong>Description of files:</strong> <strong></strong><em>Figure 2.</em> Velocity fields<br>(a) quiver_20ms.dat<br>(b) quiver_200ms.dat<br>(c) quiver_500ms.dat <em>Figure 3.</em> Constrast of energy<br>(main) <br>DeltaE_experiment.dat, <br>DeltaE_theory.dat<br>(inset) <br>DeltaE_inset_experiment.dat,<br>DeltaE_inset_theory.dat <em>Figure 4.</em> Maximal deformation<br>(main)<br>etamax_experiment_exp.dat<br>etamax_theory_exp.dat etamax_experiment_sin.dat<br>etamax_theory_sin.dat<br>(a)<br>eta-t_20ms_experiment_exp.dat <br>eta-t_20ms_theory_exp.dat <br>(b)<br>eta-t_20ms_experiment_sin.dat<br>eta-t_20ms_theory_sin.dat <br>(c)<br>eta-t_200ms_experiment_exp.dat<br>eta-t_200ms_theory_exp.dat <br>(d)<br>eta-t_200ms_experiment_sin.dat<br>eta-t_200ms_theory_sin.dat
DOI: 10.6084/m9.figshare.979429.v8
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979238.v4
title: Experiments on tsunami waves

description: Data used for figures in manuscript entitled: <em>Generation of surface waves by an underwater moving bottom: Experiments and application to tsunami modelling</em>
DOI: 10.6084/m9.figshare.979429.v9
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979190
title: The khmer software package: enabling efficient sequence analysis

description: A citation handle for the khmer software, v1.0
DOI: 10.6084/m9.figshare.979429.v10
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979429.v11
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979429.v12
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979190.v1
title: The khmer software package: enabling efficient sequence analysis

description: A citation handle for the khmer software, v1.0
DOI: 10.6084/m9.figshare.979179
title: Taking one charge off a two-dimensional Wigner crystal

description: A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distances <i>d</i> from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the <i>d</i> = 0 and <i>d</i> → ∞ limiting cases extend for finite values of <i>d</i> from the respective starting points into two sequences of stable states, with intersecting energies at some value <i>d</i><sub><i>t</i></sub>; beyond this value the branches continue as metastable states.
DOI: 10.6084/m9.figshare.979429.v13
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979190.v2
title: The khmer software package: enabling efficient sequence analysis

description: A citation handle for the khmer software, v1.0
DOI: 10.6084/m9.figshare.979429.v14
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979179.v1
title: Taking one charge off a two-dimensional Wigner crystal

description: A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distances <i>d</i> from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the <i>d</i> = 0 and <i>d</i> → ∞ limiting cases extend for finite values of <i>d</i> from the respective starting points into two sequences of stable states, with intersecting energies at some value <i>d</i><sub><i>t</i></sub>; beyond this value the branches continue as metastable states.
DOI: 10.6084/m9.figshare.979429.v15
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979179.v2
title: Taking one charge off a two-dimensional Wigner crystal

description: A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distances <i>d</i> from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the <i>d</i> = 0 and <i>d</i> → ∞ limiting cases extend for finite values of <i>d</i> from the respective starting points into two sequences of stable states, with intersecting energies at some value <i>d</i><sub><i>t</i></sub>; beyond this value the branches continue as metastable states.
DOI: 10.6084/m9.figshare.979168
title: Patterns of beetle diversity in kauri forest

description: Kauri forest represents a major ecosystem in northern New Zealand; however, the invertebrate fauna and their ecological diversity in these forests is very poorly known. This article investigates the composition and diversity of beetle communities in two kauri forest remnants, sampled by pitfall traps each month for one year. In total 4777 beetles were caught, representing 28 families, 84 genera and 107 species. Estimates of species richness indicate there were 173 species at both sites combined. The five most abundant species contributed 71%, and the top 10 species contributed 88% of all beetles caught. The abundance, richness and composition of the beetle community were consistent throughout the year. Patterns of niche overlap also show that the same set of species co-occur throughout the year, rather than temporal partitioning of the environment on an annual time scale. This data suggests that seasonality plays a limited role in explaining the composition and diversity of beetle communities in kauri forest.
DOI: 10.6084/m9.figshare.979179.v3
title: Taking one charge off a two-dimensional Wigner crystal

