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Find video protocols related to scientific articles indexed in Pubmed.
Digital suppression of both cross and inter-modulation distortion in multi-carrier RF photonic link with down-conversion.
Opt Express
PUBLISHED: 11-18-2014
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We propose and demonstrate a novel scheme to effectively suppress the cross modulation distortion (XMD) and the third-order inter-modulation distortion (IMD3) which exist in wide-band, multi-carrier analog photonic link (APL) system. Such nonlinearities, which are caused by the out-of-band and in-band signals, respectively, constrain the link's performance severely. Instead of building an extra nonlinear path in hardware, the XMD and IMD3 compensation information is extracted from the received distorted signal, and both distortions are then suppressed by digitally multiplying the distorted signal with the compensation information. After compensation in the digital domain, the down-converted XMD and IMD3 distortions are experimentally suppressed with 33 dB and 25 dB, respectively, resulting in an improved upper limit for the SFDR.
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Bandpass sampling based digital coherent receiver with free-running local oscillator laser for phase-modulated radio-over-fiber links.
Opt Express
PUBLISHED: 11-18-2014
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A bandpass sampling based digital coherent receiver is presented for phase modulated radio-over-fiber links with coherent detection. In the scheme, the bandpass sampling technique is introduced in RoF systems to overcome the high sampling rate requirement and front-end hardware dependency of conventional digtal coherent receivers. In particular, the selection rule of bandpass sampling rate was defined by taking into account the frequency offset induced by free-running optical local oscillator. Analytical assessment and simulations are used to determine the ultimate performance in terms of tolerances to ADC bit resolution and laser linewidth. Thereafter, a 40Mbps QPSK modulated data signal at 2.4GHz RF carrier frequency is experimentally demonstrated over the proposed 50.6-km radio-over-fiber link employing bandpass sampling.
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Efficient flat metasurface lens for terahertz imaging.
Opt Express
PUBLISHED: 11-18-2014
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Metamaterials offer exciting opportunities that enable precise control of amplitude, polarization and phase of the light beam at a subwavelength scale. A gradient metasurface consists of a class of anisotropic subwavelength metamaterial resonators that offer abrupt amplitude and phase changes, thus enabling new applications in optical device design such as ultrathin flat lenses. We propose a highly efficient gradient metasurface lens based on a metal-dielectric-metal structure that operates in the terahertz regime. The proposed structure consists of slotted metallic resonator arrays on two sides of a thin dielectric spacer. By varying the geometrical parameters, the metasurface lens efficiently manipulates the spatial distribution of the terahertz field and focuses the beam to a spot size on the order of a wavelength. The proposed flat metasurface lens design is polarization insensitive and works efficiently even at wide angles of incidence.
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Experimental study of the impacts of external disturbances on N2O emission from water to air.
Water Sci. Technol.
PUBLISHED: 10-30-2014
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To obtain a comprehensive understanding of nitrous oxide (N2O) emission from water to air, the impacts of external disturbances including wind, stirring and aeration on N2O emissions were investigated by continuously monitoring N2O concentration variations in water. The volumetric mass transfer coefficient of N2O from water to air (KLaN2O) under different conditions was determined by using exponential regression to fit the monitoring data. The results showed that KLaN2O was 0.0017 min(-1) at the stable condition, and with the increase of wind velocity, stirring velocity and aeration rate, the diffusion of N2O from water to air was enhanced. It was also observed that KLaN2O linearly increased with the increase of wind velocity and aeration rate, and exponentially increased with the increase of stirring velocity. The sequencing of the impacts of the three factors on N2O emission was aeration > stirring > wind. As turbulence and the mixing intensity of the liquid phase under the aeration condition were more vigorous than those of the wind and the stirring, the impact of aeration on N2O emission was greater than those of wind and stirring. When predicting N2O emissions from water to air, external disturbances, either environmental factors or operational factors, should be taken into consideration.
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Phase stabilized downlink transmission for wideband radio frequency signal via optical fiber link.
Opt Express
PUBLISHED: 10-17-2014
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In this paper, we propose and demonstrate a phase stabilized wideband downlink transmission scheme, which directly transmits the received radio frequency (RF) signals from remote antennas to central station. A reference RF tone is round-trip transferred between the central station and remote end to obtain the delay variation caused by the fiber link. The delay variation is then used to alter a tunable laser. Since optical carriers with different wavelengths propagate at different velocities in fiber, a tunable optical delay line is realized to cancel the delay variation of the fiber link. The tunable delay range is in proportion to the length of the fiber link, which means a very long delivery distance can be expected. Experimentally, a RF signal at frequency of 2.50 GHz has been downlink transferred through a 45 km fiber link, with stability of 3.3x10-13 at 1 s and 7.5x10-17 at 104 s.
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Multi-dimensional crest factor reduction and digital predistortion for multi-band radio-over-fiber links.
Opt Express
PUBLISHED: 10-17-2014
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A multi-dimensional crest factor reduction (MD-CFR) technique is proposed to improve the performance and efficiency of multi-band radio-over-fiber (RoF) links. Cooperating with multi-dimensional digital predistortion (MD-DPD), MD-CFR increases the performance of both directly-modulated and externally-modulated RoF links, in terms of error vector magnitude (EVM) and adjacent channel power ratio (ACPR). For directly-modulated RoF link, more than 5 dB output ACPR reduction is obtained, output EVMs are reduced from 11.83% and 12.47% to 7.51% and 7.26% for two bands respectively, while only a slight improvement to 11.58% and 10.78% is obtained solely using MD-DPD. Similar results are achieved in externally-modulated RoF link. Given a threshold in EVM or ACPR, the RF power transmit efficiency is also further enhanced.
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A Novel Class of Somatic Small RNAs Similar to Germ Cell Pachytene PIWI-interacting Small RNAs.
J. Biol. Chem.
PUBLISHED: 10-15-2014
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PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that bind PIWI family proteins exclusively expressed in the germ cells of mammalian gonads. MIWI2-associated piRNAs are essential for silencing transposons during primordial germ cell development, and MIWI-bound piRNAs are required for normal spermatogenesis during adulthood in mice. Although piRNAs have long been regarded as germ cell-specific, increasing lines of evidence suggest that somatic cells also express piRNA-like RNAs (pilRNAs). Here, we report the detection of abundant pilRNAs in somatic cells, which are similar to MIWI-associated piRNAs mainly expressed in pachytene spermatocytes and round spermatids in the testis. Based on small RNA deep sequencing and qPCR analyses, pilRNA expression is dynamic and displays tissue-specificity. Although, pilRNAs are similar to pachytene piRNAs in both size and genomic origins, they have a distinct ping-pong signature. Furthermore, pilRNA biogenesis appears to utilize a yet-to-be-identified pathway, which is different from all currently known small RNA biogenetic pathways. In addition, pilRNAs appear to preferentially target the 3' untranslated regions (3'UTRs) of mRNAs in a partially complementary manner. Our data suggest that pilRNAs, as an integral component of the small RNA transcriptome in somatic cell lineages, represent a distinct population of small RNAs that may have functions similar to germ cell piRNAs.
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Development of all-solid-state flash x-ray generator with photoconductive semiconductor switches.
Rev Sci Instrum
PUBLISHED: 10-03-2014
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A compact, low-jitter, and high repetitive rate all-solid-state flash x-ray generator making use of photo conductive semiconductor switches was developed recently for the diagnostic purpose of some hydrokinetical experiments. The generator consisted of twelve stages of Blumlein pulse forming networks, and an industrial cold cathode diode was used to generate intense x-ray radiations with photon energy up to 220 keV. Test experiments showed that the generator could produce >1 kA electron beam currents and x-ray pulses with ~40 ns duration under 100 Hz repetitive rates at least (limited by the triggering laser on hand), also found was that the delay time of the cathode explosive emission is crucial to the energy transfer efficiency of the whole system. In addition, factors affecting the diode impedance, how the switching synchronization and diode impedance determining the allowable operation voltage were discussed.
