cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.987086.v1
title: Data sets for UK Pulmonary Rehabilitation Programmes in real-life clinical settings

description: The data-sheet shows demographics and outcomes of patients who participated in two UK Pulmonary Rehabilitation Programmes. Hospital 1 offered 3 sessions per week over 6 weeks (Group 1) and Hospital 2 offered 2 sessions per week over 9 weeks (group 2). Data have been anonymised.
DOI: 10.6084/m9.figshare.987074
title: A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry

description: This work aims to combine chromatographic retention, high mass resolution and accuracy, MS/MS spectra, and a package for automated identification and quantitation of lipid species in one platform for lipidomic analysis. The instrumental setup elaborated comprises reversed-phase HPLC coupled to a Fourier transform ion cyclotron resonance mass spectrometer (LTQ-FT), and Lipid Data Analyzer (LDA) software. Data analysis for lipid species quantification in this platform is based on retention time, mass resolution of 200,000, and mass accuracy below 2 ppm. In addition, automatically generated MS/MS spectra provide structural information at molecular level. This LC/MS technology allows analyzing complex biological samples in a quantitative manner as shown here paradigmatically for murine lipid droplets having a huge surplus of triacylglycerol species. Chromatographic pre-separation of the bulk lipid class alleviates the problem of ion suppression of lipid species from other classes. Extension of 1D to 2D chromatography is possible, yet time consuming. The platform affords on unambiguous detection of lipid species as low as 0.1‰ within major lipid classes as low as 0.1‰. Taken together, a novel lipidomic LC/MS platform based on chromatographic retention, high mass resolution and accuracy, MS/MS analysis and quantitation software enables analysis of complex samples as demonstrated for lipid droplets.
DOI: 10.6084/m9.figshare.987076
title: The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: We showed earlier that nutritional stress like starvation or high fat diet resulted in phenotypic changes in the lipidomes of hepatocyte lipid droplets (LDs), representative for the pathophysiological status of the mouse model. Here we extend our former study by adding genetic stress due to knock-out (KO) of adipocyte triglyceride lipase (ATGL), the rate limiting enzyme in LD lipolysis. An intervention trial for 6 weeks with male wild-type (WT) and ATGL-KO mice was carried out; both genotypes were fed lab chow or were exposed to short-time starvation. Isolated LDs were analyzed by LC-MS/MS. Triacylglycerol, diacylglycerol and phosphatidylcholine lipidomes, in that order, provided best phenotypic signatures characteristic for respective stresses applied to the animals. This was evidenced at lipid species level by principal component analysis, calculation of average values for chain-lengths and numbers of double bonds, and by visualization in heat maps. Structural backgrounds for analyses and metabolic relationships were elaborated at lipid molecular species level. Relating our lipidomic data to non-alcoholic fatty liver diseases of nutritional and genetic etiologies with or without accompanying insulin resistance, phenotypic distinction in hepatocyte LDs dependent on insulin status emerged. Taken together, lipidomes of hepatocyte lipid droplets are sensitive responders to nutritional and genetic stress.
DOI: 10.6084/m9.figshare.987077
title: Suppl. Table - The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: Supplementary table
DOI: 10.6084/m9.figshare.987078.v1
title: Suppl. Fig. - The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: Supplementary Figures
DOI: 10.6084/m9.figshare.987073
title: Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Liver steatosis can be induced by fasting or high fat diet. We investigated by lipidomic analysis whether such metabolic states are reflected in the lipidome of hepatocyte lipid droplets (LD) from mice fed normal chow diet (FED), fasted before sacrifice (FAS), or fed a high fat diet (HFD). LC-MS/MS at levels of lipid species profiles and of lipid molecular species uncovered first a FAS phenotype enriched in triacylglycerol (TG) molecular species having very long-chain polyunsaturated fatty acyl (VLC-PUFA) residues and an HFD phenotype with less unsaturated TG species in addition to characteristic marker species. Nutritional stress did not result in dramatic structural alterations in diacylglycerol (DG) and phospholipid (PL) classes. Moreover, molecular species of bulk TG and of DG indicated concomitant de novo TG synthesis and lipase-catalyzed degradation to be active in LD. DG species with VLC-PUFA residues would be preferred precursors for phosphatidylcholine (PC) species, the others for TG molecular species. In addition, molecular species of PL classes fitted the hepatocyte Kennedy and PEMT pathways. We demonstrate that lipidomic analysis of lipid droplets enables phenotyping nutritional stress. TG species are best suited for such phenotyping, whereas structural analysis of TG, DG and PL molecular species furnishes metabolic insights.
DOI: 10.6084/m9.figshare.987077.v1
title: Suppl. Table - The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: Supplementary table
DOI: 10.6084/m9.figshare.987073.v1
title: Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Liver steatosis can be induced by fasting or high fat diet. We investigated by lipidomic analysis whether such metabolic states are reflected in the lipidome of hepatocyte lipid droplets (LD) from mice fed normal chow diet (FED), fasted before sacrifice (FAS), or fed a high fat diet (HFD). LC-MS/MS at levels of lipid species profiles and of lipid molecular species uncovered first a FAS phenotype enriched in triacylglycerol (TG) molecular species having very long-chain polyunsaturated fatty acyl (VLC-PUFA) residues and an HFD phenotype with less unsaturated TG species in addition to characteristic marker species. Nutritional stress did not result in dramatic structural alterations in diacylglycerol (DG) and phospholipid (PL) classes. Moreover, molecular species of bulk TG and of DG indicated concomitant de novo TG synthesis and lipase-catalyzed degradation to be active in LD. DG species with VLC-PUFA residues would be preferred precursors for phosphatidylcholine (PC) species, the others for TG molecular species. In addition, molecular species of PL classes fitted the hepatocyte Kennedy and PEMT pathways. We demonstrate that lipidomic analysis of lipid droplets enables phenotyping nutritional stress. TG species are best suited for such phenotyping, whereas structural analysis of TG, DG and PL molecular species furnishes metabolic insights.
DOI: 10.6084/m9.figshare.987074.v1
title: A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry

