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Find video protocols related to scientific articles indexed in Pubmed.
A reality check for overdiagnosis estimates associated with breast cancer screening.
J. Natl. Cancer Inst.
PUBLISHED: 12-01-2014
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The frequency of overdiagnosis associated with breast cancer screening is a topic of controversy. Published estimates vary widely, but identifying which estimates are reliable is challenging. In this article we present an approach that provides a check on these estimates. Our approach leverages the close link between overdiagnosis and lead time by identifying the average lead time most consistent with a given overdiagnosis frequency. We consider a high-profile study that suggested that 31% of breast cancers diagnosed in the United States in 2008 were overdiagnosed and show that this corresponds to an average lead time of about nine years among localized cases. Comparing this estimate with the average lead time for invasive, screen-detected breast cancers of 40 months, around which there is a relative consensus, suggests the published estimate of overdiagnosis is excessive. This approach provides a novel way to appraise estimates of overdiagnosis given knowledge of disease natural history.
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A Chemical Tuned Strategy to Develop Novel Irreversible EGFR-TK Inhibitors with Improved Safety and Pharmacokinetic Profiles.
J. Med. Chem.
PUBLISHED: 11-20-2014
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Gatekeeper T790M mutation in EGFR is the most prevalent factor underlying acquired resistance. Acrylamide-bearing quinazoline derivatives are powerful irreversible inhibitors for overcoming resistance. Nevertheless, concerns about the risk of non-specific covalent modification have motivated the development of novel cysteine-targeting inhibitors. In this paper, we demonstrate that fluoro-substituted olefins can be tuned to alter Michael addition reactivity. Incorporation of these olefins into the quinazoline templates produced potent EGFR inhibitors with improved safety and pharmacokinetic properties. A lead compound 5a was validated against EGFRWT, EGFR T790M as well as A431 and H1975 cancer cell lines. Additionally, compound 5a displayed a weaker inhibition against the EGFR-independent cancer cell line SW620 when compared withafatinib. Oral administration of 5a at a dose of 30mg/kg induced tumor regression in a murine-EGFRL858R/T790M driven H1975 xenograft model. Also, 5a exhibited improved oral bioavailability and safety, as well as favorable tissue distribution properties and enhanced brain uptake. These findings provide the basis of a promising strategy toward the treatment of NSCLC patients with drug resistance.
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Orthogonally polarized dual-wavelength Nd:YAlO3 laser at 1341 and 1339??nm and sum-frequency mixing for an emission at 670??nm.
Appl Opt
PUBLISHED: 10-17-2014
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We report a diode-pumped continuous wave (cw) orthogonally polarized dual-wavelength laser at 1339 and 1341 nm with a single b-cut Nd:YAlO3 (Nd:YAP) crystal. By adjusting the tilt angle of the uncoated glass plate inserted in the laser cavity, we can control the cavity losses of two polarized directions. The output wavelengths are 1339 nm in a-axis polarization and 1341 nm in c-axis polarization, respectively, which are orthogonal to each other. At an incident pump power of 17.3 W, the cw output power obtained at 1339 and 1341 nm is 1.6 and 2.3 W, respectively. Furthermore, intracavity sum-frequency mixing at 1339 and 1341 nm was then realized in a KTiOPO4 (KTP) crystal to reach the red range. To our knowledge, this is the first work realizing an orthogonally polarized dual-wavelength Nd:YAP laser based on the F43/2-4I13/2 transition. Such a dual-wavelength laser would be especially valuable as a compact laser source to generate terahertz emission because the frequency difference between 1339 and 1341 nm is about 0.9 THz.
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Overdetection of recurrence after radical prostatectomy: estimates based on patient and tumor characteristics.
Clin. Cancer Res.
PUBLISHED: 10-17-2014
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Prostate-specific antigen recurrence (PSA-R) after radical prostatectomy (RP) can occur years before metastasis. This study estimates the chance that an untreated PSA-R would not progress to clinical metastasis within the patient's lifetime, that is, that recurrence is overdetected.
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Characterization of single disseminated prostate cancer cells reveals tumor cell heterogeneity and identifies dormancy associated pathways.
Oncotarget
PUBLISHED: 10-11-2014
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Cancer dormancy refers to the prolonged clinical disease-free time between removal of the primary tumor and recurrence, which is common in prostate cancer (PCa), breast cancer, esophageal cancer, and other cancers. PCa disseminated tumor cells (DTC) are detected in both patients with no evidence of disease (NED) and advanced disease (ADV). However, the molecular and cellular nature of DTC is unknown. We performed a first-in-field study of single DTC transcriptomic analyses in cancer patients to identify a molecular signature associated with cancer dormancy. We profiled eighty-five individual EpCAM+/CD45- cells from the bone marrow of PCa patients with NED or ADV. We analyzed 44 DTC with high prostate-epithelial signatures, and eliminated 41 cells with high erythroid signatures and low prostate epithelial signatures. DTC were clustered into 3 groups: NED, ADV_1, and ADV_2, in which the ADV_1 group presented a distinct gene expression pattern associated with the p38 stress activated kinase pathway. Additionally, DTC from the NED group were enriched for a tumor dormancy signature associated with head and neck squamous carcinoma and breast cancer. This study provides the first clinical evidence of the p38 pathway as a potential biomarker for early recurrence and an attractive target for therapeutic intervention.
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Effect of Trichostatin A on Anti HepG2 Liver Carcinoma Cells: Inhibition of HDAC Activity and Activation of Wnt/?-Catenin Signaling.
Asian Pac. J. Cancer Prev.
PUBLISHED: 10-09-2014
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To investigate the effect of deacetylase inhibitory trichostatin A (TSA) on anti HepG2 liver carcinoma cells and explore the underlying mechanisms.
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[Regulatory effect of ginsenoside Rh2 on HDAC1/2 activity and cyclin in human erythroleukemia K562 cells].
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi
PUBLISHED: 10-02-2014
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Objective To investigate the effects of the 20(S)-ginsenoside Rh2 [Rh2(S)]on cell proliferation, histone deacetylase 1 (HDAC1) and HDAC2 activity, and expression of cyclin in human erythroleukemia K562 cells. Methods The K562 cells were treated with Rh2(S) at various concentrations (10-80 ?mol/L). Cell proliferation activity was detected by CCK-8 assay. Flow cytometry (FCM) was used to detect cell cycle and apoptotic changes. The HDAC activity of cells was measured by chemical colorimetry. The protein expressions of HDAC1, HDAC2, cyclin D1, CDK4, p16INK4A and p21 after 48 hour-treatment of Rh2 (S) (10, 20, 40, 60 ?mol/L) were examined by Western blotting. Results The proliferation of K562 cells was inhibited by Rh2 (S) (20-80 ?mol/L) in dose-and time-dependent manner. FCM analyses revealed that the number of the K562 cells treated with 60 ?mol/L Rh2(S) was arrested in G0/G1 phase. The apoptosis rates of K562 cells were respectively (8.09±0.86)%, (9.44±0.53)% and (22.80±2.16)% after induced by 20, 40, 60 ?mol/L Rh2(S), which showed statistically significant difference (P<0.05) compared with the control group (2.63±0.14)%. HDAC activity of the cells treated with Rh2(S) (40, 60 ?mol/L) was reduced. Western blotting showed that the expressions of HDAC1, HDAC2, cyclin D1 and CDK4 decreased after induced by Rh2(S), and p16INK4A, p21 proteins were enhanced significantly. Conclusion The Rh2(S) can inhibit the proliferation of K562 cells and induce its cycle arrest and apoptosis through inhibiting HDAC1 and HDAC2 activity, down-regulating the expression of cyclin D1 and activating p16INK4A and p21.
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Indium metal-organic frameworks as high-performance heterogeneous catalysts for the synthesis of amino acid derivatives.
Inorg Chem
PUBLISHED: 09-22-2014
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Indium metal-organic frameworks (MOFs) were first used as recyclable heterogeneous Lewis acid catalysts for the synthesis of amino acid derivatives with excellent conversion yields. Moreover, exposed ether groups (Lewis basic sites) on the pore walls of In-MOF 2 could activate trimethylsilyl cyanide, forming hypervalent silicate intermediates, as proven by (29)Si NMR.
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Knockdown of glucose-regulated protein 78 enhances poly(ADP-ribose) polymerase cleavage in human pancreatic cancer cells exposed to endoplasmic reticulum stress.
Oncol. Rep.
