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New items activated in the SLUB catalog in 2023

The data set is available as a gzip-compressed, line-delimited JSON file and contains the 21,137 documents with new items activated in the <a href="https://katalog.slub-dresden.de/">SLUB catalog</a> in 2023 with the fields id (document identifier), rsn_id_str_mv (record serial number), de14_new_item_act_date (timestamp) and de14_new_item_act_date_mv (timestamps). The id consists of a source id and a record id according to the scheme {source_id}-{record_id} and enables the detailed view of a document to be retrieved using the following URL scheme: https://katalog.slub-dresden.de/id/{id}. Example: <a href="https://katalog.slub-dresden.de/id/0-185178604X">https://katalog.slub-dresden.de/id/0-185178604X</a>. Since the documents in this data set originate exclusively from the Southwest German Library Network (SWB), the source id is always 0 and the record id corresponds to the Pica Production Number (PPN) of the K10plus. The value for the field rsn_id_str_mv is based on the RSN field of the corresponding title in the Libero Library Management System, it is additionally prefixed with DE-14, i.e. the ISIL identifier of the SLUB. The multi-valued string field is a dynamic field according to VuFind's Solr index schema. The RSN value also enables the detailed view of a document to be retrieved using the following URL scheme: https://katalog.slub-dresden.de/rsn/{rsn}. Example: <a href="https://katalog.slub-dresden.de/rsn/16992029">https://katalog.slub-dresden.de/rsn/16992029</a>. The values for the fields de14_new_item_act_date and de14_new_item_act_date_mv are based on the NewItemActDate field of the corresponding items in the Libero LMS. While the multi-valued field de14_new_item_act_date_mv contains all dates from the year 2023 that could be assigned to a document, only the most recent date is specified in the field de14_new_item_act_date. Both fields are dynamic fields according to VuFind's Solr index schema. Until January 2021, the date values were used to display a list of new acquisitions on the SLUB website.

opencc-by-4.0Jan 2024View details →

Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane models

This dataset presents a comprehensive collection of input data for Molecular Dynamics (MD) simulations performed using the GROMACS simulation software. The included systems cover various membrane environments, each with distinctive properties. The systems consist of: <ol> <li>IM (Inner Membrane): Simulations involving the bacteral mimicking inner membrane environment.</li> <li>IM_OM (Inner Membrane and Outer Membrane Complex): Complex systems encompassing both inner and outer bacterial membrane models.</li> <li>OM_D (Double Symmetric Outer Membrane): Simulations featuring a symmetric outer membrane structure.</li> <li>OM (Asymmetric Outer Membrane): Simulations with an asymmetric outer membrane configuration.</li> <li>PC Membrane (Phosphatidylcholine Membrane): Simulations involving membranes composed of phosphatidylcholine.</li> </ol> For each membrane type, the dataset provides three replicas. The dataset includes initial and final structures (.gro files), simulation parameter files (.mdp), index files (.ndx), and topology files (.itp and .top) applicable to all systems.

opencc-by-4.0Mar 2024View details →

Figure 4 in Grafting increases superoxide dismutase and catalase activity to overcome the impact of the two-spotted spider mite on eggplant growth and productivity

Figure 4 Influence of TSSM infestation density on CAT (A) and SOD (B) enzyme activities, as well

opencc-by-4.0Mar 2024View details →

Figure 2 in Grafting increases superoxide dismutase and catalase activity to overcome the impact of the two-spotted spider mite on eggplant growth and productivity

Figure 2 Average total number of TSSM in grafted and non-grafted eggplants. Means followed by

Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin

Pharmacological activation of hypoxia-inducible factor 1alpha (HIF-1α), a hypoxia-responsive transcription factor, has attracted increasing attention due to its efficacy not only in renal anemia but also in various disease models. Our study demonstrated that a HIF-1 activator enhanced exosome production from cultured endothelial cells synergistically with adiponectin, an adipocyte-derived factor, through both transcriptional induction and posttranscriptional stabilization of an adiponectin binding partner, T-cadherin. Increased exosome levels were observed in wild-type mice but not in T-cadherin null mice after consecutive administration of roxadustat. Adiponectin- and T-cadherin-dependent increased exosome production may be involved in the pleiotropic effects of HIF-1 activators.

