cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22209646
title: Supplementary Material for: A genetic risk score distinguishes different types of autoantibody mediated membranous nephropathy

description: =Introduction: Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults and is characterized by detectable autoantibodies against glomerular antigens, most commonly phospholipase A2 receptor-1 (PLA2R1) and thrombospondin type-1 domain containing 7A (THSD7A). In Europeans genetic variation in at least five loci, PLA2R1, HLA-DRB1, HLA-DQA1, IRF4 and NFKB1 affect the risk of disease. Here, we investigated the genetic risk differences between different autoantibody states. Methods: 1409 MN individuals were genotyped genome-wide with a dense SNV array. The genetic risk score (GRS) was calculated utilising the previously identified European MN loci and results were compared with 4929 healthy controls and 422 individuals with steroid sensitive nephrotic syndrome. Results: GRS was calculated in the 759 MN individuals in whom antibody status was known. The GRS for MN was elevated in the anti-PLA2R1 antibody positive (N=372) compared with both the unaffected control (N=4929) and anti-THSD7A positive (N=31) groups (p&lt;0.0001 for both comparisons), suggesting that this GRS reflects anti-PLA2R1 MN. Among PLA2R1 positive patients, GRS was inversely correlated with age of disease onset (p=0.009). Further, the GRS in the dual antibody negative group (N=355) was intermediate between controls and the PLA2R1 positive group (p&lt;0.0001). Conclusion: We demonstrate that the genetic risk factors for PLA2R1- and THSD7A-antibody associated MN are different. A higher GRS is associated with younger age of onset of disease. Further, a proportion of antibody negative MN cases have an elevated GRS similar to PLA2R1-positive disease. This suggests that in some individuals with negative serology the disease is driven by autoimmunity against PLA2R1.
DOI: 10.6084/m9.figshare.22209646.v1
title: Supplementary Material for: A genetic risk score distinguishes different types of autoantibody mediated membranous nephropathy

description: =Introduction: Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults and is characterized by detectable autoantibodies against glomerular antigens, most commonly phospholipase A2 receptor-1 (PLA2R1) and thrombospondin type-1 domain containing 7A (THSD7A). In Europeans genetic variation in at least five loci, PLA2R1, HLA-DRB1, HLA-DQA1, IRF4 and NFKB1 affect the risk of disease. Here, we investigated the genetic risk differences between different autoantibody states. Methods: 1409 MN individuals were genotyped genome-wide with a dense SNV array. The genetic risk score (GRS) was calculated utilising the previously identified European MN loci and results were compared with 4929 healthy controls and 422 individuals with steroid sensitive nephrotic syndrome. Results: GRS was calculated in the 759 MN individuals in whom antibody status was known. The GRS for MN was elevated in the anti-PLA2R1 antibody positive (N=372) compared with both the unaffected control (N=4929) and anti-THSD7A positive (N=31) groups (p&lt;0.0001 for both comparisons), suggesting that this GRS reflects anti-PLA2R1 MN. Among PLA2R1 positive patients, GRS was inversely correlated with age of disease onset (p=0.009). Further, the GRS in the dual antibody negative group (N=355) was intermediate between controls and the PLA2R1 positive group (p&lt;0.0001). Conclusion: We demonstrate that the genetic risk factors for PLA2R1- and THSD7A-antibody associated MN are different. A higher GRS is associated with younger age of onset of disease. Further, a proportion of antibody negative MN cases have an elevated GRS similar to PLA2R1-positive disease. This suggests that in some individuals with negative serology the disease is driven by autoimmunity against PLA2R1.
DOI: 10.6084/m9.figshare.22209652
title: Supplementary Material for: A genetic risk score distinguishes different types of autoantibody mediated membranous nephropathy

