cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8174268
title: Benchmark Data for Chemprop

description: Datasets and splits of the manuscript "Chemprop: Machine Learning Package for Chemical Property Prediction." Train, validation and test splits are located within each folder, as well as additional data necessary for some of the benchmarks. To train Chemprop models, refer to our code repository to obtain ready-to-use scripts to train machine learning models for each of the systems. Available benchmarking systems: `hiv` HIV replication inhibition from MoleculeNet and OGB with scaffold splits `pcba_random` Biological activities from MoleculeNet and OGB with random splits `pcba_scaffold` Biological activities from MoleculeNet and OGB with scaffold splits `qm9_multitask` DFT calculated properties from MoleculeNet and OGB, trained as a multi-task model `qm9_u0` DFT calculated properties from MoleculeNet and OGB, trained as a single-task model on the target U0 only `qm9_gap` DFT calculated properties from MoleculeNet and OGB, trained as a single-task model on the target gap only `sampl` Water-octanol partition coefficients, used to predict molecules from the SAMPL6, 7 and 9 challenges `atom_bond_137k` Quantum-mechanical atom and bond descriptors `bde` Bond dissociation enthalpies trained as single-task model `bde_charges` Bond dissociation enthalpies trained as multi-task model together with atomic partial charges `charges_eps_4` Partial charges at a dielectric constant of 4 (in protein) `charges_eps_78` Partial charges at a dielectric constant of 78 (in water) `barriers_e2` Reaction barrier heights of E2 reactions `barriers_sn2` Reaction barrier heights of SN2 reactions `barriers_cycloadd` Reaction barrier heights of cycloaddition reactions `barriers_rdb7` Reaction barrier heights in the RDB7 dataset `barriers_rgd1` Reaction barrier heights in the RGD1-CNHO dataset `multi_molecule` UV/Vis peak absorption wavelengths in different solvents `ir` IR Spectra `pcqm4mv2` HOMO-LUMO gaps of the PCQM4Mv2 dataset `uncertainty_ensemble` Uncertainty estimation using an ensemble using the QM9 gap dataset `uncertainty_evidential` Uncertainty estimation using evidential learning using the QM9 gap dataset `uncertainty_mve` Uncertainty estimation using mean-variance estimation using the QM9 gap dataset `timing` Timing benchmark using subsets of QM9 gap
DOI: 10.5281/zenodo.10084755
title: Light Power Resource Variability for Energy Harvesting Photovoltaics for Self-Powered IoT
DOI: 10.5281/zenodo.10084754
title: Light Power Resource Variability for Energy Harvesting Photovoltaics for Self-Powered IoT
DOI: 10.5281/zenodo.8407169
title: Data from: Cu+ transient species mediate Cu catalyst reconstruction during CO2 electroreduction

description: Understanding metal surface reconstruction is of the uttermost importance in heterogeneous<br> catalysis as this phenomenon directly affects the nature of available active sites. However,<br> surface reconstruction is notoriously difficult to study because of the dynamic nature of the<br> phenomena behind it, particularly when solid/liquid interfaces are involved. Here, we report<br> on the intermediates which drive the rearrangement of copper catalysts for the electrochemical<br> CO2 reduction reaction (CO2RR). Online mass spectrometry and UV-Vis absorption<br> spectroscopy data are consistent with a dissolution–redeposition process, previously<br> demonstrated by in-situ electron microscopy. The data indicate that the soluble transient<br> species contain copper in +1 oxidation state. Density functional theory identifies copper adsorbate<br> complexes which can exist in solution under operating conditions. Copper carbonyls and oxalates are suggested as the major reaction-specific species driving copper reconstruction during CO2RR. This work motivates future methodological studies to enable the direct detection of these compounds and strategies which specifically target them to improve the catalyst operational stability.
DOI: 10.5281/zenodo.6724738
title: Data from: Cu+ transient species mediate Cu catalyst reconstruction during CO2 electroreduction