opencc-by-4.0Jan 2024View details →

Data to "Cardiopulmonary exercise testing complements both spirometry and nuclear imaging for assessing sarcoidosis disease stage and for monitoring disease activity"

This record contains analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in: Torregiani, C., Reale, M., Confalonieri, M., Dore, F., Crisafulli, C., Baratella, E., ... & Maiello, G. (2024). Cardiopulmonary exercise testing complements both spirometry and nuclear imaging for assessing sarcoidosis stage and for monitoring disease activity. Sarcoidosis, Vasculitis, and Diffuse Lung Diseases, 41(1), e2024017-e2024017. https://doi.org/10.36141/svdld.v41i1.15125

Monosaccharide transporter OsMST6 is activated by transcription factor OsERF120 to enhance chilling tolerance in rice seedlings

Chilling stress caused by extreme weather is threatening global rice (Oryza sativa L.) production. Identifying components of the signal transduction pathways underlying chilling tolerance in rice would advance molecular breeding. Here, we report that OsMST6, which encodes a monosaccharide transporter, positively regulates the chilling tolerance of rice seedlings. The mst6 mutants showed hypersensitivity to chilling, while the OsMST6 overexpression lines were tolerant. During chilling stress, OsMST6 transported more glucose into cells to modulate sugar and ABA signal pathways. We showed that the transcription factor OsERF120 could bind to the DRE/CRT element of the OsMST6 promoter and activate the expression of OsMST6 to positively regulate chilling tolerance. Genetically, OsERF120 was functionally dependent on OsMST6 when promoting chilling tolerance. In summary, OsERF120 and OsMST6 form a new downstream chilling regulatory pathway in rice in response to chilling stress, providing valuable findings for molecular breeding aimed at achieving global food security. The stored data is the analysis results of transcriptome data from ZH11 and mst6-1 after 0 hours and 4 hours of chilling treatment. These data form the basis for the transcriptome data visualization in the article.

opencc-by-4.0Apr 2024View details →

Raman spectra from "Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model"

The uploaded files are data from Chaudhary et al, 2021 (Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model, https://doi.org/10.1016/j.saa.2020.119118). There are two files in .mat format. In one (Preprocessed.mat) the data has been completely pre-processed according to the methods described in the paper. In the second (Unpreprocessed.mat) the data has been calibrated using the methods described in the paper, but has not received further pre-processing. Within both files there are datasets for the spectral measurement from each cell (‘spectra’), together with the treatment which was applied to each sample (‘treatment’) and the wavenumber at which the spectral measurements were made (‘wavenumber’).

opencc-by-sa-4.0Apr 2024View details →

"Volcanoes and Seismic Activity Dataset"

El datset “Volcanoes and Seismic Activity Dataset” és el resultat de la PRA1 de l'assignatura de Tipologia i Cicle de Vida de les Dades, del Màster de Ciència de Dades de la UOC. El conjut de dades s'ha generat en aplicació de técniques de web scraping a la pàgina web https://www.volcanodiscovery.com/volcanoes.html, completant el registre de tots els volcans de la pàgina web, certes caracteristiques com d'ubicació, estat i morfologia bàsica i els darrers sísmes asociats a cadascún d'ells a la data dels raspat.  El total de volcans únics registrats és de 2.070. El total de registres del dataset és de 3.416. Cada volcà pot tenir diferents sísme associats.  El total de camps del dataset és de 10. Descripció dels camps: <ul> <li> Name (nom): Inclou el nom del volcà. </li> <li> URL (enllaç): Inclou els enllaços a la pàgina de cada volcà. </li> <li> Type/Height (tipus i altura): Inclou el tipus de volcà (segons morfologia) i la seva altura en metres (m) i peus (ft). </li> <li> Status (estat): Inclou l’estat del volcà, és a dir, si és un volcà actiu, extingit, i el seu grau d’activació en escala Likert del 0 (extingit) al 5 (actiu). </li> <li> Territory/Geolocation (Territori/coordenades geolocalització): Inclou la regió on es troba el volcà i les coordenades de localització. </li> <li> Eruption style (tipus d’erupcions): Inclou el tipus d’erupció observada per cada volcà. En alguns casos, pot incloure més d’un estil d’erupció. </li> <li> Earthquake date (data del terratrèmol): Si el volcà té un terratrèmol associat, la data i l’hora en què va passar el terratrèmol. En alguns casos, indica també els dies que fa des de la seva ocurrència prenent com a referència el moment en què es va realitzar l’scraping. </li> <li> Magnitude/Depth (magnitud/profunditat): Inclou la magnitud i la profunditat del terratrèmol. Cal separar els dos valors en una posterior neteja de les dades: les dues primeres xifres, normalment separades per un punt, fan referència a la magnitud i les últimes xifres, a la profunditat (ex. 3.4205 km es correspondria a una magnitud de 3.4 i una profunditat de 205 km). </li> <li> Distance (distància): Inclou la distància del terratrèmol respecte del volcà i la direcció. </li> <li> Earthquake location (ubicació del terratrèmol): Inclou el país/estat i l’àrea o regió on s’ha donat el terratrèmol. </li> </ul>