description: =Introduction: Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults and is characterized by detectable autoantibodies against glomerular antigens, most commonly phospholipase A2 receptor-1 (PLA2R1) and thrombospondin type-1 domain containing 7A (THSD7A). In Europeans genetic variation in at least five loci, PLA2R1, HLA-DRB1, HLA-DQA1, IRF4 and NFKB1 affect the risk of disease. Here, we investigated the genetic risk differences between different autoantibody states. Methods: 1409 MN individuals were genotyped genome-wide with a dense SNV array. The genetic risk score (GRS) was calculated utilising the previously identified European MN loci and results were compared with 4929 healthy controls and 422 individuals with steroid sensitive nephrotic syndrome. Results: GRS was calculated in the 759 MN individuals in whom antibody status was known. The GRS for MN was elevated in the anti-PLA2R1 antibody positive (N=372) compared with both the unaffected control (N=4929) and anti-THSD7A positive (N=31) groups (p&lt;0.0001 for both comparisons), suggesting that this GRS reflects anti-PLA2R1 MN. Among PLA2R1 positive patients, GRS was inversely correlated with age of disease onset (p=0.009). Further, the GRS in the dual antibody negative group (N=355) was intermediate between controls and the PLA2R1 positive group (p&lt;0.0001). Conclusion: We demonstrate that the genetic risk factors for PLA2R1- and THSD7A-antibody associated MN are different. A higher GRS is associated with younger age of onset of disease. Further, a proportion of antibody negative MN cases have an elevated GRS similar to PLA2R1-positive disease. This suggests that in some individuals with negative serology the disease is driven by autoimmunity against PLA2R1.
DOI: 10.6084/m9.figshare.22209652.v1
title: Supplementary Material for: A genetic risk score distinguishes different types of autoantibody mediated membranous nephropathy

description: =Introduction: Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults and is characterized by detectable autoantibodies against glomerular antigens, most commonly phospholipase A2 receptor-1 (PLA2R1) and thrombospondin type-1 domain containing 7A (THSD7A). In Europeans genetic variation in at least five loci, PLA2R1, HLA-DRB1, HLA-DQA1, IRF4 and NFKB1 affect the risk of disease. Here, we investigated the genetic risk differences between different autoantibody states. Methods: 1409 MN individuals were genotyped genome-wide with a dense SNV array. The genetic risk score (GRS) was calculated utilising the previously identified European MN loci and results were compared with 4929 healthy controls and 422 individuals with steroid sensitive nephrotic syndrome. Results: GRS was calculated in the 759 MN individuals in whom antibody status was known. The GRS for MN was elevated in the anti-PLA2R1 antibody positive (N=372) compared with both the unaffected control (N=4929) and anti-THSD7A positive (N=31) groups (p&lt;0.0001 for both comparisons), suggesting that this GRS reflects anti-PLA2R1 MN. Among PLA2R1 positive patients, GRS was inversely correlated with age of disease onset (p=0.009). Further, the GRS in the dual antibody negative group (N=355) was intermediate between controls and the PLA2R1 positive group (p&lt;0.0001). Conclusion: We demonstrate that the genetic risk factors for PLA2R1- and THSD7A-antibody associated MN are different. A higher GRS is associated with younger age of onset of disease. Further, a proportion of antibody negative MN cases have an elevated GRS similar to PLA2R1-positive disease. This suggests that in some individuals with negative serology the disease is driven by autoimmunity against PLA2R1.
DOI: 10.5281/zenodo.7672960
title: SebaSchuetz/DEMETO_Dryer: DEMETO - Dryer - Repository

description: European Union's Horizon 2020 research and innovation programme, No 768573, project DEMETO
DOI: 10.6084/m9.figshare.20407857.v5
title: CScat

description: The global long-term satellite radar backscatter dataset created by merging ERS, QSCAT, and ASCAT.
DOI: 10.6084/m9.figshare.20284713.v9
title: Data availability for Mirusviricota and the GOEV database

description: Data availability includes supplemental tables, FASTA files corresponding to the GOEV genomic database, genes, proteins, predicted 3D protein structure, and phylogenetic trees with theiur associated metadata. This data availability also includes a folder for all to Mirusviricota MAGs.
DOI: 10.5281/zenodo.7692961
title: AuTexTification

