cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.861138.v2
title: tuftIB cell , dendritic input - Neuron version

description: Trying to reproduce fig A4C from Traub et al 2005 no aditional current to soma current to apical dendrite: EPSP I =3* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) plotted in tufuIB_Neuron.png CaBurst: I =9* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) we didn't get the somatic spike like in article tuftIB_Neuron_voltage.png (green voltage in apical dendrite, black in basal dendite, red in soma) look also at : http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124
DOI: 10.6084/m9.figshare.861124.v1
title: tuftIB cell , dendritic input - Fortran version

description: Trying to reproduce A4C from Traub et al 2005 no aditional current to soma current to apical dendrite: I =3* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) we didn't get the somatic spike like in article
DOI: 10.6084/m9.figshare.861127.v2
title: tuftIB cell , strong dendritic input + additional somatic input - Fortran version

description: Compare with A4C from Traub et al 2005 and http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124 aditional current to soma 1 na and 3 times stronger current to apical dendrite: I =9* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) caused somatick spike
DOI: 10.6084/m9.figshare.861130.v1
title: tuftIB cell , strong dendritic input + small somatic input - Fortran version

description: Compare with A4C from Traub et al 2005 and http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124 and http://figshare.com/articles/tuftIB_cell_strong_dendritic_input_additional_somatick_input_Fortran_version/861127 aditional current to soma 0.5 nA and 3 times stronger current to apical dendrite: I =9* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) didn't caused somatick spike
DOI: 10.6084/m9.figshare.861133.v2
title: tuftIB cell , dendritic input + somatic input 1 nA - Fortran version

description: Compare with A4C from Traub et al 2005 and http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124 and http://figshare.com/articles/tuftIB_cell_strong_dendritic_input_additional_somatick_input_Fortran_version/861127 and http://figshare.com/articles/tuftIB_cell_strong_dendritic_input_small_somatic_input_Fortran_version/861130 just aditional current to soma 1 nA didn't caused somatick spike dendritic current : I =3* (1-exp((t0 - t)/10)) * (exp((t0-t)/20))
DOI: 10.6084/m9.figshare.861138.v1
title: tuftIB cell , dendritic input - Neuron version

description: Trying to reproduce fig A4C from Traub et al 2005 no aditional current to soma current to apical dendrite: I =3* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) plotted in tufuTB_Neuron.png we didn't get the somatic spike like in article tuftIB_Neuron_voltage.png (green voltage in apical dendrite, black in basal dendite, red in soma) look also at : http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124
DOI: 10.6084/m9.figshare.861076
title: strand cross correlation examples

description: strand cross correlation examples using phantompeakqualtools software: https://code.google.com/p/phantompeakqualtools/
DOI: 10.6084/m9.figshare.861118
title: Neuron single cell - somatic stimulus

description: Single cell test for Neuron version of Traub model single_cell_test.hoc - Neuron script to generate all of the results look at Traub at all 2005 appendix A
DOI: 10.6084/m9.figshare.861119
title: CLSM volume rendered media files showing the maxillo-labial complex of Sparasion (Hymenoptera: Platygastroidea)

description: CLSM volume rendered media files showing the maxillo-labial complex of <em>Sparasion</em>(Hymenoptera: Platygastroidea). The file set provides supporting information for Ovidiu Alin Popovici, István Mikó, Katja Seltmann and Andrew R. Deans (submitted) The maxillo-labial complex of Sparasion (Hymenoptera: Platygastroidea). <em>Journal of Hymenoptera Research</em>.
DOI: 10.6084/m9.figshare.861127.v1
title: tuftIB cell , strong dendritic input + additional somatick input - Fortran version

description: Compare with A4C from Traub et al 2005 and http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124 aditional current to soma 1 na and 3 times stronger current to apical dendrite: I =9* (1-exp((t0 - t)/10)) * (exp((t0-t)/20)) cased somatick spike
DOI: 10.6084/m9.figshare.861133.v1
title: tuftIB cell , dendritic input + somatic input 0.5 nA - Fortran version

description: Compare with A4C from Traub et al 2005 and http://figshare.com/articles/tuftIB_cell_dendritic_input_Fortran_version/861124 and http://figshare.com/articles/tuftIB_cell_strong_dendritic_input_additional_somatick_input_Fortran_version/861127 and http://figshare.com/articles/tuftIB_cell_strong_dendritic_input_small_somatic_input_Fortran_version/861130 just aditional current to soma 1 nA didn't caused somatick spike dendritic current : I =9* (1-exp((t0 - t)/10)) * (exp((t0-t)/20))
DOI: 10.6084/m9.figshare.861071
title: Simulations files for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

description: Simulations files for the article "Molecular Conformation and Bilayer Pores in a Nonionic Surfactant Lamellar Phase Studied with 1H–13C Solid-State NMR and Molecular Dynamics Simulations" Ferreira et al. Langmuir, 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r The simulation trajectories can be found from: 60 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.28595 60 wt% C12E5, T=320K http://dx.doi.org/10.5281/zenodo.28637 60 wt% C12E5, T=333K http://dx.doi.org/10.5281/zenodo.28638 70 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.20368 70 wt% C12E5, T=320K http://dx.doi.org/10.5281/zenodo.20561 70 wt% C12E5, T=333K http://dx.doi.org/10.5281/zenodo.20664 80 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.20221
DOI: 10.6084/m9.figshare.861076.v1
title: strand cross correlation examples

