cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12745456
title: Exploring the structural dynamics of the vesicle priming machinery

description: Here are the pdb files for the simulations with only 6 central SNAREs and 6 central and 6 peripheral SNAREs with C2B of Syt1 and residue 51-75 of Cpx1 shown in figure 3.

File for figure 3a: ic_6c_snares.pdb is the initial condition for simulations with only 6 central SNAREs, and the tcl file figure_3a.tcl is to show this initial condition.

File for figure 3b: ic_6c6p_snares_c2b.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a vesicle, and the tcl file figure_3b_top_view.tcl and figure_3b_side_view.tcl are to show this initial condition.

File for figure 3c: ic_6c6p_snares_c2b_nd.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a nanodisc and ic_6c6p_snares_c2b_nd.xtc file is the corresponding trajectory of this simulation. The tcl file movie_for_figure_3c.tcl is to show the movie of this simulation. If you want to look at all proteins in this simulation, the tcl file movie_for_figure_3c_all.tcl can do that.

To view these snapshots by VMD, load the corresponding .tcl file or run "vmd -e name.tcl" in your terminal.
DOI: 10.5281/zenodo.12761027
title: TALABALARNING MAʼNAVIY -AXLOQIY TARBIYASIDA OMMAVIY AXBOROT VOSITALARINING ROLI
DOI: 10.5281/zenodo.12761028
title: TALABALARNING MAʼNAVIY -AXLOQIY TARBIYASIDA OMMAVIY AXBOROT VOSITALARINING ROLI
DOI: 10.35097/tvwlylbmvdxhecrt
title: Degree of substitution of cellulose acetate and other esters: Raw ATR-FTIR spectra and DS data obtained from IR integration, 1H NMR and 31P NMR

description: # Degree of substitution of cellulose acetate and other esters: Raw ATR-FTIR spectra and DS data obtained from IR integration, 1H NMR and 31P NMR 

## Authors
Frank Rhein, Timo Sehn, Michael A.R. Meier

## About
This repository contains the raw data used in *"Efficient and accurate determination of the degree of substitution of cellulose acetate using ATR-FTIR spectrosopy and machine learning"*. For detailed information please refer to the original publication upon acceptance.

## Datasets
The following data sets are compiled in this repository and published together with raw ATR-FTIR spectra:
- `Wolfs.A`: DOI https://doi.org/10.1002/pol.20230220 
 - Raw ATR-FTIR data
 - DS data from IR integration, 1H NMR, 31P NMR methods
- `Wolfs.B`: DOI https://doi.org/10.1039/D1GC01508G
 - Raw ATR-FTIR data
 - DS data from 1H NMR, 31P NMR methods
- `Sehn.A`, `Sehn.B`, `Sehn.C`: DOI https://doi.org/10.1021/acs.biomac.3c00762 
 - Raw ATR-FTIR data
 - DS data from 1H NMR method

An overview is given in `data_overview.xlsx`.

## Structure
Raw ATR-FTIR data is contained in the `IR_data_..` folders, while DS values from different methods are found in the respective `.txt` files. 
&gt; Note: `IR_DS` refers to the integration based method reported in https://doi.org/10.1002/pol.20230220 

## Methods
For more information on data generation and analytical setups please refer to the original publications referenced above. DS data based on 1H NMR data is obtained according to the newly reported evaluation routine. 

## Evaluation Scripts
The Python scripts for data analysis are available on Github under https://github.com/pdhs-group/DS_IR_ML
DOI: 10.5281/zenodo.11968879
title: Datasets and code for Rapljenović et al. 2024: Adsorption of trace metals onto different plastics during long-term exposure in an estuarine environment: influence of time, stratified water column, and specific surface area

description: This repository contains datasets and R code to reproduce results from Rapljenović et al. 2024: Adsorption of trace metals onto different plastics during long-term exposure in an estuarine environment: influence of time, stratified water column, and specific surface area.
DOI: 10.5281/zenodo.11968880
title: Datasets and code for Rapljenović et al. 2024: Adsorption of trace metals onto different plastics during long-term exposure in an estuarine environment: influence of time, stratified water column, and specific surface area

description: This repository contains datasets and R code to reproduce results from Rapljenović et al. 2024: Adsorption of trace metals onto different plastics during long-term exposure in an estuarine environment: influence of time, stratified water column, and specific surface area.
DOI: 10.5281/zenodo.12760287
title: Article: AI-MAPE Versus SA-SGM - Complete Data Bank

