cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1489766
title: Body Position Influences Which Neural Structures Are Recruited by Lumbar Transcutaneous Spinal Cord Stimulation

description: Data used in Danner et al. 2016.Peak-to-peak amplitudes of the responses to transcutaneous spinal cord stimulation in quadriceps, hamstrings, tibialis anterior and triceps surae in prone, supine and standing positions at 25 intensity levels (5 to 125 mA in 5 mA steps) of 10 subjects. There are four dimensional arrays in the mat file, ptpFirstResponses and ptpSecondResponses for the first and second responses, respectively. The first dimension is the musce group in following sequence left quadriceps, hamstrings, tibialis anterior and triceps surae followed by same muscles on right leg. The second dimension is the stimulation intensity, 5 mA in 5 mA steps to 125 mA. The third dimension signifies the subject. Finally, the forth dimensions describes the body position in following sequence: 1) supine, 2) standing and 3) prone.<br>Danner SM, Krenn M, Hofstoetter US, Toth A, Mayr W, Minassian K (2016) Body Position Influences Which Neural Structures Are Recruited by Lumbar Transcutaneous Spinal Cord Stimulation. PLoS ONE 11(1): e0147479. doi:10.1371/journal.pone.0147479
DOI: 10.6084/m9.figshare.1489785
title: Fileset for project "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489758
title: PlosOneDataShare.xlsx

description: Data collected at the 600m2 scale to describe plant community, primary production and soil services
DOI: 10.6084/m9.figshare.1489795
title: Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases

description: Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. Δ<i>G</i> values were −15.82(12), −3.66(12), and −12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔ<i>G</i> = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔ<i>G</i> = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (<i>r</i> = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.
DOI: 10.6084/m9.figshare.1489795.v2
title: Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases

description: Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. Δ<i>G</i> values were −15.82(12), −3.66(12), and −12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔ<i>G</i> = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔ<i>G</i> = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (<i>r</i> = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.
DOI: 10.6084/m9.figshare.1489766.v1
title: Influence of body position on transcutaneous stimulation of posterior and anterior roots

description: Peak-to-peak amplitudes of the responses to transcutaneous spinal cord stimulation in quadriceps, hamstrings, tibialis anterior and triceps surae in prone, supine and standing positions at 25 intensity levels (5 to 125 mA in 5 mA steps) of 10 subjects. There are four dimensional arrays in the mat file, ptpFirstResponses and ptpSecondResponses for the first and second responses, respectively. The first dimension is the musce group in following sequence left quadriceps, hamstrings, tibialis anterior and triceps surae followed by same muscles on right leg. The second dimension is the stimulation intensity, 5 mA in 5 mA steps to 125 mA. The third dimension signifies the subject. Finally, the forth dimensions describes the body position in following sequence: 1) supine, 2) standing and 3) prone.
DOI: 10.6084/m9.figshare.1489785.v1
title: Fileset for project neuroethics

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489755
title: Dataset for Familiar face detection in 180ms

description: Dataset containing reaction times to the simultaneous presentation of personally familiar faces, stranger faces, or objects.
DOI: 10.6084/m9.figshare.1489795.v1
title: Zinc Finger Protein Binding to DNA: An Energy Perspective Using Molecular Dynamics Simulation and Free Energy Calculations on Mutants of both Zinc Finger Domains and their Specific DNA bases.

description: Energy calculations based on MM/GBSA were employed to study various zinc finger protein motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of zinc finger motifs to their sites on DNA. ΔG values were -15.82(12), -3.66(12) and ¬12.14(11.6) Kcal/mol for finger one, finger two and finger three respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 Kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation(r= 0.98). The mutations in key amino acids in the zinc finger motif in positions -1, 2, 3 and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was 0.99 and with Van der Waal was 0.93. Results agree with experimentally found selectivity which showed that Arginine in position -1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared zinc finger motifs bound to triplet bases in other reports (D J Segal, Dreier, Beerli, & Barbas, 1999), our results may help in the design of zinc finger motifs based on the established recognition codes based on energies and contributing energies to the total energy.
DOI: 10.6084/m9.figshare.1489740
title: Genetic divergence of an avian endemic on the Californian Channel Islands

description: Microsatellite data set from free-living song sparrows collected from the California Channel Islands
DOI: 10.6084/m9.figshare.1489739
title: Multiple sequence alignment of HBV complete genome sequences performed by using ClustalW in MEGA software version 6.

