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Find video protocols related to scientific articles indexed in Pubmed.
A review of corneal melting after Boston keratoprosthesis.
Semin Ophthalmol
PUBLISHED: 10-18-2014
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Abstract Use of the Boston Keratoprosthesis (B-KPro) has grown significantly, both in the United States and overseas over the course of the last decade. It is the most frequently employed keratoprosthesis for the management of complex corneal blindness. Improving outcomes and reductions in devastating complications such as corneal melting and infection have motivated this increase in use. We review the epidemiology and pathophysiology of corneal melting following B-KPro as well as the advances in B-KPro design and postoperative care that have halted the occurrence of melting. Eyes with autoimmune diseases such as Stevens-Johnson syndrome, toxic epidermal necrolysis syndrome, and mucous membrane pemphigoid remain particularly vulnerable to corneal melt, leak, and extrusion. The development of new strategies to prevent melting in eyes with autoimmune disease is crucial to improve the outcomes of this group of patients, as they are often those with the most desperate need for visual rehabilitation with a B-KPro.
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Collagen cross-linking of the Boston keratoprosthesis donor carrier to prevent corneal melting in high-risk patients.
Eye Contact Lens
PUBLISHED: 10-17-2014
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To examine the clinical relevance and pathophysiology of Boston keratoprosthesis (B-KPro)-related corneal keratolysis (cornea melt) and to describe a novel method of preventing corneal melt using ex vivo crosslinked cornea tissue carrier.
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UV cross-linking of donor corneas confers resistance to keratolysis.
Cornea
PUBLISHED: 07-12-2014
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The aim of this study was to develop a modified ex vivo corneal cross-linking method that increases stromal resistance to enzymatic degradation for use as a carrier for the Boston keratoprosthesis.
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Developmental model of suicide trajectories.
Br J Psychiatry
PUBLISHED: 05-08-2014
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Most developmental studies on suicide do not take into account individual variations in suicide trajectories.
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Transcriptomic and peptidomic analysis of protein hydrolysates from the white shrimp (L. vannamei).
J. Biotechnol.
PUBLISHED: 02-19-2014
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An RNAseq approach associated to mass spectrometry was conducted to assess the composition, molecular mass distribution and primary sequence of hydrolytic peptides issued from hydrolysates of white shrimp (Litopenaeus vannamei) by-products. High performance size exclusion chromatography (HPSEC) analyses indicated that 69.2% of the 214-nm-absorbing components had apparent molecular masses below 1000Da, and 88.3% below 2000Da. OFFGEL-nLC-MALDI-TOF/TOF and nLC-ESI-MS/MS analyses led to the identification of 808 peptides based on the NCBI EST databank (161,397 entries) completed by the new L. vannamei databank (58,508 entries) that we created from the RNAs of tissues used for hydrolysate production. Whereas most of hydrolytic peptides have a MW below 2000Da, preliminary investigations of antimicrobial properties revealed three antibacterial fractions that demonstrate functional activities. The abundance of small peptides as well as the biological activities detected could imply very interesting applications for shrimp hydrolysate in the field of aquaculture feeding.
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Residential Trajectories of Street Youth-the Montréal Cohort Study.
J Urban Health
PUBLISHED: 02-12-2014
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Little is known about the course of homelessness among youth between the ages of 18 and 25 despite the many characteristics distinguishing them from adolescents and from older street-involved populations. We examined the residential trajectories of homeless young adults in Montréal over a 21-month period and identified determinants of various trajectory profiles. The 365 study participants (79 % men, mean age 21.9 years) were followed for an average of 515 days (range 81-630 days). We assessed housing status with a questionnaire based on the residential follow-back calendar designed by the New Hampshire Dartmouth Research Center. Using latent growth analysis to examine achievement of residential stability over time, we observed three different trajectories: group 1 presented a low probability of housing throughout the entire study period; group 2 showed a high probability of early and stable housing; group 3 displayed a fluctuating pattern. Protective correlates of residential stability included high school education, birth in Canada, and presence of mental health problems. Drug abuse or dependence was associated with a decreased probability of housing.
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Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly.
Nucleic Acids Res.