description: A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distances <i>d</i> from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the <i>d</i> = 0 and <i>d</i> → ∞ limiting cases extend for finite values of <i>d</i> from the respective starting points into two sequences of stable states, with intersecting energies at some value <i>d</i><sub><i>t</i></sub>; beyond this value the branches continue as metastable states.
DOI: 10.6084/m9.figshare.979429.v16
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data suport the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979429.v17
title: Molecular dynamics of rubromycin derivatives bound to WT and mutant reverse transcriptase

description: Data labeled as mutB refer to the E138K/M184I mutant. Data labeled as mutant refer to the K103N/Y181C mutant. files containing "_0_" in their names refer to gamma-rubromycin-bound reverse transcriptase files containing "_A_" in their names refer to rilpivirine-bound reverse transcriptase *.sce file are the initial states of the simulations (including solvent and counter-ions ), saved as YASARA scenes. YASARA may be downloaded from www.yasara.org Snapshots of the trajectories at 250 ps intervals are present as PDB files. The precise timepoint of each PDB can be known by multiplying the 5-digit number in the filename by 25 ps. These data support the manuscript : Silva PJ, Bernardo CEP. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ PrePrints 2:e348v1 http://dx.doi.org/10.7287/peerj.preprints.348v1
DOI: 10.6084/m9.figshare.979168.v1
title: Patterns of beetle diversity in kauri forest

description: Kauri forest represents a major ecosystem in northern New Zealand; however, the invertebrate fauna and their ecological diversity in these forests is very poorly known. This article investigates the composition and diversity of beetle communities in two kauri forest remnants, sampled by pitfall traps each month for one year. In total 4777 beetles were caught, representing 28 families, 84 genera and 107 species. Estimates of species richness indicate there were 173 species at both sites combined. The five most abundant species contributed 71%, and the top 10 species contributed 88% of all beetles caught. The abundance, richness and composition of the beetle community were consistent throughout the year. Patterns of niche overlap also show that the same set of species co-occur throughout the year, rather than temporal partitioning of the environment on an annual time scale. This data suggests that seasonality plays a limited role in explaining the composition and diversity of beetle communities in kauri forest.
DOI: 10.6084/m9.figshare.979179.v4
title: Taking one charge off a two-dimensional Wigner crystal

description: A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distances <i>d</i> from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the <i>d</i> = 0 and <i>d</i> → ∞ limiting cases extend for finite values of <i>d</i> from the respective starting points into two sequences of stable states, with intersecting energies at some value <i>d</i><sub><i>t</i></sub>; beyond this value the branches continue as metastable states.
DOI: 10.6084/m9.figshare.979168.v3
title: Patterns of beetle diversity in kauri forest

description: Kauri forest represents a major ecosystem in northern New Zealand; however, the invertebrate fauna and their ecological diversity in these forests is very poorly known. This article investigates the composition and diversity of beetle communities in two kauri forest remnants, sampled by pitfall traps each month for one year. In total 4777 beetles were caught, representing 28 families, 84 genera and 107 species. Estimates of species richness indicate there were 173 species at both sites combined. The five most abundant species contributed 71%, and the top 10 species contributed 88% of all beetles caught. The abundance, richness and composition of the beetle community were consistent throughout the year. Patterns of niche overlap also show that the same set of species co-occur throughout the year, rather than temporal partitioning of the environment on an annual time scale. This data suggests that seasonality plays a limited role in explaining the composition and diversity of beetle communities in kauri forest.
DOI: 10.6084/m9.figshare.979168.v2
title: Patterns of beetle diversity in kauri forest

description: Kauri forest represents a major ecosystem in northern New Zealand; however, the invertebrate fauna and their ecological diversity in these forests is very poorly known. This article investigates the composition and diversity of beetle communities in two kauri forest remnants, sampled by pitfall traps each month for one year. In total 4777 beetles were caught, representing 28 families, 84 genera and 107 species. Estimates of species richness indicate there were 173 species at both sites combined. The five most abundant species contributed 71%, and the top 10 species contributed 88% of all beetles caught. The abundance, richness and composition of the beetle community were consistent throughout the year. Patterns of niche overlap also show that the same set of species co-occur throughout the year, rather than temporal partitioning of the environment on an annual time scale. This data suggests that seasonality plays a limited role in explaining the composition and diversity of beetle communities in kauri forest.