cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3899874
title: DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 2/4)

description: DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum. The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED. All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344 Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875 Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535 Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250 Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020) doi: 10.3389/fcell.2020.581016 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.3899535
title: DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 3/4)

description: DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum. The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED. All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344 Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875 Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535 Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250 Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020) doi: 10.3389/fcell.2020.581016 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.3899534
title: DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 3/4)

description: DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum. The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED. All trajectories are simulated for 1000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344 Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875 Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535 Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250 Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020) doi: 10.3389/fcell.2020.581016 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.4034250
title: DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 4/4)

description: DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169, 676, or 1521 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum. The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, number of lipids per monolayer if not 169. The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED. All trajectories are simulated for 1000 ns, except the 1521 lipid per monolayer systems for 500 ns, with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344 Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875 Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535 Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250 Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020) doi: 10.3389/fcell.2020.581016 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.4034249
title: DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 4/4)

description: DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169, 676, or 1521 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum. The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, number of lipids per monolayer if not 169. The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED. All trajectories are simulated for 1000 ns, except the 1521 lipid per monolayer systems for 500 ns, with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . Part 1 of this upload is available at: DOI:10.5281/zenodo.3898344 Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875 Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535 Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250 Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020) doi: 10.3389/fcell.2020.581016 [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.4113927
title: Liquiritigenin reduces osteoclast activity in zebrafish model of glucocorticoid-induced osteoporosis

description: Drug and therapies currently used to treat human bone diseases have a lot of severe side effects. Liquiritigenin is a flavonoid extracted from Glycyrrhiza glabra roots which has been reported to have positive effects in vitro on osteoblasts activity and bone mineralization as well as inhibitory effect on osteoclasts differentiation and activity in vitro. The present study was aimed to evaluate the in vivo effects of liquiritigenin on bone structure and metabolism in physiological and pathological conditions using Danio rerio as experimental animal model. Treatments with liquiritigenin were performed on embryos to evaluate the osteogenesis during skeletal development. Other treatments were performed on adult fish affected by glucocorticoid-induced osteoporosis to assay the therapeutic potential of liquiritigenin in the reversion of bone-loss phenotype in scale model. Liquiritigenin treatment of zebrafish embryo significantly enhances the osteogenesis during development in a dose-dependent manner. In addition, liquiritigenin inhibits the formation of the osteoporotic phenotype in adult zebrafish model of glucocorticoid-induced osteoporosis preventing osteoclast activation in scales. Interestingly, liquiritigenin does not counteract the loss of osteoblastic activity in scales. The liquiritigenin exhibits in vivo anti-osteoporotic activity on adult fish scale model. It can be considered a good candidate to develop new drugs against osteoporosis.
DOI: 10.5281/zenodo.4113926
title: Liquiritigenin reduces osteoclast activity in zebrafish model of glucocorticoid-induced osteoporosis

description: Drug and therapies currently used to treat human bone diseases have a lot of severe side effects. Liquiritigenin is a flavonoid extracted from Glycyrrhiza glabra roots which has been reported to have positive effects in vitro on osteoblasts activity and bone mineralization as well as inhibitory effect on osteoclasts differentiation and activity in vitro. The present study was aimed to evaluate the in vivo effects of liquiritigenin on bone structure and metabolism in physiological and pathological conditions using Danio rerio as experimental animal model. Treatments with liquiritigenin were performed on embryos to evaluate the osteogenesis during skeletal development. Other treatments were performed on adult fish affected by glucocorticoid-induced osteoporosis to assay the therapeutic potential of liquiritigenin in the reversion of bone-loss phenotype in scale model. Liquiritigenin treatment of zebrafish embryo significantly enhances the osteogenesis during development in a dose-dependent manner. In addition, liquiritigenin inhibits the formation of the osteoporotic phenotype in adult zebrafish model of glucocorticoid-induced osteoporosis preventing osteoclast activation in scales. Interestingly, liquiritigenin does not counteract the loss of osteoblastic activity in scales. The liquiritigenin exhibits in vivo anti-osteoporotic activity on adult fish scale model. It can be considered a good candidate to develop new drugs against osteoporosis.
DOI: 10.6084/m9.figshare.13121861
title: A Qualitative analysis of factors related to unsafe work behaviours among environmental service workers in the COVID-19 era: perspectives of workers, and safety managers. The case of government hospitals in Addis Ababa Ethiopia

description: Two qualitative data gathering methods, namely individual in-depth interviews and key informant interviews were used on purposively selected environmental service workers and infection prevention and patient safety specialists. a total of 25 participants were recruited from three Corona virus treatment facilities interviews were recorded and transcribed in Amharic (the local language) and then translated to English. open code 4.2 was used for thematic analysis.
DOI: 10.5519/qd.ief7c8so
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (109 records)
DOI: 10.6084/m9.figshare.13121897
title: Supplementary Material for: Comparison of Quality of Life among Patients with Oro-Hypopharyngeal Cancer after Tonsillectomy and Panscopy Using Transoral Robotic Surgery: A Pilot Study