PUBLISHED: 11-13-2013
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The yeast Snu13p protein and its 15.5K human homolog both bind U4 snRNA and box C/D snoRNAs. They also bind the Rsa1p/NUFIP assembly factor, proposed to scaffold immature snoRNPs and to recruit the Hsp90-R2TP chaperone complex. However, the nature of the Snu13p/15.5K-Rsa1p/NUFIP interaction and its exact role in snoRNP assembly remained to be elucidated. By using biophysical, molecular and imaging approaches, here, we identify residues needed for Snu13p/15.5K-Rsa1p/NUFIP interaction. By NMR structure determination and docking approaches, we built a 3D model of the Snup13p-Rsa1p interface, suggesting that residues R249, R246 and K250 in Rsa1p and E72 and D73 in Snu13p form a network of electrostatic interactions shielded from the solvent by hydrophobic residues from both proteins and that residue W253 of Rsa1p is inserted in a hydrophobic cavity of Snu13p. Individual mutations of residues in yeast demonstrate the functional importance of the predicted interactions for both cell growth and snoRNP formation. Using archaeal box C/D sRNP 3D structures as templates, the association of Snu13p with Rsa1p is predicted to be exclusive of interactions in active snoRNPs. Rsa1p and NUFIP may thus prevent premature activity of pre-snoRNPs, and their removal may be a key step for active snoRNP production.
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KRAS mutations are associated with specific morphologic features in colon cancer.
J. Clin. Gastroenterol.
PUBLISHED: 10-29-2013
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Mutations in the KRAS gene occur at an early stage in the development of colorectal carcinoma. Importantly, KRAS mutation predicts resistance to anti-epidermal growth factor receptor therapy in stage IV disease.
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Persistent leak after glaucoma aqueous shunt implantation.
J. Glaucoma
PUBLISHED: 08-24-2013
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To present 4 cases of persistent leak attributed to subconjunctival fistula formation after glaucoma aqueous shunt implantation. Our preferred method for management is also described.
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Debating Deposits: An Interobserver Variability Study of Lymph Nodes and Pericolonic Tumor Deposits in Colonic Adenocarcinoma.
Arch. Pathol. Lab. Med.
PUBLISHED: 07-31-2013
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Context.- The American Joint Committee on Cancers Cancer Staging Manual 7th edition defines pericolonic tumor deposits (TDs) as discrete tumor foci in pericolic fat showing no evidence of residual lymph node (LN). This definition relies on subjective features rather than size (5th edition) or shape (6th edition) and introduced the category N1c. Although typically straightforward, metastases are encountered for which the distinction between LNs and TDs is unclear. For data to be meaningful, agreement on distinguishing features between positive LNs and TDs is needed. Objectives.-To assess agreement among gastrointestinal pathologists evaluating difficult metastases and to report the distinguishing features they found helpful. Design.-Twenty-five tumor metastases from right-sided colonic adenocarcinomas were selected in which the distinction between positive LNs and TDs was challenging. Virtual slides were reviewed by 7 gastrointestinal pathologists. A list of features potentially helpful in differentiating positive LNs and TDs was ranked for usefulness by each pathologist. Every metastasis was diagnosed as positive LN or TD. For each case diagnosed as positive LN, reviewers were asked to list every feature used in diagnosis. Results.-Complete agreement was found for 11 of 25 metastases, 5 positive LNs and 6 TDs (? statistic, 0.48; 95% confidence interval, 0.28-0.67). Top-ranked features included round shape, peripheral lymphocyte rim, peripheral lymphoid follicles, possible subcapsular sinus, residual LN in surrounding fibroadipose tissue, and thick capsule. The top used features were similar among reviewers. Conclusions.-Significant agreement on positive LNs and TDs in difficult colonic adenocarcinoma metastases was found among evaluators, but inconsistency remains. Round shape, peripheral lymphocyte rim, peripheral lymphoid follicles, possible subcapsular sinus, residual LN in surrounding fibroadipose tissue, and thick capsule were most often used to aid in diagnosis.
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Endocanalicular laser dacryocystorhinostomy with mucosal flaps.
Ophthal Plast Reconstr Surg
PUBLISHED: 07-11-2013
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To describe the technique of endocanalicular laser dacryocystorhinostomy with mucosal flap creation and to report the outcomes of this technique.
