cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12850154
title: TypeRE Dataset

description: <b>TypeRE </b>is a supervised large-scale<b> relation extraction dataset</b> made from aligning public relation extraction datasets relations into a unified ontology. The public datasets used are: Wiki80, KBP37 and KnowledgeNet. The dataset includes a total of <i>30923 sentences</i> annotated with <i>28 relational</i> categories (including the no-relation category).<br><br><br>
DOI: 10.5281/zenodo.3997084
title: Trialstreamer data

description: Trialstreamer annotated collection of RCTs. This respository contains baseline files (large), and subsequent updates (daily for PubMed, weekly for ICTRP).
DOI: 10.6084/m9.figshare.12850757
title: Early prenatal diagnosis of tricuspid valve dysplasia

description: To report our experience in early prenatal diagnosis of six cases of tricuspid valve dysplasia (TVD) and to delineate echocardiographic features. This was a retrospective study which included all the women who attended our clinic for early fetal screening sonography, between 2001 and 2018. The ultrasound screening was done at 11–16 weeks of gestation, and included an anatomic fetal scan and Doppler imaging. The diagnosis of TVD was done based on sonographic features visualized on four chamber view and color mapping of the valve. Complete fetal echocardiography was carried out to rule out additional heart malformations. Out of 34,933 early prenatal transvaginal ultrasound screening examinations, six cases of TVD were diagnosed. Five of the pregnancies were terminated as per parental request, and one fetus was delivered at term and died shortly after birth. In three fetuses a chromosomal analysis was performed, one had trisomy 21, one had an abnormal CGH, and the third had a normal karyotype. In two fetuses an autopsy was performed and the diagnosis of TVD was confirmed in both. Early prenatal detection of TVD is possible and may aid in parental counseling. Larger studies, examining the outcome of TVD should be considered.
DOI: 10.6084/m9.figshare.12850757.v1
title: Early prenatal diagnosis of tricuspid valve dysplasia

description: To report our experience in early prenatal diagnosis of six cases of tricuspid valve dysplasia (TVD) and to delineate echocardiographic features. This was a retrospective study which included all the women who attended our clinic for early fetal screening sonography, between 2001 and 2018. The ultrasound screening was done at 11–16 weeks of gestation, and included an anatomic fetal scan and Doppler imaging. The diagnosis of TVD was done based on sonographic features visualized on four chamber view and color mapping of the valve. Complete fetal echocardiography was carried out to rule out additional heart malformations. Out of 34,933 early prenatal transvaginal ultrasound screening examinations, six cases of TVD were diagnosed. Five of the pregnancies were terminated as per parental request, and one fetus was delivered at term and died shortly after birth. In three fetuses a chromosomal analysis was performed, one had trisomy 21, one had an abnormal CGH, and the third had a normal karyotype. In two fetuses an autopsy was performed and the diagnosis of TVD was confirmed in both. Early prenatal detection of TVD is possible and may aid in parental counseling. Larger studies, examining the outcome of TVD should be considered.
DOI: 10.6084/m9.figshare.12850679.v1
title: Supplementary materials.docx

description: <sup>Supplementary Tables and Figure Legends</sup>
DOI: 10.6084/m9.figshare.12850679
title: Supplementary materials.docx

description: <sup>Supplementary Tables and Figure Legends</sup>
DOI: 10.17045/sthlmuni.12845876
title: Integration of Verbal Cues with Visual and Olfactory Stimuli

