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Find video protocols related to scientific articles indexed in Pubmed.
Resistance to UV-Induced Apoptosis by Beta HPV5 E6 Involves Targeting of Activated BAK for Proteolysis by Recruitment of the HERC1 Ubiquitin Ligase.
Int. J. Cancer
PUBLISHED: 06-16-2014
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UV exposure is the main etiological agent in the development of non-melanoma skin cancer (NMSC), but mounting evidence suggests a co-factorial role for ?-genus HPV types early in tumor initiation or progression. UV damage initiates an apoptotic response, driven at the mitochondrial level by BCL-2 family proteins, that eliminates damaged cells that may accumulate deleterious mutations and acquire tumorigenic properties. BAK is a pro-apoptotic BCL-2 protein that functions ultimately to form pores that permeabilize the mitochondrial outer membrane, thereby committing a cell to death, a process involving changes in BAK phosphorylation and conformation. The E6 protein of ?-type HPV5 signals BAK for proteasomal degradation, a function that confers protection from UV-induced apoptosis. We find that HPV5 E6 does not constitutively target BAK for proteolysis, but targets the latter stages of BAK activation, following changes in phosphorylation and conformation. A mutational analysis identified the lysine residue on BAK required for proteolysis, and a functional siRNA screen identified the HECT domain E3 ubiquitin ligase HERC1 as being required for E6-mediated BAK degradation. We show that HERC1 interacts with BAK in E6-expressing cells that have been damaged by UV, provide evidence that the interaction of HERC1 with BAK requires access to a hydrophobic surface on BAK that binds BH3 domains of BCL-2 proteins, and that HERC1 contains a putative BH3 domain that can bind to BAK. These findings reveal a specific and unique mechanism used by the HPV5 E6 protein to target BAK. This article is protected by copyright. All rights reserved.
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A general framework for the use of logistic regression models in meta-analysis.
Stat Methods Med Res
PUBLISHED: 05-15-2014
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Where individual participant data are available for every randomised trial in a meta-analysis of dichotomous event outcomes, "one-stage" random-effects logistic regression models have been proposed as a way to analyse these data. Such models can also be used even when individual participant data are not available and we have only summary contingency table data. One benefit of this one-stage regression model over conventional meta-analysis methods is that it maximises the correct binomial likelihood for the data and so does not require the common assumption that effect estimates are normally distributed. A second benefit of using this model is that it may be applied, with only minor modification, in a range of meta-analytic scenarios, including meta-regression, network meta-analyses and meta-analyses of diagnostic test accuracy. This single model can potentially replace the variety of often complex methods used in these areas. This paper considers, with a range of meta-analysis examples, how random-effects logistic regression models may be used in a number of different types of meta-analyses. This one-stage approach is compared with widely used meta-analysis methods including Bayesian network meta-analysis and the bivariate and hierarchical summary receiver operating characteristic (ROC) models for meta-analyses of diagnostic test accuracy.
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The influence of topographic and dynamic cyclic variables on the distribution of small cetaceans in a shallow coastal system.
PLoS ONE
PUBLISHED: 01-01-2014
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The influence of topographic and temporal variables on cetacean distribution at a fine-scale is still poorly understood. To study the spatial and temporal distribution of harbour porpoise Phocoena phocoena and the poorly known Risso's dolphin Grampus griseus we carried out land-based observations from Bardsey Island (Wales, UK) in summer (2001-2007). Using Kernel analysis and Generalized Additive Models it was shown that porpoises and Risso's appeared to be linked to topographic and dynamic cyclic variables with both species using different core areas (dolphins to the West and porpoises to the East off Bardsey). Depth, slope and aspect and a low variation in current speed (for Risso's) were important in explaining the patchy distributions for both species. The prime temporal conditions in these shallow coastal systems were related to the tidal cycle (Low Water Slack and the flood phase), lunar cycle (a few days following the neap tidal phase), diel cycle (afternoons) and seasonal cycle (peaking in August) but differed between species on a temporary but predictable basis. The measure of tidal stratification was shown to be important. Coastal waters generally show a stronger stratification particularly during neap tides upon which the phytoplankton biomass at the surface rises reaching its maximum about 2-3 days after neap tide. It appeared that porpoises occurred in those areas where stratification is maximised and Risso's preferred more mixed waters. This fine-scale study provided a temporal insight into spatial distribution of two species that single studies conducted over broader scales (tens or hundreds of kilometers) do not achieve. Understanding which topographic and cyclic variables drive the patchy distribution of porpoises and Risso's in a Headland/Island system may form the initial basis for identifying potentially critical habitats for these species.