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CBC-ARS2 stimulates 3-end maturation of multiple RNA families and favors cap-proximal processing.
Nat. Struct. Mol. Biol.
PUBLISHED: 07-02-2013
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The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small, capped RNAs such as pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, ARS2 and PHAX, and show that both CBCAP and CBC-ARS2 complexes can be reconstituted from recombinant proteins. ARS2 stimulates PHAX binding to the CBC and snRNA 3-end processing, thereby coupling maturation with export. In vivo, CBC and ARS2 bind similar capped noncoding and coding RNAs and stimulate their 3-end processing. The strongest effects are for cap-proximal polyadenylation sites, and this favors premature transcription termination. ARS2 functions partly through the mRNA 3-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. ARS2 is thus a major CBC effector that stimulates functional and cryptic 3-end processing sites.
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Hemorrhagic descemet detachment after combined canaloplasty and cataract surgery.
Cornea
PUBLISHED: 03-02-2013
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To describe a case of hemorrhagic Descemet membrane detachment following canaloplasty and to discuss its management using neodymium:yttrium-aluminum-garnet (Nd:YAG) laser Descemet membranotomy.
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Complications associated with Boston keratoprosthesis type 1 and glaucoma drainage devices.
Br J Ophthalmol
PUBLISHED: 02-23-2013
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To compare the complications leading to best-corrected visual acuity (BCVA) loss in patients with Boston keratoprosthesis type 1 (KPro) and glaucoma drainage device (GDD) and those with KPro alone.
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Long-term Visual Outcome of Methylmalonic Aciduria and Homocystinuria, Cobalamin C Type.
Ophthalmology
PUBLISHED: 02-14-2013
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To describe the long-term ophthalmologic outcomes of patients with methylmalonic aciduria and homocystinuria, cobalamin C type (cblC).
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Fibrovascular ingrowth after 25-gauge transconjunctival vitrectomy in proliferative diabetic retinopathy.
Ophthalmic Surg Lasers Imaging Retina
PUBLISHED: 02-04-2013
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The authors describe two patients with proliferative diabetic retinopathy bilaterally who were treated with transconjunctival 25-gauge pars plana vitrectomy (PPV) for dense vitreous hemorrhage (VH). After 4 and 10 months, respectively, both developed recurrent VH. They were initially managed with in-office gas-fluid exchange and anti-VEGF intravitreal injection. Soon after gas bubble resorption, the VH recurred. Color external photos revealed engorged episcleral vessels superotemporally, and ultrasound biomicroscopy confirmed the presence of fibrovascular ingrowth (FVI) at the sclerotomy site in both patients. They were successfully treated with a slightly modified 25-gauge PPV technique. Although FVI is well-recognized following conventional 20-gauge vitrectomy, this report is the first to detail FVI arising after small-gauge transconjunctival vitrectomy.
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Microbial colonization and antibacterial resistance patterns after Boston type 1 keratoprosthesis.
Ophthalmology
PUBLISHED: 01-02-2013
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To characterize the bacterial and fungal flora colonizing the ocular surface of eyes with Boston type 1 keratoprosthesis (KPro) and to determine the prevalence of resistance to antibiotics. Culture positivity and antibiotic resistance rates in eyes with KPro are compared with those of eyes after penetrating keratoplasty (PKP) as well as control eyes.
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Prospective evaluation of acute graft-versus-host disease.
Dig. Dis. Sci.
PUBLISHED: 07-12-2011
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Graft-versus-host disease (GVHD) is a common complication of allogeneic bone marrow transplantation. Severe GVHD carries significant morbidity and mortality and remains one of the leading causes of treatment failure. Unfortunately, intestinal GVHD may present with a variety of non-specific symptoms and diagnosis based on clinical presentation is often inaccurate; biopsy is therefore needed for definitive diagnosis. At present, the optimal endoscopic approach to the diagnosis of gastrointestinal GVHD remains uncertain.
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Confocal endomicroscopic examination of malignant biliary strictures and histologic correlation with lymphatics.
J. Clin. Gastroenterol.
PUBLISHED: 06-04-2011
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Current methods to diagnose malignant biliary strictures are of low sensitivity. Confocal endomicroscopy is a new approach that may improve the diagnosis of indeterminate biliary strictures. The purpose of this study was to evaluate indeterminate biliary strictures using probe-based confocal laser endomicroscopy and to understand the histologic basis for the confocal images.
