cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.18742/rdm01-110
title: The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations – Data

description: List of data files:WT_Input_Output.tar.gzE204A_Input_Ouput.tar.gzR111A_Input_Ouptut.tar.gzWT Trajectories (.dcd)E204A Trajectories (.dcd)R111A Trajectories (.dcd)The data are divided in three projects. WT: files related to the wild-type RDL receptor; E204A: files related to the Glu204Ala mutant;R111A: files related to the Arg111Ala mutant.The simulations were run with the NAMD 2.9 molecular dynamics package and the metadynamics PLUMED 1.3 plug-in. *_Input_Output.tar.gz contain the input and output files for each project for the simulations. Multiple files with the same extension are numbered in sequential order.For a full description of the data please see the accomplanying ReadMe file. Related publication: F. Comitani, V. Limongelli, and C. Molteni, “The free energy landscape ofGABA binding to a pentameric ligand-gated ion channel and its disruption bymutations,” Journal of Chemical Theory and Computation, vol. 12, pp. 3398-3406, July 2016, doi: 10.1021/acs.jctc.6b00303The Input-Output files are availalbe to download directly (see links). Due to their size the Trajectory files are stored separately. Requests to access those files should be sent to research.data@kcl.ac.uk
DOI: 10.18742/rdm01-122
title: Dataset for the publication Photo Privacy Conflicts in Social Media - A Large-Scale Empirical Study

description: This is the anonymised dataset for the publication: J. M. Such, J. Porter, S. Preibusch, A. Joinson. Photo Privacy Conflicts in Social Media: A Large-Scale Empirical Study. Accepted in ACM Conference on Human Factors in Computing Systems CHI, 2017. The Dataset contains over 1,000 multiparty privacy conflicts over co-owned photos in social media. For further details about the project, data, methods and procedures, please see the above paper. Please cite the paper if you use the dataset.
DOI: 10.18742/rdm01-159
title: Data Files for Mapping the Conformational Free Energy of Aspartic Acid in the Gas Phase and in Aqueous Solution

description: The data are divided in sub-projects where different systems were simulated with different force fields.CHARMM_: simulations run with the CHARMM36 force fieldAMBER_: simulations run with the AMBER FF99SB-ILDN force fieldOPLS_: simulations run with theOPLS-AA force fieldConformations_: ab initio (DFT-B3LYP & MP2) calculations on selected conformers_NV.tar.gz: simulations of neutral Asp in vacuo_ZW.tar.gz: simulations of zwitterionic Asp in water_NW.tar.gz: simulations of neutral Asp in water_ZV.tar.gz: simulations of zwitterionic Asp in vacuoThe simulations using force fields were run with the NAMD 2.9 molecular dynamics package and the metadynamics PLUMED 1.3 plug-in. Ab initio geometry optimization and single point calculations were run with Gaussian 09. For a full description of the data files please see the accompanying ReadMe file.
DOI: 10.18742/rdm01-194
title: Data used in paper 'An Assessment of Algorithms to Estimate Respiratory Rate from the Electrocardiogram and Photoplethysmogram'

description: This dataset contains electrocardiogram (ECG), photoplethysmogram (PPG), Impedance Pneumography (imp) and reference oral-nasal pressure (paw) signals acquired from young subjects (aged 18-39). Data were acquired for approximately 10 minutes while lying supine at rest. Following this subjects were asked to run on a treadmill (data are not provided from this period). Data were then collected during a second recording period whilst subjects recovered from the exercise, lying supine once again. An example of the signals available in the dataset is included in the accompanying ReadMe file.Further details of the dataset and acquisition procedures are provided in the published paper: Charlton P.H. and Bonnici T.B. et al., An assessment of algorithms to estimate respiratory rate from the electrocardiogram and photoplethysmogram, Physiological Measurement, 37(4), 2016. DOI: 10.1088/0967-3334/37/4/610 .Data files included in this dataset:VORTAL_rest_data.matVORTAL_rec_data.matFor access to the data files, please contact research.data@kcl.ac.uk
DOI: 10.18742/rdm01-199
title: Data used in paper Extraction of respiratory signals from the electrocardiogram and photoplethysmogram - technical and physiological determinants