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A novel mesoporous carbon@silicon-silica nanostructure for high-performance Li-ion battery anodes.
Chem. Commun. (Camb.)
PUBLISHED: 09-30-2014
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A novel hierarchical nanostructure with graphite-like carbon and small Si nanocrystals, respectively, encapsulated in the mesopores and embedded in the silica framework of mesoporous silica nanoparticles has been facilely constructed and used as an anode for Li-ion batteries, which exhibits high specific storage capacity and extraordinarily high cycling stability.
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[Effect of Fuzhenghuayu compound on hepatocyte expression of Nrf2 in a mouse model of hepatic fibrosis].
Zhonghua Gan Zang Bing Za Zhi
PUBLISHED: 09-23-2014
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To investigate the effect of Fuzhenghuayu compound (FZHc) on expression of nuclear factor E2-related factor 2 (Nrf2) in hepatocytes under conditions of hepatic fibrosis using a mouse model.
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[Correlation of carcinoembryonic antigen with prognosis of hepatocellular carcinoma after hepatectomy].
Zhonghua Zhong Liu Za Zhi
PUBLISHED: 09-23-2014
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To investigate the correlation between carcinoembryonic antigen (CEA) and prognosis of hepatocellular carcinoma after hepatectomy.
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Analysis and modeling of moisture sorption behavior for antimicrobial composite protein films.
Biomed Mater Eng
PUBLISHED: 09-18-2014
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The WPI-NaCas-GLY antimicrobial film takes full advantage of the controlled release of active or antimicrobial agents as well as demonstrates a great potential for functioning as an alternative biodegradable polymer in practical applications. The moisture sorption kinetics of the film as an important carrier of active agents was investigated at various relative humidities (RH). The results indicated that the moisture sorption characterization and procedure of this film can be described well by the empirical Peleg model with higher confidence and concordance. The model could predict the film's moisture content at any time (Mt), the time to reach any given level of R (tR), the equilibrium moisture at any RH condition (Me), and isotherm trend based upon experimental data and modeled constants k(1), k(2), a, b, c, and d without giving consideration to their physical meaning. The water vapor transmission rate of the WPI-NaCas-GLY antimicrobial film increased exponentially with increasing RH due to its hydrophilicity, which was primarily caused by the presence of glycerol in a higher content. The results also suggested that aw predominately affects the film's Me values compared with the temperature factor by fixed nonlinear multiple regression analyses.
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MicroRNA-320a inhibits cell proliferation, migration and invasion by targeting BMI-1 in nasopharyngeal carcinoma.
FEBS Lett.
PUBLISHED: 08-27-2014
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In the present study, we investigated the roles and molecular mechanisms of miR-320a in human nasopharyngeal carcinoma (NPC). miR-320a expression was strongly reduced in NPC tissues and cell lines. Overexpression of miR-320a significantly suppressed NPC cell growth, migration, invasion and tumor growth in a xenograft mouse model. A luciferase reporter assay revealed that miR-320a could directly bind to the 3' UTR of BMI-1. Overexpression of BMI-1 rescued miR-320a-mediated biological function. BMI-1 expression was found to be up-regulated and inversely correlated with miR-320a expression in NPC. Collectively, our data indicate that miR-320a plays a tumor suppressor role in the development and progression of NPC and may be a novel therapeutic target against NPC.
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Antitumor effect of a copper (II) complex of a coumarin derivative and phenanthroline on lung adenocarcinoma cells and the mechanism of action.
Mol Med Rep
PUBLISHED: 08-26-2014
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In order to investigate the effect of a copper (II) complexes of a coumarin derivative and phenanthroline (hereinafter referred to as the coumarin-copper drug) on lung adenocarcinoma cells in vivo and in vitro, along with the mechanism of action, LA795 lung adenocarcinoma cells were treated with different concentrations of coumarin-copper drug. An MTT assay was performed to determine the cell proliferation ratio, cell apoptosis was detected by Annexin V/propidium iodide staining with flow cytometric analysis and western blot analysis was employed to evaluate the expression levels of apoptosis-associated proteins. In addition, an LA795 cell xenograft tumor model was established in nude mice, with mice receiving intraperitoneal injection once a week for three weeks of either 2 or 4 mg/kg in three divided doses coumarin?copper drug, or phosphate?buffered saline. The tumor growth curves were drawn and the tumor growth inhibition rates were calculated. The apoptotic index of subcutaneously transplanted tumor cells was determined by terminal deoxynucleotidyl?transferase?mediated dUTP nick end?labeling assay. The coumarin-copper drug effectively inhibited the proliferation of LA795 cells in a dose? and time?dependent manner, with the half maximal inhibitory concentration equaling 2.0 µmol/l. The coumarin-copper drug also significantly induced LA795 cell apoptosis in a time-dependent manner (P<0.05), which was accompanied by upregulation p35 and B-cell lymphoma-2 (Bcl-2)-associated X protein (Bax), and downregulation of Bcl-2. Furthermore, the coumarin?copper drug significantly inhibited the growth of LA795 tumors in a dose dependent manner (P<0.05), in accordance with the apoptotic index. In conclusion, the coumarin-copper drug may inhibit the proliferation of LA795 cells through the induction of cell apoptosis, which may be associated with the upregulation of p53 and Bax, with concurrent downregulation of Bcl-2.
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Systematic regional variations in Purkinje cell spiking patterns.
PLoS ONE
PUBLISHED: 08-21-2014
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In contrast to the uniform anatomy of the cerebellar cortex, molecular and physiological studies indicate that significant differences exist between cortical regions, suggesting that the spiking activity of Purkinje cells (PCs) in different regions could also show distinct characteristics. To investigate this possibility we obtained extracellular recordings from PCs in different zebrin bands in crus IIa and vermis lobules VIII and IX in anesthetized rats in order to compare PC firing characteristics between zebrin positive (Z+) and negative (Z-) bands. In addition, we analyzed recordings from PCs in the A2 and C1 zones of several lobules in the posterior lobe, which largely contain Z+ and Z- PCs, respectively. In both datasets significant differences in simple spike (SS) activity were observed between cortical regions. Specifically, Z- and C1 PCs had higher SS firing rates than Z+ and A2 PCs, respectively. The irregularity of SS firing (as assessed by measures of interspike interval distribution) was greater in Z+ bands in both absolute and relative terms. The results regarding systematic variations in complex spike (CS) activity were less consistent, suggesting that while real differences can exist, they may be sensitive to other factors than the cortical location of the PC. However, differences in the interactions between SSs and CSs, including the post-CS pause in SSs and post-pause modulation of SSs, were also consistently observed between bands. Similar, though less strong trends were observed in the zonal recordings. These systematic variations in spontaneous firing characteristics of PCs between zebrin bands in vivo, raises the possibility that fundamental differences in information encoding exist between cerebellar cortical regions.
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Porcine epidemic diarrhea virus RNA present in commercial spray-dried porcine plasma is not infectious to naïve pigs.