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Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation.
J. Cell Biol.
PUBLISHED: 06-01-2011
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Splicing is a key process that expands the coding capacity of genomes. Its kinetics remain poorly characterized, and the distribution of splicing time caused by the stochasticity of single splicing events is expected to affect regulation efficiency. We conducted a small-scale survey on 40 introns in human cells and observed that most were spliced cotranscriptionally. Consequently, we constructed a reporter system that splices cotranscriptionally and can be monitored in live cells and in real time through the use of MS2-GFP. All small nuclear ribonucleoproteins (snRNPs) are loaded on nascent pre-mRNAs, and spliceostatin A inhibits splicing but not snRNP recruitment. Intron removal occurs in minutes and is best described by a model where several successive steps are rate limiting. Each pre-mRNA molecule is predicted to require a similar time to splice, reducing kinetic noise and improving the regulation of alternative splicing. This model is relevant to other kinetically controlled processes acting on few molecules.
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Residential trajectory and HIV high-risk behaviors among Montréal street youth--a reciprocal relationship.
J Urban Health
PUBLISHED: 04-16-2011
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Evidence has linked residential instability and engagement in high-risk behaviors. This paper longitudinally examines the relationship between changes in residential stability and changes in HIV risk behaviors among Montréal street youth (SY). Between April 2006 and May 2007, 419 SY (18-25 years old) were recruited in a cohort study. SY (using Montréal street youth agencies services) were eligible if they had had at least one 24-hour episode of homelessness in the previous 30 days. Baseline and follow-up interviews, carried out every 3 months, included completion of a questionnaire (based on Life History Calendar Technique) assessing daily sleeping arrangements since the last interview, and monthly sexual and drug use behaviors. Using mixed-effects logistic regression method, we examined the association between various risk behaviors and residential stability, reached when a youth resided in any of the following settings for a whole month: own place; friends/partners/parents place; any types of housing service (excluding emergency shelters). Analyses were carried out controlling for gender, age, education level, lifetime duration of homelessness, childhood sexual trauma, and lifetime mental health disorders. As of January 2009, 360 SY (79% boys) had completed at least one follow-up interview, representing 4,889 months of follow-up. Residential stability was significantly associated with the following: sex exchange (adjusted odd ratio [AOR], 0.25; 95% confidence interval [CI], 0.14-0.37), drug injection (AOR, 0.55; CI, 0.33-0.76), daily alcohol consumption (AOR, 0.58; CI, 0.42-0.74), polydrug consumption (AOR, 0.61; CI, 0.50-0.73), polydrug consumption excluding marijuana (AOR, 0.55; CI, 0.45-0.65), and multiple sex partners (?3 partners; AOR, 0.57; CI, 0.40-0.74). Our results suggest a reciprocal relationship between residential instability and HIV risk behaviors. This calls for more integrated services combining both individual and structural-level interventions to improve the health of street youth.
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Youth and young adult suicide: a study of life trajectory.
J Psychiatr Res
PUBLISHED: 02-17-2011
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Explore the unique developmental challenges and early adversity faced by youth and young adult who died of suicide.
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Pseudointraductal papillary mucinous neoplasia caused by microscopic periductal endocrine tumors of the pancreas: a report of 3 cases.
Hum. Pathol.
PUBLISHED: 02-02-2011
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Intraductal papillary mucinous neoplasms constitute histologically distinctive pancreatic tumors characterized by cystically dilated pancreatic ducts lined by papillary epithelium, often with extensive mucin production. With increasing awareness of and vigilance for these tumors, there has been a surge in the incidence of intraductal papillary mucinous neoplasms in the last few decades. However, resections of presumed intraductal papillary mucinous neoplasms sometimes reveal other types of cystic lesions. Here we describe 3 cases of small, incidentally identified pancreatic endocrine tumors that focally compressed the main pancreatic duct and presented clinically, radiologically, and grossly as intraductal papillary mucinous neoplasm. The histology of the dilated ducts in all cases lacked convincing features of intraductal papillary mucinous neoplasm, prompting more careful examination of the specimens and eventual identification of small well-differentiated endocrine neoplasms. The constellation of findings represented by pancreatic endocrine neoplasm-associated duct stricture and dilatation can mimic intraductal papillary mucinous neoplasm clinically and pathologically. Awareness of this phenomenon can potentially avoid misdiagnosis of intraductal papillary mucinous neoplasm in such cases.
