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1,035 results for “cancer invasion”
Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation: Confocal and atomic force microscopy
<p><strong>Summary</strong></p> <p>Dataset of imaging data related to the publication Raudenska, M., Kratochvilova, M., Vicar, T., Gumulec, J., Balvan, J., Polanska, H. Pribyl, J. & Masarik, M.:Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation. <em>Scientific Reports </em><strong>2019, </strong>9, 1660</p> <p>This dataset includes image data of <em>atomic force microcopy</em> (Young modulus) and <em>confocal microscopy</em>(staining of F-actin and β-tubulin) of prostate cell lines PNT1A, 22Rv1, and PC-3. </p> <p><strong>Materials and Methods</strong></p> <p><em>Cells, cell culture conditions</em></p> <p>Cells confluent up to 50–60% were washed with a FBS-free medium and treated with a fresh medium with FBS and required antineoplastic drug concentration (IC50 concentration for the particular cell line). The cells were treated with 93 µM (PC-3), 38 µM (PNT1A), and 24 µM (22Rv1) of cisplatin (Sigma-Aldrich, St. Louis, Missouri), respectively. IC50 concentrations used for treatment with docetaxel (Sigma-Aldrich, St. Louis, Missouri) were 200nM for PC-3, 70nM for PNT1A, and 150nM for 22Rv1. </p> <p><em>Long-term zinc (II) treatment of cell cultures</em></p> <p>Cells were cultivated in the constant presence of zinc(II) ions. Concentrations of zinc(II) sulphate in the medium were increased gradually by small changes of 25 or 50 µM. The cells were cultivated at each concentration no less than one week before harvesting and their viability was checked before adding more zinc. This process was used to select zinc resistant cells naturally and to ensure better accumulation of zinc within the cells (accumulation of zinc is usually poor during the short-term treatment of prostate cancer cells). Total time of the cultivation of cell lines in the zinc(II)-containing media exceeded one year. Resulting concentrations of zinc(II) in the media (IC50 for the particular cell line) were 50 µM for the PC-3 cell line, 150 µM for the PNT1A cell line, and 400 µM for the 22Rv1 cell line. The concentrations of zinc(II) in the media and FBS were taken into account. </p> <p><em>Actin and tubulin staining</em></p> <p>β-tubulin was labeled with anti- β tubulin antibody [EPR1330] (ab108342) at a working dilution of 1/300. The secondary antibody used was Alexa Fluor® 555 donkey anti-rabbit (ab150074) at a dilution of 1/1000. Actin was labeled with Alexa Fluor™ 488 Phalloidin (A12379, Invitrogen); 1 unit per slide. For mounting Duolink® In Situ Mounting Medium with DAPI (DUO82040) was used. The cells were fixed in 3.7% paraformaldehyde and permeabilized using 0.1% Triton X-100. </p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><em>Atomic force microscopy</em></p> <p>We used the bioAFM microscope JPK NanoWizard 3 (JPK, Berlin, Germany) placed on the inverted optical microscope Olympus IX‑81 (Olympus, Tokyo, Japan) equipped with the fluorescence and confocal module, thus allowing a combined experiment (AFM‑optical combined images). The maximal scanning range of the AFM microscope in X‑Y‑Z range was 100‑100‑15 µm. The typical approach/retract settings were identical with a 15 μm extend/retract length, Setpoint value of 1 nN, a pixel rate of 2048 Hz and a speed of 30 µm/s. The system operated under closed-loop control. After reaching the selected contact force, the cantilever was retracted. The retraction length of 15 μm was sufficient to overcome any adhesion between the tip and the sample and to make sure that the cantilever had been completely retracted from the sample surface. Force‑distance (FD) curve was recorded at each point of the cantilever approach/retract movement. AFM measurements were obtained at 37°C (Petri dish heater, JPK) with force measurements recorded at a pulling speed of 30 µm/s (extension time 0.5 sec).</p> <p>The Young's modulus (E) was calculated by fitting the Hertzian‑Sneddon model on the FD curves measured as force maps (64x64 points) of the region containing either a single cell or multiple cells. JPK data evaluation software was used for the batch processing of measured data. The adjustment of the cantilever position above the sample was carried out under the microscope by controlling the position of the AFM‑head by motorized stage equipped with Petri dish heater (JPK) allowing precise positioning of the sample together with a constant elevated temperature of the sample for the whole period of the experiment. Soft uncoated AFM probes HYDRA-2R-100N (Applied NanoStructures, Mountain View, CA, USA), i.e. silicon nitride cantilevers with silicon tips are used for stiffness studies because they are maximally gentle to living cells (not causing mechanical stimulation). Moreover, as compared with coated cantilevers, these probes are very stable under elevated temperatures in liquids – thus allowing long-time measurements without nonspecific changes in the measured signal.