PUBLISHED: 08-07-2014
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The present study examined the expression of glucose?regulated protein 78 (GRP78/Bip) in human pancreatic cancer cell lines and the effect of knockdown of GRP78 on the cleavage of poly(ADP-ribose) polymerase (PARP). Human pancreatic cancer cell lines (KP-2, MIAPaCa-2, Panc-1 and SUIT-2), constitutively expressed GRP78. We also demonstrated that ER stress induced by thapsigargin upregulated protein levels of GRP78. In the presence of thapsigargin, knockdown of GRP78 enhanced the PARP cleavage in the human pancreatic cancer cells. These results provide evidence that GRP78 is a potential therapeutic target for 'difficult-to-treat' pancreatic cancer, in which ER stress signaling in part falls into disorder.
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Cadmium-induced activation of high osmolarity glycerol pathway through its Sln1 branch is dependent on the MAP kinase kinase kinase Ssk2, but not its paralog Ssk22, in budding yeast.
FEMS Yeast Res.
PUBLISHED: 08-04-2014
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Cadmium ions disrupt reactive oxygen species/Ca(2+) homeostasis and subsequently elicit cell death and adaptive signaling cascades in eukaryotic cells. Through a functional genomics approach, we have identified deletion mutants of 106 yeast genes, including three MAP kinase genes (HOG1, SLT2, and KSS1), are sensitive to a sublethal concentration of cadmium, and 64 mutants show elevated intracellular cadmium concentrations upon exposure to cadmium. Hog1 is phosphorylated, reaching a peak 30 min after the cadmium treatment. Both Sln1 and Sho1 upstream branches are involved in the cadmium-induced activation of high osmolarity glycerol (HOG) pathway. Cadmium-induced HOG activation is dependent on the MAP kinase kinase kinase Ssk2, but not its paralog Ssk22, in the Sln1 branch.
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3-Deazaneplanocin?A and Neplanocin?A Analogues and Their Effects on Apoptotic Cell Death.
ChemMedChem
PUBLISHED: 07-26-2014
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3-Deazaneplanocin?A (DzNep) is a potential epigenetic drug for the treatment of various cancers. DzNep has been reported to deplete histone methylations, including oncogenic EZH2 complex, giving rise to epigenetic modifications that reactivate many silenced tumor suppressors in cancer cells. Despite its promise as an anticancer drug, little is known about the structure-activity relationships of DzNep in the context of epigenetic modifications and apoptosis induction. In this study, a number of analogues of DzNep were examined for DzNep-like ability to induce synergistic apoptosis in cancer cells in combination with trichostatin?A, a known histone deacetylase (HDAC) inhibitor. The structure-activity relationship data thus obtained provide valuable information on the structural requirements for biological activity. The studies identified three compounds that show similar activities to DzNep. Two of these compounds show good pharmacokinetics and safety profiles. Attempts to correlate the observed synergistic apoptotic activities with measured S-adenosylhomocysteine hydrolase (SAHH) inhibitory activities suggest that the apoptotic activity of DzNep might not be directly due to its inhibition of SAHH.
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[Inhibitory effect of trichostatin A on HepG2 cell proliferation and the mechanisms].
Nan Fang Yi Ke Da Xue Xue Bao
PUBLISHED: 07-25-2014
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To investigate the inhibitory effect of trichostatin A (TSA) on the proliferation of HepG2 cells and explore the underlying mechanism.
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Differential network analyses of Alzheimer's disease identify early events in Alzheimer's disease pathology.
Int J Alzheimers Dis
PUBLISHED: 07-23-2014
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In late-onset Alzheimer's disease (AD), multiple brain regions are not affected simultaneously. Comparing the gene expression of the affected regions to identify the differences in the biological processes perturbed can lead to greater insight into AD pathogenesis and early characteristics. We identified differentially expressed (DE) genes from single cell microarray data of four AD affected brain regions: entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC), and middle temporal gyrus (MTG). We organized the DE genes in the four brain regions into region-specific gene coexpression networks. Differential neighborhood analyses in the coexpression networks were performed to identify genes with low topological overlap (TO) of their direct neighbors. The low TO genes were used to characterize the biological differences between two regions. Our analyses show that increased oxidative stress, along with alterations in lipid metabolism in neurons, may be some of the very early events occurring in AD pathology. Cellular defense mechanisms try to intervene but fail, finally resulting in AD pathology as the disease progresses. Furthermore, disease annotation of the low TO genes in two independent protein interaction networks has resulted in association between cancer, diabetes, renal diseases, and cardiovascular diseases.
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Evaluating the effect of a novel molluscicide in the endemic schistosomiasis japonica area of China.
Int J Environ Res Public Health
PUBLISHED: 07-18-2014
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Oncomelania hupensis is the sole intermediate host snail of Schistosoma japonicum in China. Snail control by molluscicide remains one of the most effective measures of schistosomiasis japonica control. A 50% wettable powder of niclosamide ethanolamine salt (WPN) is widely used for snail control in China. However, WPN is costly and toxic to fish. A novel molluscicide named LDS, the salt of quinoid-2', 5-dichloro-4'-nitrosalicylanilide from niclosamide, has been developed. To evaluate the effects of large-scale field application of LDS on field snail control, tests were conducted in 15 counties of Hubei Province, China. Active adult snails, were immersed in 0.2, 0.4, and 0.6 g/m3 of 10% LDS, 1.0 g/m3 of 50% WPN was used as the molluscicide control, and then the mortality rates of snails were investigated after 1, 2, and 3 days. In addition, four active concentrations of 10% LDS (0.4, 0.6, 0.8 and 1.0 g/m2) were applied by spraying and powdering in the field. 1.0 g/m2 of 50% WPN was used as the molluscicide control, and then the mortality rates of snails were observed after 1, 3, and 7 days. The results indicated that 0.4 g/m3 LDS applied by the immersion or 0.6 g/m2 LDS applied by spraying and powdering achieved the same molluscicidal effect as that of WPN, regardless of exposure time. By using different methods, the snail mortality rates in the molluscicide groups were related to exposure time and concentration, respectively. LDS costs less than WPN; thus, LDS is suitable and applicable for use as a molluscicide in schistosomiasis japonica epidemic areas.
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Reciprocal Actions of microRNA-9 and TLX in the Proliferation and Differentiation of Retinal Progenitor Cells.
Stem Cells Dev.
PUBLISHED: 07-14-2014
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Recent research has demonstrated critical roles of a number of microRNAs (miRNAs) in stem cell proliferation and differentiation. miRNA-9 (miR-9) is a brain-enriched miRNA. Whether miR-9 has a role in retinal progenitor cell (RPC) proliferation and differentiation remains unknown. In this study, we show that miR-9 plays an important role in RPC fate determination. The expression of miR-9 was inversely correlated with that of the nuclear receptor TLX, which is an essential regulator of neural stem cell self-renewal. Overexpression of miR-9 downregulated the TLX levels in RPCs, leading to reduced RPC proliferation and increased neuronal and glial differentiation, and the effect of miR-9 overexpression on RPC proliferation and differentiation was inhibited by the TLX overexpression; knockdown of miR-9 resulted in increased TLX expression as well as enhanced proliferation of RPCs. Furthermore, inhibition of endogenous TLX by small interfering RNA suppressed RPC proliferation and promoted RPCs to differentiate into retinal neuronal and glial cells. These results suggest that miR-9 and TLX form a feedback regulatory loop to coordinate the proliferation and differentiation of retinal progenitors.
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CVD synthesis of large-area, highly crystalline MoSe2 atomic layers on diverse substrates and application to photodetectors.
Nanoscale
PUBLISHED: 06-27-2014
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Synthesis of large-area, atomically thin transition metal dichalcogenides (TMDs) on diverse substrates is of central importance for the large-scale fabrication of flexible devices and heterojunction-based devices. In this work, we successfully synthesized a large area of highly-crystalline MoSe2 atomic layers on SiO2/Si, mica and Si substrates using a simple chemical vapour deposition (CVD) method at atmospheric pressure. Atomic force microscopy (AFM) and Raman spectroscopy reveal that the as-grown ultrathin MoSe2 layers change from a single layer to a few layers. Photoluminescence (PL) spectroscopy demonstrates that while the multi-layer MoSe2 shows weak emission peaks, the monolayer has a much stronger emission peak at ? 1.56 eV, indicating the transition from an indirect to a direct bandgap. Transmission electron microscopy (TEM) analysis confirms the single-crystallinity of MoSe2 layers with a hexagonal structure. In addition, the photoresponse performance of photodetectors based on MoSe2 monolayer was studied for the first time. The devices exhibit a rapid response of ? 60 ms and a good photoresponsivity of ? 13 mA/W (using a 532 nm laser at an intensity of 1 mW mm(-2) and a bias of 10 V), suggesting that MoSe2 monolayer is a promising material for photodetection applications.
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[Ginsenoside Rh2 inhibits proliferation and promotes apoptosis of leukemia KG1-? cells].