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Nucleoplasmic calcium regulates cell proliferation through legumain.
J. Hepatol.
PUBLISHED: 01-13-2011
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Nucleoplasmic Ca(2+) regulates cell growth in the liver, but the proteins through which this occurs are unknown.
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Peptides from Lactobacillus hydrolysates of bovine milk caseins inhibit prolyl-peptidases of human colon cells.
J. Agric. Food Chem.
PUBLISHED: 12-02-2010
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Prolyl-rich peptides derived from hydrolysates of bovine caseins have been previously shown to inhibit angiotensin converting enzyme (ACE) activity, suggesting that they may also be able to inhibit the enzymatic activities of prolyl-specific peptidases. This study shows that peptides derived from ?(S1)-casein and ?-casein inhibited the enzymatic activities of purified recombinant matrix metalloprotease (MMP)-2, MMP-7, and MMP-9. The inhibitory efficacy was sequence-dependent. These peptides also selectively inhibited the enzymatic activities of prolyl-amino-peptidases, prolyl-amino-dipeptidases, and prolyl-endopeptidases in extracts of HT-29 and SW480 human colon carcinoma cells, but not in intact cells. They were not cytotoxic or growth inhibitory for these cells. Thus, the prolyl-rich selected peptides were good and selective inhibitors of MMPs and post-proline-cleaving proteases, demonstrating their potential to control inadequate proteolytic activity in the human digestive tract, without inducing cytotoxic effects.
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RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3-end processing in Saccharomyces cerevisiae.
RNA
PUBLISHED: 10-25-2010
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We describe methods for obtaining a quantitative description of RNA processing at high resolution in budding yeast. As a model gene expression system, we constructed tetON (for induction studies) and tetOFF (for repression, derepression, and RNA degradation studies) yeast strains with a series of reporter genes integrated in the genome under the control of a tetO7 promoter. Reverse transcription and quantitative real-time-PCR (RT-qPCR) methods were adapted to allow the determination of mRNA abundance as the average number of copies per cell in a population. Fluorescence in situ hybridization (FISH) measurements of transcript numbers in individual cells validated the RT-qPCR approach for the average copy-number determination despite the broad distribution of transcript levels within a population of cells. In addition, RT-qPCR was used to distinguish the products of the different steps in splicing of the reporter transcripts, and methods were developed to map and quantify 3-end cleavage and polyadenylation. This system permits pre-mRNA production, splicing, 3-end maturation and degradation to be quantitatively monitored with unprecedented kinetic detail, suitable for mathematical modeling. Using this approach, we demonstrate that reporter transcripts are spliced prior to their 3-end cleavage and polyadenylation, that is, cotranscriptionally.
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Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-07-2010
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In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km-wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO(2) and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans.
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HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II.
Mol. Cell
PUBLISHED: 05-12-2010
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RNA polymerases are key multisubunit cellular enzymes. Microscopy studies indicated that RNA polymerase I assembles near its promoter. However, the mechanism by which RNA polymerase II is assembled from its 12 subunits remains unclear. We show here that RNA polymerase II subunits Rpb1 and Rpb3 accumulate in the cytoplasm when assembly is prevented and that nuclear import of Rpb1 requires the presence of all subunits. Using MS-based quantitative proteomics, we characterized assembly intermediates. These included a cytoplasmic complex containing subunits Rpb1 and Rpb8 associated with the HSP90 cochaperone hSpagh (RPAP3) and the R2TP/Prefoldin-like complex. Remarkably, HSP90 activity stabilized incompletely assembled Rpb1 in the cytoplasm. Our data indicate that RNA polymerase II is built in the cytoplasm and reveal quality-control mechanisms that link HSP90 to the nuclear import of fully assembled enzymes. hSpagh also bound the free RPA194 subunit of RNA polymerase I, suggesting a general role in assembling RNA polymerases.
