Pärt: Chamber and Orchestral Works / Robert Cowan

Index Scriptorium Estoniae

Cowan, Robert

1994-01-01

Uuest heliplaadist "Pärt: Chamber and Orchestral Works. Bournemouth Sinfonietta, Richard Studt. EMI Eminence CD CD-EMX 2221; Fratres; Cantus in memory of Benjamin Britten; Summa; Spiegel im Spiegel; Festina lente; Tabula Rasa; Fratres - selected comparison: Bachmann, Kibonoff (12/94)(CATA) 09026 61824-2. Kremer, Jarrett (ECM) 817 764-2

Movement is the glue connecting home ranges and habitat selection.

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Van Moorter, Bram; Rolandsen, Christer M; Basille, Mathieu; Gaillard, Jean-Michel

2016-01-01

Animal space use has been studied by focusing either on geographic (e.g. home ranges, species' distribution) or on environmental (e.g. habitat use and selection) space. However, all patterns of space use emerge from individual movements, which are the primary means by which animals change their environment. Individuals increase their use of a given area by adjusting two key movement components: the duration of their visit and/or the frequency of revisits. Thus, in spatially heterogeneous environments, animals exploit known, high-quality resource areas by increasing their residence time (RT) in and/or decreasing their time to return (TtoR) to these areas. We expected that spatial variation in these two movement properties should lead to observed patterns of space use in both geographic and environmental spaces. We derived a set of nine predictions linking spatial distribution of movement properties to emerging space-use patterns. We predicted that, at a given scale, high variation in RT and TtoR among habitats leads to strong habitat selection and that long RT and short TtoR result in a small home range size. We tested these predictions using moose (Alces alces) GPS tracking data. We first modelled the relationship between landscape characteristics and movement properties. Then, we investigated how the spatial distribution of predicted movement properties (i.e. spatial autocorrelation, mean, and variance of RT and TtoR) influences home range size and hierarchical habitat selection. In landscapes with high spatial autocorrelation of RT and TtoR, a high variation in both RT and TtoR occurred in home ranges. As expected, home range location was highly selective in such landscapes (i.e. second-order habitat selection); RT was higher and TtoR lower within the selected home range than outside, and moose home ranges were small. Within home ranges, a higher variation in both RT and TtoR was associated with higher selectivity among habitat types (i.e. third-order habitat

Selection of reference genes for quantitative real time RT-PCR during dimorphism in the zygomycete Mucor circinelloides.

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Valle-Maldonado, Marco I; Jácome-Galarza, Irvin E; Gutiérrez-Corona, Félix; Ramírez-Díaz, Martha I; Campos-García, Jesús; Meza-Carmen, Víctor

2015-03-01

Mucor circinelloides is a dimorphic fungal model for studying several biological processes including cell differentiation (yeast-mold transitions) as well as biodiesel and carotene production. The recent release of the first draft sequence of the M. circinelloides genome, combined with the availability of analytical methods to determine patterns of gene expression, such as quantitative Reverse transcription-Polymerase chain reaction (qRT-PCR), and the development of molecular genetic tools for the manipulation of the fungus, may help identify M. circinelloides gene products and analyze their relevance in different biological processes. However, no information is available on M. circinelloides genes of stable expression that could serve as internal references in qRT-PCR analyses. One approach to solve this problem consists in the use of housekeeping genes as internal references. However, validation of the usability of these reference genes is a fundamental step prior to initiating qRT-PCR assays. This work evaluates expression of several constitutive genes by qRT-PCR throughout the morphological differentiation stages of M. circinelloides; our results indicate that tfc-1 and ef-1 are the most stable genes for qRT-PCR assays during differentiation studies and they are proposed as reference genes to carry out gene expression studies in this fungus.

Selection and Verification of Candidate Reference Genes for Mature MicroRNA Expression by Quantitative RT-PCR in the Tea Plant (Camellia sinensis

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Hui Song

2016-05-01

Full Text Available Quantitative reverse transcription-polymerase chain reaction (qRT-PCR is a rapid and sensitive method for analyzing microRNA (miRNA expression. However, accurate qRT-PCR results depend on the selection of reliable reference genes as internal positive controls. To date, few studies have identified reliable reference genes for differential expression analysis of miRNAs among tissues, and among experimental conditions in plants. In this study, three miRNAs and four non-coding small RNAs (ncRNA were selected as reference candidates, and the stability of their expression was evaluated among different tissues and under different experimental conditions in the tea plant (Camellia sinensis using the geNorm and NormFinder programs. It was shown that miR159a was the best single reference gene in the bud to the fifth leaf, 5S rRNA was the most suitable gene in different organs, miR6149 was the most stable gene when the leaves were attacked by Ectropis oblique and U4, miR5368n and miR159a were the best genes when the leaves were treated by methyl jasmonate (MeJA, salicylic acid (SA and abscisic acid (ABA, respectively. Our results provide suitable reference genes for future investigations on miRNA functions in tea plants.

Selection of reliable reference genes for RT-qPCR studies in Octopus vulgaris paralarvae during development and immune-stimulation.

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García-Fernández, P; Castellanos-Martínez, S; Iglesias, J; Otero, J J; Gestal, C

2016-07-01

The common octopus, Octopus vulgaris is a new candidate species for aquaculture. However, rearing of octopus paralarvae is hampered by high mortality and poor growth rates that impede its entire culture. The study of genes involved in the octopus development and immune response capability could help to understand the key of paralarvae survival and thus, to complete the octopus life cycle. Quantitative real-time PCR (RT-qPCR) is the most frequently tool used to quantify the gene expression because of specificity and sensitivity. However, reliability of RT-qPCR requires the selection of appropriate normalization genes whose expression must be stable across the different experimental conditions of the study. Hence, the aim of the present work is to evaluate the stability of six candidate genes: β-actin (ACT), elongation factor 1-α (EF), ubiquitin (UBI), β-tubulin (TUB), glyceraldehyde 3-phosphate dehydrogenase (GADPH) and ribosomal RNA 18 (18S) in order to select the best reference gene. The stability of gene expression was analyzed using geNorm, NormFinder and Bestkeeper, in octopus paralarvae of seven developmental stages (embryo, paralarvae of 0, 10, 15, 20, 30 and 34days) and paralarvae of 20days after challenge with Vibrio lentus and Vibrio splendidus. The results were validated by measuring the expression of PGRP, a stimuli-specific gene. Our results showed UBI, EF and 18S as the most suitable reference genes during development of octopus paralarvae, and UBI, ACT and 18S for bacterial infection. These results provide a basis for further studies exploring molecular mechanism of their development and innate immune defense. Copyright © 2016 Elsevier Inc. All rights reserved.

Evidence based selection of commonly used RT-qPCR reference genes for the analysis of mouse skeletal muscle.

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Kristen C Thomas

Full Text Available The ability to obtain accurate and reproducible data using quantitative real-time Polymerase Chain Reaction (RT-qPCR is limited by the process of data normalization. The use of 'housekeeping' or 'reference' genes is the most common technique used to normalize RT-qPCR data. However, commonly used reference genes are often poorly validated and may change as a result of genetic background, environment and experimental intervention. Here we present an analysis of 10 reference genes in mouse skeletal muscle (Actb, Aldoa, Gapdh, Hprt1, Ppia, Rer1, Rn18s, Rpl27, Rpl41 and Rpl7L1, which were identified as stable either by microarray or in the literature. Using the MIQE guidelines we compared wild-type (WT mice across three genetic backgrounds (R129, C57BL/6j and C57BL/10 as well as analyzing the α-actinin-3 knockout (Actn3 KO mouse, which is a model of the common null polymorphism (R577X in human ACTN3. Comparing WT mice across three genetic backgrounds, we found that different genes were more tightly regulated in each strain. We have developed a ranked profile of the top performing reference genes in skeletal muscle across these common mouse strains. Interestingly the commonly used reference genes; Gapdh, Rn18s, Hprt1 and Actb were not the most stable. Analysis of our experimental variant (Actn3 KO also resulted in an altered ranking of reference gene suitability. Furthermore we demonstrate that a poor reference gene results in increased variability in the normalized expression of a gene of interest, and can result in loss of significance. Our data demonstrate that reference genes need to be validated prior to use. For the most accurate normalization, it is important to test several genes and use the geometric mean of at least three of the most stably expressed genes. In the analysis of mouse skeletal muscle, strain and intervention played an important role in selecting the most stable reference genes.

STAR-RT: Visual attention for real-time video game playing

OpenAIRE

Kotseruba, Iuliia; Tsotsos, John K.

2017-01-01

In this paper we present STAR-RT - the first working prototype of Selective Tuning Attention Reference (STAR) model and Cognitive Programs (CPs). The Selective Tuning (ST) model received substantial support through psychological and neurophysiological experiments. The STAR framework expands ST and applies it to practical visual tasks. In order to do so, similarly to many cognitive architectures, STAR combines the visual hierarchy (based on ST) with the executive controller, working and short-...

A prospective randomized study of postoperative adjuvant chemo-radiotherapy (CT+RT) vs. radiotherapy(RT) alone in resected stage II and IIIA non-small cell lung cancer (NSCLC)

International Nuclear Information System (INIS)

Chang, Geol Lee; Joo, Hang Kim; Kyung, Young Chung; Doo, Yun Lee; Kil, Dong Kim; Won, Young Lee; Sung, Kyu Kim; Sei, Kyu Kim; Gwi, Eon Kim

1995-01-01

Objective: A prospective randomized study has been conducted to compare the results of treatment between CT+RT and RT alone as an adjuvant setting in completely resected stage II and IIIA NSCLC. Materials and Methods: Patients who had completely resected stage II and IIIA NSCLC were randomized into a CT+RT arm(arm A) and a RT alone arm(arm B) as an adjuvant setting after stratification according to cell type(squamous vs. non-squamous) and stage(II vs. IIIA). CT(Etoposide 100mg/m2 I.V. infusion d1-3, Cisplatin 20mg/m2 I.V. infusion d1-5, total 6cycles) was started in postop. 3 weeks with a 4 weeks interval. RT(5040cGy/5-6wks, 180cGy/fr) was started in postoperative 5 weeks after the first cycle of CT for group A and in postoperative 4 weeks for group B. A total of 69 patients were registered from Sep. 1990 to Jun. 1993. Sixty five of these patients were evaluable because 4 patients were ineligible due to distant metastasis before adjuvant treatment. Two patients who refused adjuvant treatment were included in this study to avoid selection bias. Results: Sixteen patients (48%) have received CT of more than 3 cycles and 51 patients(78%) have received RT of more than 50Gy. Four patients died due to treatment-related complications [broncho-pleural fistula 3(arm A:B=2:1), pneumonia 1(arm A)]. Survival and the patterns of failure are as follows: Conclusion: There is no statistical significance in either the overall survival or the patterns of failure between the CT+RT arm and RT alone arm as an adjuvant setting in resected stage II and IIIA NSCLC

Node Ranking Tool - NoRT

Science.gov (United States)

2018-03-23

NoRT) that was developed as part of the Applied Network Science 6.2 base program work unit at NRL, Code 5580. We explain the theory of NoRT and how...to use it. 23-03-2018 Memorandum Report TOPSIS, Social Network, Sensor Network, Centrality, Diffusion, Disease, Virus, Expectation , Pandemic...base program work unit at NRL. We explain the theory of NoRT and how to use it. Index Terms TOPSIS, Social Network, Sensor Network, Centrality, Diffusion

MZC Gel Inhibits SHIV-RT and HSV-2 in Macaque Vaginal Mucosa and SHIV-RT in Rectal Mucosa.

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Calenda, Giulia; Villegas, Guillermo; Barnable, Patrick; Litterst, Claudia; Levendosky, Keith; Gettie, Agegnehu; Cooney, Michael L; Blanchard, James; Fernández-Romero, José A; Zydowsky, Thomas M; Teleshova, Natalia

2017-03-01

The Population Council's microbicide gel MZC (also known as PC-1005) containing MIV-150 and zinc acetate dihydrate (ZA) in carrageenan (CG) has shown promise as a broad-spectrum microbicide against HIV, herpes simplex virus (HSV), and human papillomavirus. Previous data show antiviral activity against these viruses in cell-based assays, prevention of vaginal and rectal simian-human immunodeficiency virus reverse transcriptase (SHIV-RT) infection, and reduction of vaginal HSV shedding in rhesus macaques and also excellent antiviral activity against HSV and human papillomavirus in murine models. Recently, we demonstrated that MZC is safe and effective against SHIV-RT in macaque vaginal explants. Here we established models of ex vivo SHIV-RT/HSV-2 coinfection of vaginal mucosa and SHIV-RT infection of rectal mucosa in macaques (challenge of rectal mucosa with HSV-2 did not result in reproducible tissue infection), evaluated antiviral activity of MZC, and compared quantitative polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay readouts for monitoring SHIV-RT infection. MZC (at nontoxic dilutions) significantly inhibited SHIV-RT in vaginal and rectal mucosas and HSV-2 in vaginal mucosa when present during viral challenge. Analysis of SHIV-RT infection and MZC activity by 1-step simian immunodeficiency virus gag quantitative RT-PCR and p27 enzyme-linked immunosorbent assay demonstrated similar virus growth dynamics and MZC activity by both methods and higher sensitivity of quantitative RT-PCR. Our data provide more evidence that MZC is a promising dual compartment multipurpose prevention technology candidate.

RT-PCR Detection of HIV in Republic of Macedonia

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Golubinka Bosevska

2008-11-01

Full Text Available The aim of the study was to detect HIV RNA in seropositive patients using RT-PCR method and thus, to establish PCR methodology in the routine laboratory works.The total of 33 examined persons were divided in two groups: 1 13 persons seropositive for HIV; and 2 20 healthy persons - randomly selected blood donors that made the case control group. The subjects age was between 25 and 52 years (average 38,5.ELFA test for combined detection of HIV p24 antigen and anti HIV-1 + 2 IgG and ELISA test for detection of antibodies against HIV-1 and HIV-2, were performed for each examined person. RNA from the whole blood was extracted using a commercial kit based on salt precipitation. Detection of HIV RNA was performed using RT-PCR kit. Following nested PCR, the product was separated by electrophoresis in 1,5 % agarose gel. The result was scored positive if the band of 210bp was visible regardless of intensity Measures of precaution were taken during all the steps of the work and HIV infected materials were disposed of accordingly.In the group of blood donors ELFA, ELISA and RT-PCR were negative. Assuming that prevalence of HIV infection is zero, the clinical specificity of RT-PCR is 100 %. The analytical specificity of RT-PCR method was tested against Hepatitis C and B, Human Papiloma Virus, Cytomegalovirus, Herpes Simplex Virus, Rubella Virus, Mycobacterium tuberculosis, Chlamydia trachomatis. None of these templates yielded amplicon. In the group of 13 seropositive persons, 33 samples were analyzed. HIV RNA was detected in 15 samples. ELISA and ELFA test were positive in all samples. Different aliquots of the samples were tested independently and showed the same results. After different periods of storing the RNA samples at -70°C, RT-PCR reaction was identical to the one performed initially. The obtained amplicons were maintained frozen at -20°C for a week and the subsequently performed electrophoresis was identical to the previous one. The reaction is

Challenges in Transitioning Research Data to Operations: The SPoRT Paradigm

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Jedloved, Gary J.; Smith, Matt; McGrath, Kevin

2010-01-01

Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the NASA Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral data from EOS satellites to improve short-term weather forecasts on a regional and local scale. With the ever-broadening application of real-time high resolution satellite data from current EOS and planned NPP, JPSS, and GOES-R sensors to weather forecast problems, significant challenges arise in the acquisition, delivery, and integration of the new capabilities into the decision making process of the operational weather community. For polar orbiting sensors such as MODIS, AIRS, VIIRS, and CRiS, the use of direct broadcast ground stations is key to the real-time delivery of the data and derived products in a timely fashion. With the ABI on the geostationary GOES-R satellite, the data volume will likely increase by a factor of 5- 10 from current data streams. However, the high data volume and limited bandwidth of end user facilities presents a formidable obstacle to timely access to the data. This challenge can be addressed through the use of subsetting techniques, innovative web services, and the judicious selection of data formats. Many of these approaches have been implemented by SPoRT for the delivery of real-time products to NWS forecast offices and other weather entities. Once available in decision support systems like AWIPS II, these new data and products must be integrated into existing and new displays that allow for the integration of the data with existing operational products in these systems. SPoRT is leading the way in demonstrating this enhanced capability. This paper will highlight the ways SPoRT is overcoming many of the challenges presented by the enormous data volumes of

Short-Term Prediction Research and Transition (SPoRT) Center: Transitioning Satellite Data to Operations

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Zavodsky, Bradley

2012-01-01

The Short-term Prediction Research and Transition (SPoRT) Center located at NASA Marshall Space Flight Center has been conducting testbed activities aimed at transitioning satellite products to National Weather Service operational end users for the last 10 years. SPoRT is a NASA/NOAA funded project that has set the bar for transition of products to operational end users through a paradigm of understanding forecast challenges and forecaster needs, displaying products in end users decision support systems, actively assessing the operational impact of these products, and improving products based on forecaster feedback. Aiming for quality partnerships rather than a large quantity of data users, SPoRT has become a community leader in training operational forecasters on the use of up-and-coming satellite data through the use of legacy instruments and proxy data. Traditionally, SPoRT has supplied satellite imagery and products from NASA instruments such as the Moderate-resolution Imaging Spectroradiometer (MODIS) and the Atmospheric Infrared Sounder (AIRS). However, recently, SPoRT has been funded by the GOES-R and Joint Polar Satellite System (JPSS) Proving Grounds to accelerate the transition of selected imagery and products to help improve forecaster awareness of upcoming operational data from the Visible Infrared Imager Radiometer Suite (VIIRS), Cross-track Infrared Sounder (CrIS), Advanced Baseline Imager (ABI), and Geostationary Lightning Mapper (GLM). This presentation provides background on the SPoRT Center, the SPoRT paradigm, and some example products that SPoRT is excited to work with forecasters to evaluate.

Selection of reference genes for RT-qPCR analysis in the monarch butterfly, Danaus plexippus (L.), a migrating bio-indicator

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Quantitative real-time PCR (qRT-PCR) is a reliable and reproducible technique for measuring and evaluating changes in gene expression. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. In this study, expres...

Breath-hold technique in conventional APPA or intensity-modulated radiotherapy for Hodgkin's lymphoma. Comparison of ILROG IS-RT and the GHSG IF-RT

Energy Technology Data Exchange (ETDEWEB)

Kriz, Jan; Spickermann, Max; Lehrich, Philipp; Reinartz, Gabriele; Eich, Hans; Haverkamp, Uwe [University of Muenster, Department of Radiation Oncology, Muenster (Germany); Schmidberger, Heinz [University Mainz, Department of Radiation Oncology, Mainz (Germany)

2015-09-15

The present study addresses the role of intensity-modulated radiotherapy (IMRT) in contrast to standard RT (APPA) for patients with Hodgkin's lymphoma (HL) with a focus on deep inspiration breath-hold (DIBH) technique and a comparison between the International Lymphoma Radiation Oncology Group (ILROG) Involved Site Radiotherapy (IS-RT) versus the German Hodgkin Study Group (GHSG) Involved Field Radiotherapy (IF-RT). APPA treatment and 2 IMRT plans were compared for 11 patients with HL. Furthermore, treatment with DIBH versus free breathing (FB) and two different treatment volumes, i.e. IF-RT versus IS-RT, were compared. IMRT was planned as a sliding-window technique with 5 and 7 beam angles. For each patient 12 different treatment plans were calculated (132 plans). Following organs at risk (OAR) were analysed: lung, heart, spinal cord, oesophagus, female breast and skin. Comparisons of the different values with regard to dose-volume histograms (DVH), conformity and homogeneity indices were made. IS-RT reduces treatment volumes. With respect to the planning target volume (PTV), IMRT achieves better conformity but the same homogeneity. Regarding the D{sub mean} for the lung, IMRT shows increased doses, while RT in DIBH reduces doses. The IMRT shows improved values for D{sub max} concerning the spinal cord, whereas the APPA shows an improved D{sub mean} of the lung and the female breast. IS-RT reduces treatment volumes. Intensity-modulated radiotherapy shows advantages in the conformity. Treatment in DIBH also reduces the dose applied to the lungs and the heart. (orig.) [German] Ziel dieser Auswertung ist es, die konventionelle APPA-Feldanordnung mit der Intensitaetsmodulierten Radiotherapie (IMRT) bei Patienten mit Hodgkin-Lymphom (HL) zu vergleichen. Ein besonderer Fokus liegt hierbei auf der Bestrahlung in tiefer Inspiration und Atemanhaltetechnik (DIBH). Des Weiteren wurde die ''Involved-site''-Radiotherapie (IS-RT) der International

A Multiplex RT-PCR Assay for S. aureus, L. monocytogenes, and Salmonella spp. Detection in Raw Milk with Pre-enrichment

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Tian Ding

2017-05-01

Full Text Available This study firstly developed a multiplex real-time PCR (RT-PCR technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus (S. aureus, Listeria monocytogenes (L. monocytogenes and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water in one reaction. Brain heart infusion (BHI broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 102 CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S. aureus, L. monocytogenes, and Salmonella spp. after pre-enrichment. The newly developed multiplex RT-PCR assay was applied to 46 dairy farm environmental samples and raw milk samples covering a wide variety of sample types. The results demonstrated that the multiplex RT-PCR assay coupled with the BHI enrichment broth was suitable for the simultaneous screening of S. aureus, L. monocytogenes, and Salmonella spp. in the pasture environment and in raw milk. The multiplex RT-PCR assay clearly and successfully shortened the total detection time and reduced labor compared to conventional culture-based methods for testing natural samples.

Global Dynamics and International Cooperation Needs of RT Development and Utilization for the Establishment of the Northeast Asia RT Hub in Korea

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Kim, Y. K.; Oh, G. B.; Yun, S. W.; Yang, M. H.; Ryu, J. S.; Choi, S. J.; Choi, S. G

2005-11-15

In an effort to achieve the objectives, the following scopes were categorized for in-depth study. First, analysis framework was developed for RT capacity development and international technology cooperation strategy. RT survey checklist and international technology cooperation was analyzed with interviewing and reports of domestic participants recently. Second, RT strategic environment was analyze for East-Asia hub competition/cooperation and developing nations using analysis framework. Korean RT was analyzed using SWOT analysis for establishment of RT hub in Korea. Third, East-Asian nations were classified analyzed by RT categories in standpoint of our country. Technology status and future cooperation plan were discussed about RT application for bio-medicine. Products/technology seminar related to an export was hold about support plan of admission/sales for functional food HemoHIM. This study can be utilized in the establishment of RT hub and development strategy. And it can be also utilized in promotion devising of domestic RT and planning setup for obtaing the international competitive power.

Global Dynamics and International Cooperation Needs of RT Development and Utilization for the Establishment of the Northeast Asia RT Hub in Korea

International Nuclear Information System (INIS)

Kim, Y. K.; Oh, G. B.; Yun, S. W.; Yang, M. H.; Ryu, J. S.; Choi, S. J.; Choi, S. G.

2005-11-01

In an effort to achieve the objectives, the following scopes were categorized for in-depth study. First, analysis framework was developed for RT capacity development and international technology cooperation strategy. RT survey checklist and international technology cooperation was analyzed with interviewing and reports of domestic participants recently. Second, RT strategic environment was analyze for East-Asia hub competition/cooperation and developing nations using analysis framework. Korean RT was analyzed using SWOT analysis for establishment of RT hub in Korea. Third, East-Asian nations were classified analyzed by RT categories in standpoint of our country. Technology status and future cooperation plan were discussed about RT application for bio-medicine. Products/technology seminar related to an export was hold about support plan of admission/sales for functional food HemoHIM. This study can be utilized in the establishment of RT hub and development strategy. And it can be also utilized in promotion devising of domestic RT and planning setup for obtaing the international competitive power

Selection and validation of reference genes for qRT-PCR expression analysis of candidate genes involved in olfactory communication in the butterfly Bicyclus anynana.

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Alok Arun

Full Text Available Real-time quantitative reverse transcription PCR (qRT-PCR is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae, two developmental stages (pupal and adult and two sexes (male and female, all of which were subjected to two food treatments (food stress and control feeding ad libitum. The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the

Selection and validation of reference genes for qRT-PCR expression analysis of candidate genes involved in olfactory communication in the butterfly Bicyclus anynana.

Science.gov (United States)

Arun, Alok; Baumlé, Véronique; Amelot, Gaël; Nieberding, Caroline M

2015-01-01

Real-time quantitative reverse transcription PCR (qRT-PCR) is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera) have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae), two developmental stages (pupal and adult) and two sexes (male and female), all of which were subjected to two food treatments (food stress and control feeding ad libitum). The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the expression

Selective effects of cholinergic modulation on task performance during selective attention.

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Furey, Maura L; Pietrini, Pietro; Haxby, James V; Drevets, Wayne C

2008-03-01

The cholinergic neurotransmitter system is critically linked to cognitive functions including attention. The current studies were designed to evaluate the effect of a cholinergic agonist and an antagonist on performance during a selective visual attention task where the inherent salience of attended/unattended stimuli was modulated. Two randomized, placebo-controlled, crossover studies were performed, one (n=9) with the anticholinesterase physostigmine (1.0 mg/h), and the other (n=30) with the anticholinergic scopolamine (0.4 mc/kg). During the task, two double-exposure pictures of faces and houses were presented side by side. Subjects were cued to attend to either the face or the house component of the stimuli, and were instructed to perform a matching task with the two exemplars from the attended category. The cue changed every 4-7 trials to instruct subjects to shift attention from one stimulus component to the other. During placebo in both studies, reaction time (RT) associated with the first trial following a cued shift in attention was longer than RT associated with later trials (pattention to houses condition (pattention to faces. Scopolamine increased RT relative to placebo selectively during trials greater than one (pattention to faces condition (pselective attention (ie trials greater than 1). Moreover, effects of cholinergic manipulation depend on the selective attention condition (ie faces vs houses), which may suggest that cholinergic activity interacts with stimulus salience. The findings are discussed within the context of the role of acetylcholine both in stimulus processing and stimulus salience, and in establishing attention biases through top-down and bottom-up mechanisms of attention.

Comparison of RT-PCR-Dot blot hybridization based on radioisotope 32P with conventional RT-PCR and commercial ELISA Assays for blood screening of HIV-1

International Nuclear Information System (INIS)

Maria Lina R; Andi Yasmon

2011-01-01

There are many commercial ELISA and rapid test kits that have been used for blood screening; however, the kits can give false positive and negative results. Therefore, RT-PCR (Reverse Transcription Polymerase Chain Reaction) - Dot Blot Hybridization based on radioisotope 32 P (RDBR) method was developed in this research, to compare the method with the conventional RT-PCR and commercial ELISA Enzyme-Linked lmmunosorbent Assay) kit. This method is efficient for screening of large blood specimens and surveillance study. Eighty seven samples were used and serum of the samples were tested by ELISA to detect HIV-1. The HIV-l RNA genome was extracted from plasma samples and tested using the RT-PCR and RDBR methods. Of 87 samples that were tested, the rates of positive testing of the RT-PCR, the RDBR, and the ELISA were 71.26%, 74.71%, and 80.46%, respectively. The RDBR (a combination of RTPCR and dot blot hybridization) was more sensitive than conventional RT-PCR by showing 3.45% in increase number of positive specimens. The results showed that of 9 samples (10.34%) were negative RDBR and positive ELISA, while 4 samples (4.60%) were negative ELISA and positive RDBR. The two methods showed slightly difference in the results but further validation is still needed. However, RDBR has high potential as an alternative method for screening of blood in large quantities when compared to method of conventional RT-PCR and ELISA. (author)

NASA/SPoRt: GOES-R Activities in Support of Product Development, Management, and Training

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Fuell, Kevin; Jedlovec, Gary; Molthan, Andrew; Stano, Geoffrey

2012-01-01

SPoRT is using current capabilities of MODIS and VIIRS, combined with current GOES (i.e. Hybrid Imagery) to demonstrate mesoscale capabilities of future ABI instrument. SPoRT is transitioning RGBs from EUMETSAT standard "recipes" to demonstrate a method to more efficiently handle the increase channels/frequency of ABI. Challenges for RGB production exist. Internal vs. external production, Bit depth needed, Adding quantitative information, etc. SPoRT forming group to address these issues. SPoRT is leading efforts on the application of total lightning in operations and to educate users of this new capability. Training in many forms is used to support testbed activities and is a key part to the transition process.

Association Between RT-Induced Changes in Lung Tissue Density and Global Lung Function

International Nuclear Information System (INIS)

Ma Jinli; Zhang Junan; Zhou Sumin; Hubbs, Jessica L.; Foltz, Rodney J.; Hollis, Donna R.; Light, Kim L.; Wong, Terence Z.; Kelsey, Christopher R.; Marks, Lawrence B.

2009-01-01

Purpose: To assess the association between radiotherapy (RT)-induced changes in computed tomography (CT)-defined lung tissue density and pulmonary function tests (PFTs). Methods and Materials: Patients undergoing incidental partial lung RT were prospectively assessed for global (PFTs) and regional (CT and single photon emission CT [SPECT]) lung function before and, serially, after RT. The percent reductions in the PFT and the average changes in lung density were compared (Pearson correlations) in the overall group and subgroups stratified according to various clinical factors. Comparisons were also made between the CT- and SPECT-based computations using the Mann-Whitney U test. Results: Between 1991 and 2004, 343 patients were enrolled in this study. Of these, 111 patients had a total of 203 concurrent post-RT evaluations of changes in lung density and PFTs available for the analyses, and 81 patients had a total of 141 concurrent post-RT SPECT images. The average increases in lung density were related to the percent reductions in the PFTs, albeit with modest correlation coefficients (range, 0.20-0.43). The analyses also indicated that the association between lung density and PFT changes is essentially equivalent to the corresponding association with SPECT-defined lung perfusion. Conclusion: We found a weak quantitative association between the degree of increase in lung density as defined by CT and the percent reduction in the PFTs.

SPoRT: Transitioning NASA and NOAA Experimental Data to the Operational Weather Community

Science.gov (United States)

Jedlovec, Gary J.

2013-01-01

Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the NASA Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral data from EOS satellites to improve short-term weather forecasts on a regional and local scale. With the ever-broadening application of real-time high resolution satellite data from current EOS, Suomi NPP, and planned JPSS and GOES-R sensors to weather forecast problems, significant challenges arise in the acquisition, delivery, and integration of the new capabilities into the decision making process of the operational weather community. For polar orbiting sensors such as MODIS, AIRS, VIIRS, and CRiS, the use of direct broadcast ground stations is key to the real-time delivery of the data and derived products in a timely fashion. With the ABI on the geostationary GOES-R satellite, the data volumes will likely increase by a factor of 5-10 from current data streams. However, the high data volume and limited bandwidth of end user facilities presents a formidable obstacle to timely access to the data. This challenge can be addressed through the use of subsetting techniques, innovative web services, and the judicious selection of data formats. Many of these approaches have been implemented by SPoRT for the delivery of real-time products to NWS forecast offices and other weather entities. Once available in decision support systems like AWIPS II, these new data and products must be integrated into existing and new displays that allow for the integration of the data with existing operational products in these systems. SPoRT is leading the way in demonstrating this enhanced capability. This paper will highlight the ways SPoRT is overcoming many of the challenges presented by the enormous data

Temperature affects thrombolytic efficacy using rt-PA and eptifibatide, an in vitro study.

Science.gov (United States)

Meunier, Jason M; Chang, Wan-Tsu W; Bluett, Brent; Wenker, Evan; Lindsell, Christopher J; Shaw, George J

2012-09-01

The potential for hypothermia as a neuroprotectant during stroke has led to its increase in clinical use. At the same time, combination pharmaceutical therapies for ischemic stroke using recombinant tissue plasminogen activator (rt-PA), and GP IIb-IIIa inhibitors, such as Eptifibatide (Epf ), are under study. However, there is little data on how the reactions triggered by these agents are impacted by temperature. Here, clot lysis during exposure to the combination of rt-PA and Epf is measured in an in vitro human clot model at hypothermic temperatures. The hypothesis is that lytic efficacy of rt-PA and Epf decreases with decreasing temperature. Whole blood clots from 31 volunteers were exposed to rt-PA (0.5 μg/mL) and Epf (0.63 μg/mL) in human fresh-frozen plasma (rt-PA+Epf ), rt-PA alone in plasma (rt-PA Alone), or to plasma alone (Control), at temperatures from 30°C to 37°C, for 30 minutes. Clot lysis was measured using a microscopic imaging technique; the mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. Temperature had a significant impact on FCL in clots exposed to rt-PA+Epf, with the FCL being lower at 30°C to 36°C than at 37°C. The FCL remained significantly higher for rt-PA+Epf–treated clots than Controls regardless of temperature, with the exception of measurements made at 30°C when no significant differences in the FCL were observed between groups. The use of hypothermia as a neuroprotectant may negatively impact the therapeutic benefit of thrombolytic agents.

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L. caryopses by RT-qPCR method.

Directory of Open Access Journals (Sweden)

Izabela Ruduś

Full Text Available Molecular studies of primary and secondary dormancy in Avena fatua L., a serious weed of cereal and other crops, are intended to reveal the species-specific details of underlying molecular mechanisms which in turn may be useable in weed management. Among others, quantitative real-time PCR (RT-qPCR data of comparative gene expression analysis may give some insight into the involvement of particular wild oat genes in dormancy release, maintenance or induction by unfavorable conditions. To assure obtaining biologically significant results using this method, the expression stability of selected candidate reference genes in different data subsets was evaluated using four statistical algorithms i.e. geNorm, NormFinder, Best Keeper and ΔCt method. Although some discrepancies in their ranking outputs were noticed, evidently two ubiquitin-conjugating enzyme homologs, AfUBC1 and AfUBC2, as well as one homolog of glyceraldehyde 3-phosphate dehydrogenase AfGAPDH1 and TATA-binding protein AfTBP2 appeared as more stably expressed than AfEF1a (translation elongation factor 1α, AfGAPDH2 or the least stable α-tubulin homolog AfTUA1 in caryopses and seedlings of A. fatua. Gene expression analysis of a dormancy-related wild oat transcription factor VIVIPAROUS1 (AfVP1 allowed for a validation of candidate reference genes performance. Based on the obtained results it can be recommended that the normalization factor calculated as a geometric mean of Cq values of AfUBC1, AfUBC2 and AfGAPDH1 would be optimal for RT-qPCR results normalization in the experiments comprising A. fatua caryopses of different dormancy status.

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT-qPCR method.

Science.gov (United States)

Ruduś, Izabela; Kępczyński, Jan

2018-01-01

Molecular studies of primary and secondary dormancy in Avena fatua L., a serious weed of cereal and other crops, are intended to reveal the species-specific details of underlying molecular mechanisms which in turn may be useable in weed management. Among others, quantitative real-time PCR (RT-qPCR) data of comparative gene expression analysis may give some insight into the involvement of particular wild oat genes in dormancy release, maintenance or induction by unfavorable conditions. To assure obtaining biologically significant results using this method, the expression stability of selected candidate reference genes in different data subsets was evaluated using four statistical algorithms i.e. geNorm, NormFinder, Best Keeper and ΔCt method. Although some discrepancies in their ranking outputs were noticed, evidently two ubiquitin-conjugating enzyme homologs, AfUBC1 and AfUBC2, as well as one homolog of glyceraldehyde 3-phosphate dehydrogenase AfGAPDH1 and TATA-binding protein AfTBP2 appeared as more stably expressed than AfEF1a (translation elongation factor 1α), AfGAPDH2 or the least stable α-tubulin homolog AfTUA1 in caryopses and seedlings of A. fatua. Gene expression analysis of a dormancy-related wild oat transcription factor VIVIPAROUS1 (AfVP1) allowed for a validation of candidate reference genes performance. Based on the obtained results it can be recommended that the normalization factor calculated as a geometric mean of Cq values of AfUBC1, AfUBC2 and AfGAPDH1 would be optimal for RT-qPCR results normalization in the experiments comprising A. fatua caryopses of different dormancy status.

