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Find video protocols related to scientific articles indexed in Pubmed.
Diversity and distribution of deep-sea shrimps in the Ross Sea region of Antarctica.
PLoS ONE
PUBLISHED: 01-01-2014
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Although decapod crustaceans are widespread in the oceans, only Natantia (shrimps) are common in the Antarctic. Because remoteness, depth and ice cover restrict sampling in the South Ocean, species distribution modelling is a useful tool for evaluating distributions. We used physical specimen and towed camera data to describe the diversity and distribution of shrimps in the Ross Sea region of Antarctica. Eight shrimp species were recorded: Chorismus antarcticus; Notocrangon antarcticus; Nematocarcinus lanceopes; Dendrobranchiata; Pasiphaea scotiae; Pasiphaea cf. ledoyeri; Petalidium sp., and a new species of Lebbeus. For the two most common species, N. antarcticus and N. lanceopes, we used maximum entropy modelling, based on records of 60 specimens and over 1130 observations across 23 sites in depths from 269 m to 3433 m, to predict distributions in relation to environmental variables. Two independent sets of environmental data layers at 0.05° and 0.5° resolution respectively, showed how spatial resolution affected the model. Chorismus antarcticus and N. antarcticus were found only on the continental shelf and upper slopes, while N. lanceopes, Lebbeus n. sp., Dendrobranchiata, Petalidium sp., Pasiphaea cf. ledoyeri, and Pasiphaea scotiae were found on the slopes, seamounts and abyssal plain. The environmental variables that contributed most to models for N. antarcticus were depth, chlorophyll-a concentration, temperature, and salinity, and for N. lanceopes were depth, ice concentration, seabed slope/rugosity, and temperature. The relative ranking, but not the composition of these variables changed in models using different spatial resolutions, and the predicted extent of suitable habitat was smaller in models using the finer-scale environmental layers. Our modelling indicated that shrimps were widespread throughout the Ross Sea region and were thus likely to play important functional role in the ecosystem, and that the spatial resolution of data needs to be considered both in the use of species distribution models.
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Tolerance of the invasive tunicate Styela clava to air exposure.
Biofouling
PUBLISHED: 09-25-2013
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Styela clava is a subtidal invasive marine species in Northern Europe, Atlantic Canada, Australia and New Zealand. It grows attached to solid substrata, including boat hulls, ropes, moorings, piers and aquaculture equipment, all of which can aid its spread to new locations. It interferes with feeding of mussels and oysters, and increases their harvesting costs. Being subtidal, it could be assumed that tunicates would rapidly die in air and thus exposure to air would be a practical method to prevent their spread on boats and equipment. This study tested their survival when exposed to air for up to (1) 120?h at a constant temperature of 10?°C, (2) shade ambient 15-27?°C, and (3) full sun ambient 15-29?°C. Humidity was consistently high (78-100%). The results indicated that survival was longer when the air temperature was cooler. Larger individuals of S. clava generally survived for longer out of seawater than smaller individuals. The results predict that two weeks of exposure to air for two weeks could be an effective management method to eradicate S. clava from marine equipment when the air temperature is 10?°C. However, drying time would be less under conditions of low humidity and under direct sunlight.
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Response to comments on "Can we name Earths species before they go extinct?".
Science
PUBLISHED: 07-23-2013
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Mora et al. disputed that most species will be discovered before they go extinct, but not our main recommendations to accelerate species discoveries. We show that our conclusions would be unaltered by discoveries of more microscopic species and reinforce our estimates of species description and extinction rates, that taxonomic effort has never been greater, and that there are 2 to 8 million species on Earth.
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Biodiversity data should be published, cited, and peer reviewed.
Trends Ecol. Evol. (Amst.)
PUBLISHED: 02-25-2013
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Concerns over data quality impede the use of public biodiversity databases and subsequent benefits to society. Data publication could follow the well-established publication process: with automated quality checks, peer review, and editorial decisions. This would improve data accuracy, reduce the need for users to clean the data, and might increase data use. Authors and editors would get due credit for a peer-reviewed (data) publication through use and citation metrics. Adopting standards related to data citation, accessibility, metadata, and quality control would facilitate integration of data across data sets. Here, we propose a staged publication process involving editorial and technical quality controls, of which the final (and optional) stage includes peer review, the most meritorious publication standard in science.
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Can we name Earths species before they go extinct?
Science
PUBLISHED: 01-26-2013
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Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity.
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Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases.
PLoS ONE
PUBLISHED: 01-09-2013
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The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the scientific community, and anticipate increased taxonomic efficiency and quality control in marine biodiversity research and management.
