cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7890154
title: Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light

description: <strong>Data type</strong>: Experimental spectroscopic measurements, computer plots. Files are with filename extensions: .<strong>DSC</strong>, .<strong>DAT</strong>, .<strong>txt</strong>, .<strong>m</strong> Information on <strong>origin of the data</strong>: EPR spectroscopic measurements with filename extensions: .<strong>DSC</strong>, .<strong>DTA</strong>, .<strong>txt</strong>. EPR spectroscopic plots with filename extension: .<strong>m</strong>. CW-EPR X-band were performed on a Bruker Elexys E580 X-band spectrometer (microwave frequency 9.76 GHz) equipped with a cylindrical dielectric cavity and a helium gas-flow cryostat from Oxford Inc. The spectrum was recorded at 4.5 K and a microwave power of 1mW, a modulation amplitude of 0.7mT and a modulation frequency of 100 KHz were used. Raw and Processed Data, and Computational Protein Design files <strong>If the dataset includes multiple files that relate to each other:</strong> Files in <strong>PARACAT_WP5_20230425_CW</strong> folder includes X-band CW-EPR spectroscopic measurements, original data are in .<strong>DTA</strong>/.<strong>DSC</strong>/.<strong>txt</strong>. Files in <strong>PARACAT_WP5_20230425_MATLAB</strong> folder includes plots of the EPR measurements, data are in .<strong>m</strong> format. <strong>Information on</strong>: Specialized abbreviations: <strong>EPR</strong> – Electron Paramagnetic Resonance; <strong>CW</strong> – Continuous Wave-EPR; <strong>METP</strong> - Miniaturized Electron Transfer Protein; METP<strong>sc</strong>1 - single-chain high-potential miniaturized electron transfer protein. Definitions of variables: <strong>Magnetic field, Temperature</strong>. Units of measurement: <strong>Gauss (G), milliTesla (mT), Kelvin (K)</strong>
description:  Files with extension .m are MATLAB input files. MATLAB license can be acquired at the link https://it.mathworks.com/downloads/web_downloads/. To run the codes present in these files, it is necessary to install, in MATLAB, a free toolbox called EasySpin, which can be found at the link https://easyspin.org/.
DOI: 10.5281/zenodo.5655335
title: Información sobre elementos Tabla Periódica

description: A continuación, se muestra una base de datos que contiene información sobre los elementos de la tabla periódica. En esta, aparecen los 118 elementos ordenados en orden creciente según su número atómico. Particularmente, los atributos que componen este dataset son: N_atomico: Número atómico del elemento que lo ordena en la Tabla Periódica. Elemento: Símbolo del elemento en la Tabla Periódica. Nombre: Nombre del elemento. Masa: Masa del elemento, expresada en unidades de masa atómica (umas). Periodo: Periodo (fila) del elemento en la Tabla Periódica. Grupo: Grupo (columna) del elemento en la Tabla Periódica. Estructura: Estructura cristalina que el elemento presenta en su forma más estable. Conf_electronica: Configuración electrónica más estable del elemento. Sobre algunos elementos, además de sus últimas capas, aparece entre corchetes un gas noble del que toman su configuración inicial. Descubrimiento: Año o años de descubrimiento. En algunos elementos aparece la “Prehistoria” como época en la que fue descubierto.
DOI: 10.5281/zenodo.5655334
title: Información sobre elementos Tabla Periódica

description: A continuación, se muestra una base de datos que contiene información sobre los elementos de la tabla periódica. En esta, aparecen los 118 elementos ordenados en orden creciente según su número atómico. Particularmente, los atributos que componen este dataset son: N_atomico: Número atómico del elemento que lo ordena en la Tabla Periódica. Elemento: Símbolo del elemento en la Tabla Periódica. Nombre: Nombre del elemento. Masa: Masa del elemento, expresada en unidades de masa atómica (umas). Periodo: Periodo (fila) del elemento en la Tabla Periódica. Grupo: Grupo (columna) del elemento en la Tabla Periódica. Estructura: Estructura cristalina que el elemento presenta en su forma más estable. Conf_electronica: Configuración electrónica más estable del elemento. Sobre algunos elementos, además de sus últimas capas, aparece entre corchetes un gas noble del que toman su configuración inicial. Descubrimiento: Año o años de descubrimiento. En algunos elementos aparece la “Prehistoria” como época en la que fue descubierto.
DOI: 10.5281/zenodo.7874729
title: Penothypic integration: assessing the value of study replication

