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Find video protocols related to scientific articles indexed in Pubmed.
Identification of Microsatellites in DNA Using Adaptive S-Transform.
IEEE J Biomed Health Inform
PUBLISHED: 06-22-2014
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Microsatellites are tandem repeats of size 1-6 base pairs, associated with various diseases, DNA fingerprinting, and also useful in evolutionary studies. A signal processing algorithm for microsatellite detection, based on adaptive S-transform is proposed. The standard deviation of Gaussian window kernel of S-transform has been optimized for integer periods of interest by maximizing the concentration measure. Time-frequency plot is generated using optimal standard deviation values. Candidate repeats are marked by comparing the spectrogram values in time-frequency plot with a threshold. A preprocessing phase followed by a verification phase extracts final results from the candidate repeats. Simulation studies on DNA sequences establish the superiority of this algorithm over other existing methods. Applicability of this algorithm in the analysis of DNA sequences associated with repeat expansion diseases has also been demonstrated.
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Elimination of young erythrocytes from blood circulation and altered erythropoietic patterns during paraquat induced anemic phase in mice.
PLoS ONE
PUBLISHED: 01-01-2014
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Paraquat a widely used herbicide causes a variety of toxic effects on humans and animals. The present study is focused on the interaction of paraquat with the mouse erythroid system. Administration of paraquat (10 mg/kg body weight i.p. on alternate days in C57Bl/6 mice) induced a significant fall in blood erythrocyte count on 7, 14, and 21 day time points but the erythrocyte count reverted back to normal by 28th day indicating the emergence of refractoriness to paraquat. A marked surge in the blood reticulocyte count was observed in paraquat treated mice that also subsided by 28th day. Young erythrocytes in circulation were randomly eliminated from blood circulation in paraquat treated mice and a significant elevation in the level of reactive oxygen species (ROS) was also observed maximally the erythrocytes of this age group. Cells representing various stages of erythroid differentiation in bone marrow and spleen were identified and enumerated flow cytometrically based on their expression of Ter119 and transferrin (CD71) receptor. Proliferative activity of erythroid cells, their relative proportion as well as their absolute numbers fell significantly in bone marrow of paraquat treated mice but all these parameters were significantly elevated in spleens of paraquat treated mice. These changes were essentially restricted to the cells belonging to the two earliest stages of erythroid differentiation. Taken together our results indicate that paraquat treatment causes a transient anemia in mice resulting from random elimination of young circulating erythrocytes as well as depressed erythropoietic activity in bone marrow. Spleen erythropoietic activity however was elevated in paraquat treated mice.
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Performance analysis of MIMO-STBC systems with higher coding rate using adaptive semiblind channel estimation scheme.
ScientificWorldJournal
PUBLISHED: 01-01-2014
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Semiblind channel estimation method provides the best trade-off in terms of bandwidth overhead, computational complexity and latency. The result after using multiple input multiple output (MIMO) systems shows higher data rate and longer transmit range without any requirement for additional bandwidth or transmit power. This paper presents the detailed analysis of diversity coding techniques using MIMO antenna systems. Different space time block codes (STBCs) schemes have been explored and analyzed with the proposed higher code rate. STBCs with higher code rates have been simulated for different modulation schemes using MATLAB environment and the simulated results have been compared in the semiblind environment which shows the improvement even in highly correlated antenna arrays and is found very close to the condition when channel state information (CSI) is known to the channel.
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An Adaptive Window Length Strategy for Eukaryotic CDS Prediction.