description: Mechanistic models provide an in-depth understanding of important biophysical systems. In fields such as developmental biology, these models are inherently complex, as they require genuinely spatial-stochastic descriptions of the underlying systems. This complexity poses significant challenges for inferring model parameters. Recently, modern deep-learning techniques have been integrated with simulation-based inference, creating an exciting new approach for estimating parameters of such models. Their overall goal is to computationally replicate target empirical observations and to develop powerful prediction tools for uncovering hidden system dynamics. However, these modern approaches remain broadly general and are often difficult to implement for specific spatial-stochastic problems, particularly within developmental biology. This difficulty raises the question of how much more valuable these modern approaches are compared to classical techniques. In this study, we compare one modern approach, AI-MAPE, inspired by the sequential neural posterior estimation (SNPE) algorithm, against one classical approach, SA-SGM, inspired by the simulated annealing (SA) algorithm. Our findings show that, while the inferred parameter sets generally agree between the two approaches, the AI-powered method, at comparable computational effort, provides significantly richer and more regular inferred distributions. This results in more detailed information about parameter interactions and synergies than the SA-inspired method.
DOI: 10.5281/zenodo.12760288
title: Article: AI-MAPE Versus SA-SGM - Complete Data Bank

description: Mechanistic models provide an in-depth understanding of important biophysical systems. In fields such as developmental biology, these models are inherently complex, as they require genuinely spatial-stochastic descriptions of the underlying systems. This complexity poses significant challenges for inferring model parameters. Recently, modern deep-learning techniques have been integrated with simulation-based inference, creating an exciting new approach for estimating parameters of such models. Their overall goal is to computationally replicate target empirical observations and to develop powerful prediction tools for uncovering hidden system dynamics. However, these modern approaches remain broadly general and are often difficult to implement for specific spatial-stochastic problems, particularly within developmental biology. This difficulty raises the question of how much more valuable these modern approaches are compared to classical techniques. In this study, we compare one modern approach, AI-MAPE, inspired by the sequential neural posterior estimation (SNPE) algorithm, against one classical approach, SA-SGM, inspired by the simulated annealing (SA) algorithm. Our findings show that, while the inferred parameter sets generally agree between the two approaches, the AI-powered method, at comparable computational effort, provides significantly richer and more regular inferred distributions. This results in more detailed information about parameter interactions and synergies than the SA-inspired method.
DOI: 10.17638/datacat.liverpool.ac.uk/2751
title: Data sources for qualitative element of RADOSS associated with paper: ‘Knowledge exchange’ workshops to optimise development of a risk prediction tool to assist conveyance decisions for suspected seizures – Part of the Risk of ADverse Outcomes after a Suspected Seizure (RADOSS) project
DOI: 10.5281/zenodo.10082423
title: Dataset of the publication Phys. Chem. Chem. Phys., 2023,25, 23614-23625

description: The experimental work was partially done within the project PROMETH2O (EMPIR 20IND06), which received funding from the EMPIR programme co-financed by the Participating States and from the European Unions Horizon 2020 research and innovation programme.
DOI: 10.5281/zenodo.10082424
title: Dataset of the publication Phys. Chem. Chem. Phys., 2023,25, 23614-23625

description: The experimental work was partially done within the project PROMETH2O (EMPIR 20IND06), which received funding from the EMPIR programme co-financed by the Participating States and from the European Unions Horizon 2020 research and innovation programme.
DOI: 10.17638/datacat.liverpool.ac.uk/2748
title: Transcripts for qualitative element of SEHOM project: "In the wilderness…dealing with difficult situations": Knowledge exchange with care home staff in England on managing seizures and epilepsy - An initial exploration
DOI: 10.5066/p98r9jm3
title: Digital database for the geologic map of the Vidal, California, and Parker SW, California-Arizona quadrangles