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi
PUBLISHED: 06-10-2014
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To investigate the effect of ginsenoside Rh2 on leukemia KG1-? cells.
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Role of Central Serotonin in Anticipation of Rewarding and Punishing Outcomes: Effects of Selective Amygdala or Orbitofrontal 5-HT Depletion.
Cereb. Cortex
PUBLISHED: 06-01-2014
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Understanding the role of serotonin (or 5-hydroxytryptamine, 5-HT) in aversive processing has been hampered by the contradictory findings, across studies, of increased sensitivity to punishment in terms of subsequent response choice but decreased sensitivity to punishment-induced response suppression following gross depletion of central 5-HT. To address this apparent discrepancy, the present study determined whether both effects could be found in the same animals by performing localized 5-HT depletions in the amygdala or orbitofrontal cortex (OFC) of a New World monkey, the common marmoset. 5-HT depletion in the amygdala impaired response choice on a probabilistic visual discrimination task by increasing the effectiveness of misleading, or false, punishment and reward, and decreased response suppression in a variable interval test of punishment sensitivity that employed the same reward and punisher. 5-HT depletion in the OFC also disrupted probabilistic discrimination learning and decreased response suppression. Computational modeling of behavior on the discrimination task showed that the lesions reduced reinforcement sensitivity. A novel, unitary account of the findings in terms of the causal role of 5-HT in the anticipation of both negative and positive motivational outcomes is proposed and discussed in relation to current theories of 5-HT function and our understanding of mood and anxiety disorders.
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Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava.
BMC Genomics
PUBLISHED: 05-31-2014
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Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs.
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PEDF and PEDF-derived peptide 44mer protect cardiomyocytes against hypoxia-induced apoptosis and necroptosis via anti-oxidative effect.
Sci Rep
PUBLISHED: 05-12-2014
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Pigment epithelium-derived factor (PEDF) has many biological activities. But it's not known whether PEDF and its functional peptides could protect against hypoxia-induced cell death and the mechanisms are still unclear. We used cultured H9c2 cells and primary cardiomyocytes to show that apoptosis and necroptosis were significantly increased after hypoxia. Both PEDF and its fuctional peptides 44mer reduced apoptosis and necroptosis rates and inhibited the expression of cleaved caspase 3 and receptor-interacting protein 3 (RIP3). Furthermore, PEDF and 44mer could up-regulate super oxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) levels, promote clearing of reactive oxygen species (ROS) and malondialdehyde (MDA). While, 34mer, another functional peptides had no effect on cell apoptosis and necroptosis. Hereby this is the first evidence that PEDF and its functional peptide 44mer protect cultured H9c2 cells and primary cardiomyocytes against apoptosis and necroptosis under hypoxic condition via the anti-oxidative mechanism.
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SDF-1/CXCR7 axis enhances ovarian cancer cell invasion by MMP-9 expression through p38 MAPK pathway.
DNA Cell Biol.
PUBLISHED: 05-12-2014
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Ovarian cancer is an aggressive gynecological malignancy with high metastatic potential. Recently, the CXC receptor (CXCR7) has been identified as a new receptor for stromal-derived factor-1 (SDF-1), and exerts important roles in cancer development. However, its effect on ovarian cancer and the underlying mechanism remain unknown. In this study, we detected abundant CXCR7 expression in ovarian cancer tissues and cells. Moreover, SDF-1 induced dramatically upregulation of CXCR7 mRNA and protein levels, indicating that the SDF-1/CXCR7 axis existed in ovarian cancer. Further analysis confirmed that SDF-1 enhanced cell adhesion and subsequent invasion, which were significantly attenuated when pretreated with CXCR7 small interference RNA (siRNA), indicating the critical function of SDF-1/CXCR7 in cell invasion. Further mechanistic analysis indicated that SDF-1/CXCR7 enhanced cell invasion by matrix metalloproteinase (MMP)-9, as pretreatment with MMP-9 siRNA significantly abrogated a number of invading cells. Additionally, SDF-1/CXCR7 induced phosphorylation of the p38 MAPK pathway, which was accounted for MMP-9 expression as preconditioning with the p38 MAPK inhibitor SB203580 obviously decreased MMP-9 expression. Together, our data implied that SDF-1/CXCR7 enhanced ovarian cancer cell invasion by MMP-9 expression through the p38 MAPK pathway. Thus, these findings confirmed the critical role of SDF-1/CXCR7 during the pathological processes of ovarian cancer and supported its potential targets for further development of antiovarian cancer therapy.
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Anti-CarP antibodies in two large cohorts of patients with rheumatoid arthritis and their relationship to genetic risk factors, cigarette smoking and other autoantibodies.
Ann. Rheum. Dis.
PUBLISHED: 05-08-2014
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In rheumatoid arthritis (RA), several genetic risk factors and smoking are strongly associated with the presence of anticitrullinated protein antibodies (ACPA), while much less is known about risk factors for ACPA-negative RA. Antibodies against carbamylated proteins (anti-CarP) have been described in both ACPA-positive and ACPA-negative RA patients. In this study, we have analysed the relationships among anti-CarP antibodies, ACPA, genetic risk factors (HLA-DRB1 alleles and PTPN22) and smoking in RA.
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Ginsenoside Rg1 induces apoptosis through inhibition of the EpoR-mediated JAK2/STAT5 signalling pathway in the TF-1/ Epo human leukemia cell line.
Asian Pac. J. Cancer Prev.
PUBLISHED: 04-26-2014
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Ginsenoside Rg1 is one effective anticancer and antioxidant constituent of total saponins of Panax ginseng (TSPG), which has been shown to have various pharmacological effects. Our previous study demonstrated that Rg1 had anti-tumor activity in K562 leukemia cells. The aim of this study was designed to investigate whether Rg1 could induce apoptosis in TF-1/Epo cells and further to explore the underlying molecular mechanisms. Here we found that Rg1 could inhibit TF-1/Epo cell proliferation and induce cell apoptosis in vitro in a concentration and time dependent manner. It also suppressed the expression of EpoR on the surface membrane and inhibited JAK2/STAT5 pathway activity. Rg1 induced up-regulation of Bax, cleaved caspase-3 and C-PAPR protein and down-regulation of Bcl-2 and AG490, a JAK2 specific inhibitor, could enhance the effects of Rg1. Our studies showed that EpoR-mediated JAK2/STAT5 signaling played a key role in Rg1-induced apoptosis in TF-1/Epo cells. These results may provide new insights of Rg1 protective roles in the prevention a nd treatment of leukemia.
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A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets.
J Am Med Inform Assoc
PUBLISHED: 04-15-2014
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The objective of this investigation is to evaluate binary prediction methods for predicting disease status using high-dimensional genomic data. The central hypothesis is that the Bayesian network (BN)-based method called efficient Bayesian multivariate classifier (EBMC) will do well at this task because EBMC builds on BN-based methods that have performed well at learning epistatic interactions.
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Improved performance of epidemiologic and genetic risk models for rheumatoid arthritis serologic phenotypes using family history.
Ann. Rheum. Dis.
PUBLISHED: 03-31-2014
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To develop and validate rheumatoid arthritis (RA) risk models based on family history, epidemiologic factors and known genetic risk factors.
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Cassava genome from a wild ancestor to cultivated varieties.
Nat Commun
PUBLISHED: 03-20-2014
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Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
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Smokeless tobacco (moist snuff) use and the risk of developing rheumatoid arthritis: results from a case-control study.
Arthritis Care Res (Hoboken)
PUBLISHED: 03-13-2014
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To investigate the association between snuff use (smokeless tobacco containing nicotine) and the risk of anti–citrullinated protein/peptide antibody (ACPA)–positive and ACPA-negative rheumatoid arthritis (RA).
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Down-regulation of phosphoglucose isomerase/autocrine motility factor enhances gensenoside Rh2 pharmacological action on leukemia KG1? cells.
Asian Pac. J. Cancer Prev.
PUBLISHED: 03-11-2014
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Ginsenoside Rh2, which exerts the potent anticancer action both in vitro and in vivo, is one of the most well characterized ginsenosides extracted from ginseng. Although its effects on cancer are significant, the underlying mechanisms remain unknown. In this study, we sought to elucidate possible links between ginsenoside Rh2 and phosphoglucose isomerase/autocrine motility factor (PGI/AMF).
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Conformable amplified lead zirconate titanate sensors with enhanced piezoelectric response for cutaneous pressure monitoring.