Selection of reference genes for quantitative real-time RT-PCR studies in tomato fruit of the genotype MT-Rg1

Directory of Open Access Journals (Sweden)

Karla L. González-Aguilera

2016-09-01

Full Text Available Quantitative real-time RT-PCR (qRT-PCR has become one of the most widely used methods for accurate quantification of gene expression. Since there are no universal reference genes for normalization, the optimal strategy to normalize raw qRT-PCR data is to perform an initial comparison of a set of independent reference genes to assess the most stable ones in each biological model. Normalization of a qRT-PCR experiment helps to ensure that the results are both statistically significant and biologically meaningful. Tomato is the model of choice to study fleshy fruit development. The miniature tomato (Solanum lycopersicum L. cultivar Micro-Tom (MT is considered a model system for tomato genetics and functional genomics. A new genotype, containing the Rg1 allele, improves tomato in vitro regeneration. In this work, we evaluated the expression stability of four tomato reference genes, namely CAC, SAND, Expressed and ACTIN2. We showed that the genes CAC and Exp are the best reference genes of the four we tested during fruit development in the MT-Rg1 genotype. Furthermore, we validated the reference genes by showing that the expression profiles of the transcription factors FRUITFULL1 (FUL1 and APETALA2c (AP2c during fruit development are comparable to previous reports using other tomato cultivars.

Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR

International Nuclear Information System (INIS)

Cicinnati, Vito R; Shen, Qingli; Sotiropoulos, Georgios C; Radtke, Arnold; Gerken, Guido; Beckebaum, Susanne

2008-01-01

Reference genes, which are often referred to as housekeeping genes are frequently used to normalize mRNA levels between different samples in quantitative reverse transcription polymerase chain reaction (qRT-PCR). The selection of reference genes is critical for gene expression studies because the expression of these genes may vary among tissues or cells and may change under certain circumstances. Here, a systematic evaluation of six putative reference genes for gene expression studies in human hepatocellular carcinoma (HCC) is presented. Six genes, beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethyl-bilane synthase (HMBS), hypoxanthine phosphoribosyl-transferase 1 (HPRT1), succinate dehydrogenase complex, subunit A (SDHA) and ubiquitin C (UBC), with distinct functional characteristics and expression patterns were evaluated by qRT-PCR. Inhibitory substances in RNA samples were quantitatively assessed and controlled using an external RNA control. The stability of selected reference genes was analyzed using both geNorm and NormFinder software. HMBS and GAPDH were identified as the optimal reference genes for normalizing gene expression data between paired tumoral and adjacent non-tumoral tissues derived from patients with HCC. HMBS, GAPDH and UBC were identified to be suitable for the normalization of gene expression data among tumor tissues; whereas the combination of HMBS, B2M, SDHA and GAPDH was suitable for normalizing gene expression data among five liver cancer cell lines, namely Hep3B, HepG2, HuH7, SK-HEP-1 and SNU-182. The determined gene stability was increased after exclusion of RNA samples containing relatively higher inhibitory substances. Of six genes studied, HMBS was found to be the single best reference gene for gene expression studies in HCC. The appropriate choice of combination of more than one reference gene to improve qRT-PCR accuracy depends on the kind of liver tissues or cells under investigation

Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR

Directory of Open Access Journals (Sweden)

Radtke Arnold

2008-11-01

Full Text Available Abstract Background Reference genes, which are often referred to as housekeeping genes are frequently used to normalize mRNA levels between different samples in quantitative reverse transcription polymerase chain reaction (qRT-PCR. The selection of reference genes is critical for gene expression studies because the expression of these genes may vary among tissues or cells and may change under certain circumstances. Here, a systematic evaluation of six putative reference genes for gene expression studies in human hepatocellular carcinoma (HCC is presented. Methods Six genes, beta-2-microglobulin (B2M, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, hydroxymethyl-bilane synthase (HMBS, hypoxanthine phosphoribosyl-transferase 1 (HPRT1, succinate dehydrogenase complex, subunit A (SDHA and ubiquitin C (UBC, with distinct functional characteristics and expression patterns were evaluated by qRT-PCR. Inhibitory substances in RNA samples were quantitatively assessed and controlled using an external RNA control. The stability of selected reference genes was analyzed using both geNorm and NormFinder software. Results HMBS and GAPDH were identified as the optimal reference genes for normalizing gene expression data between paired tumoral and adjacent non-tumoral tissues derived from patients with HCC. HMBS, GAPDH and UBC were identified to be suitable for the normalization of gene expression data among tumor tissues; whereas the combination of HMBS, B2M, SDHA and GAPDH was suitable for normalizing gene expression data among five liver cancer cell lines, namely Hep3B, HepG2, HuH7, SK-HEP-1 and SNU-182. The determined gene stability was increased after exclusion of RNA samples containing relatively higher inhibitory substances. Conclusion Of six genes studied, HMBS was found to be the single best reference gene for gene expression studies in HCC. The appropriate choice of combination of more than one reference gene to improve qRT-PCR accuracy depends on the

Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR

Science.gov (United States)

Cicinnati, Vito R; Shen, Qingli; Sotiropoulos, Georgios C; Radtke, Arnold; Gerken, Guido; Beckebaum, Susanne

2008-01-01

Background Reference genes, which are often referred to as housekeeping genes are frequently used to normalize mRNA levels between different samples in quantitative reverse transcription polymerase chain reaction (qRT-PCR). The selection of reference genes is critical for gene expression studies because the expression of these genes may vary among tissues or cells and may change under certain circumstances. Here, a systematic evaluation of six putative reference genes for gene expression studies in human hepatocellular carcinoma (HCC) is presented. Methods Six genes, beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethyl-bilane synthase (HMBS), hypoxanthine phosphoribosyl-transferase 1 (HPRT1), succinate dehydrogenase complex, subunit A (SDHA) and ubiquitin C (UBC), with distinct functional characteristics and expression patterns were evaluated by qRT-PCR. Inhibitory substances in RNA samples were quantitatively assessed and controlled using an external RNA control. The stability of selected reference genes was analyzed using both geNorm and NormFinder software. Results HMBS and GAPDH were identified as the optimal reference genes for normalizing gene expression data between paired tumoral and adjacent non-tumoral tissues derived from patients with HCC. HMBS, GAPDH and UBC were identified to be suitable for the normalization of gene expression data among tumor tissues; whereas the combination of HMBS, B2M, SDHA and GAPDH was suitable for normalizing gene expression data among five liver cancer cell lines, namely Hep3B, HepG2, HuH7, SK-HEP-1 and SNU-182. The determined gene stability was increased after exclusion of RNA samples containing relatively higher inhibitory substances. Conclusion Of six genes studied, HMBS was found to be the single best reference gene for gene expression studies in HCC. The appropriate choice of combination of more than one reference gene to improve qRT-PCR accuracy depends on the kind of liver tissues

Effect of low frequency ultrasound on combined rt-PA and eptifibatide thrombolysis in human clots.

Science.gov (United States)

Meunier, Jason M; Holland, Christy K; Pancioli, Arthur M; Lindsell, Christopher J; Shaw, George J

2009-01-01

Fibrinolytics such as recombinant tissue plasminogen activator (rt-PA) are used to treat thrombotic disease such as acute myocardial infarction (AMI) and ischemic stroke. Interest in increasing efficacy and reducing side effects has led to the study of adjuncts such as GP IIb-IIIa inhibitors and ultrasound (US) enhanced thrombolysis. Currently, GP IIb-IIIa inhibitor and fibrinolytic treatment are often used in AMI, and are under investigation for stroke treatment. However, little is known of the efficacy of combined GP IIb-IIIa inhibitor, fibrinolytic and ultrasound treatment. We measure the lytic efficacy of rt-PA, eptifibatide (Epf) and 120 kHz ultrasound treatment in an in-vitro human clot model. Blood was drawn from 15 subjects after IRB approval. Clots were made in 20 microL pipettes, and placed in a water tank for microscopic visualization during lytic treatment. Clots were exposed to control, rt-PA (rt-PA), eptifibatide (Epf), or rt-PA+eptifibatide (rt-PA + Epf), with (+US) or without (-US) ultrasound for 30 minutes at 37 degrees C in human plasma. Clot lysis was measured over time, using a microscopic imaging technique. The fractional clot loss (FCL) and initial lytic rate (LR) were used to quantify lytic efficacy. LR values for (- US) treated clots were 0.8+/-0.1(control), 1.8+/-0.3 (Epf), 1.5+/-0.2 (rt-PA), and 1.3+/-0.4 (rt-PA + Epf) (% clot width/minute) respectively. In comparison, the (+ US) group exhibited LR values of 1.6+/-0.2 (control), 4.3+/-0.4 (Epf), 6.3+/-0.4 (rt-PA), and 4.6+/-0.6 (rt-PA + Epf). For (- US) treated clots, FCL was 6.0+/-0.8 (control), 9.2+/-2.5 (Epf), 15.6+/-1.7 (rt-PA), and 28.0+/-2.2% (rt-PA + Epf) respectively. FCL for (+ US) clots was 13.5+/-2.4 (control), 20.7+/-6.4 (Epf), 44.4+/-3.6 (rt-PA) and 30.3+/-3.6% (rt-PA + Epf) respectively. Although the addition of eptifibatide enhances the in-vitro lytic efficacy of rt-PA in the absence of ultrasound, the efficacy of ultrasound and rt-PA is greater than that of combined

Arvo Pärt: Kui kannatab üks inimene, siis kannatab kogu maailm! / Arvo Pärt, Nora Pärt ; intervjueerinud Yana Toom, Maarja-Liis Arujärv, Aleksandr Zukerman ; kommenteerinud Edgar Savisaar

Index Scriptorium Estoniae

Pärt, Arvo, 1935-

2010-01-01

Arvo Pärt ja tema abikaasa Nora Pärt andsid Türgis enne Pärdi uudisteose "Aadama itk" esiettekannet intervjuu, kus rääkisid nii nende raskustest Läände elama asumisel kui uudisteose sügavamast mõttest

NASA SPoRT Modeling and Data Assimilation Research and Transition Activities Using WRF, LIS and GSI

Science.gov (United States)

Case, Jonathan L.; Blankenship, Clay B.; Zavodsky, Bradley T.; Srikishen, Jayanthi; Berndt, Emily B.

2014-01-01

weather research and forecasting ===== The NASA Short-term Prediction Research and Transition (SPoRT) program has numerous modeling and data assimilation (DA) activities in which the WRF model is a key component. SPoRT generates realtime, research satellite products from the MODIS and VIIRS instruments, making the data available to NOAA/NWS partners running the WRF/EMS, including: (1) 2-km northwestern-hemispheric SST composite, (2) daily, MODIS green vegetation fraction (GVF) over CONUS, and (3) NASA Land Information System (LIS) runs of the Noah LSM over the southeastern CONUS. Each of these datasets have been utilized by specific SPoRT partners in local EMS model runs, with select offices evaluating the impacts using a set of automated scripts developed by SPoRT that manage data acquisition and run the NCAR Model Evaluation Tools verification package. SPoRT is engaged in DA research with the Gridpoint Statistical Interpolation (GSI) and Ensemble Kalman Filter in LIS for soil moisture DA. Ongoing DA projects using GSI include comparing the impacts of assimilating Atmospheric Infrared Sounder (AIRS) radiances versus retrieved profiles, and an analysis of extra-tropical cyclones with intense non-convective winds. As part of its Early Adopter activities for the NASA Soil Moisture Active Passive (SMAP) mission, SPoRT is conducting bias correction and soil moisture DA within LIS to improve simulations using the NASA Unified-WRF (NU-WRF) for both the European Space Agency's Soil Moisture Ocean Salinity and upcoming SMAP mission data. SPoRT has also incorporated real-time global GVF data into LIS and WRF from the VIIRS product being developed by NOAA/NESDIS. This poster will highlight the research and transition activities SPoRT conducts using WRF, NU-WRF, EMS, LIS, and GSI.

Comparative evaluation of conventional RT-PCR and real-time RT-PCR (RRT-PCR) for detection of avian metapneumovirus subtype A

OpenAIRE

Ferreira, HL; Spilki, FR; dos Santos, MMAB; de Almeida, RS; Arns, CW

2009-01-01

Avian metapneumovirus (AMPV) belongs to Metapneumovirus genus of Paramyxoviridae family. Virus isolation, serology, and detection of genomic RNA are used as diagnostic methods for AMPV. The aim of the present study was to compare the detection of six subgroup A AMPV isolates (AMPV/A) viral RNA by using different conventional and real time RT-PCR methods. Two new RT-PCR tests and two real time RT-PCR tests, both detecting fusion (F) gene and nucleocapsid (N) gene were compared with an establis...

Real-time RT-PCR, a necessary tool to support the diagnosis and surveillance of rotavirus in Mexico.

Science.gov (United States)

De La Cruz Hernández, Sergio Isaac; Anaya Molina, Yazmin; Gómez Santiago, Fabián; Terán Vega, Heidi Lizbeth; Monroy Leyva, Elda; Méndez Pérez, Héctor; García Lozano, Herlinda

2018-04-01

Rotavirus produces diarrhea in children under 5 years old. Most of those conventional methods such as polyacrylamide gel electrophoresis (PAGE) and reverse transcription-polymerase chain reaction (RT-PCR) have been used for rotavirus detection. However, these techniques need a multi-step process to get the results. In comparison with conventional methods, the real-time RT-PCR is a highly sensitive method, which allows getting the results in only one day. In this study a real-time RT-PCR assay was tested using a panel of 440 samples from patients with acute gastroenteritis, and characterized by PAGE and RT-PCR. The results show that the real-time RT-PCR detected rotavirus from 73% of rotavirus-negative samples analyzed by PAGE and RT-PCR; thus, the percentage of rotavirus-positive samples increased to 81%. The results indicate that this real-time RT-PCR should be part of a routine analysis, and as a support of the diagnosis of rotavirus in Mexico. Copyright © 2017 Elsevier Inc. All rights reserved.

Tantsuime: märjaks nutetud Märt Agu saab 8000 uut sõpra / Märt Agu ; intervjueerinud Rein Sikk

Index Scriptorium Estoniae

Agu, Märt, 1980-

2011-01-01

11. Noorte tantsupeo "Maa ja ilm" üldjuht ja Tallinna Tantsuakadeemia kunstiline juht Märt Agu Tallinna lauluväljakul toimuvast tantsupeost, ülevaatustest, eesti meeste rahvatantsust, oma isast Mait Agust, tema tantsust "Põhjamaa", tantsuõpetaja elukutsest, eesti tantsust, Tallinna Tantsuakadeemiast. Andmeid Märt Agu loomingu kohta

Monitoring and improving the sensitivity of dengue nested RT-PCR used in longitudinal surveillance in Thailand.

Science.gov (United States)

Klungthong, Chonticha; Manasatienkij, Wudtichai; Phonpakobsin, Thipwipha; Chinnawirotpisan, Piyawan; Rodpradit, Prinyada; Hussem, Kittinun; Thaisomboonsuk, Butsaya; Ong-ajchaowlerd, Prapapun; Nisalak, Ananda; Kalayanarooj, Siripen; Buddhari, Darunee; Gibbons, Robert V; Jarman, Richard G; Yoon, In-Kyu; Fernandez, Stefan

2015-02-01

AFRIMS longitudinal dengue surveillance in Thailand depends on the nested RT-PCR and the dengue IgM/IgG ELISA. To examine and improve the sensitivity of the nested RT-PCR using a panel of archived samples collected during dengue surveillance. A retrospective analysis of 16,454 dengue IgM/IgG ELISA positive cases collected between 2000 and 2013 was done to investigate the sensitivity of the nested RT-PCR. From these cases, 318 acute serum specimens or extracted RNA, previously found to be negative by the nested RT-PCR, were tested using TaqMan real-time RT-PCR (TaqMan rRT-PCR). To improve the sensitivity of nested RT-PCR, we designed a new primer based on nucleotide sequences from contemporary strains found to be positive by the TaqMan rRT-PCR. Sensitivity of the new nested PCR was calculated using a panel of 87 samples collected during 2011-2013. The percentage of dengue IgM/IgG ELISA positive cases that were negative by the nested RT-PCR varied from 17% to 42% for all serotypes depending on the year. Using TaqMan rRT-PCR, dengue RNA was detected in 194 (61%) of the 318 acute sera or extracted RNA previously found to be negative by the nested RT-PCR. The newly designed DENV-1 specific primer increased the sensitivity of DENV-1 detection by the nested RT-PCR from 48% to 88%, and of all 4 serotypes from 73% to 87%. These findings demonstrate the impact of genetic diversity and signal erosion on the sensitivity of PCR-based methods. Published by Elsevier B.V.

Canine distemper virus detection by different methods of One-Step RT-qPCR

Directory of Open Access Journals (Sweden)

Claudia de Camargo Tozato

2016-01-01

Full Text Available ABSTRACT: Three commercial kits of One-Step RT-qPCR were evaluated for the molecular diagnosis of Canine Distemper Virus. Using the kit that showed better performance, two systems of Real-time RT-PCR (RT-qPCR assays were tested and compared for analytical sensitivity to Canine Distemper Virus RNA detection: a One-Step RT-qPCR (system A and a One-Step RT-qPCR combined with NESTED-qPCR (system B. Limits of detection for both systems were determined using a serial dilution of Canine Distemper Virus synthetic RNA or a positive urine sample. In addition, the same urine sample was tested using samples with prior centrifugation or ultracentrifugation. Commercial kits of One-Step RT-qPCR assays detected canine distemper virus RNA in 10 (100% urine samples from symptomatic animals tested. The One-Step RT-qPCR kit that showed better results was used to evaluate the analytical sensitivity of the A and B systems. Limit of detection using synthetic RNA for the system A was 11 RNA copies µL-1 and 110 RNA copies µl-1 for first round System B. The second round of the NESTED-qPCR for System B had a limit of detection of 11 copies µl-1. Relationship between Ct values and RNA concentration was linear. The RNA extracted from the urine dilutions was detected in dilutions of 10-3 and10-2 by System A and B respectively. Urine centrifugation increased the analytical sensitivity of the test and proved to be useful for routine diagnostics. The One-Step RT-qPCR is a fast, sensitive and specific method for canine distemper routine diagnosis and research projects that require sensitive and quantitative methodology.

Reference gene identification for reliable normalisation of quantitative RT-PCR data in Setaria viridis.

Science.gov (United States)

Nguyen, Duc Quan; Eamens, Andrew L; Grof, Christopher P L

2018-01-01

Quantitative real-time polymerase chain reaction (RT-qPCR) is the key platform for the quantitative analysis of gene expression in a wide range of experimental systems and conditions. However, the accuracy and reproducibility of gene expression quantification via RT-qPCR is entirely dependent on the identification of reliable reference genes for data normalisation. Green foxtail ( Setaria viridis ) has recently been proposed as a potential experimental model for the study of C 4 photosynthesis and is closely related to many economically important crop species of the Panicoideae subfamily of grasses, including Zea mays (maize), Sorghum bicolor (sorghum) and Sacchurum officinarum (sugarcane). Setaria viridis (Accession 10) possesses a number of key traits as an experimental model, namely; (i) a small sized, sequenced and well annotated genome; (ii) short stature and generation time; (iii) prolific seed production, and; (iv) is amendable to Agrobacterium tumefaciens -mediated transformation. There is currently however, a lack of reference gene expression information for Setaria viridis ( S. viridis ). We therefore aimed to identify a cohort of suitable S. viridis reference genes for accurate and reliable normalisation of S. viridis RT-qPCR expression data. Eleven putative candidate reference genes were identified and examined across thirteen different S. viridis tissues. Of these, the geNorm and NormFinder analysis software identified SERINE / THERONINE - PROTEIN PHOSPHATASE 2A ( PP2A ), 5 '- ADENYLYLSULFATE REDUCTASE 6 ( ASPR6 ) and DUAL SPECIFICITY PHOSPHATASE ( DUSP ) as the most suitable combination of reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. To demonstrate the suitability of the three selected reference genes, PP2A , ASPR6 and DUSP , were used to normalise the expression of CINNAMYL ALCOHOL DEHYDROGENASE ( CAD ) genes across the same tissues. This approach readily demonstrated the suitably of the three

SPoRT's Participation in the GOES-R Proving Ground Activity

Science.gov (United States)

Jedlovec, Gary; Fuell, Kevin; Smith, Matthew; Stano, Geoffrey; Molthan, Andrew

2011-01-01

The next generation geostationary satellite, GOES-R, will carry two new instruments with unique atmospheric and surface observing capabilities, the Advanced Baseline Imager (ABI) and the Geostationary Lightning Mapper (GLM), to study short-term weather processes. The ABI will bring enhanced multispectral observing capabilities with frequent refresh rates for regional and full disk coverage to geostationary orbit to address many existing and new forecast challenges. The GLM will, for the first time, provide the continuous monitoring of total lightning flashes over a hemispherical region from space. NOAA established the GOES-R Proving Ground activity several years ago to demonstrate the new capabilities of these instruments and to prepare forecasters for their day one use. Proving Ground partners work closely with algorithm developers and the end user community to develop and transition proxy data sets representing GOES-R observing capabilities. This close collaboration helps to maximize refine algorithms leading to the delivery of a product that effectively address a forecast challenge. The NASA Short-term Prediction Research and Transition (SPoRT) program has been a participant in the NOAA GOES-R Proving Ground activity by developing and disseminating selected GOES-R proxy products to collaborating WFOs and National Centers. Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the SPoRT program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral data from EOS satellites to improve short-term weather forecasts on a regional and local scale. Participation in the Proving Ground activities extends SPoRT s activities and taps its experience and expertise in diagnostic weather analysis, short-term weather forecasting, and the transition of research and experimental

A376S in the connection subdomain of HIV-1 reverse transcriptase confers increased risk of virological failure to nevirapine therapy

DEFF Research Database (Denmark)

Paredes, Roger; Puertas, Maria Carmen; Bannister, Wendy

2011-01-01

Background. The clinical relevance of mutations in the connection subdomain and the ribonuclease (RNase) H domain of HIV-1 reverse transcriptase (RT) is uncertain. Methods. The risk of virological failure to nonnucleoside RT inhibitor (NNRTI)-based antiretroviral therapy (ART) was evaluated...... in NNRTI-naive patients who started NNRTIs in the EuroSIDA study after July 1997 according to preexisting substitutions in the connection subdomain and the RNase H domain of HIV-1 RT. An observed association between A376S and virological failure was further investigated by testing in vitro NNRTI...... = .013). A376S conferred selective low-level nevirapine resistance in vitro, and led to greater affinity for double-stranded DNA. Conclusions. The A376S substitution in the connection subdomain of HIV-1 RT causes selective nevirapine resistance and confers an increased risk of virological failure...

Incremental clinical value of a dedicated RT planning FDG PET-CT over staging PET-CT in non-small cell lung cancer

International Nuclear Information System (INIS)

Lin, P.; Som, S.; Vinod, S.; Lin, M.; Shon, I. H.

2009-01-01

Full text:Objectives: To evaluate whether FDG-PET performed for radiotherapy planning can detect disease progression, compared with staging PET. Methods: Thirteen patients underwent a planning PET-CT for curative RT ( R T-PET ) within eight weeks of a staging PET-CT for newly diagnosed NSCLC between 10/2007 and 1/2009. All studies were acquired on a Philips GXL PET-CT using the same protocols, except RT-PET is acquired on a RT flat bed. The images were interpreted by consensus readings of two physicians: location/number, visual grading (0-4:3> liver, 4>brain), max transverse diameter ( M ax D ) (tumour margin is delineated by a SUV threshold of 2.5) and max SUV of each lesion. Progressive disease (PD) is defined as >10% increase in max D. Results: RT-PET detected PD (primary or nodal) or new metastases in 8 pts (61%) (mean interval:30.2±14 days, range:7-54 days). For primary tumour, RT-PET detected PD in 5 pts (range: 12-32% increase in max D and 12-39% increase in SUV) and RT-CT detected PD in 3 pts (11-21% increase in max D, paired t test: p = 0.19). Stage-PET detected 28 mediastinal/hilar nodal sites. RT-PET detected PD in 11 of these lesions in 4 pts (31%) and CT detected similar progression in 8 lesions in 2 pts. RT-PET detected 10 new lesions in 3 pts (23%) resulting in upstaging to N3 in 2 pts (supraclavicular and hilar nodes) and M1 in 1 pt (bone). Conclusion: A dedicated RT PET-CT has the potential to detect disease progression and impact on RT planning in a large number of patients.

NASA SPoRT GOES-R Proving Ground Activities

Science.gov (United States)

Stano, Geoffrey T.; Fuell, Kevin K.; Jedloec, Gary J.

2010-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) program is a partner with the GOES-R Proving Ground (PG) helping prepare forecasters understand the unique products to come from the GOES-R instrument suite. SPoRT is working collaboratively with other members of the GOES-R PG team and Algorithm Working Group (AWG) scientists to develop and disseminate a suite of proxy products that address specific forecast problems for the WFOs, Regional and National Support Centers, and other NOAA users. These products draw on SPoRT s expertise with the transition and evaluation of products into operations from the MODIS instrument and the North Alabama Lightning Mapping Array (NALMA). The MODIS instrument serves as an excellent proxy for the Advanced Baseline Imager (ABI) that will be aboard GOES-R. SPoRT has transitioned and evaluated several multi-channel MODIS products. The true and false color products are being used in natural hazard detection by several SPoRT partners to provide better observation of land features, such as fires, smoke plumes, and snow cover. Additionally, many of SPoRT s partners are coastal offices and already benefit from the MODIS sea surface temperature composite. This, along with other surface feature observations will be developed into ABI proxy products for diagnostic use in the forecast process as well as assimilation into forecast models. In addition to the MODIS instrument, the NALMA has proven very valuable to WFOs with access to these total lightning data. These data provide situational awareness and enhanced warning decision making to improve lead times for severe thunderstorm and tornado warnings. One effort by SPoRT scientists includes a lightning threat product to create short-term model forecasts of lightning activity. Additionally, SPoRT is working with the AWG to create GLM proxy data from several of the ground based total lightning networks, such as the NALMA. The evaluation will focus on the vastly improved spatial

POLYCLONAL ANTIBODIES TO DETECT THE CP-RT PROTEIN OF Potato Mop-Top VIRUS ANTICUERPOS POLICLONALES PARA LA DETECCIÓN DE LA PROTEÍNA CP-RT DEL Potato Mop-Top VIRUS

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Derly Andrade Molina

2012-06-01

Full Text Available Abstract. Potato mop-top virus (PMTV causes an important re-emerging disease in potato crops in Colombia due to the increased incidence of its protozoan vector Spongospora subterranea f.sp. subterranea (Sss, the causing agent of Powdery scab disease. For an accurate detection of PMTV it is recommended to combine different diagnostic tests and evaluate multiple samples per plant or tissue. In order to increase the number of available tools for detection of PMTV, antibodies targeting the RT domain of the CP-RT protein were developed in this work. Sequencing of the RT domain from the colombian strain R25 was achieved and using bioinformatic analysis, a potential antigenic region was identified. A peptide mimicking the antigenic region was inoculated in rabbits for the production of polyclonal antibodies. The antibodies were tested by ELISA using Nicotiana benthamiana bait-plants infected with Sss cystosori and potato plants collected in La Unión (Antioquia. The validity of serological tests was confirmed by RT-PCR. A complete sequence of the RT domain and 441 nt of the CP gene were obtained. Phylogenetic analysis identified strain R25 as closely associated to the PMTV lineage distributed worldwide. A total of 19.26 mg of anti-CP-RT polyclonal antibodies useful in detecting PMTV in infected plants were obtained. As CP-RT is involved in transmission of PMTV by Sss, these antibodies will be useful for supporting not only diagnostic programs but also basic and epidemiologic studies aimed at understanding interactions between PMTV and Sss.Resumen. El Potato mop-top virus (PMTV es uno de los virus re-emergentes en los cultivos de papa de Colombia, como resultado del aumento de la incidencia de su vector natural, el protozoo Spongospora subterranea f.sp. mamarinm@unal.edu.co (Sss, agente causal de la Sarna polvosa de la papa. Para la detección del virus se recomienda la realización simultánea de diferentes pruebas, así como la evaluación de m

Reverse transcriptase-quantitative polymerase chain reaction (RT ...

African Journals Online (AJOL)

The reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a highly specific polymerase chain reaction (PCR) method that allows one to detect very low transcription levels of functional gene(s) in soil. RT-qPCR helps us to know the active members of the microbial community, and their activities can be ...

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq data

Directory of Open Access Journals (Sweden)

Perkins James R

2012-07-01

Full Text Available Abstract Background Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s. Results We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html Conclusions These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples.

Detection of ROS1 Gene Rearrangement in Lung Adenocarcinoma: Comparison of IHC, FISH and Real-Time RT-PCR

OpenAIRE

Shan, Ling; Lian, Fang; Guo, Lei; Qiu, Tian; Ling, Yun; Ying, Jianming; Lin, Dongmei

2015-01-01

Aims To compare fluorescence in situ hybridization (FISH), immunohistochemistry (IHC) and quantitative real-time reverse transcription-PCR (qRT-PCR) assays for detection of ROS1 fusion in a large number of ROS1-positive lung adenocatcinoma (ADC) patients. Methods Using IHC analysis, sixty lung ADCs including 16 cases with ROS1 protein expression and 44 cases without ROS1 expression were selected for this study. The ROS1 fusion status was examined by FISH and qRT-PCR assay. Results Among 60 ca...

Experiment vs simulation RT WFNDEC 2014 benchmark: CIVA results

International Nuclear Information System (INIS)

Tisseur, D.; Costin, M.; Rattoni, B.; Vienne, C.; Vabre, A.; Cattiaux, G.; Sollier, T.

2015-01-01

The French Atomic Energy Commission and Alternative Energies (CEA) has developed for years the CIVA software dedicated to simulation of NDE techniques such as Radiographic Testing (RT). RT modelling is achieved in CIVA using combination of a determinist approach based on ray tracing for transmission beam simulation and a Monte Carlo model for the scattered beam computation. Furthermore, CIVA includes various detectors models, in particular common x-ray films and a photostimulable phosphor plates. This communication presents the results obtained with the configurations proposed in the World Federation of NDEC 2014 RT modelling benchmark with the RT models implemented in the CIVA software

Experiment vs simulation RT WFNDEC 2014 benchmark: CIVA results

Energy Technology Data Exchange (ETDEWEB)

Tisseur, D., E-mail: david.tisseur@cea.fr; Costin, M., E-mail: david.tisseur@cea.fr; Rattoni, B., E-mail: david.tisseur@cea.fr; Vienne, C., E-mail: david.tisseur@cea.fr; Vabre, A., E-mail: david.tisseur@cea.fr; Cattiaux, G., E-mail: david.tisseur@cea.fr [CEA LIST, CEA Saclay 91191 Gif sur Yvette Cedex (France); Sollier, T. [Institut de Radioprotection et de Sûreté Nucléaire, B.P.17 92262 Fontenay-Aux-Roses (France)

2015-03-31

The French Atomic Energy Commission and Alternative Energies (CEA) has developed for years the CIVA software dedicated to simulation of NDE techniques such as Radiographic Testing (RT). RT modelling is achieved in CIVA using combination of a determinist approach based on ray tracing for transmission beam simulation and a Monte Carlo model for the scattered beam computation. Furthermore, CIVA includes various detectors models, in particular common x-ray films and a photostimulable phosphor plates. This communication presents the results obtained with the configurations proposed in the World Federation of NDEC 2014 RT modelling benchmark with the RT models implemented in the CIVA software.

Expansion of the Real-Time SPoRT-Land Information System for NOAA/National Weather Service Situational Awareness and Local Modeling Applications

Science.gov (United States)

Case, Jonathan L; White, Kristopher D.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL is running a real-time configuration of the Noah land surface model (LSM) within the NASA Land Information System (LIS) framework (hereafter referred to as the "SPoRT-LIS"). Output from the real-time SPoRT-LIS is used for (1) initializing land surface variables for local modeling applications, and (2) displaying in decision support systems for situational awareness and drought monitoring at select NOAA/National Weather Service (NWS) partner offices. The experimental CONUS run incorporates hourly quantitative precipitation estimation (QPE) from the National Severe Storms Laboratory Multi- Radar Multi-Sensor (MRMS) which will be transitioned into operations at the National Centers for Environmental Prediction (NCEP) in Fall 2014.This paper describes the current and experimental SPoRT-LIS configurations, and documents some of the limitations still remaining through the advent of MRMS precipitation analyses in the SPoRT-LIS land surface model (LSM) simulations.

Power lies in interdisciplinary cooperation / Kärt Summatavet ; interv. Kärt Blumberg

Index Scriptorium Estoniae

Summatavet, Kärt, 1963-

2008-01-01

Ehtekunstnik Kärt Summatavet oma uudsest meetodist ehete valmistamisel - paberil oleva kujutise ülekandmisest arvuti abil metallile, mille ta töötas väljas oma doktoritöö raames Soomes Helsingi Kunsti- ja Disainiülikoolis ning mis pälvis Soulis toimunud ülemaailmsel naisleiutajate konkursil hõbemedali

Reference Gene Selection for qRT-PCR Normalization Analysis in kenaf (Hibiscus cannabinus L. under Abiotic Stress and Hormonal Stimuli

Directory of Open Access Journals (Sweden)

Xiaoping Niu

2017-05-01

Full Text Available Kenaf (Hibiscus cannabinus L., an environmental friendly and economic fiber crop, has a certain tolerance to abiotic stresses. Identification of reliable reference genes for transcript normalization of stress responsive genes expression by quantitative real-time PCR (qRT-PCR is important for exploring the molecular mechanisms of plants response to abiotic stresses. In this study, nine candidate reference genes were cloned, and their expression stabilities were assessed in 132 abiotic stress and hormonal stimuli samples of kenaf using geNorm, NormFinder, and BestKeeper algorithms. Results revealed that HcPP2A (Protein phosphatase 2A and HcACT7 (Actin 7 were the optimum reference genes across all samples; HcUBC (Ubiquitin-conjugating enzyme like protein was the worst reference gene for transcript normalization. The reliability of the selected reference genes was further confirmed by evaluating the expression profile of HcWRKY28 gene at different stress durations. This work will benefit future studies on discovery of stress-tolerance genes and stress-signaling pathways in this important fiber crop.

Development and characterization of radioimmunoassay methods for the measurement of iodothyronines (T4, T3 and rT3)

International Nuclear Information System (INIS)

Russo, E.M.K.; Vieira, J.G.H.; Barros Maciel, R.M. de; Fonseca, R.M.G.