description: Training datasets for the AuTexTification shared task at IberLEF 2023. This task aims to boost research on the detection of text generated automatically by text generation models. Participants must develop models that exploit clues about linguistic form and meaning to distinguish automatically generated text from human text. It consists of two tasks, both for English and Spanish: 1) Generated or Human: determine whether the text has been automatically generated or not. 2) Model Attribution: determine what language model generated a text.
DOI: 10.5281/zenodo.7692960
title: AuTexTification

description: Training datasets for the AuTexTification shared task at IberLEF 2023. This task aims to boost research on the detection of text generated automatically by text generation models. Participants must develop models that exploit clues about linguistic form and meaning to distinguish automatically generated text from human text. It consists of two tasks, both for English and Spanish: 1) Generated or Human: determine whether the text has been automatically generated or not. 2) Model Attribution: determine what language model generated a text.
DOI: 10.6084/m9.figshare.22209679
title: Bacterial community analysis identifies K. pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

description: <strong>Background</strong>: The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism’s growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, our study aimed to determine the oral and skin microbiomes of newborn <em>Protobothrops mucrosquamatus</em> (<em>P. mucrosquamatus</em>)<em>.</em> <strong>Results:</strong> In terms of the oral and skin microbiome, the main species were <em>Klebsiella pneumoniae </em>(<em>K. pneumoniae</em>) linkages. According to subspecies/species analysis, the proportion from high to low was <em>K. quasipneumoniae</em> subsp. Similipneumoniae, <em>K. pneumoniae</em> subsp. Pneumoniae, and <em>K. pneumoniae</em> subsp. Rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of skin and oral activity, respectively. The oral microbiome of newborn<em> P. mucrosquamatus</em> did not investigate the common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the habitat environment or prey. Functional Annotation of the Prokaryotic Taxa (FAPROTAX) analysis showed that microbiome metabolism was related to human infection and intestinal bacteria owing to the dominance of <em>K. pneumoniae</em> linkages. Fermentation was predicted in this study. The characteristics of <em>K. pneumoniae </em>may impact the development of venom in venomous snakes. <strong>Conclusion:</strong> The results of the native microbiome in the oral cavity and skin of newborn <em>P. mucrosquamatus</em> demonstrated that the habitat environment and prey capture would affect the composition of bacteria in adult snakes. This explains why soil-associated bacteria and Enterobacter were dominant in the oral and skin microbiomes of adult snakes. We hypothesised that the native microbiome influences newborn venomous snakes and that <em>K. pneumoniae</em> linkages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.
DOI: 10.6084/m9.figshare.22209679.v1
title: Bacterial community analysis identifies K. pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

description: <strong>Background</strong>: The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism’s growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, our study aimed to determine the oral and skin microbiomes of newborn <em>Protobothrops mucrosquamatus</em> (<em>P. mucrosquamatus</em>)<em>.</em> <strong>Results:</strong> In terms of the oral and skin microbiome, the main species were <em>Klebsiella pneumoniae </em>(<em>K. pneumoniae</em>) linkages. According to subspecies/species analysis, the proportion from high to low was <em>K. quasipneumoniae</em> subsp. Similipneumoniae, <em>K. pneumoniae</em> subsp. Pneumoniae, and <em>K. pneumoniae</em> subsp. Rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of skin and oral activity, respectively. The oral microbiome of newborn<em> P. mucrosquamatus</em> did not investigate the common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the habitat environment or prey. Functional Annotation of the Prokaryotic Taxa (FAPROTAX) analysis showed that microbiome metabolism was related to human infection and intestinal bacteria owing to the dominance of <em>K. pneumoniae</em> linkages. Fermentation was predicted in this study. The characteristics of <em>K. pneumoniae </em>may impact the development of venom in venomous snakes. <strong>Conclusion:</strong> The results of the native microbiome in the oral cavity and skin of newborn <em>P. mucrosquamatus</em> demonstrated that the habitat environment and prey capture would affect the composition of bacteria in adult snakes. This explains why soil-associated bacteria and Enterobacter were dominant in the oral and skin microbiomes of adult snakes. We hypothesised that the native microbiome influences newborn venomous snakes and that <em>K. pneumoniae</em> linkages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.
DOI: 10.5281/zenodo.7694834
title: Ago2-RNA complex simulations in AMOEBA force field

