cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4309547.v1
title: Metadata and Data for Hogle, Brahamsha, and Barbeau. mSystems. Accepted

description: <b>Publication:</b>Hogle SL, Brahamsha B, Barbea KA. Direct heme uptake by phytoplankton-associated <i>Roseobacter </i>bacteria. mSystems. <i>Accepted</i><br><b>Description:</b>In this study we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated <i>Roseobacter</i> bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 <i>Roseobacter</i> genomes and found that nearly half contained putative complete heme transport systems with near identical synteny. We also examined a publicly available co-culture transcriptome and found that the <i>Roseobacter</i> strain, <i>Sulfitobacter</i> sp. SA11, strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of the phytoplankton-associated <i>Roseobacter</i> strain <i>Ruegeria</i> sp. TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter <i>hmuR</i> and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis.
DOI: 10.6084/m9.figshare.4309547.v3
title: Metadata and Data for https://doi.org/10.1128/mSystems.00124-16

description: <b>Citation:</b>Hogle SL, Brahamsha B, Barbeau KA. Direct heme uptake by phytoplankton-associated <i>Roseobacter</i> bacteria. <i>mSystems</i>. 2016. 2(1):e00124-16. DOI: 10.1128/mSystems.00124-16<br><br><b>Data availability:</b>Raw sequence data for reproducing all analyses can be obtained from JGI IMG Integrated Microbial Genomes & Microbiomes database (also see Dataset S1 for accession numebrs) and the NCBI Gene Expression Omnibus (GEO accession GSE65189 and see Dataset S2). For user convenience R scripts for reproducing the transcriptomes processing analysis are available here.<br><b>Description:</b>In this study we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated <i>Roseobacter</i> bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 <i>Roseobacter</i> genomes and found that nearly half contained putative complete heme transport systems with near identical synteny. We also examined a publicly available co-culture transcriptome and found that the <i>Roseobacter</i> strain, <i>Sulfitobacter</i> sp. SA11, strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of the phytoplankton-associated <i>Roseobacter</i> strain <i>Ruegeria</i> sp. TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter <i>hmuR</i> and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis.
DOI: 10.6084/m9.figshare.4309547.v2
title: Metadata and Data for Hogle, Brahamsha, and Barbeau. mSystems. Accepted

description: <b>Publication:</b>Hogle SL, Brahamsha B, Barbea KA. Direct heme uptake by phytoplankton-associated <i>Roseobacter </i>bacteria. mSystems. <i>Accepted</i><br><b>Data availability:</b>Raw sequence data for reproducing all analyses can be obtained from JGI IMG Integrated Microbial Genomes & Microbiomes database (also see Dataset S1 for accession numebrs) and the NCBI Gene Expression Omnibus (GEO accession GSE65189 and see Dataset S2). For user convenience R scripts for reproducing the transcriptomes processing analysis are available here.<br><b>Description:</b>In this study we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated <i>Roseobacter</i> bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 <i>Roseobacter</i> genomes and found that nearly half contained putative complete heme transport systems with near identical synteny. We also examined a publicly available co-culture transcriptome and found that the <i>Roseobacter</i> strain, <i>Sulfitobacter</i> sp. SA11, strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of the phytoplankton-associated <i>Roseobacter</i> strain <i>Ruegeria</i> sp. TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter <i>hmuR</i> and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis.
DOI: 10.6084/m9.figshare.4309490
title: PRYER LTN 2016.xls

description: Aerial cover estimates of four species of native perennials and four species of native grasses, seeded wither together or one year part, at three different sites in northern California, in each of five years of initiation (2011-2015).<br>
DOI: 10.6084/m9.figshare.4309490.v1
title: PRYER LTN 2016.xls

description: Aerial cover estimates of four species of native perennials and four species of native grasses, seeded wither together or one year part, at three different sites in northern California, in each of five years of initiation (2011-2015).<br>
DOI: 10.6084/m9.figshare.4309487
title: DFT study of the thermodynamics of the reactions between thymidine or xylose-derived cyclic carbonates and methanol or iso-propanol