Nat Commun
PUBLISHED: 03-08-2014
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The ability to measure subtle changes in arterial pressure using devices mounted on the skin can be valuable for monitoring vital signs in emergency care, detecting the early onset of cardiovascular disease and continuously assessing health status. Conventional technologies are well suited for use in traditional clinical settings, but cannot be easily adapted for sustained use during daily activities. Here we introduce a conformal device that avoids these limitations. Ultrathin inorganic piezoelectric and semiconductor materials on elastomer substrates enable amplified, low hysteresis measurements of pressure on the skin, with high levels of sensitivity (~0.005?Pa) and fast response times (~0.1?ms). Experimental and theoretical studies reveal enhanced piezoelectric responses in lead zirconate titanate that follow from integration on soft supports as well as engineering behaviours of the associated devices. Calibrated measurements of pressure variations of blood flow in near-surface arteries demonstrate capabilities for measuring radial artery augmentation index and pulse pressure velocity.
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Effect of ginsenoside Rh2 on the migratory ability of HepG2 liver carcinoma cells: recruiting histone deacetylase and inhibiting activator protein 1 transcription factors.
Mol Med Rep
PUBLISHED: 03-05-2014
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In previous experiments, ginsenoside Rh2 induced apoptosis and cell cycle arrest, which indicates a potential role for ginsenoside Rh2 in anticancer treatment. The effect of ginsenoside Rh2 on cancer is marked and ginsenoside Rh2 has been shown to inhibit pancreatic tumor migratory ability. In the present study, Transwell chambers were used in order to investigate whether ginsenoside Rh2 inhibits the migratory ability of HepG2 liver carcinoma cells. Furthermore, to analyze activator protein 1 (AP-1) transcription factor expression following Rh2 treatment, ten plasmids encoding Renilla luciferase coupled to the transcription factors were transiently transfected into the HepG2 cells and luciferase was detected by the Luciferase Reporter Assay system reagent. The results indicated that ginsenoside Rh2 inhibited HepG2 cell migratory ability. The expression levels of AP-1 transcription factors were increased in HepG2 cells following induction by phorbol 12-myristate 13-acetate, but ginsenoside Rh2 suppressed this induced AP?1 expression. AP-1 transcription factors recruit histone deacetylase (HDAC)4 and affect its transcription, thus, the expression levels of HDAC4 were also analyzed, and these were found to be increased in the Rh2 treatment group. Matrix metalloproteinase 3 (MMP3), a gene downstream of AP-1, was then investigated, and the treatment group expressed reduced levels of MMP3 gene and protein. Therefore, the inhibitory effect of ginsenoside Rh2 on the migratory ability of HepG2 may be presumed to occur by the recruitment of HDAC and the resulting inhibition of AP?1 transcription factors, in order to reduce the expression levels of MMP3 gene and protein.
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Concentration dependence of optical clearing on the enhancement of laser-scanning optical-resolution photoacoustic microscopy imaging.
J Biomed Opt
PUBLISHED: 02-18-2014
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Quantitative analysis of optical clearing effects (OCE) induced by hyperosmotic agents is very important to optical tissue clearing applications in biomedical diagnostic imaging and therapeutics. This study aims at investigating the effect of glycerol concentration on the laser-scanning optical-resolution photoacoustic microscopy (LSOR-PAM) imaging contrast and light penetration depth. The photoacoustic (PA) signal amplitude changes are evaluated as a function of the concentration of glycerol. The results reveal that the PA signal amplitudes are enhanced with the glycerol concentration increasing, and also show that higher concentration of glycerol produces better light penetration and OCE on a phantom. The PA signal amplitude increases only 8.1% for 20% glycerol, but for higher concentrations, the increases are 76% and 165% for 40% and 60% glycerol, respectively. This preliminary study demonstrates that application of glycerol as an optical contrast agent reduces the tissue scattering and is beneficial to PAM imaging and optical diagnosis in clinical dermatology.
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Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in cassava.
BMC Plant Biol.
PUBLISHED: 02-10-2014
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Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environment. Even though generally considered to be sensitive to low temperature, Cassava, a major tropical crop, can be tolerant to much lower temperature after chilling acclimation. Improvement to chilling resistance could be beneficial to breeding. However, the underlying mechanism and the effects of chilling acclimation on chilling tolerance remain largely unexplored.
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Multifunctional skin-like electronics for quantitative, clinical monitoring of cutaneous wound healing.
Adv Healthc Mater
PUBLISHED: 02-02-2014
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Non-invasive, biomedical devices have the potential to provide important, quantitative data for the assessment of skin diseases and wound healing. Traditional methods either rely on qualitative visual and tactile judgments of a professional and/or data obtained using instrumentation with forms that do not readily allow intimate integration with sensitive skin near a wound site. Here, an electronic sensor platform that can softly and reversibly laminate perilesionally at wounds to provide highly accurate, quantitative data of relevance to the management of surgical wound healing is reported. Clinical studies on patients using thermal sensors and actuators in fractal layouts provide precise time-dependent mapping of temperature and thermal conductivity of the skin near the wounds. Analytical and simulation results establish the fundamentals of the sensing modalities, the mechanics of the system, and strategies for optimized design. The use of this type of "epidermal" electronics system in a realistic clinical setting with human subjects establishes a set of practical procedures in disinfection, reuse, and protocols for quantitative measurement. The results have the potential to address important unmet needs in chronic wound management.
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A two-enzyme immobilization approach using carbon nanotubes/silica as support.
Biotechnol. Prog.
PUBLISHED: 01-28-2014
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Multiple enzyme mixtures are attractive for the production of many compounds at an industrial level. We report a practical and novel approach for coimmobilization of two enzymes. The system consists of a silica microsphere core coated with two layers of individually immobilized enzymes. The model enzymes ?-amylase (AA) and glucoamylase (GluA) were individually immobilized on carbon nanotubes (CNTs). A CNT-GluA layer was formed by adsorbing CNT-GluA onto silica microsphere. A sol-gel layer with entrapped CNT-AA was then formed outside the CNT-GluA/silica microsphere conjugate. The coimmobilized ?-amylase and glucoamylase exhibited 95.1% of the activity of the mixture of free ?-amylase and glucoamylase. The consecutive use exhibited a good stability of the coimmobilized enzymes. The developed approach demonstrates advantages, including controlling the ratio of coimmobilized enzymes in an easy way, facilitating diffusion of small molecules in and out of the matrix, and preventing the leaching of enzymes. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 2014.
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The central role of EED in the orchestration of polycomb group complexes.
Nat Commun
PUBLISHED: 01-25-2014
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Polycomb repressive complexes 1 and 2 (PRC1 and 2) play a critical role in the epigenetic regulation of transcription during cellular differentiation, stem cell pluripotency and neoplastic progression. Here we show that the polycomb group protein EED, a core component of PRC2, physically interacts with and functions as part of PRC1. Components of PRC1 and PRC2 compete for EED binding. EED functions to recruit PRC1 to H3K27me3 loci and enhances PRC1-mediated H2A ubiquitin E3 ligase activity. Taken together, we suggest an integral role for EED as an epigenetic exchange factor coordinating the activities of PRC1 and 2.
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Androgen receptor signaling in hepatocellular carcinoma and pancreatic cancers.
World J. Gastroenterol.
PUBLISHED: 01-17-2014
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Hepatocellular carcinoma (HCC) and pancreatic cancer remain difficult to treat, and despite the ongoing development of new treatments, the overall survival rate has only modestly improved over the past decade. Liver and pancreatic progenitors commonly develop from endoderm cells in the embryonic foregut. A previous study showed that HCC and pancreatic cancer cell lines variably express androgen receptor (AR), and these cancers and the surrounding tissues also express AR. AR is a ligand-dependent transcription factor that belongs to the nuclear receptor superfamily. Androgen response element is present in regulatory elements on the AR-responsive target genes, such as transforming growth factor beta-1 (TGF beta-1) and vascular endothelial growth factor (VEGF). It is well known that the activation of AR is associated with human carcinogenesis in prostate cancer as well as HCC and pancreatic cancer and that GRP78, TGF beta, and VEGF all play important roles in carcinogenesis and cancer development in these cancers. HCC is a male-dominant cancer irrespective of its etiology. Previous work has reported that vertebrae forkhead box A 1/2 are involved in estrogen receptors and/or AR signaling pathways, which may contribute to the gender differences observed with HCC. Our recent work also showed that AR has a critical role in pancreatic cancer development, despite pancreatic cancer not being a male dominant cancer. Aryl hydrocarbon (or dioxin) receptor is also involved in both HCC and pancreatic cancer through the formation of complex with AR. It is possible that AR might be involved in their carcinogenesis through major histocompatibility complex class?I?chain-related gene A/B. This review article describes AR and its role in HCC and pancreatic cancer and suggests that more specific AR signaling-inhibitors may be useful in the treatment of these "difficult to treat" cancers.