PLoS ONE
PUBLISHED: 08-12-2014
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Porcine epidemic diarrhea virus emerged in North America in April 2013 and has since been identified in 30 U.S. States, Canada and Mexico. The rapid spread of PEDV has raised concerns about the role of feed and particularly pork-by-product components such as spray-dried porcine plasma (SDPP) in PEDV transmission. The aim of this study was to determine the infectivity of PEDV RNA present in commercial SDPP. Specifically, 40 3-week-old PEDV naïve pigs were randomly assigned to one of five treatment groups. At day post inoculation (dpi) 0, NEG-CONTROL pigs were sham-inoculated, PEDV-CONTROL pigs received cell culture propagated PEDV, and SDPP-CONTROL pigs were switched to a diet with 5% SDPP containing 5.1±0.1 log10 PEDV RNA copies/g. To evaluate a potential positive effect of anti-PEDV antibodies in SDPP on PEDV challenge, four days prior to PEDV challenge the pigs in the SDPP-PEDV group were switched to and remained on a 5% SDPP diet through dpi 28. Another group, EGG-PEDV, was orally administered a commercial egg-derived liquid PEDV globulin product from dpi -4 through 6. All PEDV-CONTROL pigs began shedding PEDV in feces by dpi 3 and seroconverted between dpi 7 and 14, whereas pigs in NEG-CONTROL and SDPP-CONTROL groups remained PEDV RNA negative and did not seroconvert to PEDV for the study duration. This indicates no evidence of infectivity of the PEDV RNA in the SDPP lot utilized. Furthermore, under the study conditions SDPP or egg-derived liquid PEDV globulin addition did not significantly alter PEDV-shedding or overall disease course after experimental challenge.
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Distributed cooperative regulation for multiagent systems and its applications to power systems: a survey.
ScientificWorldJournal
PUBLISHED: 07-21-2014
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Cooperative regulation of multiagent systems has become an active research area in the past decade. This paper reviews some recent progress in distributed coordination control for leader-following multiagent systems and its applications in power system and mainly focuses on the cooperative tracking control in terms of consensus tracking control and containment tracking control. Next, methods on how to rank the network nodes are summarized for undirected/directed network, based on which one can determine which follower should be connected to leaders such that partial followers can perceive leaders' information. Furthermore, we present a survey of the most relevant scientific studies investigating the regulation and optimization problems in power systems based on distributed strategies. Finally, some potential applications in the frequency tracking regulation of smart grids are discussed at the end of the paper.
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[A clinicopathological and prognostic study of rare pathological subtype cases of hepatocellular carcinoma].
Zhonghua Wai Ke Za Zhi
PUBLISHED: 07-19-2014
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To investigate the clinicopathological features and prognosis of clear cell carcinoma (CCC), giant cell carcinoma (GCC) and sarcomatoid carcinoma (SC), the 3 rare cellular morphological subtypes of hepatocellular carcinoma (HCC).
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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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Preparation and characterization of novel functionalized prochloraz microcapsules using silica-alginate-elements as controlled release carrier materials.
ACS Appl Mater Interfaces
PUBLISHED: 07-07-2014
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Controlled release formulation of pesticides is an effective approach to achieve the desirable purpose of increasing the utilization of pesticides and reducing the environmental residuals. In this work, a novel functionalized microcapsule using silica cross-linked with alginate, and some beneficial elements to crops, was prepared. The microcapsules were structurally characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, thermogravimetric analysis, and X-ray photoelectron spectroscopy. The results showed that the microcapsules had a high loading efficiency of prochloraz (about 30% w/w) and could effectively protect prochloraz against degradation under UV irradiation and alkaline conditions, showed sustainable release for at least 60 days, and also likely increased disease resistance due to the element on the surface. Given the advantages of the microcapsules, this delivery system may be extended to other photosensitive or pH-sensitive pesticides in the future.
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[Detection of circulating tumor cells in patients with hepatocellular carcinoma].
Zhonghua Zhong Liu Za Zhi
PUBLISHED: 07-04-2014
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To explore the detection efficiency of circulating tumor cells (CTCs) in patients with hepatocellular carcinoma (HCC).
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Two miRNA clusters, miR-34b/c and miR-449, are essential for normal brain development, motile ciliogenesis, and spermatogenesis.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-30-2014
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Ablation of a single miRNA gene rarely leads to a discernable developmental phenotype in mice, in some cases because of compensatory effects by other functionally related miRNAs. Here, we report that simultaneous inactivation of two functionally related miRNA clusters (miR-34b/c and miR-449) encoding five miRNAs (miR-34b, miR-34c, miR-449a, miR-449b, and miR-449c) led to sexually dimorphic, partial perinatal lethality, growth retardation, and infertility. These developmental defects correlated with the dysregulation of ? 240 target genes, which are mainly involved in three major cellular functions, including cell-fate control, brain development and microtubule dynamics. Our data demonstrate an essential role of a miRNA family in brain development, motile ciliogenesis, and spermatogenesis.
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Population transcriptomics reveals a potentially positive role of expression diversity in adaptation.
J Integr Plant Biol
PUBLISHED: 06-29-2014
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While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18 503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30 609 genic SNPs. Population expression (Ep ) and expression diversity (Ed ) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.
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The spray-drying process is sufficient to inactivate infectious porcine epidemic diarrhea virus in plasma.
Vet. Microbiol.
PUBLISHED: 06-20-2014
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Porcine epidemic diarrhea virus (PEDV) is considered an emergent pathogen associated with high economic losses in many pig rearing areas. Recently it has been suggested that PEDV could be transmitted to naïve pig populations through inclusion of spray-dried porcine plasma (SDPP) into the nursery diet which led to a ban of SDPP in several areas in North America and Europe. To determine the effect of spray-drying on PEDV infectivity, 3-week-old pigs were intragastrically inoculated with (1) raw porcine plasma spiked with PEDV (RAW-PEDV-CONTROL), (2) porcine plasma spiked with PEDV and then spray dried (SD-PEDV-CONTROL), (3) raw plasma from PEDV infected pigs (RAW-SICK), (4) spray-dried plasma from PEDV infected pigs (SD-SICK), or (5) spray-dried plasma from PEDV negative pigs (SD-NEG-CONTROL). For the spray-drying process, a tabletop spray-dryer with industry-like settings for inlet and outlet temperatures was used. In the RAW-PEDV-CONTROL group, PEDV RNA was present in feces at day post infection (dpi) 3 and the pigs seroconverted by dpi 14. In contrast, PEDV RNA in feces was not detected in any of the pigs in the other groups including the SD-PEDV-CONTROL group and none of the pigs had seroconverted by termination of the project at dpi 28. This work provides direct evidence that the experimental spray-drying process used in this study was effective in inactivating infectious PEDV in the plasma. Additionally, plasma collected from PEDV infected pigs at peak disease did not contain infectious PEDV. These findings suggest that the risk for PEDV transmission through commercially produced SDPP is minimal.
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[Salvage surgery for neck recurrence or residue of nasopharyngeal carcinoma after primary radiotherapy].
Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
PUBLISHED: 06-17-2014
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To investigate the surgical procedures and prognosis for neck recurrence or residue of nasopharyngeal carcinoma(NPC) after primary radiotherapy.
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[Multiple endocrine neoplasia type 2A caused by a p.C618R RET proto-oncogene mutation in a Chinese pedigree].
Zhonghua Yi Xue Yi Chuan Xue Za Zhi
PUBLISHED: 06-15-2014
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To explore the clinical characteristics and significance of RET proto-oncogene screening in multiple endocrine neoplasia type 2A (MEN2A).
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RNA extraction from swine samples and detection of influenza A virus in swine by real-time RT-PCR.
Methods Mol. Biol.
PUBLISHED: 06-06-2014
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Real-time RT-PCR (rRT-PCR) assays are currently the method of choice in many laboratories for the detection and subtyping of influenza A virus (IAV) in swine. Traditionally, nasal swabs and lung tissues (sometimes broncho-alveolar lavage and tracheal tissues) are the primary specimens for IAV testing. However, oral fluids are becoming more common for IAV prognostic profiling. In this chapter, we describe (1) procedures of RNA extraction from the common clinical specimens, (2) two rRT-PCR assays for detection of IAV in swine, and (3) an rRT-PCR assay for subtyping swine IAV. RNA extraction procedures include a magnetic bead method optimized for extraction from nasal swabs and tissue homogenates and a magnetic bead method optimized for extraction from oral fluids. Two rRT-PCR assays for detection of swine IAV include a USDA-validated IAV rRT-PCR targeting the matrix gene and the USDA-licensed VetMAX™-Gold Swine Influenza Virus Detection rRT-PCR kit (Life Technologies) targeting the nucleoprotein and matrix genes. The swine IAV subtyping assays described here are multiplex SIV HA (H1 and H3) and NA (N1 and N2) subtyping rRT-PCR reagents from Life Technologies.