description: Multiple sequence alignment of HBV complete genome sequences performed by using ClustalW in MEGA software version 6.
DOI: 10.6084/m9.figshare.1489785.v2
title: Fileset for the study of "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489740.v1
title: Genetic divergence of an avian endemic on the Californian Channel Islands

description: Microsatellite data set from free-living song sparrows collected from the California Channel Islands
DOI: 10.6084/m9.figshare.1489709
title: How distance affects semantic integration in discourse: Evidence from Event-Related Potentials

description: data for Plos One paper
DOI: 10.6084/m9.figshare.1489715
title: "Seeing touches early in life." Dataset

description: Dataset from the article: Addabbo M., Longhi E., Bolognini N., Senna I., Tagliabue P., Macchi Cassia V., & Turati C. (2015). Seeing touches early in life. Plos one.
DOI: 10.6084/m9.figshare.1489785.v3
title: Fileset for the study of "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489703
title: Production of glycosylated human anti-Hepatitis B monoclonal antibodies in the microalgae Phaeodactylum tricornutum

description: Monoclonal antibodies (mAbs) represent actually the major class of biopharmaceuticals. They are produced recombinantly using living cells as biofactories. Among the different expression systems currently available, microalgae represent an emerging alternative which displays several biotechnological advantages. Indeed, microalgae are classified as generally recognized as safe organisms and can be grown easily in bioreactors with high growth rates similarly to CHO cells. Moreover, microalgae exhibit a phototrophic lifestyle involving low production costs as protein expression is fuelled by photosynthesis. However, questions remain to be solved before any industrial production of algae-made biopharmaceuticals. Among them, protein heterogeneity as well as protein post-translational modifications need to be evaluated. Especially, N- glycosylation acquired by the secreted recombinant proteins is of major concern since most of the biopharmaceuticals including mAbs are N-glycosylated and it is well recognized that glycosylation represent one of their critical quality attribute. In this paper, we assess the quality of the first recombinant algae-made mAbs produced in the diatom, Phaeodactylum tricornutum. We are focusing on the characterization of their C- and N-terminal extremities, their signal peptide cleavage and their post-translational modifications including N-glycosylation macro- and microheterogeneity. This study brings understanding on diatom cellular biology, especially secretion and intracellular trafficking of proteins. Overall, it reinforces the positioning of P. tricornutum as an emerging host for the production of biopharmaceuticals and prove that P. tricornutum is suitable for producing homogenous recombinant proteins bearing high mannose-type N-glycans.
DOI: 10.6084/m9.figshare.1489785.v4
title: Fileset for project neuroethics

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489785.v6
title: Fileset for project "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489785.v8
title: Fileset for project "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489562
title: Bollywood movie repository data

description: Please cite us as: 1. Sarika Jalan, Camellia Sarkar, Anagha Madhusudanan, Sanjiv K. Dwivedi. Uncovering randomness and success in society. PLoS ONE 9, e88249 (2014).<br>DOI: 10.1371/journal.pone.0088249 2. Camellia Sarkar, Sarika Jalan. Social patterns revealed through random matrix theory. EPL 108, 48003 (2014).<br>DOI: 10.1209/0295-5075/108/48003
DOI: 10.6084/m9.figshare.1489785.v7
title: Fileset for project "The First Decade of Neuroethics"

description: Files supporting the analysis presented in the paper "The First Decade of Neuroethics"
DOI: 10.6084/m9.figshare.1489525
title: Dataset examining functional assessment of animals with plant facilitation complexes

description: A systematic review examing plant facilitation by shrubs with other plant species and at least one animal species reported was done in 2014. A conceptual framework, review, and this dataset examined the capacity for positive plant interactions to scale to other taxa.
DOI: 10.6084/m9.figshare.1489525.v1
title: Dataset examining functional assessment of animals with plant facilitation complexes

description: A systematic review examing plant facilitation by shrubs with other plant species and at least one animal species reported was done in 2014. A conceptual framework, review, and this dataset examined the capacity for positive plant interactions to scale to other taxa.
DOI: 10.6084/m9.figshare.1488680
title: Directions to Quin

