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  • A reliable and unobtrusive quantification of changes in cortical activity during short-term memory (STM) task can be used to evaluate the efficacy of interfaces and to provide real-time user-state information. In this dataset, we record electroencephalogram (EEG) signals in STM and baseline activity.
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  • Nutrient transporters can be rapidly removed from cell surface via substrate-stimulated endocytosis as a way to control nutrient influx, but the molecular underpinnings have not been well understood. In this work, we focused on zinc-dependent endocytosis of human ZIP4 (hZIP4), a zinc transporter essential for dietary zinc uptake. Structure-guided mutagenesis and internalization assay revealed that hZIP4 per se acts as the exclusive zinc sensor with the transport site being responsible for zinc sensing. In an effort of seeking sorting signal, a scan of the longest cytosolic loop (L2) led to identification of a conserved LQL motif essential for endocytosis. Partial proteolysis of purified hZIP4 demonstrated a structural coupling between the transport site and the L2 upon zinc binding, which supports a working model of how zinc ions at physiological concentration trigger a conformation-dependent endocytosis of the zinc transporter. This work provides a new paradigm on post-translational regulation of nutrient transporters.
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  • Raw data for 2-choice food preference assays, FLIC assays, immunofluorescence staining, pharyngeal calcium imaging, and optogenetics.
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  • Large surveys of peptides naturally presented on major histocompatibility class I (MHC I) proteins have enabled improved MHC I ligand prediction by dramatically expanding the available data for many MHC I alleles. However, it is unclear to what extent antigen processing signals can also be learned from these datasets. Here, we developed a predictor of antigen processing by training neural networks to discriminate mass spec-identified MHC I ligands from unobserved peptides, where both classes of peptides are predicted to be strong MHC I binders. The resulting predictor shows qualitative consistency with established preferences for the transporter associated with antigen processing, proteasomal cleavage, and endoplasmic reticulum aminopeptidases. When we combined the antigen processing predictor with a novel pan-allele MHC I binding predictor in a logistic regression model, the combination model significantly outperformed the two components alone as well as the NetMHCpan 4.0 and MixMHCpred 2.0.2 tools at predicting mass spec-identified MHC I ligands. Our predictors are implemented in the open source MHCflurry package, version 1.6.0 (github.com/openvax/mhcflurry).
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  • The Zr-1.05Nb, Zr-0.85Nb-0.20Ta and Zr-0.85Nb-0.40Ta alloys with an alpha plus beta equilibrium microstructure (annealing 570 °C for 3840 h) were measured by EDS-TEM. The measurements of beta phase (precipitates) was carried out in carbon extraction replicas and alpha phase (matrix) was carried out in thin films. The EDS-TEM spectra were obtained with a field emission TEM FEI Tecnai F20 G2 (FEG) operated at 200 kV with an EDAX EDS detector, take-off angle 14.8°, sample rotation 15° and data collected from a focused spot of 15 nm diameter (spot3). The EDS-TEM measurements were made by Dra. Eugenia Zelaya in the Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, Argentina. The group of measurements in this dataset will be the main part of the manuscript: P.A. Ferreirós, P.R. Alonso, D.P. Quirós, E. Zelaya, G.H. Rubiolo, Accurate quantitative EDS-TEM analysis of precipitates and matrix in equilibrium (Alpha+Beta) Zr-1Nb alloys with Ta addition. Manuscript to be sent to Journal of Nuclear Materials (March 2020)
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  • The repository includes the dataset for the manuscript entitled A calibration framework for high-resolution hydrological models using a multiresolution and heterogeneous strategy submitted to WRR. Currently, we only deposit the data for plotting Fig4. Upon acceptance, we will store all the data in this repository.