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Isolation of swine influenza virus in cell cultures and embryonated chicken eggs.
Methods Mol. Biol.
PUBLISHED: 06-06-2014
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Influenza virus isolation is a procedure to obtain a live and infectious virus that can be used for antigenic characterization, pathogenesis investigation, and vaccine production. Embryonated chicken egg inoculation is traditionally considered the "gold standard" method for influenza virus isolation and propagation. However, many primary cells and continuous cell lines have also been examined or developed for influenza virus isolation and replication. Specifically, swine influenza virus (SIV) isolation and propagation have been attempted and compared in embryonated chicken eggs, some primary porcine cells, and a number of continuous cell lines. Currently Madin-Darby canine kidney (MDCK) cells remain the most commonly used cell line for isolation, propagation, and titration of SIV. Virus isolation in embryonated chicken eggs or in different cell lines offers alternative approaches when SIV isolation in MDCK cells is unsuccessful. Nasal swabs, lung tissues, and oral fluids are three major specimen types for SIV isolation. In this chapter, we describe the procedures of sample processing, SIV isolation in MDCK cells and in embryonated chicken eggs, as well as methods used for confirming the virus isolation results.
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Carbon sequestration by Miscanthus energy crops plantations in a broad range semi-arid marginal land in China.
Sci. Total Environ.
PUBLISHED: 06-04-2014
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Carbon sequestration is an essential ecosystem service that second-generation energy crops can provide. To evaluate the ability of carbon sequestration of Miscanthus energy crops in the Loess Plateau of China, the yield and soil organic carbon (SOC) changes were measured for three Miscanthus species in the experimental field in Qingyang of the Gansu Province (QG). With the highest yield of the three species, Miscanthus lutarioriparius contributed to the largest increase of SOC, 0.57 t ha(-1)yr(-1), comparing to the field left unplanted. Through modeling M. lutarioriparius yield across the Loess Plateau, an average increase of SOC was estimated at 0.46 t ha(-1)yr(-1) for the entire region. Based on the measurements of SOC mineralization under various temperatures and moistures for soil samples taken from QG, a model was developed for estimating SOC mineralization rates across the Loess Plateau and resulted in an average of 1.11 t ha(-1)yr(-1). Combining the estimates from these models, the average of net carbon sequestration was calculated at a rate of 9.13 t ha(-1)yr(-1) in the Loess Plateau. These results suggested that the domestication and production of M. lutarioriparius hold a great potential for carbon sequestration and soil restoration in this heavily eroded region.
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Exposure to particular matter increases susceptibility to respiratory Staphylococcus aureus infection in rats via reducing pulmonary natural killer cells.
Toxicology
PUBLISHED: 06-03-2014
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Epidemiological studies have shown a correlation between exposure to fine particular matter (PM2.5) and increased respiratory infection, but the mechanisms have remained poorly defined. By using an experimental system we evaluated the effect of PM2.5 exposure on susceptibility to subsequent pulmonary Staphylococcus aureus (S. aureus) infection and its potential mechanisms. Rats were intratracheally instilled with a single dose of PM2.5 sample or PBS followed by an intratracheal inoculation with bacteria S. aureus at 24h after PM2.5 exposure. The rats were examined at 24h post infection. We found that exposure of rats to PM2.5 significantly increased inflammatory cells and levels of IL-6 and TNF-? in bronchoalveolar lavage fluids (BALF). Prior PM2.5 exposure markedly increased the susceptibility of rats to subsequent S. aureus infection. The mechanistic studies showed that alveolar macrophages (AMs) from PM2.5-experienced lungs had depressed phagocytosis of S. aureus, and prior PM2.5 exposure significantly decreased the natural killer (NK) cells recruited into the airways following subsequent S. aureus infection. Further, adoptive transfer of naive NK cells to the lung of prior PM2.5-exposed rats restored PM2.5-impaired antibacterial host defense. The presence of NK cells markedly enhanced the ability of AMs to phagocytose S. aureus ex vivo. Thus, our study identifies PM2.5-impaired NK cell response in the lung to be a novel critical mechanism for PM2.5-mediated susceptibility to S. aureus bacterial infection, which provides a potential mechanism to explain the epidemiological findings that associate ambient air pollution and increased lung bacterial infections. Our findings also suggest that enhancing pulmonary NK cells may be considered for future therapeutic approaches to clinically antibiotic-resistant S. aureus infection in the lung.
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[Evaluations of seven different clinical staging systems for Chinese patients with hepatocellular carcinoma undergoing curative resection].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 05-24-2014
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To compare the performance of 7 prognostic staging systems in predicting the survival of surgical patients with hepatocellular carcinoma (HCC).
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An Incremental and Distributed Inference Method for Large-Scale Ontologies Based on MapReduce Paradigm.
IEEE Trans Cybern
PUBLISHED: 05-13-2014
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With the upcoming data deluge of semantic data, the fast growth of ontology bases has brought significant challenges in performing efficient and scalable reasoning. Traditional centralized reasoning methods are not sufficient to process large ontologies. Distributed reasoning methods are thus required to improve the scalability and performance of inferences. This paper proposes an incremental and distributed inference method for large-scale ontologies by using MapReduce, which realizes high-performance reasoning and runtime searching, especially for incremental knowledge base. By constructing transfer inference forest and effective assertional triples, the storage is largely reduced and the reasoning process is simplified and accelerated. Finally, a prototype system is implemented on a Hadoop framework and the experimental results validate the usability and effectiveness of the proposed approach.
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Combined treatment with erythropoietin and granulocyte colony-stimulating factor enhances neovascularization and improves cardiac function after myocardial infarction.
Chin. Med. J.
PUBLISHED: 05-06-2014
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Erythropoietin (EPO) and granulocyte colony-stimulating factor (G-CSF) are both potential novel therapeutics for use after myocardial infarction (MI). However, their underlying mechanisms remain unclear and the efficacy of monotherapy with EPO or G-CSF is also controversial. Therefore, we investigated the effects of combined treatment with EPO and G-CSF on neovascularization and cardiac function in post-infarction rats and explored the potential mechanisms.
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[Clinical characteristics and prognosis of three rare and poor-prognostic subtypes of primary liver carcinoma].
Zhonghua Zhong Liu Za Zhi
PUBLISHED: 05-03-2014
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To explore the clinicopathological features and prognostic factors of three rare and poor-prognostic pathological subtypes of primary liver carcinoma, and improve the clinical diagnosis and surgical treatment.
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Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model.
Sci Rep
PUBLISHED: 04-30-2014
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The research in microbial communities would potentially impact a vast number of applications in "bio"-related disciplines. Large-scale analyses became a clear trend in microbial community studies, thus it is increasingly important to perform efficient and in-depth data mining for insightful biological principles from large number of samples. However, as microbial communities are from different sources and of different structures, comparison and data-mining from large number of samples become quite difficult. In this work, we have proposed a data model to represent large-scale comparison of microbial community samples, namely the "Multi-Dimensional View" data model (the MDV model) that should at least include 3 aspects: samples profile (S), taxa profile (T) and meta-data profile (V). We have also proposed a method for rapid data analysis based on the MDV model and applied it on the case studies with samples from various environmental conditions. Results have shown that though sampling environments usually define key variables, the analysis could detect bio-makers and even subtle variables based on large number of samples, which might be used to discover novel principles that drive the development of communities. The efficiency and effectiveness of data analysis method based on the MDV model have been validated by the results.
