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6,144 results for “cancer treatment”
Multi-scale simulations for optimizing cancer treatment
<p>The dataset comprises the output of several simulations of a model of tumor growth with different parameter values (10.1101/2021.12.17.473136). The model is a multi-scale agent-based model of a tumor spheroid that is treated with periodic pulses of the cytokine tumor necrosis factor (TNF). The multi-scale model simulates processes including i) the diffusion, uptake, and secretion of molecular entities such as oxygen, or TNF; ii) the mechanical interaction between cells; and iii) cellular processes including cell life cycle, cell death models, signal transduction.</p> <p>The multi-scale model was implemented and simulated using the PhysiBoSS framework (Letort et al. 2019). The dataset corresponds to 425 different simulations launched and automatically tagged as Interesting/Non-Interesting based on the effect of the parameters on the simulation (see README file). Each simulation was tagged by them with the following parameters (in that order):</p> <ul> <li>oxygen_necrotic, oxygen_critical</li> <li>oxygen_no_proliferation</li> <li>oxygen_reference</li> <li>initial_uptake_rate</li> <li>protein_threshold</li> <li>secretion_rate</li> <li>oxygen_concentration</li> <li>tnf_concentration</li> </ul> <p>Details on how these files are built can be found in the <strong>Biological Use Case</strong> output format file (<a href="https://zenodo.org/record/3921049">https://zenodo.org/record/3921049</a>). </p>
Impact of paclitaxel treatment on the Triple Negative Breast Cancer Cell line HCC1143
<div>Data and code related to Zenodo repository: 10.5281/zenodo.11237850</div> <div> </div> <div>Experimental goal:</div> <div>Evaluate the impact of escalating paclitaxel dose on cell count, nuclear morphology and cellular outcome.</div> <div> </div> <div>Methods:</div> <div>Cells were plated at 3000 cells in 100ul of complete media per well in a 96 well plate (#08-772-225, FisherScientific). After 24 hours, an additional 100ul of either vehicle (0.1% DMSO) or paclitaxel containing complete media was added. After 72 hours cells were fixed with 4% Formaldehyde (#28908, ThermoFisher Scientific) for 15 minutes at room temperature, then permeabilized with 0.3% Triton X-100 (#X100-100ML, Sigma Aldrich) for 10 minutes at room temperature, then washed twice with PBS. Fixed cells were blocked with 1% BSA (A7906-100G, Millipore Sigma) in PBS for 1 hour at room temperature and then stained overnight with 1:100 anti-CDKN2A/p16INK4A+CDKN2B/p15INK4B-AF644 (#ab199756, Abcam), and 1:100 anti-cPARP-AF647 (#6987S, Cell Signaling Technology) or 1:500 anti-TUBB3-AF647 (#ab190575, Abcam) overnight at 4C. Each well was washed twice with room temp PBS then stained with 0.5ug/mL DAPI (4083S, Cell Signaling Technology) in PBS for 15 minutes at room temperature. Following DAPI staining, wells were washed once with PBS, then stained with 1:20,000 HCS CellMask in PBS (Orange: #H32713, Green: #H32714, Invitrogen) for 15 minutes at room temperature. Wells were washed twice with room temperature PBS and then 4 fields of view per well imaged on an InCell 6000 (GE Healthcare). Images were segmented with two custom Cellpose models to segment the nucleus (using parameters: diameter = 45, chan = DAPI, chan2 = Cellmask Orange) and cytoplasm (using parameters: diameter = 90, chan = Cellmask Orange, chan2 = DAPI). Image quantification was performed in R (v4.3.1) using EBImage (v4.42.0), and cells were annotated based on the number of distinct nuclei segmented within each cytoplasmic mask. </div> <div> </div> <div>Included files:</div> <div>row_#_level_1.zip : 6 zip file containing original images from InCell 6000, one zip per row</div> <div>level_2.csv : Data quantified to the nuclear level (cytoplasmic quantification is duplicates across multiplet nuclei)</div> <div>level_3.csv: Data quantified at the cellular level including number of nuclei and stain intensities for segmented compartments</div> <div>platemap.csv: Description of each well from the stained plate</div> <div>cellpose_modelz.zip: Zip file containing the two CellPose models used for segmentation</div> <div>image_quantification.rmd : R markdown file containing code for extracting and quantifying image intensities using the raw images (level_1) and segmentation masks created from cellpose.</div>
Literature search for publication: A meta-analysis on the role older adults with cancer favour in treatment decision making
<p>Dataset belonging to 10.5281/zenodo.7308287 including data of literature search regardign outcome preference scale in geriatric oncology</p>
Bevacizumab plus erlotinib versus erlotinib alone as first line treatment of patients with EGFR-mutated advanced nonsquamous non-small cell lung cancer. BEVacizumab plus ERLotinib studY (BEVERLY): an academic, multicenter, randomised phase III trial.