description: This dataset contains electrocardiogram (ECG), photoplethysmogram (PPG), Impedance Pneumography (imp) and reference oral-nasal pressure (paw) signals acquired from young subjects (aged 18-39) and elderly subjects (aged 70+). Data were acquired for approximately 10 minutes while lying supine at rest. This dataset is intended to facilitate evaluation of the performance of algorithms for estimation of respiratory rate (RR) from the ECG and PPG. It can also be used to evaluate the influence of technical and physiological factors on the performance of RR algorithms. It was collected during National Clinical Trial no. 01472133, and reported in the following publication:Charlton P.H. et al., Extraction of respiratory signals from the electrocardiogram and photoplethysmogram: technical and physiological determinants, Physiological Measurement, 38(5), 2017. DOI: 10.1088/1361-6579/aa670e .Further details of the dataset and acquisition procedures are provided in this publication.An example of the signals available in the dataset is included in the accompanying ReadMe file.For access to the files please email research.data@kcl.ac.uk
DOI: 10.18742/rdm01-244
title: Regional Multi-view Learning for Cardiac Motion Analysis

description: EPSRC funded project to investigate machine learning based methods to use MR and Ultrasound data for motion analysis. Data acquired from healthy volunteers with ethics and consent. This project belongs to the CDT in Medical Imaging Project of the School of Biomedical Engineering & Imaging Sciences, King's College of London. The CDT in Medical Imaging Project has multiple sub-projects, and this one is called Multimodal analysis of cardiac motion and deformation. The dataset contains MR and ultrasound healthy volunteer data acquired at St Thomas Hospital but not through the NHS. All volunteers have signed the consent form that allow release of the data. Furthermore, each dataset has been anonymized and stored in Nifti format.This data supports the article Puyol-Anton, E. et al, (2018) Regional Multi-view Learning for Cardiac Motion Analysis: Application to Identification of Dilated Cardiomyopathy Patients. IEEE Transactions on Biomedical Engineering. doi: 10.1109/TBME.2018.2865669.
DOI: 10.18742/rdm01-266
title: Soft, adhesive (+) alpha tocopherol phosphate planar bilayers that control oral biofilm growth through a substantive antimicrobial effect

description: Collection of 569 files that were used to generate the publication entitled 'Soft, adhesive (+) alpha tocopherol phosphate planar bilayers that control oral biofilm growth through a substantive antimicrobial effect' which is to be published in the journal of Nanomedicine in 2018. The data comprises - Atomic microscopy images- Chemical characterisation of alpha tocopherol phosphate- Light scattering analysis data of alpha tocopherol nanosystems- Micro-organism growth inhibition data- Oral biofilm growth inhibition dataTotal size of data 339MB
DOI: 10.18742/rdm01-275
title: Data files for Embroidered Electrodes for Control of Affordable Myoelectric Prostheses

description: This study reports an investigation into the use of embroidered electrodes for recording surface EMG data from amputees, and the feasibility of using that data as a discrete control interface for a prosthesis through classification of muscle patterns. During data recording, participants are asked to visualise performing one of four gestures with their ghost limb (corresponding to the desired movement of a prosthetic hand) while surface EMG data is collected using the textile-based system. The four classes of gesture are those most commonly used in human hand motion: fist contraction, index finger extension, wrist extension, wrist flexion.Total data size 54.3MB To make downloading quicker and easier the files are accessible as a single zipped folder (11.9MB)
DOI: 10.18742/rdm01-283
title: PET and CT data for 52Mn-DOXIL in a healthy mouse - 1h, 24h and 72 h post injection

description: In vivo PET-CT imaging data (as DICOM files) with [52Mn]Mn-DOXIL in a B6CBAF1 mouse.  Created using VivoQuant software (inviCRO, USA). Related publication:Gawne P, Man F, Fonslet J, Radia R, Bordoloi J, Cleveland M, Jimenez-Royo P, Gabizon A, Blower PJ, et al.,T. M. de Rosales R, Manganes e-52: applications in cell radiolabelling and liposomal nanomedicine PET imaging using oxine (8-hydroxyquinoline) as an ionophore, Dalton Transactions, 2018, IN PRESS.
DOI: 10.18742/rdm01-316
title: Dataset associated with the paper 'The Renyi divergence enables accurate and precise cluster analysis for localization microscopy'

description: Data related to the evaluation of the Renyi divergence as a clustering analysis tool.Please note most files are between 5-9GB.
DOI: 10.18742/rdm01-403
title: Mitochondrial matrix viscosity and membrane fluidity are environmentally and physiologically responsive - Dataset