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Reporting of industry funded study outcome data: comparison of confidential and published data on the safety and effectiveness of rhBMP-2 for spinal fusion.
BMJ
PUBLISHED: 06-22-2013
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To investigate whether published results of industry funded trials of recombinant human bone morphogenetic protein 2 (rhBMP-2) in spinal fusion match underlying trial data by comparing three different data sources: individual participant data, internal industry reports, and publicly available journal publications and conference abstracts.
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Safety and effectiveness of recombinant human bone morphogenetic protein-2 for spinal fusion: a meta-analysis of individual-participant data.
Ann. Intern. Med.
PUBLISHED: 06-20-2013
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Recombinant human bone morphogenetic protein-2 (rhBMP-2) is widely used to promote fusion in spinal surgery, but its safety has been questioned.
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Opioid analgesics suppress male gonadal function but opioid use in males and females does not correlate with symptoms of sexual dysfunction.
Pain Res Manag
PUBLISHED: 11-08-2011
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Opioid analgesia impairs gonadal function in men and women, but the correlation with symptoms and hormonal measurements of hypogonadism is not well established.
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Identification of bacteria and potential sources in neonates at risk of infection delivered by Caesarean and vaginal birth.
J. Med. Microbiol.
PUBLISHED: 08-26-2011
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Neonatal gastric aspirates (NGA) are routinely screened in UK hospitals to investigate fetal/neonatal infections associated with cases of adverse pregnancy outcome (APO). The aim of this study was to describe and compare the microbiology of NGA from Caesarean and vaginal deliveries using molecular methods, and to evaluate other possible clinical and non-clinical variables that may have determined the presence of the bacteria in the samples. The value of using NGA and molecular methods to investigate potential pathogens associated with the risk of early infection was also evaluated. Bacteria were identified by a combined molecular approach on the basis of the 16S rRNA gene using both clone analysis and denaturing gradient gel electrophoresis. A total of 43 and 34 different species were identified in the vaginal (n = 121) and Caesarean (n = 119) deliveries, respectively; 26 of the species observed (51 %) were common to both modalities, although usually less prevalent in the Caesarean cases. Multivariate analysis confirmed an association between infection and prolonged rupture of membranes in vaginal deliveries (odds ratio = 5.7, 95 % confidence interval = 1.1-29.0). Various associations between infection and given variables were also shown, including labour, intrapartum antibiotic prophylaxis, and time and place of sample collection. The molecular methods allowed identification of a range of bacteria and potential sources not previously observed in NGA, including possible genito-urinary, gastrointestinal and oral pathogens. NGA represents a valuable sample for investigating potential pathogens associated with APO and the risk of early infection in neonates using molecular methods.
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Screening for future cardiovascular disease using age alone compared with multiple risk factors and age.
PLoS ONE
PUBLISHED: 03-08-2011
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Risk factors such as blood pressure and serum cholesterol are used, with age, in screening for future cardiovascular disease (CVD) events. The value of using these risk factors with age compared with using age alone is not known. We compared screening for future CVD events using age alone with screening using age and multiple risk factors based on regular Framingham risk assessments.
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A randomised controlled trial of the effect of high concentration oxygen on myocardial ischaemia during exercise.
Int. J. Cardiol.
PUBLISHED: 01-20-2011
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International guidelines recommend the use of oxygen for angina, based on Level C evidence. We aimed to determine whether high concentration oxygen influences the time to exercise-induced ischaemia or angina in patients with stable ischaemic heart disease (IHD).
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Sequential methods for random-effects meta-analysis.
Stat Med
PUBLISHED: 08-23-2010
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Although meta-analyses are typically viewed as retrospective activities, they are increasingly being applied prospectively to provide up-to-date evidence on specific research questions. When meta-analyses are updated account should be taken of the possibility of false-positive findings due to repeated significance tests. We discuss the use of sequential methods for meta-analyses that incorporate random effects to allow for heterogeneity across studies. We propose a method that uses an approximate semi-Bayes procedure to update evidence on the among-study variance, starting with an informative prior distribution that might be based on findings from previous meta-analyses. We compare our methods with other approaches, including the traditional method of cumulative meta-analysis, in a simulation study and observe that it has Type I and Type II error rates close to the nominal level. We illustrate the method using an example in the treatment of bleeding peptic ulcers.
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Same-day discharge is feasible and safe in the majority of elderly patients undergoing elective percutaneous coronary intervention.
J Invasive Cardiol
PUBLISHED: 07-07-2010
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Same-day discharge after elective percutaneous coronary intervention (PCI) is safe in the majority of patients. However, the elderly have more comorbidities and less favorable coronary and peripheral arterial anatomy, which may preclude safe same-day discharge after PCI. We assessed the feasibility and safety of same-day discharge in an elderly cohort of patients.