<p>Background. Adding bevacizumab to erlotinib prolonged PFS of patients with EGFR-mutated advanced NSCLC in the Japanese NEJ026 trial, but limited data were available in non-Asian patients. BEVERLY is an Italian, multicenter, randomized phase III trial of bevacizumab plus erlotinib versus erlotinib alone as first-line treatment of advanced EGFR-mutated NSCLC.</p> <p>Methods. Eligible patients were randomized 1:1 to erlotinib (150mg daily) plus bevacizumab (15mg/kg iv q3w) or erlotinib alone, until disease progression or unacceptable toxicity. Center, ECOG PS and type of mutation (ex19 deletion vs ex21 L858R vs others) were stratification variables. Investigator-assessed PFS (IA-PFS) and blinded-independent centrally-reviewed PFS (BICR-PFS) were co-primary endpoints. With 80% power in detecting a 0·60 HR and 2–sided α error 0·05, 126 events out of 160 patients were needed. The trial was registered as NCT02633189 and EudraCT 2015-002235-17.</p> <p>Findings. From Apr 11, 2016 to Feb 27, 2019, 160 pts were randomized to erlotinib pus bevacizumab (80) or erlotinib alone (80). Baseline characteristics were balanced between arms; 34 (42·5%) patients in erlotinib plus bevacizumab arm and 43 (53·8%) in erlotinib arm were former or current smokers. At a median follow-up of 36·3 months, 140 PFS events (87·5%) were reported, 68 with erlotinib plus bevacizumab and 72 with erlotinib. Median IA-PFS was 15·4 months (95% CI 12·2–18·6) with erlotinib plus bevacizumab and 9·6 months (95% CI 8·2–10·6) with erlotinib (HR 0·66; 95%CI: 0·47–0·92). BICR-PFS analysis confirmed this result. A significant interaction with treatment effect was found for smoking habit (P=0·0323): former or current smokers receiving erlotinib plus bevacizumab had a longer PFS (16·9 months [95% CI 10·2–21·8] versus 8·8 months [95% CI 5·6–9·6]) than those receiving erlotinib alone.</p> <p>Hypertension (grade≥3: 24% vs 5%), skin rash (grade≥3: 31% vs 14%), thromboembolic events (any grade: 11% vs 4%), and proteinuria (any grade: 23% vs 6%) were more frequent with the combination treatment.</p> <p>Interpretation. The addition of bevacizumab to first-line erlotinib significantly prolonged PFS in Italian patients with EGFR-mutated NSCLC, without unexpected safety issues.</p>
Oral cancer speech corpus for the paper "Objective speech outcomes after surgical treatment for oral cancer: An acoustic analysis of a spontaneous speech corpus containing 32.850 tokens"
<p>Dataset accompanying the paper "<em>Objective speech outcomes after surgical treatment for oral cancer: An acoustic analysis of a spontaneous speech corpus containing 32.850 tokens</em>"</p> <p>The zip file contains five folders:</p> <p>- <strong>Database:</strong> contains csv files for each speaker which contain the processed features</p> <p>- <strong>Recordings: </strong>the original recording from the YouTube Oral Cancer speech dataset, without further preprocessing</p> <p>- <strong>Recordings_Normalised:</strong> same as recordings but after minimal audio preprocessing (min-max scaling)</p> <p>- <strong>Textgrids: </strong>contains the textgrids which are annotated on the word-level and on phoneme-level</p> <p>- <strong>TIMIT selection: </strong>contains the textgrids for the TIMIT speakers. We unfortunately cannot share the audio date as it is not open source. More information can be found <a href="https://catalog.ldc.upenn.edu/LDC93s1">here.</a></p>
Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing
<p>Circulating tumor DNA (ctDNA) in blood may become a generic biomarker for non-invasive cancer diagnosis and monitoring. However, detection of ctDNA is challenged by the presence of many circulating DNA molecules from healthy cells. We found that single ctDNA molecules can be sequenced with high accuracy by a three-step process consisting of capturing, copying and concatenation of the original double-stranded ctDNA molecules. This innovative approach - called CyclomicsSeq - is unparalleled by any other method in terms of cost-efficiency and speed, allowing point-of-care cancer diagnostics.</p> <p>Within this CPOC, subsidized by the Oncode institute, we have applied our CyclomicsSeq ctDNA test in patients with advanced head and neck cancer squamous cell carcinoma (HNSCC). Head and neck cancer (HNSCC) accounts for 380,000 cancer-related deaths worldwide. For these patients, determining whether a patient responds to the primary chemoradiation treatment is challenging, and non-responders are sometimes identified when other treatment options are no longer possible. By measuring the ctDNA levels in the blood of these patients prior to and during treatment, we aim to identify non-responders at an earlier stage.</p> <p>This dataset contains base calls of TP53 of 47 nanopore sequencing runs. We included 10 patients and 7 controls. For the patients, we have samples of multiple time points (0 = prior to treatment, 1 = 1 week after treatment initiation, etc).</p>