description: This repository contains the databases and scripts used to analyze the phenotypic integration of different species, populations, and sexes and assess which structural paths were generally (vs. conditionally) supported (vs. unsupported). These data were used in the following study: Irene Gaona-Gordillo, Benedikt Holtmann, Alexia Mouchet, Alexander Hutfluss, Alfredo Sánchez-Tójar, and Niels J. Dingemanse. <em>Unpublished manuscript. </em>Are animal personality, body condition, physiology, and structural size integrated? A comparison of species, populations, and sexes, and the value of study replication. J Anim Ecol. For any further information, please contact: Irene Gaona-Gordillo, email: gaona-gordillo@bio.lmu.de Niels Dingemanse, email: n.dingemanse@lmu.de
DOI: 10.5281/zenodo.7874728
title: Penothypic integration: assessing the value of study replication

description: This repository contains the databases and scripts used to analyze the phenotypic integration of different species, populations, and sexes and assess which structural paths were generally (vs. conditionally) supported (vs. unsupported). These data were used in the following study: Irene Gaona-Gordillo, Benedikt Holtmann, Alexia Mouchet, Alexander Hutfluss, Alfredo Sánchez-Tójar, and Niels J. Dingemanse. <em>Unpublished manuscript. </em>Are animal personality, body condition, physiology, and structural size integrated? A comparison of species, populations, and sexes, and the value of study replication. J Anim Ecol. For any further information, please contact: Irene Gaona-Gordillo, email: gaona-gordillo@bio.lmu.de Niels Dingemanse, email: n.dingemanse@lmu.de
DOI: 10.5281/zenodo.7886524
title: River monitoring, particulate Cs-137 measurements and rainfall monintoring of the Mano Dam catchment (Japan) from 2014 to 2019

description: This dataset is composed of river monitoring, laboratory particulate Cs-137 measurements and rainfall monitoring used in the article: Vandromme, R., Hayashi, S.,Tsuji, H., Evrard, O., Grangeon, T., Landemaine, V., Laceby, J.P., Wakiyama, Y., Cerdan, O. The unprecedented soil decontamination program in Fukushima only reduced radioactive fluxes in rivers by 17% (PNAS, under review) River measurements were conducted by Hayashi S. and Tsuji H. <br> A hydrological station was installed immediately upstream of Mano Dam Lake (Lake Hayama) in June 2014. The water height in the river was measured using an AquiStar PT12 pressure/temperature sensor (INW, Kirkland, WA, USA) at 5-min intervals and then converted into flow rate data using gage curves. Water and SS samples were also collected from the river section using an ISCO 6712 automatic water sampler (Teledyne Technologies, Lincoln, NE, USA) at 1-h intervals during flood events. The SS concentration was determined in the laboratory by filtration using a Whatman GF/F filter with 0.7-µm pores (Cytiva, Tokyo, Japan), and these concentrations were then used to convert the turbidity logs measured by a DTS-12 digital turbidity sensor (FTS Inc., Victoria, BC CANADA) at 5-min intervals into SS logs. <br> This station was damaged by Typhoon Etau in September 2015. Following this damage, the data analysis and discovery of anomalies that persisted until the end of 2016 prompted us to omit the data acquired during this period. The hydrological station was subsequently moved a few hundred meters upstream in 2017. Water flows and sediment concentrations were subsequently acquired using the same systems described above at 10-min intervals until the end of 2019. River water samples were punctually collected to measure 137Cs concentration in Suspended Sediment (SS) (66 measurements during floods) from June 2014 to December 2019 (this chronicle ends in the middle of a flood). Station location before 2017 (coordinate system:WGS84) : lat 37.738391, long 140.803943<br> Station location after 2017 (coordinate system:WGS84) : lat 37.733191, long 140.807709 Rainfall record was acquired by the Fukushima Prefecture (Maenori station, lat 37.73644, long 140.74233, coordinate system:WGS84) at 10-minute time steps.
DOI: 10.5281/zenodo.7886523
title: River monitoring, particulate Cs-137 measurements and rainfall monintoring of the Mano Dam catchment (Japan) from 2014 to 2019

