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7,125 results for “prostate cancer”
Converting between the International Prostate Symptom Score (IPSS) and the Expanded Prostate Cancer Index Composite (EPIC) urinary subscales: modeling and external validation
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miR-145-5p mimic inhibits bone metastasis of prostate cancer via the regulation of epithelial mesenchymal transition
<p><strong>Background.</strong> The bone is the most common site of distant metastasis in prostate cancer. However, treatments for the bone metastasis of prostate cancer remain unsatisfactory. MicroRNAs (miRNAs) are small noncoding RNAs that play a variety of critical roles in tumor development and progression. Studies have confirmed that miRNA mimics could regulate the response to therapy in many cancers. <strong>Methods.</strong> In this study, a set of forty-four miRNAs were reduced in prostate cancer patients with bone metastases by high-throughput sequencing analysis. Wound healing and transwell assays and western blotting analysis were used to explore the role of miRNA mimic in prostate cancer bone metastasis.<strong> Results.</strong> These mimics of down-regulated miRNAs may be able to cure prostate cancer bone metastasis, including hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-133a-3p, hsa-miR-222-5p, hsa-miR-204-3p, hsa-miR-145-5p, hsa-miR-3681-5p, hsa-miR-184, hsa-miR-144-3p, hsa-miR-204-5p, and hsa-miR-221-5p. To further investigate the role of these miRNA mimics on prostate cancer bone metastasis, miR-145-5p was randomly selected for validation. Bioinformatics analysis showed that miR-145-5p target genes significantly affected TGF-beta signaling pathway. Wound healing and transwell assays and western blotting analysis revealed that miR-145-5p mimic inhibited proliferation, migration and invasion. Importantly, miR-145-5p mimic increased the expression of E-cadherin and reduced the expression of matrix metalloproteinase 2 and 9. These results revealed that miR-145-5p mimic mediated epithelial mesenchymal transition. Meanwhile, miR-145-5p mimic enhanced the level of caspase 9, which is an important promoter of apoptosis. These results indicate that miR-145-5p mimic could inhibit the progress of prostate cancer bone metastasis via regulation of epithelial mesenchymal transition. In addition, miR-145-5p mimic could induce the apoptosis of prostate cancer cells with bone metastases. In summary, the miR-145-5p mimic is expected to become a novel strategy for the treatment of tumor metastasis.</p>
Filtered and annotated SNV and indel variants in the PC3 and LNCaP human prostate cancer cell lines
<p>150bp paired-end reads (insert size 350bp) were obtained using the Illumina HiSeqX sequencer. Samtools v1.3.1 mpileup and bcftools were used to interrogate indexed BAM files, from whole-genome reads aligned to human reference genome GRCh38 build 82, and generate a VCF (Variant Call Format) file of single nucleotide variants (SNVs) and short indel variants. Variants private, or unique to a particular cell line, or shared by both were next identified. Variants (likely to be common germline variants) present in HapMap, 1000 genomes phase 3 (2,504 human genomes), and the National Heart Lung and Blood Institute’s Exome Sequencing Project (ESP) (bundled variant data file available at https://goo.gl/mEogvD) were excluded. Variant files (VCF) were filtered using SnpSift with the following parameters: 'QUAL \textgreater= 200 \&\& DP \textgreater= 30', where QUAL denotes minimum variance confidence and DP total depth threshold. Filtered variants were annotated using SnpEff v4.3g. Please see https://github.com/sciseim/PCaWGS for associated scripts.</p> <p> </p>
de novo genome assembly of the LNCaP human prostate cancer cell line
<p>Whole-genome sequencing reads from the LNCaP human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p>
de novo genome assembly of the PC3 human prostate cancer cell line
<p>Whole-genome sequencing reads from the PC3 human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p> <p> </p> <p> </p> <p> </p>
Supplementary material: CYB561 supports the neuroendocrine phenotype in castration-resistant prostate cancer