1982-01-01

The experience acquired in the development of radioimmunoassay for T 4 , T 3 and rT 3 in unextrated serum is described. Antisera were produced in rabbits using iodothyronines conjugated to bovine serum albumin: the antisera selected provided the development of sensitive and specific radioassay methods. Stable high activity T 3 , T 4 and rT 3 tracers were prepared by iodination of 3,5 T 2 , T 3 and 3,3' T 2 by the chloramine-T method, and purified by column chromatography on Sephadex G25. Binding of those iodothyronines to endogenous serum proteins was blocked by including 8-aniline-1-naphtalene sulphonic acid (ANSA) in the T 4 and T 3 assays and thymerosal in the rT 3 assay. Normal values were defined in 46 healthy euthyroid adults of both sexes: T 4 = 7,1 +- 1,3μg/dl; T 3 = 139 +- 35ng/dl and rT 3 = 18,0 +- 7,9ng/dl. (Author) [pt

RT-PCR Protocols - Methods in Molecular Biology

Directory of Open Access Journals (Sweden)

Manuela Monti

2011-03-01

Full Text Available “The first record I have of it, is when I made a computer file which I usually did whenever I had an idea, that would have been on the Monday when I got back, and I called it Chain Reaction.POL, meaning polymerase. That was the identifier for it and later I called the thing the Polymerase Chain Reaction, which a lot of people thought was a dumb name for it, but it stuck, and it became PCR”. With these words the Nobel prize winner, Kary Mullis, explains how he named the PCR: one of the most important techniques ever invented and currently used in molecular biology. This book “RT-PCR Protocols” covers a wide range of aspects important for the setting of a PCR experiment for both beginners and advanced users. In my opinion the book is very well structured in three different sections. The first one describes the different technologies now available, like competitive RT-PCR, nested RT-PCR or RT-PCR for cloning. An important part regards the usage of PCR in single cell mouse embryos, stressing how important...........

AWIPS II Application Development, a SPoRT Perspective

Science.gov (United States)

Burks, Jason E.; Smith, Matthew; McGrath, Kevin M.

2014-01-01

The National Weather Service (NWS) is deploying its next-generation decision support system, called AWIPS II (Advanced Weather Interactive Processing System II). NASA's Short-term Prediction Research and Transition (SPoRT) Center has developed several software 'plug-ins' to extend the capabilities of AWIPS II. SPoRT aims to continue its mission of improving short-term forecasts by providing NASA and NOAA products on the decision support system used at NWS weather forecast offices (WFOs). These products are not included in the standard Satellite Broadcast Network feed provided to WFOs. SPoRT has had success in providing support to WFOs as they have transitioned to AWIPS II. Specific examples of transitioning SPoRT plug-ins to WFOs with newly deployed AWIPS II systems will be presented. Proving Ground activities (GOES-R and JPSS) will dominate SPoRT's future AWIPS II activities, including tool development as well as enhancements to existing products. In early 2012 SPoRT initiated the Experimental Product Development Team, a group of AWIPS II developers from several institutions supporting NWS forecasters with innovative products. The results of the team's spring and fall 2013 meeting will be presented. Since AWIPS II developers now include employees at WFOs, as well as many other institutions related to weather forecasting, the NWS has dealt with a multitude of software governance issues related to the difficulties of multiple remotely collaborating software developers. This presentation will provide additional examples of Research-to-Operations plugins, as well as an update on how governance issues are being handled in the AWIPS II developer community.

MINIX4RT: Real-Time Semaphores

OpenAIRE

Pessolani, Pablo Andrés

2007-01-01

MINIX4RT es una extensión del conocido Sistema Operativo MINIX que incorpora servicios de Tiempo Real Estricto en un nuevo microkernel pero manteniendo compatibilidad con las versiones anteriores del MINIX estándar. Los semáforos son el mecanismo primitivo para la sincronización y exclusion mutua en varios sistemas operativos, pero MINIX no brinda esa facilidad. Se adicionaron semáforos a MINIX4RT y, como éste es un Sistema Operativo de Tiempo Real, deben reunir ciertos requisitos de procesam...

Treatment selection for tonsillar squamous cell carcinoma

Directory of Open Access Journals (Sweden)

Yao-Yuan Kuo

2013-04-01

Conclusion: Both primary surgery and RT/CRT organ preservation are effective treatments for tonsillar SCC. Single modality treatment, either surgery or RT/CRT, can typically be provided for stage I–II diseases. Although RT/CRT organ preservation is used more frequently for stage III–IV tonsillar SCC in recent years, primary surgery combined with adjuvant therapy still achieves equivalent outcomes. Multidisciplinary pretreatment counseling and the facilities and personnel available are therefore important for decision-making. In addition, if RT/CRT organ preservation is selected as the primary treatment, tumor tonsillectomy is not indicated.

A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology.

Science.gov (United States)

Wang, Jing; Yang, Xue; Chen, Haofeng; Wang, Xuewei; Wang, Xiangyu; Fang, Yi; Jia, Zhenyu; Gao, Jidong

2017-07-11

RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples. By combining Reverse Transcription-Multiple Ligation-dependent Amplification method and next generation sequencing technology, RT-MLPSeq overcomes the limit of probe length in multiplex ligation-dependent probe amplification assay and thus could detect expression levels of transcripts without quantitative limitations. We proved that different RT-MLPSeq probes targeting on the same transcripts have highly consistent results and the starting RNA/cDNA input could be as little as 1 ng. RT-MLPSeq also presented consistent relative RNA levels of selected 13 genes with reverse transcription quantitative PCR. Finally, we demonstrated the application of the new RT-MLPSeq method by measuring the mRNA expression levels of 21 genes which can be used for accurate calculation of the breast cancer recurrence score - an index that has been widely used for managing breast cancer patients.

The incidence and functional consequences of RT-associated cardiac perfusion defects

International Nuclear Information System (INIS)

Marks, Lawrence B.; Yu Xiaoli; Prosnitz, Robert G.; Zhou Sumin; Hardenbergh, Patricia H.; Blazing, Michael; Hollis, Donna; Lind, Pehr; Tisch, Andrea; Wong, Terence Z.; Borges-Neto, Salvador

2005-01-01

Purpose: Radiation therapy (RT) for left-sided breast cancer has been associated with cardiac dysfunction. We herein assess the temporal nature and volume dependence of RT-induced left ventricular perfusion defects and whether these perfusion defects are related to changes in cardiac wall motion or alterations in ejection fraction. Methods: From 1998 to 2001, 114 patients were enrolled onto an IRB-approved prospective clinical study to assess changes in regional and global cardiac function after RT for left-sided breast cancer. Patients were imaged 30 to 60 minutes after injection of technetium 99m sestamibi or tetrofosmin. Post-RT perfusion scans were compared with the pre-RT studies to assess for RT-induced perfusion defects as well as functional changes in wall motion and ejection fraction. Two-tailed Fisher's exact test and the Cochran-Armitage test for linear trends were used for statistical analysis. Results: The incidence of new perfusion defects 6, 12, 18, and 24 months after RT was 27%, 29%, 38%, and 42%, respectively. New defects occurred in approximately 10% to 20% and 50% to 60% of patients with less than 5%, and greater than 5%, of their left ventricle included within the RT fields, respectively (p = 0.33 to 0.00008). The rates of wall motion abnormalities in patients with and without perfusion defects were 12% to 40% versus 0% to 9%, respectively; p values were 0.007 to 0.16, depending on the post-RT interval. Conclusions: Radiation therapy causes volume-dependent perfusion defects in approximately 40% of patients within 2 years of RT. These perfusion defects are associated with corresponding wall-motion abnormalities. Additional study is necessary to better define the long-term functional consequences of RT-induced perfusion defects

Pärt: Fratres / Robert Cowan

Index Scriptorium Estoniae

Cowan, Robert

1995-01-01

Uuest heliplaadist "Pärt: Fratres (seven versions). Festina Lente. Cantus in Memory of Benjamin Britten. Summa. Peter Manning (vn.), France Springuel (vc.), Mireille Gleizes (pf.), I Fiamminghi. Telare CD CD80387 (79 minutes)

Artist - analytical RT inspection simulation tool

International Nuclear Information System (INIS)

Bellon, C.; Jaenisch, G.R.

2007-01-01

The computer simulation of radiography is applicable for different purposes in NDT such as for the qualification of NDT systems, the prediction of its reliability, the optimization of system parameters, feasibility analysis, model-based data interpretation, education and training of NDT/NDE personnel, and others. Within the framework of the integrated project FilmFree the radiographic testing (RT) simulation software developed by BAM is being further developed to meet practical requirements for inspection planning in digital industrial radiology. It combines analytical modelling of the RT inspection process with the CAD-orientated object description applicable to various industrial sectors such as power generation, railways and others. (authors)

Arvo Pärt jagab preemia koolidele / Rebekka Lotman, Eva Kübar ; kommenteerinud Arvo Pärt

Index Scriptorium Estoniae

Lotman, Rebekka, 1978-

2009-01-01

Kultuuriministeerium tegi ettepaneku anda Arvo Pärdile elutööpreemia, millega kaasneva rahasumma lubas Pärt kinkida Rakvere ja Paide muusikakoolile. Elutööpreemiad saavad veel Ellen Niit ja Aarne Üksküla

Simultaneous detection of three lily viruses using Triplex IC-RT-PCR.

Science.gov (United States)

Zhang, Yubao; Wang, Yajun; Xie, Zhongkui; Yang, Guo; Guo, Zhihong; Wang, Le

2017-11-01

Viruses commonly infecting lily (Lilium spp.) include: Lily symptomless virus (LSV), Cucumber mosaic virus (CMV) and Lily mottle virus (LMoV). These viruses usually co-infect lilies causing severe economic losses in terms of quantity and quality of flower and bulb production around the world. Reliable and precise detection systems need to be developed for virus identification. We describe the development of a triplex immunocapture (IC) reverse transcription (RT) polymerase chain reaction (PCR) assay for the simultaneous detection of LSV, CMV and LMoV. The triplex IC-RT-PCR was compared with a quadruplex RT-PCR assay. Relative to the quadruplex RT-PCR, the specificity of the triplex IC-RT-PCR system for LSV, CMV and LMoV was 100% for field samples. The sensitivity of the triplex IC-RT-PCR system was 99.4%, 81.4% and 98.7% for LSV, CMV and LMoV, respectively. Agreement (κ) between the results obtained from the two tests was 0.968, 0.844 and 0.984 for LSV, CMV and LMoV, respectively. This is the first report of the simultaneous detection of LSV, CMV and LMoV in a triplex IC-RT-PCR assay. In particular we believe this convenient and reliable triplex IC-RT-PCR method could be used routinely for large-scale field surveys or crop health monitoring of lily. Copyright © 2017. Published by Elsevier B.V.

Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus.

Science.gov (United States)

Domingo-Calap, Pilar; Sentandreu, Vicente; Bracho, Maria Alma; González-Candelas, Fernando; Moya, Andrés; Sanjuán, Rafael

2009-10-01

Although viral variability studies have focused traditionally on consensus sequences, the relevance of molecular clone sequences for studying viral evolution at the intra-host level is being increasingly recognized. However, for this approach to be reliable, RT-PCR artifacts do not have to contribute excessively to the observed variability. Molecular clone sequences were obtained from an in vitro transcript to estimate the maximum error rate associated to RT-PCR for the Hepatitis C virus (HCV) E1-E2 region. On average, the frequency of RT-PCR errors was one order of magnitude lower than the level of intra-host genetic variability observed in samples from an HCV outbreak. However, RT-PCR errors were not distributed evenly along the E1-E2 region and were concentrated heavily in the hypervariable region 2 (HVR 2). Although it is concluded that RT-PCR molecular clone sequences are reliable, these results warn against extrapolation of RT-PCR error rates to different genome regions. The data suggest that the RNA sequence context or secondary structure can determine the fidelity of in vitro transcription or reverse transcription. Potentially, these factors might also modify the fidelity of the viral polymerase.

Comparative Evaluation Of Conventional Rt-pcr And Real-time Rt-pcr (rrt-pcr) For Detection Of Avian Metapneumovirus Subtype A [comparação Entre As Técnicas De Rt-pcr Convencional E Rt-pcr Em Tempo Real Para A Detecção Do Metapneumovírus Aviários Subtipo A

OpenAIRE

Ferreira H.L.; Spilki F.R.; dos Santos M.M.A.B.; de Almeida R.S.; Arns C.W.

2009-01-01

Avian metapneumovirus (AMPV) belongs to Metapneumovirus genus of Paramyxoviridae family. Virus isolation, serology, and detection of genomic RNA are used as diagnostic methods for AMPV. The aim of the present study was to compare the detection of six subgroup A AMPV isolates (AMPV/A) viral RNA by using different conventional and real time RT-PCR methods. Two new RT-PCR tests and two real time RT-PCR tests, both detecting fusion (F) gene and nucleocapsid (N) gene were compared with an establis...

Comparative evaluation of conventional RT-PCR and real-time RT-PCR (RRT-PCR for detection of avian metapneumovirus subtype A Comparação entre as técnicas de RT-PCR convencional e RT-PCR em tempo real para a detecção do metapneumovírus aviários subtipo A

Directory of Open Access Journals (Sweden)

Helena Lage Ferreira

2009-08-01

Full Text Available Avian metapneumovirus (AMPV belongs to Metapneumovirus genus of Paramyxoviridae family. Virus isolation, serology, and detection of genomic RNA are used as diagnostic methods for AMPV. The aim of the present study was to compare the detection of six subgroup A AMPV isolates (AMPV/A viral RNA by using different conventional and real time RT-PCR methods. Two new RT-PCR tests and two real time RT-PCR tests, both detecting fusion (F gene and nucleocapsid (N gene were compared with an established test for the attachment (G gene. All the RT-PCR tested assays were able to detect the AMPV/A. The lower detection limits were observed using the N-, F- based RRT-PCR and F-based conventional RT-PCR (10(0.3 to 10¹ TCID50 mL-1. The present study suggests that the conventional F-based RT-PCR presented similar detection limit when compared to N- and F-based RRT-PCR and they can be successfully used for AMPV/A detection.O metapneumovírus aviário (AMPV pertence ao gênero Metapneumovirus, família Paramyxoviridae. Isolamento viral, sorologia e detecção do RNA genômico são atualmente as técnicas utilizadas para o diagnóstico desse agente. O objetivo do presente estudo foi comparar a detecção de RNA viral de seis isolados de AMPV, subtipo A (AMPV/A, utilizando diferentes métodos de RT-PCR convencional e real time RT-PCR (RRT-PCR. Duas novas técnicas de RT-PCR convencional e duas técnicas de RRT-PCR, ambas para a detecção dos genes da nucleoproteína (N e da proteína de fusão (F, foram comparadas com um RT-PCR previamente estabelecido para a detecção do AMPV (gene da glicoproteína -G. Todos esses métodos foram capazes de detectar os isolados AMPV/A. As técnicas RRT-PCR (genes F e N mostraram os menores limites de detecção (10(0.3 to 10¹ TCID50 mL-1. Os resultados sugerem que as técnicas RT-PCR convencional (gene F e as técnicas de RRT-PCR (gene F e N desenvolvidas no presente estudo podem ser utilizadas com sucesso para a detecção do

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

Science.gov (United States)

Sang, Jian; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wenming; Bao, Yiming; Xiao, Jingfa; Hu, Songnian; Hao, Lili; Zhang, Zhang

2018-01-04

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species. Specifically, it integrates a comprehensive collection of more than 750 internal control genes for 73 animals, 115 plants, 12 fungi and 9 bacteria, and incorporates detailed information on recommended application scenarios corresponding to specific experimental conditions, which, collectively, are of great help for researchers to adopt appropriate internal control genes for their own experiments. Taken together, ICG serves as a publicly editable and open-content encyclopaedia of internal control genes and accordingly bears broad utility for reliable RT-qPCR normalization and gene expression characterization in both model and non-model organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

High selection pressure promotes increase in cumulative adaptive culture.

Directory of Open Access Journals (Sweden)

Carolin Vegvari

Full Text Available The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little attention has been paid to the role of natural selection in the evolution of cultural complexity. Here we use an agent-based simulation model to demonstrate that high selection pressure in the form of resource pressure promotes the accumulation of adaptive culture in spite of small population sizes and high innovation costs. We argue that the interaction of demography and selection is important, and that neither can be considered in isolation. We predict that an increase in cultural complexity is most likely to occur under conditions of population pressure relative to resource availability. Our model may help to explain why culture change can occur without major environmental change. We suggest that understanding the interaction between shifting selective pressures and demography is essential for explaining the evolution of cultural complexity.

Märt Haamer: Tsahknal pole Overalliga mingisugust seost / Märt Haamer ; intervjueerinud Jan Jõgis-Laats

Index Scriptorium Estoniae

Haamer, Märt, 1973-

2009-01-01

Overall Eesti juhi Märt Haameri väitel pole Anders Tsahkna ühtegi riigihanget Overalli ettevõtetele suunanud. Overalli omandusse kuuluv firma Gennet Lab on olnud alltöövõtja paaris E-tervise Sihtasutuse korraldatud hankes

Preparation of rT3 in human serum ria kit

International Nuclear Information System (INIS)

Zhang Peixuan; Han Shiquan; Zhang Liling

1991-02-01

A method for the measurement of rT 3 in serum by radioimmunoassay is presented. The double antibody plus polyethylene glycol was used as separating reagent. The method is simple, precise and sensitive. Serum rT 3 values of normal (n = 61) were 47.7 ± 11.34 x 10 -8 g/L (X-bar ± SD). Patients with hyperthyroidism (n = 8) serum rT 3 values were 272.2 ± 91.1 x 10 -8 g/L (X-bar ± SD) and patients with hypothyroidism (n = 2) serum rT 3 values were 11.4 ± 8.3 x 10 -8 g/L (X-bar ± SD). It appears to be a useful diagnostic procedure for thyroid diseases

Evaluation of candidate reference genes for gene expression normalization in Brassica juncea using real time quantitative RT-PCR.

Directory of Open Access Journals (Sweden)

Ruby Chandna

Full Text Available The real time quantitative reverse transcription PCR (qRT-PCR is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes, ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes, in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization.

Soft-Rt: software for IMRT simulations based on MCNPX

International Nuclear Information System (INIS)

Ferreira F, T. C.; Campos, T.

2015-10-01

Intensity Modulated Radiation Therapy (IMRT) is an advanced treatment technique, widely used in external radiotherapy. This paper presents the Soft-Rt which allows the simulation of an entire IMRT treatment protocol. The Soft-Rt performs a full three-dimensional rendering of a set of patient images, including the definitions of region of interest with organs in risk, and the target tumor volume and margins (PTV). Thus, a more accurate analysis and planning can be performed, taking into account the features and orientation of the radiation beams. The exposed tissues as well as the amount of absorbed dose is depicted in healthy and/or cancerous tissues. As conclusion, Soft-Rt can predict dose on the PTV accurately, preserving the surrounding healthy tissues. Soft-Rt is coupled with SISCODES code. The SISCODES code is firstly applied to segment the set of CT or MRI patient images in distinct tissues pointing out its respective density and chemical compositions. Later, the voxel model is export to the Soft-Rt IMRT planning module in which a full treatment planning is created. All geometrical parameters are sent to the general purpose Monte Carlo transport code - MCNP - to simulate the interaction of each incident beam towards to the PTV avoiding organs in risk. The normalized dose results are exported to the Soft-Rt out-module, in which the three-dimensional model visualization is shown in a transparent glass procedure adopting gray scale for the dependence on the mass density of the correlated tissue; while, a color scale to depict dose values in a superimpose protocol. (Author)

Soft-Rt: software for IMRT simulations based on MCNPX

Energy Technology Data Exchange (ETDEWEB)

Ferreira F, T. C. [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Av. Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais (Brazil); Campos, T., E-mail: tcff01@gmail.com [Universidade Federal de Minas Gerais, Departamento de Engenharia Nuclear, Programa de Pos Graduacao em Ciencias e Tecnicas Nucleares, Av. Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais (Brazil)

2015-10-15

Intensity Modulated Radiation Therapy (IMRT) is an advanced treatment technique, widely used in external radiotherapy. This paper presents the Soft-Rt which allows the simulation of an entire IMRT treatment protocol. The Soft-Rt performs a full three-dimensional rendering of a set of patient images, including the definitions of region of interest with organs in risk, and the target tumor volume and margins (PTV). Thus, a more accurate analysis and planning can be performed, taking into account the features and orientation of the radiation beams. The exposed tissues as well as the amount of absorbed dose is depicted in healthy and/or cancerous tissues. As conclusion, Soft-Rt can predict dose on the PTV accurately, preserving the surrounding healthy tissues. Soft-Rt is coupled with SISCODES code. The SISCODES code is firstly applied to segment the set of CT or MRI patient images in distinct tissues pointing out its respective density and chemical compositions. Later, the voxel model is export to the Soft-Rt IMRT planning module in which a full treatment planning is created. All geometrical parameters are sent to the general purpose Monte Carlo transport code - MCNP - to simulate the interaction of each incident beam towards to the PTV avoiding organs in risk. The normalized dose results are exported to the Soft-Rt out-module, in which the three-dimensional model visualization is shown in a transparent glass procedure adopting gray scale for the dependence on the mass density of the correlated tissue; while, a color scale to depict dose values in a superimpose protocol. (Author)

Superior sulcus non-small cell lung carcinoma: A comparison of IMRT and 3D-RT dosimetry.

Science.gov (United States)

Truntzer, Pierre; Antoni, Delphine; Santelmo, Nicola; Schumacher, Catherine; Falcoz, Pierre-Emmanuel; Quoix, Elisabeth; Massard, Gilbert; Noël, Georges

2016-01-01

A dosimetric study comparing intensity modulated radiotherapy (IMRT) by TomoTherapy to conformational 3D radiotherapy (3D-RT) in patients with superior sulcus non-small cell lung cancer (NSCLC). IMRT became the main technique in modern radiotherapy. However it was not currently used for lung cancers. Because of the need to increase the dose to control lung cancers but because of the critical organs surrounding the tumors, the gains obtainable with IMRT is not still demonstrated. A dosimetric comparison of the planned target and organs at risk parameters between IMRT and 3D-RT in eight patients who received preoperative or curative intent irradiation. In the patients who received at least 66 Gy, the mean V95% was significantly better with IMRT than 3D-RT (p = 0.043). IMRT delivered a lower D2% compared to 3D-RT (p = 0.043). The IH was significantly better with IMRT (p = 0.043). The lung V 5 Gy and V 13 Gy were significantly higher in IMRT than 3D-RT (p = 0.043), while the maximal dose (D max) to the spinal cord was significantly lower in IMRT (p = 0.043). The brachial plexus D max was significantly lower in IMRT than 3D-RT (p = 0.048). For patients treated with 46 Gy, no significant differences were found. Our study showed that IMRT is relevant for SS-NSCLC. In patients treated with a curative dose, it led to a reduction of the exposure of critical organs, allowing a better dose distribution in the tumor. For the patients treated with a preoperative schedule, our results provide a basis for future controlled trials to improve the histological complete response by increasing the radiation dose.

Kuidas sünnib pealkiri? / Pärt Lias

Index Scriptorium Estoniae

Lias, Pärt

2003-01-01

Eesti kirjanikud vastavad Pärt Liase küsimusele oma teoste pealkirjade saamisloo kohta: Doris Kareva, Ilona Laaman, Eha Lättemäe, Priidu Beier, Oskar Kruus, Jaan Kruusvall, Paul-Eerik Rummo ja Andres Vanapa (1); Triin Soomets, Priit Aimla, Aarne Puu, Einar Sander, Jüri Tuulik ja Ülo Tuulik (2); Nikolai Baturin, Leo Metsar, Toomas Vint, Leonid Stolovitš ja Pärt Lias (3)

Future of the reprocessing business at the RT-1 plant

International Nuclear Information System (INIS)

Bukharin, O.

1995-01-01

Economic viability of reprocessing operations at the RT-1 plant is provided by the contracts with nuclear utilities from Finland and Hungary. Finland will stop sending fuel to Mayak for reprocessing after 1996. Hungary will be capable to resolve the problem of spent fuel domestically some time in the future. This increases vulnerability of the reprocessing business at Mayak to future political uncertainties. (author)

Avaliação das técnicas de RT-PCR e heminested RT-PCR em cérebros de cães com sinais neurológicos compatíveis com cinomose

Directory of Open Access Journals (Sweden)

Adriana Cortez

2015-12-01

Full Text Available The diagnostic value of RT-PCR and hemi-nested RT-PCR (hnRT-PCR was compared in brain samples of dogs presenting neurological signs compatible with canine distemper. Samples of central nervous system (CNS were collected from 68 dogs and tested by direct immunofluorescence test (RFID and, independent of the results, they were stored at -20°C for at least three years. They were submitted to the RT-PCR and hnRT-PCR techniques aiming to determine the gene responsible for the viral nucleoprotein decoding. Fifty-nine samples were positive for RIFD, 40 for RT-PCR (Kappa = 0.358 and 54 for hnRT-PCR (Kappa = 0.740. All nine RIFD negative samples were also negative for RT-PCR and hnRT-PCR. In spite of the storage duration and proper sample conditions, the estimated accordance between hnRT-PCR and RIFD demonstrated that hnRT-PCR technique can be applied in retrospective studies.

E-government strategy of Surabaya city government through e-rt / rw to improve the quality of public service

Science.gov (United States)

Oktariyanda, T. A.; Rahaju, T.

2018-01-01

The use of information technology by Surabaya City Government has generated various innovations of public services such as “e-Sapa Warga”, e-Commerce, “e-RT/RW”, e-Budgeting, e-Project, e-Procurement, “e-Pendidikan”. Among the many innovations, e-RT/RW (Rukun Tetangga / Rukun Warga) is an innovation that is quite prominent because there are still many areas that have not implemented. This research can be classified as literature review and critical research. The aims of this research are to describe and analyze e-government strategy in Surabaya City through e-RT / RW to improve public service quality. The result of this research is e-government strategy in Surabaya City through e-RT / RW is already relevant and in accordance with Goldsmith’s theory of e-government. The positive impact of the implementation of e-RT / RW is the increasing quality of public services to bring benefits to all citizens Surabaya City.

Post-RT CT results as a predictive model for the necessity of planned post-RT neck dissection in patients with cervical metastatic disease from squamous cell carcinoma

International Nuclear Information System (INIS)

Ojiri, Hiroya; Mendenhall, William M.; Stringer, Scott P.; Johnson, Patches L.; Mancuso, Anthony A.

2002-01-01

Purpose: To establish whether the extent of neck disease on postradiation therapy (RT) computed tomography (CT) can predict the likelihood of positive neck nodes and, thereby, the necessity of planned post-RT neck dissection. Methods and Materials: Ninety-five patients who underwent post-RT neck dissection within 2 months for squamous cell carcinoma of the head and neck were eligible. Of the 95 patients, 37 (32.7%) of 113 hemineck specimens were pathologically positive. On post-RT CT imaging studies, the number and size of lymph nodes >1 cm were recorded. Internal focal defects and the likelihood of extracapsular spread were graded. Results: If lymph nodes on post-RT CT were ≤15 mm, free of significant internal focal low-attenuation or calcification, and without imaging evidence of extracapsular spread, the surgical hemineck specimen was positive in 1 (3.4%) of the 29 hemineck specimens. A focal low-attenuation defect (p=0.0078) and evidence of extracapsular spread (p=0.0721) seen in the residual nodal mass on CT were independent predictors of a positive surgical specimen by multivariate analysis. Conclusion: CT findings on post-RT neck studies can help predict the likelihood of residual disease and, thereby, the necessity of planned post-RT neck dissection

Pärt: Berliner Messe / Rob Cowan

Index Scriptorium Estoniae

Cowan, Rob

1998-01-01

Uuest heliplaadist "Pärt: Berliner Messe. The Beatitudes. Annum per Annum. Magnificat. Seven Magnificat Antiphons. De profundis. Polyphony / Steven Layton with Andrew Lucas" Hyperion CDA66960 (74 minutes:DDD)

Arvo Pärt. Litany / Peter Korfmacher

Index Scriptorium Estoniae

Korfmacher, Peter

1996-01-01

Uuest heliplaadist "Pärt, Arvo. Litany; Psalom; Trisagion. Hilliard Ensemble, Estonian Philharmonic Chamber Choir, Tallinn Chamber Orchestra, Tõnu Kaljuste"; Lithuanian Chamber Orchestra, Saulius Sondeckis. ECM 1592/449 810-2

Profiling structured product labeling with NDF-RT and RxNorm

Science.gov (United States)

2012-01-01

Background Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product information. The SPL drug labels contain rich information about FDA approved clinical drugs. However, the lack of linkage to standard drug ontologies hinders their meaningful use. NDF-RT (National Drug File Reference Terminology) and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. Methods In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. We established the classification and relevant linkage for SPL drug labels using the following three approaches. First, we retrieved NDF-RT categorical information from the External Pharmacologic Class (EPC) indexing SPLs. Second, we used the RxNorm and NDF-RT mappings to classify and link SPLs with NDF-RT categories. Third, we profiled SPLs using RxNorm term type information. In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. Meanwhile, we imported RxNorm data into MySQL relational database. Results In total, 96.0% SPL drug labels were mapped with NDF-RT categories whereas 97.0% SPL drug labels are linked to RxNorm codes. We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. Conclusions The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical applications through

Profiling structured product labeling with NDF-RT and RxNorm

Directory of Open Access Journals (Sweden)

Zhu Qian

2012-12-01

Full Text Available Abstract Background Structured Product Labeling (SPL is a document markup standard approved by Health Level Seven (HL7 and adopted by United States Food and Drug Administration (FDA as a mechanism for exchanging drug product information. The SPL drug labels contain rich information about FDA approved clinical drugs. However, the lack of linkage to standard drug ontologies hinders their meaningful use. NDF-RT (National Drug File Reference Terminology and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. Methods In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. We established the classification and relevant linkage for SPL drug labels using the following three approaches. First, we retrieved NDF-RT categorical information from the External Pharmacologic Class (EPC indexing SPLs. Second, we used the RxNorm and NDF-RT mappings to classify and link SPLs with NDF-RT categories. Third, we profiled SPLs using RxNorm term type information. In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. Meanwhile, we imported RxNorm data into MySQL relational database. Results In total, 96.0% SPL drug labels were mapped with NDF-RT categories whereas 97.0% SPL drug labels are linked to RxNorm codes. We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. Conclusions The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical

Profiling structured product labeling with NDF-RT and RxNorm.

Science.gov (United States)

Zhu, Qian; Jiang, Guoqian; Chute, Christopher G

2012-12-20

Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product information. The SPL drug labels contain rich information about FDA approved clinical drugs. However, the lack of linkage to standard drug ontologies hinders their meaningful use. NDF-RT (National Drug File Reference Terminology) and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. We established the classification and relevant linkage for SPL drug labels using the following three approaches. First, we retrieved NDF-RT categorical information from the External Pharmacologic Class (EPC) indexing SPLs. Second, we used the RxNorm and NDF-RT mappings to classify and link SPLs with NDF-RT categories. Third, we profiled SPLs using RxNorm term type information. In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. Meanwhile, we imported RxNorm data into MySQL relational database. In total, 96.0% SPL drug labels were mapped with NDF-RT categories whereas 97.0% SPL drug labels are linked to RxNorm codes. We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical applications through standard drug ontologies such as NDF-RT and

SPARCL1 Expression Increases With Preoperative Radiation Therapy and Predicts Better Survival in Rectal Cancer Patients

Energy Technology Data Exchange (ETDEWEB)

Kotti, Angeliki, E-mail: angkotti@yahoo.gr; Holmqvist, Annica; Albertsson, Maria; Sun, Xiao-Feng, E-mail: xiao-feng.sun@liu.se

2014-04-01

Purpose: The secreted protein acidic and rich in cysteine-like 1 (SPARCL1) is expressed in various normal tissues and many types of cancers. The function of SPARCL1 and its relationship to a patient's prognosis have been studied, whereas its relationship to radiation therapy (RT) is not known. Our aim was to investigate the expression of SPARCL1 in rectal cancer patients who participated in a clinical trial of preoperative RT. Methods and Materials: The study included 136 rectal cancer patients who were randomized to undergo preoperative RT and surgery (n=63) or surgery alone (n=73). The expression levels of SPARCL1 in normal mucosa (n=29), primary tumor (n=136), and lymph node metastasis (n=35) were determined by immunohistochemistry. Results: Tumors with RT had stronger SPARCL1 expression than tumors without RT (P=.003). In the RT group, strong SPARCL1 expression was related to better survival than weak expression in patients with stage III tumors, independent of sex, age, differentiation, and margin status (P=.022; RR = 18.128; 95% confidence interval, 1.512-217.413). No such relationship was found in the non-RT group (P=.224). Further analysis of interactions among SPARCL1 expression, RT, and survival showed statistical significance (P=.024). In patients with metastases who received RT, strong SPARCL1 expression was related to better survival compared to weak expression (P=.041) but not in the non-RT group (P=.569). Conclusions: SPARCL1 expression increases with RT and is related to better prognosis in rectal cancer patients with RT but not in patients without RT. This result may help us to select the patients best suited for preoperative RT.

The effect of sexual selection on adaptation and extinction under increasing temperatures.

Science.gov (United States)

Parrett, Jonathan M; Knell, Robert J

2018-04-25

Strong sexual selection has been reported to both enhance and hinder the adaptive capacity and persistence of populations when exposed to novel environments. Consequently, how sexual selection influences population adaption and persistence under stress remains widely debated. Here, we present two empirical investigations of the fitness consequences of sexual selection on populations of the Indian meal moth, Plodia interpunctella, exposed to stable or gradually increasing temperatures. When faced with increasing temperatures, strong sexual selection was associated with both increased fecundity and offspring survival compared with populations experiencing weak sexual selection, suggesting sexual selection acts to drive adaptive evolution by favouring beneficial alleles. Strong sexual selection did not, however, delay extinction when the temperature became excessively high. By manipulating individuals' mating opportunities during fitness assays, we were able to assess the effect of multiple mating independently from the effect of population-level sexual selection, and found that polyandry has a positive effect on both fecundity and offspring survival under increasing temperatures in those populations evolving with weak sexual selection. Within stable temperatures, there were some benefits from strong sexual selection but these were not consistent across the entire experiment, possibly reflecting changing costs and benefits of sexual selection under stabilizing and directional selection. These results indicate that sexual selection can provide a buffer against climate change and increase adaptation rates within a continuously changing environment. These positive effects of sexual selection may, however, be too small to protect populations and delay extinction when environmental changes are relatively rapid. © 2018 The Author(s).

Optimisation of the RT-PCR detection of immunomagnetically enriched carcinoma cells

International Nuclear Information System (INIS)

Raynor, Michael; Stephenson, Sally-Anne; Walsh, David CA; Pittman, Kenneth B; Dobrovic, Alexander

2002-01-01

Immunomagnetic enrichment followed by RT-PCR (immunobead RT-PCR) is an efficient methodology to identify disseminated carcinoma cells in the blood and bone marrow. The RT-PCR assays must be both specific for the tumor cells and sufficiently sensitive to enable detection of single tumor cells. We have developed a method to test RT-PCR assays for any cancer. This has been investigated using a panel of RT-PCR markers suitable for the detection of breast cancer cells. In the assay, a single cell line-derived tumor cell is added to 100 peripheral blood mononuclear cells (PBMNCs) after which mRNA is isolated and reverse transcribed for RT-PCR analysis. PBMNCs without added tumor cells are used as specificity controls. The previously studied markers epidermal growth factor receptor (EGFR), mammaglobin 1 (MGB1), epithelial cell adhesion molecule (EpCAM/TACSTD1), mucin 1 (MUC1), carcinoembryonic antigen (CEA) were tested. Two new epithelial-specific markers ELF3 and EphB4 were also tested. MUC1 was unsuitable as strong amplification was detected in 100 cell PBMNC controls. Expression of ELF3, EphB4, EpCAM, EGFR, CEA and MGB1 was found to be both specific for the tumor cell, as demonstrated by the absence of a signal in most 100 cell PBMNC controls, and sensitive enough to detect a single tumor cell in 100 PBMNCs using a single round of RT-PCR. ELF3, EphB4, EpCAM, EGFR, CEA and MGB1 are appropriate RT-PCR markers for use in a marker panel to detect disseminated breast cancer cells after immunomagnetic enrichment

Multiple bottlenecks in hierarchical control of action sequences: what does "response selection" select in skilled typewriting?