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First report of anterior pallial tentacles in Solen dactylus (Bivalvia: Solenidae) from the Northern Persian Gulf, Iran.
PLoS ONE
PUBLISHED: 01-01-2013
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Solenidae are deep burrowing bivalves inhabiting intertidal and shallow sub-tidal soft bottom sediments mostly in tropical and sub-tropical areas. Solen dactylus has a restricted distribution within the Indian Ocean. Solen dactylus is frequently found on the sandy-muddy coast of the northern Persian Gulf, Iran. Specimens of S. dactylus were collected since 2006 from Bandar Abbas to study their biology and ecology. During these studies, an unexpected pair of anterior pallial tentacles at the dorsal end of the anterior pallial crest of the mantle was found. In the tentacles, two kinds of epithelial cells (pyramidal and vacuolated) and fibres (radial and longitudinal), and a branch of the pallial nerve located in the centre of a haemocoel, were determined. A possible coherence of a furrow parallel to the anterior shell margin with the presence of anterior pallial tentacles is discussed. All species with long anterior pallial tentacles have anterior shell furrows. Anterior pallial tentacles were found in 10 species of Solenidae from Asia to the Middle East and Europe. The function of the tentacles is unknown. However, more species need to be examined for anterior pallial tentacles and anterior shell furrows to determine if they reflect a common evolutionary history or ecology.
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Predicting total global species richness using rates of species description and estimates of taxonomic effort.
Syst. Biol.
PUBLISHED: 08-18-2011
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We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased, reflecting the less explored nature of the oceans. From the mid-19th century, the cumulative number of species described has been linear, with the highest number of species described in the decade of 1900, and fewer species described and fewer authors active during the World Wars. There were more authors describing species since the 1960s, indicating greater taxonomic effort. There were fewer species described per author since the 1920s, suggesting it has become more difficult to discover new species. There was no evidence of any change in individual effort by taxonomists. Using a nonhomogeneous renewal process model we predicted that 24-31% to 21-29% more marine and terrestrial species remain to be discovered, respectively. We discuss why we consider that marine species comprise only 16% of all species on Earth although the oceans contain a greater phylogenetic diversity than occurs on land. We predict that there may be 1.8-2.0 million species on Earth, of which about 0.3 million are marine, significantly less than some previous estimates.
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Endothelial cells create a stem cell niche in glioblastoma by providing NOTCH ligands that nurture self-renewal of cancer stem-like cells.
Cancer Res.
PUBLISHED: 07-25-2011
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One important function of endothelial cells in glioblastoma multiforme (GBM) is to create a niche that helps promote self-renewal of cancer stem-like cells (CSLC). However, the underlying molecular mechanism for this endothelial function is not known. Since activation of NOTCH signaling has been found to be required for propagation of GBM CSLCs, we hypothesized that the GBM endothelium may provide the source of NOTCH ligands. Here, we report a corroboration of this concept with a demonstration that NOTCH ligands are expressed in endothelial cells adjacent to NESTIN and NOTCH receptor-positive cancer cells in primary GBMs. Coculturing human brain microvascular endothelial cells (hBMEC) or NOTCH ligand with GBM neurospheres promoted GBM cell growth and increased CSLC self-renewal. Notably, RNAi-mediated knockdown of NOTCH ligands in hBMECs abrogated their ability to induce CSLC self-renewal and GBM tumor growth, both in vitro and in vivo. Thus, our findings establish that NOTCH activation in GBM CSLCs is driven by juxtacrine signaling between tumor cells and their surrounding endothelial cells in the tumor microenvironment, suggesting that targeting both CSLCs and their niche may provide a novel strategy to deplete CSLCs and improve GBM treatment.
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Re-structuring of marine communities exposed to environmental change: a global study on the interactive effects of species and functional richness.
PLoS ONE
PUBLISHED: 04-08-2011
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Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research.
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Glycoproteomic analysis of glioblastoma stem cell differentiation.
J. Proteome Res.
PUBLISHED: 12-16-2010
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Cancer stem cells are responsible for tumor formation through self-renewal and differentiation into multiple cell types and thus represent a new therapeutic target for tumors. Glycoproteins play a critical role in determining the fates of stem cells such as self-renewal, proliferation, and differentiation. Here we applied a multilectin affinity chromatography and quantitative glycoproteomics approach to analyze alterations of glycoproteins relevant to the differentiation of a glioblastoma-derived stem cell line HSR-GBM1. Three lectins including concanavalin A (Con A), wheat germ agglutinin (WGA), and peanut agglutinin (PNA) were used to capture glycoproteins, followed by LC-MS/MS analysis. A total of 73 and 79 high-confidence (FDR < 0.01) glycoproteins were identified from the undifferentiated and differentiated cells, respectively. Label-free quantitation resulted in the discovery of 18 differentially expressed glycoproteins, wherein 9 proteins are localized in the lysosome. All of these lysosomal glycoproteins were up-regulated after differentiation, where their principal function was hydrolysis of glycosyl residues. Protein-protein interaction and functional analyses revealed the active involvement of lysosomes during the process of glioblastoma stem cell differentiation. This work provides glycoprotein markers to characterize differentiation status of glioblastoma stem cells that may be useful in stem-cell therapy of glioblastoma.