IEEE/ACM Trans Comput Biol Bioinform
PUBLISHED: 02-03-2013
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Signal processing-based algorithms for identification of coding sequences (CDS) in eukaryotes are non-data driven and exploit the presence of three-base periodicity in these regions for their detection. Three-base periodicity is commonly detected using short time Fourier transform (STFT) that uses a window function of fixed length. As the length of the protein coding and noncoding regions varies widely, the identification accuracy of STFT-based algorithms is poor. In this paper, a novel signal processing-based algorithm is developed by enabling the window length adaptation in STFT of DNA sequences for improving the identification of three-base periodicity. The length of the window function has been made adaptive in coding regions to maximize the magnitude of period-3 measure, whereas in the noncoding regions, the window length is tailored to minimize this measure. Simulation results on bench mark data sets demonstrate the advantage of this algorithm when compared with other non-data-driven methods for CDS prediction.
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Relative efficacy of uptake and presentation of Mycobacterium bovis BCG antigens by type I mouse lung epithelial cells and peritoneal macrophages.
Infect. Immun.
PUBLISHED: 06-06-2011
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Flow cytometric studies indicated that both peritoneal macrophages (PMs) and primary lung epithelial (PLE) cells isolated from mouse lungs could take up fluorescence-tagged Mycobacterium bovis BCG. BCG uptake in both cases was significantly inhibited by cytochalasin D, indicating active internalization of BCG by these cells. Confocal microscopy data further confirmed that BCG was internalized by PLE cells. BCG sonicate antigen (sBCG) had marked toxicity toward PMs but was relatively nontoxic to PLE cells. Accordingly, BCG sonicate antigen induced a significantly higher apoptotic and necrotic response in PMs compared to that in PLE cells. Both PMs and PLE cells exposed to BCG antigens and fixed thereafter could efficiently present antigens to purified BCG-sensitized T helper cells, as assessed by the release of interleukin-2 (IL-2) and gamma interferon (IFN-?). If, however, PLE cells were fixed before exposure to BCG, antigen presentation was abrogated, indicating that the PLE cells may in some way process the BCG antigen. A comparison of efficacies of BCG-pulsed PLE cells and PMs to present antigen at various antigen-presenting cell (APC)/T cell ratios indicated that PMs had only marginally greater APC function than that of PLE cells. Staining with specific monoclonal antibodies indicated that the cultured PLE cells used for antigen presentation essentially comprised type I epithelial cells. Our results suggest that type I lung epithelial cells may present BCG antigens to sensitized T helper cells and that their performance as APCs is comparable with that of PMs.
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Quantitative assessment of elemental carbon in the lungs of never smokers, cigarette smokers, and coal miners.
J. Toxicol. Environ. Health Part A
PUBLISHED: 04-12-2011
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Inhalation exposure to particulates such as cigarette smoke and coal dust is known to contribute to the development of chronic lung disease. The purpose of this study was to estimate the amount of elemental carbon (EC) deposits from autopsied lung samples from cigarette smokers, miners, and control subjects and explore the relationship between EC level, exposure history, and the extent of chronic lung disease. The samples comprised three subgroups representing never smokers (8), chronic cigarette smokers (26), and coal miners (6). Following the dissolution of lung tissue, the extracted EC residue was quantified using a thermal-optical transmission (TOT) carbon analyzer. Mean EC levels in the lungs of the control group were 56.68 ± 24.86 (SD) ?g/g dry lung weight. Respective mean EC values in lung samples from the smokers and coal miners were 449.56 ± 320.3 ?g/g and 6678.2 ± 6162 ?g/g. These values were significantly higher than those obtained from the never-smoker group. EC levels in the lung and pack-years of cigarette smoking correlated significantly, as did EC levels and the severity of small airway disease. This study provides one of the first quantitative assessments of EC in human lungs from populations at high relative risk for the development of chronic lung disease.
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Cytotoxic effect of poly-dispersed single walled carbon nanotubes on erythrocytes in vitro and in vivo.