description: Data to support article:<br><br>CO<sub>2</sub>-driven stereochemical inversion of sugars to create thymidine-based polycarbonates by ring-opening polymerisation<br><br>DOI: 10.6084/m9.figshare.4309487<br><br><br>Authors:<br><br> Georgina L. Gregory,<sup>a</sup> Elizabeth M. Hierons,<sup>a</sup> Gabriele Kociok-Köhn,<sup>a</sup> Ram Sharma<sup>b</sup> and Antoine Buchard<sup>a,</sup>* <sup>a</sup> Department of Chemistry, University of Bath, Bath BA2 7AY <sup>b</sup> Department of Chemical Engineering, University of Bath, Bath BA2 7AY <br>DFT study: - DFT optimised geometries and computed free enthalpies were used to calculate the thermodynamics of the ring-opening of N-methylthymidine cyclic carbonates trans-<b>1</b> or cis-<b>1</b>, or N-benzoylthymidine cyclic carbonate cis-<b>1-</b>Bz, or ᴅ-xylose-based cyclic carbonate IPXTC <b><sub> </sub></b>(from Shen et al., Macromolecules 1999, 32, 2799 - 280), by methanol or iso-propanol, to evaluate the thermodynamics of ROP and the regioselectivity of the reactions. <b><sub><br><br></sub></b> Protocol: <br>rwB97XD/6-311+G(2d,p)/cpcm=dichloromethane/T=298.15K Content: - Gaussian09 rev D.01 output files- Thermodynamics_ROP.pdf, illustrating the calculations made and summarising the enthalpies computed.
DOI: 10.6084/m9.figshare.4309475
title: Interactive Locomotion

description: The dataset is made up of full-body kinematics data of 6 subjects performing two main tasks: - walking alone (Solo Trial); - walking together with another subject while mechanically coupled through a stretcher-like object (Paired Trial).<br> Data were collected by using the VICON system with 14 infrared bonita camera. Subjects were fully instrumented by 34 passive markers placed according to the Plug-In-Gait marker placement. The stretcher like object used to mechanically coupled a pair of subjects was also instrumented with 6 markers in order to detect its position during the trials. The experiment parameters and subject metadata are provided in the files Subject_Disposition.xlsx and Database_Subjects_CoMTrajectory.xlsx. The trajectory of each marker placed on each subject within a pair is stored in Pair*.mat while the trajectory and the velocity of the CoM for each subject evaluated at each gait cycle can be found in CoM_trajectories and CoM_velocities.<br> In detail: - Pair*.mat: For each pair (*=1,2,3,...,7), the cells represent the trials performed by the pair. By opening one cell (trial) it is possible to find several fields. The relevant one is the ‘DATA’ field (hdl*{1,#trial}.DATA) where it is possible to find several parameters related to the Subject in front of the stretcher (1) or behind it (2), For simplicity we will refer only to the Subject in front to explain the rest of the fields (same can be said for the Subject behind just by replacing 1 with 2 or A with B). The main field to be analyzed are: o hdl*{1,#trial}.DATA.Pos1-&gt;it contains all the markers’ trajectories, related to markers on the right (R) or on the left (L) or in the center (C). o hdl*{1,#trial}.DATA.CoMs01A.C.CoM-&gt;it contains CoM trajectory o hdl*{1,#trial}.DATA.CoM_Table-&gt;it contains Table CoM trajectory. - CoM_trajectories: each field is a Subject that is identified by a number (pair to which he/she belongs) and a letter A/B to indicate whether the subject is in front of the stretcher (A) or behind (B). o COM_GCT.Subject**.Single-&gt;contains a nuber of cells corresponding to the total number of trials that the Subject** did during the ‘Solo Trial’. Since some of the 6 analyzed subjects can compare in different pairs or in the same pair but in different position, in order to map the subject inside a pair to the real subject (whose parameters are stored in Database_Subjects_CoM_Trajectory.xlsx) please refer to Subject_Disposition.xlsx. In each trial one can access to the COM traejectory along the forward direction; oCOM_GCT.Subject**.Coupled -&gt;contains a nuber of cells corresponding to the total number of trials that the Subject** did during the ‘Paired Trial’; In each trial one can access to the COM traejectory along the forward direction; o COM_GCT.Subject**.Media-&gt;it is the mean CoM trajectory for both Single and Paired trials. - CoM_velocities: same scheme of CoM_trajectories.
DOI: 10.6084/m9.figshare.4309475.v1
title: Interactive Locomotion