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Pathology reporting of neuroendocrine tumors: application of the Delphic consensus process to the development of a minimum pathology data set.
Am. J. Surg. Pathol.
PUBLISHED: 02-02-2010
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Epithelial neuroendocrine tumors (NETs) have been the subject of much debate regarding their optimal classification. Although multiple systems of nomenclature, grading, and staging have been proposed, none has achieved universal acceptance. To help define the underlying common features of these classification systems and to identify the minimal pathology data that should be reported to ensure consistent clinical management and reproducibility of data from therapeutic trials, a multidisciplinary team of physicians interested in NETs was assembled. At a group meeting, the participants discussed a series of "yes" or "no" questions related to the pathology of NETs and the minimal data to be included in the reports. After discussion, anonymous votes were taken, using the Delphic principle that 80% agreement on a vote of either yes or no would define a consensus. Questions that failed to achieve a consensus were rephrased once or twice and discussed, and additional votes were taken. Of 108 questions, 91 were answerable either yes or no by more than 80% of the participants. There was agreement about the importance of proliferation rate for tumor grading, the landmarks to use for staging, the prognostic factors assessable by routine histology that should be reported, the potential for tumors to progress biologically with metastasis, and the current status of advanced immunohistochemical and molecular testing for treatment-related biomarkers. The lack of utility of a variety of immunohistochemical stains and pathologic findings was also agreed upon. A consensus could not be reached for the remaining 17 questions, which included both minor points related to extent of disease assessment and some major areas such as terminology, routine immunohistochemical staining for general neuroendocrine markers, use of Ki67 staining to assess proliferation, and the relationship of tumor grade to degree of differentiation. On the basis of the results of the Delphic voting, a minimum pathology data set was developed. Although there remains disagreement among experts about the specific classification system that should be used, there is agreement about the fundamental pathology data that should be reported. Examination of the areas of disagreement reveals significant opportunities for collaborative study to resolve unanswered questions.
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Processivity and coupling in messenger RNA transcription.
PLoS ONE
PUBLISHED: 01-28-2010
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The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. In this simple on/off model, the many processes involved in active transcription are represented by a single reaction. These processes include elongation, which has a minimum time for completion and processing that is not captured in the model.
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Crystal growth of proteins, nucleic acids, and viruses in gels.
Prog. Biophys. Mol. Biol.
PUBLISHED: 11-27-2009
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Medium-sized single crystals with perfect habits and no defect producing intense and well-resolved diffraction patterns are the dream of every protein crystallographer. Crystals of biological macromolecules possessing these characteristics can be prepared within a medium in which mass transport is restricted to diffusion. Chemical gels (like polysiloxane) and physical gels (such as agarose) provide such an environment and are therefore suitable for the crystallisation of biological macromolecules. Instructions for the preparation of each type of gel are given to urge crystal growers to apply diffusive media for enhancing crystallographic quality of their crystals. Examples of quality enhancement achieved with silica and agarose gels are given. Results obtained with other substances forming gel-like media (such as lipidic phases and cellulose derivatives) are presented. Finally, the use of gels in combination with capillary tubes for counter-diffusion experiments is discussed. Methods and techniques implemented with proteins can also be applied to nucleic acids and nucleoprotein assemblies such as viruses.
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Prevalence and predictors of hepatic steatosis in adults with newly diagnosed chronic liver disease due to hepatitis C.