PLoS ONE
PUBLISHED: 03-11-2011
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Single wall Carbon Nanotubes (SWCNTs) are hydrophobic and do not disperse in aqueous solvents. Acid functionalization of SWCNTs results in attachment of carboxy and sulfonate groups to carbon atoms and the resulting acid functionalized product (AF-SWCNTs) is negatively charged and disperses easily in water and buffers. In the present study, effect of AF-SWCNTs on blood erythrocytes was examined. Incubation of mouse erythrocytes with AF-SWCNTs and not with control SWCNTs, resulted in a dose and time dependent lysis of erythrocyte. Using fluorescence tagged AF-SWCNTs, binding of AF-SWCNTs with erythrocytes could be demonstrated. Confocal microscopy results indicated that AF-SWCNTs could enter the erythrocytes. Treatment with AF-SWCNTs resulted in exposure of hydrophobic patches on erythrocyte membrane that is indicative of membrane damage. A time and dose dependent increase in externalization of phosphatidylserine on erythrocyte membrane bilayer was also found. Administration of AF-SWCNTs through intravenous route resulted in a transient anemia as seen by a sharp decline in blood erythrocyte count accompanied with a significant drop in blood haemoglobin level. Administration of AF-SWCNTs through intratracheal administration also showed significant decline in RBC count while administration through other routes (gavage and intra-peritoneal) was not effective. By using a recently developed technique of a two step in vivo biotinylation of erythrocytes that enables simultaneous enumeration of young (age <10 days) and old (age>40 days) erythrocytes in mouse blood, it was found that the in vivo toxic effect of AF-SWCNTs was more pronounced on older subpopulation of erythrocytes. Subpopulation of old erythrocytes fell after treatment with AF-SWCNTs but recovered by third day after the intravenous administration of AF-SWCNTs. Taken together our results indicate that treatment with AF-SWCNTs results in acute membrane damage and eventual lysis of erythrocytes. Intravenous administration of AF-SWCNTs resulted in a transient anemia in which older erythrocytes are preferably lysed.
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Technique of abdominal hysterectomy for non-puerperal uterine inversion.
BMJ Case Rep
PUBLISHED: 01-01-2011
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A 52-year-old postmenopausal woman presented with lower abdominal pain, bleeding per-vaginum and a mass protruding per-vaginum of 1-week duration. A clinical diagnosis of non-puerperal uterine inversion due to fundal leiomyoma was made. Non-puerperal uterine inversion is a rare clinical condition and usually follows a benign or malignant mass attached to the fundus of uterus. Surgical procedures described in the literature use different techniques to first reposition the uterus followed by hysterectomy. However, repositioning the uterus is not always successful. Surgery for inverted uterus is technically difficult due to close proximity of the ureters to the ovarian and uterine vessels due to traction on the vascular pedicles, difficulty in repositioning the uterus and constraints of mobilising the bladder down due to the inverted uterus. This paper illustrates the salient steps of surgery to safely accomplish abdominal hysterectomy without repositioning the uterus to treat this rare condition.
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Differential pulmonary retention of diesel exhaust particles in Wistar Kyoto and spontaneously hypertensive rats.
Toxicol. Sci.
PUBLISHED: 07-27-2009
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Spontaneously hypertensive (SH) and normotensive Wistar Kyoto (WKY) rats have been used for understanding the mechanisms of variations in susceptibility to airborne pollutants. We examined the lung burden of diesel exhaust particles (DEP) following inhalation of diesel engine exhaust (DEE) in both strains. The kinetics of clearance was also examined after single intratracheal (IT) instillation of DEP. Lungs were analyzed for DEP elemental carbon (EC) after exposure to DEE (0, 500, or 2000 microg/m(3) 4 h/day, 5 days/week x 4 weeks). SH rats had 16% less DEP-EC at 500 and 32% less at 2000 microg/m(3) in the lungs, despite having 50% higher than the average minute volume. No strain-related differences were noted in number of alveolar macrophages or their average DEP load as evident from examining cells in bronchoalveolar lavage fluid (BALF). The kinetics of DEP clearance from lungs of male WKY and SH rats was studied following a single instillation at 0.0 or 8.33 mg/kg of DEP standard reference material (SRM 2975) from the National Institute of Standards Technology. SH rats cleared 60% DEP over 112 days while minimal clearance occurred from the lungs of WKY. The pattern of DEP-induced inflammatory response assessed by BALF analysis was similar in both strains, although the overall protein leak was slightly greater in SH rats. A time-dependent accumulation of DEP occurred in tracheal lymph nodes of both strains (SH > WKY). Thus, SH rats may clear DEP more efficiently from their lungs than normotensive WKY rats, with a small contribution of more effective lymphatic drainage.