description: FLIM images in SPCImage Document format, originally analysed SPCImage from Becker & Hickl. Includes IRF. FLIM images with accompanying IRFs of: - HeLa cells stained with mitochondrial matrix targeting molecular rotor (control, nystatin and histamine conditions) - Extracted mitochondria stained with membrane targeting molecular rotor (high and low glucose growth conditions)Data supports Steinmark, E. 'Mitochondrial matrix viscosity and membrane fluidity are environmentally and physiologically responsive', PLOS One, Submitted.
DOI: 10.18742/rdm01-407
title: Diminishing biofilm resistance to antimicrobial nanomaterials through electrolyte screening of electrostatic interactions

description: Raw scientific data that was collected using a Langmuir trough, a confocal microscope and a UV spectrophotometer.
DOI: 10.18742/rdm01-423
title: Data supporting paper - Modelling left atrial flow, energy, blood heating distribution in response to catheter ablation therapy

description: Two patients pressure, velocity and particle tracking data pre and post catheter ablation therapy. As above submitted to Frontiers.
DOI: 10.18742/rdm01-451
title: Kapiti research farm and ranch map

description: This is a digital data used to create the maps of the ILRI research farm 'Kapiti Ranch' in 2018. Mapping was carried out on aerial photos taken in 2014 and then updated using high resolution satellite images captured in 2018. Watercourse mapping was carried out using a LiDAR derived digital terrain model also captured in 2014. Note that only within the farm borders is fully mapped. The area around the borders is given for context but not fully mapped.
DOI: 10.18742/rdm01-456
title: Data for paper 'Hand-made embroidered electromyography towards a solution for low-income countries'

description: PLEASE NOTE: AN UPDATED VERSION OF THIS DATASET HAS BEEN PUBLISHED AT http://doi.org/doi:10.18742/RDM01-597This study presents the first work into the hand-sewing of electrodes for surface electromyography to assess its feasibility as an affordable, alternative means of production. In experiments reported here, batches of hand-sewn electrodes from Nm = 6 novice embroiderers are tested for (i) manufacturing consistency, and (ii) myographic data acquisition against conventional gelled and machine-sewn electrodes.
DOI: 10.18742/rdm01-47
title: Model Optimisation for Feature--Class allocation using MDEOptimiser  A TTC 2016 Submission

description: This dataset contains the results of experimental runs of the MDEOptimiser tool as described in the corresponding paper submitted to TTC 2016 (the Transformation Tool Contest associated to the STAF conference in Vienna). The tool uses evolutionary optimisation algorithms directly on software models (expressed using the MDE approach to software modelling) to solve multi-objective optimisation problems. In this case, the problem was the class—feature allocation problem and the solutions presented are for five specific instances of this problem as were given with the TTC challenge case.Related publication: A. Burdusel, S. Zschaler:  Model Optimisation for Feature--Class allocation using MDEOptimiser: A TTC 2016 Submission. Accepted at TTC’16, 2016. To be published.
DOI: 10.18742/rdm01-472
title: Bubblewrap synthesis of quantum dots

description: Excel spreadsheets of raw data
DOI: 10.18742/rdm01-478
title: Learning Singularity Avoidance - Data using a real world 7 link sawyer robot and simulated 3 link planar system

description: This dataset contains both real world and simulated data. The real world data consists of 50 trajectories of 7DOF Jointspace data recorded kinaesthetically using the Sawyer robot. Each demonstration has 1) a task space component where the sawyer moves from a starting position to anywhere on a drawer and 2) a null space component where the system is closing the drawer. The constraint in the null space limits movement of the system to the x-axis. These can be read as text files. The simulated data consists of 3 sets of 50 trajectories of 3DOF Jointspace data in a planar system. In each set the system is constrained by one of the 3 constraints: 1) X and Y, 2) X and Theta and 3) Y and Theta. These are stored as matlab data.For further details please refer to the paper: Learning Singularity Avoidance Manavalan, J. & Howard, M. J. W., 2019, IEEE/RSJ International Conference on Intelligent Robots and Systems.
DOI: 10.18742/rdm01-497
title: The English and Romanian Adoptees Brain Imaging Study – Alterations in adult brain structure associated with early childhood deprivation