Medicine (Baltimore)
PUBLISHED: 09-12-2009
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Obesity appears to be a risk factor for hepatic steatosis, which has been implicated in the development of hepatic fibrosis in patients with hepatitis C virus infection. We conducted the current study to examine whether obesity is associated with hepatic steatosis among patients with chronic hepatitis C identified from a population-based cohort. Study participants were persons with chronic hepatitis C who had had a liver biopsy, identified from a population-based study of persons with newly identified chronic liver disease conducted in gastroenterology practices. Data were collected through patient interviews, medical record abstraction, and review of previously performed liver biopsies. The outcome variable of interest was significant steatosis, defined as steatosis grade > or =2 determined from liver biopsy samples. Univariate and multivariate analyses were performed using logistic regression techniques. The analysis included 450 patients with chronic hepatitis C with available liver biopsy slides. Overall, only 15.8% of subjects had significant hepatic steatosis (grade > or =2), while 35.9% of obese subjects had significant steatosis. In multivariate analysis, significant fibrosis (defined as > or = grade 2) (odds ratio [OR], 3.43; 95% confidence interval [CI], 1.59-7.37), obesity (OR, 3.32; 95% CI, 1.84-5.98), genotype 3 (OR, 2.5; 95% CI, 1.09-5.75), and the presence of multiple metabolic comorbidities (OR, 1.91; 95% CI, 0.88-4.11) were independently associated with steatosis. In this unique United States cohort of patients with newly diagnosed chronic liver disease due to hepatitis C, obesity was independently associated with hepatic steatosis. The results of this study provide additional evidence that obesity worsens liver damage in patients with chronic hepatitis C, and suggest a role for weight loss as a treatment modality in these patients.
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N-(4-(6,7-Disubstituted-quinolin-4-yloxy)-3-fluorophenyl)-2-oxo-3-phenylimidazolidine-1-carboxamides: a novel series of dual c-Met/VEGFR2 receptor tyrosine kinase inhibitors.
Bioorg. Med. Chem. Lett.
PUBLISHED: 08-21-2009
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A series of N-(4-(6,7-disubstituted-quinolin-4-yloxy)-3-fluorophenyl)-2-oxo-3-phenylimidazolidine-1-carboxamides targeting c-Met and VEGFR2 tyrosine kinases was designed and synthesized. The compounds were potent against these two enzymes with IC(50) values in the low nanomolar range in vitro, possessed favorable pharmacokinetic profiles and showed high efficacy in vivo in several human tumor xenograft models in mice.
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1,2-Diamines as inhibitors of co-activator associated arginine methyltransferase 1 (CARM1).
Bioorg. Med. Chem. Lett.
PUBLISHED: 08-16-2009
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We have identified the N(1)-benzyl-N(2)-methylethane-1,2-diamine unit as a substitute for the (S)-alanine benzylamide moiety for the design of co-activator associated arginine methyltransferase 1 (CARM1) inhibitors. The potency of these inhibitors is in the same order of magnitude as their predecessors and their clearance, volume of distribution, and half lives were greatly improved.
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Spectrum of histologic changes in colonic biopsies in patients treated with mycophenolate mofetil.
Mod. Pathol.
PUBLISHED: 03-27-2009
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Mycophenolate mofetil, an immunosuppressive agent, is frequently used following bone marrow and solid organ transplantation. Diarrhea is a commonly seen side effect of mycophenolate mofetil, which may necessitate colonic biopsy in some patients. The histologic changes found in this setting have been reported to mimic self-limited colitis, graft-vs-host disease or inflammatory bowel disease in isolated case reports, and could pose diagnostic and management difficulties. The goal of this study is to define the spectrum of histologic changes in colonic biopsies associated with mycophenolate mofetil usage. All solid organ transplant patients who received mycophenolate mofetil and underwent colonic biopsy for gastrointestinal symptoms from 1999 to 2007 were included in the study. Patients who did not receive mycophenolate mofetil were used as controls. Various histologic features including architectural distortion, apoptosis, inflammatory infiltrate, Paneth cell metaplasia and mucin depletion were subjectively evaluated and scored (scale: 0-3) by two independent reviewers in a blinded fashion. Forty solid organ transplant patients underwent colonic biopsy for gastrointestinal symptoms during the study period. Biopsies from 69% of patients on mycophenolate mofetil showed histologic changes. Apoptosis (41%) and architectural distortion (66%) were seen more frequently in patients receiving mycophenolate mofetil as compared to the control group (13%). The histologic changes in patients receiving mycophenolate mofetil were categorized as normal/near normal (31%), inflammatory bowel disease-like (28%), graft-vs-host disease-like (19%), ischemia-like (3%) and self-limited colitis-like (16%) changes. Of the controls, only one patient showed a graft-vs-host disease-like histologic pattern. In conclusion, histologic changes are frequently associated with mycophenolate mofetil use and can resemble self-limited colitis, graft-vs-host disease and inflammatory bowel disease leading to diagnostic difficulties. Increased awareness of the histologic spectrum of mycophenolate mofetil-induced changes is required by the pathologist to avoid diagnostic errors.