description: This geologic database is a digitized version of the original 1:24,000-scale analog geologic map titled &quot;Geologic map of the Vidal, California, and Parker SW, California-Arizona quadrangles&quot;, published by the U.S. Geological Survey (USGS) in 1980. The map area straddles the Arizona-California border, and is located approximately 9.0 km (5.6 mi) west-southwest of Parker, CA, immediately south of the unincorporated communities of Vidal and Vidal Junction, CA. The map area includes the northern Riverside Mountains, which contain a prominent suite of Permian, Mesozoic, and potentially Precambrian metamorphic and metasedimentary rocks. These rocks predominantly consist of gneisses, schists, limestones, and dolomites, separated by three mapped structural discontinuities and the prominent Whipple Mountains Detachment Fault. The map area additionally contains small outcrops of Miocene intermediate-to-felsic volcanic rocks consisting of basaltic andesite flows, andesitic porphyry, rhyolitic intrusives, and the Peach Springs Tuff. The Riverside Mountains are surrounded by numerous sedimentary units, largely consisting of fluvial deposits, that record the arrival and subsequent fluctuations of the Colorado River in the region from the Pliocene through the Holocene. These sedimentary units additionally record Quaternary alluvial fan processes on the flanks of the Riverside Mountains and in the lower Vidal Valley.
DOI: 10.6084/m9.figshare.26319307
title: Data for conditions (1)-(32)

description: Data from working conditions (1)-(32) monitored by CO2 and PM2.5 sensors.
DOI: 10.6084/m9.figshare.26319307.v1
title: Data for conditions (1)-(32)

description: Data from working conditions (1)-(32) monitored by CO2 and PM2.5 sensors.
DOI: 10.17638/datacat.liverpool.ac.uk/2527
title: The Collaborate project: Developing feasible person-centred care alternatives to emergency department responses for adults with epilepsy: a discrete choice analysis mixed methods study
DOI: 10.5281/zenodo.12755129
title: Global Daily River Discharge product at 0.5° resolution from ISBA-CTRIP simulations based on ERA5-GPCC forcing from 1950 to 2023

description: This product provides global daily river discharge at a resolution of 0.5 degree from 1950 to 2023. It is derived from an offline simulation conducted with the ISBA-CTRIP global land surface modeling system (Decharme et al. 2019) embedded in the SURFEX version 8 modeling platform. It was designed for use in large-scale hydrological applications, as well as in the the CNRM climate models that participate in CMIP6 but also in large scale hydrological applications. The model is driven by meteorological forcing data (temperature, precipitation, humidity, winds, etc) derived from the ERA5 global atmospheric reanalysis, but where montly precipitation is corrected to align with the GPPC observed precipitation product. GPCC Full Data Monthly Product Version 2022  at 0.5 degree resolution are used from 1950 to 2020. For the last three years (2021 to 2023), we used the GPCC Monitoring Product Version 2022, which is only available at 1 degree resolution, and then interpolated at 0.5 degree using a conservative remapping.
description: outlet = river flows at the mouth of each river basin flowing into the ocean, inland sea or lake (m3/s) -> derived from rivo

rivo = river flows at each point of the the hydrological network (m3/s)

rivv = river velocity (m/s)

river-parameters



flowdir = flow direction at each point of the hydrological network -> North (1), North East (2), East (3), South East (4), South (5), South West (6), West (7), North West (8), Sea Outlet (9), Inland Outlet (12)

areacellr = grid-cell area (m2)

drarea = upstream drainage area at each point of the hydrological network (m2)

basin_boundaries = River basin boundaries referenced by its number
description: Please also reference Decharme et al. (2019) in your reports or articles if you use these data.
DOI: 10.6084/m9.figshare.24628596.v1
title: Numerical simulation of particle and bubble detachment process in turbulent flow environment using CFD-DEM

description: Three-dimensional discrete element method (DEM) models were developed to simulate particle-bubble interactions by utilizing the API function within the EDEM software platform. Geometric grids were constructed using FLUENT software to induce isotropic turbulence, and this turbulence environment was incorporated into the CFD-DEM framework. The simulations focused on the detachment of particles and bubbles, with particle sizes ranging from 0.10 to 0.30 mm, particle densities ranging from 1500 to 2500 kg/m³, and fixed bubble sizes of 1.00, 1.20, 1.60, and 2.00 mm. The detachment processes occurred within a turbulent flow field at distances of 1, 1.5, 2, and 3 mm from the grid. It is found that the particle-bubble bond required more capillary force to maintain attachment equilibrium as the particle density and size, bubble size, and flow field turbulence environment increased, the smaller the initial flow velocity to bring the bubble and particle to a critical desorption state, indicating the increase in all these factors were not conducive to attachment stability.
DOI: 10.6084/m9.figshare.24628596
title: Numerical simulation of particle and bubble detachment process in turbulent flow environment using CFD-DEM