Science.gov (United States)

Yamaguchi, Motonori; Logan, Gordon D; Li, Vanessa

2013-08-01

Does response selection select words or letters in skilled typewriting? Typing performance involves hierarchically organized control processes: an outer loop that controls word level processing, and an inner loop that controls letter (or keystroke) level processing. The present study addressed whether response selection occurs in the outer loop or the inner loop by using the psychological refractory period (PRP) paradigm in which Task1 required typing single words and Task2 required vocal responses to tones. The number of letters (string length) in the words was manipulated to discriminate selection of words from selection of keystrokes. In Experiment 1, the PRP effect depended on string length of words in Task1, suggesting that response selection occurs in the inner loop. To assess contributions of the outer loop, the influence of string length was examined in a lexical-decision task that also involves word encoding and lexical access (Experiment 2), or to-be-typed words were preexposed so outer-loop processing could finish before typing started (Experiment 3). Response time for Task2 (RT2) did not depend on string length with lexical decision, and RT2 still depended on string length with typing preexposed strings. These results support the inner-loop locus of the PRP effect. In Experiment 4, typing was performed as Task2, and the effect of string length on typing RT interacted with stimulus onset asynchrony superadditively, implying that another bottleneck also exists in the outer loop. We conclude that there are at least two bottleneck processes in skilled typewriting. 2013 APA, all rights reserved

Modelling Dynamic Topologies via Extensions of VDM-RT

DEFF Research Database (Denmark)

Nielsen, Claus Ballegård

Only a few formal methods include descriptions of the network topology that the modelled system is deployed onto. In VDM Real-Time (VDM-RT) this has been enabled for distributed systems that have a static structure. However, when modelling dynamic systems this fixed topology becomes an issue....... Systems with highly distributed and alternating relationships cannot be expressed correctly in a static model. This document describes how VDM-RT can be extended with new language constructs to enable the description of dynamic reconfiguration of the network topology during the runtime execution...... of a model. The extension is developed on the basis of a case study involving a dynamic system that has a constant changing system topology. With a basis in the case study a model is developed that uses the static version of VDM-RT in order to reveal the limitations of the language. The case study...

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

Science.gov (United States)

Bell, Jordan R.; Case, Jonathan L.; Molthan, Andrew L.

2011-01-01

for areas with lower GVF in the SPoRT model runs. These differences in the heating and evaporation rates produced subtle yet quantifiable differences in the simulated convective precipitation systems for the selected severe weather case examined.

Food restriction but not fish oil increases fertility in hens: role of RARRES2?

Science.gov (United States)

Mellouk, Namya; Ramé, Christelle; Delaveau, Joël; Rat, Christophe; Marchand, Maxime; Mercerand, Frédéric; Travel, Angélique; Brionne, Aurélien; Chartrin, Pascal; Ma, Linlin; Froment, Pascal; Dupont, Joëlle

2018-04-01

Overfed hens selected for their rapid growth become fatter and develop reproductive disorders. Herein, we aimed to demonstrate that food restriction leading to a weight reduction and/or a supplementation with fish oil may be effective in preventing reproductive disorders through the regulation of adipokine expression in broiler hens. This study included four groups of food restricted (Rt) or ad libitum hens (Ad, feeding at a rate 1.7 times greater than Rt hens) supplemented or unsupplemented with fish oil (1%). The Rt diet significantly increased plasma chemerin (RARRES2) levels during the laying period, delayed sexual maturity by one week and improved egg quality and fertility. These effects were associated with higher progesterone production in response to IGF1 (or LH) in cultured granulosa cells and in vivo egg yolk, as compared with Ad hens. Fish oil supplementation had similar effects to the Rt diet on progesterone ( P  food restriction but not fish oil supplementation improved fertility, and this was associated with variations in RARRES2 plasma and ovarian expression in hens. © 2018 Society for Reproduction and Fertility.

Common Starlings (Sturnus vulgaris) increasingly select for grazed areas with increasing distance-to-nest.

Science.gov (United States)

Heldbjerg, Henning; Fox, Anthony D; Thellesen, Peder V; Dalby, Lars; Sunde, Peter

2017-01-01

The abundant and widespread Common Starling (Sturnus vulgaris) is currently declining across much of Europe due to landscape changes caused by agricultural intensification. The proximate mechanisms causing adverse effects to breeding Starlings are unclear, hampering our ability to implement cost-efficient agri-environmental schemes to restore populations to former levels. This study aimed to show how this central foraging farmland bird uses and selects land cover types in general and how use of foraging habitat changes in relation to distance from the nest. We attached GPS-loggers to 17 breeding Starlings at a Danish dairy cattle farm in 2015 and 2016 and analysed their use of different land cover types as a function of distance intervals from the nest and their relative availability. As expected for a central place forager, Starlings increasingly avoided potential foraging areas with greater distance-to-nest: areas ≥ 500 m were selected > 100 times less frequently than areas within 100 m. On average, Starlings selected the land cover category Grazed most frequently, followed by Short Grass, Bare Ground, Meadow and Winter Crops. Starlings compensated for elevated travel costs by showing increasing habitat selection the further they foraged from the nest. Our results highlight the importance of Grazed foraging habitats close to the nest site of breeding Starlings. The ecological capacity of intensively managed farmlands for insectivorous birds like the Starling is decreasing through conversion of the most strongly selected land cover type (Grazed) to the least selected (Winter Crops) which may be further exacerbated through spatial segregation of foraging and breeding habitats.

Common Starlings (Sturnus vulgaris increasingly select for grazed areas with increasing distance-to-nest.

Directory of Open Access Journals (Sweden)

Henning Heldbjerg

Full Text Available The abundant and widespread Common Starling (Sturnus vulgaris is currently declining across much of Europe due to landscape changes caused by agricultural intensification. The proximate mechanisms causing adverse effects to breeding Starlings are unclear, hampering our ability to implement cost-efficient agri-environmental schemes to restore populations to former levels. This study aimed to show how this central foraging farmland bird uses and selects land cover types in general and how use of foraging habitat changes in relation to distance from the nest. We attached GPS-loggers to 17 breeding Starlings at a Danish dairy cattle farm in 2015 and 2016 and analysed their use of different land cover types as a function of distance intervals from the nest and their relative availability. As expected for a central place forager, Starlings increasingly avoided potential foraging areas with greater distance-to-nest: areas ≥ 500 m were selected > 100 times less frequently than areas within 100 m. On average, Starlings selected the land cover category Grazed most frequently, followed by Short Grass, Bare Ground, Meadow and Winter Crops. Starlings compensated for elevated travel costs by showing increasing habitat selection the further they foraged from the nest. Our results highlight the importance of Grazed foraging habitats close to the nest site of breeding Starlings. The ecological capacity of intensively managed farmlands for insectivorous birds like the Starling is decreasing through conversion of the most strongly selected land cover type (Grazed to the least selected (Winter Crops which may be further exacerbated through spatial segregation of foraging and breeding habitats.

Forført af hjernen?

DEFF Research Database (Denmark)

Lieberoth, Andreas

2013-01-01

Blandingen af offentlig interesse, gode mediehistorier og smarte sælgere har ført til sejlivede neuromyter, der ikke bare distraherer almindelige mennesker, men også fører til udbredte misforståelser blandt professionelle som lærere og plejepersonale. I bedste fald leder neuromyter til spild af t...

DeepRT: deep learning for peptide retention time prediction in proteomics

OpenAIRE

Ma, Chunwei; Zhu, Zhiyong; Ye, Jun; Yang, Jiarui; Pei, Jianguo; Xu, Shaohang; Zhou, Ruo; Yu, Chang; Mo, Fan; Wen, Bo; Liu, Siqi

2017-01-01

Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Herein, we present DeepRT, a deep learning based software for peptide retention time prediction. DeepRT automatically learns features directly from the peptide sequences using the deep convolutional Neural Network (CNN) and Recurrent Neural Network (RNN) model, which eliminates the need to use hand-crafted features or rules. After the feature learning, pr...

Development of duplex real-time RT-PCR based on Taqman technology for detecting simultaneously the genome of pan-enterovirus and enterovirus 71.

Science.gov (United States)

Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung

2013-07-01

Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.

Pärt, Arvo. Fratres / Rainer Wagner

Index Scriptorium Estoniae

Wagner, Rainer

1995-01-01

Uuest heliplaadist "Pärt, Arvo. Fratres, Cantus (in Memory of Benjamin Britten), summa, Festina Lente; Peter Manning, France Springuel, Mireille Gleizes, Huub Righarts, I Fiamminghi, Rudolf Werthen" (AD: 1994) Telarc/in-akustik CD 80 387 (WD: 79'00")

Molecular analysis of dolphin morbillivirus: A new sensitive detection method based on nested RT-PCR.

Science.gov (United States)

Centelleghe, Cinzia; Beffagna, Giorgia; Zanetti, Rossella; Zappulli, Valentina; Di Guardo, Giovanni; Mazzariol, Sandro

2016-09-01

Cetacean Morbillivirus (CeMV) has been identified as the most pathogenic virus for cetaceans. Over the past three decades, this RNA virus has caused several outbreaks of lethal disease in odontocetes and mysticetes worldwide. Isolation and identification of CeMV RNA is very challenging in whales because of the poor preservation status frequently shown by tissues from stranded animals. Nested reverse transcription polymerase chain reaction (nested RT-PCR) is used instead of conventional RT-PCR when it is necessary to increase the sensitivity and the specificity of the reaction. This study describes a new nested RT-PCR technique useful to amplify small amounts of the cDNA copy of Cetacean morbillivirus (CeMV) when it is present in scant quantity in whales' biological specimens. This technique was used to analyze different tissues (lung, brain, spleen and other lymphoid tissues) from one under human care seal and seven cetaceans stranded along the Italian coastline between October 2011 and September 2015. A well-characterized, 200 base pair (bp) fragment of the dolphin Morbillivirus (DMV) haemagglutinin (H) gene, obtained by nested RT-PCR, was sequenced and used to confirm DMV positivity in all the eight marine mammals under study. In conclusion, this nested RT-PCR protocol can represent a sensitive detection method to identify CeMV-positive, poorly preserved tissue samples. Furthermore, this is also a rather inexpensive molecular technique, relatively easy to apply. Copyright © 2016 Elsevier B.V. All rights reserved.

Helical Tomotherapy-Based STAT RT: Dosimetric Evaluation for Clinical Implementation of a Rapid Radiation Palliation Program

International Nuclear Information System (INIS)

McIntosh, Alyson; Dunlap, Neal; Sheng, Ke; Geezey, Constance; Turner, Benton; Blackhall, Leslie; Weiss, Geoffrey; Lappinen, Eric; Larner, James M.; Read, Paul W.

2010-01-01

Helical tomotherapy-based STAT radiation therapy (RT) uses an efficient software algorithm for rapid intensity-modulated treatment planning, enabling conformal radiation treatment plans to be generated on megavoltage computed tomography (MVCT) scans for CT simulation, treatment planning, and treatment delivery in one session. We compared helical tomotherapy-based STAT RT dosimetry with standard linac-based 3D conformal plans and standard helical tomotherapy-based intensity-modulated radiation therapy (IMRT) dosimetry for palliative treatments of whole brain, a central obstructive lung mass, multilevel spine disease, and a hip metastasis. Specifically, we compared the conformality, homogeneity, and dose with regional organs at risk (OARs) for each plan as an initial step in the clinical implementation of a STAT RT rapid radiation palliation program. Hypothetical planning target volumes (PTVs) were contoured on an anthropomorphic phantom in the lung, spine, brain, and hip. Treatment plans were created using three planning techniques: 3D conformal on Pinnacle 3 , helical tomotherapy, and helical tomotherapy-based STAT RT. Plan homogeneity, conformality, and dose to OARs were analyzed and compared. STAT RT and tomotherapy improved conformality indices for spine and lung plans (CI spine = 1.21, 1.17; CI lung = 1.20, 1.07, respectively) in comparison with standard palliative anteroposterior/posteroanterior (AP/PA) treatment plans (CI spine = 7.01, CI lung = 7.30), with better sparing of heart, esophagus, and spinal cord. For palliative whole-brain radiotherapy, STAT RT and tomotherapy reduced maximum and mean doses to the orbits and lens (maximum/mean lens dose: STAT RT = 2.94/2.65 Gy, tomotherapy = 3.13/2.80 Gy, Lateral opposed fields = 7.02/3.65 Gy), with an increased dose to the scalp (mean scalp dose: STAT RT = 16.19 Gy, tomotherapy = 15.61 Gy, lateral opposed fields = 14.01 Gy). For bony metastatic hip lesions, conformality with both tomotherapy techniques (CI = 1

Early diagnosis of dengue in travelers: comparison of a novel real-time RT-PCR, NS1 antigen detection and serology.

Science.gov (United States)

Huhtamo, Eili; Hasu, Essi; Uzcátegui, Nathalie Y; Erra, Elina; Nikkari, Simo; Kantele, Anu; Vapalahti, Olli; Piiparinen, Heli

2010-01-01

The increased traveling to dengue endemic regions and the numerous epidemics have led to a rise in imported dengue. The laboratory diagnosis of acute dengue requires several types of tests and often paired samples are needed for obtaining reliable results. Although several diagnostic methods are available, proper comparative data on their performance are lacking. To compare the performance of novel methods including a novel pan-DENV real-time RT-PCR and a commercially available NS1 capture-EIA in regard to IgM detection for optimizing the early diagnosis of DENV in travelers. A panel of 99 selected early phase serum samples of dengue patients was studied by real-time RT-PCR, NS1 antigen ELISA, IgM-EIA, IgG-IFA and cell culture virus isolation. The novel real-time RT-PCR was shown specific and sensitive for detection of DENV-1-4 RNA and suitable for diagnostic use. The diagnostic rate using combination of RNA and IgM detection was 99% and using NS1 and IgM detection 95.9%. The results of RNA and NS1 antigen detection disagreed in 15.5% of samples that had only RNA or NS1 antigen detected. The diagnostic rates of early samples are higher when either RNA or NS1 antigen detection is combined with IgM detection. Besides the differences in the RNA and NS1 detection assays, the observed discrepancy of results could suggest individual variation or differences in timing of these markers in patient serum. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Enhanced control of dorsolateral prefrontal cortex neurophysiology with real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback training and working memory practice.

Science.gov (United States)

Sherwood, Matthew S; Kane, Jessica H; Weisend, Michael P; Parker, Jason G

2016-01-01

Real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback can be used to train localized, conscious regulation of blood oxygen level-dependent (BOLD) signals. As a therapeutic technique, rt-fMRI neurofeedback reduces the symptoms of a variety of neurologic disorders. To date, few studies have investigated the use of self-regulation training using rt-fMRI neurofeedback to enhance cognitive performance. This work investigates the utility of rt-fMRI neurofeedback as a tool to enhance human cognition by training healthy individuals to consciously control activity in the left dorsolateral prefrontal cortex (DLPFC). A cohort of 18 healthy participants in the experimental group underwent rt-fMRI neurofeedback from the left DLPFC in five training sessions across two weeks while 7 participants in the control group underwent similar training outside the MRI and without rt-fMRI neurofeedback. Working memory (WM) performance was evaluated on two testing days separated by the five rt-fMRI neurofeedback sessions using two computerized tests. We investigated the ability to control the BOLD signal across training sessions and WM performance across the two testing days. The group with rt-fMRI neurofeedback demonstrated a significant increase in the ability to self-regulate the BOLD signal in the left DLPFC across sessions. WM performance showed differential improvement between testing days one and two across the groups with the highest increases observed in the rt-fMRI neurofeedback group. These results provide evidence that individuals can quickly gain the ability to consciously control the left DLPFC, and this training results in improvements of WM performance beyond that of training alone. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.

Science.gov (United States)

Panero, Riccardo; Rinaldi, Antonio; Memoli, Domenico; Nassa, Giovanni; Ravo, Maria; Rizzo, Francesca; Tarallo, Roberta; Milanesi, Luciano; Weisz, Alessandro; Giurato, Giorgio

2017-03-15

The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). aweisz@unisa.it or ggiurato@unisa.it. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Milan Kundera poeediparukaga faun / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

1996-01-01

Arvustus: Kundera, Milan. Surematus. Tln. : Monokkel, 1995. Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 176-179

WE-H-207B-00: MRgRT

Energy Technology Data Exchange (ETDEWEB)

NONE

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.

WE-H-207B-00: MRgRT

International Nuclear Information System (INIS)

2016-01-01

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A

Physics of Gate Modulated Resonant Tunneling (RT)-FETs: Multi-barrier MOSFET for steep slope and high on-current

Science.gov (United States)

Afzalian, Aryan; Colinge, Jean-Pierre; Flandre, Denis

2011-05-01

A new concept of nanoscale MOSFET, the Gate Modulated Resonant Tunneling Transistor (RT-FET), is presented and modeled using 3D Non-Equilibrium Green's Function simulations enlightening the main physical mechanisms. Owing to the additional tunnel barriers and the related longitudinal confinement present in the device, the density of state is reduced in its off-state, while remaining comparable in its on-state, to that of a MOS transistor without barriers. The RT-FET thus features both a lower RT-limited off-current and a faster increase of the current with V G, i.e. an improved slope characteristic, and hence an improved Ion/ Ioff ratio. Such improvement of the slope can happen in subthreshold regime, and therefore lead to subthreshold slope below the kT/q limit. In addition, faster increase of current and improved slope occur above threshold and lead to high thermionic on-current and significant Ion/ Ioff ratio improvement, even with threshold voltage below 0.2 V and supply voltage V dd of a few hundreds of mV as critically needed for future technology nodes. Finally RT-FETs are intrinsically immune to source-drain tunneling and are therefore promising candidate for extending the roadmap below 10 nm.

qRT-PCR quantification of the biological control agent Trichoderma harzianum in peat and compost-based growing media.

Science.gov (United States)

Beaulieu, Robert; López-Mondéjar, Rubén; Tittarelli, Fabio; Ros, Margarita; Pascual, José Antonio

2011-02-01

To ensure proper use of Trichoderma harzianum in agriculture, accurate data must be obtained in population monitoring. The effectiveness of qRT-PCR to quantify T. harzianum in different growing media was compared to the commonly used techniques of colony counting and qPCR. Results showed that plate counting and qPCR offered similar T. harzianum quantification patterns of an initial rapid increase in fungal population that decreased over time. However, data from qRT-PCR showed a population curve of active T. harzianum with a delayed onset of initial growth which then increased throughout the experiment. Results demonstrated that T. harzianum can successfully grow in these media and that qRT-PCR can offer a more distinct representation of active T. harzianum populations. Additionally, compost amended with T. harzianum exhibited a lower Fusarium oxysporum infection rate (67%) and lower percentage of fresh weight loss (11%) in comparison to amended peat (90% infection rate, 23% fresh weight loss). Copyright © 2010 Elsevier Ltd. All rights reserved.

Quantitative real-time RT-PCR and chromogenic in situ hybridization

DEFF Research Database (Denmark)

Rosa, Fabíola E; Silveira, Sara M; Silveira, Cássia G T

2009-01-01

. METHODS: To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR) and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. RESULTS: The concordance...

Selection of reference genes for qRT-PCR analysis of gene expression in sea cucumber Apostichopus japonicus during aestivation

Science.gov (United States)

Zhao, Ye; Chen, Muyan; Wang, Tianming; Sun, Lina; Xu, Dongxue; Yang, Hongsheng

2014-11-01

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a technique that is widely used for gene expression analysis, and its accuracy depends on the expression stability of the internal reference genes used as normalization factors. However, many applications of qRT-PCR used housekeeping genes as internal controls without validation. In this study, the expression stability of eight candidate reference genes in three tissues (intestine, respiratory tree, and muscle) of the sea cucumber Apostichopus japonicus was assessed during normal growth and aestivation using the geNorm, NormFinder, delta CT, and RefFinder algorithms. The results indicate that the reference genes exhibited significantly different expression patterns among the three tissues during aestivation. In general, the β-tubulin (TUBB) gene was relatively stable in the intestine and respiratory tree tissues. The optimal reference gene combination for intestine was 40S ribosomal protein S18 (RPS18), TUBB, and NADH dehydrogenase (NADH); for respiratory tree, it was β-actin (ACTB), TUBB, and succinate dehydrogenase cytochrome B small subunit (SDHC); and for muscle it was α-tubulin (TUBA) and NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 (NDUFA13). These combinations of internal control genes should be considered for use in further studies of gene expression in A. japonicus during aestivation.

Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice.

Science.gov (United States)

da Silva, Paula Renata Alves; Vidal, Marcia Soares; de Paula Soares, Cleiton; Polese, Valéria; Simões-Araújo, Jean Luís; Baldani, José Ivo

2016-11-01

Among the members of the genus Burkholderia, Burkholderia tropica has the ability to fix nitrogen and promote sugarcane plant growth as well as act as a biological control agent. There is little information about how this bacterium metabolizes carbohydrates as well as those carbon sources found in the sugarcane juice that accumulates in stems during plant growth. Reverse transcription quantitative PCR (RT-qPCR) can be used to evaluate changes in gene expression during bacterial growth on different carbon sources. Here we tested the expression of six reference genes, lpxC, gyrB, recA, rpoA, rpoB, and rpoD, when cells were grown with glucose, fructose, sucrose, mannitol, aconitic acid, and sugarcane juice as carbon sources. The lpxC, gyrB, and recA were selected as the most stable reference genes based on geNorm and NormFinder software analyses. Validation of these three reference genes during strain Ppe8 growth on the same carbon sources showed that genes involved in glycogen biosynthesis (glgA, glgB, glgC) and trehalose biosynthesis (treY and treZ) were highly expressed when Ppe8 was grown in aconitic acid relative to other carbon sources, while otsA expression (trehalose biosynthesis) was reduced with all carbon sources. In addition, the expression level of the ORF_6066 (gluconolactonase) gene was reduced on sugarcane juice. The results confirmed the stability of the three selected reference genes (lpxC, gyrB, and recA) during the RT-qPCR and also their robustness by evaluating the relative expression of genes involved in glycogen and trehalose biosynthesis when strain Ppe8 was grown on different carbon sources and sugarcane juice.

Direct recovery of infectious Pestivirus from a full-length RT-PCR amplicon

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, Ilona; Hoffmann, Bernd

2008-01-01

This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro, and the result......This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro......, and the resulting RNA transcripts were electroporated into ovine cells. Infectious virus was obtained after one cell culture passage. The rescued viruses had a phenotype similar to the parental Border Disease virus strain. Therefore, direct generation of infectious pestiviruses from full-length RT-PCR cDNA products...

Pärt, Arvo: "Litany" / Patric Wiklacz

Index Scriptorium Estoniae

Wiklacz, Patric

1996-01-01

Uuest heliplaadist "Pärt, Arvo: "Litany". Litany. Psalom. Trisagion. The Hilliard Ensemble, Orchestre de chambre de Tallinn, Choeur de chambre Philharmonique d'Estonie, Tõnu Kaljuste. Orchestre de chambre de Lituanie, Saulius Sondeckis. ECM New Series ECM 1592, distribution Polygram 449 810-2 (CD:158F)

Pärt, Arvo: "Litany" / Barry Witherden

Index Scriptorium Estoniae

Witherden, Barry

1996-01-01

Uuest heliplaadist "Pärt, Arvo: "Litany". Litany. Psalom. Trisagion. The Hilliard Ensemble, Tallinn Chamber Orchestra, Estonian Philharmonic Chamber Orchestra, Estonian Philharmonic Chamber Choir, Tõnu Kaljuste. Orchestre de chambre de Lituanie, Saulius Sondeckis". ECM New Series ECM 1592, distribution Polygram 449 810-2 (CD:158F)

The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

Science.gov (United States)

Zavodsky, Bradley; Kozlowski, Danielle; Case, Jonathan; Molthan, Andrew

2012-01-01

Short-term Prediction Research and Transition (SPoRT) seeks to improve short-term, regional weather forecasts using unique NASA products and capabilities SPoRT has developed a unique, real-time configuration of the NASA Unified Weather Research and Forecasting (WRF)WRF (ARW) that integrates all SPoRT modeling research data: (1) 2-km SPoRT Sea Surface Temperature (SST) Composite, (2) 3-km LIS with 1-km Greenness Vegetation Fraction (GVFs) (3) 45-km AIRS retrieved profiles. Transitioned this real-time forecast to NOAA's Hazardous Weather Testbed (HWT) as deterministic model at Experimental Forecast Program (EFP). Feedback from forecasters/participants and internal evaluation of SPoRT-WRF shows a cool, dry bias that appears to suppress convection likely related to methodology for assimilation of AIRS profiles Version 2 of the SPoRT-WRF will premier at the 2012 EFP and include NASA physics, cycling data assimilation methodology, better coverage of precipitation forcing, and new GVFs

Teekond Kirjasõna Vabariigis / Märt Väljataga ; intervjueerinud Marek Tamm

Index Scriptorium Estoniae

Väljataga, Märt, 1965-

2015-01-01

Märt Väljataga tõlgitud R. Rorty artiklist "Pragmatism ja filosoofia", mis ilmus Akadeemia 1992, nr. 2, lk. 281-282, 285, tema filosoofiast ja Märt Väljataga tööst ajakirja "Vikerkaar" toimetajana ning tõlkijana

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

Science.gov (United States)

Bell, Jordan R.; Case, Jonathan L.; LaFontaine, Frank J.; Kumar, Sujay V.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed a Greenness Vegetation Fraction (GVF) dataset, which is updated daily using swaths of Normalized Difference Vegetation Index data from the Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA EOS Aqua and Terra satellites. NASA SPoRT began generating daily real-time GVF composites at 1-km resolution over the Continental United States (CONUS) on 1 June 2010. The purpose of this study is to compare the National Centers for Environmental Prediction (NCEP) climatology GVF product (currently used in operational weather models) to the SPoRT-MODIS GVF during June to October 2010. The NASA Land Information System (LIS) was employed to study the impacts of the SPoRT-MODIS GVF dataset on a land surface model (LSM) apart from a full numerical weather prediction (NWP) model. For the 2010 warm season, the SPoRT GVF in the western portion of the CONUS was generally higher than the NCEP climatology. The eastern CONUS GVF had variations both above and below the climatology during the period of study. These variations in GVF led to direct impacts on the rates of heating and evaporation from the land surface. In the West, higher latent heat fluxes prevailed, which enhanced the rates of evapotranspiration and soil moisture depletion in the LSM. By late Summer and Autumn, both the average sensible and latent heat fluxes increased in the West as a result of the more rapid soil drying and higher coverage of GVF. The impacts of the SPoRT GVF dataset on NWP was also examined for a single severe weather case study using the Weather Research and Forecasting (WRF) model. Two separate coupled LIS/WRF model simulations were made for the 17 July 2010 severe weather event in the Upper Midwest using the NCEP and SPoRT GVFs, with all other model parameters remaining the same. Based on the sensitivity results, regions with higher GVF in the SPoRT model runs had higher evapotranspiration and

Factors influencing the use of RT in NSW: a qualitative study exploring consumer and health professional practices

International Nuclear Information System (INIS)

Sundaresan, Puma; Milross, Christopher G.; Stockler, Martin R.; Smith, Andrea; Evans, Alison; King, Madeleine T.

2014-01-01

Radiotherapy (RT) is an essential and cost-effective cancer treatment. It is underutilised in Australia. Bridging the gap between actual and optimal RT utilisation requires not only provision of adequate RT infrastructure but also an understanding of the factors that influence the extent to which this opportunity for RT is utilised. This study explored factors perceived to affect RT-related decision making by consumers and health professionals (HPs). Six semi-structured focus groups (FGs) and 13 interviews were conducted at three geographical locations in NSW, Australia (n=26 consumers and 30 HPs). Audio recordings of FGs and interviews were transcribed verbatim and analysed thematically. An exhaustive list of issues perceived to affect consumer and HP RT decisions was identified. There were common themes across participant groups and locations. Perceptions of RT and its benefits, as well as accurate communication of the expected benefits and risks of RT, were highlighted as important to decision making. Perceived factors relating to 'inconvenience' of RT were multifaceted and included travel, relocation, accommodation, time away from work and financial challenges. Perceived potential barriers to RT referral included knowledge of RT and RT services, availability of a local or visiting RT service, referrer bias, and the low profile of RT. Important drivers during RT decisions appear to include the perceived benefit, risks and inconvenience of RT. Underutilisation of RT may also result from multiple barriers at the referrer level. Further research into whether these factors influence actual RT decisions is needed.

Development and implementation of the quality control panel of RT-PCR and real-time RT-PCR for avian influenza A (H5N1 surveillance network in mainland China

Directory of Open Access Journals (Sweden)

Wang Wei

2011-03-01

Full Text Available Abstract Background Reverse transcription PCR (RT-PCR and real time RT-PCR (rRT-PCR have been indispensable methods for influenza surveillance, especially for determination of avian influenza. The movement of testing beyond reference lab introduced the need of quality control, including the implementation of an evaluation system for validating personal training and sample proficiency testing. Methods We developed a panel with lysates of seasonal influenza virus (H1N1, H3N2 and B, serials of diluted H5N1 virus lysates, and in-vitro transcribed H5 hemaglutinin (HA and an artificial gene RNAs for RT-PCR and rRT-PCR quality control assessment. The validations of stability and reproducibility were performed on the panel. Additionally, the panel was implemented to assess the detection capability of Chinese human avian influenza networks. Results The panel has relatively high stability and good reproducibility demonstrated by kappa's tests. In the implementation of panel on Chinese human avian influenza networks, the results suggested that there were a relatively low number of discrepancies for both concise and reproducibility in Chinese avian influenza virus net works. Conclusions A quality control panel of RT-PCR and real-time RT-PCR for avian influenza A (H5N1 surveillance network was developed. An availably statistical data, which are used to assess the detection capability of networks on avian influenza virus (H5N1, can be obtained relatively easily through implementation of the panel on networks.

A study on the establishment of practical program for the RT promotion plan

Energy Technology Data Exchange (ETDEWEB)

Kim, Seong Yen; Jin, J. H.; Beyn, M. W.; Han, H. S.; Park, C.; Lee, J. W.; Yang, M. S.; Jeong, I. H.; Nho, Y. C

2003-03-01

The present state of RT utilizations in Korea is categorized into radioisotope applications to treat incurable diseases, food irradiation, and nondestructive test, and radiation applications by radiation generators such as cyclotrons to produce short half-life radioisotopes for medical uses and electron accelerators to make better products of cables and radial tiers. In order to activate more utilizations of RT, the followings should be carried out: 1. Establishment of RT Research Institute and RT Industrial Complex - Establishment of the tentatively named [Radiation Science and Technology Research Center] and 'Cyclotron Center' in four provinces should be effectively carried out as scheduled. - Successful pursuing design and construction of the proton accelerator for research and technology development, and CNS research facility. - Radiation area workers training participating the RT projects; Participation and training of university graduates to the on-going and planned RT projects, Classes for special skills and experts to radiation could be designed at the Consociated Graduate School, being established by joining national research organizations, if necessary. - Secure minimum number of R and D man power for RT development 2. Review design and construction of RI production reactor and construct distribution and transportation of RIs - Constructions of distribution lines and a central depository site with the establishment of Cyclotron Centers and RI production reactor - Designation, as early as possible, of the organization to handle the constructions of the distribution lines and the central depository site. 3. Establishment of an organization to appeal RT industries' concerns - An organization composed of governmental officials, researchers from national research institutes and/or private research institutes, representatives from associations and RT industries should be formed to define the issues to promote radiation uses. 4. Establishment of

A study on the establishment of practical program for the RT promotion plan

International Nuclear Information System (INIS)

Kim, Seong Yen; Jin, J. H.; Beyn, M. W.; Han, H. S.; Park, C.; Lee, J. W.; Yang, M. S.; Jeong, I. H.; Nho, Y. C.

2003-03-01

The present state of RT utilizations in Korea is categorized into radioisotope applications to treat incurable diseases, food irradiation, and nondestructive test, and radiation applications by radiation generators such as cyclotrons to produce short half-life radioisotopes for medical uses and electron accelerators to make better products of cables and radial tiers. In order to activate more utilizations of RT, the followings should be carried out: 1. Establishment of RT Research Institute and RT Industrial Complex - Establishment of the tentatively named [Radiation Science and Technology Research Center] and 'Cyclotron Center' in four provinces should be effectively carried out as scheduled. - Successful pursuing design and construction of the proton accelerator for research and technology development, and CNS research facility. - Radiation area workers training participating the RT projects; Participation and training of university graduates to the on-going and planned RT projects, Classes for special skills and experts to radiation could be designed at the Consociated Graduate School, being established by joining national research organizations, if necessary. - Secure minimum number of R and D man power for RT development 2. Review design and construction of RI production reactor and construct distribution and transportation of RIs - Constructions of distribution lines and a central depository site with the establishment of Cyclotron Centers and RI production reactor - Designation, as early as possible, of the organization to handle the constructions of the distribution lines and the central depository site. 3. Establishment of an organization to appeal RT industries' concerns - An organization composed of governmental officials, researchers from national research institutes and/or private research institutes, representatives from associations and RT industries should be formed to define the issues to promote radiation uses. 4. Establishment of Pan-ministry PR

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

Science.gov (United States)

Goldman, N

1994-09-01

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

Combination of RT-PCR and proteomics for the identification of Crimean-Congo hemorrhagic fever virus in ticks

Directory of Open Access Journals (Sweden)

Isabel G. Fernández de Mera

2017-07-01

Full Text Available Crimean-Congo hemorrhagic fever (CCHF is an emerging tick-borne zoonotic disease caused by the CCHF virus (CCHFV. In this study, an experimental approach combining RT-PCR and proteomics was used for the identification and characterization of CCHFV in 106 ticks from 7 species that were collected from small ruminants in Greece. The methodological approach included an initial screening for CCHFV by RT-PCR followed by proteomics analysis of positive and control negative tick samples. This novel approach allowed the identification of CCHFV-positive ticks and provided additional information to corroborate the RT-PCR findings using a different approach. Two ticks, Dermacentor marginatus and Haemaphysalis parva collected from a goat and a sheep, respectively were positive for CCHFV. The sequences for CCHFV RNA segments S and L were characterized by RT-PCR and proteomics analysis of tick samples, respectively. These results showed the possibility of combining analyses at the RNA and protein levels using RT-PCR and proteomics for the characterization of CCHFV in ticks. The results supported that the CCHFV identified in ticks are genetic variants of the AP92 strain. Although the AP92-like strains probably do not represent a high risk of CCHF to the population, the circulation of genetically diverse CCHFV strains could potentially result in the appearance of novel viral genotypes with increased pathogenicity and fitness.

Incremental clinical value of a dedicated RT planning FDG PET-CT over staging PET-CT in non-small cell lung cancer

International Nuclear Information System (INIS)

Lin, P.; Som, S.; Vinod, S.; Lin, M.; Shon, I. H.