description: Understanding metal surface reconstruction is of the uttermost importance in heterogeneous
catalysis as this phenomenon directly affects the nature of available active sites. However,
surface reconstruction is notoriously difficult to study because of the dynamic nature of the
phenomena behind it, particularly when solid/liquid interfaces are involved. Here, we report
on the intermediates which drive the rearrangement of copper catalysts for the electrochemical
CO2 reduction reaction (CO2RR). Online mass spectrometry and UV-Vis absorption
spectroscopy data are consistent with a dissolution–redeposition process, previously
demonstrated by in-situ electron microscopy. The data indicate that the soluble transient
species contain copper in +1 oxidation state. Density functional theory identifies copper adsorbate
complexes which can exist in solution under operating conditions. Copper carbonyls and oxalates are suggested as the major reaction-specific species driving copper reconstruction during CO2RR. This work motivates future methodological studies to enable the direct detection of these compounds and strategies which specifically target them to improve the catalyst operational stability.
DOI: 10.5281/zenodo.6724739
title: Data from: Cu+ transient species mediate Cu catalyst reconstruction during CO2 electroreduction

description: Understanding metal surface reconstruction during operation is of the uttermost importance in heterogeneous catalysis as it directly affects the available active sites. However, surface reconstruction is notoriously difficult to study because of the dynamic nature of the phenomena behind it. Here, we report on the intermediates, which drive the rearrangement of copper catalysts during the electrochemical CO<sub>2</sub> reduction reaction (CO<sub>2</sub>RR). In-situ methods, including mass spectrometry and fluorescence spectroscopy, evidence a dissolution – redeposition process mediated by transient species containing copper in +1 oxidation state. Density functional theory simulations identify copper-adsorbate complexes which form in solution under operating conditions. Copper carbonyls and oxalates are suggested as the major reaction-specific species driving copper reconstruction during CO<sub>2</sub>RR. This work motivates future studies to confirm the identity of these compounds and specifically target them to improve the catalyst operational stability.
DOI: 10.5281/zenodo.8407241
title: Data from: Cu+ transient species mediate Cu catalyst reconstruction during CO2 electroreduction

description: Understanding metal surface reconstruction is of the uttermost importance in heterogeneous
catalysis as this phenomenon directly affects the nature of available active sites. However,
surface reconstruction is notoriously difficult to study because of the dynamic nature of the
phenomena behind it, particularly when solid/liquid interfaces are involved. Here, we report
on the intermediates which drive the rearrangement of copper catalysts for the electrochemical
CO2 reduction reaction (CO2RR). Online mass spectrometry and UV-Vis absorption
spectroscopy data are consistent with a dissolution–redeposition process, previously
demonstrated by in-situ electron microscopy. The data indicate that the soluble transient
species contain copper in +1 oxidation state. Density functional theory identifies copper adsorbate
complexes which can exist in solution under operating conditions. Copper carbonyls and oxalates are suggested as the major reaction-specific species driving copper reconstruction during CO2RR. This work motivates future methodological studies to enable the direct detection of these compounds and strategies which specifically target them to improve the catalyst operational stability.
DOI: 10.5281/zenodo.10086283
title: Gastric Neurotransmiss data Di Natale 2023

description: Data supporting Publication:  Di Natale et al, Characterization of neuromuscular transmission and projections of muscle motor neurons in the rat stomach
DOI: 10.5281/zenodo.10086284
title: Gastric Neurotransmiss data Di Natale 2023

description: Data supporting Publication:  Di Natale et al, Characterization of neuromuscular transmission and projections of muscle motor neurons in the rat stomach
DOI: 10.5281/zenodo.10014608
title: Combined continuous nanoparticle synthesis with chromatographic size classification

description: In this paper, we report a combination of the continuous flow synthesis of gold nanoparticles (AuNPs) with subsequent purification and narrowing of the particle size distribution (PSD) by size-exclusion chromatography (SEC) by adapting the flow rates of synthesis and classification. First, we show scalability of chromatographic classification with respect to column dimension and the absence of irreversible nanoparticle adhesion on the column material. Two different syntheses lead to a large and widely distributed and a small and narrowly distributed AuNP dispersion, which are classified by a semipreparative column. The PSDs of individual fractions are characterized by analytical SEC. The broadly distributed AuNP dispersion was classified into three fractions with distinct PSDs. For the narrowly distributed AuNPs, the separation is almost independent of the mobile phase flow rate: coarse and fine fractions with almost identical PSDs and separation efficiency curves are observed irrespective of the flow rate. Even NP samples with narrow PSDs can be classified into multiple fractions with tailored PSDs while simultaneously removing dissolved impurities from the dispersion. With our study, we demonstrate the potential of a direct combination of continuous NP synthesis with chromatographic classification for the optimization of final PSDs and the simultaneous purification of nanoparticulate dispersions.
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)– Project-ID 416229255 – SFB 1411
DOI: 10.5281/zenodo.10014607
title: Combined continuous nanoparticle synthesis with chromatographic size classification

