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Find video protocols related to scientific articles indexed in Pubmed.
A Novel Representation of Genomic Sequences for taxonomic clustering and visualization by means of Self-Organizing Maps.
Bioinformatics
PUBLISHED: 10-24-2014
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Self-Organizing Maps (SOMs) are readily-available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To increase the usefulness of SOM-based approaches for the analysis of genomic sequence data, novel representation methods are required that automatically and bijectively transform aligned nucleotide sequences into numeric vectors, dealing with both nucleotide ambiguity and gaps derived from sequence alignment.
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A comparative analysis of computational approaches and algorithms for protein subcomplex identification.
Sci Rep
PUBLISHED: 02-14-2014
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High-throughput AP-MS methods have allowed the identification of many protein complexes. However, most post-processing methods of this type of data have been focused on detection of protein complexes and not its subcomplexes. Here, we review the results of some existing methods that may allow subcomplex detection and propose alternative methods in order to detect subcomplexes from AP-MS data. We assessed and drew comparisons between the use of overlapping clustering methods, methods based in the core-attachment model and our own prediction strategy (TRIBAL). The hypothesis behind TRIBAL is that subcomplex-building information may be concealed in the multiple edges generated by an interaction repeated in different contexts in raw data. The CACHET method offered the best results when the evaluation of the predicted subcomplexes was carried out using both the hypergeometric and geometric scores. TRIBAL offered the best performance when using a strict meet-min score.
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European multicenter analytical evaluation of the Abbott ARCHITECT STAT high sensitive troponin I immunoassay.
Clin. Chem. Lab. Med.
PUBLISHED: 01-29-2014
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International recommendations highlight the superior value of cardiac troponins (cTns) for early diagnosis of myocardial infarction along with analytical requirements of improved precision and detectability. In this multicenter study, we investigated the analytical performance of a new high sensitive cardiac troponin I (hs-cTnI) assay and its 99th percentile upper reference limit (URL).
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Separate and combined effects of DNMT and HDAC inhibitors in treating human multi-drug resistant osteosarcoma HosDXR150 cell line.
PLoS ONE
PUBLISHED: 01-01-2014
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Understanding the molecular mechanisms underlying multi-drug resistance (MDR) is one of the major challenges in current cancer research. A phenomenon which is common to both intrinsic and acquired resistance, is the aberrant alteration of gene expression in drug-resistant cancers. Although such dysregulation depends on many possible causes, an epigenetic characterization is considered a main driver. Recent studies have suggested a direct role for epigenetic inactivation of genes in determining tumor chemo-sensitivity. We investigated the effects of the inhibition of DNA methyltransferase (DNMT) and hystone deacethylase (HDAC), considered to reverse the epigenetic aberrations and lead to the re-expression of de novo methylated genes in MDR osteosarcoma (OS) cells. Based on our analysis of the HosDXR150 cell line, we found that in order to reduce cell proliferation, co-treatment of MDR OS cells with DNMT (5-Aza-dC, DAC) and HDAC (Trichostatin A, TSA) inhibitors is more effective than relying on each treatment alone. In re-expressing epigenetically silenced genes induced by treatments, a very specific regulation takes place which suggests that methylation and de-acetylation have occurred either separately or simultaneously to determine MDR OS phenotype. In particular, functional relationships have been reported after measuring differential gene expression, indicating that MDR OS cells acquired growth and survival advantage by simultaneous epigenetic inactivation of both multiple p53-independent apoptotic signals and osteoblast differentiation pathways. Furthermore, co-treatment results more efficient in inducing the re-expression of some main pathways according to the computed enrichment, thus emphasizing its potential towards representing an effective therapeutic option for MDR OS.
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KANTS: A Stigmergic Ant Algorithm for Cluster Analysis and Swarm Art.
IEEE Trans Cybern
PUBLISHED: 07-30-2013
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KANTS is a swarm intelligence clustering algorithm inspired by the behavior of social insects. It uses stigmergy as a strategy for clustering large datasets and, as a result, displays a typical behavior of complex systems: self-organization and global patterns emerging from the local interaction of simple units. This paper introduces a simplified version of KANTS and describes recent experiments with the algorithm in the context of a contemporary artistic and scientific trend called swarm art, a type of generative art in which swarm intelligence systems are used to create artwork or ornamental objects. KANTS is used here for generating color drawings from the input data that represent real-world phenomena, such as electroencephalogram sleep data. However, the main proposal of this paper is an art project based on well-known abstract paintings, from which the chromatic values are extracted and used as input. Colors and shapes are therefore reorganized by KANTS, which generates its own interpretation of the original artworks. The project won the 2012 Evolutionary Art, Design, and Creativity Competition.
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A survey of protein interaction data and multigenic inherited disorders.
BMC Bioinformatics
PUBLISHED: 02-05-2013
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Multigenic diseases are often associated with protein complexes or interactions involved in the same pathway. We wanted to estimate to what extent this is true given a consolidated protein interaction data set. The study stresses data integration and data representation issues.
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Retinol-binding protein 4 levels are associated with measures of liver and renal function and oxidant/antioxidant status in obese children.
J. Pediatr.
PUBLISHED: 02-04-2013
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Serum retinol-binding protein 4 (RBP4) has been proposed as a metabolic risk factor in obesity. We found that RBP4 levels also were associated with liver enzymes and cystatin C. Oxidant stress is a significant feature in obese children with greater values of RBP4 that can mediate the development of comorbidities.
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Deep-sea bioluminescence blooms after dense water formation at the ocean surface.
