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Find video protocols related to scientific articles indexed in Pubmed.
Analysis of compound heterozygous CYP2C19 genotypes to determine cis and trans configurations.
Pharmacogenomics
PUBLISHED: 08-22-2014
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Through allele specific PCR we studied 220 CYP2C19 compound heterozygous samples, of unknown ethnicity, to determine the haplotype for each of the variations within a sample.
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Alternative method of allelic discrimination.
BioTechniques
PUBLISHED: 08-01-2014
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5' nuclease assays for allelic discrimination use both a wild-type and a mutant probe. Here we present a new method for genotyping by 5' nuclease assays that dispenses with the mutant probe, using the wild-type probe together with a probe for a reference gene known to be present in two copies to determine the copy number of the wild type allele relative to the reference gene. The copy number of the wild-type allele then determines the genotype: two copies indicates homozygous wild-type; one copy indicates heterozygous; and zero copies indicates homozygous mutant. We were able to use our method to correctly genotype three alleles of the thiopurine methyl transferase (TPMT) gene: TPMT *2 (c.G238C), *3B (c.G460A) and *3C (c.A719G). Our approach can be used as an alternate allelic discrimination strategy that is cost effective when multiple TaqMan assays are performed on a sample.
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AIDS-related mycoses: the way forward.
Trends Microbiol.
PUBLISHED: 03-04-2014
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The contribution of fungal infections to the morbidity and mortality of HIV-infected individuals is largely unrecognized. A recent meeting highlighted several priorities that need to be urgently addressed, including improved epidemiological surveillance, increased availability of existing diagnostics and drugs, more training in the field of medical mycology, and better funding for research and provision of treatment, particularly in developing countries.
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Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol.
Mayo Clin. Proc.
PUBLISHED: 01-07-2014
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To report the design and implementation of the Right Drug, Right Dose, Right Time-Using Genomic Data to Individualize Treatment protocol that was developed to test the concept that prescribers can deliver genome-guided therapy at the point of care by using preemptive pharmacogenomics (PGx) data and clinical decision support (CDS) integrated into the electronic medical record (EMR).
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The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.
Database (Oxford)
PUBLISHED: 01-01-2014
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The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. The CGHub currently contains >1.4?PB of data, has grown at an average rate of 50?TB a month and serves >100?TB per week. The architecture of CGHub is designed to support bulk searching and downloading through a Web-accessible application programming interface, enforce patient genome confidentiality in data storage and transmission and optimize for efficiency in access and transfer. In this article, we describe the design of these three components, present performance results for our transfer protocol, GeneTorrent, and finally report on the growth of the system in terms of data stored and transferred, including estimated limits on the current architecture. Our experienced-based estimates suggest that centralizing storage and computational resources is more efficient than wide distribution across many satellite labs. Database URL: https://cghub.ucsc.edu.
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In situ damage assessment using synchrotron X-rays in materials loaded by a Hopkinson bar.
Philos Trans A Math Phys Eng Sci
PUBLISHED: 01-01-2014
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Split Hopkinson or Kolsky bars are common high-rate characterization tools for dynamic mechanical behaviour of materials. Stress-strain responses averaged over specimen volume are obtained as a function of strain rate. Specimen deformation histories can be monitored by high-speed imaging on the surface. It has not been possible to track the damage initiation and evolution during the dynamic deformation inside specimens except for a few transparent materials. In this study, we integrated Hopkinson compression/tension bars with high-speed X-ray imaging capabilities. The damage history in a dynamically deforming specimen was monitored in situ using synchrotron radiation via X-ray phase contrast imaging. The effectiveness of the novel union between these two powerful techniques, which opens a new angle for data acquisition in dynamic experiments, is demonstrated by a series of dynamic experiments on a variety of material systems, including particle interaction in granular materials, glass impact cracking, single crystal silicon tensile failure and ligament-bone junction damage.
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Associations between serotonin transporter gene polymorphisms and heat pain perception in adults with chronic pain.
BMC Med. Genet.
PUBLISHED: 07-23-2013
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The triallelic serotonin transporter gene linked polymorphic region (5-HTTLPR) has been associated with alterations in thermal pain perception. The primary aim of this study was to investigate the associations between heat pain (HP) perception and the triallelic 5-HTTLPR in a large cohort of adults with chronic pain.