description: In this paper, we report a combination of the continuous flow synthesis of gold nanoparticles (AuNPs) with subsequent purification and narrowing of the particle size distribution (PSD) by size-exclusion chromatography (SEC) by adapting the flow rates of synthesis and classification. First, we show scalability of chromatographic classification with respect to column dimension and the absence of irreversible nanoparticle adhesion on the column material. Two different syntheses lead to a large and widely distributed and a small and narrowly distributed AuNP dispersion, which are classified by a semipreparative column. The PSDs of individual fractions are characterized by analytical SEC. The broadly distributed AuNP dispersion was classified into three fractions with distinct PSDs. For the narrowly distributed AuNPs, the separation is almost independent of the mobile phase flow rate: coarse and fine fractions with almost identical PSDs and separation efficiency curves are observed irrespective of the flow rate. Even NP samples with narrow PSDs can be classified into multiple fractions with tailored PSDs while simultaneously removing dissolved impurities from the dispersion. With our study, we demonstrate the potential of a direct combination of continuous NP synthesis with chromatographic classification for the optimization of final PSDs and the simultaneous purification of nanoparticulate dispersions.
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)– Project-ID 416229255 – SFB 1411
DOI: 10.5281/zenodo.10089781
title: Hormone profiles of the African pygmy mouse Mus minutoides, a species with XY female sex reversal.
DOI: 10.5281/zenodo.10089782
title: Hormone profiles of the African pygmy mouse Mus minutoides, a species with XY female sex reversal.
DOI: 10.5281/zenodo.10089705
title: ShapeNet: An Information-Rich 3D Model Repository
DOI: 10.5281/zenodo.10089706
title: ShapeNet: An Information-Rich 3D Model Repository
DOI: 10.5281/zenodo.10089677
title: 32 mix_Post-column oxidation with EC cell

description: Qexactive HF
DOI: 10.5281/zenodo.10058129
title: MNIST dataset
DOI: 10.5281/zenodo.10058130
title: MNIST dataset
DOI: 10.5281/zenodo.10089676
title: 32 mix_Post-column oxidation with EC cell

description: Qexactive HF
DOI: 10.5281/zenodo.10089910
title: 32Mix_Postcolumn_Reduction_ECell

description: Q exactive HF
DOI: 10.5281/zenodo.10089911
title: 32Mix_Postcolumn_Reduction_ECell

description: Q exactive HF
DOI: 10.5281/zenodo.10089975
title: Tuebingen Compounds Library_Postcolumn_Reduction_ECell

description: Q exactive HF
DOI: 10.5281/zenodo.10089974
title: Tuebingen Compounds Library_Postcolumn_Reduction_ECell

description: Q exactive HF
DOI: 10.5281/zenodo.7994906
title: Low-frequency somatic mutations are heritable in plants

description: <strong>The Weismann theory (</strong><strong>1</strong><strong>) states that hereditary traits are transmitted exclusively from the germline. The theory is valid in many animals (</strong><strong>15</strong><strong>) where germline cells are set aside early in development (</strong><strong>1</strong><strong>). In plants, germline segregation is generally assumed to occur late in development (</strong><strong>2</strong><strong>,</strong><strong>4</strong><strong>,</strong><strong>10</strong><strong>), which leads to several predictions on the fate of mutations occurring in plant tissues: mutations have generally low frequency in plant tissues (</strong><strong>8</strong><strong>); mutations at high frequency have a higher chance of transmission; branching topology of the tree dictates mutation distribution (</strong><strong>9</strong><strong>); and, exposure to UV radiation increases mutagenesis (</strong><strong>18</strong><strong>). We produced new genomes for two tropical tree species from the Amazon rainforest and resequenced 60 tissue samples to identify 18,274 unique mutations, almost all at low tissue frequency. We show that: 1) low-frequency mutations are transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.</strong>
DOI: 10.5281/zenodo.7184983
title: Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter"

description: Full-length hCtr1 models used to perform classical molecular dynamics (MD) simulations described in the article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" by Aupič et al.