Christian Tamburini, Miquel Canals, Xavier Durrieu de Madron, Loïc Houpert, Dominique Lefèvre, Séverine Martini, Fabrizio D'Ortenzio, Anne Robert, Pierre Testor, Juan Antonio Aguilar, Imen Al Samarai, Arnaud Albert, Michel André, Marco Anghinolfi, Gisela Anton, Shebli Anvar, Miguel Ardid, Ana Carolina Assis Jesus, Tri L Astraatmadja, Jean-Jacques Aubert, Bruny Baret, Stéphane Basa, Vincent Bertin, Simone Biagi, Armando Bigi, Ciro Bigongiari, Claudio Bogazzi, Manuel Bou-Cabo, Boutayeb Bouhou, Mieke C Bouwhuis, Jürgen Brunner, Jose Busto, Francisco Camarena, Antonio Capone, Christina Cârloganu, Giada Carminati, John Carr, Stefano Cecchini, Ziad Charif, Philippe Charvis, Tommaso Chiarusi, Marco Circella, Rosa Coniglione, Heide Costantini, Paschal Coyle, Christian Curtil, Patrick Decowski, Ivan Dekeyser, Anne Deschamps, Corinne Donzaud, Damien Dornic, Hasankiadeh Q Dorosti, Doriane Drouhin, Thomas Eberl, Umberto Emanuele, Jean-Pierre Ernenwein, Stéphanie Escoffier, Paolo Fermani, Marcelino Ferri, Vincenzo Flaminio, Florian Folger, Ulf Fritsch, Jean-Luc Fuda, Salvatore Galatà, Pascal Gay, Giorgio Giacomelli, Valentina Giordano, Juan-Pablo Gómez-González, Kay Graf, Goulven Guillard, Garadeb Halladjian, Gregory Hallewell, Hans van Haren, Joris Hartman, Aart J Heijboer, Yann Hello, Juan Jose Hernández-Rey, Bjoern Herold, Jurgen Hößl, Ching-Cheng Hsu, Marteen de Jong, Matthias Kadler, Oleg Kalekin, Alexander Kappes, Uli Katz, Oksana Kavatsyuk, Paul Kooijman, Claudio Kopper, Antoine Kouchner, Ingo Kreykenbohm, Vladimir Kulikovskiy, Robert Lahmann, Patrick Lamare, Giuseppina Larosa, Dario Lattuada, Gordon Lim, Domenico Lo Presti, Herbert Loehner, Sotiris Loucatos, Salvatore Mangano, Michel Marcelin, Annarita Margiotta, Juan Antonio Martinez-Mora, Athina Meli, Teresa Montaruli, Luciano Moscoso, Holger Motz, Max Neff, Emma Nuel Nezri, Dimitris Palioselitis, Gabriela E Păvălaş, Kevin Payet, Patrice Payre, Jelena Petrovic, Paolo Piattelli, Nicolas Picot-Clemente, Vlad Popa, Thierry Pradier, Eleonora Presani, Chantal Racca, Corey Reed, Giorgio Riccobene, Carsten Richardt, Roland Richter, Colas Rivière, Kathrin Roensch, Andrei Rostovtsev, Joaquin Ruiz-Rivas, Marius Rujoiu, Valerio G Russo, Francisco Salesa, Augustin Sánchez-Losa, Piera Sapienza, Friederike Schöck, Jean-Pierre Schuller, Fabian Schussler, Rezo Shanidze, Francesco Simeone, Andreas Spies, Maurizio Spurio, Jos J M Steijger, Thierry Stolarczyk, Mauro G F Taiuti, Simona Toscano, Bertrand Vallage, Véronique Van Elewyck, Giulia Vannoni, Manuela Vecchi, Pascal Vernin, Guus Wijnker, Jorn Wilms, Els de Wolf, Harold Yepes, Dmitry Zaborov, Juan De Dios Zornoza, Juan Zúñiga.
PLoS ONE
PUBLISHED: 01-01-2013
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The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as "open-sea convection". It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms. Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts.
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iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database.
BMC Bioinformatics
PUBLISHED: 07-22-2011
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The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment.
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iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.
BMC Bioinformatics
PUBLISHED: 07-22-2011
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The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were quantified in our previous studies.
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[Geospatial distribution and detection of dengue virus in Aedes (Stegomyia) aegypti mosquitos in Ciudad Juárez, Chihuahua, Mexico].
Salud Publica Mex
PUBLISHED: 05-21-2010
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To determine the distribution of Aedes aegypti in Ciudad Juárez, Mexico and evaluate it as a carrier of the dengue virus.
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Relapsing massive metal bezoar: a case report.
J Med Case Rep
PUBLISHED: 02-10-2009
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Bezoars are uncommon findings in the gastrointestinal tract and are composed of a wide variety of materials. We report a case of a relapsing metal bezoar in a man with schizophrenia.
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Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction.
BMC Bioinformatics
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Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different source databases, data integration strategies, representation of proteins and complexes, and data reliability assumptions. Here we examined how the use of different data integration and representation techniques, or different notions of reliability, may affect the efficacy of degree and centrality as features in drug target prediction.
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The neurofibromin 1 type I isoform predominance characterises female population affected by sporadic breast cancer: preliminary data.
J. Clin. Pathol.
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Neurofibromin 1 (NF1) as a tumour suppressor gene can give rise to several transcripts by an alternative splicing event, generated at least for CELF cofactors. At present, the NF1 isoforms and CELF splicing transcripts in sporadic breast cancer are unknown. The aim of the authors was to detect NF1 gene expression, the NF1 isoform ratio and the CELF transcripts present in sporadic breast cancer.
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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.