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Antibiotic Stewardship Ward Rounds and a Dedicated Prescription Chart Reduce Antibiotic Consumption and Pharmacy Costs without Affecting Inpatient Mortality or Re-Admission Rates.
PLoS ONE
PUBLISHED: 01-01-2013
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Antibiotic consumption is a major driver of bacterial resistance. To address the increasing burden of multi-drug resistant bacterial infections, antibiotic stewardship programmes are promoted worldwide to rationalize antibiotic prescribing and conserve remaining antibiotics. Few studies have been reported from developing countries and none from Africa that report on an intervention based approach with outcomes that include morbidity and mortality.
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Frequency of undetected CYP2D6 hybrid genes in clinical samples: impact on phenotype prediction.
Drug Metab. Dispos.
PUBLISHED: 10-17-2011
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Cytochrome P450 2D6 (CYP2D6) is highly polymorphic. CYP2D6-2D7 hybrid genes can be present in samples containing CYP2D6*4 and CYP2D6*10 alleles. CYP2D7-2D6 hybrid genes can be present in samples with duplication signals and in samples with homozygous genotyping results. The frequency of hybrid genes in clinical samples is unknown. We evaluated 1390 samples for undetected hybrid genes by polymerase chain reaction (PCR) amplification, PCR fragment analysis, TaqMan copy number assays, DNA sequencing, and allele-specific primer extension assay. Of 508 CYP2D6*4-containing samples, 109 (21.5%) harbored CYP2D6*68 + *4-like, whereas 9 (1.8%) harbored CYP2D6*4N + *4-like. Of 209 CYP2D6*10-containing samples, 44 (21.1%) were found to have CYP2D6*36 + *10. Of 332 homozygous samples, 4 (1.2%) harbored a single CYP2D7-2D6 hybrid, and of 341 samples with duplication signals, 25 (7.3%) harbored an undetected CYP2D7-2D6 hybrid. Phenotype before and after accurate genotyping was predicted using a method in clinical use. The presence of hybrid genes had no effect on the phenotype prediction of CYP2D6*4- and CYP2D6*10-containing samples. Four of four (100%) homozygous samples containing a CYP2D7-2D6 gene had a change in predicted phenotype, and 23 of 25 (92%) samples with a duplication signal and a CYP2D7-2D6 gene had a change in predicted phenotype. Four novel genes were identified (CYP2D6*13A1 variants 1 and 2, CYP2D6*13G1, and CYP2D6*13G2), and two novel hybrid tandem structures consisting of CYP2D6*13B + *68×2 + *4-like and CYP2D6*13A1 variant 2 + *1×N were observed.
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SULT1A1, CYP2C19 and disease-free survival in early breast cancer patients receiving tamoxifen.
Pharmacogenomics
PUBLISHED: 10-03-2011
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Tamoxifen biotransformation to endoxifen, a potent antiestrogen, is catalyzed by CYP2D6. In addition, CYP2C19 and SULT1A1 have also been implicated in the metabolism of tamoxifen. We sought to evaluate the importance of SULT1A1 copy number and CYP2C19*17 on disease-free survival (DFS) in postmenopausal women randomized to tamoxifen monotherapy in North Central Cancer Treatment Group 89-30-52 from January 1991 to April 1995.
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Relationship between FKBP5 polymorphisms and depression symptoms among kidney transplant recipients.
Depress Anxiety
PUBLISHED: 05-03-2011
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Several polymorphisms in FK506 Binding Protein gene (FKBP5) and a history of child abuse have been shown to be associated with an increased risk for posttraumatic stress disorder (PTSD). It has also been demonstrated that the same polymorphisms of FKBP5 are associated with increased recurrence of depressive episodes and rapid response to antidepressant treatment. However, there are only limited numbers of studies replicating the polymorphisms as vulnerability factors for the development of mental illnesses, such as PTSD and depression after stressful life event, especially with a specific incidence, such as kidney transplant surgery.
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CYP2C19 variation and citalopram response.
Pharmacogenet. Genomics
PUBLISHED: 04-01-2011
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Variations in cytochrome P450 (CYP) genes have been shown to be associated with both accelerated and delayed pharmacokinetic clearance of many psychotropic medications. Citalopram is metabolized by three CYP enzymes. CYP2C19 and CYP3A4 play a primary role in citalopram metabolism, whereas CYP2D6 plays a secondary role.
