cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10547538
title: data from: Genomic architecture controls multivariate adaptation to climate change

description: All data used for the 2024 study "Genomic architecture controls multivariate adaptation to climate change" by Drew E. Terasaki Hart and Ian J. Wang.

The study presents simulation results (created using [Geonomics](https://geonomics.readthedocs.io/)) across 18 simulation scenarios of interest, defined by the complete cross of 3 values of linkage (strong, weak, independent), 3 values of polygenicity (low, moderate, high) and 2 values of genotypic redundancy (low and high).

The archived data is a single zipfile comprising two subdirectories:



`output_100_final_for_analysis`, which contains all simulation outputs from each of the 100 main and null (i.e., control) iterations run for the high-genotypic-redundancy scenarios, and all identical outputs for the lo1-genotypic-redundancy scenarios:



3 CSV files:



a table of directional gene flow data, for all 9 main and 9 null scenarios for the given iteration's redundancy level (filename formatted as 'output_PID-<COMPUTE_PROCESS_ID>_DIR.csv')

 a table of summary statistic time series, for all 9 main and 9 null scenarios for the given iteration's redundancy level (filename formatted as 'output_PID-<COMPUTE_PROCESS_ID>_TS_DATA.csv'

a table of summary statistics (single values per iteration, rather than time series), for all 9 main and 9 null scenarios for the given iteration's redundancy level (filename formatted as 'output_PID-<COMPUTE_PROCESS_ID>_TS_DATA.csv'



a set of 180 directories (with names formatted as 'GNX_mod-<ITERATION_NULLNESS>_L<LINKAGE>_G<POLYGENICITY>_its0_randID<RANDOM_ID>_<COMPUTE_PROCESS_ID>'), generated by Geonomics, containing the automated CSV and VCF outputs produced by Geonomics.



`analysis` contains all analysis outputs (processed and summarized data, statistical tests, and figures) derived from that data and used to produce the results presented in the paper.
DOI: 10.21227/sbwe-k671
title: Hybrid Thermal Modeling with LPTN-Informed Neural Network for Multi-Node Temperature Estimation in PMSM

description: To achieve improved multi-node temperature estimation with limited training data in Permanent Magnet Synchronous Motors (PMSMs), a novel approach of a Lumped-Parameter Thermal Network (LPTN)-informed neural network is proposed in this paper. Firstly, the parameter and model uncertainties of third or higher-order LPTNs with global parameter identification for temperature estimation are systematically stated based on numerical analysis. Then, a two-step parameter identification strategy for a third-order LPTN with simplified thermal transfer paths is proposed to resolve parameter uncertainty. This strategy uses only air-gap structure information to make all parameters converge to their unique solutions without the need for additional geometrical parameters or material features. In response to model uncertainty, an LPTN-informed Long Short-Term Memory (LSTM) framework is designed to compensate for model unaccounted errors and extend temperature estimation nodes that the highly abstract low-order LPTN does not consider.Experimental temperature estimation results validate the effectiveness of the proposed LPTN-informed LSTM framework under a limited 23.8 hours of training data.
DOI: 10.6084/m9.figshare.24559522.v1
title: Digital cultural heritage museums

description: A concept for a tourist trail of digital cultural heritage in Poland
DOI: 10.6084/m9.figshare.8981924
title: Thermodynamic factor of quaternary mixtures from Kirkwood–Buff integration

description: Expressions for the thermodynamic factor matrix Γ of quaternary mixtures are derived in terms of Kirkwood–Buff integrals and implemented into the massively parallel simulation tool <i>ms</i>2. To assess these expressions, a liquid-like supercritical quaternary Lennard–Jones mixture is sampled throughout its entire composition range, employing molecular dynamics in the canonical ensemble. Good agreement is found between numerical chemical potential derivatives and the results from the present Kirkwood–Buff integral expressions. Moreover, the limits of the thermodynamic factor matrix for pure, binary and ternary subsystems are discussed.
DOI: 10.6084/m9.figshare.9164207
title: Studies on coherent and incoherent spin dynamics that control the magnetic field effect on photogenerated radical pairs

description: Since 1970s, magnetic field effects (MFEs) on photogenerated radical pairs have been the centre of focus in the field of spin chemistry. The MFE attributes to quantum mechanical interconversion between the singlet and triplet radical pair states and subsequent spin-selective recombination reactions. In this New View article, the author picks up two hot topics studied during the last two decades, which are (i) so-called low field effect (LFE) and (ii) 2<i>J</i>-resonance MFE on fixed distance donor–acceptor linked molecules. In both of the topics, quantum mechanical explanations are given referring to recent reports, and some novel calculations have been carried out for bridging theoretical and experimental data for long-lived radical pairs. For the first topic, time domain calculations of coherent state mixing have been carried out for elucidation of hyperfine (HF) structure dependence of the LFE. For the second topic, Monte Carlo simulations of the torsional motion of polyaromatic linker unit have been carried out for the demonstration of fast decoherence in such rigid molecules. From these considerations, future possibilities of MFE studies on photo-functional materials and biomolecules have been indicated.
DOI: 10.6084/m9.figshare.9164207.v2
title: Studies on coherent and incoherent spin dynamics that control the magnetic field effect on photogenerated radical pairs