description: 10*100ns simulations of Ago2-RNA complex in the AMOEBA force field. The simulations were conducted using OpenMM.
DOI: 10.5281/zenodo.7694833
title: Ago2-RNA complex simulations in AMOEBA force field

description: 10*100ns simulations of Ago2-RNA complex in the AMOEBA force field. The simulations were conducted using OpenMM.
DOI: 10.5281/zenodo.7692493
title: Dataset for "Quantum spin models for numerosity perception"

description: Data to recreate the figures 2-3, 6-9 of the manuscript "Quantum spin models for numerosity perception". For figure 5, we provide all of the numerically simulated data for the time evolution of our system whose average, spectrum and analysis is presented in the figure. The data is structured in individual folders for every figure and we provide a README file for each folder.
description: Additional funding sources include: Italian national program PON 2014-2020 - Istruzione e ricerca per il recupero - REACT-EU, DM MUR 1062/2021 Italian Ministry of Education PRIN2017 Grants 2017SBCPZY FLAG-ERA Joint Transnational Call 2019 Grant DOMINO European Union - Next Generation EU through the "Centro Nazionale per Simulazioni, calcolo e analisi dei dati ad alte prestazioni" by the SPOKE on QC for the PNRR.
DOI: 10.5281/zenodo.7692492
title: Dataset for "Quantum spin models for numerosity perception"

description: Data to recreate the figures 2-3, 6-9 of the manuscript "Quantum spin models for numerosity perception". For figure 5, we provide all of the numerically simulated data for the time evolution of our system whose average, spectrum and analysis is presented in the figure. The data is structured in individual folders for every figure and we provide a README file for each folder.
description: Additional funding sources include: Italian national program PON 2014-2020 - Istruzione e ricerca per il recupero - REACT-EU, DM MUR 1062/2021 Italian Ministry of Education PRIN2017 Grants 2017SBCPZY FLAG-ERA Joint Transnational Call 2019 Grant DOMINO European Union - Next Generation EU through the "Centro Nazionale per Simulazioni, calcolo e analisi dei dati ad alte prestazioni" by the SPOKE on QC for the PNRR.
DOI: 10.25345/c5n58cw5s
title: MassIVE MSV000091400 - Critical assessment of an N-glycopeptide MS/MS data analysis workflow incorporating two complementary software tools for more confident identification and assignments
title: LC-MS and MS/MS analysis results of recombinant SARS-CoV-2 spike proteins produced in HEK293 cells
DOI: 10.6084/m9.figshare.22209718
title: The essential role of biodiversity in the key axes of ecosystem function

description: We present here the data used in our analysis, all of which are standardized.
DOI: 10.12751/g-node.ee1twn
title: A Predictive Circuit for Novelty Detection in Songbird Auditory Cortex

description: In order to make sense of complicated sensory landscapes, the brain privileges the processing of novel stimuli. Detecting novelty is therefore a fundamental problem for the brain to solve. And it turns out to be complicated, as stimuli can be completely novel, or just novel relative to certain certain contexts or expectations. To better understand how the brain detects both types of novelty, we studied an auditory region of the avian brain that performs both absolute and relative novelty detection. We introduce a predictive model, called the Agnotron, that is capable of performing both kinds of novelty detection with the same circuit mechanism. Armed with predictions made by the Agnotron, we perform experiments to confirm the existence of Agnotron- like circuitry in the brain. While we fail to find evidence that the various novelty signals in this brain area are produced by the same mechanism, we do find support for predictive circuitry for some novelty signals. We continue with an advanced investigation of one absolute novelty signal in particular, known as the Song-Specific Adaptation. After recapitulating classical results with state-of-the-art technology, we report novel phenomena that rule out predictive circuit mechanisms for the SSA. Taken together, our results suggest that predictive mechanisms can explain some novelty signals in the avian brain, but not the SSA, which seems to have a more simplistic feed-forward mechanism of generation.
description: IsSupplementTo: Happ, Michael Liu (March 1, 2023). A predictive circuit for novelty detection in Songbird Auditory Cortex. Massachusetts Institute of Technology, Cambridge, MA, USA.
DOI: 10.5281/zenodo.7536523
title: Canopy Height Model Dresden 2017