Selpercatinib treatment of RET mutated thyroid cancers is associated with gastrointestinal adverse effects
<p><strong>Background:</strong></p> <p>Metastatic medullary thyroid carcinoma (MTC) and radioactive iodine refractory differentiated thyroid carcinoma (RAI-R DTC) have poor prognosis and limited treatment options. Selpercatinib (LOXO-292), a selective kinase inhibitor targeting the <em>RET</em> gene, has shown a 69-79% objective responses have been observed in this cohort (1) with benefits in other tumours harbouring the same oncogenic driver (2). Published reports describe only 17% of patients experiencing gastrointestinal Adverse effects (AE) which is in contrast to our local experience. Here we characterise the AE and correlate with radiological and histopathological findings. </p> <p><strong>Methods:</strong></p> <p>Sequential patients enrolled in LIBRETTO-001 at Royal North Shore Hospital, Sydney with available imaging (n=22) were recruited. Patients had regular visits with AE documented and CT scans 3 monthly. CT at screening, at time of gastrointestinal AE and at most recent follow up were reviewed and scored. Endoscopic examination was performed in five patients.</p> <p><strong>Results:</strong></p> <p>Of 22 patients in this cohort, the majority had somatic <em>RET </em>alterations (n=18), most commonly <em>p.Met918Thr</em> (n=14). Ten patients (50%) developed gastrointestinal adverse effects. Dose reduction was required in 8 of the 10 patients, but none discontinued therapy. The majority had stable disease (n=17). Gastric and small bowel oedema was evident in symptomatic patients after a median time of 67 weeks’ treatment. Histological correlation in five patients revealed mucosal oedema correlating with radiological evidence of congestion and oedema.</p> <p><strong>Discussion: </strong></p> <p>Gastrointestinal AEs with selpercatinib may be more common than previously described. Most are self-limiting but often require dose adjustments. Histological evidence of mucosal oedema observed in conjunction with the radiological findings of congestion and wall thickening suggest that bowel wall oedema is a predominant mechanism of abdominal pain in these patients.</p>
A Study to Compare the Safety and Efficacy of an Aromatase Inhibitor in Combination With Lapatinib, Trastuzumab or Both for the Treatment of Hormone Receptor Positive, HER2+ Metastatic Breast Cancer
ClinicalTrials.gov study NCT01160211. IPD Sharing: YES. Countries: 29. Publications: 2.
Sleep Treatment Education Program for Young Adult Cancer Survivors (STEP-YA)
ClinicalTrials.gov study NCT05358951. IPD Sharing: YES. Countries: 1. Publications: 1.
Study Assessing the Efficacy and Safety of Alpelisib Plus Fulvestrant in Men and Postmenopausal Women With Advanced Breast Cancer Which Progressed on or After Aromatase Inhibitor Treatment.
ClinicalTrials.gov study NCT02437318. IPD Sharing: YES. Countries: 31. Publications: 6.
A Study of SAR444245 Combined With Other Anticancer Therapies for the Treatment of Participants With Gastrointestinal Cancer (Master Protocol) (Pegathor Gastrointestinal 203)
ClinicalTrials.gov study NCT05104567. IPD Sharing: YES. Countries: 9. Publications: 0.
177Lu-PSMA-617 vs. Androgen Receptor-Directed Therapy in the Treatment of Progressive Metastatic Castrate Resistant Prostate Cancer
ClinicalTrials.gov study NCT04689828. IPD Sharing: YES. Countries: 14. Publications: 2.
Treatment in Preventing Anal Cancer in Patients With HIV and Anal High-Grade Lesions
ClinicalTrials.gov study NCT02135419. IPD Sharing: YES. Countries: 2. Publications: 4.
Everolimus in Combination With Trastuzumab and Paclitaxel in the Treatment of HER2 Positive Locally Advanced or Metastatic Breast Cancer
ClinicalTrials.gov study NCT00876395. IPD Sharing: UNDECIDED. Countries: 28. Publications: 3.