description: Since 1970s, magnetic field effects (MFEs) on photogenerated radical pairs have been the centre of focus in the field of spin chemistry. The MFE attributes to quantum mechanical interconversion between the singlet and triplet radical pair states and subsequent spin-selective recombination reactions. In this New View article, the author picks up two hot topics studied during the last two decades, which are (i) so-called low field effect (LFE) and (ii) 2<i>J</i>-resonance MFE on fixed distance donor–acceptor linked molecules. In both of the topics, quantum mechanical explanations are given referring to recent reports, and some novel calculations have been carried out for bridging theoretical and experimental data for long-lived radical pairs. For the first topic, time domain calculations of coherent state mixing have been carried out for elucidation of hyperfine (HF) structure dependence of the LFE. For the second topic, Monte Carlo simulations of the torsional motion of polyaromatic linker unit have been carried out for the demonstration of fast decoherence in such rigid molecules. From these considerations, future possibilities of MFE studies on photo-functional materials and biomolecules have been indicated.
DOI: 10.6084/m9.figshare.8981924.v1
title: Thermodynamic factor of quaternary mixtures from Kirkwood–Buff integration

description: Expressions for the thermodynamic factor matrix Γ of quaternary mixtures are derived in terms of Kirkwood–Buff integrals and implemented into the massively parallel simulation tool <i>ms</i>2. To assess these expressions, a liquid-like supercritical quaternary Lennard–Jones mixture is sampled throughout its entire composition range, employing molecular dynamics in the canonical ensemble. Good agreement is found between numerical chemical potential derivatives and the results from the present Kirkwood–Buff integral expressions. Moreover, the limits of the thermodynamic factor matrix for pure, binary and ternary subsystems are discussed.
DOI: 10.6084/m9.figshare.9164207.v1
title: Studies on coherent and incoherent spin dynamics that control the magnetic field effect on photogenerated radical pairs

description: Since 1970s, magnetic field effects (MFEs) on photogenerated radical pairs have been the centre of focus in the field of spin chemistry. The MFE attributes to quantum mechanical interconversion between the singlet and triplet radical pair states and subsequent spin-selective recombination reactions. In this New View article, the author picks up two hot topics studied during the last two decades, which are (i) so-called low field effect (LFE) and (ii) 2<i>J</i>-resonance MFE on fixed distance donor–acceptor linked molecules. In both of the topics, quantum mechanical explanations are given referring to recent reports, and some novel calculations have been carried out for bridging theoretical and experimental data for long-lived radical pairs. For the first topic, time domain calculations of coherent state mixing have been carried out for elucidation of hyperfine (HF) structure dependence of the LFE. For the second topic, Monte Carlo simulations of the torsional motion of polyaromatic linker unit have been carried out for the demonstration of fast decoherence in such rigid molecules. From these considerations, future possibilities of MFE studies on photo-functional materials and biomolecules have been indicated.
DOI: 10.5281/zenodo.10397868
title: MD data for "CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism"

description: MD simulations for "Mengyuan Xu, Torben Neelands, Alexander S Powers, Yan Liu, Steven D Miller, Grigore Pintilie, J Du Bois, Ron O Dror, Wah Chiu, Merritt Maduke. CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. eLife (2023)"

 

Data provided as .psf and .dcd files for each simulation trajectory.
DOI: 10.5281/zenodo.10397869
title: MD data for "CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism"

description: MD simulations for "Mengyuan Xu, Torben Neelands, Alexander S Powers, Yan Liu, Steven D Miller, Grigore Pintilie, J Du Bois, Ron O Dror, Wah Chiu, Merritt Maduke. CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. eLife (2023)"

 