2009-01-01

Full text:Objectives: To evaluate whether FDG-PET performed for radiotherapy planning can detect disease progression, compared with staging PET. Methods: Thirteen patients underwent a planning PET-CT for curative RT ( R T-PET ) within eight weeks of a staging PET-CT for newly diagnosed NSCLC between 10/2007 and 1/2009. All studies were acquired on a Philips GXL PET-CT using the same protocols, except RT-PET is acquired on a RT flat bed. The images were interpreted by consensus readings of two physicians: location/number, visual grading (0-4:3> liver, 4>brain), max transverse diameter ( M ax D ) (tumour margin is delineated by a SUV threshold of 2.5) and max SUV of each lesion. Progressive disease (PD) is defined as >10% increase in max D. Results: RT-PET detected PD (primary or nodal) or new metastases in 8 pts (61%) (mean interval:30.2±14 days, range:7-54 days). For primary tumour, RT-PET detected PD in 5

Computerization of nuclear material accounting and control at storage facilities of RT-1 plant, PA Mayak

International Nuclear Information System (INIS)

Krakhmal'nik, V.I.; Menshchikov, Yu.L.; Mozhaev, D.A.

1999-01-01

Computerized system for nuclear material (NM) accounting and control at RT-1 plant is being created on the basis of advanced engineering and programming tools, which give a possibility to ensure prompt access to the information required, to unify the accounting and report documentation, make statistical processing of the data, and trace the NM transfers in the chain of its storage at facilities of RT-1 plant. Currently, the accounting is performed in parallel, both by the old methods and with computerized system. The following functions are performed by the system at the current stage: input of data on the end product's (plutonium dioxide) quantitative and qualitative composition; data input on the localization of containers with finished products at storage facilities of the plant and the product's temporary characteristics; selective verification of the data on containers and batches, according to the criteria prespecified by the user; data protection against unauthorized access; data archiving; report documents formation and providing [ru

RT-PCR for detection of all seven genotypes of Lyssavirus genus.

Science.gov (United States)

Vázquez-Morón, S; Avellón, A; Echevarría, J E

2006-08-01

The Lyssavirus genus includes seven species or genotypes named 1-7. Rabies genotypes correlate with geographical distribution and specific hosts. Co-circulation of different lyssaviruses, imported cases, and the presence of unknown viruses, such as Aravan, Khujand, Irkut and West Caucasian Bat Virus, make it necessary to use generic methods able to detect all lyssaviruses. Primer sequences were chosen from conserved regions in all genotypes in order to optimise a generic RT-PCR. Serial dilutions of 12 RNA extracts from all seven Lyssavirus genotypes were examined to compare the sensitivity of the RT-PCR standardised in this study with a published RT-PCR optimised for EBLV1 detection and capable of amplifying RNA from all seven lyssaviruses. All seven genotypes were detected by both RT-PCRs, however, the sensitivity was higher with the new version of the test. Twenty samples submitted for rabies diagnosis were tested by the new RT-PCR. Eight out of 20 samples from six dogs, one horse and one bat were found positive, in agreement with immunofluorescence results. Seven samples from terrestrial mammals were genotype 1 and one from a bat was genotype 5. In conclusion, this method can be used to complement immunofluorescence for the diagnosis of rabies, enabling the detection of unexpected lyssaviruses during rabies surveillance.

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

Science.gov (United States)

Mehta, Rohini; Birerdinc, Aybike; Hossain, Noreen; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair; Baranova, Ancha

2010-05-21

Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

Directory of Open Access Journals (Sweden)

Afendy Arian

2010-05-01

Full Text Available Abstract Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

Benign meningiomas: primary treatment selection affects survival

International Nuclear Information System (INIS)

Condra, Kellie S.; Buatti, John M.; Mendenhall, William M.; Friedman, William A.; Marcus, Robert B.; Rhoton, Albert L.

1997-01-01

Purpose: To examine the effect of primary treatment selection on outcomes for benign intracranial meningiomas at the University of Florida. Methods and Materials: For 262 patients, the impact of age, Karnofsky performance status, pathologic features, tumor size, tumor location, and treatment modality on local control and cause-specific survival was analyzed (minimum potential follow-up, 2 years; median follow-up, 8.2 years). Extent of surgery was classified by Simpson grade. Treatment groups: surgery alone (n = 229), surgery and postoperative radiotherapy (RT) (n = 21), RT alone (n = 7), radiosurgery alone (n = 5). Survival analysis: Kaplan-Meier method with univariate and multivariate analysis. Results: At 15 years, local control was 76% after total excision (TE) and 87% after subtotal excision plus RT (SE+RT), both significantly better (p = 0.0001) than after SE alone (30%). Cause-specific survival at 15 years was reduced after treatment with SE alone (51%), compared with TE (88%) or SE+RT (86%) (p = 0.0003). Recurrence after primary treatment portended decreased survival, independent of initial treatment group or salvage treatment selection (p = 0.001). Atypical pathologic features predicted reduced 15-year local control (54 vs. 71%) and cause-specific survival rates (57 vs. 86%). Multivariate analysis for cause-specific survival revealed treatment group (SE vs. others; p = 0.0001), pathologic features (atypical vs. typical; p = 0.0056), and Karnofsky performance status (≥80 vs. <80; p = 0.0153) as significant variables. Conclusion: Benign meningiomas are well managed by TE or SE+RT. SE alone is inadequate therapy and adversely affects cause-specific survival. Atypical pathologic features predict a poorer outcome, suggesting possible benefit from more aggressive treatment. Because local recurrence portends lower survival rates, primary treatment choice is important

Dose optimization with first-order total-variation minimization for dense angularly sampled and sparse intensity modulated radiation therapy (DASSIM-RT)

Energy Technology Data Exchange (ETDEWEB)

Kim, Hojin; Li Ruijiang; Lee, Rena; Goldstein, Thomas; Boyd, Stephen; Candes, Emmanuel; Xing Lei [Department of Electrical Engineering, Stanford University, Stanford, California 94305-9505 (United States) and Department of Radiation Oncology, Stanford University, Stanford, California 94305-5847 (United States); Department of Radiation Oncology, Stanford University, Stanford, California 94305-5847 (United States); Department of Radiation Oncology, Ehwa University, Seoul 158-710 (Korea, Republic of); Department of Electrical Engineering, Stanford University, Stanford, California 94305-9505 (United States); Department of Statistics, Stanford University, Stanford, California 94305-4065 (United States); Department of Radiation Oncology, Stanford University, Stanford, California 94305-5304 (United States)

2012-07-15

Purpose: A new treatment scheme coined as dense angularly sampled and sparse intensity modulated radiation therapy (DASSIM-RT) has recently been proposed to bridge the gap between IMRT and VMAT. By increasing the angular sampling of radiation beams while eliminating dispensable segments of the incident fields, DASSIM-RT is capable of providing improved conformity in dose distributions while maintaining high delivery efficiency. The fact that DASSIM-RT utilizes a large number of incident beams represents a major computational challenge for the clinical applications of this powerful treatment scheme. The purpose of this work is to provide a practical solution to the DASSIM-RT inverse planning problem. Methods: The inverse planning problem is formulated as a fluence-map optimization problem with total-variation (TV) minimization. A newly released L1-solver, template for first-order conic solver (TFOCS), was adopted in this work. TFOCS achieves faster convergence with less memory usage as compared with conventional quadratic programming (QP) for the TV form through the effective use of conic forms, dual-variable updates, and optimal first-order approaches. As such, it is tailored to specifically address the computational challenges of large-scale optimization in DASSIM-RT inverse planning. Two clinical cases (a prostate and a head and neck case) are used to evaluate the effectiveness and efficiency of the proposed planning technique. DASSIM-RT plans with 15 and 30 beams are compared with conventional IMRT plans with 7 beams in terms of plan quality and delivery efficiency, which are quantified by conformation number (CN), the total number of segments and modulation index, respectively. For optimization efficiency, the QP-based approach was compared with the proposed algorithm for the DASSIM-RT plans with 15 beams for both cases. Results: Plan quality improves with an increasing number of incident beams, while the total number of segments is maintained to be about the

System of programming units for the K556RT4 and K556RT5 fixed programmed memory devices

International Nuclear Information System (INIS)

Bobkov, S.G.; Ermolin, Yu.V.; Kantserov, V.A.; Strigin, V.B.

1983-01-01

The programming system of constant programmable memory devices K556RT4 and K556RT5 that consist of two units (a programming device and an electrothermotraining unit) is described. The modules are made in the KAMAK standard. The programming device takes up 2 normal places, while the electrothermotraining block takes up 1 place. As information recording is done using a computer the time for programming is reduced and the possibility of errors is limited as compared with the manual method. The computer introduces the whole word to be recorded, not the separate parts, in the programming device. The transition to a new digit of a given word in the programming device is done automatically. This reduces the expense of computer time and accelerates the programming of microdiagrams

An RT distribution analysis of relatedness proportion effects in lexical decision and semantic categorization reveals different mechanisms.

Science.gov (United States)

de Wit, Bianca; Kinoshita, Sachiko

2015-01-01

The magnitude of the semantic priming effect is known to increase as the proportion of related prime-target pairs in an experiment increases. This relatedness proportion (RP) effect was studied in a lexical decision task at a short prime-target stimulus onset asynchrony (240 ms), which is widely assumed to preclude strategic prospective usage of the prime. The analysis of the reaction time (RT) distribution suggested that the observed RP effect reflected a modulation of a retrospective semantic matching process. The pattern of the RP effect on the RT distribution found here is contrasted to that reported in De Wit and Kinoshita's (2014) semantic categorization study, and it is concluded that the RP effect is driven by different underlying mechanisms in lexical decision and semantic categorization.

Clinical application of RT-nested PCR integrated with RFLP in Hantavirus detection and genotyping: a prospective study in Shandong Province, PR China.

Science.gov (United States)

Liu, Yun-Xi; Zhao, Zhong-Tang; Cao, Wu-Chun; Xu, Xiao-Qun; Suo, Ji-Jiang; Xing, Yu-Bin; Jia, Ning; Du, Ming-Mei; Liu, Bo-Wei; Yao, Yuan

2013-01-01

The aim of the present study was to evaluate the clinical usefulness of applying RT-nested PCR along with RFLP as a method for diagnosis and genotypic differentiation of Hantavirus in the acute-stage sera of HFRS patients as compared to the ELISA technique. A prospective study of patients with suspected HFRS patients was carried out. Sera were collected for serological evaluation by ELISA and RT-nested PCR testing. Primers were selected from the published sequence of the S segment of HTNV strain 76-118 and SEOV strain SR-11, which made it possible to obtain an amplicon of 403 bp by RT-nested PCR. The genotypic differentiations of the RT-nested PCR amplicons were carried out by RFLP. Sequence analyses of the amplicons were used to confirm the accuracy of the results obtained by RFLP. Of the 48 acute-stage sera from suspected HFRS patients, 35 were ELISA-positive while 41 were positive by RT-nested PCR. With Hind III and Hinf I, RFLP profiles of the RT-nested PCR amplicons of the 41 positive sera exhibited two patterns. 33 had RFLP profiles similar to the reference strain R22, and thus belonged to the SEOV type. The other 8 samples which were collected during October-December had RFLP profiles similar to the reference strain 76-118, and thus belonged to the HTNV type. Sequence phylogenetic analysis of RT-nested PCR amplicons revealed sdp1, sdp2 YXL-2008, and sdp3 as close relatives of HTNV strain 76-118, while sdp22 and sdp37 as close relatives of SEOV strain Z37 and strain R22 located in two separate clusters in the phylogenetic tree. These results were identical to those acquired by RFLP. RT-nested PCR integrated with RFLP was a rapid, simple, accurate method for detecting and differentiating the genotypes of Hantavirus in the acute-stage sera of suspected HFRS patients. In Shandong province, the main genotypes of Hantavirus belonged to the SEOV types, while the HTNV types were observed during the autumn-winter season.

Application and evaluation of RT-PCR-ELISA for the nucleoprotein and RT-PCR for detection of low-pathogenic H5 and H7 subtypes of avian influenza virus

DEFF Research Database (Denmark)

Dybkær, Karen; Munch, Mette; Handberg, Kurt J.

2004-01-01

Three 1-tube Reverse Transcriptase Polymerase Chain Reactions (RT-PCR) directed against the genes encoding the nucleoprotein (NP) and the H5 and H7 hemagglutinin (HA) gene, respectively, were used for detection of avian influenza virus (AIV) in various specimens. A total of 1,040 samples...... originating from chickens experimentally infected with 2 different low pathogenic avian influenza viruses, from domestic ducks and from wild aquatic birds were examined. The outcome of 1) the universal AIV RT-PCR including a PCR-enzyme-linked immunosorbent assay (ELISA) procedure directed against NP (NP RT...

Kirjanduskriitikute suvemängud / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

2007-01-01

Arvustus: Lodge, David. Ühest kohast teise / tlk. Aet Varik. Tallinn : Varrak, 2005 ; Lodge, David. Väike maailm / tlk. Kersti Unt. Tallinn : Varrak, 1996 ; Lodge, David. Väärt töö / tlk. Kersti Unt. Tallinn : Varrak, 2006

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

Science.gov (United States)

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

Reverse transcriptase-quantitative polymerase chain reaction (RT ...

African Journals Online (AJOL)

zino

2014-02-05

Feb 5, 2014 ... ecological studies - A review ... The objective of this review is to assess the importance of RT-qPCR in soil related ... phenol extraction step with heat inactivation of the added .... Real time polymerase chain reaction (PCR).

A novel mean-centering method for normalizing microRNA expression from high-throughput RT-qPCR data

Directory of Open Access Journals (Sweden)

Wylie Dennis

2011-12-01

Full Text Available Abstract Background Normalization is critical for accurate gene expression analysis. A significant challenge in the quantitation of gene expression from biofluids samples is the inability to quantify RNA concentration prior to analysis, underscoring the need for robust normalization tools for this sample type. In this investigation, we evaluated various methods of normalization to determine the optimal approach for quantifying microRNA (miRNA expression from biofluids and tissue samples when using the TaqMan® Megaplex™ high-throughput RT-qPCR platform with low RNA inputs. Findings We compared seven normalization methods in the analysis of variation of miRNA expression from biofluid and tissue samples. We developed a novel variant of the common mean-centering normalization strategy, herein referred to as mean-centering restricted (MCR normalization, which is adapted to the TaqMan Megaplex RT-qPCR platform, but is likely applicable to other high-throughput RT-qPCR-based platforms. Our results indicate that MCR normalization performs comparable to or better than both standard mean-centering and other normalization methods. We also propose an extension of this method to be used when migrating biomarker signatures from Megaplex to singleplex RT-qPCR platforms, based on the identification of a small number of normalizer miRNAs that closely track the mean of expressed miRNAs. Conclusions We developed the MCR method for normalizing miRNA expression from biofluids samples when using the TaqMan Megaplex RT-qPCR platform. Our results suggest that normalization based on the mean of all fully observed (fully detected miRNAs minimizes technical variance in normalized expression values, and that a small number of normalizer miRNAs can be selected when migrating from Megaplex to singleplex assays. In our study, we find that normalization methods that focus on a restricted set of miRNAs tend to perform better than methods that focus on all miRNAs, including

Evaluation of selection criteria for graduate students in radiation therapy.

Science.gov (United States)

Schneider-Kolsky, Michal; Wright, Caroline; Baird, Marilyn

2006-12-01

Selection of suitable students into graduate medical and specialist health professional courses can be difficult. Historically, selection of students was primarily based on prior academic performance. Recently, however, more emphasis has been placed on considering broader academic backgrounds and personal characteristics and attitudes of students, but no reliable measurement tool is available to predict student success and satisfaction with their choice of profession. The aim of this study was to survey practising radiation therapists in Australia to seek their opinions regarding suitable selection criteria for graduate entry radiation therapy (RT) students in order to optimize selection procedures for future applicants. Four hundred questionnaires were sent to nine RT centres in three states within Australia. All nine clinics participated in the survey and 189 questionnaires were returned. Results show that the majority of radiation therapists place a high level of importance upon a sound knowledge of physics and mathematics, as well as life experience, and agree that a visit to an RT clinic plus an interview comprise important components of the selection process. Humanities, psychology and a psychometric test were not viewed as essential entry requirements. Experienced radiation therapists placed less value on academic performance in the primary degree and were more likely to include an interview as a selection criterion than junior practitioners. Empathy for patients was identified as the most important personal attribute. It is thus recommended that not only cognitive but also personal skills be evaluated during the selection of prospective radiation therapists.

MIV-150-containing intravaginal rings protect macaque vaginal explants against SHIV-RT infection.

Science.gov (United States)

Ouattara, Louise A; Barnable, Patrick; Mawson, Paul; Seidor, Samantha; Zydowsky, Thomas M; Kizima, Larisa; Rodriguez, Aixa; Fernández-Romero, José A; Cooney, Michael L; Roberts, Kevin D; Gettie, Agegnehu; Blanchard, James; Robbiani, Melissa; Teleshova, Natalia

2014-05-01

Recent studies demonstrated that intravaginal rings (IVRs) containing 100 mg of the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 significantly protect macaques against a chimeric simian-human immunodeficiency virus that expresses the HIV-1 HxB2 reverse transcriptase (SHIV-RT) when present before and after vaginal challenge. The objectives of this study were to (i) evaluate the pharmacodynamics (PD) of MIV-150 in vaginal fluids (VF) and in ectocervical and vaginal tissues following 100-mg MIV-150 IVR exposure and to (ii) gain more insight whether pharmacokinetics (PK) of MIV-150 can predict PD. MIV-150 in VF collected at 1 day and 14 days post-MIV-150 IVR insertion inhibited ex vivo SHIV-RT infection in vaginal biopsy specimens from untreated animals (not carrying IVRs) in a dose-dependent manner. Previous PK studies demonstrated a significant increase of ectocervical and vaginal tissue MIV-150 concentrations 14 days versus 1 day post-IVR insertion, with the highest increase in vaginal tissue. Therefore, we tested PD of MIV-150 in tissues 14 days post-MIV-150 IVR insertion. Ex vivo SHIV-RT infection of vaginal, but not ectocervical, tissues collected 14 days post-MIV-150 IVR insertion was significantly inhibited compared to infection at the baseline (prior to MIV-150 IVR exposure). No changes in vaginal and ectocervical tissue infection were observed after placebo IVR exposure. Overall, these data underscore the use of the ex vivo macaque explant challenge models to evaluate tissue and VF PK/PD of candidate microbicides before in vivo animal efficacy studies. The data support further development of MIV-150-containing IVRs.

Pärt, Arvo. Litany; Psalom; Trisagion / Andreas Obst

Index Scriptorium Estoniae

Obst, Andreas

1996-01-01

Pärt, Arvo. Litany; Psalom; Trisagion. Hilliard Ensemble, Estonian Philharmonic Chamber Choir, Tallinn Chamber Orchestra, Tõnu Kaljuste; Lithuanian Chamber Orchestra, Saulius Sondeckis. ECM 1592/449 810-2

Used mixed oxide fuel reprocessing at RT-1 plant

Energy Technology Data Exchange (ETDEWEB)

Kolupaev, D.; Logunov, M.; Mashkin, A.; Bugrov, K.; Korchenkin, K. [FSUE PA ' Mayak' , 30, Lenins str, Ozersk, 460065 (Russian Federation); Shadrin, A.; Dvoeglazov, K. [ITCP ' PRORYV' , 2/8 Malaya Krasmoselskay str, Moscow, 107140 (Russian Federation)

2016-07-01

Reprocessing of the mixed uranium-plutonium spent nuclear fuel of the BN-600 reactor was performed at the RT-1 plant twice, in 2012 and 2014. In total, 8 fuel assemblies with a burn-up from 73 to 89 GW day/t and the cooling time from 17 to 21 years were reprocessed. The reprocessing included the stages of dissolution, clarification, extraction separation of U and Pu with purification from the fission products, refining of uranium and plutonium at the relevant refining cycles. Dissolution of the fuel composition of MOX used nuclear fuel (UNF) in nitric acid solutions in the presence of fluoride ion has occurred with the full transfer of actinides into solution. Due to the high content of Pu extraction separation of U and Pu was carried out on a nuclear-safe equipment designed for the reprocessing of highly enriched U spent nuclear fuel and Pu refining. Technological processes of extraction, separation and refining of actinides proceeded without deviations from the normal mode. The output flow of the extraction outlets in their compositions corresponded to the regulatory norms and remained at the level of the compositions of the streams resulting from the reprocessing of fuel types typical for the RT-1 plant. No increased losses of Pu into waste have been registered during the reprocessing of BN-600 MOX UNF an compare with VVER-440 uranium UNF reprocessing. (authors)

Narcisisma saistība ar pašnovērtējumu.

OpenAIRE

Strode, Indra

2008-01-01

Pētījuma mēķis ir noskaidrot narcisisma saistību ar pašvērtējumu. Pētījuma respondentu skaits – 60 cilvēki (30 sievietes, 30vīrieši). Vecuma ierobežojums – no 20 līdz 30 gadi. Pašvērtējuma līmeņa noteikšanai tika izmantota Rozenberga pašnovērtējuma aptauja („Rosenberg Self-Esteem Scale”, Rosenberg, 1965), narcisisma noteikšanai tik izmantota Narcistiskas personības aptauja (Raskin & Terry, 1988). Vīriešu narcisisma un pašvērtējuma rādītāji uzrādīja statistiski nozīmīgu korelāciju, tāpat kā si...

Mamma diagnostics for MTRA (medical-radiological personnel)/RT (radiologists); Mammadiagnostik fuer MTRA/RT

Energy Technology Data Exchange (ETDEWEB)

Fischer, Uwe; Baum, Friedemann

2014-07-01

The text book on mamma diagnostics for MTRA (medical-radiological personnel)/RT (radiologists) covers the following issues: Anatomy, development and physiology of mammary glands; tumor development an breast cancer risk; pathology, non-imaging diagnostics; mammography: physical-technical fundamentals; mammography: analogue technique; mammography: digital technique; mammography: quality assurance; mammography: legal questions and radiation protection; mammography: new developments; mammography: setting technique; mammography: use and appraisal; mamma-sonography: technique and methodology; mamma-sonography: assignment and appraisal, mamma-NMR: technique and methodology; mamma-NMR: assignment and appraisal lymph node diagnostics; mamma interventions; biopsy; mamma interventions: marking examination concepts; therapeutic concepts; hygienic concepts; communication and interaction.

Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus.

Science.gov (United States)

Santiago, Gilberto A; Vergne, Edgardo; Quiles, Yashira; Cosme, Joan; Vazquez, Jesus; Medina, Juan F; Medina, Freddy; Colón, Candimar; Margolis, Harold; Muñoz-Jordán, Jorge L

2013-01-01

Dengue is an acute illness caused by the positive-strand RNA dengue virus (DENV). There are four genetically distinct DENVs (DENV-1-4) that cause disease in tropical and subtropical countries. Most patients are viremic when they present with symptoms; therefore, RT-PCR has been increasingly used in dengue diagnosis. The CDC DENV-1-4 RT-PCR Assay has been developed as an in-vitro diagnostic platform and was recently approved by the US Food and Drug Administration (FDA) for detection of dengue in patients with signs or symptoms of mild or severe dengue. The primers and probes of this test have been designed to detect currently circulating strains of DENV-1-4 from around the world at comparable sensitivity. In a retrospective study with 102 dengue cases confirmed by IgM anti-DENV seroconversion in the convalescent sample, the RT-PCR Assay detected DENV RNA in 98.04% of the paired acute samples. Using sequencing as a positive indicator, the RT-PCR Assay had a 97.92% positive agreement in 86 suspected dengue patients with a single acute serum sample. After extensive validations, the RT-PCR Assay performance was highly reproducible when evaluated across three independent testing sites, did not produce false positive results for etiologic agents of other febrile illnesses, and was not affected by pathological levels of potentially interfering biomolecules. These results indicate that the CDC DENV-1-4 RT-PCR Assay provides a reliable diagnostic platform capable for confirming dengue in suspected cases.

Pärt, Arvo: "Miserere", "Festina lente" / Volkmar Fischer

Index Scriptorium Estoniae

Fischer, Volkmar

1991-01-01

Uuest heliplaadist Pärt, Arvo: "Miserere", "Festina lente", "Sarah Was Ninety Years Old". The Hilliard Ensemble. Orchester der Beethovenhalle Bonn. Dirigent Dennis Russel Davies (ECM Records, distr Amigo)

An Evidence-Based Approach to Detection by DASI-ELISA and RT-PCR in Dormant Period

Directory of Open Access Journals (Sweden)

Antonio Olmos

2008-01-01

Full Text Available An evidence-based approach, such as those developed in clinical and veterinary medicine, was applied to the detection of Plum pox virus (PPV during the dormant period. A standardized methodology was used for the calculation of parameters of the operational capacity of DASI-ELISA and RT-PCR in wintertime. These methods are routinely handled to test the sanitary status of plants in national or international trading and in those cases concerning export-import of plant materials. Diagnosis often has to be performed during the dormant period, when plant material is commercialized. Some guidelines to interpret diagnostic results of wintertime are provided in an attempt to minimize risks associated with the methods and over-reliance on the binary outcome of a single assay. In order to evaluate if a complementary test increased the confidence of PPV diagnosis when discordant results between DASI-ELISA and RT-PCR are obtained, NASBA-FH also was included. Likelihood ratios of each method were estimated based on the sensitivity and specificity obtained in wintertime. Subsequently, a Bayesian approach was performed to calculate post-test probability of PPV infection in spring. Results of evidence-based approach show that different PPV prevalences require different screening tests. Thus, at very low PPV prevalence levels DASI-ELISA should be used as the election method, whilst at the highest PPV prevalence levels RT-PCR should be performed. NASBA-FH could be used at medium prevalences to clarify discordances between DASI-ELISA and RT-PCR.

Detection of Tomato black ring virus by real-time one-step RT-PCR.

Science.gov (United States)

Harper, Scott J; Delmiglio, Catia; Ward, Lisa I; Clover, Gerard R G

2011-01-01

A TaqMan-based real-time one-step RT-PCR assay was developed for the rapid detection of Tomato black ring virus (TBRV), a significant plant pathogen which infects a wide range of economically important crops. Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA-2. The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants. The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA. A comparison with conventional RT-PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT-PCR was approximately ten-fold less sensitive than the real-time RT-PCR assay. Finally, the real-time RT-PCR assay was tested using five different RT-PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found. The development of this rapid assay should aid in quarantine and post-border surveys for regulatory agencies. Copyright © 2010 Elsevier B.V. All rights reserved.

Pärt, Arvo: Seven Magnificat Antiphons / Barry Witherden

Index Scriptorium Estoniae

Witherden, Barry

1996-01-01

Uuest heliplaadist "Pärt, Arvo: Seven Magnificat Antiphons. Magnificat. Summa; Tormis, Veljo: The Curse Upon Iron. Karelian Destiny. BBC Singers, Bo Holton". Collins Classics 1472-2 (61 minutes: DDD)

Use of RT-PCR and elisa techniques for the diagnostic of infectious bronchitis virus in broilers at slaughter

Directory of Open Access Journals (Sweden)

Davi de Oliveira Almeida

2015-03-01

Full Text Available ABSTRACT. Almeida D.O., Tortely R., Nascimento E.R., Khan M., Pereira V.L.A & Babapoor S. [Use of RT-PCR and elisa techniques for the diagnostic of infectious bronchitis virus in broilers at slaughter.] Uso das técnicas de RT-PCR e elisa no diagnóstico da bronquite infecciosa em frangos de corte ao abate. Revista Brasileira de Medicina Veterinária, 37(1:55-59, 2015. Departamento de Saúde Coletiva Veterinária e Saúde Pública, Universidade Federal Fluminense, Rua Vital Brazil Filho, 64, Santa Rosa, Niterói, RJ 24230-340, Brasil. E-mail: elmiro@vm.uff.br Avian infectious bronchitis (IB is a viral, acute and highly contagious disease caused by infectious bronchitis virus (IBV. The disease affects broilers improvement and performance causing major economic losses in the world poultry industry. Generally, IBV infections can be diagnosed by detection of IBV itself or the specific antibody response. This study aimed to detect IBV in broilers under Sanitary Inspection by RT-PCR and ELISA, comparing the results and relating them with the average weight of the flock. Samples were collected from 40 vaccinated broiler flocks under Sanitary Inspection at slaughter. Ten birds from every flock were randomly selected and blood samples were collected for ELISA as well three birds had their trachea and caecal tonsils collected for RT- -PCR test. From 40 flocks, 30 were IBV positive by ELISA and 26 by RT-PCR, in which 15 were detected simultaneously in trachea and caecal tonsil and 5 in each sample. There was no agreement between ELISA and RT-PCR results regarding IBV diagnosis as well positivity in both tests was not statistically significant with the average weight of the flock. There was an improvement on IBV diagnosis when caecal tonsils and tracheas were used instead of just one of them. Considering the only vaccine serotype allowed by Brazilian government is the Mass serotype and its persistence in broilers would only be detected up to 28 days

Selective targeting of brain tumors with gold nanoparticle-induced radiosensitization.

Directory of Open Access Journals (Sweden)

Daniel Y Joh

Full Text Available Successful treatment of brain tumors such as glioblastoma multiforme (GBM is limited in large part by the cumulative dose of Radiation Therapy (RT that can be safely given and the blood-brain barrier (BBB, which limits the delivery of systemic anticancer agents into tumor tissue. Consequently, the overall prognosis remains grim. Herein, we report our pilot studies in cell culture experiments and in an animal model of GBM in which RT is complemented by PEGylated-gold nanoparticles (GNPs. GNPs significantly increased cellular DNA damage inflicted by ionizing radiation in human GBM-derived cell lines and resulted in reduced clonogenic survival (with dose-enhancement ratio of ~1.3. Intriguingly, combined GNP and RT also resulted in markedly increased DNA damage to brain blood vessels. Follow-up in vitro experiments confirmed that the combination of GNP and RT resulted in considerably increased DNA damage in brain-derived endothelial cells. Finally, the combination of GNP and RT increased survival of mice with orthotopic GBM tumors. Prior treatment of mice with brain tumors resulted in increased extravasation and in-tumor deposition of GNP, suggesting that RT-induced BBB disruption can be leveraged to improve the tumor-tissue targeting of GNP and thus further optimize the radiosensitization of brain tumors by GNP. These exciting results together suggest that GNP may be usefully integrated into the RT treatment of brain tumors, with potential benefits resulting from increased tumor cell radiosensitization to preferential targeting of tumor-associated vasculature.

Red blood cells in cerebrospinal fluid as possible inhibitory factor for enterovirus RT-PCR

Directory of Open Access Journals (Sweden)

Sérgio Monteiro de Almeida

Full Text Available ABSTRACT The presence of hemoglobin in samples are considered an important inhibitory factor for polymerase chain reaction (PCR. The aim of this study was to examine the influence of red blood cells (RBCs in cerebrospinal fluid (CSF as an inhibitory factor to reverse transcription polymerase chain reaction (RT-PCR for enteroviruses (EV. Forty-four CSF samples from patients showing characteristics of viral meningitis were assessed for EV by RT-PCR. Viral RNA extracted with guanidine isothyocianate buffer and virus detection was performed by in-house nested PCR. Positivity for EV RT-PCR was higher in CSF samples without RBCs than in samples with RBCs: 13(26% and 36(9.2%, p = 0.001. In the group with positive EV RT-PCR, the mean + SD CSF RBC was 37 ± 183 cell/mm3; the group with negative results had 580 + 2,890 cell/mm3 (p = 0.007. The acceptable upper limit for CSF RBCs that could not influence RT-PCR was 108 cells/mm3. CSF samples with negative results for EV RT-PCR have more erythrocytes.

SPoRT - An End-to-End R2O Activity

Science.gov (United States)

Jedlovec, Gary J.

2009-01-01

Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral observational data applications from EOS satellites to improve short-term weather forecasts on a regional and local scale. SPoRT currently partners with several universities and other government agencies for access to real-time data and products, and works collaboratively with them and operational end users at 13 WFOs to develop and test the new products and capabilities in a "test-bed" mode. The test-bed simulates key aspects of the operational environment without putting constraints on the forecaster workload. Products and capabilities which show utility in the test-bed environment are then transitioned experimentally into the operational environment for further evaluation and assessment. SPoRT focuses on a suite of data and products from MODIS, AMSR-E, and AIRS on the NASA Terra and Aqua satellites, and total lightning measurements from ground-based networks. Some of the observations are assimilated into or used with various versions of the WRF model to provide supplemental forecast guidance to operational end users. SPoRT is enhancing partnerships with NOAA / NESDIS for new product development and data access to exploit the remote sensing capabilities of instruments on the NPOESS satellites to address short term weather forecasting problems. The VIIRS and CrIS instruments on the NPP and follow-on NPOESS satellites provide similar observing capabilities to the MODIS and AIRS instruments on Terra and Aqua. SPoRT will be transitioning existing and new capabilities into the AWIIPS II environment to continue the continuity of its activities.

Märt Agu: "Isa vari käib mul kogu aeg kannul" / Märt Agu ; interv. Aigi Viira

Index Scriptorium Estoniae

Agu, Märt

2006-01-01

1. okt. tähistas oma 30-aastast sünnipäeva ja oma ellukutsuja Mait Agu 55-sünniaastapäeva Tallinna Ülikooli koreograafiaosakond. Sel puhul esitati Estonias Mait Agu tantsulavastus "Kodalased ja kaasaegsed", mille seadis uuesti lavale Märt Agu oma isa loodud koreograafia põhjal

A Formal Approach for RT-DVS Algorithms Evaluation Based on Statistical Model Checking

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Shengxin Dai

2015-01-01

Full Text Available Energy saving is a crucial concern in embedded real time systems. Many RT-DVS algorithms have been proposed to save energy while preserving deadline guarantees. This paper presents a novel approach to evaluate RT-DVS algorithms using statistical model checking. A scalable framework is proposed for RT-DVS algorithms evaluation, in which the relevant components are modeled as stochastic timed automata, and the evaluation metrics including utilization bound, energy efficiency, battery awareness, and temperature awareness are expressed as statistical queries. Evaluation of these metrics is performed by verifying the corresponding queries using UPPAAL-SMC and analyzing the statistical information provided by the tool. We demonstrate the applicability of our framework via a case study of five classical RT-DVS algorithms.

Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in north Mesopotamia since the Neolithic.

Science.gov (United States)

Yaka, Reyhan; Birand, Ayşegül; Yılmaz, Yasemin; Caner, Ceren; Açan, Sinan Can; Gündüzalp, Sidar; Parvizi, Poorya; Erim Özdoğan, Aslı; Togan, İnci; Somel, Mehmet

2018-05-01

North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region. A total of 16 Çemialo Sırtı individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI-HVRII sequences. We studied haplotype diversity and pairwise genetic distances using F ST , comparing the Çemialo Sırtı population with ancient and modern-day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons. Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present-day populations of the region. Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian

A Diagnostic Approach to Increase Reusable Dinnerware Selection in a Cafeteria

Science.gov (United States)

Manuel, Jennifer C.; Sunseri, Mary Anne; Olson, Ryan; Scolari, Miranda

2007-01-01

The current project tested a diagnostic approach to selecting interventions to increase patron selection of reusable dinnerware in a cafeteria. An assessment survey, completed by a sample of 43 patrons, suggested that the primary causes of wasteful behavior were (a) environmental arrangement of dinnerware options and (b) competing motivational…

Ring trial 2016 for Bluetongue virus detection by real-time RT-PCR in France.

