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CIC-DUX4 chromatin prolfiling reveals new epigenetic dependencies and actionable therpaeutic targets in CIC-rearranged sarcomas
<p>CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here we generated a genome wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites. This property is in contrast with the repressive function of the wild type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation, and its pharmacological inhibition to significantly impact tumor growth in vitro and in vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation and suggests a potential therapeutic approach for the clinical management of CDS patients. </p>
Temperature-dependence and genetic variation in resource acquisition strategies in a model freshwater plant
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The activation of Wnt signaling by a STAT6-dependent macrophage phenotype promotes mucosal repair in murine IBD
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Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging
<p><a href="https://zenodo.org/api/files/edf611c5-3daa-479a-8470-3406cf4df3b5/example_data.zip?versionId=43aab935-acd9-4b81-9a0d-298eaae73fd1">example data</a></p>
Multivocal Study on Microservice Dependencies
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Sustained macrophage reprogramming is required for CD8 T cell-dependent long-term tumor resolution
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FIG. 1 in Density-Dependent Fitness Attributes and Carry-Over Effects in Crawfish Frogs (Rana areolata), a Species of Conservation Concern
FIG. 1. Results of enclosure experiments to determine effects of intraspecific competition, interspecific competition, and predation treatments on larval survivorship, size (SVL and mass), and time to metamorphosis. In the two Intraspecific treatments, Low ¼ 30 Crawfish Frog tadpoles/enclosure (0.09 tadpoles/L) and High ¼ 90 Crawfish Frog tadpoles/enclosure (0.27 tadpoles/L). In the two Interspecific treatments, Lc ¼ Green Frog tadpoles and Ls ¼ Southern Leopard Frog tadpoles. In these treatments, in each enclosure we placed 45 Crawfish Frog and 45 Leopard Frog tadpoles (0.13 tadpoles/L/species), and 45 Crawfish Frog (0.13 tadpoles/L) and 20 Green Frog tadpoles (0.06 tadpoles/L), respectively. In the Predation treatment (At), we placed 90 Crawfish Frog tadpoles (0.27 tadpoles/L) and 5 Small-mouthed Salamander larvae (0.02 larvae/L) per enclosure. Lowercase letters above each column reflect statistical significance using ANOVA. Columns with different letters are statistically significant (P, 0.05).
B Cell Differentiation and Anti-Tumor Humoral Responses Depend on Cathepsin S Activity
<p>This repository contains the processed data and codes for the manuscript <br>"<strong><span>B Cell Differentiation and Anti-Tumor Humoral Responses Depend on Cathepsin S Activity</span></strong>"</p> <p>The data is AnnData object stored in h5ad format. The codes are Python jupyter notebooks. </p>
Dependence of the molecular interactions between cyanoacrylate and native copper surfaces on the process atmosphere
<p>This dataset containts the research data for the figures and publication with the title "Dependence of the molecular interactions between cyanoacrylate and native copper surfaces on the process atmosphere", a paper to be published in the MDPI journal "Adhesives".</p>
Temperature Dependence of Young's Modulus of Kaolin-Based Silicate Ceramics with Mullite Addition
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Type II-Plateau supernova radiation: dependences on progenitor and explosion properties
<p>Model spectra from <a href="https://ui.adsabs.harvard.edu/abs/2013MNRAS.433.1745D">Dessart et al. 2013, MNRAS, 433, 1745</a></p>
Fig. 1 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways
Fig. 1. Symptoms of the soybean leaves from the transgenic overexpressing BiP (C9) and untransformed (WT) genotypes submitted to inoculation by P. syringae pv. tomato. In (A) Leaves from plants after 8 and 36 hai (hour after inoculation) and in (B) after 15 and 30 dai (day after inoculation).
Fig. 55 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 55. Reduction of NADP þ by ferredoxin-dependent reductase. The FAD cofactor is reduced in two consecutive steps by single electron transfer from reduced ferredoxin. The two-electron reduced (hydroquinone) FAD subsequently transfers a hydride to NADP+ to yield NADPH. The reaction may also run in the reverse direction, i.e. NADPH serves as the reductant to generate reduced ferredoxin, which is used to drive a number of biochemical reactions.
Fig. 48 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 48. Reaction catalyzed by sarcosine/pipecolate oxidase. A. Oxidation of sarcosine generates the imine, which spontaneously hydrolyzes to glycine and formaldehyde. In contrast to mammalian sarcosine oxidase, the A. thaliana enzyme does not utilize tetrahydrofolate to capture the reactive formaldehyde. B. Oxidation of pipecolate to Δ1-piperideine-6-carboxylate. In both reactions the reoxidation of the reduced FAD occurs by dioxygen leading to the production of hydrogen peroxide (not shown).
Fig. 43 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 43. Reaction of N-monooxygenation by flavin-containing monooxygenases. The single flavin-containing monooxygenase belonging to clade 1 is involved in pathogen defense, as it catalyzes the N-oxygenation of pipecolic acid to NHP, a key metabolite required for the initiation of pathogen-induced immune response (Hartmann et al., 2018).
Fig. 46 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 46. Reactions catalyzed by NADPH oxidases. The two electrons delivered by NADPH are either used for the reduction of dioxygen to hydrogen peroxide (top reaction) or the reduction of two molecules of dioxygen to two molecules of superoxide (bottom reaction).
Fig. 5 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 5. Reaction of glycerol 3-phosphate dehydrogenase. The secondary alcohol group is oxidized to the keto-group (shown in red) generating dihydroxyacetone phosphate, which is further converted by triose phosphate isomerase, a glycolytic enzyme, to glyceraldehyde 3-phosphate. The reduced FAD is reoxidized by membrane-associated CoQ and thus the electrons enter the mETC. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 1. Association with other cofactors (A) and mode of flavin binding (B). (A) In 36 A. thaliana flavoenzymes additional iron-dependent cofactors are part of the functional enzyme and contain either heme (18), iron-sulfur (Fe–S) clusters (10) or a combination of the molypdocofactor (Moco) with 2Fe–2S clusters (6) or heme (2). In acetohydroxyacid synthase the FAD cofactor is associated with thiamine pyrophosphate (TPP). (B) In most cases the FMN and FAD cofactor is bound non-colavently (FMN = 44 and FAD = 180), while mono-covalent (exclusively to the 8α-position of FAD) and bi-covalent linkage (to the 6- and 8α-position of FAD) are comparatively rare (9 and 10.3% of the FAD-containing flavoenzymes, respectively). The insert shows the isoalloxazine ring with the numbering scheme and indicates the positions of covalent attachment. The FMN cofactor is not involved in covalent bond formation in the flavoenzymes of A. thaliana.
Fig. 3 in Assessing the Old-Growth Dependency of Two Saproxylic Beetle Species in the Southern Appalachian Mountains
Fig. 3. (A) Megalodacne heros, dorsal habitks. (B) Ganoderma tsugae. (C) Records of M. heros acd host Ganoderma spp. withic Great Smoky Mokctaics Natiocal Park with historic lacd kses. Oktliced areas oc the map icdicate areas searched dkricg this stkdy ic 2019 acd 2021.All records oktside acd some records icside of the areas searched are from iNatkralist.
Otolith reliability is context dependent for estimating warming and CO2 acidification impacts on fish growth
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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.