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Role of transportation in spread of porcine epidemic diarrhea virus infection, United States.
Emerging Infect. Dis.
PUBLISHED: 04-23-2014
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After porcine epidemic diarrhea virus (PEDV) was detected in the United States in 2013, we tested environmental samples from trailers in which pigs had been transported. PEDV was found in 5.2% of trailers not contaminated at arrival, , suggesting that the transport process is a source of transmission if adequate hygiene measures are not implemented.
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Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734.
Genome Announc
PUBLISHED: 04-12-2014
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Porcine deltacoronavirus (PDCoV) was detected in feces from diarrheic sows during an epidemic of acute and transmissible diarrhea. No transmissible gastroenteritis virus or porcine epidemic diarrhea virus was detected. The PDCoV USA/IA/2014/8734 from the herd was sequenced for full-length genomic RNA to further characterize PDCoV in U.S. swine.
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"Seesaw balloon-wire cutting" technique as a novel approach to "balloon-uncrossable" chronic total occlusions.
J Invasive Cardiol
PUBLISHED: 04-11-2014
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Balloon crossing failure after passing a guidewire usually leads to unsuccessful percutaneous recanalization of chronic total occlusions (CTOs). We sought to investigate a novel technique for solving this problem.
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V?9V?2 TCR-activation by phosphorylated antigens requires butyrophilin 3 A1 (BTN3A1) and additional genes on human chromosome 6.
Eur. J. Immunol.
PUBLISHED: 04-02-2014
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Pyrophosphorylated metabolites of isoprenoid-biosynthesis (phosphoantigens, PAgs) activate V?9V?2 T cells during infections and trigger antitumor activity. This activation depends on expression of butyrophilin 3 A1 (BTN3A1) by antigen-presenting cells. This report defines the minimal genetic requirements for activation of V?9V?2 T cells by PAgs and mAb 20.1. We compared PAg-presentation by BTN3A1-transduced CHO hamster cells with that of CHO cells containing the complete human chromosome 6 (Chr6). BTN3A1 expression alone was sufficient for activation of V?9V?2 T-cell receptor transductants by mAb 20.1., while activation by PAgs also required the presence of Chr6. We take this finding as evidence that gene(s) on Chr6 in addition to BTN3A1 are mandatory for PAg-mediated activation of V?9V?2 T cells. This observation is important for the design of animal models for PAg-mediated immune responses and provokes speculations about the analogy between genes controlling PAg presentation and MHC-localized genes controlling peptide-antigen presentation.
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Experimental investigation on multi-dimensional digital predistortion for multi-band radio-over-fiber systems.
Opt Express
PUBLISHED: 03-26-2014
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The recently-proposed multi-dimensional digital predistortion (DPD) technique is experimentally investigated in terms of nonlinearity order, memory length, oversampling rate, digital-to-analog conversion resolution, carrier frequency dependence and RF input power tolerance, in both directly-modulated and externally-modulated multi-band radio-over-fiber (RoF) systems. Similar characteristics of the multi-dimensional digital predistorter are identified in directly-modulated and externally-modulated RoF systems. The experimental results suggest implementing a memory-free multi-dimensional digital predistorter involving nonlinearity orders up to 5 at 2 × oversampling rate for practical multi-band RoF systems. Using the suggested parameters, the multi-dimensional DPD is able to improve the RF input power tolerance by greater than 3dB for each band in a two-band RoF system, indicating an enhancement of RF power transmitting efficiency.
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Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis.
Sci Rep
PUBLISHED: 03-25-2014
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Nannochloropsis spp. are a group of oleaginous microalgae that harbor an expanded array of lipid-synthesis related genes, yet how they are transcriptionally regulated remains unknown. Here a phylogenomic approach was employed to identify and functionally annotate the transcriptional factors (TFs) and TF binding-sites (TFBSs) in N. oceanica IMET1. Among 36 microalgae and higher plants genomes, a two-fold reduction in the number of TF families plus a seven-fold decrease of average family-size in Nannochloropsis, Rhodophyta and Chlorophyta were observed. The degree of similarity in TF-family profiles is indicative of the phylogenetic relationship among the species, suggesting co-evolution of TF-family profiles and species. Furthermore, comparative analysis of six Nannochloropsis genomes revealed 68 "most-conserved" TFBS motifs, with 11 of which predicted to be related to lipid accumulation or photosynthesis. Mapping the IMET1 TFs and TFBS motifs to the reference plant TF-"TFBS motif" relationships in TRANSFAC enabled the prediction of 78 TF-"TFBS motif" interaction pairs, which consisted of 34 TFs (with 11 TFs potentially involved in the TAG biosynthesis pathway), 30?TFBS motifs and 2,368 regulatory connections between TFs and target genes. Our results form the basis of further experiments to validate and engineer the regulatory network of Nannochloropsis spp. for enhanced biofuel production.
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Investigation of a novel biomarker, neuropilin-1, and its application for poor prognosis in acute myeloid leukemia patients.
Tumour Biol.
PUBLISHED: 03-07-2014
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According to the previous studies, numerous biomarkers impact on the prognosis of acute myeloid leukemia (AML) and the prediction for AML had been improved tremendously in the past decades. However, accurate risk-stratification at diagnosis or prognosis remained difficult. In order to further investigate the prognosis evaluation biomarker, the transcription or expression of neuropilin-1 (NRP-1) in 87 AML patients and 32 non-malignant controls were examined. Real-time quantitative polymerase chain reaction (RT-PCR) and Western blot were used to detect the NRP-1 expression. Clinical data were collected and analyzed for the 87 AML patients. The results indicated that high NRP-1 expression discriminated the complete remission (CR) rate of AML patients (22.12 % vs. 68.04 % for AML, P < 0.01). De novo AML patients tended to express higher NRP-1 proteins than relapsed AML patients. The overall survival (OS) and relapse-free survival (RFS) rate of the high NRP-1 expression patients decreased significantly compared with the low NRP-1 expression patients (P < 0.001). NRP-1 was revealed to be an independent risk factor for OS in AML (P = 0.003). In conclusion, NRP-1 could predict the shorter OS and RFS rate, and also related with the CR response in AML. Therefore, NRP-1 may act as a more aggressive and promising predictor for the poor prognosis of AML.
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Analysis of the steps in single-molecule photobleaching traces by using the hidden markov model and maximum-likelihood clustering.
Chem Asian J
PUBLISHED: 02-28-2014
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The step analysis of single-molecule photobleaching data offers a new approach for studying protein stoichiometry under physiological conditions. As such, it is important to develop suitable algorithms that can accurately extract the step events from the noisy single-molecule data. Herein, we report a HMM method that combines maximum-likelihood clustering for initializing the emission-probability distribution of the HMMs with an extended silhouette clustering criterion for estimating the state number of single molecules. In this way, the limitations of standard HMM in terms of processing typical single-molecule data with a short sequence are overcome. By using this method, the number and time points of the step events are automatically determined, without the introduction of any subjectivity. Simulation experiments on the experimental photobleaching data indicate that our method is very effective and robust in the analysis of single-molecule fluorescence photobleaching curves if the signal/noise ratio is larger than 2:1. This method was employed for processing photobleaching data that were obtained from single-molecule fluorescence imaging of transforming growth factor typeII receptors on a cell surface. This method is also expected to be applicable to the analysis of other stepwise events.
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Jaundice as a prognostic factor in patients undergoing radical treatment for carcinomas of the ampulla of Vater.
Chin. Med. J.