Science.gov (United States)

Sailleau, Corinne; Viarouge, Cyril; Breard, Emmanuel; Vitour, Damien; Zientara, Stephan

2017-05-01

Since the unexpected emergence of BTV-8 in Northern Europe and the incursion of BTV-8 and 1 in France in 2006-2007, molecular diagnosis has considerably evolved. Several real-time RT-PCR (rtRT-PCR) methods have been developed and published, and are currently being used in many countries across Europe for BTV detection and typing. In France, the national reference laboratory (NRL) for orbiviruses develops and validates 'ready-to-use' kits with private companies for viral RNA detection. The regional laboratories network that was set up to deal with a heavy demand for analyses has used these available kits. From 2007, ring tests were organized to monitor the performance of the French laboratories. This study presents the results of 63 regional laboratories in the ring trial organized in 2016. Blood samples were sent to the laboratories. Participants were asked to use the rtRT-PCR methods in place in their laboratory, for detection of all BTV serotypes and specifically BTV-8. The French regional laboratories are able to detect and genotype BTV in affected animals. Despite the use of several methods (i.e. RNA extraction and different commercial rtRT-PCRs), the network is homogeneous. The ring trial demonstrated that the French regional veterinary laboratories have reliable and robust BTV diagnostic tools for BTV genome detection.

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

Science.gov (United States)

Chalabala, Jan; Uhlig, Frank; Slavíček, Petr

2018-03-29

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

PpRT1: the first complete gypsy-like retrotransposon isolated in Pinus pinaster.

Science.gov (United States)

Rocheta, Margarida; Cordeiro, Jorge; Oliveira, M; Miguel, Célia

2007-02-01

We have isolated and characterized a complete retrotransposon sequence, named PpRT1, from the genome of Pinus pinaster. PpRT1 is 5,966 bp long and is closely related to IFG7 gypsy retrotransposon from Pinus radiata. The long terminal repeats (LTRs) have 333 bp each and show a 5.4% sequence divergence between them. In addition to the characteristic polypurine tract (PPT) and the primer binding site (PBS), PpRT1 carries internal regions with homology to retroviral genes gag and pol. The pol region contains sequence motifs related to the enzymes protease, reverse transcriptase, RNAseH and integrase in the same typical order known for Ty3/gypsy-like retrotransposons. PpRT1 was extended from an EST database sequence indicating that its transcription is occurring in pine tissues. Southern blot analyses indicate however, that PpRT1 is present in a unique or a low number of copies in the P. pinaster genome. The differences in nucleotide sequence found between PpRT1 and IFG7 may explain the strikingly different copy number in the two pine species genome. Based on the homologies observed when comparing LTR region among different gypsy elements we propose that the highly conserved LTR regions may be useful to amplify other retrotransposon sequences of the same or close retrotransposon family.

Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated associated virus 3 variant groups I, II, III and VI

Directory of Open Access Journals (Sweden)

Bester Rachelle

2012-09-01

Full Text Available Abstract Background Grapevine leafroll-associated virus 3 (GLRaV-3 is the main contributing agent of leafroll disease worldwide. Four of the six GLRaV-3 variant groups known have been found in South Africa, but their individual contribution to leafroll disease is unknown. In order to study the pathogenesis of leafroll disease, a sensitive and accurate diagnostic assay is required that can detect different variant groups of GLRaV-3. Methods In this study, a one-step real-time RT-PCR, followed by high-resolution melting (HRM curve analysis for the simultaneous detection and identification of GLRaV-3 variants of groups I, II, III and VI, was developed. A melting point confidence interval for each variant group was calculated to include at least 90% of all melting points observed. A multiplex RT-PCR protocol was developed to these four variant groups in order to assess the efficacy of the real-time RT-PCR HRM assay. Results A universal primer set for GLRaV-3 targeting the heat shock protein 70 homologue (Hsp70h gene of GLRaV-3 was designed that is able to detect GLRaV-3 variant groups I, II, III and VI and differentiate between them with high-resolution melting curve analysis. The real-time RT-PCR HRM and the multiplex RT-PCR were optimized using 121 GLRaV-3 positive samples. Due to a considerable variation in melting profile observed within each GLRaV-3 group, a confidence interval of above 90% was calculated for each variant group, based on the range and distribution of melting points. The intervals of groups I and II could not be distinguished and a 95% joint confidence interval was calculated for simultaneous detection of group I and II variants. An additional primer pair targeting GLRaV-3 ORF1a was developed that can be used in a subsequent real-time RT-PCR HRM to differentiate between variants of groups I and II. Additionally, the multiplex RT-PCR successfully validated 94.64% of the infections detected with the real-time RT-PCR HRM

Enzymatic and viability RT-qPCR assays for evaluation of enterovirus, hepatitis A virus and norovirus inactivation: Implications for public health risk assessment.

Science.gov (United States)

Monteiro, S; Santos, R

2018-04-01

To assess the potential of a viability dye and an enzymatic reverse transcription quantitative PCR (RT-qPCR) pretreatment to discriminate between infectious and noninfectious enteric viruses. Enterovirus (EntV), norovirus (NoV) GII.4 and hepatitis A virus (HAV) were inactivated at 95°C for 10 min, and four methods were used to compare the efficiency of inactivation: (i) cell culture plaque assay for HAV and EntV, (ii) RT-qPCR alone, (iii) RT-qPCR assay preceded by RNase treatment, and (iv) pretreatment with a viability dye (reagent D (RD)) followed by RT-qPCR. In addition, heat-inactivated NoV was treated with RD coupled with surfactants to increase the efficiency of the viability dye. No treatment was able to completely discriminate infectious from noninfectious viruses. RD-RT-qPCR reduced more efficiently the detection of noninfectious viruses with little to no removal observed with RNase. RD-RT-qPCR method was the closest to cell culture assay. The combination of surfactants and RD did not show relevant improvements on the removal of inactivated viruses signal compared with viability RT-qPCR, with the exception of Triton X-100. The use of surfactant/RD-RT-qPCR, although not being able to completely remove the signal from noninfectious viral particles, yielded a better estimation of viral infectivity. Surfactant/RD-RT-qPCR may be an advantageous tool for a better detection of infectious viruses with potential significant impact in the risk assessment of the presence of enteric viruses. © 2017 The Society for Applied Microbiology.

NASA SPoRT JPSS PG Activities in Alaska

Science.gov (United States)

Berndt, Emily; Molthan, Andrew; Fuell, Kevin; McGrath, Kevin; Smith, Matt; LaFontaine, Frank; Leroy, Anita; White, Kris

2018-01-01

SPoRT (NASA's Short-term Prediction Research and Transition Center) has collaboratively worked with Alaska WFOs (Weather Forecast Offices) to introduce RGB (Red/Green/Blue false color image) imagery to prepare for NOAA-20 (National Oceanic and Atmospheric Administration, JPSS (Joint Polar Satellite System) series-20 satellite) VIIRS (Visible Infrared Imaging Radiometer Suite) and improve forecasting aviation-related hazards. Last R2O/O2R (Research-to-Operations/Operations-to-Research) steps include incorporating NOAA-20 VIIRS in RGB suite and fully transitioning client-side RGB processing to GINA (Geographic Information Network of Alaska) and Alaska Region. Alaska Region WFOs have been part of the successful R2O/O2R story to assess the use of NESDIS (National Environmental Satellite, Data, and Information Service) Snowfall Rate product in operations. SPoRT introduced passive microwave rain rate and IMERG (Integrated Multi-satellitE Retrievals for GPM (Global Precipitation Measurement)) (IMERG) to Alaska WFOs for use in radar-void areas and assessing flooding potential. SPoRT has been part of the multi-organization collaborative effort to introduce Gridded NUCAPS (NOAA Unique CrIS/ATMS (Crosstrack Infrared Sounder/Advanced Technology Microwave Sounder) Processing System) to the Anchorage CWSU (Center Weather Service Unit) to assess Cold Air Aloft events, [and as part of NOAA's PG (Product Generation) effort].

Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus.

Directory of Open Access Journals (Sweden)

Gilberto A Santiago

Full Text Available Dengue is an acute illness caused by the positive-strand RNA dengue virus (DENV. There are four genetically distinct DENVs (DENV-1-4 that cause disease in tropical and subtropical countries. Most patients are viremic when they present with symptoms; therefore, RT-PCR has been increasingly used in dengue diagnosis. The CDC DENV-1-4 RT-PCR Assay has been developed as an in-vitro diagnostic platform and was recently approved by the US Food and Drug Administration (FDA for detection of dengue in patients with signs or symptoms of mild or severe dengue. The primers and probes of this test have been designed to detect currently circulating strains of DENV-1-4 from around the world at comparable sensitivity. In a retrospective study with 102 dengue cases confirmed by IgM anti-DENV seroconversion in the convalescent sample, the RT-PCR Assay detected DENV RNA in 98.04% of the paired acute samples. Using sequencing as a positive indicator, the RT-PCR Assay had a 97.92% positive agreement in 86 suspected dengue patients with a single acute serum sample. After extensive validations, the RT-PCR Assay performance was highly reproducible when evaluated across three independent testing sites, did not produce false positive results for etiologic agents of other febrile illnesses, and was not affected by pathological levels of potentially interfering biomolecules. These results indicate that the CDC DENV-1-4 RT-PCR Assay provides a reliable diagnostic platform capable for confirming dengue in suspected cases.

Structural Evolution of the R-T Phase Boundary in KNN-Based Ceramics

KAUST Repository

Lv, Xiang

2017-10-04

Although a rhombohedral-tetragonal (R-T) phase boundary is known to substantially enhance the piezoelectric properties of potassium-sodium niobate ceramics, the structural evolution of the R-T phase boundary itself is still unclear. In this work, the structural evolution of R-T phase boundary from -150 °C to 200 °C is investigated in (0.99-x)K0.5Na0.5Nb1-ySbyO3-0.01CaSnO3-xBi0.5K0.5HfO3 (where x=0~0.05 with y=0.035, and y=0~0.07 with x=0.03) ceramics. Through temperature-dependent powder X-ray diffraction (XRD) patterns and Raman spectra, the structural evolution was determined to be Rhombohedral (R, <-125 °C) → Rhombohedral+Orthorhombic (R+O, -125 °C to 0 °C) → Rhombohedral+Tetragonal (R+T, 0 °C to 150 °C) → dominating Tetragonal (T, 200 °C to Curie temperature (TC)) → Cubic (C, >TC). In addition, the enhanced electrical properties (e.g., a direct piezoelectric coefficient (d33) of ~450±5 pC/N, a conversion piezoelectric coefficient (d33*) of ~580±5 pm/V, an electromechanical coupling factor (kp) of ~0.50±0.02, and TC~250 °C), fatigue-free behavior, and good thermal stability were exhibited by the ceramics possessing the R-T phase boundary. This work improves understanding of the physical mechanism behind the R-T phase boundary in KNN-based ceramics and is an important step towards their adoption in practical applications. This article is protected by copyright. All rights reserved.

Narr kui ajastu metafoor / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

2001-01-01

William Shakespeare'i "Kuningas Lear" (lav. Priit Pedajas) ja Pedro Calder̤n de la Barca "Elu on unenägu" (lav. Ingo Normet) Eesti Draamateatris. Ilmunud ka kogumikus : Hellerma, Kärt. Avanenud ruum. Tallinn : Eesti Keele Sihtasutus, 2006, lk. 213-216. Pealk. Narr kui meie aja kangelane

Pärt, Arvo: De profundis / Barry Witherden

Index Scriptorium Estoniae

Witherden, Barry

1997-01-01

Uuest heliplaadist "Pärt, Arvo: De profundis. Missa Sillabica. Solfeggio. And one of the Pharisees. Cantate Domino. Summa. Seven Magnificat Antiphons. The Beautitudes. Magnificat. Christopher Bowers-Broadbent (org.), Daniel Kennedy (perc.). Theatre of Voices / Paul Hillier (bass)". Harmonia Mundi HMU40 7182; HMU90 7182 (76 minutes:DDD)

Cell-type-specific responses of RT4 neural cell lines to dibutyryl-cAMP: branch determination versus maturation

International Nuclear Information System (INIS)

Droms, K.; Sueoka, N.

1987-01-01

This report describes the induction of cell-type-specific maturation, by dibutyryl-cAMP and testololactone, of neuronal and glial properties in a family of cell lines derived from a rat peripheral neurotumor, RT4. This maturation allows further understanding of the process of determination because of the close lineage relationship between the cell types of the RT4 family. The RT4 family is characterized by the spontaneous conversion of one of the cell types, RT4-AC (stem-cell type), to any of three derivative cell types, RT4-B, RT4-D, or RT4-E, with a frequency of about 10(-5). The RT4-AC cells express some properties characteristic of both neuronal and glial cells. Of these neural properties expressed by RT4-AC cells, only the neuronal properties are expressed by the RT4-B and RT4-E cells, and only the glial properties are expressed by the RT4-D cells. This in vitro cell-type conversion of RT4-AC to three derivative cell types is a branch point for the coordinate regulation of several properties and seems to resemble determination in vivo. In our standard culture conditions, several other neuronal and glial properties are not expressed by these cell types. However, addition of dibutyryl-cAMP induces expression of additional properties, in a cell-type-specific manner: formation of long cellular processes in the RT4-B8 and RT4-E5 cell lines and expression of high-affinity uptake of gamma-aminobutyric acid, by a glial-cell-specific mechanism, in the RT4-D6-2 cell line. These new properties are maximally expressed 2-3 days after addition of dibutyryl-cAMP

Aplicación de RT-Linux en el control de motores de pasos. Parte II; Appication of RT-Linux in the Control of Steps Motors. Part II

Directory of Open Access Journals (Sweden)

Ernesto Duany Renté

2011-02-01

Full Text Available Este trabajo complementa al presentado anteriormente: "Aplicación de RT-Linux en el control de motoresde pasos. Primera parte", de manera que se puedan relacionar a las tareas de adquisición y control para laobtención de un sistema lo más exacto posible. Las técnicas empleadas son las de tiempo real aprovechandolas posibilidades del microkernel RT-Linux y los software libres contenidos en sistemas Unix/Linux. Lasseñales se obtienen mediante un conversor AD y mostradas en pantalla empleando el Gnuplot.  The work presented in this paper is a complement to the control and acquisition tasks which were explainedin "Application of RT-Linux in the Control of Steps Motors. First Part", so that those both real time taskscan be fully related in order to make the whole control system more accurate. The employed techniquesare those of Real Time Taking advantage of the possibilities of the micro kernel RT-Linux and the freesoftware distributed in the Unix/Linux operating systems. The signals are obtained by means of an ADconverter and are shown in screen using Gnuplot.

RT-PCR-ELISA as a tool for diagnosis of low-pathogenicity avian influenza

DEFF Research Database (Denmark)

Dybkaer, Karen; Munch, Mette; Handberg, Kurt Jensen

2003-01-01

A one-tube reverse transcriptase/polymerase chain reaction coupled with an enzyme-linked immunosorbent assay (RT-PCR-ELISA) was developed for the rapid detection of avian influenza virus (AIV) in clinical specimens. A total of 419 swab pools were analyzed from chickens experimentally infected wit...... of the twenty-three VI-positive specimens were negative when tested by RT-PCR-ELISA. The diagnostic sensitivity and specificity of the RT-PCR-ELISA was 91% and 97%, respectively, using VI in SPF eggs as the gold reference standard....

SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

International Nuclear Information System (INIS)

Yao, R; Chisela, W; Dorbu, G

2016-01-01

Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mm on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.

Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L..

Directory of Open Access Journals (Sweden)

Roberta Fogliatto Mariot

Full Text Available Potato (Solanum tuberosum yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3 and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A. According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.

Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L.).

Science.gov (United States)

Mariot, Roberta Fogliatto; de Oliveira, Luisa Abruzzi; Voorhuijzen, Marleen M; Staats, Martijn; Hutten, Ronald C B; Van Dijk, Jeroen P; Kok, Esther; Frazzon, Jeverson

2015-01-01

Potato (Solanum tuberosum) yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3) and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A). According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.

Specificiteit van de Mantoux-reactie op het nieuwe tuberculine RT23 ten opzichte van de reactie op het oude PPD-RIVM; vergelijkend onderzoek onder ziekenhuispersoneel

NARCIS (Netherlands)

Cobelens, F. G.; de Boer, H. E.

1999-01-01

OBJECTIVE: In the Netherlands, an increase in prevalence of tuberculin positivity has been noted since the replacement of the Dutch PPD-RIVM preparation by RT23. This investigation was carried out to assess the specificity of RT23 compared with PPD-RIVM. DESIGN: Comparative. METHOD: In 90 hospital

Development of single step RT-PCR for detection of Kyasanur forest disease virus from clinical samples

Directory of Open Access Journals (Sweden)

Gouri Chaubal

2018-02-01

Discussion and conclusion: The previously published sensitive real time RT-PCR assay requires higher cost in terms of reagents and machine setup and technical expertise has been the primary reason for development of this assay. A single step RT-PCR is relatively easy to perform and more cost effective than real time RT-PCR in smaller setups in the absence of Biosafety Level-3 facility. This study reports the development and optimization of single step RT-PCR assay which is more sensitive and less time-consuming than nested RT-PCR and cost effective for rapid diagnosis of KFD viral RNA.

Pärt, Arvo: Litany. Psalom. Trisagion / Robert Cowan

Index Scriptorium Estoniae

Cowan, Robert

1996-01-01

Uuest heliplaadist "Pärt, Arvo: Litany. Psalom. Trisagion. Hilliard Ensemble, Estonian Philharmonic Chamber Choir, Tallinn Chamber Orchestra, Tõnu Kaljuste; Lithuanian Chamber Orchestra, Saulius Sondeckis" ECM New Series 449 810-4; 449 810-2 (42 minutes: DDD)

Performance of nested RT-PCR on CSF for tuberculous meningitis diagnosis in HIV-infected patients.

Science.gov (United States)

Gualberto, F A S; Gonçalves, M G; Fukasawa, L O; Santos, A M Ramos Dos; Sacchi, C T; Harrison, L H; Boulware, D R; Vidal, J E

2017-10-01

Timely diagnosis of tuberculous meningitis (TBM) in patients with human immunodeficiency virus (HIV) infection remains a challenge. Despite the current scale-up of the Xpert® MTB/RIF assay, other molecular diagnostic tools are necessary, particularly in referral centres in low- and middle-income countries without Xpert testing. To determine the diagnostic performance of nested real-time polymerase chain reaction (nRT-PCR) in HIV-infected TBM patients categorised according to standardised clinical case definitions. Based on clinical, laboratory and imaging data, HIV-infected patients with suspected TBM were prospectively categorised as 'definite TBM', 'probable TBM', 'possible TBM' or 'not TBM'. We evaluated nRT-PCR sensitivity and specificity in diagnosing TBM among definite TBM cases, and among definite + probable TBM cases. Ninety-two participants were enrolled in the study. nRT-PCR sensitivity for definite TBM (n = 8) was 100% (95%CI 67-100) and 86% (95%CI 60-96) for both definite and probable TBM (n = 6). Assuming that 'not TBM' patients (n = 74) were true-negatives, nRT-PCR specificity was 100% (95%CI 95-100). The possible TBM group (n = 4) had no nRT-PCR positives. The nRT-PCR is a useful rule-in test for HIV-infected patients with TBM according to international consensus case definitions. As nRT-PCR cannot exclude TBM, studies comparing and combining nRT-PCR with other assays are necessary for a rule-out test.

SASqPCR: robust and rapid analysis of RT-qPCR data in SAS.

Directory of Open Access Journals (Sweden)

Daijun Ling

Full Text Available Reverse transcription quantitative real-time PCR (RT-qPCR is a key method for measurement of relative gene expression. Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization. Currently no computer program for RT-qPCR data analysis is suitable for analytical optimization and user-controllable customization based on data quality, experimental design as well as specific research aims. Here I introduce an all-in-one computer program, SASqPCR, for robust and rapid analysis of RT-qPCR data in SAS. This program has multiple macros for assessment of PCR efficiencies, validation of reference genes, optimization of data normalizers, normalization of confounding variations across samples, and statistical comparison of target gene expression in parallel samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. In addition, it is highly automatic and functionally extendable. Thus users are the actual decision-makers controlling RT-qPCR data analyses. SASqPCR and its tutorial are freely available at http://code.google.com/p/sasqpcr/downloads/list.

NASA/SPoRT's GOES-R Activities in Support of Product Development, Management, and Training

Science.gov (United States)

Fuell, K. K.; Jedlovec, G.; Molthan, A.; Stano, G. T.

2012-12-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center supports many activities within the GOES-R Proving Grounds (PG). These include the development of imagery from existing instrumentation as a proxy to future Advanced Baseline Imager (ABI) capabilities on GOES-R. The Moderate Resolution Imaging Spectroradiometer (MODIS) and the Visible/Infrared Imager/Radiometer Suite (VIIRS) instruments are used to provide a glimpse of the multi-spectral capabilities that will become the norm as the number of channels and data rate dramatically increase with GOES-R. The NOAA/NWS has plans to provide operational users with all ABI channels at the highest resolution. Data fusion of individual channels into composite red, green, and blue imagery products will assist the end user with this future wave of information. While increasing the efficiency in the operational use of ABI channels, these composites provide only qualitative information. Within the GOES-R PG, SPoRT and other partners are exploring ways to include quantitative information as part of the composite imagery. However, limitations in local hardware processing and/or data bandwidth for users of the GOES-R data stream are challenges to overcome. This presentation will discuss the creation of these composite images as well as possible solutions to address these processing challenges. In a similar manner the Geostationary Lightning Mapper (GLM) to be launched on GOES-R presents several data management challenges. The GLM is a pioneering instrument to quantify total lightning from a geostationary platform. The expected data frequency from the GLM is to be at a sub-minute interval. Users of such a data set may have little experience in handling such a rapid update of information. To assist users, SPoRT is working with the NWS to develop tools within the user's decision support system to allow tracking and analysis of total lightning from a storm-based perspective. This presentation will discuss the

NASA/SPoRT's GOES-R Activities in Support of Product Development, Management, and Training

Science.gov (United States)

Fuell, Kevin K.; Jedlovec, Gary; Molthan, Andrew L.; Stano, Geoffrey T.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center supports many activities within the GOES-R Proving Grounds (PG). These include the development of imagery from existing instrumentation as a proxy to future Advanced Baseline Imager (ABI) capabilities on GOES-R. The Moderate Resolution Imaging Spectroradiometer (MODIS) and the Visible/Infrared Imager/Radiometer Suite (VIIRS) instruments are used to provide a glimpse of the multi-spectral capabilities that will become the norm as the number of channels and data rate dramatically increase with GOES-R. The NOAA/NWS has plans to provide operational users with all ABI channels at the highest resolution. Data fusion of individual channels into composite red, green, and blue imagery products will assist the end user with this future wave of information. While increasing the efficiency in the operational use of ABI channels, these composites provide only qualitative information. Within the GOES-R PG, SPoRT and other partners are exploring ways to include quantitative information as part of the composite imagery. However, limitations in local hardware processing and/or data bandwidth for users of the GOES-R data stream are challenges to overcome. This presentation will discuss the creation of these composite images as well as possible solutions to address these processing challenges. In a similar manner the Geostationary Lightning Mapper (GLM) to be launched on GOES-R presents several data management challenges. The GLM is a pioneering instrument to quantify total lightning from a geostationary platform. The expected data frequency from the GLM is to be at a sub-minute interval. Users of such a data set may have little experience in handling such a rapid update of information. To assist users, SPoRT is working with the NWS to develop tools within the user fs decision support system to allow tracking and analysis of total lightning from a storm-based perspective. This presentation will discuss the

Do extra-group fertilizations increase the potential for sexual selection in male mammals?

Science.gov (United States)

Isvaran, Kavita; Sankaran, Sumithra

2017-10-01

Fertilizations by males outside the social breeding group (extra-group paternity, EGP) are widespread in birds and mammals. EGP is generally proposed to increase male reproductive skew and thereby increase the potential for sexual selection, but the generality of this relationship is unclear. We extracted data from 27 mammals in seven orders and used phylogenetic comparative methods to investigate the influence of EGP and social mating system on measures of inequality in male fertilization success, which are indices of the potential for sexual selection. We find that EGP and social mating system can predict the potential for sexual selection in mammalian populations, but only when considered jointly and not individually. EGP appears to increase the potential for sexual selection but only when the degree of social polygyny is relatively low. When social polygyny is high, EGP appears to result in a more uniform distribution of reproduction and a decrease in the potential for sexual selection. A possible explanation to be investigated is that the phenotype of extra-group fathers differs systematically across social mating systems. Our findings have implications for the use of EGP and social mating system as indices of sexual selection in comparative analyses of trait evolution under sexual selection. © 2017 The Author(s).

Karje kunstniku südamest / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

1997-01-01

Arvustus: Dinesen, Isak [Blixen, Karen]. Babette'i pidusöök / tlk. Piret Peiker. Tallinn : Varrak, 1996. Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 167-169

Quantitative RT-PCR for titration of replication-defective recombinant Semliki Forest virus.

Science.gov (United States)

Puglia, Ana L P; Rezende, Alexandre G; Jorge, Soraia A C; Wagner, Renaud; Pereira, Carlos A; Astray, Renato M

2013-11-01

Virus titration may constitute a drawback in the development and use of replication-defective viral vectors like Semliki Forest virus (SFV). The standardization and validation of a reverse transcription quantitative PCR (qRT-PCR) method for SFV titration is presented here. The qRT-PCR target is located within the nsp1 gene of the non-structural polyprotein SFV region (SFV RNA), which allows the strategy to be used for several different recombinant SFV constructs. Titer determinations were carried out by performing virus titration and infection assays with SFVs containing an RNA coding region for the rabies virus glycoprotein (RVGP) or green fluorescent protein (GFP). Results showed that the standardized qRT-PCR is applicable for different SFV constructs, and showed good reproducibility. To evaluate the correlation between the amount of functional SFV RNA in a virus lot and its infectivity in BHK-21 cell cultures, a temperature mediated titer decrease was performed and successfully quantitated by qRT-PCR. When used for cell infection at the same multiplicity of infection (MOI), the temperature treated SFV-RVGP samples induced the same levels of RVGP expression. Similarly, when different SFV-GFP lots with different virus titers, as accessed by qRT-PCR, were used for cell infection at the same MOI, the cultures showed comparable amounts of fluorescent cells. The data demonstrate a good correlation between the amount of virus used for infection, as measured by its SFV RNA, and the protein synthesis in the cells. In conclusion, the qRT-PCR method developed here is accurate and enables the titration of replication-defective SFV vectors, an essential aid for viral vector development as well as for establishment of production bioprocesses. Copyright © 2013 Elsevier B.V. All rights reserved.

Study of rt-PA therapy for acute stroke in older patients

International Nuclear Information System (INIS)

Ono, Yasuhiro; Toyoshima, Atsuhiko; Toyota, Yasunori; Kuramoto, Satoshi; Katsumata, Atsushi; Kawauchi, Masamitsu; Matsumoto, Yuzo

2011-01-01

Intravenous alteplase (rt-PA) therapy has been widely approved for acute ischemic stroke. We examined symptomatic intracranial hemorrhage (SICH) and outcomes in older patients treated with rt-PA therapy. We divided 130 consecutive patients treated with rt-PA into two groups: 72 patients younger than 80 years (age <80 group) and 58 patients older than 80 years (age ≥80 group). On CT and MRI scans, SICH was observed in 5 patients (7.1%) in the age <80 group and 4 patients (6.9%) in the age ≥80 group. The SICH rate did not differ significantly between the two groups (odds ratio (OR) 1.21, 95% confidence interval (CI) 0.04-2.39, P=0.6174). The patients in the age ≥80 group had a significantly lower mRS 0-1 rate (8.8 vs. 30.0%; OR 7.20, 95% CI 6.05-8.34, P=0.0009) and significantly higher mRS 6 (mortality) rate (19.3 vs. 9.0%; OR 6.52, 95% CI 5.39-7.65, P=0.0015) compared with those in the age <80 group. These data suggest that the factor of age is not related to SICH but is related to patients' outcomes in rt-PA therapy. (author)

Modulations of the processing of line discontinuities under selective attention conditions?

Science.gov (United States)

Giersch, Anne; Fahle, Manfred

2002-01-01

We examined whether the processing of discontinuities involved in figure-ground segmentation, like line ends, can be modulated under selective attention conditions. Subjects decided whether a gap in collinear or parallel lines was located to the right or left. Two stimuli were displayed in immediate succession. When the gaps were on the same side, reaction times (RTs) for the second stimulus increased when collinear lines followed parallel lines, or the reverse, but only when the two stimuli shared the same orientation and location. The effect did not depend on the global form of the stimuli or on the relative orientation of the gaps. A frame drawn around collinear elements affected the results, suggesting a crucial role of the "amodal" orthogonal lines produced when line ends are aligned. Including several gaps in the first stimulus also eliminated RT variations. By contrast, RT variations remained stable across several experimental blocks and were significant for interstimulus intervals from 50 to 600 msec between the two stimuli. These results are interpreted in terms of a modulation of the processing of line ends or the production of amodal lines, arising when attention is selectively drawn to a gap.

GOKaRT: Graphical Online Search Tool for Maps

Directory of Open Access Journals (Sweden)

Mechthild Schüler

2008-09-01

Full Text Available The map department of the Staats- und Universitätsbibliothek Göttingen together with the Berlin State Library propose a project to develop a web-based graphic cataloguing and search system for maps, to be funded by the German Research Foundation. This tool shall be made available to all map holdings in archives, libraries, university departments and museums in Germany as a comfortable means for the administration of map holdings and as a search tool. Sheets belonging to map series as well as single maps (old and new will be registered cooperatively by the participants with simple tools. This cooperation in data maintenance will facilitate the work especially for understaffed map holdings. Depending on the type of map there are four different mechanisms for map reference. For map series electronic index sheets are used which will show information regarding the various issues of the map sheets. Due to the intuitive graphic search entry GOKaRT-users will easily find the required maps of a certain region available in a chosen holding. User administration modules ensure comfortable handling. GOKaRT is being developed on the basis of licence-free open source programmes. In case financing is provided by the German Research Foundation, GOKaRT can be used free of charge internationally. This would require a contract stipulating data exchange between the partners as well as permanent storage and usability of the data.

Data acquisition and real-time bolometer tomography using LabVIEW RT

International Nuclear Information System (INIS)

Giannone, L.; Eich, T.; Fuchs, J.C.; Ravindran, M.; Ruan, Q.; Wenzel, L.; Cerna, M.; Concezzi, S.

2011-01-01

The currently available multi-core PCI Express systems running LabVIEW RT (real-time), equipped with FPGA cards for data acquisition and real-time parallel signal processing, greatly shorten the design and implementation cycles of large-scale, real-time data acquisition and control systems. This paper details a data acquisition and real-time tomography system using LabVIEW RT for the bolometer diagnostic on the ASDEX Upgrade tokamak (Max Planck Institute for Plasma Physics, Garching, Germany). The transformation matrix for tomography is pre-computed based on the geometry of distributed radiation sources and sensors. A parallelized iterative algorithm is adapted to solve a constrained linear system for the reconstruction of the radiated power density. Real-time bolometer tomography is performed with LabVIEW RT. Using multi-core machines to execute the parallelized algorithm, a cycle time well below 1 ms is reached.

DaRT: A CALL System to Help Students Practice and Develop Reasoning Skills in Choosing English Articles.

Science.gov (United States)

Yoshii, Rika; Milne, Alastair

1998-01-01

Describes DaRT, a computer assisted language-learning system for helping English-as-a-Second-Language students master English articles. DaRT uses a diagrammatic reasoning tool to present communicative contexts for exercises in choosing appropriate articles. This paper describes the development of DaRT and DaRT's system components and concludes…

Thermal regulation 2000: one year later; RT 2000: un an apres

Energy Technology Data Exchange (ETDEWEB)

NONE

2002-05-01

This meeting, organized by the research center of Gaz de France (Cegibat), aims at drawing up a progress status of the French thermal regulation (RT 2000), one year after its enforcement on June 1, 2000: status, experience feedback and recommendations; Gaz de France assistance and solutions; tools at the disposition of designers (labelling of equipments, simulation softwares..); practical examples of implementation of the RT 2000 in office buildings, residential buildings and sport complexes. (J.S.)

L. Harrison: Mass (to St. Anthony); A. Pärt: Berliner Messe / Robert Cowan

Index Scriptorium Estoniae

Cowan, Robert

1994-01-01

Uuest heliplaadist "L. Harrison: Mass (to St. Anthony); A. Pärt: Berliner Messe. Oregon Repertory Singers / Gilbert Seeley. Koch International Classics CD 37 177-2; Pärt - comparative version: Estonian Phil. Chbr. Ch., Tallinn CO / Kaljuste" (11/93)(ECM) 439 162-2

WE-H-207B-04: Strategies for Adaptive RT

Energy Technology Data Exchange (ETDEWEB)

Green, O. [Washington University School of Medicine (United States)

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.

WE-H-207B-02: MR-Driven RT Planning

Energy Technology Data Exchange (ETDEWEB)

Cao, M. [UCLA School of Medicine (United States)

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.

WE-H-207B-04: Strategies for Adaptive RT

International Nuclear Information System (INIS)

Green, O.

2016-01-01

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A

WE-H-207B-02: MR-Driven RT Planning

International Nuclear Information System (INIS)

Cao, M.

2016-01-01

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the session was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A

Simultaneous detection of enteropathogenic viruses in buffalos faeces using multiplex reverse transcription-polymerase chain reaction (mRT-PCR

Directory of Open Access Journals (Sweden)

U. Pagnini

2010-02-01

Full Text Available A multiplex reverse transcription- polymerase chain reaction (mRT-PCR assay that detects Bovine Viral Diarrhoea Virus, Bovine Coronavirus, and Group A Rotaviruses in infected cell-culture fluids and clinical faecal samples is described. One hundred twenty faecal samples from buffalo calves with acute gastroenteritis were tested. The mRT-PCR was validated against simplex RT-PCR with published primers for Pestivirus, Coronavirus and Rotavirus. The multiplex RT-PCR was equally sensitive and specific in detecting viral infections compared with simplex RT-PCR. The mRT-PCR readily identified viruses by discriminating the size of their amplified gene products. This mRT-PCR may be a sensitive and rapid assay for surveillance of buffalo enteric viruses in field specimens. This novel multiplex RT-PCR is an attractive technique for the rapid, specific, and cost-effective laboratory diagnosis of acute gastroenteritis.