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Involvement of androgen receptor and glucose-regulated protein 78 kDa in human hepatocarcinogenesis.
Exp. Cell Res.
PUBLISHED: 01-09-2014
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Previous studies demonstrated that androgen receptor (AR) is expressed in human hepatocellular carcinoma (HCC), one of the male-dominant diseases. Glucose-regulated protein 78 kDa (GRP78/Bip), which has a role in cancer development, is one of the androgen response genes in prostate cell lines. The aim of this study was to investigate the impact of AR on endoplasmic reticulum (ER)-stress signaling in human hepatoma. AR and GRP78 expressions were examined in human liver tissue panels. Human hepatoma cells stably expressing short hairpin RNA targeting AR and cells over-expressing AR were generated. The expressions of ER-stress molecules and AR were measured by real-time RT-PCR and Western blotting. The effect of AR on ER-stress responsive gene expression was examined by reporter assay. Strong positive correlation between AR mRNA and GRP78 mRNA was observed in stage I/II-HCCs. AR enhanced ER-stress responsive element activities and GRP78 expression, and regulated ER-stress response in hepatocytes. Sorafenib strongly induced significant apoptosis in HepG2 cells by the inhibition of AR and inhibition of the downstream GRP78. AR seems a co-regulator of GRP78 especially in earlier-stage HCC. AR plays a critical role in controlling ER-stress, providing new therapeutic options against HCC.
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Downregulation of microRNA-431 by human interferon-? inhibits viability of medulloblastoma and glioblastoma cells via upregulation of SOCS6.
Int. J. Oncol.
PUBLISHED: 01-07-2014
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miRNAs are small non-coding RNAs that inhibit gene expression by cleaving or hindering the translation of target mRNAs. In this study, we focused on miR-431, which mediated inhibition of cell viability by human interferon-? (HuIFN-?). We aimed to demonstrate an antineoplastic effect of HuIFN-? via miR-431 expression against medulloblastoma and glioblastoma, because HuIFN-? is frequently used in adjuvant therapy of these tumors. Addition of HuIFN-? to medulloblastoma and glioblastoma cells reduced viability, significantly decreased miR-431 expression, upregulated expression of SOCS6 (putative miR-431 target genes) and inhibited Janus kinase (JAK) 1 and signal transducer and activator of transcription (STAT) 2. The mitogen-activated protein kinase (MAPK) pathway, but not the phosphoinositide 3-kinase (PI3K)-Akt pathway, was downregulated in medulloblastoma cells, whereas the PI3K-Akt pathway, but not the MAPK pathway, was downregulated in glioblastoma cells. Addition of HuIFN-? and transient transfection with miR-431 to medulloblastoma and glioblastoma cells did not reduce viability, downregulated expression of SOCS6, and concomitantly activated the JAK1 and STAT2. We propose that, in medulloblastoma and glioblastoma cells, HuIFN-? decreases miR-431 expression and upregulates SOCS6 expression, and consequently inhibit cell proliferation by suppressing the JAK-STAT signaling pathway.
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Regulation of microRNA by hepatitis B virus infection and their possible association with control of innate immunity.
World J. Gastroenterol.
PUBLISHED: 01-03-2014
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Hepatitis B virus (HBV) chronically infects more than 350 million people worldwide. HBV causes acute and chronic hepatitis, and is one of the major causes of cirrhosis and hepatocellular carcinoma. There exist complex interactions between HBV and the immune system including adaptive and innate immunity. Toll-like receptors (TLRs) and TLR-signaling pathways are important parts of the innate immune response in HBV infections. It is well known that TLR-ligands could suppress HBV replication and that TLRs play important roles in anti-viral defense. Previous immunological studies demonstrated that HBV e antigen (HBeAg) is more efficient at eliciting T-cell tolerance, including production of specific cytokines IL-2 and interferon gamma, than HBV core antigen. HBeAg downregulates cytokine production in hepatocytes by the inhibition of MAPK or NF-?B activation through the interaction with receptor-interacting serine/threonine protein kinase. MicroRNAs (miRNAs) are also able to regulate various biological processes such as the innate immune response. When the expressions of approximately 1000 miRNAs were compared between human hepatoma cells HepG2 and HepG2.2.15, which could produce HBV virion that infects chimpanzees, using real-time RT-PCR, we observed several different expression levels in miRNAs related to TLRs. Although we and others have shown that HBV modulates the host immune response, several of the miRNAs seem to be involved in the TLR signaling pathways. The possibility that alteration of these miRNAs during HBV infection might play a critical role in innate immunity against HBV infection should be considered. This article is intended to comprehensively review the association between HBV and innate immunity, and to discuss the role of miRNAs in the innate immune response to HBV infection.
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Emissions of ammonia and greenhouse gases during combined pre-composting and vermicomposting of duck manure.
Waste Manag
PUBLISHED: 01-03-2014
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Combined pre-composting and vermicomposting has shown potential for reclamation of solid wastes, which is a significant source of ammonia (NH3), and greenhouse gases (GHG), including nitrous oxide (N2O), methane (CH4), and carbon dioxide (CO2). Earthworms and amendments may both affect physico-chemical characteristics that control gas-producing processes, and thus affect NH3 and GHG emissions. Here, we used two-way ANOVA to test the effects of addition of reed straw and combined addition of reed straw and zeolite on NH3 and GHG emissions during pre-composting of duck manure, either with or without a follow-up phase of vermicomposting. Results showed that cumulative N2O, CH4, and CO2 emissions during pre-composting and vermicomposting ranged from 92.8, 5.8, and 260.6 mg kg(-)(1) DM to 274.2, 30.4, and 314.0 mg kg(-1) DM, respectively. Earthworms and amendments significantly decreased N2O and CH4 emissions. Emission of CO2 was not affected by earthworms, but increased in responses to addition of reed straw. Cumulative NH3 emission ranged from 3.0 to 8.1 g kg(-1) DM, and was significantly decreased by reed straw and zeolite addition. In conclusion, combined pre-composting and vermicomposting with reed straw and zeolite addition would be strongly recommended in mitigating emissions of N2O, CH4, and NH3 from duck manure. Moreover, this method also provides nutrient-rich products that can be used as a fertilizer.
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Hepatitis C Virus Nonstructural Protein 5A Inhibits Thapsigargin-Induced Apoptosis.
PLoS ONE
PUBLISHED: 01-01-2014
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We previously reported that the hepatitis C virus (HCV) nonstructural protein 5A (NS5A) down-regulates TLR4 signaling and lipopolysaccharide-induced apoptosis of hepatocytes. There have been several reports regarding the association between HCV infection and endoplasmic reticulum (ER) stress. Here, we examined the regulation of HCV NS5A on the apoptosis of hepatocytes induced by thapsigargin, an inducer of ER stress.
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Development of aminoglycoside and ?-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin.
Front Microbiol
PUBLISHED: 01-01-2014
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Lincomycin, chlortetracycline, and amoxicillin are commonly used antimicrobials for growth promotion and infectious disease prophylaxis in swine production. In this study, we investigated the shifts and resistance development among intestinal microbiota in pregnant sows before and after lincomycin, chlortetracycline, and amoxicillin treatment by using phylogenetic analysis, bacterial enumeration, and PCR. After the antimicrobial treatment, shifts in microbial community, an increased proportion of resistant bacteria, and genes related to antimicrobial resistance as compared to the day before antimicrobial administration (day 0) were observed. Importantly, a positive correlation between antimicrobial resistance gene expression in different categories, especially those encoding aminoglycoside and ?-lactamase and antimicrobial resistance, was observed. These findings demonstrate an important role of antimicrobial usage in animals in the development of antimicrobial resistance, and support the notion that prudent use of antimicrobials in swine is needed to reduce the risk of the emergence of multi-drug resistant zoonotic pathogens.
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Modeling signal transduction from protein phosphorylation to gene expression.
Cancer Inform
PUBLISHED: 01-01-2014
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Signaling networks are of great importance for us to understand the cell's regulatory mechanism. The rise of large-scale genomic and proteomic data, and prior biological knowledge has paved the way for the reconstruction and discovery of novel signaling pathways in a data-driven manner. In this study, we investigate computational methods that integrate proteomics and transcriptomic data to identify signaling pathways transmitting signals in response to specific stimuli. Such methods can be applied to cancer genomic data to infer perturbed signaling pathways.
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Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data.