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Surface area and the seabed area, volume, depth, slope, and topographic variation for the worlds seas, oceans, and countries.
Environ. Sci. Technol.
PUBLISHED: 10-29-2010
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Depth and topography directly and indirectly influence most ocean environmental conditions, including light penetration and photosynthesis, sedimentation, current movements and stratification, and thus temperature and oxygen gradients. These parameters are thus likely to influence species distribution patterns and productivity in the oceans. They may be considered the foundation for any standardized classification of ocean ecosystems and important correlates of metrics of biodiversity (e.g., species richness and composition, fisheries). While statistics on ocean depth and topography are often quoted, how they were derived is rarely cited, and unless calculated using the same spatial resolution the resulting statistics will not be strictly comparable. We provide such statistics using the best available resolution (1-min) global bathymetry, and open source digital maps of the worlds seas and oceans and countries Exclusive Economic Zones, using a standardized methodology. We created a terrain map and calculated sea surface and seabed area, volume, and mean, standard deviation, maximum, and minimum, of both depth and slope. All the source data and our database are freely available online. We found that although the ocean is flat, and up to 71% of the area has a < 1 degree slope. It had over 1 million approximately circular features that may be seamounts or sea-hills as well as prominent mountain ranges or ridges. However, currently available global data significantly underestimate seabed slopes. The 1-min data set used here predicts there are 68,669 seamounts compared to the 30,314 previously predicted using the same method but lower spatial resolution data. The ocean volume exceeds 1.3 billion km(3) (or 1.3 sextillion liters), and sea surface and seabed areas over 354 million km(2). We propose the coefficient of variation of slope as an index of topographic heterogeneity. Future studies may improve on this database, for example by using a more detailed bathymetry, and in situ measured data. The database could be used to classify ocean features, such as abyssal plains, ridges, and slopes, and thus provide the basis for a standards based classification of ocean topography.
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KIT expression and methylation in medulloblastoma and PNET cell lines and tumors.
J. Neurooncol.
PUBLISHED: 01-17-2010
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The stem cell factor/kit tyrosine kinase receptor pathway is related to tumor growth and progression in several cancers including Ewing sarcoma, a peripheral PNET (pPNET). Identifying additional groups of tumors that may use the pathway is important as they might be responsive to imatinib mesylate treatment. MB and central PNET (cPNET) are embryonal tumors of the CNS that share similar undifferentiated morphology with Ewing sarcomas and display aggressive clinical behavior. cPNET outcome is significantly lower than MB outcome, even for localized tumors treated with high-risk MB therapy. The elucidation of signaling pathways involved in MB and cPNET pathogenesis, and the discovery of new therapeutic targets is necessary to improve the treatment of these neoplasms. We analyzed KIT expression in 2 MB, one pPNET, one cPNET and 2 rhabdomyosarcoma (RMS) cell lines. Also, in 13 tumor samples (12 MB and one cPNET), we found KIT overexpression in the most aggressive cell lines (metastatic MB and pPNET). Hypermethylation of KIT was clear in the RMS non-expressing cell lines. Among MB tumors, we could see variable levels of KIT expression; a subset of them (25%) might be related in its growth pattern to KIT up-regulation. No methylated KIT was detected in the tumors expressing the lowest levels of KIT. Our results point to methylation as an epigenetic regulatory mechanism for KIT inhibition only in the KIT non-expressing RMS cell lines, and neither in the rest of the cell lines nor in the tumor samples.
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How sea lice from salmon farms may cause wild salmonid declines in Europe and North America and be a threat to fishes elsewhere.
Proc. Biol. Sci.