Data provided as .psf and .dcd files for each simulation trajectory.
DOI: 10.6084/m9.figshare.25038476
title: Supplementary Material for: Systematic Development of National Guidelines for Obesity Care: the Swedish Approach

description: Introduction: With the rapid development of treatment modalities for obesity management, there is a growing need for guidelines. This was acknowledged by the Swedish National Board of Health and Welfare and in 2020 the process of producing the first national guidelines for obesity care, including both children and adults, was initiated. The main aim was to ensure equal high standard care throughout Sweden by supporting decision makers to allocate resources to the best knowledge-based care. 
Methods: The standardized procedures of the National Board of Health and Welfare were applied to construct guidelines in a systematic and transparent way, including priority setting of recommendations and quality indicators to evaluate the progress of implementation. The process involved independent expert committees including professionals and patient representatives, and the guidelines were reviewed through an open public consultation. 
Results: In total, 20 recommendations were issued encompassing a broad scope, from identification and diagnosis to multiple treatment modalities, embedded in a life course perspective from pregnancy to the elderly, as well as highlighting the need for improved knowledge and competence of health care providers. 
Conclusions: National guidelines for improved standard care and evidence based and efficient use of health care resources for obesity treatment can be developed in a systematic way with professionals and patient representatives.
DOI: 10.6084/m9.figshare.24966534.v1
title: data.xlsx

description: In this study, a combination model of Convolutional Neural Network (CNN) and Light Gradient Boosting Machine (LightGBM) integrating multi-attraction search index was proposed, which performed feature extraction of historical tourist volume of the target attraction and multi-attraction internet search index by CNN, and utilized LightGBM to predict tourist volume of the Oriental Pearl TV Tower in Shanghai, China.
DOI: 10.5281/zenodo.10479388
title: Data for Paper "Analysis of Longitudinal Wrinkle Formation During Calendering of NMC811 Cathodes Under Variation of Different Process Parameters"

description: Dataset for paper 10.1007/s11740-023-01258-8
DOI: 10.5281/zenodo.10479389
title: Data for Paper "Analysis of Longitudinal Wrinkle Formation During Calendering of NMC811 Cathodes Under Variation of Different Process Parameters"

description: Dataset for paper 10.1007/s11740-023-01258-8
DOI: 10.6084/m9.figshare.25038494
title: Supplementary Material for: Catabolic network of the fermentative gut bacterium Phocaeicola vulgatus (phylum Bacteroidetes) from a physiologic-proteomic perspective

description: Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary fiber-fueled, fermentative metabolism the microbial community as well as the host health. To refine the current understanding of the P. vulgatus physiology, 14 different growth-supporting carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars, were selected for two major lines of investigation, which were based on substrate-adapted cells. Firstly, the range of growth performance was quantitatively assessed, revealing, e.g., doubling times [h] from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields [gCDW/mmolS] from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields [mMATP/mMC] from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one-sided (with rhamnose or fucose: mainly propane-1,2-diol). Secondly, based on proteogenomic analyses a fermentation network serving all tested compounds was reconstructed. This network is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate-specificity (e.g., conversion of arabinose to D-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. Taken together, insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols are provided.
DOI: 10.6084/m9.figshare.25038494.v1
title: Supplementary Material for: Catabolic network of the fermentative gut bacterium Phocaeicola vulgatus (phylum Bacteroidetes) from a physiologic-proteomic perspective

description: Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary fiber-fueled, fermentative metabolism the microbial community as well as the host health. To refine the current understanding of the P. vulgatus physiology, 14 different growth-supporting carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars, were selected for two major lines of investigation, which were based on substrate-adapted cells. Firstly, the range of growth performance was quantitatively assessed, revealing, e.g., doubling times [h] from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields [gCDW/mmolS] from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields [mMATP/mMC] from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one-sided (with rhamnose or fucose: mainly propane-1,2-diol). Secondly, based on proteogenomic analyses a fermentation network serving all tested compounds was reconstructed. This network is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate-specificity (e.g., conversion of arabinose to D-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. Taken together, insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols are provided.
DOI: 10.5281/zenodo.10547781
title: Three-dimensional simulation results of Perkins instability in the midlatitude F-region ionosphere

description: The simulated results for Perkins instability
DOI: 10.5281/zenodo.10159898
title: Three-dimensional simulation results of Perkins instability in the midlatitude F-region ionosphere

description: The simulated results for Perkins instability
DOI: 10.5281/zenodo.10159899
title: Three-dimensional simulation results of Perkins instability in the midlatitude F-region ionosphere

description: The simulated results for Perkins instability
DOI: 10.20372/aau_rd
title: Socio-Economic RD TEST
DOI: 10.15151/esrf-es-1409495605
title: iNEXT Discovery-Instruct ESRF-ERIC; Structural biology for translational research and discovery.