The zipped file contains three folders named alpha, beta and unfolded. Each contains the full-length all-atom model of the human copper transporter 1 (hCtr1) with the N-terminal domains in the alpha, beta or the unfolded conformational state. We provide both the initial model (initial-model.pdb) created with MODELLER (version 10.0) homology modelling software (B. Webb, A. Sali, Comparative Protein Structure Modeling Using MODELLER. Curr. Protoc. Bioinforma. 54, 5–6 (2016)) and the model structure embedded in the lipid bilayer as obtained after a 1 μs MD simulation (after-md.pdb).
DOI: 10.5281/zenodo.7184984
title: Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter"

description: Full-length hCtr1 models used to perform classical molecular dynamics (MD) simulations described in the article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" by Aupič et al.


The zipped file contains three folders named alpha, beta and unfolded. Each contains the full-length all-atom model of the human copper transporter 1 (hCtr1) with the N-terminal domains in the alpha, beta or the unfolded conformational state. We provide both the initial model (initial-model.pdb) created with MODELLER (version 10.0) homology modelling software (B. Webb, A. Sali, Comparative Protein Structure Modeling Using MODELLER. Curr. Protoc. Bioinforma. 54, 5–6 (2016)) and the model structure embedded in the lipid bilayer as obtained after a 1 μs MD simulation (after-md.pdb).
DOI: 10.5281/zenodo.10090342
title: Supplementary material to "Signalling molecules and extracellular DNA elicit chemotactic and regulatory responses in surface-associated Roseobacteraceae
DOI: 10.5281/zenodo.10090341
title: Supplementary material to "Signalling molecules and extracellular DNA elicit chemotactic and regulatory responses in surface-associated Roseobacteraceae
DOI: 10.5281/zenodo.7962145
title: ComplexEye - a multi lens array microscope for High-Throughput embedded immune cell migration analysis

description: This dataset contains raw high-resolution movies of migrating neutrophils, which were recorded using an array microscope with 16 independent aberration-corrected glass lenses spaced at the pitch of a 96-well plate.
DOI: 10.5281/zenodo.7962144
title: ComplexEye - a multi lens array microscope for High-Throughput embedded immune cell migration analysis

description: This dataset contains raw high-resolution movies of migrating neutrophils, which were recorded using the ComplexEye, an array microscope with 16 independent aberration-corrected glass lenses spaced at the pitch of a 96-well plate. Please see the manuscript "ComplexEye - a multi lens array microscope for High-Throughput embedded immune cell migration analysis" for more information.
The movies can be assigned to the following figures in the manuscript:

96-well_plate_movies_n=1_complexeye.zip: Figure 3a
96-well_plate_movies_n=1_leica.zip: Figure 3a
384-well_plate_movies_n=1_complexeye.zip: Figure 3b
384-well_plate_movies_n=16_complexeye.zip: Figure 3c
R01.zip - R17.zip: Figure 4 and 5
DOI: 10.5281/zenodo.10082674
title: ComplexEye - a multi lens array microscope for High-Throughput embedded immune cell migration analysis

description: This dataset contains raw high-resolution movies of migrating neutrophils, which were recorded using the ComplexEye, an array microscope with 16 independent aberration-corrected glass lenses spaced at the pitch of a 96-well plate. Please see the manuscript "ComplexEye - a multi lens array microscope for High-Throughput embedded immune cell migration analysis" for more information.
The movies can be assigned to the following figures in the manuscript:

