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6,467 results for “process”
Overexpression of miR-155-5p can upregulate antigen processing and presentation pathway via targeting tapasin
<p><strong>Background </strong>Dysregulation of major histocompatibility complex (MHC) class I antigen processing and presentation machinery (APM) components in the tumor as one main molecular mechanism of immune escape leading to deactivation of T cell immune surveillance could be due to post-transcriptional regulation via immune-modulatory microRNAs (miRNA). It is now well established from a variety of studies that several miRNAs could effectively modulate the expression of some MHC class I APM components in tumors. Tapasin is an important APM molecule involved in the association of MHC class I with transporter associated with antigen processing (TAP) and peptide loading. Since so far no detailed investigation of the posttranscriptional regulation of tapasin exists, the aim of this study is to identify and functionally characterize miRNAs targeting tapasin in melanoma.</p> <p><strong>Methods </strong>Using miRNA trapping by RNA <em>in vitro</em> affinity purification (miTRAP) and <em>in silico </em>as well as small RNA sequencing, miRNAs will be identified, which bind to the 3'untranslated region (3' UTR) of tapasin. Dual luciferase assays will be performed to determine binding of the miRNA. <em>In silico</em> analysis was performed to predict the effect of miRNAs on the survival of melanoma patients in correlation to tapasin. RT-qPCR, Western blot, flow cytometry and other functional assays were performed after transfecting miRNA mimics in three melanoma cell lines.</p> <p><strong>Results </strong>Using the combination strategy of miTRAP and RNA seq we identified miR-155-5p to bind to the 3’UTR of tapasin, which was further confirmed by <em>in silico analysis</em> and dual luciferase reporter assay. Transfection of miR-155-5p mimics demonstrated that miR-155-5p upregulate tapasin protein level, which was accompanied by an upregulation of the MHC class I (HLA-ABC) surface expression. Simultaneously, in several different types of cancer, including melanoma, the expression of miR-155-5p is significantly positively correlated with the patient's survival and HLA-A protein.</p>
Batch-processing Abstraction for Raw Data Integration
BARDI is a data engineering tool to make clinical data "AI-ready" by transforming raw, unstructured inputs (like pathology reports) into structured, model-friendly formats. It provides modular pipelines for preprocessing tasks such as tokenization, normalization, and batch data handling, simplifying the development and maintenance of large-scale data workflows for machine learning. Overall, prepares clinical text and related data so downstream model frameworks can efficiently perform tasks such as information extraction and prediction.
SDC1 processed catalogue
<p>Science data challenge 1 catalogue</p>
Dataset - Dissolved organic matter sources and processing in the endorheic Lake Nam Co catchment (Tibet) as assessed by ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)
<p> </p> <p>Disclaimer 2022-01-04: Associated full text in preparation</p>
Pupal epidermis ATAC-seq (D. melanogaster) (processed BAM files)
<p>Processed Binary Alignment Map files for fruitfly pupal epidermis ATAC-seq data</p>
AfroMAFT unpre-processed
<p>Unpre-processed mC4 and news corpus we used for the <a href="https://aclanthology.org/2022.naacl-main.223/">MAFAND paper</a></p>
Sex-specific speed-accuracy tradeoffs shape neural processing of acoustic signals
<p>Speed-accuracy tradeoffs – being fast at the risk of being wrong – are fundamental to many decisions and natural selection is expected to resolve these tradeoffs according to the costs and benefits of behavior. We here test the prediction that females and males should integrate information from courtship signals differently because they experience different payoffs along the speed-accuracy continuum. We fitted a neural model of decision making (a drift-diffusion model of integration to threshold) to behavioral data from the grasshopper <i>Chorthippus biguttulus</i> to determine the parameters of temporal integration of acoustic directional information used by male grasshoppers to locate receptive females. The model revealed that males had a low threshold for initiating a turning response, yet a large integration time constant enabled them to continue to gather information when cues were weak. This contrasts with parameters estimated for females of the same species when evaluating potential mates, in which response thresholds were much higher and behavior was strongly influenced by unattractive stimuli. Our results reveal differences in neural integration consistent with the sex-specific costs of mate search: Males often face competition and need to be fast. Females often pay high error costs and need to be deliberate.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.