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Replication Data for: "Atomistic description of the OCTN1 recognition mechanism via in silico methods"
No full textReplication Data for "Atomistic description of the OCTN1 recognition mechanism via in silico methods, PLOS ONE, 2024, 19(6): e0304512".
The dataset includes two distinct types of PDB files, identified by their naming convention.
1. Docking poses
Files:
22a4_*_pose.pdb
Description:
These files contain the docking poses of individual ligands bound to OCTN1. Each PDB file corresponds to a different compound (indicated by * in the file name) and represents the selected binding pose obtained from molecular docking calculations. The structures include OCTN1 and the docked ligand in the predicted binding configuration.
Docking poses are useful to reproduce MD simulations.
2. MD equilibration cluster medoids
Files:
r1_22a4_*.pdb
r2_22a4_*.pdb
Description:
These files contain representative structures (medoids) of conformational clusters extracted from independent equilibration molecular dynamics replicas of OCTN1–ligand complexes.
The prefix r1 and r2 identifies different MD replicas, while * denotes the ligand name. For each ligand, the medoid corresponds to the most representative structure of the dominant cluster sampled during the equilibration phase, and captures the stabilized binding mode of the compound within OCTN1.
MD clusters are useful to asses the rearrangements of the complexes
Replication Data for: Ferroptosis-Induced Oxidative Stress Overcomes Therapy Resistance in Glioblastoma: Evidence from In Vitro and In Vivo Models
No full textThis dataset includes the Tandem mass tag LC-MS/MS proteomics data of changed proteins generated in the study: “Ferroptosis-Induced Oxidative Stress Overcomes Therapy Resistance in Glioblastoma: Evidence from In Vitro and In Vivo Models” by Sofia Remedia, Cristina Martelli, Francesca Servidio, Marcella Bonanomi, Clarissa Gervasoni, Bruno Giovanni Galuzzi, Martina Nespoli, Chiara Pellizzer, Alessandro Giammona, Daniela Gaglio, Daniele Capitanio, Gloria Bertoli, Luisa Ottobrini, and Alessia Lo Dico. Data were generated by LC-ESI-MS/MS with TMT isobaric labeling quantitation. Mass spectra generated on a orbitrap Fusion tribrid mass spectrometer (Thermo) were analyzed using MaxQuant software (Max-Planck-Institute of Biochemistry, Munich, Germany, version 1.6.17.0). Statistical analyses were performed using the Perseus software (Max Planck Institute of Biochemistry, Munich, Germany, version 1.6.15.0). For statistical analysis, ANOVA test and Tukey's multicomparison analysis with a p-value threshold of 0.05 were applied. To exclude the presence of false positives from the analysis, Benjamini–Hochberg false discovery rate test was applied
Mediterranean AR over northern Italy
No full text Content
This dataset contains atmospheric rivers (ARs) identified over the Mediterranean and impacting northern Italy. ARs have been identified as objects and the dataset contains shape, axis, date and time of each identified object.
ERA5 gridded reanalyses (0.25°) provide the Integrated Vapour Transport (IVT) every 6 hours. The algorithm of Guan and Walliser (2015) has been adopted to identify ARs as objects characterized by adiacent grid points with IVT exceeding the 85th percentile, and satisfying geometrical requirements (lenght > 2000 km, aspect ratio >2). The algorithm was slighly modified to adapt to the Mediterranean (see Davolio et al., 2025 for further details).
Among all the ARs identified over the full domain (-30 to 30 E; 20 to 60 N), only those affecting the target area of northern/central Italy (Italian peninsula north of about 42.5N) and at the same time extending well ouside the Mediterranean basin (defind as an arc-shaped area, see againg Davolio et al., 2025, Figure 3), have been selected. This latter requirement is devised to intercept ARs reaching the Mediterranean from either Africa tropical areas or the North Atlantic and assures a length of at least 2000 km.
Also, a temporal requirement is imposed: an AR must persist for at least three 6-hourly time steps. It means that only AR objects persisting longer than 12 hours are considered in the dataset.
The dataset covers the period 1961-2024.
Data are provided on a regular lat-lon grid, 0.25° grid-spacing, on the domain -30 to 30 E; 20 to 60 N
Files
Data are in netcdf format and divided in decades.
Naming is as yyyy_YYYY_AR.nc where
yyyy is the initial year
YYYY is the final year of the decades.
Figures of the IVT field and the shape identifying the AR object are also provided in png format. All the AR instants of the netcdf files have been plotted. Figures are grouped for decades (as the netcdf files) in a tgz file.
A list of the events is also provided as pdf, with initial/final time of each event, max IVT and duration.
Software:
- The code developed by Guan and Walliser (2015) has been adopted "Global Atmospheric River Detection" v2016.07.02
- The selection of AR satisfying our requirements was performed through python codes.
- Finally, a careful manual check was necessary to remove some objects that did not resemble AR (but survived the selection for "bugs" in the code).