    Data Types:
    • Software/Code
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    • Document
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  • The barred knifejaw, Oplegnathus fasciatus (Teleostei: Centrarchiformes Oplegnathidae), is an important species in marine cage culture and fish stocking for marine ranching in East Asia. The males of Oplegnathidae (O. fasciatus and O. punctatus) species are characterized by an X1X2Y system with a neo-Y chromosome based on male karyotype analyses. Release of the chromosome-level reference genome of female O. fasciatus has facilitated insights into the origin of the X1X2Y system of male O. fasciatus. In the present study, we applied PacBio long-read sequencing and high-throughput chromosome interaction mapping (Hi-C) to assemble a chromosome-level genome of male O. fasciatus. A highly contiguous genome with a size of 795 Mb, 2,295 contigs, and a contig N50 of 2.13 Mb was obtained. The 1,355 ordered contigs combined with the draft genome were further assembled into 23 chromosomes approximately 762 Mb in length with a contig and scaffold N50 length of 2.18 and 32.43 Mb, respectively. A large neo-chromosome (Ch9) of 94.2 Mb was assembled from 444 contigs, and found to be more than three times larger than the rest chromosomes in O. fasciatus genome. In addition, 63.1 Mb of the Ch9 sequences of male O. fasciatus had high identity (~99.0%) to the Ch8 and Ch10 sequences of female O. fasciatus based on a whole-genome synteny analysis, showing that the neo-Y chromosome shared significant homology with Ch8 and Ch10 based on male/female genome comparison. Significant fission tracks at the terminal point of the chromosomes were also identified between Ch9 and Ch8/Ch10 using synteny analyses, which showed chromosome rearrangements events had happened in the neo-chromosome Ch9. Our present results accurately demonstrated that the X1X2Y system of male O. fasciatus originated from the fusions of the non-homologous chromosomes Ch8 and Ch10. According to the synteny analyses and previous karyotypes results, which characterized acrocentric chromosomes, we suggested that a centric fusion of acrocentric chromosomes Ch8 and Ch10 was responsible for the formation of the X1X2Y system of male O. fasciatus.
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  • The retinal OCT images ofr rare diseases were extracted by using the Google image and Google dataset search that included English keywords including central serous chorioretinopathy, macular telangiectasia, macular hole, Stargadt’s disease, retinitis pigmentosa. These rare diseases were selected according to a previous review article about OCT diagnosis. The images possessing rare diseases were manually classified by two board-certified ophthalmologists, and ambiguous images were removed to clarify the image domains. Additional file "Segmentation_manual.zip" offers manually segmentedOCT images for pathologic lesions.
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  • RIS file with 148 key sources used in the literature review of the article "Defining, articulating, and operationalizing the new urban water paradigm" Abstract: Urban water systems (UWSs) in industrialized countries have underpinned unprecedented improvements in urban living standards through effective drinking water supply, sanitation and drainage. However, conventional UWSs are increasingly regarded as too rigid and not sufficiently resilient to confront growing social, technological and environmental complexity and uncertainty, manifested, for example, in the maladaptation to climate change, limited resources, and degrading urban livability. In response, a new urban water paradigm has emerged in the last two decades, which, so far, has remained ambiguous and incoherently articulated. Based on a review of 148 peer-reviewed sources, this article proposes and applies an analytical framework to coherently describe the new paradigm and contrast it with the old urban water paradigm. The framework includes a philosophical foundation and set of methodological principles that shape the new paradigm’s approach to governance, management, and infrastructure. Our proposed definition and articulation of the paradigm helps to bridge the numerous proposed alternative water management frameworks, which offer useful directions forward but are often fragmented and ambiguous.
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  • We presents a dataset of 100 fundus digital images of retina. The retinal images are taken from Armed Forces Institute of Ophthalmology (AFIO), Rawalpindi, Pakistan and annotated with the help of four expert ophthalmologists for the purpose of computer aided diagnosis of hypertensive retinopaty, diabetic retinopathy and papilledema. This dataset contains retinal blood vessels network, segmented artery/ vein network to calculate Arteriovenous Ratio (AVR), annotation of Optic Nerve Head (ONH) and various retinal abnormalities such as hard exudates (HE) and cotton wool spots. The dataset is valuable for those researchers who are developing automated systems for vessels segmentation, artery/ vein classification, diagnosis of hypertensive retinopathy, diabetic retinopathy and papilledema. Please cite the following article if you want to use this dataset: Muhammad Usman Akram, Shahzad Akbar, Taimur Hassan, Sajid Gul Khawaja, Ubaidullah Yasin, Imran Basit, "Data on fundus images for vessels segmentation, detection of hypertensive retinopathy, diabetic retinopathy and papilledema", Data in Brief, Volume 29, 105282, ISSN 2352-3409, 2020.
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