description: These are directions to the play Quin; a commentry, or footnote, to Beckett's play Quad, written as part of a lecture / performance of Quad staged by Pan Pan Theatre Company at the Edinburgh Festival in 2013 and the Dublin Dance Festival in 2014.
DOI: 10.6084/m9.figshare.1488676
title: Supporting Data for A world at risk: Aggregating development trends to forecast global habitat conversion

description: These data support research described within Oakleaf JR, Kennedy CM, Baruch-Mordo S, West PC, Gerber JS, et al. (2015) A World at Risk: Aggregating Development Trends to Forecast Global Habitat Conversion. PLOS ONE 10(10): e0138334. https://doi.org/10.1371/journal.pone.0138334.
DOI: 10.6084/m9.figshare.1488677
title: Digital cranial endocast of <i>Pseudoplohophorus absolutus</i> (Xenarthra, Cingulata) and its systematic and evolutionary implications

description: ABSTRACTGlyptodonts are a group of extinct xenarthrans with several anatomical features that make them one of the most bizarre groups of mammals. By the late 19th century, some authors began to analyze the brain of Pleistocene glyptodonts using natural endocranial casts. These studies revealed the small size of the brain of the large Pleistocene forms. However, the evolution of the brain in glyptodonts and how it fits in a phylogenetic context has not been analyzed. In order to evaluate the evolution of the brain in this group, we described the first digital endocranial cast of the late Miocene glyptodont <i>Pseudoplohophorus absolutus</i> and compared it with digital endocranial casts of the Pleistocene glyptodonts <i>Glyptodon, Doedicurus</i>, and <i>Panochthus</i> and the extant armadillos <i>Dasypus, Euphractus, Chaetophractus</i>, and <i>Zaedyus</i>. The endocast morphology of <i>P. absolutus</i> is similar to that of Pleistocene glyptodonts: large olfactory bulbs, a small cerebrum with a single neocortical sulcus, and a large cerebellum. However, the relative brain size is larger than in the Pleistocene forms, with values of the encephalization quotient (EQ) close to that of extant armadillos. A comparison between xenarthrans orders shows that Cingulata (glyptodonts and armadillos) have lower EQ values than Pilosa (sloths and vermilinguas). This could possibly be related to certain restrictions and benefits imposed by the presence of the carapace in cingulates. Furthermore, because the carapace restricts the development of the cervical musculature that supports the skull, the small size of the brain in glyptodonts could be a trade-off (along with others) to reduce the weight of the skull.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1488674
title: ATT based flow territories

description: These flow territories were created based on the Tatu et al. Neurology 1998 vascular territories, using arterial transit time (ATT) data from a population of elderly with hypertension. They correspond to Figure 2 of Plos One paper "Cerebral perfusion measurements in elderly with hypertension using arterial spin labeling". Data is stored in a regular nifti-file, without compression. Regions are encoded as follows: 1 = proximal ACA<br>2 = middle ACA<br>3 = distal ACA<br>4 = proximal MCA<br>5 = middle MCA<br>6 = distal MCA<br>7 = proximal PCA<br>8 = middle PCA<br>9 = distal PCA
DOI: 10.6084/m9.figshare.1488676.v1
title: Supporting Data for A world at risk: Aggregating development trends to forecast global habitat conversion

description: These data support research described within Oakleaf JR, Kennedy CM, Baruch-Mordo S, West PC, Gerber JS, et al. (2015) A World at Risk: Aggregating Development Trends to Forecast Global Habitat Conversion. PLOS ONE 10(10): e0138334. https://doi.org/10.1371/journal.pone.0138334.
DOI: 10.6084/m9.figshare.1488677.v1
title: Digital cranial endocast of <i>Pseudoplohophorus absolutus</i> (Xenarthra, Cingulata) and its systematic and evolutionary implications