</p> <p><em>Image analysis</em></p> <p>Fluorescence microscopy data were analyzed in ImageJ 1.52h and Python 3.7.1 as follows: cells were manually segmented using actin fluorescence channel, two regions were created for analysis: whole cell and cell periphery, lining a 4 μm thick region around cell border and including most of periphery actin cytoskeleton. In these two regions following parameters were measured for both actin and tubulin fluorescence: Integrated intensity, median intensity, and following regions were measured to describe cell morphology: Cell area, Maximum caliper (max feret diameter), roundness, and aspect ratio. Moreover, stress fibers were manually segmented in every cell and following parameters were measured: number of fibers per cell, feret angle of fiber, integrated intensity, fiber length, mean intensity. Next, a standard deviation of feret angles of individual fibers was calculated relatively to mean of feret angle using a circstd function from scipy package for Python.</p> <p><strong>Identification of files</strong></p> <p><em>Microscopy data</em></p> <p>Files are separated into individual zip files. The dataset of <em>confocal microscopy </em>is separated based on treatments: untreated control, docetaxel-treated cells, cisplatin-treated cells, zinc-treated cells. Filenames actin_tubulin_Zstack_cisplatin.zip, actin_tubulin_Zstack_untreated_control.zip, actin_tubulin_Zstack_zinc.zip, actin_tubulin_Zstack_docetaxel.zip. Files included in these ZIP archives are named as follows: "cellline_treatment_FOV". Files are 3-layer 16bit tiff files with layer sequence as follows: F-Actin (Phalloidin)/b-tubulin/Hoechst 33342. The dataset contains 242 FOVs of three cell line types/three treatments + one control, files are Z-stacks made of 50 slices.</p> <p>The dataset of <em>atomic force microscopy </em>(AFM) is included in one ZIP archive "AFM_YoungModulus_SetpointHeight.zip", which includes data on Young modulus and Setpoint Height of cell lines 22Rv1, PNT1A and PC-3 and treatments zinc, docetaxel, cisplatin (+control), i.e. identical like for confocal microscopy. The file naming is as follows: "AFM_cellline_treatment_FOV_Youngmodulus.tif" for Young modulus and "AFM_cellline_treatment_FOV_setpointheight.tif" for setpoint height. The data are filtered 32-bit tiff images, where the pixel value correspond to cell stiffness (young modulus) in Pa or setpoint height in m.</p> <p><em>Confocal microscopy analysis files</em></p> <p>Following files are csv tables including image analysis of actin/tubulin staining captured by confocal microscope:</p> <p>Cytoskeleton_fluo_analysis_Cell_Cell_periphery_morphology.csv: table includes analyzed data for actin and tubulin staining in following cellular regions: cell, cell periphery. Standard ImageJ parameters regarding intensity and morphology included.</p> <p>Cytoskeleton_fluo_analysis_Fibers.csv: table includes results of manual segmentation and consequent analysis of actin stres fibers in the cells. Apart from standard ImageJ parameters, also number of stress fibers per cell and standard deviation of fiber angle relative to the cell mean angle (for details see methods) are included.</p>
Supplementary material - Non-invasive Multimodal Imaging Reveals Early Therapy-Induced Senescence in Human Cancer Cells
<p>The repository features .xls and .txt worksheets including all the data used through this work and reported in the manuscript figures and graphs. More precisely, we included the following: </p> <ul> <li>Figure 2. Raw pixel-wise signals detected in NLO images of TIS cells control cells that were used to perform the colocalization graphs and analyses reported. We describe the average colocalization of SRS and F-CARS signals, and TPEF and E-CARS signals, in both phenotypes.</li> <li>Figure 4. Raw data from image analyses of TPEF and SRS channels of multimodal NLO images, divided in 5 different time points over the therapy follow-up period. The data describe the early rearrangement of mitochondria (TPEF) and lipid vesicles (SRS) in TIS cells, with respect to control counterparts.</li> <li>Figure 6. Raw data from image analyses of QPI images, divided in 4 different time points over the therapy follow-up period. The data describe the early morphological modifications of TIS cells, with respect to control counterparts.</li> </ul>
18Fluorine-Fluciclovine PET/CT for Staging Muscle Invasive Bladder Cancer Preceding Radical Cystectomy
ClinicalTrials.gov study NCT04018053. IPD Sharing: YES. Countries: 1. Publications: 1.