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Effect of folic acid, with or without other B vitamins, on cognitive decline: meta-analysis of randomized trials.
Am. J. Med.
PUBLISHED: 01-15-2010
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We aimed to quantify the effect of folic acid supplementation on the prevention of cognitive decline.
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The effect of single-dose propofol injection on pain and quality of life in chronic daily headache: a randomized, double-blind, controlled trial.
Anesth. Analg.
PUBLISHED: 11-20-2009
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On the basis of a small number of case studies, IV propofol has been advocated for the treatment of chronic daily headache (CDH). There has been no randomized controlled trial of this therapy. Our objective in this randomized, double-blind, placebo-controlled trial was to determine whether a single IV dose of propofol 2.4 mg/kg results in clinically significant reduction in disability or pain in CDH for the next 30 days.
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Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.
BMC Genomics
PUBLISHED: 07-07-2009
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The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has been recovered from human infections in both North America and Australia. Recently, Pa has been shown to have a nematode vector that can also infect insects, like its sister species the insect pathogen P. luminescens (Pl). To understand the relationship between pathogenicity to insects and humans in Photorhabdus we have sequenced the complete genome of Pa strain ATCC43949 from North America. This strain (formerly referred to as Xenorhabdus luminescens strain 2) was isolated in 1977 from the blood of an 80 year old female patient with endocarditis, in Maryland, USA. Here we compare the complete genome of Pa ATCC43949 with that of the previously sequenced insect pathogen P. luminescens strain TT01 which was isolated from its entomopathogenic nematode vector collected from soil in Trinidad and Tobago.
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Systematic review of studies of the effect of hyperoxia on coronary blood flow.
Am. Heart J.
PUBLISHED: 05-25-2009
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International guidelines recommend the routine use of oxygen in the initial treatment of myocardial infarction, yet it is uncertain what effect this might have on physiologic and clinical outcomes.
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A critique of the UKs JNCC seismic survey guidelines for minimising acoustic disturbance to marine mammals: best practise?
Mar. Pollut. Bull.
PUBLISHED: 02-26-2009
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The United Kingdoms statutory conservation agency, the Joint Nature Conservation Committee (JNCC), developed guidelines in 1995 to minimise acoustic disturbance of marine mammals by oil and gas industry seismic surveys. These were the first national guidelines to be developed and have subsequently become the standard, or basis, of international mitigation measures for noise pollution during seismic surveys. However, relatively few aspects of these measures have a firm scientific basis or proven efficacy. Existing guidelines do not offer adequate protection to marine mammals, given the complex propagation of airgun pulses; the difficulty of monitoring in particular the smaller, cryptic, and/or deep-diving species, such as beaked whales and porpoises; limitations in monitoring requirements; lack of baseline data; and other biological and acoustical complications or unknowns. Current guidelines offer a common sense approach to noise mitigation, but in light of recent research and ongoing concerns, they should be updated, with broader measures needed to ensure adequate species protection and to address data gaps.
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Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens.
PLoS Pathog.
PUBLISHED: 02-24-2009
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The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.
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Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi.
BMC Genomics
PUBLISHED: 01-21-2009
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Of the > 2000 serovars of Salmonella enterica subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, S. enterica serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi.
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Risk estimation versus screening performance: a comparison of six risk algorithms for cardiovascular disease.
J Med Screen
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Risk of future cardiovascular disease (CVD) events is typically estimated from risk factors such as age, sex, blood pressure and cholesterol. Many risk algorithms exist to estimate CVD risk. All should have similar screening performances because of the dominant effect of age in predicting who will and will not have a CVD event, regardless of the accuracy of CVD risk estimation. Six CVD risk algorithms were compared (Framingham 1991, Framingham 2008, Reynolds risk, ASSIGN, SCORE and QRISK2), each differing in the risk factors used and in CVD outcomes.
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Statistical analysis of individual participant data meta-analyses: a comparison of methods and recommendations for practice.
PLoS ONE
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Individual participant data (IPD) meta-analyses that obtain "raw" data from studies rather than summary data typically adopt a "two-stage" approach to analysis whereby IPD within trials generate summary measures, which are combined using standard meta-analytical methods. Recently, a range of "one-stage" approaches which combine all individual participant data in a single meta-analysis have been suggested as providing a more powerful and flexible approach. However, they are more complex to implement and require statistical support. This study uses a dataset to compare "two-stage" and "one-stage" models of varying complexity, to ascertain whether results obtained from the approaches differ in a clinically meaningful way.
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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.