96-well_plate_movies_n=1_complexeye.zip: Figure 3a
96-well_plate_movies_n=1_leica.zip: Figure 3a
384-well_plate_movies_n=1_complexeye.zip: Figure 3b
384-well_plate_movies_n=16_complexeye.zip: Figure 3c
R01.zip - R17.zip: Figure 4 and 5
DOI: 10.5281/zenodo.10057181
title: Jedeschule
DOI: 10.5281/zenodo.10066962
title: Exploring the Impact of SOD1 Transcript Variants on Amyotrophic Lateral Sclerosis

description: The database includes the raw data of the article "Exploring the Impact of SOD1 Transcript Variants on Amyotrophic Lateral Sclerosis". Aim of this work was to investigate the role of SOD1 transcripts in amyotrophic lateral sclerosis. The database contains the data obtained by the following evaluations:
 a) immunofluorescence analysis for the evaluation of total, transfected and endogenous SOD1 in transfected SHYSY5Y and Hela cells, b) Multiplex analysis for the evaluation of SOD1 transcripts in SYSY5Y cells and in PBMCs patients, c) correlation analysis for the correlation between SOD1 transcripts and ages of patients, ALSFRS_R value, PRB value and PRL value.
We found that the shortest transcript is upregulated in stress condition in both the cellular model and the patients' cells. Moreover, we found a possible correlation between the SOD1 short transcript and the severity of the pathology, which correlates also with the age of patients at symptoms onset. No correlation was found between SOD1 transcripts and the progression of the disease. Our data suggest a toxic effect of SOD1 short transcript in patients affects by amyotrophic lateral sclerosis.
DOI: 10.5281/zenodo.10066963
title: Exploring the Impact of SOD1 Transcript Variants on Amyotrophic Lateral Sclerosis

description: The database includes the raw data of the article "Exploring the Impact of SOD1 Transcript Variants on Amyotrophic Lateral Sclerosis". Aim of this work was to investigate the role of SOD1 transcripts in amyotrophic lateral sclerosis. The database contains the data obtained by the following evaluations:
 a) immunofluorescence analysis for the evaluation of total, transfected and endogenous SOD1 in transfected SHYSY5Y and Hela cells, b) Multiplex analysis for the evaluation of SOD1 transcripts in SYSY5Y cells and in PBMCs patients, c) correlation analysis for the correlation between SOD1 transcripts and ages of patients, ALSFRS_R value, PRB value and PRL value.
We found that the shortest transcript is upregulated in stress condition in both the cellular model and the patients' cells. Moreover, we found a possible correlation between the SOD1 short transcript and the severity of the pathology, which correlates also with the age of patients at symptoms onset. No correlation was found between SOD1 transcripts and the progression of the disease. Our data suggest a toxic effect of SOD1 short transcript in patients affects by amyotrophic lateral sclerosis.
DOI: 10.5281/zenodo.10090384
title: Example dataset to illustrate metric learning for ReID in maDLC

description: Example data to illustrate ReID transformer in Lauer et al. Nature Methods 2022. 
Link: https://www.nature.com/articles/s41592-022-01443-0
 
NOTE: This same data is also here: https://zenodo.org/records/7883589 (we realized this only afterwards)
DOI: 10.5281/zenodo.10090385
title: Example dataset to illustrate metric learning for ReID in maDLC

description: Example data to illustrate ReID transformer in Lauer et al. Nature Methods 2022. 
Link: https://www.nature.com/articles/s41592-022-01443-0
 
NOTE: This same data is also here: https://zenodo.org/records/7883589 (we realized this only afterwards)
DOI: 10.5281/zenodo.10057180
title: OPA
DOI: 10.5281/zenodo.10090402
title: OPA
DOI: 10.5281/zenodo.5148254
title: Jianyong Ma/BNF in grain legumes in LPJ-GUESS

description: This file contains the input data for model runs on global scale and the measured results for BNF evaluation at site scales presented in Geoscientific Model Development (GMD) paper: https://doi.org/10.5194/gmd-15-815-2022
DOI: 10.5281/zenodo.5148255
title: Jianyong Ma/BNF in grain legumes in LPJ-GUESS

description: This file contains the input data for model runs on global scale and the measured results for BNF evaluation at site scales presented in Geoscientific Model Development (GMD) paper: https://doi.org/10.5194/gmd-15-815-2022
DOI: 10.5517/ccdc.csd.cc2d9rzg
title: CCDC 2213926: Experimental Crystal Structure Determination

description: Related Article: Kakoli Malakar, Balasubramaniam Selvakumaran, Mariappan Murali, Pitchan Arul Prakash, Somasundaram Sangeetha, Winaki P. Sohtun, Mohamed Sultan Mohamed Jaabir, Marappan Velusamy|2023|New J.Chem.|47|20070|doi:10.1039/D2NJ06170H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.