description: The dataset is made up of full-body kinematics data of 6 subjects performing two main tasks: - walking alone (Solo Trial); - walking together with another subject while mechanically coupled through a stretcher-like object (Paired Trial).<br> Data were collected by using the VICON system with 14 infrared bonita camera. Subjects were fully instrumented by 34 passive markers placed according to the Plug-In-Gait marker placement. The stretcher like object used to mechanically coupled a pair of subjects was also instrumented with 6 markers in order to detect its position during the trials. The experiment parameters and subject metadata are provided in the files Subject_Disposition.xlsx and Database_Subjects_CoMTrajectory.xlsx. The trajectory of each marker placed on each subject within a pair is stored in Pair*.mat while the trajectory and the velocity of the CoM for each subject evaluated at each gait cycle can be found in CoM_trajectories and CoM_velocities.<br> In detail: - Pair*.mat: For each pair (*=1,2,3,...,7), the cells represent the trials performed by the pair. By opening one cell (trial) it is possible to find several fields. The relevant one is the ‘DATA’ field (hdl*{1,#trial}.DATA) where it is possible to find several parameters related to the Subject in front of the stretcher (1) or behind it (2), For simplicity we will refer only to the Subject in front to explain the rest of the fields (same can be said for the Subject behind just by replacing 1 with 2 or A with B). The main field to be analyzed are: o hdl*{1,#trial}.DATA.Pos1-&gt;it contains all the markers’ trajectories, related to markers on the right (R) or on the left (L) or in the center (C). o hdl*{1,#trial}.DATA.CoMs01A.C.CoM-&gt;it contains CoM trajectory o hdl*{1,#trial}.DATA.CoM_Table-&gt;it contains Table CoM trajectory. - CoM_trajectories: each field is a Subject that is identified by a number (pair to which he/she belongs) and a letter A/B to indicate whether the subject is in front of the stretcher (A) or behind (B). o COM_GCT.Subject**.Single-&gt;contains a nuber of cells corresponding to the total number of trials that the Subject** did during the ‘Solo Trial’. Since some of the 6 analyzed subjects can compare in different pairs or in the same pair but in different position, in order to map the subject inside a pair to the real subject (whose parameters are stored in Database_Subjects_CoM_Trajectory.xlsx) please refer to Subject_Disposition.xlsx. In each trial one can access to the COM traejectory along the forward direction; oCOM_GCT.Subject**.Coupled -&gt;contains a nuber of cells corresponding to the total number of trials that the Subject** did during the ‘Paired Trial’; In each trial one can access to the COM traejectory along the forward direction; o COM_GCT.Subject**.Media-&gt;it is the mean CoM trajectory for both Single and Paired trials. - CoM_velocities: same scheme of CoM_trajectories.
DOI: 10.6084/m9.figshare.4309469
title: DFT study of the thermodynamics of the reaction between dimethyl carbonate and thymidine and xylose-derived cyclic carbonates

description: Data to support article:<br><br>CO<sub>2</sub>-driven stereochemical inversion of sugars to create thymidine-based polycarbonates by ring-opening polymerisation<br><br>DOI: 10.6084/m9.figshare.4309469<br><br><br>Authors:<br><br> Georgina L. Gregory,<sup>a</sup> Elizabeth M. Hierons,<sup>a</sup> Gabriele Kociok-Köhn,<sup>a</sup> Ram Sharma<sup>b</sup> and Antoine Buchard<sup>a,</sup>* <sup>a</sup> Department of Chemistry, University of Bath, Bath BA2 7AY <sup>b</sup> Department of Chemical Engineering, University of Bath, Bath BA2 7AY <br>DFT study: - DFT optimised geometries and computed enthalpies were used to calculate the thermodynamics of the isodesmic reactions between dimethyl carbonate and N-methylthymidine cyclic carbonates trans-<b>1</b> or cis-<b>1</b>, or N-benzoylthymidine cyclic carbonate cis-<b>1-</b>Bz, or ᴅ-xylose-based cyclic carbonate IPXTC <b><sub> </sub></b>(from Shen et al., Macromolecules 1999, 32, 2799 - 280), so as to evaluate the ring-strains of the 4 monomers.<b><sub><br></sub></b> Protocol: <br>rwB97XD/6-311+G(2d,p)/cpcm=dichloromethane/T=298.15K Content: - Gaussian09 rev D.01 output files- Ring_Strain_Evaluation.pdf, illustrating the calculations made and summarising the enthalpies computed.
DOI: 10.6084/m9.figshare.4309469.v1
title: DFT study of the thermodynamics of the reaction between dimethyl carbonate and thymidine and xylose-derived cyclic carbonates