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Influence of acid functionalization on the cardiopulmonary toxicity of carbon nanotubes and carbon black particles in mice.
Toxicol. Appl. Pharmacol.
PUBLISHED: 05-14-2009
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Engineered carbon nanotubes are being developed for a wide range of industrial and medical applications. Because of their unique properties, nanotubes can impose potentially toxic effects, particularly if they have been modified to express functionally reactive chemical groups on their surface. The present study was designed to evaluate whether acid functionalization (AF) enhanced the cardiopulmonary toxicity of single-walled carbon nanotubes (SWCNT) as well as control carbon black particles. Mice were exposed by oropharyngeal aspiration to 10 or 40 microg of saline-suspended single-walled carbon nanotubes (SWCNTs), acid-functionalized SWCNTs (AF-SWCNTs), ultrafine carbon black (UFCB), AF-UFCB, or 2 microg LPS. 24 hours later, pulmonary inflammatory responses and cardiac effects were assessed by bronchoalveolar lavage and isolated cardiac perfusion respectively, and compared to saline or LPS-instilled animals. Additional mice were assessed for histological changes in lung and heart. Instillation of 40 microg of AF-SWCNTs, UFCB and AF-UFCB increased percentage of pulmonary neutrophils. No significant effects were observed at the lower particle concentration. Sporadic clumps of particles from each treatment group were observed in the small airways and interstitial areas of the lungs according to particle dose. Patches of cellular infiltration and edema in both the small airways and in the interstitium were also observed in the high dose group. Isolated perfused hearts from mice exposed to 40 microg of AF-SWCNTs had significantly lower cardiac functional recovery, greater infarct size, and higher coronary flow rate than other particle-exposed animals and controls, and also exhibited signs of focal cardiac myofiber degeneration. No particles were detected in heart tissue under light microscopy. This study indicates that while acid functionalization increases the pulmonary toxicity of both UFCB and SWCNTs, this treatment caused cardiac effects only with the AF-carbon nanotubes. Further experiments are needed to understand the physico-chemical processes involved in this phenomenon.
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Voltage gated calcium channels negatively regulate protective immunity to Mycobacterium tuberculosis.
PLoS ONE
PUBLISHED: 01-16-2009
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Mycobacterium tuberculosis modulates levels and activity of key intracellular second messengers to evade protective immune responses. Calcium release from voltage gated calcium channels (VGCC) regulates immune responses to pathogens. In this study, we investigated the roles of VGCC in regulating protective immunity to mycobacteria in vitro and in vivo. Inhibiting L-type or R-type VGCC in dendritic cells (DCs) either using antibodies or by siRNA increased calcium influx in an inositol 1,4,5-phosphate and calcium release calcium activated channel dependent mechanism that resulted in increased expression of genes favoring pro-inflammatory responses. Further, VGCC-blocked DCs activated T cells that in turn mediated killing of M. tuberculosis inside macrophages. Likewise, inhibiting VGCC in infected macrophages and PBMCs induced calcium influx, upregulated the expression of pro-inflammatory genes and resulted in enhanced killing of intracellular M. tuberculosis. Importantly, compared to healthy controls, PBMCs of tuberculosis patients expressed higher levels of both VGCC, which were significantly reduced following chemotherapy. Finally, blocking VGCC in vivo in M. tuberculosis infected mice using specific antibodies increased intracellular calcium and significantly reduced bacterial loads. These results indicate that L-type and R-type VGCC play a negative role in M. tuberculosis infection by regulating calcium mobilization in cells that determine protective immunity.