description: The English and Romanian Adoptees Brain Imaging Study investigates the effects of early institutional deprivation on brain structure in young adulthood. This study analysed MRI data of young adults, who were exposed to severe deprivation in early childhood in the Romanian orphanages of the Ceaușescu era before being adopted by UK families. This dataset contains brain structural summary data of 67 Romanian adoptees and 21 non-deprived UK adoptees. Additionally, this dataset contains information on neurodevelopmental symptom domains, deprivation duration, birth weight, weight at entry into the UK and polygenic scores for total brain volume.
DOI: 10.18742/rdm01-502
title: Simulation data for 'Extraction and high-throughput sequencing of oak heartwood DNA - assessing the feasibility of genome-wide DNA methylation profiling'

description: Studies of the methylation state of DNA preserved in oak heartwood can help identify epigenetic tree ring features informing on past environmental conditions. Heartwood contains little DNA; large amounts of phenolic compounds are known to hinder the preparation of high-throughput sequencing libraries. To complement experiments, we simulated the interaction of double-stranded DNA (dsDNA) with a potential PCR inhibitor, the phenolic compound ellagic acid, by molecular dynamics and metadynamics techniques. Specifically, we investigated with molecular dynamics: (i) ellagic acid in water and in methanol; (ii) a model of dsDNA in water; (iii) multiple ellagic acids interacting with dsDNA in water and in methanol; (iv) dsDNA with an intercalated ellagic acid in water and in methanol. Moreover, with metadynamics, we explored the unbinding of an intercalated ellagic acid in dsDNA in water and in methanol.
DOI: 10.18742/rdm01-503
title: Simulation data I (molecular dynamics) for 'Trans–Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel - How They Are Affected by and How They Affect the Biomolecular Environment'

description: Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans–cis isomerization of a proline at the interface between the extracellular and transmembrane domain. We investigate this switch within the receptor with molecular dynamics (data reported here) and metadynamics simulations. The molecular dynamics simulations regard four different models, named 5Trans (with Pro281 in the trans conformation for all the five subunits), 3Cis (with Pro281 in the cis conformation in subunits 1, 3 and 4), 5Cis (with the five Pro281 in cis), and 5Trans5Cis (with the five Pro281 in trans and the five Pro274 in cis).
DOI: 10.18742/rdm01-504
title: Simulation data II (metadynamics) for 'Trans–Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel - How They Are Affected by and How They Affect the Biomolecular Environment'

description: Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans–cis isomerization of a proline at the interface between the extracellular and transmembrane domain. We investigate this switch within the receptor with metadynamics simulations (data reported here) and molecular dynamics. The metadynamics simulations regard the isomerisation process of Pro281 in subunit 3.
DOI: 10.18742/rdm01-55
title: CoA_MRIData

description: This datasets contains cardiac MRI images for 20 patients post-coarctation repair. For each patient 2 images of cardiac geometry, and 2-3 phase-contrast flow images are available. This data is suitable for pulse wave velocity measurements. All data is acquired under ethics 09-H0802-78 as approved by the London - Westminster research ethics committee, and has been fully anonymised.Related publication - Van Engelen, Arna, Silva Vieira, Miguel, Rafiq, Isma, Cecelja, Marina, Schneider, Torben, de Bliek, Hubrecht, Figueroa, C. Alberto, Hussain, Tarique, Botnar, Rene M. Alastruey, Jordi, (2017), “Aortic length measurements for pulse wave velocity calculation: manual 2D vs automated 3D centreline extraction", Journal of Cardiovascular Magnetic Resonance, 2017, v 19, n 1, p32. http://dx.doi.org/10.1186/s12968-017-0341-y
DOI: 10.18742/rdm01-597
title: Data for paper 'Hand-made embroidered electromyography towards a solution for low-income countries', version 2

description: This study presents the first work into the hand-sewing of electrodes for surface electromyography to assess its feasibility as an affordable, alternative means of production. In experiments reported here, batches of hand-sewn electrodes from Nm = 6 novice embroiderers are tested for (i) manufacturing consistency, and (ii) myographic data acquisition against conventional gelled and machine-sewn electrodes.
DOI: 10.18742/rdm01-667
title: Dataset used in paper ‘Evaluation of [13N]ammonia positron emission tomography as a potential method for quantifying glutamine synthetase activity in the human brain.’ (Egerton A and Dunn JT et al 2020)