PUBLISHED: 07-08-2009
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Fishes farmed in sea pens may become infested by parasites from wild fishes and in turn become point sources for parasites. Sea lice, copepods of the family Caligidae, are the best-studied example of this risk. Sea lice are the most significant parasitic pathogen in salmon farming in Europe and the Americas, are estimated to cost the world industry euro300 million a year and may also be pathogenic to wild fishes under natural conditions. Epizootics, characteristically dominated by juvenile (copepodite and chalimus) stages, have repeatedly occurred on juvenile wild salmonids in areas where farms have sea lice infestations, but have not been recorded elsewhere. This paper synthesizes the literature, including modelling studies, to provide an understanding of how one species, the salmon louse, Lepeophtheirus salmonis, can infest wild salmonids from farm sources. Three-dimensional hydrographic models predicted the distribution of the planktonic salmon lice larvae best when they accounted for wind-driven surface currents and larval behaviour. Caligus species can also cause problems on farms and transfer from farms to wild fishes, and this genus is cosmopolitan. Sea lice thus threaten finfish farming worldwide, but with the possible exception of L. salmonis, their host relationships and transmission adaptations are unknown. The increasing evidence that lice from farms can be a significant cause of mortality on nearby wild fish populations provides an additional challenge to controlling lice on the farms and also raises conservation, economic and political issues about how to balance aquaculture and fisheries resource management.
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Development of an in vitro culture method for cells and tissues from the zebra mussel (Dreissena polymorpha).
Cytotechnology
PUBLISHED: 05-26-2009
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Despite the successful transfer of mammalian in vitro techniques for use with fish and other vertebrates, little progress has been made in the area of invertebrate tissue culture. This paper describes the development of an in vitro technique for the culture of both cells in suspension and tissue explants from the gill, digestive gland and mantle of the zebra mussel (Dreissena polymorpha) and their successful maintenance in culture for up to 14 days. Cell suspensions from the gills and digestive gland were the most successful technique developed with viability >80% maintained for up to 8 days in culture, suitable for use in short term toxicity tests. Tissue explants from the mantle were also maintained in culture for up to 14 days. This paper describes the challenges involved in the development of a novel in vitro culture technique for aquatic invertebrates.
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The magnitude of global marine species diversity.
Ward Appeltans, Shane T Ahyong, Gary Anderson, Martin V Angel, Tom Artois, Nicolas Bailly, Roger Bamber, Anthony Barber, Ilse Bartsch, Annalisa Berta, Magdalena Błażewicz-Paszkowycz, Phil Bock, Geoff Boxshall, Christopher B Boyko, Simone Nunes Brandão, Rod A Bray, Niel L Bruce, Stephen D Cairns, Tin-Yam Chan, Lanna Cheng, Allen G Collins, Thomas Cribb, Marco Curini-Galletti, Farid Dahdouh-Guebas, Peter J F Davie, Michael N Dawson, Olivier De Clerck, Wim Decock, Sammy De Grave, Nicole J de Voogd, Daryl P Domning, Christian C Emig, Christer Erséus, William Eschmeyer, Kristian Fauchald, Daphne G Fautin, Stephen W Feist, Charles H J M Fransen, Hidetaka Furuya, Oscar Garcia-Alvarez, Sarah Gerken, David Gibson, Arjan Gittenberger, Serge Gofas, Liza Gómez-Daglio, Dennis P Gordon, Michael D Guiry, Francisco Hernández, Bert W Hoeksema, Russell R Hopcroft, Damiá Jaume, Paul Kirk, Nico Koedam, Stefan Koenemann, Jürgen B Kolb, Reinhardt M Kristensen, Andreas Kroh, Gretchen Lambert, David B Lazarus, Rafael Lemaitre, Matt Longshaw, Jim Lowry, Enrique Macpherson, Laurence P Madin, Christopher Mah, Gill Mapstone, Patsy A McLaughlin, Jan Mees, Kenneth Meland, Charles G Messing, Claudia E Mills, Tina N Molodtsova, Rich Mooi, Birger Neuhaus, Peter K L Ng, Claus Nielsen, Jon Norenburg, Dennis M Opresko, Masayuki Osawa, Gustav Paulay, William Perrin, John F Pilger, Gary C B Poore, Phil Pugh, Geoffrey B Read, James D Reimer, Marc Rius, Rosana M Rocha, José I Saiz-Salinas, Victor Scarabino, Bernd Schierwater, Andreas Schmidt-Rhaesa, Kareen E Schnabel, Marilyn Schotte, Peter Schuchert, Enrico Schwabe, Hendrik Segers, Caryn Self-Sullivan, Noa Shenkar, Volker Siegel, Wolfgang Sterrer, Sabine Stöhr, Billie Swalla, Mark L Tasker, Erik V Thuesen, Tarmo Timm, M Antonio Todaro, Xavier Turon, Seth Tyler, Peter Uetz, Jacob van der Land, Bart Vanhoorne, Leen P van Ofwegen, Rob W M van Soest, Jan Vanaverbeke, Genefor Walker-Smith, T Chad Walter, Alan Warren, Gary C Williams, Simon P Wilson, Mark J Costello.
Curr. Biol.
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The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered.
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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.