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Dataset results
19 results for “Protein diffusion”
Supplementary materials for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding"
<h1>Info</h1> <p>This dataset contains the supplementary materials for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding". </p> <p>For <strong>source code </strong>and <strong>detailed instructions on usage, </strong>please refer to our <a href="https://github.com/meneshail/TopoDiff/tree/main" target="_blank" rel="noopener">github</a> .</p> <h1>Supplementary data</h1> <h2>weights.tar.gz</h2> <p>The trained model weights used in the paper.</p> <h2>dataset.zip</h2> <p>CATH-60 Dataset used in the paper. In the notebook directory of our <a href="https://github.com/meneshail/TopoDiff/tree/main" target="_blank" rel="noopener">github</a> , we provide an example on encoding and visualize it with our trained encoder.</p> <h2>design.zip</h2> <p>The 21 novel mainly-beta designs selected for experiment validation. Along with the generated backbone, we also provide the prediction results from AlphaFold and ESMFold.</p> <h2>benchmark_sample.zip</h2> <p>Sampled backbones used for all benchmark experiment (All methods and variants included).</p> <h2>evaluation.tar.gz</h2> <p>Precomputed CATH reference data for coverage metric computation. Need to be downloaded for using evaluation scripts. </p>
Single Cell Phenotypic Profiling to Identify a Set of Immune Cell Protein Biomarkers for Relapsed and Refractory Diffuse Large B Cell Lymphoma: A Single-Center Study
<p>Diffuse large B-cell lymphoma (DLBCL) is the most common invasive type of non-Hodgkin lymphoma. Cell-of-origin (COO) classification is related to patients’ prognoses. Primary drug resistance in treatment for DLBCL has been observed. The specific serum biomarkers in these patients who suffer from relapsed and refractory (R/R)-DLBCL remains unclear. In the current study, using single-cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF), we determined and verified immune cell biomarkers at the mRNA and protein levels in single-cell resolution from 18 diagnostic peripheral blood mononuclear cell (PBMC) specimens collected from patients with R/R DLBCL. As controls, five PBMC specimens from healthy volunteers were obtained. We identified a panel of 35 surface marker genes for the features of R/R DLBCL unique cell cluster by scRNA-seq of eight R/R DLBCL patient samples and validated its efficiency in an external cohort consisting of 10 R/R DLBCL patients by CyTOF. The cell clustering and dimension reduction were compared among R/R DLBCL samples in CyTOF Space with COO as well as the C-MYC expression designation. Immune cells from each patient occupied unique regions in the 32-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Significant heterogeneity observed in subgroups was mainly attributed to individual differences among samples and not to expression differences in a single, homogeneous immune cell subpopulation. The marker panel showed reliability in labeling R/R DLBCL without any influence from COO stratification and C-MYC expression designation. Furthermore, we compared all the markers between R/R DLBCL and normal samples. A total of 12 biomarkers were significantly overexpressed in R/R DLBCL relative to the normal samples. Therefore, we further optimized the diagnostic biomarker panel of R/R DLBCL comprising CD82, CD55, CD36, CD63, CD59, IKZF1, CD69, CD163, CD14, CD226, CD84, and CD31. In summary, we developed a novel set of biomarkers for the diagnoses of patients with R/R DLBCL. Detections procedures at single-cell resolution provide precise biomarkers which may substantially overcome intertumoral and intratumoral heterogeneity among primary samples. The findings confirmed that each case was unique and may comprise multiple, genetically distinct subclones.</p> <p>Here we uploaded the dataset of CyTOF for external validation. For more detailed information, please contact Dr zheng (zenki_zheng@163.com)</p> <p> </p>
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Sampled Structures from Diffusion Models for Protein SHAPES
<p>Data associated with SHAPES (Structural and Hierarchical Assessment of Proteins with Embedding Similarity)</p> <ul> <li><code>rmsd.tar.gz</code> : RMSD and TM scores of ESMFold predicted structures with original designed backbones.</li> <li><code>mpnn.tar.gz</code> : ProteinMPNN designed sequences.</li> <li><code>raster.tar.gz</code> : CATH and sampled structures annotated with the grid square label after rasterization. Also includes the specific structures which are displayed in the raster plots.</li> <li><code>dssp.tar.gz</code> : Secondary structure frequences computed by DSSP.</li> <li><code>samples.tar.gz</code> : All sampled structures.</li> </ul> <p>Due to size, the ESMFold predicted structures for eight ProteinMPNN-designed sequences per sampled backbone are not included.</p> <p> </p> <p>Code: <code>proteinshapes-main.zip</code></p>
Clinicopathological differences in MYC and BCL2 protein expression between primary extranodal and nodal diffuse large B-cell lymphoma
Open the record for dataset details and reuse information.
Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [RNA-Seq]
GEO Series GSE154462. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
Targeting Non-proteolytic Protein Ubiquitination for the Treatment of Diffuse Large B Cell Lymphoma (Agilent Arrays)
GEO Series GSE73281. Homo sapiens. 20 samples. Type: Expression profiling by array.
A Phase I/II Study of the Tumor-targeting Human L19-IL2 Monoclonal Antibody-cytokine Fusion Protein in Combination With Rituximab in Relapsed or Refractory Diffuse Large B-cell Lymphoma (DLBCL)
ClinicalTrials.gov study NCT02957019. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of AEB071 (a Protein Kinase C Inhibitor) in Patients With CD79-mutant Diffuse Large B-Cell Lymphoma
ClinicalTrials.gov study NCT01402440. IPD Sharing: Not stated. Countries: 10. Publications: 0.
Data from: Tau protein as a diagnostic marker for diffuse axonal injury
Open the record for dataset details and reuse information.
Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [ChIP-Seq]
GEO Series GSE154457. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma
GEO Series GSE154463. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Targeting Non-proteolytic Protein Ubiquitination for the Treatment of Diffuse Large B Cell Lymphoma (Affy SNP6.0 Arrays)
GEO Series GSE73639. Homo sapiens. 5 samples. Type: Genome variation profiling by SNP array.
Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [ATAC-Seq]
GEO Series GSE154456. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A Feasibility Study of Gallium-68 Citrate PET to Detect Aberrant MYC Proto-Oncogene, BHLH Transcription Factor (MYC) Protein Expression in Diffuse Large B-Cell Lymphoma
ClinicalTrials.gov study NCT02776891. IPD Sharing: NO. Countries: 0. Publications: 0.
Clinicopathological characteristics and genomic profile of primary sinonasal tract diffuse large B cell lymphoma (DLBCL) reveals gain at 1q31 and RGS1 encoding protein; high RGS1 immunohistochemical expression associates with poor overall survival in DLBCL not otherwise specified (NOS)
<p>Raw annonymized data, OncoScan CEL files of the manuscript.</p> <p>PMID: 27775850</p> <p>DOI: 10.1111/his.13106</p> <p>ABSTRACT:</p> <p><strong>Aims: </strong> We aimed to define the clinicopathological characteristics of 29 primary sinonasal diffuse large B cell lymphoma (DLBCL<sup>sn</sup> ) in a series of 240 cases of DLBCL not otherwise specified [DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> ], including DLBCL<sup>sn</sup> training set (n = 11) and validation set (n = 18), and DLBCL<sup>non-sn</sup> (n = 211).</p> <p><strong>Methods and results: </strong> In the training set, 82% had a non-germinal center B-cell-like (Hans' Classifier) (non-GCB) phenotype and 18% were Epstein-Barr virus-encoded small RNAs (EBER)<sup>+</sup> . The genomic profile showed gains<sup>(+)</sup> of 1q21.3q31.2 (55%), 10q24.1 (46%), 11q14.1 (46%) and 18q12.1q23 (46%); losses<sup>(-)</sup> of 6q26q27 (55%) and 9p21.3 (64%); and copy number neutral loss of heterozygosity (LOH) (acquired uniparental disomy, UPD) at 6p25.3p21.31 (36%). This profile is comparable to DLBCL<sup>NOS</sup> (GSE11318, n = 203.) and closer to non-GCB/activated B-cell-like subtype (ABC). Nevertheless, +1q31, -9p21.3 and -10q11.1q26.2 were more characteristic of DLBCL<sup>sn</sup> (P < 0.001). Array results were verified successfully by fluorescence in situ hybridization (FISH) on +1q21.3 (CKS1B), -6q26 (PARK2), +8q24.21 (MYC), -9p21.3 (MTAP, CDKN2A/B), -17p13.1 (TP53) and +18q21.33 (BCL2) with 82-91% agreement. Minimal common regions included biologically relevant genes of MNDA (+1q23.1), RGS1 and RGS13 (+1q31.2), FOXP1 (+3p13), PRDM1 (BLIMP1) and PARK2 (-6q21q26), MYC (+8q24.21), CDKN2A (-9p21.3), PTEN (-10q23.31), MDM2 (+12q15), TP53 (-17p13.1) and BCL2 (+18q21.33). Correlation between DNA copy number and protein immunohistochemistry was confirmed for RGS1, RGS13, FOXP1, PARK2 and BCL2. The microenvironment had high infiltration of M2-like tumour associated macrophages (TAMs) and CD8<sup>+</sup> T lymphocytes that associated with higher genomic instability. The DLBCL<sup>sn</sup> validation set confirmed the clinicopathological characteristics, all FISH loci and immunohistochemistry (IHC) for RGS1. RGS1, one of the most frequently altered genes, was analysed by IHC in DLBCL<sup>all</sup> and high RGS1 expression associated with non-GCB, EBER<sup>+</sup> and unfavourable overall survival (hazard ratio = 1.794; P = 0.016).</p> <p><strong>Conclusions: </strong> DLBCL<sup>sn</sup> has a characteristic genomic profile. High RGS1 IHC expression associates with poor overall survival in DLBCL<sup>all (</sup><sup>NOS</sup><sup>)</sup> .</p>
Transducin β-like protein 1 controls multiple oncogenic networks in diffuse large B cell lymphoma
GEO Series GSE148232. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Movies used in manuscript "Cellular glycosaminoglycans and viral protein glycosylation regulate diffusion and entry of herpesvirus at cell surface
<p>Movies S1. Timelapses of HSV-1 (KOS strain) diffusing at the surface of (A) wt CHO-K1 cells expressing both herapan sulfate (HS) and chondroitin sulfate (CS), (B) wt CHO cells treated with chondroitinase ABC, lacking chondroitin sulfate (CHO-ΔCS), (C) pgsD-677 lacking HS (CHO-ΔHS). (D) Timelapse of HSV-1 (KOS strain) on wt HaCat cells. (E) Timelapse of the mutant HSV-1 (KOS-gCΔmuc) on wt HaCat cells. The scale bar represents 10 μm. Using Fiji, all movies were corrected for uneven background using the same procedure with a rolling ball of 50 and the noise was despeckled. The LUT thresholds were set to be 10 as minimum and 50 as maximum for all videos. Finally, the movies were then saved as .avi using an acceleration of 50 frame per second. (F) The virus trajectories reconstructed using Trackmate are shown on the movie corresponding to A for wt CHO. The colors of the trajectory are arbitrary.</p>
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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)
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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.