description: This work aims to combine chromatographic retention, high mass resolution and accuracy, MS/MS spectra, and a package for automated identification and quantitation of lipid species in one platform for lipidomic analysis. The instrumental setup elaborated comprises reversed-phase HPLC coupled to a Fourier transform ion cyclotron resonance mass spectrometer (LTQ-FT), and Lipid Data Analyzer (LDA) software. Data analysis for lipid species quantification in this platform is based on retention time, mass resolution of 200,000, and mass accuracy below 2 ppm. In addition, automatically generated MS/MS spectra provide structural information at molecular level. This LC/MS technology allows analyzing complex biological samples in a quantitative manner as shown here paradigmatically for murine lipid droplets having a huge surplus of triacylglycerol species. Chromatographic pre-separation of the bulk lipid class alleviates the problem of ion suppression of lipid species from other classes. Extension of 1D to 2D chromatography is possible, yet time consuming. The platform affords on unambiguous detection of lipid species as low as 0.1‰ within major lipid classes as low as 0.1‰. Taken together, a novel lipidomic LC/MS platform based on chromatographic retention, high mass resolution and accuracy, MS/MS analysis and quantitation software enables analysis of complex samples as demonstrated for lipid droplets.
DOI: 10.6084/m9.figshare.987076.v1
title: The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: We showed earlier that nutritional stress like starvation or high fat diet resulted in phenotypic changes in the lipidomes of hepatocyte lipid droplets (LDs), representative for the pathophysiological status of the mouse model. Here we extend our former study by adding genetic stress due to knock-out (KO) of adipocyte triglyceride lipase (ATGL), the rate limiting enzyme in LD lipolysis. An intervention trial for 6 weeks with male wild-type (WT) and ATGL-KO mice was carried out; both genotypes were fed lab chow or were exposed to short-time starvation. Isolated LDs were analyzed by LC-MS/MS. Triacylglycerol, diacylglycerol and phosphatidylcholine lipidomes, in that order, provided best phenotypic signatures characteristic for respective stresses applied to the animals. This was evidenced at lipid species level by principal component analysis, calculation of average values for chain-lengths and numbers of double bonds, and by visualization in heat maps. Structural backgrounds for analyses and metabolic relationships were elaborated at lipid molecular species level. Relating our lipidomic data to non-alcoholic fatty liver diseases of nutritional and genetic etiologies with or without accompanying insulin resistance, phenotypic distinction in hepatocyte LDs dependent on insulin status emerged. Taken together, lipidomes of hepatocyte lipid droplets are sensitive responders to nutritional and genetic stress.
DOI: 10.6084/m9.figshare.987079.v1
title: Suppl. Table - Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Supplementary tables
DOI: 10.6084/m9.figshare.987041
title: Suat ATAN