Cancer Inform
PUBLISHED: 01-01-2014
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This paper concerns a new method for identifying aberrant signal transduction pathways (STPs) in cancer using case/control gene expression-level datasets, and applying that method and an existing method to an ovarian carcinoma dataset. Both methods identify STPs that are plausibly linked to all cancers based on current knowledge. Thus, the paper is most appropriate for the cancer informatics community. Our hypothesis is that STPs that are altered in tumorous tissue can be identified by applying a new Bayesian network (BN)-based method (causal analysis of STP aberration (CASA)) and an existing method (signaling pathway impact analysis (SPIA)) to the cancer genome atlas (TCGA) gene expression-level datasets. To test this hypothesis, we analyzed 20 cancer-related STPs and 6 randomly chosen STPs using the 591 cases in the TCGA ovarian carcinoma dataset, and the 102 controls in all 5 TCGA cancer datasets. We identified all the genes related to each of the 26 pathways, and developed separate gene expression datasets for each pathway. The results of the two methods were highly correlated. Furthermore, many of the STPs that ranked highest according to both methods are plausibly linked to all cancers based on current knowledge. Finally, CASA ranked the cancer-related STPs over the randomly selected STPs at a significance level below 0.05 (P = 0.047), but SPIA did not (P = 0.083).
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Prostate cancer characteristics associated with response to pre-receptor targeting of the androgen axis.
PLoS ONE
PUBLISHED: 01-01-2014
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Factors influencing differential responses of prostate tumors to androgen receptor (AR) axis-directed therapeutics are poorly understood, and predictors of treatment efficacy are needed. We hypothesized that the efficacy of inhibiting DHT ligand synthesis would associate with intra-tumoral androgen ratios indicative of relative dependence on DHT-mediated growth.
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Suppression of La antigen exerts potential antiviral effects against hepatitis A virus.
PLoS ONE
PUBLISHED: 01-01-2014
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Despite the development and availability of hepatitis A virus (HAV) vaccine, HAV infection is still a major cause of acute hepatitis that occasionally leads to fatal liver disease. HAV internal ribosomal entry-site (IRES) is one of the attractive targets of antiviral agents against HAV. The aim of the present study is to evaluate the impact of La, one of the cellular proteins, on HAV IRES-mediated translation and HAV replication.
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Modeling the altered expression levels of genes on signaling pathways in tumors as causal bayesian networks.
Cancer Inform
PUBLISHED: 01-01-2014
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This paper concerns a study indicating that the expression levels of genes in signaling pathways can be modeled using a causal Bayesian network (BN) that is altered in tumorous tissue. These results open up promising areas of future research that can help identify driver genes and therapeutic targets. So, it is most appropriate for the cancer informatics community. Our central hypothesis is that the expression levels of genes that code for proteins on a signal transduction network (STP) are causally related and that this causal structure is altered when the STP is involved in cancer. To test this hypothesis, we analyzed 5 STPs associated with breast cancer, 7 STPs associated with other cancers, and 10 randomly chosen pathways, using a breast cancer gene expression level dataset containing 529 cases and 61 controls. We identified all the genes related to each of the 22 pathways and developed separate gene expression datasets for each pathway. We obtained significant results indicating that the causal structure of the expression levels of genes coding for proteins on STPs, which are believed to be implicated in both breast cancer and in all cancers, is more altered in the cases relative to the controls than the causal structure of the randomly chosen pathways.
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Occurrence and Recurrence of Hepatocellular Carcinoma Were Not Rare Events during Phlebotomy in Older Hepatitis C Virus-Infected Patients.
Case Rep Oncol
PUBLISHED: 01-01-2014
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The use of phlebotomy is relatively common for 'difficult-to-treat by antiviral therapies' hepatitis C virus (HCV)-infected patients and for certain patients having chronic liver diseases with an iron overload of the liver. In the present study, we retrospectively analyzed patients treated with phlebotomy and their adverse events. We observed the occurrence and recurrence of hepatocellular carcinoma, and the appearance of ascites in some patients infected with HCV as well as the reduction of serum ferritin and alanine aminotransferase levels. Severe adverse events necessitating a cessation of phlebotomy occurred independently of ?-fetoprotein (>10 ng/ml) in patients infected with HCV according to multivariate logistic regression analysis. These findings may serve as a basis for phlebotomy especially in older patients with chronic hepatitis C.
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A new method for predicting patient survivorship using efficient bayesian network learning.
Cancer Inform
PUBLISHED: 01-01-2014
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The purpose of this investigation is to develop and evaluate a new Bayesian network (BN)-based patient survivorship prediction method. The central hypothesis is that the method predicts patient survivorship well, while having the capability to handle high-dimensional data and be incorporated into a clinical decision support system (CDSS). We have developed EBMC_Survivorship (EBMC_S), which predicts survivorship for each year individually. EBMC_S is based on the EBMC BN algorithm, which has been shown to handle high-dimensional data. BNs have excellent architecture for decision support systems. In this study, we evaluate EBMC_S using the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset, which concerns breast tumors. A 5-fold cross-validation study indicates that EMBC_S performs better than the Cox proportional hazard model and is comparable to the random survival forest method. We show that EBMC_S provides additional information such as sensitivity analyses, which covariates predict each year, and yearly areas under the ROC curve (AUROCs). We conclude that our investigation supports the central hypothesis.
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Ultra-deep sequencing analysis of the hepatitis A virus 5'-untranslated region among cases of the same outbreak from a single source.
Int J Med Sci
PUBLISHED: 01-01-2014
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Hepatitis A virus (HAV) is a causative agent of acute viral hepatitis for which an effective vaccine has been developed. Here we describe ultra-deep pyrosequences (UDPSs) of HAV 5'-untranslated region (5'UTR) among cases of the same outbreak, which arose from a single source, associated with a revolving sushi bar. We determined the reference sequence from HAV-derived clone from an attendant by the Sanger method. Sixteen UDPSs from this outbreak and one from another sporadic case were compared with this reference. Nucleotide errors yielded a UDPS error rate of < 1%. This study confirmed that nucleotide substitutions of this region are transition mutations in outbreak cases, that insertion was observed only in non-severe cases, and that these nucleotide substitutions were different from those of the sporadic case. Analysis of UDPSs detected low-prevalence HAV variations in 5'UTR, but no specific mutations associated with severity in these outbreak cases. To our surprise, HAV strains in this outbreak conserved HAV IRES sequence even if we performed analysis of UDPSs. UDPS analysis of HAV 5'UTR gave us no association between the disease severity of hepatitis A and HAV 5'UTR substitutions. It might be more interesting to perform ultra-deep sequencing of full length HAV genome in order to reveal possible unknown genomic determinants associated with disease severity. Further studies will be needed.
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Genetic risk scores and number of autoantibodies in patients with rheumatoid arthritis.
Ann. Rheum. Dis.
PUBLISHED: 12-17-2013
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Certain HLA-DRB1 alleles and single-nucleotide polymorphisms (SNPs) are associated with rheumatoid arthritis (RA). Our objective was to examine the combined effect of these associated variants, calculated as a cumulative genetic risk score (GRS) on RA predisposition, as well as the number of autoantibodies (none, one or two present).
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[The treatment effect of immunoglobulin in AIDS with Guillain-Barre syndrome].
Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi
PUBLISHED: 12-11-2013
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To discuss the treatment effect of immunoglobulin in acquired immune deficiency syndrome (AIDS) with Guillain-Barre syndrome (GBS).
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MicroRNAs in normal and psoriatic skin.
Physiol. Genomics
PUBLISHED: 12-10-2013
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Psoriasis is a chronic and common human skin disorder currently with no cure. Psoriatic skin displays inflammatory, raised and scaly lesions with widely aberrant gene expression. Recent studies have revealed critical roles that microRNAs play as a class of post-transcriptional gene regulator in skin development and skin diseases. A substantial number of novel microRNAs have been identified in skin, and much has been learned about the dysregulated expression and functional roles of microRNAs in psoriasis, as well as the robustness and plasticity of microRNA-mediated gene expression regulation. Here we review recent progresses in discovery, profiling and characterization of microRNAs in human psoriatic skin, discuss insights to their biological functions and share our view on remaining challenges to be addressed.
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[Heavy metal speciation and stability in the sediment of Lihu Lake].
Huan Jing Ke Xue
PUBLISHED: 12-03-2013
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The spatial occurrence characteristics of the speciation of Cr, Ni, Cu, Zn, As, Cd, Hg and Pb in sediments of the lake body and river mouths of Lihu Lake were studied. Meanwhile, combined with the spatial distribution of metals in interstitial water, the stability and bio-availability of various forms of studied metals were discussed. The results showed that metals in interstitial water and extractable metals in surface sediments both had obvious spatial heterogeneity, and the metal contents in retreated fishery district were lower. High value areas of Cr, Cu and Zn distributed in belt along Baojie Bridge and Lihu Lake Bridge, and the high value areas of Ni, As, Cd, Hg distributed in sector extending from river mouths to the lake body. Most metals mainly existed in residue state except for Cd, Cu and Ni, the extractable content of which respectively accounted for 71.02%, 54.79% and 50.62% of the total content. The stability of eight studied metals was in the order of Cr > Pb > Hg > As > Cu > Ni > Zn > Cd. Cd and Zn were unstable in most studied sites, so there was higher risk of quick desorption and release. Toxicity assessment of interstitial water showed that the tested metals would not pose acute toxicity for aquatic ecosystem, but Hg and Pb in some districts, especially in the river mouths, might pose chronic toxicity for the benthonic organisms.