description: Data to support article:<br><br>CO<sub>2</sub>-driven stereochemical inversion of sugars to create thymidine-based polycarbonates by ring-opening polymerisation<br><br>DOI: 10.6084/m9.figshare.4309469<br><br><br>Authors:<br><br> Georgina L. Gregory,<sup>a</sup> Elizabeth M. Hierons,<sup>a</sup> Gabriele Kociok-Köhn,<sup>a</sup> Ram Sharma<sup>b</sup> and Antoine Buchard<sup>a,</sup>* <sup>a</sup> Department of Chemistry, University of Bath, Bath BA2 7AY <sup>b</sup> Department of Chemical Engineering, University of Bath, Bath BA2 7AY <br>DFT study: - DFT optimised geometries and computed enthalpies were used to calculate the thermodynamics of the isodesmic reactions between dimethyl carbonate and N-methylthymidine cyclic carbonates trans-<b>1</b> or cis-<b>1</b>, or N-benzoylthymidine cyclic carbonate cis-<b>1-</b>Bz, or ᴅ-xylose-based cyclic carbonate IPXTC <b><sub> </sub></b>(from Shen et al., Macromolecules 1999, 32, 2799 - 280), so as to evaluate the ring-strains of the 4 monomers.<b><sub><br></sub></b> Protocol: <br>rwB97XD/6-311+G(2d,p)/cpcm=dichloromethane/T=298.15K Content: - Gaussian09 rev D.01 output files- Ring_Strain_Evaluation.pdf, illustrating the calculations made and summarising the enthalpies computed.
DOI: 10.6084/m9.figshare.4309442
title: Association of pulmonary tuberculosis and HIV in the Mexican Institute of Social Security 2006-2014

description: Supporting information.
DOI: 10.6084/m9.figshare.4309439
title: Citalopram connectivity DMN component

description: DMN component, identified using ICA.<br>
DOI: 10.6084/m9.figshare.4309442.v1
title: Association of pulmonary tuberculosis and HIV in the Mexican Institute of Social Security 2006-2014

description: Supporting information.
DOI: 10.6084/m9.figshare.4309430
title: DFT study of the reaction between TBD, 4-methyl benzylalcohol initiator, and one molecule of N-methylthymidine cyclic carbonate (ring-opening polymerisation initiation step)

description: Data to support article:<br><br>CO<sub>2</sub>-driven stereochemical inversion of sugars to create thymidine-based polycarbonates by ring-opening polymerisation<br><br>DOI: 10.6084/m9.figshare.4309430<br><br><br>Authors:<br><br> Georgina L. Gregory,<sup>a</sup> Elizabeth M. Hierons,<sup>a</sup> Gabriele Kociok-Köhn,<sup>a</sup> Ram Sharma<sup>b</sup> and Antoine Buchard<sup>a,</sup>* <sup>a</sup> Department of Chemistry, University of Bath, Bath BA2 7AY <sup>b</sup> Department of Chemical Engineering, University of Bath, Bath BA2 7AY <br>- DFT optimised geometries and computed free enthalpies of local minima (intermediates) and local maxima (transition states) were used to investigate the mechanism of the reaction between TBD, 4-methylbenzyl alcohol and 1 molecule of N-methylthymidine cyclic carbonate to account for the initiation step of ring-opening polymerisation.<br> <br><br>Protocols:<br>rwB97XD/6-311++G(d,p)/6-31+G(d)cpcm=dichloromethane/T=298.15K<br><br><br>Content:<br><br>- Gaussian09 rev D.01 output files<br>- ROP_initiation.pdf, illustrating the calculations made and summarising the free enthalpies computed.
DOI: 10.6084/m9.figshare.4309439.v1
title: Citalopram connectivity DMN component

description: DMN component, identified using ICA.<br>
DOI: 10.6084/m9.figshare.4309439.v2
title: Citalopram connectivity DMN component

description: DMN component, identified using ICA.<br>
DOI: 10.6084/m9.figshare.4309328
title: Supplemental Materails: A mechanically-coupled reaction diffusion model that incorporates intra-tumoral heterogeneity to predict in vivo glioma growth

description: This is Matlab code and data that reproduces panels from figures 3-8 in the Journal of the Royal Society Interface submission <i>A mechanically-coupled reaction diffusion model that incorprates intra-tumoral heterogenity to predict in vivo glioma growth. </i>Authors: Hormuth II, DA; Weis JA; Barnes SL; Miga MI; Rericha EC: Quaranta V: Yankeelov TE.<br><br>
DOI: 10.6084/m9.figshare.4309328.v1
title: Supplemental Materails: A mechanically-coupled reaction diffusion model that incorporates intra-tumoral heterogeneity to predict in vivo glioma growth