This dataset has been produced within the PRIN2022 Project ARMEX "Exploring Atmospheric Rivers in the Mediterranean and their connection with EXtreme hydrometeorological events over Italy: observation, modelling and impacts"
Project Next Generation EU, Mission 4, Component 1, CUP B53D23007490006 funded by Ministero dell'Università e della Ricerca
https://sites.google.com/view/armexproject
References:
- Davolio, S., Sala, I., Comunian, A., Mastrangelo, D., Miglietta, M. M., Drago Pitura, L., and Grazzini, F.: Detection of atmospheric rivers affecting the Mediterranean and producing extreme rainfall over northern-central Italy, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2025-3447, 2025.
- Guan, B. and Waliser, D. E.: Detection of atmospheric rivers—evaluation and application of an algorithm for global studies. J. Geophys. Res. (Atmosphere), 120, 12514–12535, https://doi.org/10.1002/2015JD0245257, 2015
Activity 1 - HEA Neuroevolution Potential - NEP input and output files
No full textInput and output files of the Neuroevolution Potential code
https://gpumd.org/potentials/nep.html
The generated MLIP consists in the nep.txt file.
The dataset contains three files corresponding to three versions of the MLIP.
NEP_Jan08_maxF10_80percent and NEP_Jan08_maxF10_alltrain
obtained by training on 80% or on 100% of the dft data, using the default NEP parameters.
NEP_Jan08_maxF10_alltrain_alt
obtained by training on 100% of the dft data using and improved parameters (larger basis set, more neurons), see nep.in
For an estimate of the MLIP quality one can refer to the RMSE reported in loss.out
The present MLIP should be able to describe a generic alloy of Mn Co Fe Ni Cu atoms.
It can e.g. be used in LAMMPS with the nep pair_style:
https://deepwiki.com/brucefan1983/NEP_CPU/5.1-lammps-integration-buil
Replication data for synthesis of: "Natural and Nature-Inspired Catechol Siderophores: A Promising Strategy for Rice Blast Management"
No full textFor the preparation of catechol-bearing natural compounds protected 2,3-dihydroxybenzoic acid was used as a key precursor. Aminochelin was obtained as a trifluoroaceatate by reaction with N-Boc-1,4-diaminobutane using HATU and DIPEA in THF. The protecting groups were removed by hydrogenation (10% Pd/C catalyst), followed by treatment with TFA in dichloromethane.
The analogue containing a hydroxy group in place of the amino group on the side chain was obtained following a similar procedure with different aminobutanols. Same procedure for analogues containing the 3,4-dihydroxy substituted moiety in place of the 2,3-substituted one were obtained starting from the protected 3,4-dihydroxybenzoic
acid. The protecting groups were removed by hydrogenation (10% Pd/C catalyst).
Azotochelin was synthesized via amide coupling between protected 2,3-dihydroxybenzoic acid and L-lysine, followed by deprotection of the phenolic groups. In this case, the use of BBr3 resulted to be more advantageous than hydrogenation, which did not give a complete deprotection.
The reaction of protected 2,3-dihydroxybenzoic acid with L-lysine ethyl ester gave an intermediate, which was reduced with LiBH4 to obtain another compound which the removal of benzyl protecting groups by BBr3 afforded Myxochelin A.
Myxochelin A analogues were prepared following the same synthetic pathway reported above.
The reaction of the protected 2,3-dihydroxybenzoic acid with pentane-1,5-diamine,
followed by removal of the protecting group by BBr3 in dichloromethane, gave the corresponding diamide, which contained the same skeleton of Azotochelin and Myxochelin A, without the substituent on the connecting chain. The same approach was
followed to obtain other analogs
Activity1 - HEA Structures and DFT data
No full textThis dataset containes a number of high entropy alloy (HEA) structures made by Mn, Fe, Co, Ni, Cu, in different geometrical and compositional combinations.
Each structure is in a separate subfolder containing the SIESTA input (with extension .fdf) and output (with extension .out) files.
Information of coordinates and cell vectors are contained in the siesta input file, as well as the parameters of the SIESTA calculation.
DFT data (one-shot-energy calculations) are in the SIESTA output file
Replication data for chelating ability of: "Natural and Nature-Inspired Catechol Siderophores: A Promising Strategy for Rice Blast Management"
No full textPreparation of CAS Reagent. 100 mL graduated glass cylinder was previously washed with 6 M HCl. Six mL of 10 mM solution of hexadecyltrimethylammonium bromide (HDTMA) (22 mg in 6 mL distilled water) was poured into the cylinder and diluted to 40 mL with distilled water. While stirring, 1.5 mL of 1 mM ferric iron solution (2.7 mg of FeCl3·6 H2O in 10 mL HCl 1 M) was added, whereupon 7.5 mL of 2 mM Chrome Azurol S (CAS) solution (9.1 mg in 7.5 mL distilled water) was slowly added.