description: The aim of this proposal is to provide user access to automated protein-to-structure and fragment screening pipelines based on the combination of EMBL HTX lab services and CrystalDirect technology and automated data collection at ESRF’s MX beamlines. Access modalities will include 1) Online-Crystallography (Protein-to-Structure pipeline) 2) Large-Scale ligand and Fragment Screening and 3) new Plate-to-beam data collection modalities enabled by the integration of CrystalDirect at MASSIF1. User access to these modalities will require competitive application and peer-review through the E.C. funded iNEXT Discovery and Instruct-ERIC consortia. Moreover, new approaches for high density ligand screening will be implemented and the experimental opportunities enabled by the Integration of CrystalDirect at the MASSIF-1 station will be further developed. This work will be carried out in the context of international collaborative projects.
DOI: 10.15151/esrf-es-1409589257
title: Molecular machines in energy transduction, cellular signaling and defense processes

description: Since this BAG is composed of seven different working groups from three different locations (university of Cologne, university of Bochum, university of Düsseldorf), the projects for this proposal are of rather heterogeneous nature. Nonetheless, we are focusing on 5 main topics:
1.) proteins involved in transport processes, transporters or channels, either embedded in the membrane or acting in the cytosol (e.g. ABC transporters, fusion proteins, regulators)
2.) proteins involved in the immune system, pathogen invasion or defense/resistance processes (dehydratases, toxins, binding proteins)
3.) proteins involved or associated with diseases like cancer or developmental disorders (e.g. protein kinase, toxins, antibodies)
4.) enzymes of putative industrial use to encounter increasing environmental pollution (e.g. transaminases, estereases)
5.) proteins involved in light harvesting, photosynthesis (C3/C4 pathways) and chromophore binding proteins (e.g. synthases, photosensor domains)
DOI: 10.15151/esrf-es-1428654017
title: CO2 uptake/retention/release by an iron cation-exchanged clay mineral

description: Previously our group found, that the synthetic clay mineral Ni-Fluorohectorite (Ni-Hec, where Ni2+ is the charge-compensating cation in the clay interlayer) is competitive with alternative materials (MOFs, activated carbon etc.) with respect to CO2 volumetric adsorption capacity. It was also recently demonstrated that the CO2 adsorption mechanism in Ni-Hec is due to an intercalated nickel hydroxide species, and that Ni-Hec with lower charge layer adsorbs more CO2 and at lower pressure compared to higher layer charges. Recently we in addition found that Fe3+ or Fe2+ (instead of Ni2+) demonstrate CO2 interaction similar to Ni-Hec. In this proposed experiment we want to do a detailed temperature-pressure study of Fe-Hec powders. Fe is particularly interesting here because it is much more abundant and available than Ni and has much less environmental concerns. The experiment will study prepared Fe-Mt powder samples.
DOI: 10.15151/esrf-es-1428654043
title: Temporomandibular Joint 3D-investigation for the development of bio inspired scaffold materials

description: The temporomandibular joint (TMJ) is responsible for chewing movements, sound articulation, facial expression, and facial symmetry. Therefore, dysfunction in this joint leads to issues in food intake, aesthetics, and communication besides causing high levels of pain in the individual. The few treatments available for TMJ disorders comprise the administration of intra-articular injections, which can result in TMJ degeneration and the need for a joint replacement using commercially available faulty prostheses. The present work aims to characterize the intricate anatomic structure of human TMJs by using hierarchical phase-contrast tomography. Data collection will be essential to our Horizon 2020 project (http://www.interlynk-h2020.eu/) which targets creating scaffolds for improving TMJ replacements. The collected images will be used to enable the creation of bio-inspired, more efficient TMJ replacements in the future.
DOI: 10.15151/esrf-es-1428654668
title: Unravelling "explosion upon melting" mechanism through SAXS-XPCS investigation of induction-heated Fe-nanoparticles filled UHMWPE

description: We aim to characterize the structure evolution of highly industrially relevant Ultra High Molecular Weight Polyethylene (UHMWPE) during fast-sintering through an innovative heating method: magnetic hyperthermia. By combining SAXS, XPCS, thermal imaging and induction heating of responsive particles, our experiments aim to bring decisive insights to apprehend the “explosion upon melting” phenomenon predicted by de Gennes in 1995.
DOI: 10.15151/esrf-es-1428656386
title: Tracking the temperature dependence of paramagnons in cuprate supeconductors

description: Among the others, spin fluctuations are considered as the most promising candidate to mediate the pairing interaction in high Tc superconducting cuprates. The role of spin is nonetheless still debated, particularly as for the interplay with other degrees of freedom. Although high energy paramagnon excitations have been vastly studied in their doping dependence with RIXS, a temperature dependence study across the phase diagram is still missing. In this regard, we hereby propose to perform a full temperature dependence study of YBa2Cu3O7-δ samples at two distinct doping, also exploiting the unique capability of ID32 to measure the scattered photons polarization to disentangle the spin temperature effects to the charge excitations. If successful the experiment will represent the first study of high energy paramagnetic excitations across the superconducting transition in a cuprate superconductor, elucidating further their role in the unconventional pairing of these systems.