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Find video protocols related to scientific articles indexed in Pubmed.
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.
Bioinformatics
PUBLISHED: 08-31-2014
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DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.
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Targeting PI3-kinase (PI3K), AKT and mTOR axis in lymphoma.
Br. J. Haematol.
PUBLISHED: 08-06-2014
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Targeted therapy represents a transformation in oncology, a field that has relied primarily on non-selective cytotoxic therapies. Phosphatidylinositol 3-kinase (PI3K) is a family of ubiquitous signalling molecules involved in a wide variety of cellular processes and likewise, in a broad selection of human cancers. The discovery that the p110-? form of PI3K is differentially expressed in normal and malignant lymphocytes has led to the development of specific inhibitors that are currently in clinical trials for lymphoma. Downstream effectors of PI3K, including v-akt murine thymoma viral oncogene homolog 1 (AKT; also termed AKT1) and mechanistic target of rapamycin (serine/threonine kinase) (mTOR) are similarly important in lymphoma, and agents targeting these components of the PI3K-AKT-mTOR axis are also underway, although at earlier stages of development. In this review we examine the role of PI3K-AKT-mTOR in normal and malignant lymphocytes, as well as the preclinical and clinical status of a number of inhibitors of this pathway.
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Hairy cell leukemia: Update on molecular profiling and therapeutic advances.
Blood Rev.
PUBLISHED: 07-11-2014
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Hairy cell leukemia was initially described as a clinicopathologic entity more than 50 years ago. We have subsequently discovered that HCL is really at least two diseases: classical HCL and the hairy cell leukemia variant. The former is among a small group of cancers exceptional for being (nearly) unified by a single genetic lesion, the BRAF V600E mutation. Over the past three decades, tremendous progress in both diagnostic and prognostic clarification has been accompanied by therapeutic advances in classical HCL. Consequently, this once uniformly fatal disease has been converted in most cases into a chronic illness enabling patients to live long and productive lives. In response to standard therapy, patients have high complete remission rates. Unfortunately, the long-term survival curves have not plateaued, revealing that this disease is controlled but not cured. Though rare and representing only about 10% of an already rare disease, those patients with the variant fare exceptionally poorly with standard therapy: complete response rates to purine nucleoside analogs are reported to be less than 50%, whereas the complete response rates in classical HCL are up to 90%. Novel small molecules targeting BRAF and the B-cell receptor signaling complex, and biologic agents like antibodies and immunotoxin conjugates are being explored for those patients who have relapsed. Substantial opportunities for continued research remain. This complex and multi-faceted disease incorporates challenges from altered immunity associated with the underlying disease and its treatments. Considering the rarity of this malignancy, optimization of patient management requires multi-institutional collaboration. The Hairy Cell Leukemia Foundation (www.hairycellleukemia.org) was formed to coordinate these efforts.
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PKC-? as a therapeutic target in CLL: PKC inhibitor AEB071 demonstrates preclinical activity in CLL.
Blood
PUBLISHED: 07-07-2014
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Targeting B-cell receptor (BCR) signaling in chronic lymphocytic leukemia (CLL) has been successful with durable remissions observed with several targeted therapeutics. Protein kinase C-? (PKC-?) is immediately downstream of BCR and has been shown to be essential to CLL cell survival and proliferation in vivo. We therefore evaluated sotrastaurin (AEB071), an orally administered potent PKC inhibitor, on CLL cell survival both in vitro and in vivo. AEB071 shows selective cytotoxicity against B-CLL cells in a dose-dependent manner. Additionally, AEB071 attenuates BCR-mediated survival pathways, inhibits CpG-induced survival and proliferation of CLL cells in vitro, and effectively blocks microenvironment-mediated survival signaling pathways in primary CLL cells. Furthermore, AEB071 alters ?-catenin expression, resulting in decreased downstream transcriptional genes as c-Myc, Cyclin D1, and CD44. Lastly, our preliminary in vivo studies indicate beneficial antitumor properties of AEB071 in CLL. Taken together, our results indicate that targeting PKC-? has the potential to disrupt signaling from the microenvironment contributing to CLL cell survival and potentially drug resistance. Future efforts targeting PKC with the PKC inhibitor AEB071 as monotherapy in clinical trials of relapsed and refractory CLL patients are warranted.
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Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.
Cancer Inform
PUBLISHED: 01-01-2014
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QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/.
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Emerging drug profile: cyclin-dependent kinase inhibitors.
Leuk. Lymphoma
PUBLISHED: 07-29-2013
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Abstract As the rational application of targeted therapies in cancer supplants traditional cytotoxic chemotherapy, there is an ever-greater need for a thorough understanding of the complex machinery of the cell and an application of this knowledge to the development of novel therapeutics and combinations of agents. Here, we review the current state of knowledge of the class of targeted agents known as cyclin-dependent kinase (CDK) inhibitors, with a focus on chronic lymphocytic leukemia (CLL). Flavopiridol (alvocidib) is the best studied of the CDK inhibitors, producing a dramatic cytotoxic effect in vitro and in vivo, with the principal limiting factor of acute tumor lysis. Unfortunately, flavopiridol has a narrow therapeutic window and is relatively non-selective with several off-target (i.e. non-CDK) effects, which prompted development of the second-generation CDK inhibitor dinaciclib. Dinaciclib appears to be both more potent and selective than flavopiridol, with at least an order of magnitude greater therapeutic index, and is currently in phase III clinical trials. In additional to flavopiridol and dinaciclib, we also review the current status of other members of this class, and provide commentary as to the future direction of combination therapy including CDK inhibitors.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.