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N-(3-fluoro-4-(2-arylthieno[3,2-b]pyridin-7-yloxy)phenyl)-2-oxo-3-phenylimidazolidine-1-carboxamides: a novel series of dual c-Met/VEGFR2 receptor tyrosine kinase inhibitors.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-20-2009
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A series of N-(3-fluoro-4-(2-arylthieno[3,2-b]pyridin-7-yloxy)phenyl)-2-oxo-3-phenylimidazolidine-1-carboxamides targeting c-Met and VEGFR2 tyrosine kinases was designed and synthesized. The compounds were potent against these two enzymes with IC(50) values in the low nanomolar range in vitro, possessed favorable pharmacokinetic profiles and showed high efficacy in vivo in several human tumor xenograft models in mice.
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N-Benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides as inhibitors of co-activator associated arginine methyltransferase 1 (CARM1).
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-10-2009
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A series of N-benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides targeting co-activator associated arginine methyltransferase 1 (CARM1) have been designed and synthesized. The potency of these inhibitors was influenced by the nature of the heteroaryl fragment with the thiophene analogues being superior to thiazole, pyridine, isoindoline and benzofuran based inhibitors.
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Efficacy of an ibuprofen/codeine combination for pain management in children presenting to the emergency department with a limb injury: a pilot study.
J Emerg Med
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Fractures and severe sprains generate moderate to severe pain (>3/10). Despite this fact, pain management in children presenting to the Emergency Department (ED) with a musculoskeletal trauma is still suboptimal. Few studies have focused on the efficacy of a combination of an opioid with an anti-inflammatory drug to relieve this type of pain.
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Intraocular lens position following in-the-bag implantation of single-piece versus three-piece acrylic intraocular lenses.
Ophthalmic Surg Lasers Imaging
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To report the position of the single-piece and three-piece intraocular lenses (IOLs) following in-the-bag implantation.
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Nuclear retention prevents premature cytoplasmic appearance of mRNA.
Mol. Cell
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In S. cerevisiae cells debilitated in mRNA nuclear export, transcripts are retained in nuclear foci ("dots"). The ultimate fate of dot-mRNA has remained elusive. Here, we use single molecule counting microscopy and (35)S-methionine pulse-labeling assays to quantify cytoplasmic HSP104 RNA levels and estimate HSP104 RNA translation status. HSP104 transcripts, retained in dots as a consequence of the mex67-5 mutation, are slowly released over time for cytoplasmic translation. Thus, dot-mRNA retains function. However, forcing its nuclear export, by overexpressing the Sub2p mRNA export factor, does not elevate Hsp104p protein levels but is instead paralleled by growth deficiency. Nuclear export and growth phenotypes are both counteracted by coexpressing the nuclear RNA quality control factor Rrp6p. Thus, prematurely released dot-mRNA is translationally inactive and possibly toxic. Accordingly, nuclear retention of mRNA may serve a precautionary role during stressful situations such as, e.g., decreased mRNA maturation competence.
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Review of endophthalmitis following Boston keratoprosthesis type 1.
Br J Ophthalmol
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Endophthalmitis remains one of the most damaging and challenging complications following Boston keratoprosthesis type 1 (KPro) surgery. The authors reviewed the literature from 2001 onward to identify cases of endophthalmitis following KPro surgery and present an additional case of endophthalmitis in a patient with Stevens Johnson syndrome. The prevalence of endophthalmitis between 2001 and 2011 was 5.4%. Gram-positive bacteria are the most common agents responsible for endophthalmitis in this patient population while gram-negative bacteria and fungi are emerging pathogens. Risk factors for endophthalmitis include preoperative diagnosis of cicatricial disease and postoperative infectious keratitis, glaucoma drainage device erosion and non-compliance with antibiotic prophylaxis. Additional studies on the prevention and treatment of endophthalmitis are required to improve the overall prognosis of these patients.
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Boston keratoprosthesis type 1 surgery: use of frozen versus fresh corneal donor carriers.
Cornea
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This study aims to determine whether frozen corneas can be successfully used as carriers of the Boston keratoprosthesis (KPro).
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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.

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

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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.