description: There are 69 .csv files included in this dataset. Each raw data .csv file contains the raw data for a single participant. An R file was then used to combine the raw data and condense it for analyses. The R file is included with the data and is called ObjectCategoryAnalysis.Rmd. Additionally, there is a ReadMe file titled DataSharingREADME.txt.<br>DATA-SPECIFIC INFORMATION FOR: Each raw data file.<br>1. Number of variables: 11<br>2. Number of cases/rows: 192 x 69 = 13248<br>3. Variable List:<br>Participant: 101-169<br>Block: Their are 4 blocktypes: VisualStimulus (blocks with object-cues and visual targets), VisualCategory (blocks with category-cues and visual targets), OlfactoryStimulus (blocks with object-cues and olfactory targets), OlfactoryCategory (blocks with category-cues and olfactorytargets).<br>Cue: One of six possible auditory cues participants heard prior to target onset: "lavender", "lilac", "pear", "lemon", "flower", "fruit".<br>Target: One of four possible targets presented to each participant. These can either be visual or olfactory: lavender, lilac, pear, lemon.<br>Match: Informs about whether the Cue and Target matched (yes) or were different (no).<br>Accuracy: 1 if participant answered correctly, 0 if participant answered incorrectly.<br>ReactionTime: Response latency on that particular trial.<br>Modality: Whether the target was Visual or Olfactory.<br>CueType: Whether the cue was object-based (Object) or category-based (Category).<br>Congruency: Provides the same information as Match. If cue and target match it says Congruent, if cue and target do not match it says Incongruent.<br>LogRT: Reaction Times on a logarithmic scale.<br><br>R InformationThe analysis uses both R and R Studio (although only R is required to run the .Rmd file.)R reference: https://www.r-project.org/<br>R Studio: https://rstudio.com/
DOI: 10.6084/m9.figshare.12850682
title: AggregatedNewsRE Dataset

description: <b>AggregatedNewsRE</b> is a Relation Extraction corpus with data from 11 clusters of articles.It is composed by a total of 400 candidate facts, manually annotated with 18 relational categories (including no-relation category).
DOI: 10.6084/m9.figshare.12850682.v1
title: AggregatedNewsRE Dataset

description: <b>AggregatedNewsRE</b> is a Relation Extraction corpus with data from 11 clusters of articles.It is composed by a total of 400 candidate facts, manually annotated with 18 relational categories (including no-relation category).
DOI: 10.6084/m9.figshare.12851081
title: Expt1068_Training

description: Dataset for Training Cohort (Experiment 1068). Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851081.v1
title: Expt1068_Training

description: Dataset for Training Cohort (Experiment 1068). Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12782504
title: Fig2D_1.tif

description: Cartographic projection of a Histone-eGFP labelled embryo imaged with multi-view SPIM.The progressively deeper onion layers of the projection are color-coded to distinguish superficial and internal nuclei. The nuclei participating in closing of the serosa window were back-tracked to the uniform blastoderm stage to reveal their spatial origin. Tracks are color-coded by time as indicated by the color scale.
DOI: 10.6084/m9.figshare.12782504.v1
title: Fig2D_1.tif

description: Cartographic projection of a Histone-eGFP labelled embryo imaged with multi-view SPIM.The progressively deeper onion layers of the projection are color-coded to distinguish superficial and internal nuclei. The nuclei participating in closing of the serosa window were back-tracked to the uniform blastoderm stage to reveal their spatial origin. Tracks are color-coded by time as indicated by the color scale.
DOI: 10.6084/m9.figshare.12851318.v1
title: The anti-cancer drug ABTL0812 induces ER stress-mediated cytotoxic autophagy by increasing dihydroceramide levels in cancer cells