description: This dataset is composed of river monitoring, laboratory particulate Cs-137 measurements and rainfall monitoring used in the article: Vandromme, R., Hayashi, S.,Tsuji, H., Evrard, O., Grangeon, T., Landemaine, V., Laceby, J.P., Wakiyama, Y., Cerdan, O. The unprecedented soil decontamination program in Fukushima only reduced radioactive fluxes in rivers by 17% (PNAS, under review) River measurements were conducted by Hayashi S. and Tsuji H. <br> A hydrological station was installed immediately upstream of Mano Dam Lake (Lake Hayama) in June 2014. The water height in the river was measured using an AquiStar PT12 pressure/temperature sensor (INW, Kirkland, WA, USA) at 5-min intervals and then converted into flow rate data using gage curves. Water and SS samples were also collected from the river section using an ISCO 6712 automatic water sampler (Teledyne Technologies, Lincoln, NE, USA) at 1-h intervals during flood events. The SS concentration was determined in the laboratory by filtration using a Whatman GF/F filter with 0.7-µm pores (Cytiva, Tokyo, Japan), and these concentrations were then used to convert the turbidity logs measured by a DTS-12 digital turbidity sensor (FTS Inc., Victoria, BC CANADA) at 5-min intervals into SS logs. <br> This station was damaged by Typhoon Etau in September 2015. Following this damage, the data analysis and discovery of anomalies that persisted until the end of 2016 prompted us to omit the data acquired during this period. The hydrological station was subsequently moved a few hundred meters upstream in 2017. Water flows and sediment concentrations were subsequently acquired using the same systems described above at 10-min intervals until the end of 2019. River water samples were punctually collected to measure 137Cs concentration in Suspended Sediment (SS) (66 measurements during floods) from June 2014 to December 2019 (this chronicle ends in the middle of a flood). Station location before 2017 (coordinate system:WGS84) : lat 37.738391, long 140.803943<br> Station location after 2017 (coordinate system:WGS84) : lat 37.733191, long 140.807709 Rainfall record was acquired by the Fukushima Prefecture (Maenori station, lat 37.73644, long 140.74233, coordinate system:WGS84) at 10-minute time steps.
DOI: 10.6084/m9.figshare.22737083
title: Well-to-Well variation in qPCR amplification curves is suggestive of dysfunction in thermal cycler heat block

description: Modern quantitative polymerase chain reaction (qPCR) instrument typically has a 96 well heat block where the PCR tubes are placed for thermal cycling. With time and continued usage, there may be faster degradation of some wells relative to others, thereby, resulting in ineffective heating in some wells over others. This effect will manifest in different temperature cycling for different wells, which will likely result in different qPCR curves. Thus, observation of different qPCR amplification curves for different wells for the same experimental conditions is suggestive of dysfunction of the thermal heat block, or a more serious malfunction in the main system board that controls the temperature cycling of the heat block. This work presents a couple of representative amplification curves indicative of the effect.
DOI: 10.6084/m9.figshare.22737083.v1
title: Well-to-Well variation in qPCR amplification curves is suggestive of dysfunction in thermal cycler heat block

description: Modern quantitative polymerase chain reaction (qPCR) instrument typically has a 96 well heat block where the PCR tubes are placed for thermal cycling. With time and continued usage, there may be faster degradation of some wells relative to others, thereby, resulting in ineffective heating in some wells over others. This effect will manifest in different temperature cycling for different wells, which will likely result in different qPCR curves. Thus, observation of different qPCR amplification curves for different wells for the same experimental conditions is suggestive of dysfunction of the thermal heat block, or a more serious malfunction in the main system board that controls the temperature cycling of the heat block. This work presents a couple of representative amplification curves indicative of the effect.
DOI: 10.6084/m9.figshare.20170811
title: Master accelerometer data from brainwear participants. Data only included if passed threshold for high-quality.

description: Master accelerometer data from brainwear participants. Data only included if passed threshold for high-quality.
DOI: 10.6084/m9.figshare.20170811.v1
title: Master accelerometer data from brainwear participants. Data only included if passed threshold for high-quality.

description: Master accelerometer data from brainwear participants. Data only included if passed threshold for high-quality.
DOI: 10.5066/p9fdulxj
title: Fault Zones in the Gulf Coast [gcfltzoneg]

description: These data represent major fault zones as indicated on Plate 2, Principal structural features, Gulf of Mexico Basin (compiled by T.E. Ewing and R.F. Lopez) in volume J, The Geology of North America (1991). This dataset contains basic data and interpretations developed and compiled by the U.S. Geological Survey's Framework Studies and Assessment of the Gulf Coast Project. Other major sources of data include publicly available information from state agencies as well as publications of the U.S. Geological Survey and other scientific organizations. In cases where company proprietary data were used to produce various derivatives such as contour surfaces, the source is cited but the data are not displayed.
DOI: 10.5281/zenodo.1020240
title: Popc Bilayer With 10% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs

description: POPC bilayer with 10% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.