<p>Castration-resistant prostate cancer (CRPC) is associated with resistance to androgen deprivation therapy, and an increase in the population of neuroendocrine (NE) differentiated cells. It is hypothesized that NE differentiated cells secrete neuropeptides that support androgen-independent tumor growth and induce aggressiveness of adjacent proliferating tumor cells through a paracrine mechanism. The cytochrome b561 (<em>CYB561</em>) gene, which codes for a secretory vesicle transmembrane protein, is constitutively expressed in NE cells and highly expressed in CRPC. CYB561 is involved in the α-amidation-dependent activation of neuropeptides and contributes to regulating iron metabolism which is often dysregulated in cancer. These findings led us to hypothesize that CYB561 may be a key player in the NE differentiation process that drives the progression and maintenance of the highly aggressive NE phenotype in CRPC. In our study, we found that <em>CYB561</em> expression is upregulated in metastatic and NE prostate cancer (NEPC) tumors and cell lines compared to normal prostate epithelia and that its expression is independent of androgen regulation. Knockdown of <em>CYB561</em> in androgen-deprived LNCaP cells dampened NE differentiation potential and transdifferentiation-induced increase in iron levels. In NEPC PC-3 cells, depletion of CYB561 reduced the secretion of growth-promoting factors, lowered intracellular ferrous iron concentration, and mitigated the highly aggressive nature of these cells in complementary assays for cancer hallmarks. These findings demonstrate the role of CYB561 in facilitating transdifferentiation and maintenance of NE phenotype in CRPC through its involvement in neuropeptide biosynthesis and iron metabolism pathways.</p>
Papers & Videos Prostate Cancer Studies
<p>El dataset incluye artículos y videos relacionados con investigaciones sobre el cáncer de próstata, publicados en diversas revistas científicas. Este conjunto de datos tiene como objetivo analizar la frecuencia y el enfoque de los estudios realizados en esta área, así como corroborar la relevancia que la comunidad científica otorga al estudio del cáncer de próstata.</p> <p>La data se obtuvo de un website especializado en la publicación de revistas cientificas, revisadas por pares de acceso abierto: http://www.dovepress.com</p>
Metascape Results for Prostate Cancer Multiomics Data
<p><strong>ABSTRACT </strong></p> <p>Large <em>p</em> small <em>n</em> problem is a challenging problem in big data analytics. There are no de facto standard methods available to it. In this study, we propose a tensor decomposition (TD) based unsupervised feature extraction (FE) formalism applied to multiomics datasets, where the number of features is more than 100000 while the number of instances is as small as about 100. The proposed TD based unsupervised FE outperformed other conventional supervised feature selection methods, such as random forest, categorical regression (also known as analysis of variance, ANOVA), and penalized linear discriminant analysis when they are applied to not only multiomics datasets but also synthetic datasets. Genes selected by TD based unsupervised FE were biologically reliable. TD based unsupervised FE turned out to be not only the superior feature selection method but also the method that can select biologically reliable genes. </p> <p><strong>Instructions: </strong></p> <p>This is a supplementary file of paper submitted to bigdata2020</p> <p> </p> <p><strong>Inspiration:</strong></p> <p>This dataset uploaded to U-BRITE for "AI against CANCER DATA SCIENCE HACKATHON"</p> <p>https://cancer.ubrite.org/hackathon-2021/</p> <p><strong>Acknowledgements</strong></p> <p>Y-h. Taguchi, July 17, 2020, "Metascape results for Prostate cancer multiomics data", IEEE Dataport, doi: https://dx.doi.org/10.21227/rdmb-jm40.</p> <p>https://ieee-dataport.org/documents/metascape-results-prostate-cancer-multiomics-data</p> <p><strong>U-BRITE last update date:</strong> 07/21/2021</p>
Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression.
<p>This file contains vst-normalized gene expression data along with annotations which can be used to reproduce our findings.</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>
Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
<p>Full results datasets for Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility:</p> <p>ALL*all_pheno.csv are TOPMed-MESA combined-ancestry models, discovery and replication cohorts</p> <p>ARIC_EA_all_pheno.csv is ARIC European-American ancestry models, discovery cohort</p> <p>ARIC*meta_all.txt is ARIC European-American ancestry models, discovery and replication cohorts, with meta-analysis of disc+rep</p>
Automated diagnosis of prostate cancer using artificial intelligence. A systematic literature review. Extraction and Summary Forms.