All simulation results, figures and code regarding the manuscript: Calibrating models of cancer invasion: parameter estimation using Approximate Bayesian Computation and gradient matching
<p>We present two different methods to estimate parameters within a partial differential equation (PDE) model of cancer invasion. The model describes the spatio-temporal evolution of three variables -- tumour cell density, extracellular matrix density and matrix degrading enzyme concentration -- in a one-dimensional tissue domain. The first method is a likelihood-free approach associated with Approximate Bayesian Computation (ABC); the second is a two-stage gradient matching method based on smoothing the data with a Generalized Additive Model (GAM) and matching gradients from the GAM to those from the model. Both methods performed well on simulated data. To increase realism, additionally we tested the gradient matching scheme with simulated measurement error and found that the ability to estimate some model parameters deteriorated rapidly as measurement error increased.</p>
Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection
<p>Processed data (feature-by-sample matrices) of non-disruptive bisulfite-free methylation sequencing for cfDNA samples from 4 clinical cohorts (Cohort 1, Cohort 2, Cohort 3, and cfTAPS dataset). Codes used to repeat the results in our paper can be found https://rpubs.com/LiYumei/926228 and https://github.com/ChaorongC/MESA. </p>
Dataset from the Study: "A non-invasive approach to skin cancer diagnosis via graphene electrical tattoos and electrical impedance tomography"
<p>This repository contains the scripts and other resources used in:</p> <p>“A non-invasive approach to skin cancer diagnosis via graphene electrical tattoos and electrical impedance tomography”, Lee H et al. 10.1088/1361-6579/ad3d26</p> <p> </p> <p>>> THIS DATA IS FREE FOR USE IN ANY SCIENTIFIC RESEARCH WITH CITATION (PLEASE USE THE DOI FOR PRECISE CITATION): DOI 10.1088/1361-6579/ad3d26</p> <p> </p> <p>>> IF YOU USE THESE RESOURCES, CITE!!!</p> <p> </p> <p>The repository contains the phantom experimental data and the code and resources to generate the numerical/computational models.</p> <p> </p> <p>Note:</p> <p>Software used in this study:</p> <ul> <li>MATLAB</li> <li>EIDORS </li> </ul> <p>Measurement system used in this study:</p> <ul> <li>Sciospec EIT32 system</li> </ul>
Mutation and methylation data for study: Assessment of the molecular heterogeneity of E-cadherin expression in invasive lobular breast cancer
<p>Processed mutation data and DNA methylation beta values published with this study.</p>
Dataset of "Interclonal mutually beneficial cooperation mediated by TGF-β1 enhances invasion of breast cancer cells"
<p>Original pictures from Figures 1A and 1B.</p> <p>Dataset from Figure 2-6 with data analysis (including Wound Healing assay, Transwell migration and invasion assay) on MCF7, MDA and H2122 AS cell lines</p>
EFFECTIVENESS OF PELVIC FLOOR EXERCISE TO PREVENT LARS (LOW ANTERIOR RESECTION SYNDROME) AFTER MINI-INVASIVE LOW ANTERIOR RESECTION IN PATIENTS WITH RECTAL CANCER. Adherence to prescribed home exercise. Quality of life after low anterior resection.
<p><span>Advances in the surgical treatment of rectal diseases lead to better oncological results, a higher chance of preserving the sphincters, and thus a lower number of permanent stomas. However, the preserved anus does not always have to perform its original function fully. All patients after a low anterior resection are at risk of developing functional disorders - low anterior resection syndrome (LARS). The prevalence of LARS ranges from 41-80% and is a significant factor in reducing the quality of life. </span><span>According to the available data, it is possible to prevent LARS through postoperative pelvic floor exercises, however, relevant studies are missing. </span><span>The pelvic floor is a ligament-muscle system that provides dynamic support for the organ systems located in the small pelvis. </span><span>Strengthening the muscles can serve as a follow-up treatment after surgical procedures including prevention of LARS.</span></p> <p><span>The main goal of this randomized study will be to determine the effectiveness of pelvic floor exercises on the incidence or severity of LARS in patients after mini-invasive rectal resection. Secondary goal is to identify the adherence of patients to prescribed home exercise and quality of life. </span></p> <p><span>Researchers will compare the group of patients with pelvic floor exercises to those without. Under the professional guidance of a physiotherapist, participants will be educated the day before surgery and in the first 4 postoperative days to exercise the pelvic floor exercise and continue at home for a month. </span><span>The resulting knowledge will have a fundamental impact on clinical practice and patient management.</span></p>
Supplementary files for "Tristetraprolin Affects Invasion-Associated Genes Expression and Cell Motility in Triple-Negative Breast Cancer Model"
<p>Track1 and Track3 - raw numerical data on cell tracking; Morphology-DXR treated - raw images of the cells, treated with DXR; Morphology ecTTP+WT - morphology of wild-type and TTP-overexpressing cells; RAW data qPCR - rew data of gene expression experiments</p>