description: Nonlinear Programming (Turkish)
DOI: 10.6084/m9.figshare.987052
title: Assessment of harmful algal species using different approaches: the case study of the Sardinian coasts

description: The presence and distribution of harmful algal species were investigated along the coasts of Sardinia in the summer of 2012. Fourteen potentially noxious taxa were identified at 74 beaches. The majority of the recovered taxa were potentially toxic and/or high biomass producers. <i>Alexandrium taylorii</i>, <i>Gymnodinium instriatum</i>, and <i>Ostreopsis</i> cf. <i>ovata</i> were the most frequent and abundant taxa, although <i>Barrufeta bravensis</i> reached the highest density (4.4 × 10<sup>6</sup> cells L<sup>−1</sup>). <i>Barrufeta bravensis</i>, <i>A. taylorii</i>, and <i>G. instriatum</i> were responsible for intense water discoloration at two of the beaches sampled. Polymerase chain reaction (PCR) analyses supported the identification of several taxa and decisively identified <i>B. bravensis</i>. PCR assays increased the information available on the species distributions. The locations studied were heterogeneous in their prevailing environmental conditions and their morphodynamic profiles. Statistical analyses indicated that the distributions of harmful algal species correlated with gravel and medium-fine sand substrata. These data provide substantial knowledge on the distributions of harmful algal species on beaches, which have been poorly studied on a global scale. The apparent relationship between noxious species and grain size suggests that vegetative cells may be recruited from cyst beds in beach sediments.
DOI: 10.6084/m9.figshare.987036
title: Longer-Term Effects of ADAS Use on Speed and Headway Control in Drivers Diagnosed With Parkinson's Disease

description: <b>Objective:</b> An advanced driver assistance system (ADAS) provided information about speed limits, speed, speeding, and following distance. Information was presented to the participants by means of a head-up display.<b>Methods:</b> Effects of the information on speed and headway control were studied in a longer-term driving simulator study including 12 repeated measures spread out over 4 weeks. Nine healthy older drivers between the ages of 65 and 82 years and 9 drivers between the ages of 68 and 82 years diagnosed with Parkinson's disease (PD) participated in the study. Within the 4 weeks, groups completed 12 consecutive sessions (10 with ADAS and 2 without ADAS) in a driving simulator.<b>Results:</b> Results indicate an effect of ADAS use on performance. Removing ADAS after short-term exposure led to deterioration of performance in all speed measures in the group of drivers diagnosed with PD.<b>Conclusions:</b> These results suggest that provision of traffic information was utilized by drivers diagnosed with PD in order to control their speed.
DOI: 10.6084/m9.figshare.987052.v1
title: Assessment of harmful algal species using different approaches: the case study of the Sardinian coasts