See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B10%25DHMDMAB/T313K/MODEL_LIPID14
DOI: 10.5281/zenodo.1020593
title: Popc Bilayer With 20% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs

description: POPC bilayer with 20% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.

See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B20%25DHMDMAB/T313K/MODEL_LIPID14
DOI: 10.5281/zenodo.1020623
title: Popc Bilayer With 30% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs

description: POPC bilayer with 30% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.

See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B30%25DHMDMAB/T313K/MODEL_LIPID14
DOI: 10.5281/zenodo.1020689
title: Popc Bilayer With 50% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs

description: POPC bilayer with 50% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 180ns of 200ns long simulation.

See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B50%25DHMDMAB/T313K/MODEL_LIPID14
DOI: 10.5281/zenodo.1020709
title: Popc Bilayer Simulated At T313K With The Lipid14 Model Using Gromacs

description: POPC bilayer with 50% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. 70ns long simulation.

See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC/T313K/MODEL_LIPID14
DOI: 10.5281/zenodo.1118265
title: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field

description: Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions. file names report molar fraction of cations (i.e. not bulk concentrations) simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files) simulation length 300 ns temperature 313 K (otherwise noted) Gromacs simulation setting is in the file npt_lipid_bilayer.mdp
DOI: 10.5281/zenodo.12767
title: Md Simulation Trajectory And Related Files For Popc Bilayer (Lipid14, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Lipid14 force field (http://dx.doi.org/10.1021/ct4010307), 50ns, T=303K, 72 POPC molecules, 2234 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project.
description: {"references": ["nmrlipids.blogspot.fi", "Dickson et al. J. Chem. Theory Comput., 2014, 10 (2), pp 865\u2013879"]}
DOI: 10.5281/zenodo.259376
title: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Ecc-Scaled Ions

description: Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the recent ion parameters by Kohagen et al. [3] for CaCl_2.

The Charmm36 force field parameters were obtained Charmm-GUI [4], and the ion parameters are available at https://bitbucket.org/hseara/ions/ . IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br>
––––––––––––––––––––––––––––––––––––––––––––––––––––––<br>
The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 800 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0-&gt;) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br>
––––––––––––––––––––––––––––––––––––––––––––––––––––––<br>
[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q

[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m

[3] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693

[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br>
Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935
DOI: 10.5281/zenodo.30865
title: Popc_Amber_Lipid14_Nacl_1Mol

description: MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M NaCl. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 77 Na, 77 Cl. 200ns trajectory  (preceded by 5ns NPT equillibration) (2 files of 100ns).

This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi
DOI: 10.5281/zenodo.30898
title: Popc_Amber_Lipid14_Verlet

description: MD simulation trajectory and related files for fully hydrated POPC bilayer with runned with Verlet scheme. The LIPID14 force field was used with Gromacs 5.0.3. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters. 200ns trajectory  (preceded by 5ns NPT equillibration) (2 files of 100ns).

This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi
DOI: 10.5281/zenodo.34415
title: Popc_Amber_Lipid14_Cacl2_035Mol

description: MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.35M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory  (preceded by 5ns NPT equillibration) (2 files of 100ns).

THE TRAJECTORY "035M_CaCl2_POPC_AMB_100_200ns.xtc" IS CORRUPTED. FOR THE UNCORRUPTED FILE PLEASE FOLLOW THE LINK: https://zenodo.org/record/46234

This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi
DOI: 10.5281/zenodo.5236640
title: MSM/RD generated data/plots

description: This repository holds the data generated with the MSM/RD software to produce the plots for the paper: ``Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics'' by Mauricio J. del Razo, Manuel Dibak, Christof Schütte and Frank Noé. The plots are stored in the plots directory. The plotting scripts are written using jupyter notebooks and require numpy and matplotlib. To produce the plots yourself, just run the notebooks included in this folder. The MSM/RD code is written in c++ with python bindings. The code is still in constant development, and there is no official release. Active development of the code is done on this github repository. The exact version of the code used for the paper can be found on this Zenodo repository.