<p>Extraction and summary forms of a systematic literature review protocol detailed by Barbara Kitchenham for automated diagnosis of prostate cancer using artificial intelligence articles. </p>
Search strategies for generic justification of 18F-PSMA PET/CT in the staging of primary prostate cancer and the restaging of recurrent and metastatic prostate cancer
<p>The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The search strategies address the following research questions:</p> <p>RQ 1: In the primary staging of patients with high risk prostate cancer, what is the sensitivity, specificity and diagnostic accuracy of 18F-PSMA?</p> <p>RQ 2: In patients with biochemically recurrrent prostate cancer, what is the sensitivity, specificity and diagnostic accuracy of 18F-PSMA?</p> <p>RQ 3: What is the risk of adverse events (including dose) associated with receiving 18F-PSMA?</p> <p>RQ 4: Is 18F-PSMA uptake associated with response to treatments for metastatic prostate cancer?</p>
Single Cell RNA sequencing data of ADT treated Prostate cancer patients
<p>The data was generated from a study that was conducted according to guidelines approved by the Review Board at the University of Texas Southwestern Medical Center. We procured patient biopsy samples from two distinct studies. The first is titled "Tissue Collection and Results Gathering for Radiotherapy Patients & Healthy Individuals" (STU 072010-098), and the second is a Phase I Clinical Study on Stereotactic Ablative Radiotherapy (SABR) for Pelvic and Prostate Areas in High-Risk Prostate Cancer Patients (STU062014-027). The single-cell RNA sequencing (scRNA-seq) took place in Dr. Douglas Strand's laboratory, adhering to the method outlined in Henry et al<sup>1</sup>. We used a 1-hour treatment with 5mg/ml of collagenase type I, 10mM of ROCK inhibitor, and 1mg of DNase. Barcode labeling for 3' GEX was done using a 10X machine, and the sequencing process utilized an Illumina NextSeq 500 device.</p> <p> </p> <p>1. Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J., ... & Strand, D. W. (2018). A cellular anatomy of the normal adult human prostate and prostatic urethra. <em>Cell reports</em>, <em>25</em>(12), 3530-3542.</p>
Search strategies for 177 lu-PSMA in the treatment of metastatic castrate-resistant prostate cancer
<p>The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The search strategies were designed to answer the following research questions:</p> <p><strong>RQ1.</strong> Does the use of radioligand therapy using <sup>177</sup>Lu-PSMA lead to improved overall survival and progression-free survival, compared with other available treatment(s) in patients with metastatic, castrate-resistant prostate cancer?</p> <p><strong>RQ2.</strong> Does the use of radioligand therapy using <sup>177</sup>Lu-PSMA lead to improved quality of life or symptom control, compared with other available treatment(s), in patients with metastatic, castrate-resistant prostate cancer?</p> <p><strong>RQ3. </strong> What is the risk of adverse events and toxicity associated with radioligand therapy using <sup>177</sup>Lu-PSMA, compared with other available treatment in patients with metastatic, castrate-resistant prostate cancer?</p>
Oxaliplatin and Pemetrexed Disodium in Treating Patients With Refractory Hormone-Resistant Prostate Cancer
ClinicalTrials.gov study NCT01338792. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Selinexor in Treating Patients With Abiraterone Acetate and/or Enzalutamide Refractory Metastatic Castration-Resistant Prostate Cancer
ClinicalTrials.gov study NCT02215161. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Hormone Suppression and Radiation Therapy for 6 Months With/Without Docetaxel for High Risk Prostate Cancer
ClinicalTrials.gov study NCT00116142. IPD Sharing: NO. Countries: 1. Publications: 4.
The Effect of High-dose Silybin-phytosome in Men With Prostate Cancer
ClinicalTrials.gov study NCT00487721. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Aflibercept in Combination With Docetaxel in Metastatic Androgen Independent Prostate Cancer
ClinicalTrials.gov study NCT00519285. IPD Sharing: Not stated. Countries: 31. Publications: 3.
ScienceDex guides
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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)
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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.