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A Double in vivo Biotinylation Technique for Objective Assessment of Aging and Clearance of Mouse Erythrocytes in Blood Circulation.
Transfus Med Hemother
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We have recently developed a new technique to objectively identify erythrocyte cohorts of defined age in mouse blood. The technique (termed double in vivo biotinylation, DIB) involves an initial biotinylation of all erythrocytes in circulation, followed after a few days by a second biotinylation, at a lower density, that labels the biotin-negative erythrocytes that have entered since the first biotinylation. The proportions of biotin(high), biotin(low), and biotin(negative) erythrocytes are enumerated by flow cytometry. The DIB technique allows us to track age-related changes on erythrocyte cohorts (Protocol A), and to simultaneously identify very young and older erythrocyte populations in the blood (Protocol B). Using this technique, we have reexamined: i) the relationship between age and buoyant density of erythrocytes, ii) erythrocyte destruction through a random removal mechanism, and iii) the expression of phosphatidylserine on aging erythrocytes. We have also used the DIB technique to study age-related changes in the expression of various markers like CD47 and CD147 and green autofluorescence in aging erythrocyte populations.
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Interactions of polydispersed single-walled carbon nanotubes with T cells resulting in downregulation of allogeneic CTL responses in vitro and in vivo.
Nanotoxicology
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Addition of polydispersed acid functionalised single-walled carbon nanotubes (AF-SWCNTs) significantly suppressed alloimmune cytotoxic T cell (CTL) response generated in a mixed lymphocyte reaction (MLR) between spleen cells from C57BL/6 (H-2(b)) and BALB/c (H-2(d)) mice. AF-SWCNTs treatment also decreased CD69 expression, enhanced apoptotic response in T cells and reduced significantly the recovery of live CD4? and CD8? T cells from MLR cultures. A two to threefold increase was noticed in the binding/uptake of AF-SWCNTs by T cells in MLR cultures as compared with control cultured T cells. Confocal microscopy confirmed the internalization of AF-SWCNTs by live CD8? T cells in MLR cultures. Administration of AF-SWCNTs suppressed the generation of anti-P815 CTL response in C57BL/6 mice and the recovery of T-cell populations from the spleens. The results demonstrate a suppressive effect of AF-SWCNTs on CTL response and provide an insight into the mechanism of this suppression.
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Loss of proliferation and antigen presentation activity following internalization of polydispersed carbon nanotubes by primary lung epithelial cells.
PLoS ONE
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Interactions between poly-dispersed acid functionalized single walled carbon nanotubes (AF-SWCNTs) and primary lung epithelial (PLE) cells were studied. Peritoneal macrophages (PMs, known phagocytic cells) were used as positive controls in this study. Recovery of live cells from cultures of PLE cells and PMs was significantly reduced in the presence of AF-SWCNTs, in a time and dose dependent manner. Both PLE cells as well as PMs could take up fluorescence tagged AF-SWCNTs in a time dependent manner and this uptake was significantly blocked by cytochalasin D, an agent that blocks the activity of acto-myosin fibers and therefore the phagocytic activity of cells. Confocal microscopic studies confirmed that AF-SWCNTs were internalized by both PLE cells and PMs. Intra-trachially instilled AF-SWCNTs could also be taken up by lung epithelial cells as well as alveolar macrophages. Freshly isolated PLE cells had significant cell division activity and cell cycling studies indicated that treatment with AF-SWCNTs resulted in a marked reduction in S-phase of the cell cycle. In a previously standardized system to study BCG antigen presentation by PLE cells and PMs to sensitized T helper cells, AF-SWCNTs could significantly lower the antigen presentation ability of both cell types. These results show that mouse primary lung epithelial cells can efficiently internalize AF-SWCNTs and the uptake of nanotubes interfered with biological functions of PLE cells including their ability to present BCG antigens to sensitized T helper cells.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.