description: ABSTRACTGlyptodonts are a group of extinct xenarthrans with several anatomical features that make them one of the most bizarre groups of mammals. By the late 19th century, some authors began to analyze the brain of Pleistocene glyptodonts using natural endocranial casts. These studies revealed the small size of the brain of the large Pleistocene forms. However, the evolution of the brain in glyptodonts and how it fits in a phylogenetic context has not been analyzed. In order to evaluate the evolution of the brain in this group, we described the first digital endocranial cast of the late Miocene glyptodont <i>Pseudoplohophorus absolutus</i> and compared it with digital endocranial casts of the Pleistocene glyptodonts <i>Glyptodon, Doedicurus</i>, and <i>Panochthus</i> and the extant armadillos <i>Dasypus, Euphractus, Chaetophractus</i>, and <i>Zaedyus</i>. The endocast morphology of <i>P. absolutus</i> is similar to that of Pleistocene glyptodonts: large olfactory bulbs, a small cerebrum with a single neocortical sulcus, and a large cerebellum. However, the relative brain size is larger than in the Pleistocene forms, with values of the encephalization quotient (EQ) close to that of extant armadillos. A comparison between xenarthrans orders shows that Cingulata (glyptodonts and armadillos) have lower EQ values than Pilosa (sloths and vermilinguas). This could possibly be related to certain restrictions and benefits imposed by the presence of the carapace in cingulates. Furthermore, because the carapace restricts the development of the cervical musculature that supports the skull, the small size of the brain in glyptodonts could be a trade-off (along with others) to reduce the weight of the skull.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1488677.v3
title: Digital cranial endocast of <i>Pseudoplohophorus absolutus</i> (Xenarthra, Cingulata) and its systematic and evolutionary implications

description: ABSTRACTGlyptodonts are a group of extinct xenarthrans with several anatomical features that make them one of the most bizarre groups of mammals. By the late 19th century, some authors began to analyze the brain of Pleistocene glyptodonts using natural endocranial casts. These studies revealed the small size of the brain of the large Pleistocene forms. However, the evolution of the brain in glyptodonts and how it fits in a phylogenetic context has not been analyzed. In order to evaluate the evolution of the brain in this group, we described the first digital endocranial cast of the late Miocene glyptodont <i>Pseudoplohophorus absolutus</i> and compared it with digital endocranial casts of the Pleistocene glyptodonts <i>Glyptodon, Doedicurus</i>, and <i>Panochthus</i> and the extant armadillos <i>Dasypus, Euphractus, Chaetophractus</i>, and <i>Zaedyus</i>. The endocast morphology of <i>P. absolutus</i> is similar to that of Pleistocene glyptodonts: large olfactory bulbs, a small cerebrum with a single neocortical sulcus, and a large cerebellum. However, the relative brain size is larger than in the Pleistocene forms, with values of the encephalization quotient (EQ) close to that of extant armadillos. A comparison between xenarthrans orders shows that Cingulata (glyptodonts and armadillos) have lower EQ values than Pilosa (sloths and vermilinguas). This could possibly be related to certain restrictions and benefits imposed by the presence of the carapace in cingulates. Furthermore, because the carapace restricts the development of the cervical musculature that supports the skull, the small size of the brain in glyptodonts could be a trade-off (along with others) to reduce the weight of the skull.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1488663
title: New Gateway-compatible vectors for a high-throughput protein–protein interaction analysis by a bimolecular fluorescence complementation (BiFC) assay in plants and their application to a plant clathrin structure analysis

description: Protein–protein interactions (PPI) play key roles in various biological processes. The bimolecular fluorescence complementation (BiFC) assay is an excellent tool for routine PPI analyses in living cells. We developed new Gateway vectors for a high-throughput BiFC analysis of plants, adopting a monomeric Venus split just after the tenth β-strand, and analyzed the interaction between <i>Arabidopsis thaliana</i> coated vesicle coatmers, the clathrin heavy chain (CHC), and the clathrin light chain (CLC). In competitive BiFC tests, CLC interacted with CHC through a coiled-coil motif in the middle section of CLC. R1340, R1448, and K1512 in CHC and W94 in CLC are potentially key amino acids underlying the inter-chain interaction, consistent with analyses based on homology modeling. Our Gateway BiFC system, the V10-BiFC system, provides a useful tool for a PPI analysis in living plant cells. The CLC–CHC interaction identified may facilitate clathrin triskelion assembly needed for cage formation.