PUBLISHED: 02-28-2014
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Carcinomas of the ampulla of Vater (CAV) is a relatively rare malignant gastrointestinal tumor, and its postoperative prognostic factors have been well studied. However, as its first symptom, the impact of jaundice on the prognosis of CAV is not so clear. This study aims to explore the role of jaundice as a prognostic factor in patients undergoing radical treatment for CAV.
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Protecting location privacy for outsourced spatial data in cloud storage.
ScientificWorldJournal
PUBLISHED: 02-25-2014
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As cloud computing services and location-aware devices are fully developed, a large amount of spatial data needs to be outsourced to the cloud storage provider, so the research on privacy protection for outsourced spatial data gets increasing attention from academia and industry. As a kind of spatial transformation method, Hilbert curve is widely used to protect the location privacy for spatial data. But sufficient security analysis for standard Hilbert curve (SHC) is seldom proceeded. In this paper, we propose an index modification method for SHC (SHC(?)) and a density-based space filling curve (DSC) to improve the security of SHC; they can partially violate the distance-preserving property of SHC, so as to achieve better security. We formally define the indistinguishability and attack model for measuring the privacy disclosure risk of spatial transformation methods. The evaluation results indicate that SHC(?) and DSC are more secure than SHC, and DSC achieves the best index generation performance.
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Effects of biochar and the geophagous earthworm Metaphire guillelmi on fate of (14)C-catechol in an agricultural soil.
Chemosphere
PUBLISHED: 02-19-2014
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Both biochar and earthworms can exert influence on behaviors of soil-borne monomeric phenols in soil; however, little was known about the combined effects of biochar and earthworm activities on fate of these chemicals in soil. Using (14)C-catechol as a representative, the mineralization, transformation and residue distribution of phenolic humus monomer in soil amended with different amounts of biochar (0%, 0.05%, 0.5%, and 5%) without/with the geophagous earthworm Metaphire guillelmi were investigated. The results showed biochar at amendment rate <0.5% did not affect (14)C-catechol mineralization, whereas 5% biochar amendment significantly inhibited the mineralization. Earthworms did not affect the mineralization of (14)C-catechol in soil amended with <0.5% biochar, but significantly enhanced the mineralization in 5% biochar amended soil when they were present in soil for 9 d. When earthworms were removed from the soil, the mineralization of (14)C-catechol was significantly lower than that of in earthworm-free soil indicating that (14)C-catecholic residues were stabilized during their passage through earthworm gut. The assimilation of (14)C by earthworms was low (1.2%), and was significantly enhanced by biochar amendment, which was attributed to the release of biochar-associated (14)C-catecholic residues during gut passage of earthworm.
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An unconditionally stable, positivity-preserving splitting scheme for nonlinear Black-Scholes equation with transaction costs.
ScientificWorldJournal
PUBLISHED: 02-12-2014
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This paper deals with the numerical analysis of nonlinear Black-Scholes equation with transaction costs. An unconditionally stable and monotone splitting method, ensuring positive numerical solution and avoiding unstable oscillations, is proposed. This numerical method is based on the LOD-Backward Euler method which allows us to solve the discrete equation explicitly. The numerical results for vanilla call option and for European butterfly spread are provided. It turns out that the proposed scheme is efficient and reliable.
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Phase-conjugation-based fast RF phase stabilization for fiber delivery.
Opt Express
PUBLISHED: 02-12-2014
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In this paper, we propose a phase-conjugation-based fast radio frequency (RF) phase auto stabilization technique for long-distance fiber delivery. By phase conjugation at the center site, the proposed scheme pre-phase-promotes the RF signal with the shift which is acquired by round-trip transferring another RF whose frequency is half of the one to be sent. Such phase pre-promotion is then used to counteract exactly the following retard induced by one-way delivery. Different from the previous phase-locking-loop-based schemes, the proposed open-loop design avoids the use of any tunable parts and dynamic phase tracking, enabling a fast phase stabilization at the remote site. An end-less compensation capacity can also be achieved. Our design is analyzed by theory. Experimentally, the new scheme is verified by transferring a frequency of 2.42 GHz through a 30-km optical fiber link. Significant phase drift compression is observed. The rapid phase stabilization is verified by introducing sudden time delay change into the link. The recovery time equals to the round-trip time of the link plus the transitional duration of the delay change, which is much shorter than the traditional trial-and-error phase locking loop. Important issues of the system design are discussed.
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Optical frequency comb based multi-band microwave frequency conversion for satellite applications.
Opt Express
PUBLISHED: 02-12-2014
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Based on optical frequency combs (OFC), we propose an efficient and flexible multi-band frequency conversion scheme for satellite repeater applications. The underlying principle is to mix dual coherent OFCs with one of which carrying the input signal. By optically channelizing the mixed OFCs, the converted signal in different bands can be obtained in different channels. Alternatively, the scheme can be configured to generate multi-band local oscillators (LO) for widely distribution. Moreover, the scheme realizes simultaneous inter- and intra-band frequency conversion just in a single structure and needs only three frequency-fixed microwave sources. We carry out a proof of concept experiment in which multiple LOs with 2 GHz, 10 GHz, 18 GHz, and 26 GHz are generated. A C-band signal of 6.1 GHz input to the proposed scheme is successfully converted to 4.1 GHz (C band), 3.9 GHz (C band) and 11.9 GHz (X band), etc. Compared with the back-to-back (B2B) case measured at 0 dBm input power, the proposed scheme shows a 9.3% error vector magnitude (EVM) degradation at each output channel. Furthermore, all channels satisfy the EVM limit in a very wide input power range.
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Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics.
Nat Commun
PUBLISHED: 01-27-2014
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Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has ~25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen-host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens.
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Effects of oxysophoridine on amino acids after cerebral ischemic injury in mice.
Ann Indian Acad Neurol
PUBLISHED: 01-26-2014
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Our previous studies demonstrated that oxysophoridine (OSR) had neuroprotective effects on mice through antioxidant and anti-apoptotic mechanisms. In this study, we investigated whether OSR could influence the release of amino acids in ischemic mice brains.
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Experiences with infectious cDNA clones of equine arteritis virus: lessons learned and insights gained.
Virology
PUBLISHED: 01-24-2014
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The advent of recombinant DNA technology, development of infectious cDNA clones of RNA viruses, and reverse genetic technologies have revolutionized how viruses are studied. Genetic manipulation of full-length cDNA clones has become an especially important and widely used tool to study the biology, pathogenesis, and virulence determinants of both positive and negative stranded RNA viruses. The first full-length infectious cDNA clone of equine arteritis virus (EAV) was developed in 1996 and was also the first full-length infectious cDNA clone constructed from a member of the order Nidovirales. This clone was extensively used to characterize the molecular biology of EAV and other Nidoviruses. The objective of this review is to summarize the characterization of the virulence (or attenuation) phenotype of the recombinant viruses derived from several infectious cDNA clones of EAV in horses, as well as their application for characterization of the molecular basis of viral neutralization, persistence, and cellular tropism.
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A high efficiency gene disruption strategy using a positive-negative split selection marker and electroporation for Fusarium oxysporum.
Microbiol. Res.
PUBLISHED: 01-16-2014
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The Fusarium oxysporum species complex consists of fungal pathogens that cause serial vascular wilt disease on more than 100 cultivated species throughout the world. Gene function analysis is rapidly becoming more and more important as the whole-genome sequences of various F. oxysporum strains are being completed. Gene-disruption techniques are a common molecular tool for studying gene function, yet are often a limiting step in gene function identification. In this study we have developed a F. oxysporum high-efficiency gene-disruption strategy based on split-marker homologous recombination cassettes with dual selection and electroporation transformation. The method was efficiently used to delete three RNA-dependent RNA polymerase (RdRP) genes. The gene-disruption cassettes of three genes can be constructed simultaneously within a short time using this technique. The optimal condition for electroporation is 10?F capacitance, 300? resistance, 4kV/cm field strength, with 1?g of DNA (gene-disruption cassettes). Under these optimal conditions, we were able to obtain 95 transformants per ?g DNA. And after positive-negative selection, the transformants were efficiently screened by PCR, screening efficiency averaged 85%: 90% (RdRP1), 85% (RdRP2) and 77% (RdRP3). This gene-disruption strategy should pave the way for high throughout genetic analysis in F. oxysporum.