description: strand cross correlation examples using phantompeakqualtools software: https://code.google.com/p/phantompeakqualtools/
DOI: 10.6084/m9.figshare.861119.v1
title: CLSM volume rendered media files showing the maxillo-labial complex of Sparasion (Hymenoptera: Platygastroidea)

description: CLSM volume rendered media files showing the maxillo-labial complex of <em>Sparasion</em>(Hymenoptera: Platygastroidea). The file set provides supporting information for Ovidiu Alin Popovici, István Mikó, Katja Seltmann and Andrew R. Deans (submitted) The maxillo-labial complex of Sparasion (Hymenoptera: Platygastroidea). <em>Journal of Hymenoptera Research</em>.
DOI: 10.6084/m9.figshare.861071.v1
title: Simulations files for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

description: Simulations files for the article "Molecular Conformation and Bilayer Pores in a Nonionic Surfactant Lamellar Phase Studied with 1H–13C Solid-State NMR and Molecular Dynamics Simulations" Ferreira et al. Langmuir, 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r The simulation trajectories can be found from: 60 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.28595 60 wt% C12E5, T=320K http://dx.doi.org/10.5281/zenodo.28637 60 wt% C12E5, T=333K http://dx.doi.org/10.5281/zenodo.28638 70 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.20368 70 wt% C12E5, T=320K http://dx.doi.org/10.5281/zenodo.20561 70 wt% C12E5, T=333K http://dx.doi.org/10.5281/zenodo.20664 80 wt% C12E5, T=298K http://dx.doi.org/10.5281/zenodo.20221
DOI: 10.6084/m9.figshare.861118.v2
title: Neuron single cell - somatic stimulus

description: Single cell test for Neuron version of Traub model single_cell_test.hoc - Neuron script to generate all of the results look at Traub at all 2005 appendix A
DOI: 10.6084/m9.figshare.861118.v1
title: Neuron single cell

description: Single cell test for Neuron version of Traub model single_cell_test.hoc - Neuron script to generate all of the results
DOI: 10.6084/m9.figshare.861055
title: Posner test using Arduino and Python

description: This fileset contains all information to run a Posner's test (exogenous cues), using an Arduino and Python. Data is generated using Arduino (measurement of reaction times) and fed via USB to a computer running Python to read in and record the data.
DOI: 10.6084/m9.figshare.861045
title: Mouse PyX kinematic dataset

description: Raw data of over 200 gait-related variables obtained via high-speed kinematic analysis in mice with unilateral corticospinal tract injury (or sham-injured mice). Please contact me with any questions/further details. Associated with publication: Harel NY, Yigitkanli K, Fu Y, Cafferty WB, Strittmatter SM. Multimodal exercises simultaneously stimulating cortical and brainstem pathways after unilateral corticospinal lesion. Brain Res. 2013 Nov 13;1538:17-25. doi: 10.1016/j.brainres.2013.07.012.
DOI: 10.6084/m9.figshare.861046
title: Mouse PyX kinematic data - SPSS analysis

description: SPSS output for analysis of gait-related variables obtained via high-speed kinematic analysis in mice with unilateral corticospinal tract injury (or sham-injured mice). Please contact me with any questions or for further details. Associated with publication: Harel NY, Yigitkanli K, Fu Y, Cafferty WB, Strittmatter SM. Multimodal exercises simultaneously stimulating cortical and brainstem pathways after unilateral corticospinal lesion. Brain Res. 2013 Nov 13;1538:17-25. doi: 10.1016/j.brainres.2013.07.012.
DOI: 10.6084/m9.figshare.861055.v1
title: Posner test using Arduino and Python

description: This fileset contains all information to run a Posner's test (exogenous cues), using an Arduino and Python. Data is generated using Arduino (measurement of reaction times) and fed via USB to a computer running Python to read in and record the data.
DOI: 10.6084/m9.figshare.861044
title: Neural injury and repair

description: Lecture given as part of "Brain and Behavior" course at Icahn School of Medicine at Mount Sinai
DOI: 10.6084/m9.figshare.861047.v1
title: Gaussian Job Archive for CsF3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.861041
title: Association Data

description: Asosciations, deleterious variants in maize genes.
DOI: 10.6084/m9.figshare.861046.v1
title: SPSS analysis of mouse kinematic data

description: SPSS output for analysis of gait-related variables obtained via high-speed kinematic analysis in mice with unilateral corticospinal tract injury (or sham-injured mice). Please contact me with any questions or for further details. Associated with publication: Harel NY, Yigitkanli K, Fu Y, Cafferty WB, Strittmatter SM. Multimodal exercises simultaneously stimulating cortical and brainstem pathways after unilateral corticospinal lesion. Brain Res. 2013 Nov 13;1538:17-25. doi: 10.1016/j.brainres.2013.07.012.
DOI: 10.6084/m9.figshare.861041.v2
title: Association Data