description: Studies have shown lower treatment-related morbidity when using transoral robotic surgery (TORS) compared to conventional surgery. Patients investigated for oro- and hypopharyngeal cancer (T1, T2) were compared concerning quality of life (QoL) after tonsillectomy and TORS using validated QoL questionnaires: QLQ-C30 and QLQ-H&N35. The patients treated with TORS showed a higher pain score and thus also a higher need for painkillers, whereas they had lower values on self-assessment of anxiety/depression using the Hospital Anxiety and Depression Scale score. The pre- and postoperative information given did not meet the expectations of the patients treated with conventional surgery. The present data show advantages of the TORS technique from the patients’ perspective. Even if patients treated with TORS are in need of more painkilling treatment, they cope better with the long-term effects of treatment, as judged by self-assessment of anxiety and depression.
DOI: 10.15129/28a67ac3-0daf-4c8d-81c7-3af6a847c211
title: Data for: "Experimental investigation of the thermoelastic performance of an aerospace aluminium honeycomb composite panel"

description: Open source data for the paper 'Experimental investigation of the thermoelastic performance of an aerospace aluminium honeycomb composite panel' by Olga A. Ganilova, Matthew P. Cartmell, and Andrew Kiley
DOI: 10.5281/zenodo.4110278
title: Roussillon MPS 2020 dataset Dall'Alba

description: The folder is composed of the data set used for the modelization of the Roussillon Pliocene Continental aquifer using a multiple-point statistics approach coupled to the DeeSse algorithm. This data set is linked to the article "Dall'Alba, V., Renard, P., Straubhaar, J., Issautier, B., Duvail, C., and Caballero, Y.: 3D Multiple-point Statistics Simulations of the Roussillon Continental Pliocene Aquifer using DeeSse, Hydrol. Earth Syst. Sci., 2020". Grid Information : <em>- dimension (nx/ny/nz) : 409/512/110</em> <em>- spacing (x/y/z) : 100/100/2m</em> <em>- origin (ox/oy/oz) : 664328.1865/6153000.2413/-210.0</em>
DOI: 10.5281/zenodo.4110277
title: Roussillon MPS 2020 dataset Dall'Alba

description: The folder is composed of the data set used for the modelization of the Roussillon Pliocene Continental aquifer using a multiple-point statistics approach coupled to the DeeSse algorithm. This data set is linked to the article "Dall'Alba, V., Renard, P., Straubhaar, J., Issautier, B., Duvail, C., and Caballero, Y.: 3D Multiple-point Statistics Simulations of the Roussillon Continental Pliocene Aquifer using DeeSse, Hydrol. Earth Syst. Sci., 2020". Grid Information : <em>- dimension (nx/ny/nz) : 409/512/110</em> <em>- spacing (x/y/z) : 100/100/2m</em> <em>- origin (ox/oy/oz) : 664328.1865/6153000.2413/-210.0</em>
DOI: 10.6084/m9.figshare.13121906.v1
title: SPA-R.dat

description: Spa-r database of spanish athletes
DOI: 10.6084/m9.figshare.13121906.v2
title: SPA-R.dat

description: Spa-r database of spanish athletes
DOI: 10.6084/m9.figshare.12206270
title: A large-scale optical microscopy image dataset of potato tuber for deep learning based plant cell assessment

description: This dataset includes 9,811 natural (unstained) and 6,127 stained brightfield microscopy images with three fold annotation such as physical, morphological and tissue grading based on weight, different section area and tissue zone respectively. The tuber weight ranging from 80-100 gm, 40-50 gm, 15-25 gm have been considered as large (L), medium (M), and small (S) respectively. Furthermore, the images have been labelled with L, M, and S to specify their respective weights. Further, the samples associated with each label have been numbered from 1 to 5, such as L1 refers to the first sample of a large tuber. For morphological grading, the tubers have been divided into three parts namely Z1, Z2, and Z3 which specify the bud, middle, and stem areas respectively. In tissue grading, the images have been captured from inner and outer core and labelled as IC and OC. We have used three types of staining agents such as Safranin O and Toluidine Blue O for visualizing cell walls and Lugols Iodine for distinguishing starch granules prominently. In addition, we prepared ground truth segmentation labels for three different potato tuber weights. The dataset contains three folders named as “stain”, “unstain” and “segmentation”. All the images are in JPG format. The raw microscopy images of potato tubers can be found in “stain” and “unstain” folder; whereas, the segmentation folder provides raw images with ground truth segmentation labels. The “stain” folder contains different stained images in the respective folders named as “safranin”, “toluidine” and “lugols”. The image labels information can be extracted from the image filenames itself. The file naming format for unstained image is as physical grading with sample no_ morphological grading_ tissue grading_ section no._ image no.; for example, M1_Z1_IC_Sec1_02.jpg refers to an image (first section out of five) taken from the inner core of Z1 of medium weight potato tuber (sample no 1). Similarly, the stained image file naming format is asphysical grading with sample no_ morphological grading_ tissue grading_ section no._ stain type_ image no.; for example, S1_Z2_OC_Sec3_lugol_02.jpg refers to an lugol’s iodine stained image (third section out of five) taken from the outer core of Z2 of small weight potato tuber (sample no 1). The segmentation folder contains two subfolders, named as “images” and “groundtruth”. The image files naming format is as physical grading_ image no.; for example, “L_2.jpg” represents the second image of a large potato tuber sample.
DOI: 10.6084/m9.figshare.12206270.v1
title: A large-scale optical microscopy image dataset of potato tuber for deep learning based plant cell assessment