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Metabolism of fungicide 2-allylphenol in Rhizoctonia cerealis.
Ecotoxicol. Environ. Saf.
PUBLISHED: 01-15-2014
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2-Allylphenol is a biomimetic synthetic fungicide that mimics the compound ginkgol found in gingko fruit (Gingko biloba L.). This systemic fungicide can effectively suppress a wide range of plant diseases, including wheat sharp eyespot (Rhizoctonia cerealis). However, its degradation in environment after application is still unknown. To understand this fungicide degradation, major metabolites of 2-allylphenol in R. cerealis were examined. The parent and metabolites of 2-allylphenol were detected and quantified in the mycelia and liquid medium. Results showed that 2-allylphenol was metabolized and bio-transformed by R. cerealis, and four metabolites were found, including 2-(2-hydroxyphenyl) acetic acid (M1), 2-(2, 3-dihydroxypropyl) phenol (M2), 2-(2-hydroxypropyl)-phenol (M3) and 2-(3-hydroxypropyl)-phenol (M4). Based on the results, we propose that the biodegradation pathway is that 2-allylphenol is rapidly oxidized into metabolite M2 and hydrolyzed into M3 and M4, which formed M2, and carboxylation of M2 to 2-hydroxy-3-(2?-hydroxyphenyl) propionic acid which undergo hydrolyzation and decarboxylation to form M1. 2-Allylphenol can be bio-transformed to new compounds by R. cerealis, suggesting the existence of microbe metabolic pathways for 2-allylphenol.
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Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.
J Biomed Inform
PUBLISHED: 01-15-2014
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Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach.
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Significance of CD44 expression in head and neck cancer: a systemic review and meta-analysis.
BMC Cancer
PUBLISHED: 01-06-2014
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CD44 has been reported to be involved with tumor growth and metastasis and has also been implicated as a CSC marker in head and neck squamous cell cancer (HNSCC). However, the prognostic value of CD44 still remains controversial; hence, we investigated the correlation between CD44 and the clinicopathological features of HNSCC by meta-analysis.
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Modulation of Purkinje cell complex spike waveform by synchrony levels in the olivocerebellar system.
Front Syst Neurosci
PUBLISHED: 01-01-2014
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Purkinje cells (PCs) generate complex spikes (CSs) when activated by the olivocerebellar system. Unlike most spikes, the CS waveform is highly variable, with the number, amplitude, and timing of the spikelets that comprise it varying with each occurrence. This variability suggests that CS waveform could be an important control parameter of olivocerebellar activity. The origin of this variation is not well known. Thus, we obtained extracellular recordings of CSs to investigate the possibility that the electrical coupling state of the inferior olive (IO) affects the CS waveform. Using multielectrode recordings from arrays of PCs we showed that the variance in the recording signal during the period when the spikelets occur is correlated with CS synchrony levels in local groups of PCs. The correlation was demonstrated under both ketamine and urethane, indicating that it is robust. Moreover, climbing fiber reflex evoked CSs showed an analogous positive correlation between spikelet-related variance and the number of cells that responded to a stimulus. Intra-IO injections of GABA-A receptor antagonists or the gap junction blocker carbenoxolone produced correlated changes in the variance and synchrony levels, indicating the presence of a causal relationship. Control experiments showed that changes in variance with synchrony were primarily due to changes in the CS waveform, as opposed to changes in the strength of field potentials from surrounding cells. Direct counts of spikelets showed that their number increased with synchronization of CS activity. In sum, these results provide evidence of a causal link between two of the distinguishing characteristics of the olivocerebellar system, its ability to generate synchronous activity and the waveform of the CS.
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LSF expression and its prognostic implication in colorectal cancer.
Int J Clin Exp Pathol
PUBLISHED: 01-01-2014
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Colorectal cancer (CRC) is the third most common cancer worldwide and the fourth most common cause of cancer death. Therapy failure was the first cause of death. LSF is a transcription factor regulating gene expression of angiogenesis, tumor invasion and proliferation, and is identified as a chemoresistant gene. Real-time PCR and Western blot to analyze mRNA and protein expression of LSF in 23 paired CRC samples. Immunohistochemistry was used to detect protein expression of LSF in 166 paired CRC samples. Both LSF mRNA and protein were upregulated in CRC. High LSF expression in CRC correlated with large tumor size, advanced pN stage, advanced AJCC stage and high Ki-67 index (P < 0.001). High expression of LSF favored worse prognosis. 5-year survival rates of LSF high and low expression were 39.6% and 78.6%, respectively. The 5-year median OS were 34 months and 57 months, respectively. LSF is an important mediator in CRC tumorigenesis and progression, and LSF expression is an important index for and prognostic prediction.
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Lin28a Protects against Hypoxia/Reoxygenation Induced Cardiomyocytes Apoptosis by Alleviating Mitochondrial Dysfunction under High Glucose/High Fat Conditions.
PLoS ONE
PUBLISHED: 01-01-2014
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The aim of the present study was to investigate the role of Lin28a in protecting against hypoxia/reoxygenation (H/R)-induced cardiomyocytes apoptosis under high glucose/high fat (HG/HF) conditions.
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Variants identified by hepatocellular carcinoma and chronic hepatitis B virus infection susceptibility GWAS associated with survival in HBV-related hepatocellular carcinoma.
PLoS ONE
PUBLISHED: 01-01-2014
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Recent genome-wide association studies (GWAS) have identified several common susceptibility loci associated with the risk of hepatocellular carcinoma (HCC) or chronic hepatitis B infection (CHB). However, the relationship between these genetic variants and survival of patients with hepatitis B virus (HBV)-related HCC is still unknown. In this study, 22 single nucleotide polymorphisms (SNPs) were genotyped among 330 HBV-related HCC patients using the MassARRAY system from Sequenom. Cox proportional hazards regression was used to examine the effects of genotype on survival time under an additive model with age, sex, smoking status and clinical stage as covariates. We identified four SNPs on 6p21 (rs1419881 T>C, rs7453920 G>A,rs3997872 G>A and rs7768538 T>C), and two SNPs on 8p12 (rs2275959 C>T and rs7821974 C>T) significantly associated with survival time of HBV-related HCC patients. Our results suggest that HCC or CHB susceptibility loci might also affect the prognosis of patients with HBV-related HCC.
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Prognosis of patients with hepatocellular carcinoma and hypersplenism after surgery: a single-center experience from the People's Republic of China.
Onco Targets Ther
PUBLISHED: 01-01-2014
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As prognosis of patients with hepatocellular carcinoma (HCC) and hypersplenism is rarely reported, this study examined prognostic factors for patients who underwent surgery for this condition.
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A security-awareness virtual machine management scheme based on Chinese wall policy in cloud computing.
ScientificWorldJournal
PUBLISHED: 01-01-2014
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Cloud computing gets increasing attention for its capacity to leverage developers from infrastructure management tasks. However, recent works reveal that side channel attacks can lead to privacy leakage in the cloud. Enhancing isolation between users is an effective solution to eliminate the attack. In this paper, to eliminate side channel attacks, we investigate the isolation enhancement scheme from the aspect of virtual machine (VM) management. The security-awareness VMs management scheme (SVMS), a VMs isolation enhancement scheme to defend against side channel attacks, is proposed. First, we use the aggressive conflict of interest relation (ACIR) and aggressive in ally with relation (AIAR) to describe user constraint relations. Second, based on the Chinese wall policy, we put forward four isolation rules. Third, the VMs placement and migration algorithms are designed to enforce VMs isolation between the conflict users. Finally, based on the normal distribution, we conduct a series of experiments to evaluate SVMS. The experimental results show that SVMS is efficient in guaranteeing isolation between VMs owned by conflict users, while the resource utilization rate decreases but not by much.