description: Asosciations, deleterious variants in maize genes.
DOI: 10.6084/m9.figshare.861038.v1
title: Gaussian Job Archive for CsF3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.861041.v1
title: Association Data

description: Asosciations, deleterious variants in maize genes.
DOI: 10.6084/m9.figshare.861029.v1
title: Gaussian Job Archive for CsF3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.861030.v1
title: Gaussian Job Archive for CsF3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.861021
title: Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions

description: Recent technological breakthroughs in medicinal chemistry arena had ameliorated the perspectives of quantitative structure–activity relationship (QSAR) methods. In this direction, we developed a group-based QSAR method based on pharmacophore-similarity concept which takes into account the 2D topological pharmacophoric descriptors and predicts the group-specific biological activities. This activity prediction may assist the contribution of certain pharmacophore features encoded by respective fragments toward activity improvement and/or detrimental effects. We termed this method as pharmacophore-similarity-based QSAR (PS-QSAR) and studied the activity contribution of fragments from 3-hydroxypyridinones derivatives possessing antimalarial activities.
DOI: 10.6084/m9.figshare.861022
title: Visible periodicity of strong nucleosome DNA sequences

description: Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10–11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes – i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms – nucleosome positioning motifs – are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.
DOI: 10.6084/m9.figshare.861021.v1
title: Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions

description: Recent technological breakthroughs in medicinal chemistry arena had ameliorated the perspectives of quantitative structure–activity relationship (QSAR) methods. In this direction, we developed a group-based QSAR method based on pharmacophore-similarity concept which takes into account the 2D topological pharmacophoric descriptors and predicts the group-specific biological activities. This activity prediction may assist the contribution of certain pharmacophore features encoded by respective fragments toward activity improvement and/or detrimental effects. We termed this method as pharmacophore-similarity-based QSAR (PS-QSAR) and studied the activity contribution of fragments from 3-hydroxypyridinones derivatives possessing antimalarial activities.
DOI: 10.6084/m9.figshare.861022.v1
title: Visible periodicity of strong nucleosome DNA sequences

description: Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10–11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes – i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms – nucleosome positioning motifs – are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.
DOI: 10.6084/m9.figshare.861021.v2
title: Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions

description: Recent technological breakthroughs in medicinal chemistry arena had ameliorated the perspectives of quantitative structure–activity relationship (QSAR) methods. In this direction, we developed a group-based QSAR method based on pharmacophore-similarity concept which takes into account the 2D topological pharmacophoric descriptors and predicts the group-specific biological activities. This activity prediction may assist the contribution of certain pharmacophore features encoded by respective fragments toward activity improvement and/or detrimental effects. We termed this method as pharmacophore-similarity-based QSAR (PS-QSAR) and studied the activity contribution of fragments from 3-hydroxypyridinones derivatives possessing antimalarial activities.
DOI: 10.6084/m9.figshare.861022.v2
title: Visible periodicity of strong nucleosome DNA sequences

description: Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10–11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes – i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms – nucleosome positioning motifs – are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.
DOI: 10.6084/m9.figshare.861022.v4
title: Visible periodicity of strong nucleosome DNA sequences

description: Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10–11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes – i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms – nucleosome positioning motifs – are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.
DOI: 10.6084/m9.figshare.861022.v3
title: Visible periodicity of strong nucleosome DNA sequences

description: Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10–11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes – i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms – nucleosome positioning motifs – are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.
DOI: 10.6084/m9.figshare.860448
title: Statistical Comparison of Two ROC Curves

description: This excel file will do a statistical tests of whether two ROC curves are different from each other based on the Area Under the Curve. You'll need the coefficient from the presented table in the following article to enter the correct AUC value for the comparison: Hanley JA, McNeil BJ (1983) A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 148:839-843.
DOI: 10.6084/m9.figshare.860449
title: Gaussian Job Archive for C36H44ClMnN2O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.860458
title: RDS in Thailand: webRDS and Contact Patterns

description: Web based respondent driven sampling conducted among students in Thailand, to investigate contact patterns relevant for the spread of close-contact infections.
DOI: 10.6084/m9.figshare.861021.v3
title: Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions

description: Recent technological breakthroughs in medicinal chemistry arena had ameliorated the perspectives of quantitative structure–activity relationship (QSAR) methods. In this direction, we developed a group-based QSAR method based on pharmacophore-similarity concept which takes into account the 2D topological pharmacophoric descriptors and predicts the group-specific biological activities. This activity prediction may assist the contribution of certain pharmacophore features encoded by respective fragments toward activity improvement and/or detrimental effects. We termed this method as pharmacophore-similarity-based QSAR (PS-QSAR) and studied the activity contribution of fragments from 3-hydroxypyridinones derivatives possessing antimalarial activities.
DOI: 10.6084/m9.figshare.860446
title: Gaussian Job Archive for C36H44ClMnN2O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.860449.v1
title: Gaussian Job Archive for C36H44ClMnN2O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.