description: ABTL0812 is a first-in-class small molecule with anti-cancer activity, which is currently in clinical evaluation in a phase 2 trial in patients with advanced endometrial and squamous non-small cell lung carcinoma (NCT03366480). Previously, we showed that ABTL0812 induces TRIB3 pseudokinase expression, resulting in the inhibition of the AKT-MTORC1 axis and macroautophagy/autophagy-mediated cancer cell death. However, the precise molecular determinants involved in the cytotoxic autophagy caused by ABTL0812 remained unclear. Using a wide range of biochemical and lipidomic analyses, we demonstrated that ABTL0812 increases cellular long-chain dihydroceramides by impairing DEGS1 (delta 4-desaturase, sphingolipid 1) activity, which resulted in sustained ER stress and activated unfolded protein response (UPR) via ATF4-DDIT3-TRIB3 that ultimately promotes cytotoxic autophagy in cancer cells. Accordingly, pharmacological manipulation to increase cellular dihydroceramides or incubation with exogenous dihydroceramides resulted in ER stress, UPR and autophagy-mediated cancer cell death. Importantly, we have optimized a method to quantify mRNAs in blood samples from patients enrolled in the ongoing clinical trial, who showed significant increased <i>DDIT3</i> and <i>TRIB3</i> mRNAs. This is the first time that UPR markers are reported to change in human blood in response to any drug treatment, supporting their use as pharmacodynamic biomarkers for compounds that activate ER stress in humans. Finally, we found that MTORC1 inhibition and dihydroceramide accumulation synergized to induce autophagy and cytotoxicity, phenocopying the effect of ABTL0812. Given the fact that ABTL0812 is under clinical development, our findings support the hypothesis that manipulation of dihydroceramide levels might represents a new therapeutic strategy to target cancer. 4-PBA: 4-phenylbutyrate; AKT: AKT serine/threonine kinase; ATG: autophagy related; ATF4: activating transcription factor 4; Cer: ceramide; DDIT3: DNA damage inducible transcript 3; DEGS1: delta 4-desaturase, sphingolipid 1; dhCer: dihydroceramide; EIF2A: eukaryotic translation initiation factor 2 alpha; EIF2AK3: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; HSPA5: heat shock protein family A (Hsp70) member 5; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryonic fibroblast; MTORC1: mechanistic target of rapamycin kinase complex 1; NSCLC: non-small cell lung cancer; THC: Δ<sup>9</sup>-tetrahydrocannabinol; TRIB3: tribbles pseudokinase 3; XBP1: X-box binding protein 1; UPR: unfolded protein response.
DOI: 10.6084/m9.figshare.12851351.v1
title: Autophagy coupled to translation is required for long-term memory

description: An increase in protein synthesis following learning is a fundamental and evolutionarily conserved mechanism of long-term memory. To maintain homeostasis, this protein synthesis must be counterbalanced by mechanisms such as protein degradation. Recent studies reported that macroautophagy/autophagy, a major protein degradation mechanism, is required for long-term memory formation. However, how learning regulates autophagy and recruits it into long-term memory formation remains to be established. Here, we show that inhibitory avoidance in rats significantly increases the levels of autophagy and lysosomal degradation proteins, including BECN1/beclin 1, LC3-II, SQSTM1/p62 and LAMP1, as well as autophagic flux in the hippocampus. Moreover, pharmacological inhibition or targeted molecular disruption of the learning-induced autophagy impairs long-term memory, leaving short-term memory intact. The increase in autophagy proteins results from active translation of their mRNA and not from changes in their total mRNA levels. Additionally, the induction of autophagy requires the immediate early gene <i>Arc</i>/<i>Arg3.1</i>. Finally, in contrast to classical regulation of autophagy in other systems, we found that the increase in autophagy upon learning is dispensable for the increase in protein synthesis. We conclude that coupling between learning-induced translation and autophagy, rather than translation <i>per se</i>, is an essential mechanism of long-term memory.
DOI: 10.5281/zenodo.3997093
title: Taxonomic and functional annotations of the Integrated non-redundant Gene Catalog 9.9

description: The Integrated non-redundant Gene Catalog (<strong>IGC</strong>) 9.9 is a database of 9.9 million genes from 1267 individual fecal samples together with the Homo sapiens database (MetaHIT project, grant agreement 201052). This repository contains the taxonomic and functional annotation of the IGC database. <strong>full_taxonomy_MetaHIT99.tsv </strong>: Taxonomic assignment of proteins from IGC database with the sequence aligner DIAMOND against the non-redundant NCBI database, with an e-value threshold of 10<sup>-4</sup> <strong>KEGG89_IGC_hs99.table</strong> : Functional annotation of proteins from IGC database with KEGG resource with an e-value threshold of 10<sup>-5</sup>, a bit-score threshold of 60 and using the sensitive mode of DIAMOND
description: Funding sources This work was supported by the Agence Nationale de la Recherche (ANR) as part of the MICRO-Obes (ANR-07-GMGE-002.1-01) and the ProteoCardis (ANR-15-CE14-0013) projects, and by the Métaprogramme INRA as part of the ObOmics project.
DOI: 10.5281/zenodo.3997092
title: Taxonomic and functional annotations of the Integrated non-redundant Gene Catalog 9.9