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Correlation of CYP2B6, CYP2C19, ABCC4 and SOD2 genotype with outcomes in allogeneic blood and marrow transplant patients.
Leuk. Res.
PUBLISHED: 03-14-2011
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CYP2B6, CYP2C19, ABCC4, and SOD2 have been implicated in adverse drug reactions and survival after cyclophosphamide (CPA) treatment. 110 BMT patients who received high dose CPA treatment were genotyped for variants in these genes and the results were correlated with toxicity and relapse. CYP2B6 genotype significantly influenced overall toxicity suggesting active CYP2B6 alleles led to higher rates of overall toxicity. The p.R487C deficiency allele was significantly associated with a lower rate of overall toxicity and a higher rate of relapse. SOD2 rs4880 V16A polymorphism was associated with significantly less CPA-related overall toxicity and significantly lower relapse rates by Kaplan-Meier analysis although the SOD2 finding regarding relapse was not significant when evaluated by the cumulative incidence function.
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Coprescription of tamoxifen and medications that inhibit CYP2D6.
J. Clin. Oncol.
PUBLISHED: 05-03-2010
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Evidence has emerged that the clinical benefit of tamoxifen is related to the functional status of the hepatic metabolizing enzyme cytochrome P450 2D6 (CYP2D6). CYP2D6 is the key enzyme responsible for the generation of the potent tamoxifen metabolite, endoxifen. Multiple studies have examined the relationship of CYP2D6 status to breast cancer outcomes in tamoxifen-treated women; the majority of studies demonstrated that women with impaired CYP2D6 metabolism have lower endoxifen concentrations and a greater risk of breast cancer recurrence. As a result, practitioners must be aware that some of the most commonly prescribed medications coadministered with tamoxifen interfere with CYP2D6 function, thereby reducing endoxifen concentrations and potentially increasing the risk of breast cancer recurrence. After reviewing the published data regarding tamoxifen metabolism and the evidence relating CYP2D6 status to breast cancer outcomes in tamoxifen-treated patients, we are providing a guide for the use of medications that inhibit CYP2D6 in patients administered tamoxifen.
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CYP2D6: novel genomic structures and alleles.
Pharmacogenet. Genomics
PUBLISHED: 09-11-2009
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CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today.
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Microglial inhibition of neuroprotection by antagonists of the EP1 prostaglandin E2 receptor.
J Neuroinflammation
PUBLISHED: 02-17-2009
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The EP1 receptor for the prostanoid PGE2 is a G-protein coupled receptor that has been shown to contribute to excitotoxic neuronal death. In this study we examined the influence of non-neuronal cells on neuroprotective properties of EP1 receptor antagonists (Ono 8711 and SC 51089).
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Serotonin transporter gene status and electroconvulsive therapy outcomes: a retrospective analysis of 83 patients.
J Clin Psychiatry
PUBLISHED: 02-05-2009
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The length of the promoter polymorphism of the serotonin transporter gene has been shown to have an impact on response to some selective serotonin reuptake inhibitor antidepressants. Carrier status for the long allele has been associated with a better response to serotonin reuptake inhibitor antidepressant medications in most studies.
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Sequence variations of the human MPDZ gene and association with alcoholism in subjects with European ancestry.
Alcohol. Clin. Exp. Res.
PUBLISHED: 01-21-2009
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Mpdz gene variations are known contributors of acute alcohol withdrawal severity and seizures in mice.
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H3+ at the interface between astrochemistry and astroparticle physics.
Philos Trans A Math Phys Eng Sci
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The H(3)(+) molecular ion has been used by Oka and collaborators to trace the rate of ionization by cosmic rays in the interstellar medium. More energetic cosmic rays also produce diffuse ?-radiation. Now that several supernova remnants (SNRs) have been identified as ?-ray sources, it is possible to use spectroscopy of molecular ions to search for enhanced ionization rates that would pinpoint the SNRs as the accelerators of cosmic rays. It is proposed that the warm, dilute molecular gas revealed by H(3)(+) absorption in the central molecular zone of the Galaxy can also be investigated via radio recombination lines of atoms and possibly triatomic hydrogen.