description: The canopy height model (CHM) represents area-wide tree canopy heights within the City of Dresden (Germany). The CHM provides spatially explicit information on urban forest structure enabling the assessment of the small-scale impacts of urban trees and strategically managing the ecosystem services they provide. The high-resolution raster layer has a cell size of 0.5 meter and maps the height of the upper crown layer above the underlying ground. The CHM was derived from a classification of the urban forest in a LiDAR point cloud using a data fusion approach combining LiDAR with multispectral imagery and a 3D building model. LiDAR data were acquired in 2017. The classification is described in detail in this article. The raster is available as a single-band GeoTIFF in the coordinate system ETRS89/UTM zone 33 (EPSG: 25833). The source data used was made freely available by the “Landesamt für Geobasisinformation Sachsen” (GeoSN) under the license "Data license Germany - attribution - Version 2.0" and can be downloaded under the following links:<br> LiDAR: https://www.geodaten.sachsen.de/downloadbereich-digitale-hoehenmodelle-4851.html<br> 3D Building Model: https://www.geodaten.sachsen.de/downloadbereich-digitale-3d-stadtmodelle-4875.html<br> Aerial Imagery: https://www.geodaten.sachsen.de/downloadbereich-dop-4826.html
description: The City of Dresden supported generation and validation of the dataset by providing the municipal tree inventory. The research contributed to the project "Standard-BIPV-System" (FKZ: 03EE1061C) funded by the German Federal Ministry for Economic Affairs and Climate Action.
DOI: 10.5281/zenodo.7536549
title: Parameterized Tree Positions Dresden 2017

description: The parameterized tree positions represent the location of all trees detected on the basis of a laser scan survey from 2017 within the City of Dresden (Germany). Geometric attributes such as tree height and crown diameter were derived for each tree. For this purpose, the urban forest was classified in the point cloud and then individual tree crowns were segmented. Based on these segments, geometric attributes were determined from the LiDAR point cloud. In total, this automated inventory contains ~ 3 million tree positions. This is an overestimation of the actual number of trees which is due to inaccuracies in the segmentation of individual trees, especially in dense tree stands. Despite this overestimation, the tree volumes detected in the point cloud are realistically reproduced. The methodology is described in detail in this article. Each tree has the following attributes: "treeID_utm33_tiles" - ID "H_Tree" – tree height (m) "H_Crown" – crown height (m) "H_Trunk" – trunk height (m) "D_Crown" – crown diameter (m) "X", "Y","Z" – position The dataset is available either as a Shapefile or GeoJSON in the coordinate system ETRS89/UTM zone 33 (EPSG: 25833).<br> The dataset was divided into tiles. The tile number results from the coordinate of the lower left corner in the coordinate reference system. The source data used was made freely available by the “Landesamt für Geobasisinformation Sachsen” (GeoSN) under the license "Data license Germany - attribution - Version 2.0" and can be downloaded under the following links:<br> LiDAR: https://www.geodaten.sachsen.de/downloadbereich-digitale-hoehenmodelle-4851.html<br> 3D Building Model: https://www.geodaten.sachsen.de/downloadbereich-digitale-3d-stadtmodelle-4875.html<br> Aerial Imagery: https://www.geodaten.sachsen.de/downloadbereich-dop-4826.html
description: The City of Dresden supported generation and validation of the dataset by providing the municipal tree inventory. The research contributed to the project "Standard-BIPV-System" (FKZ: 03EE1061C) funded by the German Federal Ministry for Economic Affairs and Climate Action.