description: The presence and distribution of harmful algal species were investigated along the coasts of Sardinia in the summer of 2012. Fourteen potentially noxious taxa were identified at 74 beaches. The majority of the recovered taxa were potentially toxic and/or high biomass producers. <i>Alexandrium taylorii</i>, <i>Gymnodinium instriatum</i>, and <i>Ostreopsis</i> cf. <i>ovata</i> were the most frequent and abundant taxa, although <i>Barrufeta bravensis</i> reached the highest density (4.4 × 10<sup>6</sup> cells L<sup>−1</sup>). <i>Barrufeta bravensis</i>, <i>A. taylorii</i>, and <i>G. instriatum</i> were responsible for intense water discoloration at two of the beaches sampled. Polymerase chain reaction (PCR) analyses supported the identification of several taxa and decisively identified <i>B. bravensis</i>. PCR assays increased the information available on the species distributions. The locations studied were heterogeneous in their prevailing environmental conditions and their morphodynamic profiles. Statistical analyses indicated that the distributions of harmful algal species correlated with gravel and medium-fine sand substrata. These data provide substantial knowledge on the distributions of harmful algal species on beaches, which have been poorly studied on a global scale. The apparent relationship between noxious species and grain size suggests that vegetative cells may be recruited from cyst beds in beach sediments.
DOI: 10.6084/m9.figshare.987041.v1
title: Suat ATAN

description: Nonlinear Programming (Turkish)
DOI: 10.6084/m9.figshare.987036.v1
title: Longer-term effects of ADAS use on speed and headway control in drivers diagnosed with Parkinson's disease

description: <b>Objective:</b> An Advanced Driver Assistance System (ADAS) provided information about speed limits, speed, speeding, and following distance. Information was presented to the participants by means of a head up display (HUD).<b>Methods:</b> Effects of the information on speed and headway control were studied in a longer-term driving simulator study including twelve repeated measures spread out over four weeks. Nine healthy older drivers between the ages of 65 and 82 years making up one group and nine drivers diagnosed with Parkinson's disease (PD) between the ages of 68 and 82 years making up another group participated in the study. Within the four weeks, groups completed twelve consecutive sessions (ten with ADAS and two without ADAS) in a driving simulator.<b>Results:</b> Results indicate an effect of ADAS use on performance. Removing ADAS after short-term exposure led to deterioration of performance in all speed measures in the group of drivers diagnosed with PD.<b>Conclusions:</b> These results suggest that provision of traffic information was utilized by drivers diagnosed with PD in order to control their speed.
DOI: 10.6084/m9.figshare.987036.v3
title: Longer-Term Effects of ADAS Use on Speed and Headway Control in Drivers Diagnosed With Parkinson's Disease

description: <b>Objective:</b> An advanced driver assistance system (ADAS) provided information about speed limits, speed, speeding, and following distance. Information was presented to the participants by means of a head-up display.<b>Methods:</b> Effects of the information on speed and headway control were studied in a longer-term driving simulator study including 12 repeated measures spread out over 4 weeks. Nine healthy older drivers between the ages of 65 and 82 years and 9 drivers between the ages of 68 and 82 years diagnosed with Parkinson's disease (PD) participated in the study. Within the 4 weeks, groups completed 12 consecutive sessions (10 with ADAS and 2 without ADAS) in a driving simulator.<b>Results:</b> Results indicate an effect of ADAS use on performance. Removing ADAS after short-term exposure led to deterioration of performance in all speed measures in the group of drivers diagnosed with PD.<b>Conclusions:</b> These results suggest that provision of traffic information was utilized by drivers diagnosed with PD in order to control their speed.
DOI: 10.6084/m9.figshare.987036.v2
title: Longer-Term Effects of ADAS Use on Speed and Headway Control in Drivers Diagnosed With Parkinson's Disease

description: <b>Objective:</b> An advanced driver assistance system (ADAS) provided information about speed limits, speed, speeding, and following distance. Information was presented to the participants by means of a head-up display.<b>Methods:</b> Effects of the information on speed and headway control were studied in a longer-term driving simulator study including 12 repeated measures spread out over 4 weeks. Nine healthy older drivers between the ages of 65 and 82 years and 9 drivers between the ages of 68 and 82 years diagnosed with Parkinson's disease (PD) participated in the study. Within the 4 weeks, groups completed 12 consecutive sessions (10 with ADAS and 2 without ADAS) in a driving simulator.<b>Results:</b> Results indicate an effect of ADAS use on performance. Removing ADAS after short-term exposure led to deterioration of performance in all speed measures in the group of drivers diagnosed with PD.<b>Conclusions:</b> These results suggest that provision of traffic information was utilized by drivers diagnosed with PD in order to control their speed.
DOI: 10.6084/m9.figshare.987030
title: Computer generated rat kidney arterial trees