In a separate flask, 2.5 M solution of piperazine (4.31 g in 20 mL distilled water) was prepared and cooled to 0 °C and 6.25 mL of concentrated HCl was carefully added. The piperazine solution was added to the CAS/Fe3+ solution in the cylinder and then brought to a final volume of 100 mL with distilled water. Lastly, sulfosalicylic acid (102 mg) was added. The final blue solution was stored in a polyethylene falcon in a cool and dark place.
Compounds. The assay was done in triplicate. EDTA was selected as a positive control, whereas the negative control (N.C.) was the blank solution of H2O:DMSO 9:1 v/v.
Results: The chelating ability of the synthesized compounds was evaluated by the Chrome azurol S (CAS) assay. The tested compounds were dissolved in H2O:DMSO
9:1 v/v at 1 mg/mL concentration. 100 μL of the solution of the tested compound and 100 μL of CAS reagent were added into the same well of the 96 Microwell plate (final
concentration 0.5 mg/mL) and allowed to react for 30 min. The results evidenced that the 2,3-dihydroxy substituted benzamides have a significant chelating capability, comparable to the reference compound EDTA except for aminochelin. Conversely,
3,4-dihydroxy benzamides, with the catechol group shifted away from the amide moiety, had a lower chelating activity.
The results evidenced that the 2,3-dihydroxy substituted benzamides have a significant chelating capability, comparable to the reference compound EDTA. (see compounds 2, 3, 7a−c, 11, 16a−b) except for the natural compound 1. Conversely, 3,4-dihydroxy benzamides, with the catechol group shifted away from the amide moiety, had a lower chelating activity (7d−e, 16c). As expected, compounds 14a−e, lacking the catechol group, did not show any significant ability to chelate iron
Aurona and Leone Glaciers and Proglacial areas
No full textThe dataset contains the elaborated file related to the evolution of Aurona and Leone Glaciers in the Piedmont Region (Italian Alps) and the relative proglacial areas. In particular, the file contains
1. Shape files of the glacial and proglacial historical monitoring (1872-2020)
2. CSV files of the Leone and Aurona moraines crests displacement (1958-1981)
3. CSV file of the boulder displacement in the Leone proglacial area (1958-2020)
4. Tif files of the DOD respectively for glaciers (2010-2021), Aurona (2000-2010; 2010-2021; 2021-2023) and Leone (2000-2010; 2010-2021) proglacial areas.
5. .bin files related to the cloud-to-cloud comparisons for the Aurona proglacial area and two sub zones (debris flow-APA 1; subsiding zone-APA 2)
SkyTEM survey in dune area
No full textSkyTEM data in dune area in the Netherlands. The two uploaded files comprise the airborne electromagnetic (AEM) survey dataset and the corresponding AEM system parameter information. Specifically, File 1 contains AEM system parameters in the standard GEX format, including the transmitter waveform, system model, transmitter coil geometry and dimensions, the number of transmitter coil turns, and filter specifications. File 2 contains the survey data published in the standard XYZ format, including relative transmitter–receiver positions, data units, flight altitude, gate times, low-moment and high-moment measurements, and the corresponding data standard deviation (STD) information
Degree of Urbanisation (DEGURBA) level 1 for 16 countries in Sub-Saharan Africa and the Caribbean
No full textThis data release contains four harmonised gridded population datasets as well as the derived gridded "DEGURBA Level 1" datasets and associated spatial entities for 15 countries in sub-Saharan Africa and one country in the Caribbean (refer to the 'Geospatial Metadata' section).
The gridded population datasets comprise the "Global Human Settlement Population" dataset (GHS-POP) and three WorldPop products: "WorldPop Constrained Global Population", "WorldPop Unconstrained Global Population", and "WorldPop Bespoke National Population" datasets (refer to the "Reletaed Datasets" section) . The four population datasets were harmonised, partially using the "GHS-POPWARP v3" tool, to ensure consistency in coordinate reference system, spatial resolution, extent, and alignment, as well as population total referring to 2020. The gridded "DEGURBA Level 1" datasets were derived for each population grid using the "GHS-DUG v6.1" tool. The harmonisation process enables the comparability of the derived "DEGURBA Level 1" datasets. Details about the harmonisation process and the comparison between the "DEGURBA Level 1" datasets are given in Zhang et al. (2025; refer to the "Related Publication" section).
These data were produced by the WorldPop Research Group at the University of Southampton in partnership with the Department of Earth Science “A. Desio” of the University of Milan in the framework of the DEGURBA project, with funding from the European Commission's Directorate-General for Regional and Urban Policy (DG REGIO), under grant agreement "Population and SDG indicators by Degree of Urbanisation" (2022CE16BAT035). Project partners included the WorldPop Research Group at the University of Southampton, the Department of Earth Science "A. Desio" of the University of Milan, and the European Commission Joint Research Centre (EC-JRC; as a no-cost project partner). The data processing was performed by Dorothea Woods, Iyanuloluwa Deborah Olowe, Alessandro Sorichetta, and Maksym Bondarenko. Project lead, coordination and oversight were provided by Alessandro Sorichetta and Andrew J. Tatem