description: This dataset includes 9,811 natural (unstained) and 6,127 stained brightfield microscopy images with three fold annotation such as physical, morphological and tissue grading based on weight, different section area and tissue zone respectively. The tuber weight ranging from 80-100 gm, 40-50 gm, 15-25 gm have been considered as large (L), medium (M), and small (S) respectively. Furthermore, the images have been labelled with L, M, and S to specify their respective weights. Further, the samples associated with each label have been numbered from 1 to 5, such as L1 refers to the first sample of a large tuber. For morphological grading, the tubers have been divided into three parts namely Z1, Z2, and Z3 which specify the bud, middle, and stem areas respectively. In tissue grading, the images have been captured from inner and outer core and labelled as IC and OC. We have used three types of staining agents such as Safranin O and Toluidine Blue O for visualizing cell walls and Lugols Iodine for distinguishing starch granules prominently. In addition, we prepared ground truth segmentation labels for three different potato tuber weights. The dataset contains three folders named as “stain”, “unstain” and “segmentation”. All the images are in JPG format. The raw microscopy images of potato tubers can be found in “stain” and “unstain” folder; whereas, the segmentation folder provides raw images with ground truth segmentation labels. The “stain” folder contains different stained images in the respective folders named as “safranin”, “toluidine” and “lugols”. The image labels information can be extracted from the image filenames itself. The file naming format for unstained image is as physical grading with sample no_ morphological grading_ tissue grading_ section no._ image no.; for example, M1_Z1_IC_Sec1_02.jpg refers to an image (first section out of five) taken from the inner core of Z1 of medium weight potato tuber (sample no 1). Similarly, the stained image file naming format is asphysical grading with sample no_ morphological grading_ tissue grading_ section no._ stain type_ image no.; for example, S1_Z2_OC_Sec3_lugol_02.jpg refers to an lugol’s iodine stained image (third section out of five) taken from the outer core of Z2 of small weight potato tuber (sample no 1). The segmentation folder contains two subfolders, named as “images” and “groundtruth”. The image files naming format is as physical grading_ image no.; for example, “L_2.jpg” represents the second image of a large potato tuber sample.
DOI: 10.34740/kaggle/dsv/1576546
title: Musical Emotions Classification
DOI: 10.6084/m9.figshare.13121807
title: GPS RINEX data and Space weather data files for the manuscripts: Atmospheric wave energy of the 2020 August 4 explosion in Beirut, Lebanon, from ionospheric disturbances

description: GPS RINEX data and Space weather data from Israel and Palestine during the August 4, 2020 chemical explosion in Beirut, Lebanon
DOI: 10.21227/f7cb-0q23
title: AURORA, A multi sensor dataset for robotic ocean exploration

description: The current maturity of autonomous underwater vehicles (AUVs) has made their deployment practical and cost-effective, such that many scientific, industrial and military applications now include AUV operations. However, the logistical difficulties and high costs of operating at-sea are still critical limiting factors in further technology development, the benchmarking of new techniques and the reproducibility of research results. To overcome this problem, we present a freely available dataset suitable to test control, navigation, sensor processing algorithms and others tasks. This dataset combines AUV navigation data, side-scan sonar, multibeam echosounder data and seafloor camera image data, and associated sensor acquisition meta-data to provide a detailed characterisation of surveys carried out by the National Oceanography Centre (NOC) in the Greater Haig Fras Marine Conservazion Zone (MCZ) of the U.K in 2015.
DOI: 10.6084/m9.figshare.13121906
title: Spanish SPA-R.dat

description: Spa-r database of spanish athletes
DOI: 10.6084/m9.figshare.13121906.v4
title: Spanish SPA-R.dat

description: Spa-r database of spanish athletes
DOI: 10.6084/m9.figshare.13121906.v3
title: Spanish SPA-R.dat

description: Spa-r database of spanish athletes