description: The Integrated non-redundant Gene Catalog (<strong>IGC</strong>) 9.9 is a database of 9.9 million genes from 1267 individual fecal samples together with the Homo sapiens database (MetaHIT project, grant agreement 201052). This repository contains the taxonomic and functional annotation of the IGC database. <strong>full_taxonomy_MetaHIT99.tsv </strong>: Taxonomic assignment of proteins from IGC database with the sequence aligner DIAMOND against the non-redundant NCBI database, with an e-value threshold of 10<sup>-4</sup> <strong>KEGG89_IGC_hs99.table</strong> : Functional annotation of proteins from IGC database with KEGG resource with an e-value threshold of 10<sup>-5</sup>, a bit-score threshold of 60 and using the sensitive mode of DIAMOND
description: Funding sources This work was supported by the Agence Nationale de la Recherche (ANR) as part of the MICRO-Obes (ANR-07-GMGE-002.1-01) and the ProteoCardis (ANR-15-CE14-0013) projects, and by the Métaprogramme INRA as part of the ObOmics project.
DOI: 10.6084/m9.figshare.12851376.v1
title: Model-free Feature Screening and FDR Control with Knockoff Features

description: This paper proposes a model-free and data-adaptive feature screening method for ultra-high dimensional data. The proposed method is based on the projection correlation which measures the dependence between two random vectors. This projection correlation based method does not require specifying a regression model, and applies to data in the presence of heavy tails and multivariate responses. It enjoys both sure screening and rank consistency properties under weak assumptions. A two-step approach, with the help of knockoff features, is advocated to specify the threshold for feature screening such that the false discovery rate (FDR) is controlled under a pre-specified level. The proposed two-step approach enjoys both sure screening and FDR control simultaneously if the pre-specified FDR level is greater or equal to 1/s, where <i>s</i> is the number of active features. The superior empirical performance of the proposed method is illustrated by simulation examples and real data applications.
DOI: 10.6084/m9.figshare.12851423.v1
title: SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

description: SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in <i>SETX</i> result in either of two distinct neurodegenerative disorders. <i>SETX</i> dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed the effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX-depleted cells. Importantly, we discovered a strong connection between SETX and the macroautophagy/autophagy pathway, reflecting a direct effect on transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2. 3ʹREADS: 3ʹ region extraction and deep sequencing; ACTB: actin beta; ALS4: amyotrophic lateral sclerosis type 4; AOA2: ataxia with oculomotor apraxia type 2; APA: alternative polyadenylation; AS: alternative splicing; ATG7: autophagy-related 7; ATP6V0D2: ATPase H+ transporting V0 subunit D2; BAF: bafilomycin A<sub>1</sub>; BECN1: beclin 1; ChIP: chromatin IP; Chloro: chloroquine; CPT: camptothecin; DDR: DNA damage response; DNMT1: DNA methyltransferase 1; DRIP: DNA/RNA IP; DSBs: double strand breaks; EBs: embryoid bodies; FTD: frontotemporal dementia; GABARAP: GABA type A receptor-associated protein; GO: gene ontology; HR: homologous recombination; HTT: huntingtin; IF: immunofluorescence; IP: immunoprecipitation; iPSCs: induced pluripotent stem cells; KD: knockdown; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MN: motor neuron; MTORC1: mechanistic target of rapamycin kinase complex 1; PASS: PolyA Site Supporting; PFA: paraformaldehyde; RNAPII: RNA polymerase II; SCA: spinocerebellar ataxia; SETX: senataxin; SMA: spinal muscular atrophy; SMN1: survival of motor neuron 1, telomeric; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TSS: transcription start site; TTS: transcription termination site; ULK1: unc-51 like autophagy activating kinase 1; WB: western blot; WIPI2: WD repeat domain, phosphoinositide interacting 2; XRN2: 5ʹ-3ʹ exoribonuclease 2.
DOI: 10.17632/m32kz6jjcx.1
title: Digital Psychological Platform for Mass Web-Surveys