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Trehalose maintains vitality of mouse epididymal epithelial cells and mediates gene transfer.
PLoS ONE
PUBLISHED: 01-01-2014
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In the present study, trehalose was utilized to improve primary culture of mouse epididymal epithelial cells in vitro, and to enhance naked DNA delivery in epididymis in vivo. During the six-day culture, the proliferation activity of the cells in the medium with addition of trehalose was higher than that of those cells cultured in absence of trehalose (p<0.01). To determine the optimal concentration for cell proliferation, a series of trehalose concentrations (0, 60, 120, 180 mM) were tested, and the result indicated that the cell in the medium with 120 mM trehalose showed the highest proliferation potential. The epididymis epithelial cells were cultured in the medium containing 120 mM trehalose upon 16th passage, and they continued expressing markers of epididymal epithelial cell, such as rE-RABP, AR and ER-beta. Our study also indicated that trehalose concentrations of 120-240 mM, especially 180 mM, could effectively enhance DNA delivery into the mouse epididymis epithelial cell in vitro. Moreover, trehalose could induce in vivo expression of exogenous DNA in epididymal epithelial cells and help to internalize plasmid into sperm,which did not influence motility of sperm when the mixture of trehalose (180 mM) and DNA was injected into epididymal lumen through efferent tubule. This study suggested that trehalose, as an effective and safer reagent, could be employed potentially to maintain vitality of mouse epididymal epithelial cells during long-term culture in vitro and to mediate in vitro and in vivo gene transfer.
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Recent advances in the ARID family: focusing on roles in human cancer.
Onco Targets Ther
PUBLISHED: 01-01-2014
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The human AT-rich interaction domain (ARID) family contains seven subfamilies and 15 members characterized by having an ARID. Members of the ARID family have the ability to regulate transcription and are involved in cell differentiation and proliferation. Accumulating evidence suggests that ARID family members are involved in cancer-related signaling pathways, highly mutated or differentially expressed in tumor tissues, and act as predictive factors for cancer prognosis or therapeutic outcome. Here we review the molecular biology and clinical studies concerned with the role played by the ARID family in cancer. This may contribute to our understanding of the initiation and progression of cancer from a novel point of view, as well as providing potential targets for cancer therapy.
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Nannochloropsis genomes reveal evolution of microalgal oleaginous traits.
PLoS Genet.
PUBLISHED: 01-01-2014
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Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.
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Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China.
Arch. Virol.
PUBLISHED: 01-01-2014
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The complete genome sequence of a novel monopartite begomovirus, isolate G-YU-12-10, was obtained from sweet potato samples exhibiting severe leaf curl symptoms in Xinxiang, Henan Province, China. The genome sequence consisted of 2766 nucleotides and encoded two open reading frames (ORFs) (AV1 and AV2) in the viral-sense strand and four ORFs (AC1-AC4) in the complementary-sense strand. The genome of isolate G-YU-12-10 was closely related to other sweet-potato-infecting begomoviruses (sweepoviruses) and shared the highest nucleotide sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316). Thus, the G-YU-12-10 isolate represents a novel species according to the demarcation criteria of species in the genus Begomovirus, for which the name Sweet potato leaf curl Henan virus (SPLCHnV) is proposed. Interspecific recombination analysis supported the recombination hypothesis, indicating that recombination with other begomoviruses had taken place within AC2 and AC3 ORFs of SPLCHnV and also in the non-coding intergenic region (IR).
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Isolation and Characterization of Porcine Epidemic Diarrhea Viruses Associated with the 2013 Disease Outbreak among Swine in the United States.
J. Clin. Microbiol.
PUBLISHED: 11-06-2013
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Porcine epidemic diarrhea virus (PEDV) was detected in May 2013 for the first time in U.S. swine and has since caused significant economic loss. Obtaining a U.S. PEDV isolate that can grow efficiently in cell culture is critical for investigating pathogenesis and developing diagnostic assays and for vaccine development. An additional objective was to determine which gene(s) of PEDV is most suitable for studying the genetic relatedness of the virus. Here we describe two PEDV isolates (ISU13-19338E and ISU13-22038) successfully obtained from the small intestines of piglets from sow farms in Indiana and Iowa, respectively. The two isolates have been serially propagated in cell culture for over 30 passages and were characterized for the first 10 passages. Virus production in cell culture was confirmed by PEDV-specific real-time reverse-transcription PCR (RT-PCR), immunofluorescence assays, and electron microscopy. The infectious titers of the viruses during the first 10 passages ranged from 6 × 10(2) to 2 × 10(5) 50% tissue culture infective doses (TCID50)/ml. In addition, the full-length genome sequences of six viruses (ISU13-19338E homogenate, P3, and P9; ISU13-22038 homogenate, P3, and P9) were determined. Genetically, the two PEDV isolates were relatively stable during the first 10 passages in cell culture. Sequences were also compared to those of 4 additional U.S. PEDV strains and 23 non-U.S. strains. All U.S. PEDV strains were genetically closely related to each other (?99.7% nucleotide identity) and were most genetically similar to Chinese strains reported in 2011 to 2012. Phylogenetic analyses using different genes of PEDV suggested that the full-length spike gene or the S1 portion is appropriate for sequencing to study the genetic relatedness of these viruses.
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Multifrequency radio frequency sensing with photonics-assisted spectrum compression.
Opt Lett
PUBLISHED: 11-02-2013
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We propose and demonstrate a multifrequency radio frequency (RF) spectrum estimation technology. With photonic assistance, a multifrequency RF signal ranging from 0 to 1 GHz is highly spectrally compressed and sensed using a single analog-to-digital converter with analog bandwidth of 42.6 MHz. By calculating the cross correlation of pseudo random binary sequence and the encoded signal, up to 40 RF tones are precisely recognized without large computational load. The employment of optical mixing decreased the cost and increased the performance compared to its electrical counterpart. The theory and performance are also discussed.
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[3.0T-MR high resolution proton density weighted imaging for transverse cervical ligament in healthy adolescents].
Zhong Nan Da Xue Xue Bao Yi Xue Ban
PUBLISHED: 10-30-2013
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Objective: To explore the imaging characteristics of the transverse ligament in healthy adolescents, and further understand the imaging characteristics of the ligament injury. Methods: We used 3.0T-MR to scan the transverse ligament with proton-weighted sequence in 32 young volunteers, scanned coronally, horizontally and sagittally, and then observed the morphology, thickness, running and signal characteristics of the ligament. Results: The anatomy and signal characteristics of the transverse cervical ligament were clearly displayed by high resolution proton density weighted imaging (PDWI). The whole picture of the transverse ligament was effectively displayed by coronal combined with horizontal image. The transverse ligament was located in the rear of the odontoid, and connected to the inside of both sides of the block like half-arc. The length was (20.4±3.3) mm, the ligament center was the thickest, and both sides gradually became thinner. The middle width of the ligament was (7.3±0.6) mm, the ligament ends narrowed down, and the middle was (2.1±0.4) mm thick; 75% of the transverse ligament showed homogeneous low signal in PDWI, while 25% of the local transverse ligament had high signal. Conclusion: High resolution PDWI with 3.0T-MR is a effective method to evaluate the structure of the transverse cervical ligament. Local high signal may not necessarily be the sign of ligament injure. There may also be some high signal in the normal adolescent ligament, so we must pay much attention to clinical diagnosis and treatment.
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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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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.