description: Dynamic PET & structural MRI images with accompanying blood sample data for repeatability study investigating human cerebral ammonia metabolism with 15O-H2O and 13N-NH3 PET tracers. Data from eight healthy subjects. Each subject had a 15O-H2O PET-CT brain scan followed by a 13N-NH3 scan; both scans repeated same day. Continuous and manual arterial blood sampling was acquired on all scans, with metabolite analysis on the NH3 scan blood manual samples. This data was used in the paper: “Evaluation of [13N]ammonia positron emission tomography as a potential method for quantifying glutamine synthetase activity in the human brain” by Egerton A and Dunn JT et al in EJNMMI Research.
DOI: 10.18742/rdm01-690
title: Safety beliefs and knowledge of cognitive enhancers in UK university students

description: Cognitive enhancers (CE) are prescription drugs taken, either without a prescription or at a dose exceeding that which is prescribed, to improve cognitive functions such as concentration, vigilance or memory. Previous research suggests that users believe the drugs to be safer than non-users and that they have sufficient knowledge to judge safety. However, no research had actually compared the information sources used and safety knowledge of users and non-users. This study therefore compared users and non-users of CE in terms of i) their sources of knowledge about the safety of CE and ii) the accuracy of their knowledge of possible adverse effects of a typical cognitive enhancer (modafinil); and iii) how the accuracy of knowledge relates to their safety beliefs. Students (N=148) from King’s College London (UK) completed an anonymous online survey assessing safety beliefs, sources of knowledge and knowledge of the safety of modafinil; and indicated whether they used CE, and, if so, which drug(s).
DOI: 10.18742/rdm01-697
title: Data for paper 'Identification of the Design Parameters for a Spacer Fabric Pressure-Mapping Sensor’

description: Excel data for paper 'Identification of the Design Parameters for a Spacer Fabric Pressure-Mapping Sensor’. The data are experiment 1 result and experiment 2 result.
DOI: 10.18742/rdm01-717
title: Supplemental material for 'The effect of plaque control in the treatment of Oral Lichen Planus (OLP) with gingival manifestations - a Systematic Review'

description: Supplemental material for systematic review paper published in journal Community Dental Health (ref CDH 00220-2020)
DOI: 10.18742/rdm01-720
title: HAWKMAN test data and simulations

description: Simulated and experimental image sequences and super resolution reconstructions
DOI: 10.18742/rdm01-731
title: Potential energy surfaces, absorption and emission spectra of three fluorescent molecular rotors

description: Ground and excited state potential energy surfaces and absorption and emission spectra of BODIPY-C10, BODIPY-Cyclopropyl-A and BODIPY-Cyclopropyl-B, calculated using the Gaussian 09 Code.Type of data: Quantum mechanical simulation files
DOI: 10.18742/rdm01-746
title: Data files for ‘Breeding habitat selection of urban peregrine falcons (Falco peregrinus) in London’

description: Understanding habitat selection by individual animals within their home range is crucial to facilitating their conservation. Peregrine falcon (Falco peregrinus) populations are increasingly urbanised, but little is known about their urban habitat use. Thus, we analysed the breeding habitat selection and nest spacing of peregrine falcons in London, United Kingdom, based on nest site locations identified through records of public sightings submitted to an online database between 2003-2018.
DOI: 10.18742/rdm01-750
title: Modulation of pulsatile GnRH dynamics along the reproductive cycle - the role of excitability within the arcuate kisspeptin network

description: Pulsatile LH data set
DOI: 10.18742/rdm01-753
title: Summaries of electrophysiological data in support of manuscript published in Science Translational Medicine, entitled 'Neuromodulation using ultra-low frequency current waveform reversibly blocks axonal conduction and chronic pain'

description: The database consists of two Excel spreadsheet files containing values recorded during electrophysiological experiments to investigate the effects of a novel form of polarising nerve conduction block, developed Presidio Medical Inc. The experiments were performed at King's College London as part of a collaborative investigation between King's College, Zenith Neurotech Ltd., and Presidio Medical Inc.
DOI: 10.18742/rdm01-757
title: Brief sensory deprivation triggers cell type-specific structural and functional plasticity in olfactory bulb neurons

description: Confocal microscopy images, electrophysiological traces, annotated MatLab code, and analysis done in MS Excel.All zipped data folders include readme files explaining how to navigate them.