description: This is Matlab code and data that reproduces panels from figures 3-8 in the Journal of the Royal Society Interface submission <i>A mechanically-coupled reaction diffusion model that incorprates intra-tumoral heterogenity to predict in vivo glioma growth. </i>Authors: Hormuth II, DA; Weis JA; Barnes SL; Miga MI; Rericha EC: Quaranta V: Yankeelov TE.<br><br>
DOI: 10.6084/m9.figshare.4309379.v3
title: Implantes dentales - Grup Dr. Bladé

description: Somos una clínica dental con varios centros en Barcelona y alrededores para dar un mayor servicio dental a todo el mundo con el mejor precio y garantías.Somos un equipo de profesionales altamente preparados en salud bucodental y estética dental. Expertos en implantes dentales. No dude en ponerse en contacto con nosotros para conocer cuáles son nuestros servicios.<br>
DOI: 10.6084/m9.figshare.4309379.v2
title: implante.jpg

description: Somos una clínica dental con varios centros en Barcelona y alrededores para dar un mayor servicio dental a todo el mundo con el mejor precio y garantías.Somos un equipo de profesionales altamente preparados en salud bucodental y estética dental. Expertos en implantes dentales. No dude en ponerse en contacto con nosotros para conocer cuáles son nuestros servicios.https://youtu.be/BUCYvdokDak?list=PLrIV-agFeQF56n7RVbeDP6he2vJguEn0h
DOI: 10.6084/m9.figshare.4309310
title: Comparison of valsartan and amlodipine on ambulatory blood pressure variability in hypertensive patients

description: We tested the hypothesis that calcium channel blockers (CCBs: amlodipine group, <i>n =</i> 38)) are superior to angiotensin receptor blockers (ARBs: valsartan group, <i>n =</i> 38) against ambulatory blood pressure variability (BPV) in untreated Japanese hypertensive patients. Both drugs significantly reduced ambulatory systolic and diastolic BP values. With regard to BPV, standard deviation (SD) in SBP did not change with the administration of either drug, but the ARB significantly increased SD in awake DBP (12 ± 4–14 ± 4 mmHg). The ARB also significantly increased the coefficients of variation (CVs)in awake and 24-h SBP/DBP (all P &lt; 0.05), but <i>amlodipine</i> did not change the CV. CCB significantly reduced the maximum values of awake SBP (193 ± 24–182 ± 27 mmHg, P = 0.02), sleep SBP (156 ± 18–139 ± 14 mmHg, P &lt; 0 .001), and awake and sleep DBP (P &lt; 0.01 in both cases), but the ARB did not change the maximum BP values. In conclusion, a once-daily morning dose of CCB amlodipine was more effective at controlling ambulatory BPV than ARB valsartan, especially in reducing maximum BP levels.
DOI: 10.6084/m9.figshare.4309310.v1
title: Comparison of valsartan and amlodipine on ambulatory blood pressure variability in hypertensive patients

description: We tested the hypothesis that calcium channel blockers (CCBs: amlodipine group, <i>n =</i> 38)) are superior to angiotensin receptor blockers (ARBs: valsartan group, <i>n =</i> 38) against ambulatory blood pressure variability (BPV) in untreated Japanese hypertensive patients. Both drugs significantly reduced ambulatory systolic and diastolic BP values. With regard to BPV, standard deviation (SD) in SBP did not change with the administration of either drug, but the ARB significantly increased SD in awake DBP (12 ± 4–14 ± 4 mmHg). The ARB also significantly increased the coefficients of variation (CVs)in awake and 24-h SBP/DBP (all P &lt; 0.05), but <i>amlodipine</i> did not change the CV. CCB significantly reduced the maximum values of awake SBP (193 ± 24–182 ± 27 mmHg, P = 0.02), sleep SBP (156 ± 18–139 ± 14 mmHg, P &lt; 0 .001), and awake and sleep DBP (P &lt; 0.01 in both cases), but the ARB did not change the maximum BP values. In conclusion, a once-daily morning dose of CCB amlodipine was more effective at controlling ambulatory BPV than ARB valsartan, especially in reducing maximum BP levels.