opencc-by-4.0Jul 2023View details →

A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice

Raw Data for An atypical phosphoswitch in specific neurons of the suprachiasmatic nucleus gates locomotor activity at the light/dark transition in mice <ol> <li>Multi-electrode array data from PiT2+/+ and PiT2-/- mice</li> <li>Locomotor activity from PiT2+/+ and PiT2-/- mice in LD 12:12, DD, LD 4:20, LD 20:4 and DD with light pulses</li> <li>Phosphoproteome data</li> </ol>

opencc-by-4.0Apr 2024View details →

Utilization of outdoor spaces for specific activities (Barcelona, Rotterdam, Gothenburg): ratings and reasoning

What outdoor spaces are more likely to be used for different activities? In this repository, we share the data we collected and analysed to explore the impact of physical characteristics of outdoor spaces on the probability of utilization across diverse individuals, considering various age and gender groups. To collect this data we performed a crowdsourcing campaign. We recruited 409 participants from 21 European countries. To ensure a diverse range of outdoor spaces’ physical characteristics, our selection includes a range of spaces such as public squares, open marketplaces, greenspaces, pocket parks, play spaces, and streets, sourced from three European cities: Rotterdam, Barcelona, and Gothenburg. In our experiments, we presented to participants five different outdoor spaces and asked them to indicate to what degree, and why, they consider them suitable for any of the aforementioned activities. In total we collected data for 413 spaces representing 102 public open spaces, 107 streets, 114 greenspaces, 91 pocket parks, and 84 play spaces. In particular this dataset includes: <ul> <li>9700 ratings of outdoor spaces likely use for different activities (Likert scale 1-5)</li> <li>6388 short explanations of these ratings</li> <li>Each space is assigned a geolocation and a gsv_id which links this location to its corresponding google street view image</li> </ul>

opencc-by-4.0Apr 2024View details →

A Conserved Inhibitory Interdomain Interaction Regulates DNA-binding Activities of Hybrid Two-component Systems in Bacteroides

The study reveals a highly conserved inhibitory mechanism to regulate the activities of hybrid two-component systems (HTCSs) in Bacteroides. HTCSs comprise a major class of transcription regulators of polysaccharide utilization genes in Bacteroides. A conserved sequence motif has been discovered to correlate with the interdomain arrangement of HTCS domains. Presence or absence of this motif is likely predictive of the regulatory mechanism evolved for utilization of different glycans.   This dataset includes sequence analyses and structure predictions of HTCSs. List of files: ·        AlphaFold-HTCS-RR.zip                             AlphaFold results of all HTCS-RR fragments in B. theta ·        AlphaFold-HTCS-cyto-dimer.zip                AlphaFold results of all HTCS-cyto dimers in B. theta ·        HTCSbacteroides-MAFFT-fasta                  Sequence alignment of 6908 HTCSs from Bacteroides ·        HMM-AllHTCS.hmm                                  HMM of HTCSs generated from the MAFFT alignment ·        HMM-DBD-PF12833                                 HMM of HTH18 (Pfam: PF12833) from Interpro ·        HMM-REC-PF00072                                  HMM of REC (Pfam: PF00072) from Interpro ·        B_theta_RR_fasta                                       Sequence alignment of 32 HTCS-RRs in B. theta ·        B_theta_RR-tree                                         A neighbor-joining phylogenetic tree of 32 HTCS-RRs in B. theta

Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

PfRH5-induced human monoclonal antibodies show broadly neutralizing activity in P. falciparum clinical isolates

Vaccines to the Plasmodium falciparum reticulocyte binding-like protein homolog 5 (PfRH5) target the blood stage of the parasite's life cycle. PfRH5 has the potential to trigger the production of strain-transcendent antibodies and has proven its efficacy both in pre-clinical and early clinical studies. Vaccine-induced monoclonal antibodies (mAbs) to PfRH5 showed promising outcomes in cultured P. falciparum strains from distinct geographic areas. Here, we assessed the functional impact of vaccine-induced mAbs to PfRH5 on the genetically more complex P. falciparum clinical isolates. We used mAbs isolated from single-cell sorted B-cells of volunteers enrolled in the phase 1a (NCT02181088) clinical trial of the viral-vectored PfRH5 vaccine and used ex-vivo growth inhibition assays (GIA) to assess their efficacy in P. falciparum clinical isolates. Next-generation sequencing (NGS) was used to assess the breadth of genetic diversity in P. falciparum clinical isolates and to infer the genotype/phenotype relationship involved in antibody susceptibility. We showed a dose-dependent inhibition of clinical isolates with three main GIA groups, high, medium, and low. Except for one isolate, our data shows no significant differences in antibody GIA profile between the P. falciparum clinical isolates and the 3D7 reference strain, which harbours the vaccine allele. We observed an additive relationship, where the combination of GIA-low and GIA-medium antibodies resulted in increased GIA activities, having important implications for the contribution of specific monoclonal antibodies in polyclonal IgG responses. While our NGS analysis showed the occurrence of novel mutations in the pfrh5 gene, these mutations were predicted to have little or no functional impact on the antigen's structure or recognition by known mAbs. Our present findings complement earlier reports on the strain transcendent potential of mAbs to PfRH5 and constitute, to our knowledge, the first report on the susceptibility of P. falciparum clinical isolates from natural infections to vaccine-induced mAbs to PfRH5.

Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 02)

Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. Instruction The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example, `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` They can be decompressed with  `cat Nolig_Respawn00a.tar.* | tar xzpvf -`     Remarks <ul> <li>Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.</li> <li>There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest</li> <li>For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. </li> </ul>   Please cite us if you find this data useful!

Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 03)

Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. Instruction The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example, `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` They can be decompressed with  `cat Nolig_Respawn00a.tar.* | tar xzpvf -`   Remarks <ul> <li>Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.</li> <li>There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest</li> <li>For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. </li> </ul>   Please cite us if you find this data useful!

Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 01)

Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. Instruction The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example, `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` They can be decompressed with  `cat Nolig_Respawn00a.tar.* | tar xzpvf -`   Remarks <ul> <li>Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.</li> <li>There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest</li> <li>For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. </li> </ul> Please cite us if you find this data useful!

Light curves included in "Broad-Line Region Characterization in Dozens of Active Galactic Nuclei Using Small-Aperture Telescopes"

This repository is for the paper "Broad-Line Region Characterization in Dozens of Active Galactic Nuclei Using Small-Aperture Telescopes" by Catalina Sobrino Figaredo. It is associated with the manuscript number AAS557954. Table Information: EXTNAME: Name as a combination of the object name and the year of observation (e.g., HE2128-0221_YEAR=2016) Columns: MJD: Modified Julian Date FLUX: Flux in mJy ERRFLUX: Flux uncertainty in mJy FILTER: The observation filter (B_j, V_j, r_s, R_j, 670, 680, 690, SII)

Supplementary Table 1 Interview flow and description of activities

Supplementary table 1

Spatiotemporal dynamics of grassland aboveground biomass in northern China and the alpine region: Impacts of climate change and human activities

We employed CASA model to estimate grassland Net Primary Productivity and aboveground biomass A(AGB) from meteorological and GIMMS Normalized Difference Vegetation Index (NDVI) remote sensing  data in northern China. We analyzed the dynamics of grassland AGB and impacts climate change and human activites.