description: Three-dimensional discrete element method (DEM) models were developed to simulate particle-bubble interactions by utilizing the API function within the EDEM software platform. Geometric grids were constructed using FLUENT software to induce isotropic turbulence, and this turbulence environment was incorporated into the CFD-DEM framework. The simulations focused on the detachment of particles and bubbles, with particle sizes ranging from 0.10 to 0.30 mm, particle densities ranging from 1500 to 2500 kg/m³, and fixed bubble sizes of 1.00, 1.20, 1.60, and 2.00 mm. The detachment processes occurred within a turbulent flow field at distances of 1, 1.5, 2, and 3 mm from the grid. It is found that the particle-bubble bond required more capillary force to maintain attachment equilibrium as the particle density and size, bubble size, and flow field turbulence environment increased, the smaller the initial flow velocity to bring the bubble and particle to a critical desorption state, indicating the increase in all these factors were not conducive to attachment stability.
DOI: 10.6075/j0f76crk
title: Data from: Airborne observations of surface winds, waves and currents from meso to submesoscales

description: Data were collected using the SIO Modular Aerial Sensing System (MASS) and processed using Matlab (R2021b).
description: This collection contains the data sets needed to generate each figure presented in the publication "Lenain, Luc; Smeltzer, Benjamin K.; Pizzo, Nick; Freilich, Mara; Colosi, Luke; Ellingsen, Simen; Grare, Laurent; Peyriere, Hugo; Statom, Nick (2023). Airborne observations of surface winds, waves and currents from meso to submesoscales. Submitted to Geophysical Research Letters". In this work we present a unique set of coincident and collocated high-resolution observations of surface currents and directional properties of surface waves collected from an airborne instrument, the Modular Aerial Sensing System (MASS), collected off the coast of Southern California. High-resolution observations of near surface current profiles and shear are obtained using a new instrument, DoppVis, capable of capturing horizontal spatial current variability down to 128m resolution. This data set provides a unique opportunity to examine how currents at scales ranging from 1-100 km modulate bulk (e.g. significant wave height), directional and spectral properties of surface gravity waves. Such observations are a step toward developing better understanding of the underlying physics of submesoscale processes (e.g. frontogenesis and frontal arrest) and the nature of transitions between mesoscale and submesoscale dynamics.
DOI: 10.6075/j0g16118
title: Data and Code from: 3D Reconstruction and Segmentation of Barely Visible Impact Damage in Composites from Pulse-Echo Ultrasonic C-Scans

description: This dataset is a set of processed pulse-echo ultrasonic C-scans of composite samples with barely visible impact damage. The samples have varying layups and impact energies and have been processed using an open-source MATLAB code developed as an alternative to commercial ultrasonic C-scan processing software. The data included are (1) raw data from the ultrasonic C-scan, in .csv file format in .zip folder, (2) the processed C-scan from a commercial software, Mistras/UTWin, in .png format, (3) output figures from the open source code, in .png format (specifically, time-of-flight map, damage layers map, inflection points map & mask, 3D reconstruction of damage state, and hybrid 3D reconstruction), (4) a static version of the open source MATLAB code, in a .zip folder, (5) all the outputs and figures produced by the code, in .mat and .png/.fig format in two separate .zip folders.
DOI: 10.5281/zenodo.12761060
title: Dataset for Study: Negotiating Visibility: Mediating Presence through Zoom Camera Choices in Post-Secondary Students during COVID-19
DOI: 10.5281/zenodo.12761061
title: Dataset for Study: Negotiating Visibility: Mediating Presence through Zoom Camera Choices in Post-Secondary Students during COVID-19
DOI: 10.6084/m9.figshare.26319169
title: Vegetation cover data in PASTFORWARD experiment from 2016 to 2023. Data used for the analysis in 'Forest floor environment overrules global change treatment effects on understorey communities in a mesocosm experiment' (Lorer et al., Global Change Biology, 2024).