SU-F-J-219: Predicting Ventilation Change Due to Radiation Therapy: Dependency On Pre-RT Ventilation and Effort Correction

Energy Technology Data Exchange (ETDEWEB)

Patton, T; Du, K; Bayouth, J [University of Wisconsin, Madison, WI (United States); Christensen, G; Reinhardt, J [University of Iowa, Iowa City, IA (United States)

2016-06-15

Purpose: Ventilation change caused by radiation therapy (RT) can be predicted using four-dimensional computed tomography (4DCT) and image registration. This study tested the dependency of predicted post-RT ventilation on effort correction and pre-RT lung function. Methods: Pre-RT and 3 month post-RT 4DCT images were obtained for 13 patients. The 4DCT images were used to create ventilation maps using a deformable image registration based Jacobian expansion calculation. The post-RT ventilation maps were predicted in four different ways using the dose delivered, pre-RT ventilation, and effort correction. The pre-RT ventilation and effort correction were toggled to determine dependency. The four different predicted ventilation maps were compared to the post-RT ventilation map calculated from image registration to establish the best prediction method. Gamma pass rates were used to compare the different maps with the criteria of 2mm distance-to-agreement and 6% ventilation difference. Paired t-tests of gamma pass rates were used to determine significant differences between the maps. Additional gamma pass rates were calculated using only voxels receiving over 20 Gy. Results: The predicted post-RT ventilation maps were in agreement with the actual post-RT maps in the following percentage of voxels averaged over all subjects: 71% with pre-RT ventilation and effort correction, 69% with no pre-RT ventilation and effort correction, 60% with pre-RT ventilation and no effort correction, and 58% with no pre-RT ventilation and no effort correction. When analyzing only voxels receiving over 20 Gy, the gamma pass rates were respectively 74%, 69%, 65%, and 55%. The prediction including both pre- RT ventilation and effort correction was the only prediction with significant improvement over using no prediction (p<0.02). Conclusion: Post-RT ventilation is best predicted using both pre-RT ventilation and effort correction. This is the only prediction that provided a significant

Kaks vaadet Ameerikast Jacques Derridale / Märt Väljataga

Index Scriptorium Estoniae

Väljataga, Märt, 1965-

1998-01-01

Kommentaariks Vikerkaares 1998, nr. 7-8 ilmunud artiklitele: Mark Lilla 'Jacques Derrida poliitika' ja Richard Rorty 'Ironistlikust teooriast privaatsete allusioonideni' (mõlemad tõlkinud Märt Väljataga)

Zidovudine (AZT monotherapy selects for the A360V mutation in the connection domain of HIV-1 reverse transcriptase.

Directory of Open Access Journals (Sweden)

Jessica H Brehm

Full Text Available We previously demonstrated in vitro that zidovudine (AZT selects for A371V in the connection domain and Q509L in ribonuclease H (RNase H domain of HIV-1 reverse transcriptase (RT which, together with the thymidine analog mutations D67N, K70R and T215F, confer greater than 100-fold AZT resistance. The goal of the current study was to determine whether AZT monotherapy in HIV-1 infected patients also selects the A371V, Q509L or other mutations in the C-terminal domains of HIV-1 RT.Full-length RT sequences in plasma obtained pre- and post-therapy were compared in 23 participants who received AZT monotherapy from the AIDS Clinical Trials Group study 175. Five of the 23 participants reached a primary study endpoint. Mutations significantly associated with AZT monotherapy included K70R (p = 0.003 and T215Y (p = 0.013 in the polymerase domain of HIV-1 RT, and A360V (p = 0.041 in the connection domain of HIV-1 RT. HIV-1 drug susceptibility assays demonstrated that A360V, either alone or in combination with thymidine analog mutations, decreased AZT susceptibility in recombinant viruses containing participant-derived full-length RT sequences or site-directed mutant RT. Biochemical studies revealed that A360V enhances the AZT-monophosphate excision activity of purified RT by significantly decreasing the frequency of secondary RNase H cleavage events that reduce the RNA/DNA duplex length and promote template/primer dissociation.The A360V mutation in the connection domain of RT was selected in HIV-infected individuals that received AZT monotherapy and contributed to AZT resistance.

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

Science.gov (United States)

Jia, Yi; Jannink, Jean-Luc

2012-01-01

Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored. PMID:23086217

Long term selection for reduced or increased pecking behaviour in laying hens

DEFF Research Database (Denmark)

Buitenhuis, A J; Kjaer, J B

2008-01-01

Feather pecking in laying hens is an important issue in animal welfare. Four studies in laying hens were selected which investigated increased or reduced pecking behaviour using direct or indirect measures of feather pecking behaviour. Direct comparison of the selected experiments is difficult......, as the selection criteria and even the selection procedures varied. Keeping these differences in mind, the results of the experiments showed that a) It is possible to change pecking behaviour in the desired direction using selection, b) Aggressive pecking is not related to feather pecking, c) There is no clear...... that dopamine also plays a role in the regulation of pecking behaviour, and finally e) There are differences between the selected lines and their control lines with regard to the immune parameters both in the individual selected lines as the group selected lines, indicating that direct as well as indirect...

The HYP-RT Hypoxic Tumour Radiotherapy Algorithm and Accelerated Repopulation Dose per Fraction Study

Directory of Open Access Journals (Sweden)

W. M. Harriss-Phillips

2012-01-01

Full Text Available The HYP-RT model simulates hypoxic tumour growth for head and neck cancer as well as radiotherapy and the effects of accelerated repopulation and reoxygenation. This report outlines algorithm design, parameterisation and the impact of accelerated repopulation on the increase in dose/fraction needed to control the extra cell propagation during accelerated repopulation. Cell kill probabilities are based on Linear Quadratic theory, with oxygenation levels and proliferative capacity influencing cell death. Hypoxia is modelled through oxygen level allocation based on pO2 histograms. Accelerated repopulation is modelled by increasing the stem cell symmetrical division probability, while the process of reoxygenation utilises randomised pO2 increments to the cell population after each treatment fraction. Propagation of 108 tumour cells requires 5–30 minutes. Controlling the extra cell growth induced by accelerated repopulation requires a dose/fraction increase of 0.5–1.0 Gy, in agreement with published reports. The average reoxygenation pO2 increment of 3 mmHg per fraction results in full tumour reoxygenation after shrinkage to approximately 1 mm. HYP-RT is a computationally efficient model simulating tumour growth and radiotherapy, incorporating accelerated repopulation and reoxygenation. It may be used to explore cell kill outcomes during radiotherapy while varying key radiobiological and tumour specific parameters, such as the degree of hypoxia.

PEMBERDAYAAN EKONOMI MASYARAKAT RT 05 RW IX KELURAHAN KROBOKAN KECAMATAN SEMARANG BARAT MELALUI PENGOLAHAN BAHAN PANGAN LOKAL DAN PEMASARANNYA

Directory of Open Access Journals (Sweden)

Mei Sulistyoningsih

2015-09-01

Full Text Available Abstract ?é?á The purpose of this activity is to increase of people?óÔé¼Ôäós income through local food processing and its marketing by empowerment of communities. Participants of these activities include member of RT 05 RW IX, Kelurahan Krobokan, sub-district of West Semarang, Semarang City. The method are discussion, practice, and simulation. Implementation of activities is to encourage community to be entrepreneurs in increasing family incomes not only just relying on the income from the work as laborers or workers. Training activities of local food into a healthy diet has a positive response from family group in RT 05 RW IX, Kelurahan Krobokan, sub-district of West Semarang, Semarang City. ?é?á Keywords : family income, local food, entrepreneur, marketing

Small prizes increased healthful school lunch selection in a Midwestern school district.

Science.gov (United States)

Siegel, Robert; Lockhart, Mary Kate; Barnes, Allison S; Hiller, Elizabeth; Kipp, Roger; Robison, Debora L; Ellsworth, Samantha C; Hudgens, Michelle E

2016-04-01

As obesity has become a pressing health issue for American children, greater attention has been focused on how schools can be used to improve how students eat. Previously, we piloted the use of small prizes in an elementary school cafeteria to improve healthful food selection. We hoped to increase healthful food selection in all the elementary schools of a small school district participating in the United States Department of Agriculture Lunch Program by offering prizes to children who selected a Power Plate (PP), which consisted of an entrée with whole grains, a fruit, a vegetable, and plain low-fat milk. In this study, the PP program was introduced to 3 schools sequentially over an academic year. During the kickoff week, green, smiley-faced emoticons were placed by preferred foods, and children were given a prize daily if they chose a PP on that day. After the first week, students were given a sticker or temporary tattoo 2 days a week if they selected a PP. Combining data from the 3 schools in the program, students increased PP selection from 4.5% at baseline to 49.4% (p small prizes as rewards dramatically improves short-term healthful food selection in elementary school children.

Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence.

Science.gov (United States)

Lotos, Leonidas; Efthimiou, Konstantinos; Maliogka, Varvara I; Katis, Nikolaos I

2014-03-01

In this study a two-step RT-PCR assay was developed for the generic detection of poleroviruses. The RdRp coding region was selected as the primers' target, since it differs significantly from that of other members in the family Luteoviridae and its sequence can be more informative than other regions in the viral genome. Species specific RT-PCR assays targeting the same region were also developed for the detection of the six most widespread poleroviral species (Beet mild yellowing virus, Beet western yellows virus, Cucurbit aphid-borne virus, Carrot red leaf virus, Potato leafroll virus and Turnip yellows virus) in Greece and the collection of isolates. These isolates along with other characterized ones were used for the evaluation of the generic PCR's detection range. The developed assay efficiently amplified a 593bp RdRp fragment from 46 isolates of 10 different Polerovirus species. Phylogenetic analysis using the generic PCR's amplicon sequence showed that although it cannot accurately infer evolutionary relationships within the genus it can differentiate poleroviruses at the species level. Overall, the described generic assay could be applied for the reliable detection of Polerovirus infections and, in combination with the specific PCRs, for the identification of new and uncharacterized species in the genus. Copyright © 2013 Elsevier B.V. All rights reserved.

Feasibility of small animal cranial irradiation with the microRT system

International Nuclear Information System (INIS)

Kiehl, Erich L.; Stojadinovic, Strahinja; Malinowski, Kathleen T.; Limbrick, David; Jost, Sarah C.; Garbow, Joel R.; Rubin, Joshua B.; Deasy, Joseph O.; Khullar, Divya; Izaguirre, Enrique W.; Parikh, Parag J.; Low, Daniel A.; Hope, Andrew J.

2008-01-01

Purpose: To develop and validate methods for small-animal CNS radiotherapy using the microRT system. Materials and Methods: A custom head immobilizer was designed and built to integrate with a pre-existing microRT animal couch. The Delrin couch-immobilizer assembly, compatible with multiple imaging modalities (CT, microCT, microMR, microPET, microSPECT, optical), was first imaged via CT in order to verify the safety and reproducibility of the immobilization method. Once verified, the subject animals were CT-scanned while positioned within the couch-immobilizer assembly for treatment planning purposes. The resultant images were then imported into CERR, an in-house-developed research treatment planning system, and registered to the microRTP treatment planning space using rigid registration. The targeted brain was then contoured and conformal radiotherapy plans were constructed for two separate studies: (1) a whole-brain irradiation comprised of two lateral beams at the 90 degree sign and 270 degree sign microRT treatment positions and (2) a hemispheric (left-brain) irradiation comprised of a single A-P vertex beam at the 0 degree sign microRT treatment position. During treatment, subject animals (n=48) were positioned to the CERR-generated treatment coordinates using the three-axis microRT motor positioning system and were irradiated using a clinical Ir-192 high-dose-rate remote after-loading system. The radiation treatment course consisted of 5 Gy fractions, 3 days per week. 90% of the subjects received a total dose of 30 Gy and 10% received a dose of 60 Gy. Results: Image analysis verified the safety and reproducibility of the immobilizer. CT scans generated from repeated reloading and repositioning of the same subject animal in the couch-immobilizer assembly were fused to a baseline CT. The resultant analysis revealed a 0.09 mm average, center-of-mass translocation and negligible volumetric error in the contoured, murine brain. The experimental use of the head

Metallographic anlaysis and strength investigation of different Be-Cu joints in the temperature range RT-3500C

International Nuclear Information System (INIS)

Gervash, A.A.; Giniatouline, R.N.; Mazul, I.V.

1995-01-01

The goal of this work is to estimate the strength and structure of different Be-Cu joining techniques. Brazing, diffusion bonding and joint rolling methods were chosen as ITER Be-Cu joint method candidates. Selected for ITER application Be-Cu joints were produced as technological plates (30-50 mm x 50-100 mm x thickness). AR samples for farther investigations were cutted out from initial technological plates. To compare mechanical strength of selected Be-Cu joints tensile and shearing tests of chosen candidates were carried out in the temperature range RT - 350 degrees C. The metallographic analysis of Be-Cu crosssection was also done. Preliminary results of these tests as well as metallographic analysis data are presented. The industrial possibilities of producing required for ITER full scale Be-Cu joints are discussed

A competitive trade-off limits the selective advantage of increased antibiotic production.

Science.gov (United States)

Gerardin, Ylaine; Springer, Michael; Kishony, Roy

2016-09-26

In structured environments, antibiotic-producing microorganisms can gain a selective advantage by inhibiting nearby competing species 1 . However, despite their genetic potential 2,3 , natural isolates often make only small amounts of antibiotics, and laboratory evolution can lead to loss rather than enhancement of antibiotic production 4 . Here, we show that, due to competition with antibiotic-resistant cheater cells, increased levels of antibiotic production can actually decrease the selective advantage to producers. Competing fluorescently labelled Escherichia coli colicin producers with non-producing resistant and sensitive strains on solid media, we found that although producer colonies can greatly benefit from the inhibition of nearby sensitive colonies, this benefit is shared with resistant colonies growing in their vicinity. A simple model, which accounts for such local competitive and inhibitory interactions, suggests that the advantage of producers varies non-monotonically with the amount of production. Indeed, experimentally varying the amount of production shows a peak in selection for producers, reflecting a trade-off between benefit gained by inhibiting sensitive competitors and loss due to an increased contribution to resistant cheater colonies. These results help explain the low level of antibiotic production observed for natural species and can help direct laboratory evolution experiments selecting for increased or novel production of antibiotics.

SU-E-J-42: Customized Deformable Image Registration Using Open-Source Software SlicerRT

Energy Technology Data Exchange (ETDEWEB)

Gaitan, J Cifuentes; Chin, L; Pignol, J [Sunnybrook Health Sciences Centre, Toronto, Ontario (Canada); Kirby, N; Pouliot, J [UC San Francisco, San Francisco, CA (United States); Lasso, A; Pinter, C; Fichtinger, G [Queen' s University, Kingston, Ontario (Canada)

2014-06-01

Purpose: SlicerRT is a flexible platform that allows the user to incorporate the necessary images registration and processing tools to improve clinical workflow. This work validates the accuracy and the versatility of the deformable image registration algorithm of the free open-source software SlicerRT using a deformable physical pelvic phantom versus available commercial image fusion algorithms. Methods: Optical camera images of nonradiopaque markers implanted in an anatomical pelvic phantom were used to measure the ground-truth deformation and evaluate the theoretical deformations for several DIR algorithms. To perform the registration, full and empty bladder computed tomography (CT) images of the phantom were obtained and used as fixed and moving images, respectively. The DIR module, found in SlicerRT, used a B-spline deformable image registration with multiple optimization parameters that allowed customization of the registration including a regularization term that controlled the amount of local voxel displacement. The virtual deformation field at the center of the phantom was obtained and compared to the experimental ground-truth values. The parameters of SlicerRT were then varied to improve spatial accuracy. To quantify image similarity, the mean absolute difference (MAD) parameter using Hounsfield units was calculated. In addition, the Dice coefficient of the contoured rectum was evaluated to validate the strength of the algorithm to transfer anatomical contours. Results: Overall, SlicerRT achieved one of the lowest MAD values across the algorithm spectrum, but slightly smaller mean spatial errors in comparison to MIM software (MIM). On the other hand, SlicerRT created higher mean spatial errors than Velocity Medical Solutions (VEL), although obtaining an improvement on the DICE to 0.91. The large spatial errors were attributed to the poor contrast in the prostate bladder interface of the phantom. Conclusion: Based phantom validation, SlicerRT is capable of

Table 1. Primer sequences used for real-time qRT-PCR analysis of ...

Indian Academy of Sciences (India)

User

TGTCCCAGTAAACCGCTC. GAATCCAGCACGATACCAGT. Figure 1. Expression analysis of candidate CsActin and CsFbox genes by qRT-PCR in response to 4°C treatment. The y-axis indicates Cq values, and error bars represent standard deviations of the mean values of four replicates. Rt, roots; St, stems; Le, leaves; Fl ...

Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

Directory of Open Access Journals (Sweden)

Porceddu Enrico

2009-02-01

Full Text Available Abstract Background Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. Results The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and α-tubulin. Conclusion The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability

Cognitive load during route selection increases reliance on spatial heuristics.

Science.gov (United States)

Brunyé, Tad T; Martis, Shaina B; Taylor, Holly A

2018-05-01

Planning routes from maps involves perceiving the symbolic environment, identifying alternate routes and applying explicit strategies and implicit heuristics to select an option. Two implicit heuristics have received considerable attention, the southern route preference and initial segment strategy. This study tested a prediction from decision-making theory that increasing cognitive load during route planning will increase reliance on these heuristics. In two experiments, participants planned routes while under conditions of minimal (0-back) or high (2-back) working memory load. In Experiment 1, we examined how memory load impacts the southern route heuristic. In Experiment 2, we examined how memory load impacts the initial segment heuristic. Results replicated earlier results demonstrating a southern route preference (Experiment 1) and initial segment strategy (Experiment 2) and further demonstrated that evidence for heuristic reliance is more likely under conditions of concurrent working memory load. Furthermore, the extent to which participants maintained efficient route selection latencies in the 2-back condition predicted the magnitude of this effect. Together, results demonstrate that working memory load increases the application of heuristics during spatial decision making, particularly when participants attempt to maintain quick decisions while managing concurrent task demands.

25 kaadrit sekundis / Liis Auväärt

Index Scriptorium Estoniae

Auväärt, Liis

2009-01-01

Nukufilmis käib töö filmiga "Lisa Limone & Maroc Orange", režissöör Mait Laas, animaatorid Triin Sarapik-Kivi, Märt Kivi, operaator Ragnar Neljandi, nukumeistrid Heigo Eeriksoo, Taivo Müürsep, Ene Mellow ja Kreeta Käeri. Dekoratsioonimeistrid Mait Erik ja Roman Kuznetsov

A novel and highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus.

Science.gov (United States)

Shen, Xin-Xin; Qiu, Fang-Zhou; Zhao, Huai-Long; Yang, Meng-Jie; Hong, Liu; Xu, Song-Tao; Zhou, Shuai-Feng; Li, Gui-Xia; Feng, Zhi-Shan; Ma, Xue-Jun

2018-03-01

The sensitivity of qRT-PCR assay is not adequate for the detection of the samples with lower viral load, particularly in the cerebrospinal fluid (CSF) of patients. Here, we present the development of a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of human enterovirus (HEV). The clinical performance of both RTN RT-PCR and qRT-PCR was also tested and compared using 140 CSF and fecal specimens. The sensitivities of RTN RT-PCR assay for EV71, Coxsackievirus A (CVA)16, CVA6 and CVA10 achieved 10 -8 dilution with a corresponding Ct value of 38.20, 36.45, 36.75, and 36.45, respectively, which is equal to traditional two-step nested RT-PCR assay and approximately 2-10-fold lower than that of qRT-PCR assay. The specificity of RTN RT-PCR assay was extensively analyzed insilico and subsequently verified using the reference isolates and clinical samples. Sixteen qRT-PCR-negative samples were detected by RTN RT-PCR and a variety of enterovirus serotypes was identified by sequencing of inner PCR products. We conclude RTN RT-PCR is more sensitive than qRT-PCR for the detection of HEV in clinical samples. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

Science.gov (United States)

Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

2002-01-01

A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

Performance effects of nicotine during selective attention, divided attention, and simple stimulus detection: an fMRI study.

Science.gov (United States)

Hahn, Britta; Ross, Thomas J; Wolkenberg, Frank A; Shakleya, Diaa M; Huestis, Marilyn A; Stein, Elliot A

2009-09-01

Attention-enhancing effects of nicotine appear to depend on the nature of the attentional function. Underlying neuroanatomical mechanisms, too, may vary depending on the function modulated. This functional magnetic resonance imaging study recorded blood oxygen level-dependent (BOLD) activity in minimally deprived smokers during tasks of simple stimulus detection, selective attention, or divided attention after single-blind application of a transdermal nicotine (21 mg) or placebo patch. Smokers' performance in the placebo condition was unimpaired as compared with matched nonsmokers. Nicotine reduced reaction time (RT) in the stimulus detection and selective attention but not divided attention condition. Across all task conditions, nicotine reduced activation in frontal, temporal, thalamic, and visual regions and enhanced deactivation in so-called "default" regions. Thalamic effects correlated with RT reduction selectively during stimulus detection. An interaction with task condition was observed in middle and superior frontal gyri, where nicotine reduced activation only during stimulus detection. A visuomotor control experiment provided evidence against nonspecific effects of nicotine. In conclusion, although prefrontal activity partly displayed differential modulation by nicotine, most BOLD effects were identical across tasks, despite differential performance effects, suggesting that common neuronal mechanisms can selectively benefit different attentional functions. Overall, the effects of nicotine may be explained by increased functional efficiency and downregulated task-independent "default" functions.

CYCLIC VARIATIONS OF ORBITAL PERIOD AND LONG-TERM LUMINOSITY IN CLOSE BINARY RT ANDROMEDAE

International Nuclear Information System (INIS)

Manzoori, Davood

2009-01-01

Solutions of standard VR light curves for the eclipsing binary RT And were obtained using the PHOEBE program (ver. 0.3a). Absolute parameters of the stellar components were then determined, enabling them to be positioned on the mass-luminosity diagram. Times of minima data ( O - C curve ) were analyzed using the method of Kalimeris et al. A cyclic variation in the orbital period and brightness, with timescales of about 11.89 and 12.50 yr were found, respectively. This is associated with a magnetic activity cycle modulating the orbital period of RT And via the Applegate mechanism. To check the consistency of the Applegate model, we have estimated some related parameters of the RT And system. The calculated parameters were in accordance with those estimated by Applegate for other similar systems, except B, the subsurface magnetic field of which shows a rather high value for RT And.

Arvo Pärt tänavu Holland-Festivali keskmes

Index Scriptorium Estoniae

2005-01-01

Klassikalise muusika festivalil "Holland-Festival" 1.-26. juun. Amsterdamis on aukülaliseks Arvo Pärt, kelle muusikat esitatakse 7.-10. ja 18. juunil Amsterdami Uues kirikus (Nieuwe Kerk), Muziekgebouw aan het Ij-is ja Concertgebouw's

Pärt, Arvo: "Beatus". Statuit ei Dominus / Patric Wiklacz

Index Scriptorium Estoniae

Wiklacz, Patric

1997-01-01

Uuest heliplaadist "Pärt, Arvo: "Beatus". Statuit ei Dominus. Missa syllabica. Beatus Petronius. 7 Magnificat-Antiphonen. De profundis. Memento. Cantate Domino. Solfeggio. Estonian Philharmonic Chamber Choir, T. Kaljuste". Virgin Classics 545 276-2 (CD:167F)

Gemcitabine: Selective cytotoxicity, induction of inflammation and effects on urothelial function

Energy Technology Data Exchange (ETDEWEB)

Farr, Stefanie E; Chess-Williams, Russ; McDermott, Catherine M, E-mail: camcderm@bond.edu.au

2017-02-01

Intravesical gemcitabine has recently been introduced for the treatment of superficial bladder cancer and has a favourable efficacy and toxicity profile in comparison to mitomycin c (MMC), the most commonly used chemotherapeutic agent. The aim of this study was to assess the cytotoxic potency of gemcitabine in comparison to MMC in urothelial cell lines derived from non-malignant (UROtsa) and malignant (RT4 and T24) tissues to assess selectivity. Cells were treated with gemcitabine or mitomycin C at concentrations up to the clinical doses for 1 or 2 h respectively (clinical duration). Treatment combined with hyperthermia was also examined. Cell viability, ROS formation, urothelial function (ATP, acetylcholine and PGE2 release) and secretion of inflammatory cytokines were assessed. Gemcitabine displayed a high cytotoxic selectivity for the two malignant cell lines (RT4, T24) compared to the non-malignant urothelial cells (UROtsa, proliferative and non-proliferative). In contrast, the cytotoxic effects of MMC were non-selective with equivalent potency in each of the cell lines. The cytotoxic effect of gemcitabine in the malignant cell lines was associated with an elevation in free radical formation and was significantly decreased in the presence of an equilibrative nucleoside transporter inhibitor. Transient changes in urothelial ATP and PGE{sub 2} release were observed, with significant increase in release of interleukin-6, interleukin-8 and interleukin-1β from urothelial cells treated with gemcitabine. The selectivity of gemcitabine for malignant urothelial cells may account for the less frequent adverse urological effects with comparison to other commonly used chemotherapeutic agents. - Highlights: • Intravesical gemcitabine has recently been introduced to treat bladder cancer. • Gemcitabine is selectively toxic for malignant urothelial cells. • Urothelial ATP, PGE{sub 2} and inflammatory cytokines were altered by gemcitabine. • Selectivity of gemcitabine

Are PEI-coated SWCNTs conjugated with hepatitis A virus? A chemical study with SEM, Z-potential, EDXD and RT-PCR

International Nuclear Information System (INIS)

Carbone, M; Valentini, F; Palleschi, G; Caminiti, R; Petrinca, A R; Donia, D; Divizia, M

2010-01-01

The conjugation between nanotubes, coated with different doses of polyethylene imine (PEI) and hepatitis A virus (HAV) was investigated by scanning electron microscopy, Z-potential, thermogravimetric and differential thermal analysis, transmission electron microscopy, energy dispersive x-ray diffraction (EDXD) and reverse transcript polymerase chain reaction (RT-PCR). For the first time, to our knowledge, evidence is obtained that conjugation between the nanotubes and the HAV occurs and that it has an (at least a partial) electrostatic character. Since all components of the conjugated systems, nanotubes, coating material and virus are characterized by different peak shapes in the selected q range, it was possible to infer that conjugation occurred. RT-PCR measurements confirmed that the conjugation of the coated nanotubes and HAV occurred and the result was stable. This opens up the prospect of probing the coated nanotubes as intra-cellular carriers in transfection processes of the virus. Further biological applications will concern a possible vaccine especially for non-replicative viruses.

Thoracic radiation therapy (RT) before autologous bone marrow transplantation (ABMT) in relapsed or refractory Hodgkin's disease (HD)

International Nuclear Information System (INIS)

Tsang, Richard W.; Gospodarowicz, Mary K.; Sutcliffe, Simon B.; Crump, Michael; Keating, Armand

1997-01-01

Purpose: To assess the relationship between peri-ABMT RT and treatment-related mortality in patients receiving high-dose chemotherapy (HDCT) and ABMT for recurrent/refractory HD. Materials and Methods: Between 12/1986 and 12/1992, 90 patients (pts) with HD were treated with HDCT (etoposide 60 mg/kg, melphalan 160 mg/m 2 ) +ABMT in Toronto. Fifty-nine of these had all or part of their treatment (RT and/or CT) at the PMH, and they form the basis of this report. HDCT + ABMT was performed for refractory (11 pts) or relapsed (48 pts) HD. The median age at ABMT was 29 (range 16-47), F:M ratio was 1:1.2. Salvage chemotherapy consisted of DHAP (36), mini-BEAM (7), both (8), other chemotherapy (5), and no chemotherapy (3). RT have been incorporated in the salvage treatment with the intent to achieve complete disease control of active disease at relapse or disease progression. RT was given pre-ABMT in 33 pts (3 mantle, 8 mantle with lung, 7 modified mantle excluding axillae, 4 involved field, 1 mantle with TBI, 1 TBI, and 9 non-thoracic), and post-ABMT in 4 pts (2 mantle, 2 modified mantle). Planned RT tumor dose was 35 Gy over 4 weeks (median 35 Gy, range 25-40 Gy), lower doses were used for lung RT (15-17.5 Gy). Treatment-related (TR) mortality was defined as any death occurring within 100 days of ABMT. Autopsies were performed for all patients with TR deaths. Results: We observed 36 deaths, and 10 of these were treatment-related (TR) deaths. With an average follow-up of 4.9 years (range 1.2-7.4 years), the actuarial overall survival was 52% ± 13% at 3 years, and 41% ± 14% at 5 years. Among the 24 patients who received thoracic RT before ABMT, there were 8 TR deaths, with 3 solely attributable to radiation pneumonitis. The remaining 5 TR deaths all had respiratory failure as a major medical problem with complicating sepsis and pancytopenia. The interval from RT to ABMT was shorter for 8 patients dying of TR death (mean 37 days; range 0-103 days), than for the 16 pts with

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling

DEFF Research Database (Denmark)

Simonsen, Martin; Maetschke, S.R.; Ragan, M.A.

2012-01-01

Motivation: Phylogenetic profiling methods can achieve good accuracy in predicting protein–protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly......: We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...... phylogenetic profiles often require very different RT sets to support high prediction accuracy....

Detection and Analysis of Circular RNAs by RT-PCR.

Science.gov (United States)

Panda, Amaresh C; Gorospe, Myriam

2018-03-20

Gene expression in eukaryotic cells is tightly regulated at the transcriptional and posttranscriptional levels. Posttranscriptional processes, including pre-mRNA splicing, mRNA export, mRNA turnover, and mRNA translation, are controlled by RNA-binding proteins (RBPs) and noncoding (nc)RNAs. The vast family of ncRNAs comprises diverse regulatory RNAs, such as microRNAs and long noncoding (lnc)RNAs, but also the poorly explored class of circular (circ)RNAs. Although first discovered more than three decades ago by electron microscopy, only the advent of high-throughput RNA-sequencing (RNA-seq) and the development of innovative bioinformatic pipelines have begun to allow the systematic identification of circRNAs (Szabo and Salzman, 2016; Panda et al ., 2017b; Panda et al ., 2017c). However, the validation of true circRNAs identified by RNA sequencing requires other molecular biology techniques including reverse transcription (RT) followed by conventional or quantitative (q) polymerase chain reaction (PCR), and Northern blot analysis (Jeck and Sharpless, 2014). RT-qPCR analysis of circular RNAs using divergent primers has been widely used for the detection, validation, and sometimes quantification of circRNAs (Abdelmohsen et al ., 2015 and 2017; Panda et al ., 2017b). As detailed here, divergent primers designed to span the circRNA backsplice junction sequence can specifically amplify the circRNAs and not the counterpart linear RNA. In sum, RT-PCR analysis using divergent primers allows direct detection and quantification of circRNAs.

Dynamic expression of desmin, α-SMA and TGF-β1 during hepatic fibrogenesis induced by selective bile duct ligation in young rats

Energy Technology Data Exchange (ETDEWEB)

Gonçalves, J.O.; Tannuri, A.C.A.; Coelho, M.C.M.; Bendit, I.; Tannuri, U. [Laboratório de Pesquisa em Cirurgia Pediátrica (LIM-30), Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP (Brazil)

2014-08-15

We previously described a selective bile duct ligation model to elucidate the process of hepatic fibrogenesis in children with biliary atresia or intrahepatic biliary stenosis. Using this model, we identified changes in the expression of alpha smooth muscle actin (α-SMA) both in the obstructed parenchyma and in the hepatic parenchyma adjacent to the obstruction. However, the expression profiles of desmin and TGF-β1, molecules known to be involved in hepatic fibrogenesis, were unchanged when analyzed by semiquantitative polymerase chain reaction (RT-PCR). Thus, the molecular mechanisms involved in the modulation of liver fibrosis in this experimental model are not fully understood. This study aimed to evaluate the molecular changes in an experimental model of selective bile duct ligation and to compare the gene expression changes observed in RT-PCR and in real-time quantitative PCR (qRT‐PCR). Twenty-eight Wistar rats of both sexes and weaning age (21-23 days old) were used. The rats were separated into groups that were assessed 7 or 60 days after selective biliary duct ligation. The expression of desmin, α-SMA and TGF-β1 was examined in tissue from hepatic parenchyma with biliary obstruction (BO) and in hepatic parenchyma without biliary obstruction (WBO), using RT-PCR and qRT‐PCR. The results obtained in this study using these two methods were significantly different. The BO parenchyma had a more severe fibrogenic reaction, with increased α-SMA and TGF-β1 expression after 7 days. The WBO parenchyma presented a later, fibrotic response, with increased desmin expression 7 days after surgery and increased α-SMA 60 days after surgery. The qRT‐PCR technique was more sensitive to expression changes than the semiquantitative method.

Dynamic expression of desmin, α-SMA and TGF-β1 during hepatic fibrogenesis induced by selective bile duct ligation in young rats

International Nuclear Information System (INIS)

Gonçalves, J.O.; Tannuri, A.C.A.; Coelho, M.C.M.; Bendit, I.; Tannuri, U.

2014-01-01

We previously described a selective bile duct ligation model to elucidate the process of hepatic fibrogenesis in children with biliary atresia or intrahepatic biliary stenosis. Using this model, we identified changes in the expression of alpha smooth muscle actin (α-SMA) both in the obstructed parenchyma and in the hepatic parenchyma adjacent to the obstruction. However, the expression profiles of desmin and TGF-β1, molecules known to be involved in hepatic fibrogenesis, were unchanged when analyzed by semiquantitative polymerase chain reaction (RT-PCR). Thus, the molecular mechanisms involved in the modulation of liver fibrosis in this experimental model are not fully understood. This study aimed to evaluate the molecular changes in an experimental model of selective bile duct ligation and to compare the gene expression changes observed in RT-PCR and in real-time quantitative PCR (qRT‐PCR). Twenty-eight Wistar rats of both sexes and weaning age (21-23 days old) were used. The rats were separated into groups that were assessed 7 or 60 days after selective biliary duct ligation. The expression of desmin, α-SMA and TGF-β1 was examined in tissue from hepatic parenchyma with biliary obstruction (BO) and in hepatic parenchyma without biliary obstruction (WBO), using RT-PCR and qRT‐PCR. The results obtained in this study using these two methods were significantly different. The BO parenchyma had a more severe fibrogenic reaction, with increased α-SMA and TGF-β1 expression after 7 days. The WBO parenchyma presented a later, fibrotic response, with increased desmin expression 7 days after surgery and increased α-SMA 60 days after surgery. The qRT‐PCR technique was more sensitive to expression changes than the semiquantitative method

The value of research : telling the R&T story

Science.gov (United States)

2009-07-01

The Federal Highway Administration (FHWA) plays a leadership role in shaping and executing a National Research and Technology (R&T) program. The agency also acts as a convener; collaborations with State, industry, and academic partners provide the fo...

Metodiskā darba organizēšana un izvērtēšana skolā.

OpenAIRE

Jakubovska, Solvita

2010-01-01

Maģistra darbā „Metodiskā darba organizēšana un izvērtēšana skolā” aplūkoti jautājumi par metodiskā darba organizēšanu valsts, pašvaldības un skolas līmenī, kā arī metodisko komisiju darbības izvērtēšanu, balstoties uz skolu darba kvalitātes izvērtēšanu akreditācijas procesā. Maģistra darba mērķis ir izpētīt skolas metodiskā darba organizēšanas un izvērtēšanas iespējas, veidojot priekšlikumus darba uzlabošanai. Pētījuma ietveros tika izstrādāti skolas metodisko komisiju darbības izvērtēša...

Novel HBV recombinants between genotypes B and C in 3'-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients.

Science.gov (United States)

Liu, Baoming; Yang, Jing-Xian; Yan, Ling; Zhuang, Hui; Li, Tong

2018-01-01

As one of the major global public health concerns, hepatitis B virus (HBV) can be divided into at least eight genotypes, which may be related to disease severity and treatment response. We previously demonstrated that genotypes B and C HBV, with distinct geographical distribution in China, had divergent genotype-dependent amino acid polymorphisms and variations in reverse transcriptase (RT) gene region, a target of antiviral therapy using nucleos(t)ide analogues. Recently recombination between HBV genotypes B and C was reported to occur in the RT region. However, their frequency and clinical significance is poorly understood. Here full-length HBV RT sequences from 201 Chinese chronic hepatitis B (CHB) patients were amplified and sequenced, among which 31.34% (63/201) were genotype B whereas 68.66% (138/201) genotype C. Although no intergenotypic recombination was detected among C-genotype HBV, 38.10% (24/63) of B-genotype HBV had recombination with genotype C in the 3'-terminal RT sequences. The patients with B/C intergenotypic recombinants had significantly (Pdistribution feature in China. Our findings provide novel insight into the virological, clinical and epidemiological features of new HBV B/C intergenotypic recombinants at the 3' end of RT sequences among Chinese CHB patients. The highly complex genetic background of the novel recombinant HBV carrying new mutations affecting RT protein may contribute to an enhanced heterogeneity in treatment response or prognosis among CHB patients. Published by Elsevier B.V.