description: Web surveys using digital platforms are one of the popular ways to conduct mass research. However, the intelligent analysis of the answers has a number of features based on the subject area of the conducted surveys. The dataset presents consist from mass web surveys with open-ended questions.
DOI: 10.17632/k3t2kwz53y.2
title: Competition between chiral solvents and chiral monomers in the helical bias of supramolecular polymers

description: Raw data of all figures mentioned in the text of the paper.
DOI: 10.17632/3p28zvpx58.1
title: Chuya-Kurai Source Code

description: This is an open-source code for finite-difference analysis of faulting and seismicity near the Chuya and Kurai depressions, Gorny Altai. Published as a supplementary material for reproducibility of the results.
DOI: 10.17632/kw4wzp4b4z.1
title: Supplementary data for rituximab treatment of pemphigus in a Chinese population

description: Pemphigus is a life-threatening autoimmune dermatosis due to both extensive skin damage and the side effects of conventional high-dose corticosteroid treatment. Rituximab has been reported to be effective for the treatment of severe pemphigus. The combination of rituximab and short-term prednisone has recently been evaluated as a first-line treatment for pemphigus and reported to be safer and more effective than prednisone alone. However, little has been reported on the use of rituximab in Chinese patients with pemphigus. The data include the supplementary materials of a long-term observation of 74 Chinese pemphigus patients treated with rituximab under two established treatment protocols.
DOI: 10.17632/z9zfhzk8cr.5
title: PopClusters

description: Population clusters for sub-Saharan Africa. The population clusters include the following data: 1. id – The IDs are given as a unique number for each cluster 2. Country - Name of the country. 3. Population – This is the population in each cluster obtained from the population dataset (GHSL for Somalia, Sudan and South Sudan and HRSL for the rest of the countries). The population in these clusters are calibrated to 2016 population values 4. NightLight – This value is obtained from the night-time light map and represents the maximum luminance detected in each cluster based on the 2016 stable light product available. 5. ElecPop – The number of people in each cluster who live in areas in which the stable light product detect light sources. 6. Area – The area of each cluster given in square kilometrers. 7. IsUrban – Classifies areas as either urban (2), peri-urban (1) or rural (0). Change log: 24/08-2020 - Clusters published
DOI: 10.17632/6j3mwdsysz.2
title: C-SPLPO-2 benchmark instances

description: Benchmark instances used in paper: Calvete, H.I.; Galé, C.; Iranzo, J.A.; Camacho-Vallejo, J.F; Casas-Ramírez, M.S. A matheuristic for solving the bilevel approach of the capacitated facility location problem with preferences. Computers & Operations Research. https://doi.org/10.1016/j.cor.2020.105066
DOI: 10.6084/m9.figshare.12782510
title: Fig4A_B_SqshGFP.tif

description: Cartographic projection of Tribolium embryos injected with Tc-sqh-eGFP and imaged withmulti-view SPIM.
DOI: 10.6084/m9.figshare.12782510.v1
title: Fig4A_B_SqshGFP.tif

description: Cartographic projection of Tribolium embryos injected with Tc-sqh-eGFP and imaged withmulti-view SPIM.
DOI: 10.17632/zm4c4y4yz5.1
title: Under pressure: the extraordinary survival of seal lice in the deep sea. Leonardi et al. Journal of Experimental Biology, 2020

description: Experimental data and analysis
DOI: 10.17632/7j35c2rs9m.2
title: Geant4 model of OSCAR

description: Geant4 model of OSCAR, the Oslo Scintillator Array This include the simulation code and results for the response function on a incident energy grid op to 20 MeV. See also https://doi.org/10.5281/zenodo.1153985