description: This dataset contains the vegetation cover data collected in mesocosm plant communities subjected to experimental microclimate warming, illumination and nitrogen deposition in ancient and post-agricultural forest soils in the PASTFORWARD experiment, set in the Aelmoeseneie forest in Belgium (50°58′30″N, 3°48′16″E). The data were collected from 2016 to 2023. Metadata explaining different columns is provided on the second tab of the excel file.<br>Species characteristics data (CCI, thermal niche optimum, Ellenberg L and N) can be found in Table S1 of the supplementary information of the publication.<br>Data used for the analysis in 'Forest floor environment overrules global change treatment effects on understorey communities in a mesocosm experiment' (Lorer et al., Global Change Biology, 2024).
DOI: 10.6084/m9.figshare.26319169.v1
title: Vegetation cover data in PASTFORWARD experiment from 2016 to 2023. Data used for the analysis in 'Forest floor environment overrules global change treatment effects on understorey communities in a mesocosm experiment' (Lorer et al., Global Change Biology, 2024).

description: This dataset contains the vegetation cover data collected in mesocosm plant communities subjected to experimental microclimate warming, illumination and nitrogen deposition in ancient and post-agricultural forest soils in the PASTFORWARD experiment, set in the Aelmoeseneie forest in Belgium (50°58′30″N, 3°48′16″E). The data were collected from 2016 to 2023. Metadata explaining different columns is provided on the second tab of the excel file.<br>Species characteristics data (CCI, thermal niche optimum, Ellenberg L and N) can be found in Table S1 of the supplementary information of the publication.<br>Data used for the analysis in 'Forest floor environment overrules global change treatment effects on understorey communities in a mesocosm experiment' (Lorer et al., Global Change Biology, 2024).
DOI: 10.5281/zenodo.12761034
title: Suplementary_Data_1.zip

description: The 4 completed expert review sheets used to parameterise the main model in Tosh et al (2024) Biotic stress and yield stability in English organic silvoarable agroforestry. Agronomy for Sustainable Development.
DOI: 10.5281/zenodo.12761035
title: Suplementary_Data_1.zip

description: The 4 completed expert review sheets used to parameterise the main model in Tosh et al (2024) Biotic stress and yield stability in English organic silvoarable agroforestry. Agronomy for Sustainable Development.
DOI: 10.48366/r705692
title: Art therapy activities (based on PLOS ONE publications)

description: What are the main art activities as the therapy tool.  What types of participants underwent art therapy. 
The comparison is the basis for the future Research Question: to what art therapy the Virtual Reality can be applied to. 
Contributions from PLOS ONE publisher.  
https://journals.plos.org/plosone/
DOI: 10.57770/yqiy2h
title: Defect Engineered Bi2Te3 Nanosheets with Enhanced Haloperoxidase Activity for Marine Antibiofouling

description: Defective bismuth telluride (Bi2Te3) nanosheets, an artificial nanozyme mimicking haloperoxidase activity (hPOD), show promise as eco-friendly, bactericidal, and antimicrofouling materials by enhancing cytotoxic hypohalous acid production from halides and H2O2. Microscopic and spectroscopic characterization reveals that controlled NaOH (upto X = 250 µL) etching of the nearly inactive non-transition metal chalcogenide Bi2Te3 nanosheets creates controlled defects (d), such as Bi3+species, in d-Bi2Te3-X that induces enhanced hPOD activity. d-Bi2Te3-250 exhibits approximately eight-fold improved hPOD than the as-grown Bi2Te3 nanosheets. The antibacterial activity of d-Bi2Te3-250 nanozymes, studied by bacterial viability, show 1, and 45% viability for Staphylococcus aureus and Pseudomonas aeruginosa, respectively, prevalent in marine environments. The hPOD mechanism is confirmed using scavengers, implicating HOBr and singlet oxygen for the effect. The antimicrofouling property of the d-Bi2Te3-250 nanozyme has been studied on Pseudomonas aeruginosa biofilm in a lab setting by multiple assays, and also on titanium (Ti) plates coated with the nanozyme mixed commercial paint, exposed to seawater in a real setting. All studies, including direct microscopic evidence, exhibit inhibition of microfouling, up to ≈73%, in the presence of nanozymes. This approach showcases that defect engineering can induce antibacterial, and antimicrofouling activity in non-transition metal chalcogenides, offering an inexpensive alternative to noble metals.
DOI: 10.5281/zenodo.12760688
title: Data of figures from: Berard et al, Effect of Crystalline Phase and Facet Nature on the Adsorption of Phosphate Species onto TiO2 Nanoparticles, Langmuir 2024
DOI: 10.5281/zenodo.12760689
title: Data of figures from: Berard et al, Effect of Crystalline Phase and Facet Nature on the Adsorption of Phosphate Species onto TiO2 Nanoparticles, Langmuir 2024