description: STL files generated by kidney artery branching algorithm
DOI: 10.6084/m9.figshare.985646
title: 4G Value Watch (Australia) - March 2014

description: This dataset shows prices of 4G mobile broadband and mobile phone data in Australia in March 2014. Fields include: telco, price per month, data per month, price per GB of data (calculated), excess price per GB, description, link to URL. The iPhone 5C is used as a comparison across several telco's pricing. Prices are included for plans including a phone, without a phone, for a mobile broadband (wifi router) device, and for phone data topup plans.
DOI: 10.6084/m9.figshare.985916
title: QUAST contig report

description: Contig report generated by QUAST describing location of contig mapping onto the reference genome (including the heterochromatic reference chromosome arms, but excluding the reference sequence Uextra) with NUCmer and contigs affected by putative mis-assembly.
DOI: 10.6084/m9.figshare.985645
title: Drosophila melanogaster TruSeq synthetic long-read assembly (34x)

description: FASTA file containing contigs from the assembly of the <em>Drosophila melanogaster</em> (strain <em>y;cn,bw,sp</em>) genome using TruSeq synthetic long-reads. Celera assembler parameters and other code used for the assembly and analysis can be found at: https://github.com/rmccoy7541/dmel-longread-assembly
DOI: 10.6084/m9.figshare.987030.v1
title: branching

description: STL files generated by kidney artery branching algorithm
DOI: 10.6084/m9.figshare.987030.v2
title: Computer generated rat kidney arterial trees

description: STL files generated by kidney artery branching algorithm
DOI: 10.6084/m9.figshare.985645.v1
title: Drosophila melanogaster TruSeq synthetic long-read assembly (34x)

description: FASTA file containing contigs from the assembly of the <em>Drosophila melanogaster</em> (strain <em>y;cn,bw,sp</em>) genome using TruSeq synthetic long-reads. Celera assembler parameters and other code used for the assembly and analysis can be found at: https://github.com/rmccoy7541/dmel-longread-assembly
DOI: 10.6084/m9.figshare.985604
title: Anolis data with twig ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985646.v1
title: 4G Value Watch (Australia) - March 2014

description: This dataset shows prices of 4G mobile broadband and mobile phone data in Australia in March 2014. Fields include: telco, price per month, data per month, price per GB of data (calculated), excess price per GB, description, link to URL. The iPhone 5C is used as a comparison across several telco's pricing. Prices are included for plans including a phone, without a phone, for a mobile broadband (wifi router) device, and for phone data topup plans.
DOI: 10.6084/m9.figshare.985603
title: Anolis data with trunk-ground ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985604.v1
title: Anolis data with twig ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985601
title: Anolis data with grass-bush ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985602
title: Anolis data with trunk-crown ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985603.v1
title: Anolis data with trunk-ground ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985600
title: Anolis data with crown-giant ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985599
title: RBM trained on MNIST data

description: Weights and biases for a Restricted Boltzmann Machine trained on the MNIST dataset. This RBM was trained by Charlie Tang as part of the original model on nengo.ca.
DOI: 10.6084/m9.figshare.985600.v1
title: Anolis data with crown-giant ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985601.v1
title: Anolis data with grass-bush ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985602.v1
title: Anolis data with trunk-crown ecotype coded as focals

description: A simple measure of the strength of convergent evolution
DOI: 10.6084/m9.figshare.985599.v1
title: RBM weights and biases, trained on MNIST data

description: Weights and biases for a Restricted Boltzmann Machine trained on the MNIST dataset. This RBM was trained by Charlie Tang as part of the original model on nengo.ca.