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Plasma surface modification of rigid contact lenses decreases bacterial adhesion.
Eye Contact Lens
PUBLISHED: 11-01-2013
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Contact lens safety is an important topic in clinical studies. Corneal infections usually occur because of the use of bacteria-carrying contact lenses. The current study investigated the impact of plasma surface modification on bacterial adherence to rigid contact lenses made of fluorosilicone acrylate materials.
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A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5-isoforms in four model species.
Nucleic Acids Res.
PUBLISHED: 10-30-2013
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MicroRNA (miRNA) 5-isoforms, or 5-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5 ends shifted from the 5 ends of the miRNAs by a few nucleotides. Although 5-isomiRs have been reported, their origins, properties and potential functions remain to be examined. We systematically studied 5-isomiRs in human, mouse, fruitfly and worm by analysing a large collection of small non-coding RNA and mRNA profiling data. The results revealed a broad existence of 5-isomiRs in the four species, many of which were conserved and could arise from genomic loci of canonical and non-canonical miRNAs. The well-conserved 5-isomiRs have several features, including a preference of the 3p over the 5p arms of hairpins of conserved mammalian miRNAs, altered 5-isomiRs across species and across tissues, and association with structural variations of miRNA hairpins. Importantly, 5-isomiRs and their major miRNAs may have different mRNA targets and thus potentially play distinct roles of gene regulation, as shown by an integrative analysis combining miRNA and mRNA profiling data from psoriatic and normal human skin and from murine miRNA knockout assays. Indeed, 18 5-isomiRs had aberrant expression in psoriatic human skin, suggesting their potential function in psoriasis pathogenesis. The results of the current study deepened our understanding of the diversity and conservation of miRNAs, their plasticity in gene regulation and potential broad function in complex diseases.
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Controlled synthesis of novel Au@MIL-100(Fe) core-shell nanoparticles with enhanced catalytic performance.
Chem. Commun. (Camb.)
PUBLISHED: 10-25-2013
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A novel porous Au@MIL-100(Fe) core-shell nanocatalyst with controllable MIL-100(Fe) shell thickness has been fabricated by using a versatile step-by-step fashion. Catalytic studies show that the Au@MIL-100(Fe) nanocatalyst exhibits much higher catalytic activity than the pure Au nanoparticles, suggesting that the MIL-100(Fe) shell enhances the catalytic activity via a synergistic effect.
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Activation of sirtuin 1 attenuates cerebral ventricular streptozotocin-induced tau hyperphosphorylation and cognitive injuries in rat hippocampi.
Age (Dordr)
PUBLISHED: 10-07-2013
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Patients with diabetes in the aging population are at high risk of Alzheimers disease (AD), and reduction of sirtuin 1 (SIRT1) activity occurs simultaneously with the accumulation of hyperphosphorylated tau in the AD-affected brain. It is not clear, however, whether SIRT1 is a suitable molecular target for the treatment of AD. Here, we employed a rat model of brain insulin resistance with intracerebroventricular injection of streptozotocin (ICV-STZ; 3 mg/kg, twice with an interval of 48 h). The ICV-STZ-treated rats were administrated with resveratrol (RSV; SIRT1-specific activator) or a vehicle via intraperitoneal injection for 8 weeks (30 mg/kg, once per day). In ICV-STZ-treated rats, the levels of phosphorylated tau and phosphorylated extracellular signal-regulated kinases 1 and 2 (ERK1/2) at the hippocampi were increased significantly, whereas SIRT1 activity was decreased without change of its expression level. The capacity of spatial memory was also significantly lower in ICV-STZ-treated rats compared with age-matched control. RSV, a specific activator of SIRT1, which reversed the ICV-STZ-induced decrease in SIRT1 activity, increases in ERK1/2 phosphorylation, tau phosphorylation, and impairment of cognitive capability in rats. In conclusion, SIRT1 protects hippocampus neurons from tau hyperphosphorylation and prevents cognitive impairment induced by ICV-STZ brain insulin resistance with decreased hippocampus ERK1/2 activity.
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[Investigation on the endemic foci of new emerged tick-borne encephalitis in Charles Hilary, Xinjiang].
Zhonghua Liu Xing Bing Xue Za Zhi
PUBLISHED: 09-11-2013
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To investigate the recent emerged endemic region of tick-borne encephalitis (TBE) regarding its natural reserves, in Charles Hilary, northern Xinjiang and to isolate and characterize the viral geographic strain.
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[Clinical and experimental characteristics of 20 patients with acute myeloid leukemia with complex variant of t(8; 21)].
Zhongguo Shi Yan Xue Ye Xue Za Zhi
PUBLISHED: 09-04-2013
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This study was aimed to summarize and analyze the morphology, immunophenotype, cytogenetics, molecular biology (MICM), tyrosine kinase (TK) gene mutations and clinical features of acute myeloid leukemia(AML) with complex variant of t(8;21). A retrospective study was performed for 20 AML patients with complex variant of t(8;21) in our hospital from January 1994 to April 2012, including analysis of clinical feature, immunophenotype, chromosome karyotype, treatment regimen, as well as the overall survival (OS) and relapse-free survival (RFS). Mutations of C-KIT, FLT3-ITD, FLT3-TKD and JAK2V617F were detected by genomic DNA PCR and the sequencing was per-formed in 13 AML patients with complex variant of t(8;21). The results showed that (1) the incidence of 20 AML patients with complex variant of t(8; 21) was 2.4% of total t(8; 21) AML patients. In 20 AML patients with complex variant of t(8;21), 1 case was M1, 17 cases were M2, 2 cases were M4; 10 cases were myeloid phenotype and the other 3 were myeloid plus lymphoid phenotype. There were 16 kinds of cytogenetics additional involvement of chromosomal breakpoints: lp22, 1p32, 2q35, 2q14, 3p25, 5q13, 6p22, 7q21, llq11, 1lq13, 12q14, 12q24, 12p12, 14q32, 15p13, 20q12. (2) C-KIT aberrations were detected in 30.8% cases, all mutated in exon 17 (mutkit 17), only 1 case had JAK2V617F mutation. The result of FLT3 mutation screenings in AML patients with complex variant of t(8; 21) was negative. Of 5 patients with gene mutations, 1 patient (20%) achieved complete remission (CR), the median RFS and median OS time were 6.5 months and 8.9 months respectively. Of the 8 patients without gene mutations, 6 patietns (75%) achieved CR; the median RFS and median OS time were 26.6 months and 27.7 months respectively. It is concluded that the AML patients with complex variant of t(8;21) shows typical features of t(8;21) AML, but the existence of the tyrosine kinase-related gene mutation has important implications on remission rate and long-term survival of patients treated by induction chemotherapy.
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IL-28B polymorphisms and treatment response in hepatitis C virus patients with persistently normal alanine aminotransferase.
World J Hepatol
PUBLISHED: 09-01-2013
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To examine the association between the interleukin 28B (IL-28B) genotype and treatment response in hepatitis C virus (HCV)-infected patients with persistently normal alanine aminotransferase (PNALT).
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Isolation, identification and expression of specific human CD133 antibodies.
Sci Rep
PUBLISHED: 08-30-2013
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CD133, a 120?KDa glycoprotein is a transmembrane glycoprotein which has been recently used as a cancer stem cell (CSCs) marker in a variety of carcinomas. CD133(+) cells possess strong tumorigenicity, responsible for tumor initiation and maintenance. Therefore, the goal of our study was to develop a novel CD133 humanized antibody as a promising target for cancer therapy. CD133 purified proteins were used for panning the naive human-semi-synthetic Tomlinson I + J phagemid library. The second extracellular domain (loop1) and the third extracellular domain (loop2) of CD133 were expressed in E. coli. In this study, we adopted a novel five-round selection strategy based on moderate stringent selection during the first rounds. This unique strategy was aimed at avoiding the loss of rare phages with high affinity to target proteins. After the five rounds of specific panning, six phage-antibody clones which specifically recognized recombinant human CD133 protein were obtained. The desirable phage clone named CD133-scFv-1 was cloned into the expression vector, then induced and purified. We show that CD133-scFv-1 and commercial murine antibody 293C3 could compete with each other in the indirect competitive immunoassay. Our work may lay the groundwork for future studies involving biological functions and applications of the CD133 humanized antibody.