Dataset of High-Resolution Micro-CT Imaging of Tumor Invasion and Metastasis in a Murine Esophageal Cancer PDX Model
<p>This dataset features high-resolution micro-CT imaging data capturing the progression of tumor invasion and metastasis in an orthotopic patient-derived xenograft (PDX) model of esophageal cancer. Using contrast-enhanced micro-CT, we visualized detailed patterns of tumor invasion, including budding, multicellular streaming, and expansive growth, across multiple abdominal organs such as the stomach, pancreas, liver, and spleen. The dataset includes two specimens, highlighting both the primary tumor site and extensive metastases throughout the abdominal cavity. Our imaging preserved the native tissue architecture, providing a unique three-dimensional view of tumor-host interactions. This collection offers valuable insights for researchers studying the dynamics of esophageal cancer invasion and metastasis. Detailed descriptions of the micro-CT scanning parameters, image analysis, and sample preparation are provided within the dataset archive.</p>
The role of TAp63g and p53 point mutations in regulating DNA repair, mutational susceptibility and invasion of bladder cancer cell
<p>Raw data set for the manuscript submitted to e-Life (10-06-2021-RA-eLife-71184 ) for peer-review. </p>
Mass spectrometry- based biomarkers to detect prostate cancer: A multicentric study based on non- invasive urine collection without prior intervention
<p>These are datasets related to mass spectrometry proteomics analysis, in particular Capillary Electrophoresis coupled to Mass Spectrometery (CE-MS). CE-MS was employed to acquire proteomics profiles from 970 patients from two different clinical centers. with the aim to develop a biomarker model to detect Prostate Cancer. </p>
Data from: Novel methods to define invasive procedures at the end-of-life were developed to improve quality of end of life care research: A population-based cohort study in colorectal cancer
<p><strong>Background</strong></p> <p>Understanding the use of invasive procedures (IPs) at the end-of-life (EoL) is important to avoid under- and overtreatment, but epidemiologic analysis is hampered by limited methods to define treatment intent and EoL phase. This study applied novel methods to report IPs at the EoL using a colorectal cancer (CRC) case study.</p> <p><strong>Methods</strong></p> <p>An English population-based cohort of adult patients diagnosed between 2013 and 2015 was used with follow-up to 2018. Procedure intent (curative, non-curative, diagnostic) by cancer site and stage at diagnosis was classified by two surgeons independently. Joinpoint regression modelled weekly rates of IPs for 36 sub-cohorts of patients with incremental survival of 0-36 months. EoL phase was defined by a significant IP rate change before death. Zero-inflated Poisson regression explored associations between IP rates and clinical/sociodemographic variables.</p> <p><strong>Results</strong></p> <p>Of 87,731 patients included, 41,972 (48%) died. 9,492 procedures were classified by intent (interrater agreement 99.8%). Patients received 502,895 IPs (1.39 and 3.36 per person year for survivors and decedents). Joinpoint regression identified significant increases in IPs four weeks before death in those living 3-6 months, and eight weeks before death in those living 7–36 months from diagnosis. 7,908 (18.8%) patients underwent IPs at the EoL, with stoma formation the most common major procedure. Younger age, early-stage disease, men, lower comorbidity, those receiving chemotherapy and living longer from diagnosis were associated with IPs.</p> <p><strong>Conclusions</strong></p> <p>Methods to identify and classify IPs at the EoL were developed and tested within a CRC population. This approach can be now extended and validated to identify potential under- and overtreatment. </p>
Atezolizumab in Treating Patients With Recurrent BCG-Unresponsive Non-muscle Invasive Bladder Cancer
ClinicalTrials.gov study NCT02844816. IPD Sharing: UNDECIDED. Countries: 2. Publications: 1.
Gamma-secretase/Notch Signalling Pathway Inhibitor RO4929097 in Treating Patients With Advanced, Metastatic, or Recurrent Triple Negative Invasive Breast Cancer
ClinicalTrials.gov study NCT01151449. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Fluciclovine and PSMA PET/CT for the Classification and Improved Staging of Invasive Lobular Breast Cancer
ClinicalTrials.gov study NCT04750473. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Phase 3 Study of UGN-102 for Low-Grade Intermediate-Risk Non-Muscle Invasive Bladder Cancer
ClinicalTrials.gov study NCT04688931. IPD Sharing: Not stated. Countries: 10. Publications: 1.
Phase II Study of Fluorine-18 3'-Deoxy-3'-Fluorothymidine (F-18-FLT) in Invasive Breast Cancer
ClinicalTrials.gov study NCT00572728. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cryoablation Therapy in Treating Patients With Invasive Ductal Breast Cancer
ClinicalTrials.gov study NCT00723294. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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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)
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.