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Failure to eradicate Isospora belli diarrhoea despite immune reconstitution in adults with HIV--a case series.
PLoS ONE
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Isospora belli causes diarrhoea in patients with AIDS. Most respond to targeted therapy and recommendations are that secondary prophylaxis can be stopped following immune reconstitution with ART. We report eight cases of chronic isosporiasis that persisted despite standard antimicrobial therapy, secondary prophylaxis, and good immunological and virological response to ART. Median CD4 nadir was 175.5 cells/mm(3) and median highest CD4 while symptomatic was 373 cells/mm(3). Overall 34% of stool samples and 63% of duodenal biopsy specimens were positive for oocytes. Four patients died, two remain symptomatic and two recovered. Possible explanations for persistence of symptoms include host factors such as antigen specific immune deficiency or generalised reduction in gut immunity. Parasite factors may include accumulating resistance to co-trimoxazole. Research is required to determine the optimum dose and duration of co-trimoxazole therapy and whether dual therapy may be necessary. Mortality was high and pending more data we recommend extended treatment with high-dose co-trimoxazole in similar cases.
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Reinforcing outpatient medical student learning using brief computer tutorials: the Patient-Teacher-Tutorial sequence.
BMC Med Educ
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At present, what students read after an outpatient encounter is largely left up to them. Our objective was to evaluate the education efficacy of a clinical education model in which the student moves through a sequence that includes immediately reinforcing their learning using a specifically designed computer tutorial.
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Measurement of drug in small particles from aqueous nasal sprays by Andersen Cascade Impactor.
Pharm. Res.
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To determine if cascade impactor (CI) measurement of drug in small particles from aqueous nasal sprays, described in FDAs 2003 draft Nasal Bioavailability/Bioequivalence Guidance, can be optimized to reduce measurement variability. To examine the influence of flow rate configurations and number of impactor stages on CI deposition and explore the importance of inlet volume.
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Those, that die by reason of their madness: dying insane in London, 1629-1830.
Hist Psychiatry
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Dying insane provoked great fear, and apprehension in the minds of men and women. Death as a lunatic disrupted deathbed performance and rendered the victim incapable at law. This article examines lunacy as a cause of death in the metropolis between 1629 and 1830. It draws on new material from the admission registers of St Lukes Hospital, existing data from Bethlem and the London Bills of Mortality and unique biographical data on pauper lunatics dying in the parish of St Martin in the Fields. The article argues that lunacy being ascribed as a cause of death had a distinctive chronology in this period. Those most vulnerable to the stigma of lunacy at death were those dying as parish paupers and those who inhabited metropolitan institutions.
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CYP2D6*11 and challenges in clinical genotyping of the highly polymorphic CYP2D6 gene.
Pharmacogenomics
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CYP2D6 is genotyped clinically for prediction of response to tamoxifen, psychotropic drugs and other medications. Phenotype prediction is dependent upon accurate genotyping. The CYP Allele Nomenclature Committee maintains the allelic nomenclature for CYP2D6; however, in some cases, the list of polymorphisms associated with a given allele is incomplete. Clinical laboratories and in vitro diagnostic manufacturers rely upon this nomenclature, in addition to the literature, to infer allelic function and haplotypes and when they design CYP2D6-testing platforms. This article provides more complete sequencing data for the CYP2D6*11 allele and describes the difficulties encountered in genotyping CYP2D6 when incomplete data are available. The CYP Allele Nomenclature Committee should provide clear information about the completeness of the original data used to define each allele.
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Testing a diathesis-stress model: potential genetic risk factors for development of distress in context of acute leukemia diagnosis and transplant.
Psychosomatics
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Brain-derived neurotrophic factor (BDNF) is a nerve growth factor that has antidepressant-like effects in animals and may be implicated in the etiology of mood-related phenotypes, specifically in the context of stressful life events. We hypothesized that this single-nucleotide polymorphism will predict the development of psychological distress among patients diagnosed with acute leukemia and preparing for hematopoietic stem cell transplant (HSCT). We also explored the relationship of other genetic factors to psychological distress, including 5HTTLPR and STin2, FKBP5, and the CRHR1 TAT haplotype.
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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.