A Study of SAR444245 Combined With Cemiplimab for the Treatment of Participants With Various Advanced Skin Cancers (Pegathor Skin 201)
ClinicalTrials.gov study NCT04913220. IPD Sharing: YES. Countries: 7. Publications: 0.
The Effect of Surgeon Emotional Support on Treatment Choice for Low-risk Thyroid Cancer
ClinicalTrials.gov study NCT05132478. IPD Sharing: YES. Countries: 1. Publications: 0.
Lapatinib +Capecitabine Treatment for Advanced Metastatic Breast Cancer in Women From China
ClinicalTrials.gov study NCT00508274. IPD Sharing: YES. Countries: 2. Publications: 1.
Molecular dynamics dataset for pharmacological repositioning in the treatment of non-small-cell lung cancer
<p><span>Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK<sup>+</sup>. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK<sup>+ </sup>NSCLC patients.</span> <span>However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an <em>in silico</em> approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling to obtain a structural model of cdALK<sup>+</sup> protein and then performed molecular docking and molecular dynamics of the complex cdALK<sup>+</sup>-iALKs to generate the pharmacophore model. The pharmacophore was used to identify potential iALKs from FDA-approved drugs library by ligand-based virtual screening. Four pharmacophores with different atomistic characteristics were generated, resulting in six drugs that satisfied the proposed atomistic positions</span> <span>and coupled at the ATP-binding site. Mitoxantrone, riboflavin and abacavir exhibit the best interaction energies with 228.29, 165.40 and 133.48 kjoul/mol respectively. In addition, the special literature proposed these drugs for other types of diseases due to pharmacological repositioning. This study proposes FDA-approved drugs with ALK inhibitory characteristics. Moreover, we identified pharmacophores sites that can be tested with other pharmacological libraries</span><span>.</span></p>
Exploratory mass cytometry analysis reveals immunophenotypes of cancer treatment-related pneumonitis
<p>Anti-cancer treatments can result in various adverse effects, including infections due to immune suppression/dysregulation and drug-induced toxicity in the lung. One of the major opportunistic infections is <em>Pneumocystis jirovecii</em> pneumonia (PCP), which can cause severe respiratory complications and high mortality rates. Cytotoxic drugs and immune-checkpoint inhibitors (ICIs) can induce interstitial lung diseases (ILDs). Nonetheless, the differentiation of these diseases can be difficult, and the pathogenic mechanisms of such diseases are not yet fully understood. To better comprehend the immunophenotypes, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid from patients with PCP, cytotoxic drug-induced ILD (DI-ILD), and ICI-associated ILD (ICI-ILD) using two panels containing 64 markers. In PCP, we observed an expansion of the CD16<sup>+</sup> T cell population, with the highest CD16<sup>+</sup> T proportion in a fatal case. In ICI-ILD, we found an increase in CD57<sup>+</sup> CD8<sup>+</sup> T cells expressing immune checkpoints (TIGIT<sup>+</sup> LAG3<sup>+</sup> TIM-3<sup>+</sup> PD-1<sup>+</sup>), FCRL5<sup>+</sup> B cells, and CCR2<sup>+</sup> CCR5<sup>+</sup> CD14<sup>+</sup> monocytes. These findings uncover the diverse immunophenotypes and possible pathomechanisms of cancer treatment-related pneumonitis.</p>
Data for article "Personal approach for cancer treatment: a meta-analysis of Phase II Clinical trials"
<p>We conducted systematic review and meta-analysis to provide a comprehensive overview of outcomes in patients who underwent personalized genomics-based versus non-personalized treatment in oncology. The PubMed searches detected 803 studies based on phase II clinical trials’ results published from 2010 to 2021. We selected 50 studies, having 81 arms and 6536 patients for the analysis. We compared Response Rate (RR), medians and 1-year rates of Overall Survival (OS) and Progression-Free Survival (PFS) between genomics-based personalized and non-personalized arms. This repository contains final dataset (Dataset file) and t<span lang="EN-US">he information on 803 studies identified in the literature search (803 studies description file)</span>. </p> <p>The searches, study selection, data extraction and synthesis were performed in accordance to PRISMA (preferred reporting items for systematic review and meta-analysis) guidelines. The research protocol was registered in PROSPERO (International prospective register of systematic reviews, <a href="https://www.crd.york.ac.uk/PROSPERO" rel="nofollow">https://www.crd.york.ac.uk/PROSPERO</a>), record ID CRD42024504021. </p> <p>We performed proportional meta-analysis using the RStudio program, utilizing the R programming language and packages "meta", "metafor," and "tidyverse", the code is available at github: https://github.com/MikhailPot/PreciseOnco_meta-analysis </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.