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[Temporal-spatial distribution of algal cells during drought period in Daning River of Three Gorges].
Huan Jing Ke Xue
PUBLISHED: 08-17-2013
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In order to provide basic data for algal bloom warning system, the study on temporal-spatial distribution of algal cells was carried out in Daning River of Three Gorges form April to September, 2011. The results of temporal distribution were as follows: the dominant algal species were blue algal, green algal and diatom. During the test, the density proportion of blue algae increased continuously, the density proportion of diatom decreased, while the density proportion of green algae did not change significantly. The results of spatial distribution were as follows: algal density was extremely significantly correlated with water temperature and chlorophyll a (Chl a), the correlation coefficient were 0.97 and 0.95, respectively; algal density was significantly correlated with light intensity (LI), dissolved oxygen (DO), pH and dissoluble total phosphorus (DTP), the correlation coefficient were 0.87, 0.83, 082 and 0.82, respectively; the algal density in 0 m of Caziba was higher than those in other water depths, and in Baishuihe the highest algal density occurred at 2.0 m water depth in June and July, in Shuanglong most algal cells were found in 0 m and 2.0 m in July, August and September, in Dachang algal density in different water depth did not change significantly during the test; the proportion of different algal species in vertical direction was different in the test, probably because different algal species fitted different environments.
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A novel artificial neural network method for biomedical prediction based on matrix pseudo-inversion.
J Biomed Inform
PUBLISHED: 08-09-2013
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Biomedical prediction based on clinical and genome-wide data has become increasingly important in disease diagnosis and classification. To solve the prediction problem in an effective manner for the improvement of clinical care, we develop a novel Artificial Neural Network (ANN) method based on Matrix Pseudo-Inversion (MPI) for use in biomedical applications. The MPI-ANN is constructed as a three-layer (i.e., input, hidden, and output layers) feed-forward neural network, and the weights connecting the hidden and output layers are directly determined based on MPI without a lengthy learning iteration. The LASSO (Least Absolute Shrinkage and Selection Operator) method is also presented for comparative purposes. Single Nucleotide Polymorphism (SNP) simulated data and real breast cancer data are employed to validate the performance of the MPI-ANN method via 5-fold cross validation. Experimental results demonstrate the efficacy of the developed MPI-ANN for disease classification and prediction, in view of the significantly superior accuracy (i.e., the rate of correct predictions), as compared with LASSO. The results based on the real breast cancer data also show that the MPI-ANN has better performance than other machine learning methods (including support vector machine (SVM), logistic regression (LR), and an iterative ANN). In addition, experiments demonstrate that our MPI-ANN could be used for bio-marker selection as well.
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Nonaggressive and adapted social cognition is controlled by the interplay between noradrenergic and nicotinic receptor mechanisms in the prefrontal cortex.
FASEB J.
PUBLISHED: 07-23-2013
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Social animals establish flexible behaviors and integrated decision-making processes to adapt to social environments. Such behaviors are impaired in all major neuropsychiatric disorders and depend on the prefrontal cortex (PFC). We previously showed that nicotinic acetylcholine receptors (nAChRs) and norepinephrine (NE) in the PFC are necessary for mice to show adapted social cognition. Here, we investigated how the cholinergic and NE systems converge within the PFC to modulate social behavior. We used a social interaction task (SIT) in C57BL/6 mice and mice lacking ?2*nAChRs (?2(-/-) mice), making use of dedicated software to analyze >20 social sequences and pinpoint social decisions. We performed specific PFC NE depletions before SIT and measured monoamines and acetylcholine (ACh) levels in limbic corticostriatal circuitry. After PFC-NE depletion, C57BL/6 mice exhibited impoverished and more rigid social behavior and were 6-fold more aggressive than sham-lesioned animals, whereas ?2(-/-) mice showed unimpaired social behavior. Our biochemical measures suggest a critical involvement of DA in SIT. In addition, we show that the balance between basal levels of monoamines and of ACh modulates aggressiveness and this modulation requires functional ?2*nAChRs. These findings demonstrate the critical interplay between prefrontal NE and nAChRs for the development of adapted and nonaggressive social cognition.
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A comparison of spectral magnitude and phase-locking value analyses of the frequency-following response to complex tones.
J. Acoust. Soc. Am.
PUBLISHED: 07-19-2013
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Two experiments, both presenting diotic, harmonic tone complexes (100?Hz fundamental), were conducted to explore the envelope-related component of the frequency-following response (FFRENV), a measure of synchronous, subcortical neural activity evoked by a periodic acoustic input. Experiment 1 directly compared two common analysis methods, computing the magnitude spectrum and the phase-locking value (PLV). Bootstrapping identified which FFRENV frequency components were statistically above the noise floor for each metric and quantified the statistical power of the approaches. Across listeners and conditions, the two methods produced highly correlated results. However, PLV analysis required fewer processing stages to produce readily interpretable results. Moreover, at the fundamental frequency of the input, PLVs were farther above the metrics noise floor than spectral magnitudes. Having established the advantages of PLV analysis, the efficacy of the approach was further demonstrated by investigating how different acoustic frequencies contribute to FFRENV, analyzing responses to complex tones composed of different acoustic harmonics of 100?Hz (Experiment 2). Results show that the FFRENV response is dominated by peripheral auditory channels responding to unresolved harmonics, although low-frequency channels driven by resolved harmonics also contribute. These results demonstrate the utility of the PLV for quantifying the strength of FFRENV across conditions.
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Role of gas vesicles and intra-colony spaces during the process of algal bloom formation.
Water Environ. Res.
PUBLISHED: 07-10-2013
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Aggregation morphology, vertical distribution, and algal density were analyzed during the algal cell floating process in three environments. The role of gas vesicles and intra-colony spaces was distinguished by algal blooms treated with ultrasonic waves and high pressure. Results demonstrated that the two buoyancy providers jointly provide buoyancy for floating algal cells. The results were also confirmed by force analysis. In the simulation experiment, the buoyancy acting on algal cells was greater than its gravity at sample ports 2 and 3 of a columnar-cultivated cell vessel, and intra-colony spaces were not detected. In Taihu Lake, gas vesicle buoyancy was notably less than total algal cell gravity. Buoyancy provided by intra-colony spaces exceeded total algal cell gravity at the water surface, but not at other water depths. In the Daning River, total buoyancies provided by the two buoyancy providers were less than total algal cell gravity at different water depths.
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Biodesulfurization of Model Compounds and De-asphalted Bunker Oil by Mixed Culture.
Appl. Biochem. Biotechnol.
PUBLISHED: 07-03-2013
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In this study, complicated model sulfur compounds in bunker oil and de-asphalted bunker oil were biodesulfurized in a batch process by microbial consortium enriched from oil sludge. Dibenzothiophene (DBT) and benzo[b]naphtho[1,2-d]thiophene (BNT1) were selected as model sulfur compounds. The results show that the mixed culture was able to grow by utilizing DBT and BNT1 as the sole sulfur source, while the cell density was higher using DBT than BNT1 as the sulfur source. GC-MS analysis of their desulfurized metabolites indicates that both DBT and BNT1 could be desulfurized through the sulfur-specific degradation pathway with the selective cleavage of carbon-sulfur bonds. When DBT and BNT1 coexisted, the biodesulfurization efficiency of BNT1 decreased significantly as the DBT concentrations increased (>0.1 mmol/L). BNT1 desulfurization efficiency also decreased along with the increase of 2-hydroxybiphenyl as the end product of DBT desulfurization. For real bunker oil, only 2.8 % of sulfur was removed without de-asphalting after 7 days of biotreatment. After de-asphalting, the biodesulfurization efficiency was significantly improved (26.2-36.5 %), which is mainly attributed to fully mixing of the oil and water due to the decreased viscosity of bunker oil.
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Surface hall effect and nonlocal transport in SmB?: evidence for surface conduction.
Sci Rep
PUBLISHED: 07-02-2013
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A topological insulator (TI) is an unusual quantum state in which the insulating bulk is topologically distinct from vacuum, resulting in a unique metallic surface that is robust against time-reversal invariant perturbations. The surface transport, however, remains difficult to isolate from the bulk conduction in most existing TI crystals (particularly Bi?Se?, Bi?Te? and Sb?Te?) due to impurity caused bulk conduction. We report in large crystals of topological Kondo insulator (TKI) candidate material SmB? the thickness-independent surface Hall effects and non-local transport, which persist after various surface perturbations. These results serve as proof that at low temperatures SmB? has a metallic surface that surrounds an insulating bulk, paving the way for transport studies of the surface state in this proposed TKI material.
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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.