Endogenous reverse transcriptase (RT) activity and Chromatin remodeling in normal and transformed cells and early embryos

International Nuclear Information System (INIS)

Spadafora, C.; Sciamanna, I.; Misteli, T.

2009-01-01

Endogenous Reverse Transcriptase (RT) is an enzyme encoded by two classes of genomic retro-elements: retro-transposons and endogenous retroviruses. Basal levels of RT are expressed in all non pathological, differentiated tissues while high RT expression levels characterize tumorigenic cells, germ cells and embryonic tissues. Preliminary studies carried out in our laboratory have shown that RT inhibition using pharmacological inhibitors (nevirapine and efavirenz, two drugs currently used in AIDS therapy) drastically reduces cell proliferation, promotes differentiation of tumorigenic cells in vitro, induces a reprogrammed gene expression and antagonizes tumor progression in nude mice inoculated with tumorigenic human cell lines, including melanoma, prostate and colon carcinoma and microcitoma

Detecting Newcastle disease virus in combination of RT-PCR with red blood cell absorption

Directory of Open Access Journals (Sweden)

Liu Chengqian

2011-05-01

Full Text Available Abstract Reverse transcription-polymerase chain reaction (RT-PCR has limited sensitivity when treating complicated samples, such as feces, waste-water in farms, and nucleic acids, protein rich tissue samples, all the factors may interfere with the sensitivity of PCR test or generate false results. In this study, we developed a sensitive RT-PCR, combination of red blood cell adsorption, for detecting Newcastle disease virus (NDV. One pair of primers which was highly homologous to three NDV pathotypes was designed according to the consensus nucleocapsid protein (NP gene sequence. To eliminate the interfere of microbes and toxic substances, we concentrated and purified NDV from varied samples utilizing the ability of NDV binding red blood cells (RBCs. The RT-PCR coupled with red blood cell adsorption was much more sensitive in comparison with regular RT-PCR. The approach could also be used to detect other viruses with the property of hemagglutination, such as influenza viruses.

Real-Time RT-PCR for the Detection of Lyssavirus Species

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A. Deubelbeiss

2014-01-01

Full Text Available The causative agents of rabies are single-stranded, negative-sense RNA viruses in the genus Lyssavirus of Rhabdoviridae, consisting of twelve classified and three as yet unclassified species including classical rabies virus (RABV. Highly neurotropic RABV causes rapidly progressive encephalomyelitis with nearly invariable fatal outcome. Rapid and reliable diagnosis of rabies is highly relevant for public and veterinary health. Due to growing variety of the genus Lyssavirus observed, the development of suitable molecular assays for diagnosis and differentiation is challenging. This work focused on the establishment of a suitable real-time RT-PCR technique for rabies diagnosis as a complement to fluorescent antibody test and rabies tissue culture infection test as gold standard for diagnosis and confirmation. The real-time RT-PCR was adapted with the goal to detect the whole spectrum of lyssavirus species, for nine of which synthesized DNA fragments were used. For the detection of species, seven probes were developed. Serial dilutions of the rabies virus strain CVS-11 showed a 100-fold higher sensitivity of real-time PCR compared to heminested RT-PCR. Using a panel of thirty-one lyssaviruses representing four species, the suitability of the protocol could be shown. Phylogenetic analysis of the sequences obtained by heminested PCR allowed correct classification of all viruses used.

Performance Evaluation of Irbene RT-16 Radio Telescope Receiving System

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Bleiders M.

2017-12-01

Full Text Available In the present paper, recent measurement results of refurbished Irbene RT-16 radio telescope receiving system performance are presented. The aim of the research is to evaluate characteristics of RT-16, which will allow carrying out necessary amplitude calibration in both single dish and VLBI observations, to improve the performance of existing system as well as to monitor, control and compare performance if possible changes in the receiving system will occur in future. The evaluated receiving system is 16 m Cassegrain antenna equipped with a cryogenic receiver with frequency range from 4.5 to 8.8 GHz, which is divided into four sub-bands. Multiple calibration sessions have been carried out by observing stable astronomical sources with known flux density by using in-house made total power registration backend. First, pointing offset calibration has been carried out and pointing model coefficients calculated and applied. Then, amplitude calibration, namely antenna sensitivity, calibration diode equivalent flux density and gain curve measurements have been carried out by observing calibration sources at different antenna elevations at each of the receiver sub-bands. Beam patterns have also been evaluated at different frequency bands. As a whole, acquired data will serve as a reference point for comparison in future performance evaluation of RT-16.

Detection of avian metapneumovirus subtypes in turkeys using RT-PCR.

Science.gov (United States)

Ongor, H; Karahan, M; Kalin, R; Bulut, H; Cetinkaya, B

2010-03-20

This study investigated the prevalence of avian metapneumovirus (aMPV) and the detection of molecular subtypes of field strains of the virus using RT-PCR in clinically healthy turkeys and those showing signs of respiratory disease. In the RT-PCR examination of 624 tracheal tissue samples collected from a local turkey abattoir, 2.9 per cent (18/624) of samples tested positive. In the examination of tracheal swab samples collected from flocks with respiratory problems, 18 of 20 samples tested positive. When the results were assessed at flock level, aMPV infection was detected in only one of the 23 clinically healthy turkey flocks, whereas all four flocks with respiratory problems were infected. Molecular typing using primers specific to the attachment glycoprotein (G) gene showed that all 36 positive samples belonged to subtype B. Partial sequence analysis of DNA samples showed 95 per cent homology between the field types and the reference strain aMPV subtype B. Whereas clinically healthy turkeys had been vaccinated with a subtype A virus vaccine, the flocks with respiratory problems had been vaccinated with a subtype B virus vaccine. Despite four blind passages of RT-PCR-positive samples on Vero and chicken embryo fibroblast cells, no cytopathic effect was detected by microscopic examination.

Detection of respiratory bacterial pathogens causing atypical pneumonia by multiplex Lightmix® RT-PCR.

Science.gov (United States)

Wagner, Karoline; Springer, Burkard; Imkamp, Frank; Opota, Onya; Greub, Gilbert; Keller, Peter M

2018-04-01

Pneumonia is a severe infectious disease. In addition to common viruses and bacterial pathogens (e.g. Streptococcus pneumoniae), fastidious respiratory pathogens like Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella spp. can cause severe atypical pneumonia. They do not respond to penicillin derivatives, which may cause failure of antibiotic empirical therapy. The same applies for infections with B. pertussis and B. parapertussis, the cause of pertussis disease, that may present atypically and need to be treated with macrolides. Moreover, these fastidious bacteria are difficult to identify by culture or serology, and therefore often remain undetected. Thus, rapid and accurate identification of bacterial pathogens causing atypical pneumonia is crucial. We performed a retrospective method evaluation study to evaluate the diagnostic performance of the new, commercially available Lightmix ® multiplex RT-PCR assay that detects these fastidious bacterial pathogens causing atypical pneumonia. In this retrospective study, 368 clinical respiratory specimens, obtained from patients suffering from atypical pneumonia that have been tested negative for the presence of common agents of pneumonia by culture and viral PCR, were investigated. These clinical specimens have been previously characterized by singleplex RT-PCR assays in our diagnostic laboratory and were used to evaluate the diagnostic performance of the respiratory multiplex Lightmix ® RT-PCR. The multiplex RT-PCR displayed a limit of detection between 5 and 10 DNA copies for different in-panel organisms and showed identical performance characteristics with respect to specificity and sensitivity as in-house singleplex RT-PCRs for pathogen detection. The Lightmix ® multiplex RT-PCR assay represents a low-cost, time-saving and accurate diagnostic tool with high throughput potential. The time-to-result using an automated DNA extraction device for respiratory specimens followed by multiplex RT-PCR detection was

An Evidence-Based Approach to Plum Pox Virus Detection by DASI-ELISA and RT-PCR in Dormant Period

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Antonio Olmos

2008-01-01

Full Text Available An evidence-based approach, such as those developed in clinical and veterinary medicine, was applied to the detection of Plum pox virus (PPV during the dormant period. A standardized methodology was used for the calculation of parameters of the operational capacity of DASI-ELISA and RT-PCR in wintertime. These methods are routinely handled to test the sanitary status of plants in national or international trading and in those cases concerning export-import of plant materials. Diagnosis often has to be performed during the dormant period, when plant material is commercialized. Some guidelines to interpret diagnostic results of wintertime are provided in an attempt to minimize risks associated with the methods and over-reliance on the binary outcome of a single assay. In order to evaluate if a complementary test increased the confidence of PPV diagnosis when discordant results between DASI-ELISA and RT-PCR are obtained, NASBA-FH also was included. Likelihood ratios of each method were estimated based on the sensitivity and specificity obtained in wintertime. Subsequently, a Bayesian approach was performed to calculate post-test probability of PPV infection in spring. Results of evidence-based approach show that different PPV prevalences require different screening tests. Thus, at very low PPV prevalence levels DASI-ELISA should be used as the election method, whilst at the highest PPV prevalence levels RT-PCR should be performed. NASBA-FH could be used at medium prevalences to clarify discordances between DASIELISA and RT-PCR.

The cost-effectiveness of routine radiation therapy (RT) following conservative surgery (CS) for early-stage breast cancer

International Nuclear Information System (INIS)

Hayman, James A.; Hillner, Bruce E.; Harris, Jay R.; Weeks, Jane C.

1996-01-01

Purpose: The routine use of RT following CS has been shown to decrease the rate of LR by at least 75%, but its ultimate impact on survival remains less clear. Given concerns about its toxicity, inconvenience, and cost, the need for routine RT has been questioned. These concerns, however, need to be balanced against the improved quality of life and reduced salvage costs associated with routine RT. We performed an incremental cost-utility analysis to evaluate whether, even in the assumed absence of a survival advantage, the use of RT in this situation would be considered cost-effective. Materials and Methods: A Markov decision analytic model was developed to examine the incremental impact of the addition of RT to CS on the relevant outcomes and costs from a societal perspective. Using a cycle length of one year, the analysis was performed on a theoretical cohort of 60 year old patients over a 10 year time horizon. To account for quality of life benefits, outcomes were measured in Quality Adjusted Life Years (QALYs). The LR, distant recurrence (DR), and overall survival rates used in the model were drawn principally from NSABP B-06. It was assumed for the baseline analysis that the addition of RT reduces the rate of LR by 75%, but has no impact on overall survival. Salvage for LR following CS and RT consisted of mastectomy and reconstructive surgery (MRS), while, following CS alone, it was assumed that equal numbers of patients would be salvaged by CS and RT and by MRS. The rate of DR was assumed to be constant with and without RT. The utilities of 97 patients with early-stage breast cancer treated with CS and RT were used to adjust the relevant local outcomes for quality of life, while expert judgement was used to estimate the utilities for the DR states. Baseline costs were determined using Medicare charges, ratios of costs to charges and RVUs, all at the Medical College of Virginia. When uncertainties existed, the model was biased against RT. Both benefits and

A one-step multiplex RT-PCR assay for simultaneous detection of four viruses that infect peach.

Science.gov (United States)

Yu, Y; Zhao, Z; Jiang, D; Wu, Z; Li, S

2013-10-01

A multiplex reverse transcription polymerase chain reaction (mRT-PCR) assay was developed to enable the simultaneous detection and differentiation of four viruses that infect peach, namely Apple chlorotic leaf spot virus (ACLSV), Cherry green ring mottle virus (CGRMV), Prunus necrotic ringspot virus (PNRSV) and Apricot pseudo-chlorotic leaf spot virus (APCLSV). In this study, four pairs of primers, one specific for each virus, were designed; the corresponding PCR products were 632, 439, 346 and 282 bp in length for ACLSV, CGRMV, PNRSV and APCLSV, respectively, and the fragments could be distinguished clearly by agarose gel electrophoresis. The sensitivity and specificity of the method were tested using individual RT-PCR and enzyme-linked immunosorbent assay (ELISA), and the identity of the RT-PCR amplification products was also confirmed by DNA sequencing. The results of RT-PCR and ELISA, along with batch detection using samples collected from peach orchards, revealed that this rapid and simple technique is an effective way to identify the four viruses simultaneously. The mRT-PCR assay described in this study was developed for the simultaneous detection of four peach viruses from infected peach samples is reliable and sensitive. In contrast to conventional uniplex RT-PCR, mRT-PCR is more efficient, reducing costs, time and handling when testing large numbers of samples. This rapid and simple method is useful for large-scale surveys of viruses that infect peach. © 2013 The Society for Applied Microbiology.

Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

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André F A Santos

Full Text Available BACKGROUND: Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H is poorly understood. METHODS AND FINDINGS: We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI. CONCLUSIONS: This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon.

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Qiusheng Kong

Full Text Available Watermelon is one of the major Cucurbitaceae crops and the recent availability of genome sequence greatly facilitates the fundamental researches on it. Quantitative real-time reverse transcriptase PCR (qRT-PCR is the preferred method for gene expression analyses, and using validated reference genes for normalization is crucial to ensure the accuracy of this method. However, a systematic validation of reference genes has not been conducted on watermelon. In this study, transcripts of 15 candidate reference genes were quantified in watermelon using qRT-PCR, and the stability of these genes was compared using geNorm and NormFinder. geNorm identified ClTUA and ClACT, ClEF1α and ClACT, and ClCAC and ClTUA as the best pairs of reference genes in watermelon organs and tissues under normal growth conditions, abiotic stress, and biotic stress, respectively. NormFinder identified ClYLS8, ClUBCP, and ClCAC as the best single reference genes under the above experimental conditions, respectively. ClYLS8 and ClPP2A were identified as the best reference genes across all samples. Two to nine reference genes were required for more reliable normalization depending on the experimental conditions. The widely used watermelon reference gene 18SrRNA was less stable than the other reference genes under the experimental conditions. Catalase family genes were identified in watermelon genome, and used to validate the reliability of the identified reference genes. ClCAT1and ClCAT2 were induced and upregulated in the first 24 h, whereas ClCAT3 was downregulated in the leaves under low temperature stress. However, the expression levels of these genes were significantly overestimated and misinterpreted when 18SrRNA was used as a reference gene. These results provide a good starting point for reference gene selection in qRT-PCR analyses involving watermelon.

Sequencing of chemotherapy (CT) and radiotherapy (RT) following conservative surgery (CS) for patients with early-stage breast cancer: results of a randomized trial

Energy Technology Data Exchange (ETDEWEB)

Recht, A; Come, SE; Silver, B; Gelman, RS; Hayes, DF; Shulman, LN; Henderson, IC; Harris, JR

1995-07-01

Purpose: To determine the effects of different sequences of CT and RT following CS for pts with clinical Stage I or II breast carcinoma. Methods and Materials: From 6/84-12/92, 244 pts were randomized following CS to receive CT (4 cycles of CAMFP at 3-wk intervals) either before or after RT. Median pt age was 45 yrs (range, 20-68). 164 pts were pre-, 18 pts peri-, and 62 pts were postmenopausal. 209 pts were node-positive (61 had 4 or more positive nodes); after 6/88, 35 selected node-negative pts were also included. 45 Gy was prescribed to the entire breast, followed by a boost of 16 Gy; nodal RT was optional. The medians ( and ranges) of the surgery-radiotherapy interval (SRI) according to assigned arm were: RT-first, 36 days (14-234); CT-first, 126 days (98-185). Drug doses were based on ideal body weight. Doses (per square meter) and schedule were: methotrexate, 200 mg, d.1 and 15; leucovorin, 10 mg, q6H x 12, start d.2 and 16; 5-fluorouracil, 500 mg, d.1; cyclophosphamide, 500 mg, d.1; prednisone, 40 mg/day x 5d, start d.1; and doxorubicin, 45 mg, d.3. All except leucovorin and prednisone were given by IV bolus. Dose reductions were based on the granulocyte nadir from the previous cycle, with an attempt to reescalate doses in subsequent cycles. Tamoxifen 10 mg BID was prescribed to postmenopausal pts with ER+ tumors following both RT and CT. 4 pts were ineligible due to prior malignancies, 2 pts on the RT-first arm refused their assigned sequence and received CT first, 2 pts on the RT-first arm and 1 pt on the CT-first arm refused to start or complete CT, 1 pt on the CT-arm underwent elective mastectomy prior to starting RT, and 1 pt on each arm received nonprotocol CT. Possible prognostic factors including age, menopausal status, ERP status, nodal status, and lymphatic vessel invasion were distributed nearly uniformly between the 2 arms. There was an excess of pts with EIC-positive tumors on the RT-first arm (25%) compared to the CT-first arm (11%) (p-bar=0

Sequencing of chemotherapy (CT) and radiotherapy (RT) following conservative surgery (CS) for patients with early-stage breast cancer: results of a randomized trial

International Nuclear Information System (INIS)

Recht, A; Come, SE; Silver, B; Gelman, RS; Hayes, DF; Shulman, LN; Henderson, IC; Harris, JR

1995-01-01

Purpose: To determine the effects of different sequences of CT and RT following CS for pts with clinical Stage I or II breast carcinoma. Methods and Materials: From 6/84-12/92, 244 pts were randomized following CS to receive CT (4 cycles of CAMFP at 3-wk intervals) either before or after RT. Median pt age was 45 yrs (range, 20-68). 164 pts were pre-, 18 pts peri-, and 62 pts were postmenopausal. 209 pts were node-positive (61 had 4 or more positive nodes); after 6/88, 35 selected node-negative pts were also included. 45 Gy was prescribed to the entire breast, followed by a boost of 16 Gy; nodal RT was optional. The medians ( and ranges) of the surgery-radiotherapy interval (SRI) according to assigned arm were: RT-first, 36 days (14-234); CT-first, 126 days (98-185). Drug doses were based on ideal body weight. Doses (per square meter) and schedule were: methotrexate, 200 mg, d.1 and 15; leucovorin, 10 mg, q6H x 12, start d.2 and 16; 5-fluorouracil, 500 mg, d.1; cyclophosphamide, 500 mg, d.1; prednisone, 40 mg/day x 5d, start d.1; and doxorubicin, 45 mg, d.3. All except leucovorin and prednisone were given by IV bolus. Dose reductions were based on the granulocyte nadir from the previous cycle, with an attempt to reescalate doses in subsequent cycles. Tamoxifen 10 mg BID was prescribed to postmenopausal pts with ER+ tumors following both RT and CT. 4 pts were ineligible due to prior malignancies, 2 pts on the RT-first arm refused their assigned sequence and received CT first, 2 pts on the RT-first arm and 1 pt on the CT-first arm refused to start or complete CT, 1 pt on the CT-arm underwent elective mastectomy prior to starting RT, and 1 pt on each arm received nonprotocol CT. Possible prognostic factors including age, menopausal status, ERP status, nodal status, and lymphatic vessel invasion were distributed nearly uniformly between the 2 arms. There was an excess of pts with EIC-positive tumors on the RT-first arm (25%) compared to the CT-first arm (11%) (p-bar=0

Selection for increased voluntary wheel-running affects behavior and brain monoamines in mice

Science.gov (United States)

Waters, R.Parrish; Pringle, R.B.; Forster, G.L.; Renner, K.J.; Malisch, J.L.; Garland, T.; Swallow, J.G.

2013-01-01

Selective-breeding of house mice for increased voluntary wheel-running has resulted in multiple physiological and behavioral changes. Characterizing these differences may lead to experimental models that can elucidate factors involved in human diseases and disorders associated with physical inactivity, or potentially treated by physical activity, such as diabetes, obesity, and depression. Herein, we present ethological data for adult males from a line of mice that has been selectively bred for high levels of voluntary wheel-running and from a non-selected control line, housed with or without wheels. Additionally, we present concentrations of central monoamines in limbic, striatal, and midbrain regions. We monitored wheel-running for 8 weeks, and observed home-cage behavior during the last 5 weeks of the study. Mice from the selected line accumulated more revolutions per day than controls due to increased speed and duration of running. Selected mice exhibited more active behaviors than controls, regardless of wheel access, and exhibited less inactivity and grooming than controls. Selective-breeding also influenced the longitudinal patterns of behavior. We found statistically significant differences in monoamine concentrations and associated metabolites in brain regions that influence exercise and motivational state. These results suggest underlying neurochemical differences between selected and control lines that may influence the observed differences in behavior. Our results bolster the argument that selected mice can provide a useful model of human psychological and physiological diseases and disorders. PMID:23352668

Transitioning NPOESS Data to Weather Offices: The SPoRT Paradigm with EOS Data

Science.gov (United States)

Jedlovec, Gary

2009-01-01

Real-time satellite information provides one of many data sources used by NWS weather forecast offices (WFOs) to diagnose current weather conditions and to assist in short-term forecast preparation. While GOES satellite data provides relatively coarse spatial resolution coverage of the continental U.S. on a 10-15 minute repeat cycle, polar orbiting imagery has the potential to provide snapshots of weather conditions at high-resolution in many spectral channels. Additionally, polar orbiting sounding data can provide additional information on the thermodynamic structure of the atmosphere in data sparse regions of at asynoptic observation times. The NASA Short-term Prediction Research and Transition (SPoRT) project has demonstrated the utility of polar orbiting MODIS and AIRS data on the Terra and Aqua satellites to improve weather diagnostics and short-term forecasting on the regional and local scales. SPoRT scientists work directly forecasters at selected WFOS in the Southern Region (SR) to help them ingest these unique data streams into their AWIPS system, understand how to use the data (through on-site and distance learn techniques), and demonstrate the utility of these products to address significant forecast problems. This process also prepares forecasters for the use of similar observational capabilities from NPOESS operational sensors. NPOESS environmental data records (EDRs) from the Visible 1 Infrared Imager I Radiometer Suite (VIIRS), the Cross-track Infrared Sounder (CrlS) and Advanced Technology Microwave Sounder (ATMS) instruments and additional value-added products produced by NESDIS will be available in near real-time and made available to WFOs to extend their use of NASA EOS data into the NPOESS era. These new data streams will be integrated into the NWs's new AWIPS II decision support tools. The AWIPS I1 system to be unveiled in WFOs in 2009 will be a JAVA-based decision support system which preserves the functionality of the existing systems and

Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay.

Science.gov (United States)

Lyu, Xiaodong; Wang, Xianwei; Zhang, Lina; Chen, Zhenzhu; Zhao, Yu; Hu, Jieying; Fan, Ruihua; Song, Yongping

2017-07-25

Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management. We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization. Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL). We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an

Kuu plaat : Märt Sults "Kõigest koolipapa...". Plaadid kauplusest Lasering

Index Scriptorium Estoniae

2005-01-01

Heliplaatidest : Märt Sults "Kõigest koolipapa...", Madonna "Confessions on a Dance Floor", Tõnis Mägi "Vestlus Hermanniga", Rammstein "Rosenrot", a-ha "Analogue", Darkness "One Way Ticket to Hell...And Back"

Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

Science.gov (United States)

Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

2012-01-01

past year. The domain was expanded slightly to extend further west, north, and east to improve coverage over parts of southern Canada. Minor adjustments were also made to the manner in which GVF is calculated from the distribution of maximum Normalized Difference Vegetation Index from MODIS. The presentation will highlight some examples of the substantial inter-annual change in GVF that occurred from 2010 to 2011 in the U.S. Southern Plains as a result of the summer 2011 drought, and the early vegetation green up across the eastern U.S. due to the very warm conditions in March 2012. Finally, the SPoRT LIS runs the operational Noah land surface model (LSM) in real time over much of the eastern half of the CONUS. The Noah LSM is continually cycled in real time, uncoupled to any model, and driven by operational atmospheric analyses over a long-term, multi-year integration. The LIS-Noah provides the STRC EMS with high-resolution (3 km) LSM initialization data that are in equilibrium with the operational analysis forcing. The Noah LSM within the SPoRT LIS has been upgraded from version 2.7.1 to version 3.2, which has improved look-up table attributes for several land surface quantities. The surface albedo field is now being adjusted based on the input real-time MODIS GVF, thereby improving the net radiation. Also, the LIS-Noah now uses the newer MODIS-based land use classification scheme (i.e. the International Biosphere-Geosphere Programme [IGBP]) that has a better depiction of urban corridors in areas where urban sprawl has occurred. STRC EMS users interested in initializing their LSM fields with high-resolution SPoRT LIS data should set up their model domain with the MODIS-IGBP 20-class land use database and select Noah as the LSM.

Torm Balti merel / Märt Treier ; interv. Inge Pitsner

Index Scriptorium Estoniae

Treier, Märt, 1975-

2004-01-01

TV3 näitab saksa poliitilist põnevusfilmi "Balti torm" ("Baltic Storm"), mis kujutab parvlaev "Estonia" hukku : stsenarist, produtsent Jutta Rabe : režissöör Reuben Leder. Filmi eel on teles Märt Treieri saade "Tormist sündinud tormid"

A dose-volume comparison of prostate cancer (PC) radiotherapy (RT) techniques for penile-structures (PNS) - a neglected critical organ in PC RT

International Nuclear Information System (INIS)

Dabrowski, Jolanta; Myrianthopoulos, Leon; Nguyen, Ai; Chen, George; Vijayakumar, Srinivasan

1996-01-01

Purpose/Objective: Three-dimensional conformal RT(3DCRT) is revolutionizing the use of RT in PC. Rectum and bladder, and in some studies femoral heads are included as critical structures (CS) in comparing rival plans in 3DCRT. Although RT-induced impotence is a major complication of conventional RT, with 30-50% incidence, to date no study has included PNS as a CS. This study is an attempt to remedy this deficiency in the 3DCRT planning in PC. Materials and Methods: After immobilization with Aquaplast, computed-tomography (CT) scans were obtained in supine treatment position from top of lumbar-3 vertebra to lesser-trochanter of the femora with 5-8mm slice-thicknesses; IV contrast was used in all patients. Prostate, seminal vesicles (GTV), and CSs were outlined, including PNS. Corpora cavernosa and bulbous spongiosum together were identified as PNS. Appropriate margins for CTV and PTV were used; total margin to the block from GTV was 2cm. Tumor-minimum doses were prescribed to the 100% isodose line. Dose-volume histograms (DVHs) were obtained to compare three different techniques: 1. Conventional 4 field box technique (4FC) with equal weighting; 2. Six field (2 laterals and 4 obliques [45 degrees from midline] (6FO), with 50% dose delivery from the laterals; and 3. Four equally weighted, non-axial fields [2 laterals and 2 inferior anterior obliques at 45 degree couch and gantry rotations] (4FN). Results: A total of 12 patients are included in the study. The mean and range of percentage volume of PNS receiving more than 30, 60, and 90% of the prescribed dose are shown in the table below: Box plots, such as the example shown above, were used to compare techniques overall. The 6-field coplanar technique treated the least PNS volume beyond a given dose, followed by 4FC and 4FN techniques. The order of least to maximum percent of PNS treated in most individual patients also followed the same trend. In the majority, 6FO and 4FN delivered relatively comparable doses to

Comprehensive evaluation of candidate reference genes for gene expression studies in Lysiphlebia japonica (Hymenoptera: Aphidiidae) using RT-qPCR.

Science.gov (United States)

Gao, Xue-Ke; Zhang, Shuai; Luo, Jun-Yu; Wang, Chun-Yi; Lü, Li-Min; Zhang, Li-Juan; Zhu, Xiang-Zhen; Wang, Li; Lu, Hui; Cui, Jin-Jie

2017-12-30

Lysiphlebia japonica (Ashmead) is a predominant parasitoid of cotton-melon aphids in the fields of northern China with a proven ability to effectively control cotton aphid populations in early summer. For accurate normalization of gene expression in L. japonica using quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), reference genes with stable gene expression patterns are essential. However, no appropriate reference genes is L. japonica have been investigated to date. In the present study, 12 selected housekeeping genes from L. japonica were cloned. We evaluated the stability of these genes under various experimental treatments by RT-qPCR using four independent (geNorm, NormFinder, BestKeeper and Delta Ct) and one comparative (RefFinder) algorithm. We identified genes showing the most stable levels of expression: DIMT, 18S rRNA, and RPL13 during different stages; AK, RPL13, and TBP among sexes; EF1A, PPI, and RPL27 in different tissues, and EF1A, RPL13, and PPI in adults fed on different diets. Moreover, the expression profile of a target gene (odorant receptor 1, OR1) studied during the developmental stages confirms the reliability of the chosen selected reference genes. This study provides for the first time a comprehensive list of suitable reference genes for gene expression studies in L. japonica and will benefit subsequent genomics and functional genomics research on this natural enemy. Copyright © 2017. Published by Elsevier B.V.

School Psychologists' Willingness to Implement RtI: The Role of Philosophical and Practical Readiness

Science.gov (United States)

Fan, Chung-Hau; Denner, Peter R.; Bocanegra, Joel O.; Ding, Yi

2016-01-01

After the change in IDEIA, different models of response to intervention (RtI) have been practiced widely in American school systems. School psychologists are in an important position to facilitate RtI practice and provide professional development in order to help their school systems successfully undergo this transformation. However, there is a…

Pärt, Arvo: "Summa". Collage sur BACH. Fratres / Patric Wiklacz

Index Scriptorium Estoniae

Wiklacz, Patric

1997-01-01

Uuest heliplaadist "Pärt, Arvo: "Summa". Collage sur BACH. Fratres. Cantus in Memoriam Benjamin Britten. Summa. Festina Lente. Tabula rasa. Tapiola Sinfonietta / Jean-Jacques Kantorow". BIS-CD-834. 62:30 DDD

A combination of resistance and endurance training increases leg muscle strength in COPD

DEFF Research Database (Denmark)

Iepsen, Ulrik Winning; Jørgensen, Karsten Juhl; Ringbæk, Thomas

2015-01-01

Resistance training (RT) is thought to be effective in preventing muscle depletion, whereas endurance training (ET) is known to improve exercise capacity and health-related quality of life (HRQoL) in chronic obstructive pulmonary disease (COPD). Our objectives were to assess the efficiency...... improvements in HRQoL, walking distance and exercise capacity. However, we found moderate quality evidence of a significant increase in leg muscle strength favouring a combination of RT and ET (standardized mean difference of 0.69 (95% confidence interval: 0.39-0.98). In conclusion, we found significantly...... increased leg muscle strength favouring a combination of RT with ET compared with ET alone. Therefore, we recommend that RT should be incorporated in rehabilitation of COPD together with ET....

Uss uuristab inimese südame kallal / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

2003-01-01

Arvustus: [Õnnepalu, Tõnu] Tode, Emil. Raadio. Tallinn : Eesti Keele Sihtasutus, 2002. Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 47-53

Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat.

Science.gov (United States)

Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2018-01-01

To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat ( Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.

Hippocampal brain-derived neurotrophic factor but not neurotrophin-3 increases more in mice selected for increased voluntary wheel running.

Science.gov (United States)

Johnson, R A; Rhodes, J S; Jeffrey, S L; Garland, T; Mitchell, G S

2003-01-01

Voluntary wheel running in rats increases hippocampal brain-derived neurotrophic factor (BDNF) expression, a neurochemical important for neuronal survival, differentiation, connectivity and synaptic plasticity. Here, we report the effects of wheel running on BDNF and neurotrophin-3 (NT-3) protein levels in normal control mice, and in mice selectively bred (25 generations) for increased voluntary wheel running. We hypothesized that increased voluntary wheel running in selected (S) mice would increase CNS BDNF and NT-3 protein levels more than in control (C) mice. Baseline hippocampal BDNF levels (mice housed without running wheels) were similar in S and C mice. Following seven nights of running, hippocampal BDNF increased significantly more in S versus C mice, and levels were correlated with distance run (considering C and S mice together). Spinal and cerebellar BDNF and hippocampal NT-3 levels were not significantly affected by wheel running in any group, but there was a small, positive correlation between spinal C3-C6 BDNF levels and distance run (considering C and S mice together). This is the first study to demonstrate that mice which choose to run more have greater elevations in hippocampal BDNF, suggesting enhanced potential for exercise-induced hippocampal neuroplasticity.

OR.NET RT: how service-oriented medical device architecture meets real-time communication.

Science.gov (United States)

Pfeiffer, Jonas H; Kasparick, Martin; Strathen, Benjamin; Dietz, Christian; Dingler, Max E; Lueth, Tim C; Timmermann, Dirk; Radermacher, Klaus; Golatowski, Frank

2018-02-23

Today's landscape of medical devices is dominated by stand-alone systems and proprietary interfaces lacking cross-vendor interoperability. This complicates or even impedes the innovation of novel, intelligent assistance systems relying on the collaboration of medical devices. Emerging approaches use the service-oriented architecture (SOA) paradigm based on Internet protocol (IP) to enable communication between medical devices. While this works well for scenarios with no or only soft timing constraints, the underlying best-effort communication scheme is insufficient for time critical data. Real-time (RT) networks are able to reliably guarantee fixed latency boundaries, for example, by using time division multiple access (TDMA) communication patterns. However, deterministic RT networks come with their own limitations such as tedious, inflexible configuration and a more restricted bandwidth allocation. In this contribution we overcome the drawbacks of both approaches by describing and implementing mechanisms that allow the two networks to interact. We introduce the first implementation of a medical device network that offers hard RT guarantees for control and sensor data and integrates into SOA networks. Based on two application examples we show how the flexibility of SOA networks and the reliability of RT networks can be combined to achieve an open network infrastructure for medical devices in the operating room (OR).

TMPA Products 3B42RT & 3B42V6: Evaluation and Application in Qinghai-Tibet Plateau

Science.gov (United States)

Hao, Z.; Sun, L.; Wang, J.

2012-04-01

Hydrological researchers in Qinghai-Tibet Plateau tend to be haunted by deficiency of station gauged precipitation data for the sparse and uneven distribution of local meteorological stations. Fortunately, alternative data can be obtained from TRMM (Tropic Rainfall Measurement Mission) satellite. Preliminary evaluation and necessary correction of TRMM satellite rainfall products is required for the sake of reliability and suitability considering that TRMM precipitation is unconventional and natural condition in Qinghai-Tibet Plateau is unusually complicated. 3B42RT and 3B42V6 products from TRMM Multisatellite Precipitation Analysis(TMPA) are evaluated in northeast Qinghai-Tibet Plateau with 50 stations quality-controlled gauged daily precipitation as the benchmark precipitation set. It is found that the RT data overestimates the actual precipitation greatly while V6 only overestimates it slightly. RT data shows different seasonal and inter-annual accuracies. Summer and autumn see better accuracies than winter and spring and wet years see higher accuracies than dry years. Latitude is believed to be an important factor that influences the accuracy of satellite precipitation. Both RT and V6 can reflect the general pattern of the spatial distribution of precipitation even though RT overestimates the quantity greatly. A new parameter, accumulated precipitation weight point (APWP), was introduced to describe the temporal-spatial pattern evolution of precipitation. The APWP of both RT and V6 were moving from south to north in the past decade, but they are all in the west of station gauged precipitation APWP(s).V6 APWP track fit gauged precipitation perfectly while RT APWP track has over-exaggerated legs, indicating that spatial distribution of RT precipitation experienced unreasonable sharp changes. A practical and operational procedure to correct satellite precipitation data is developed. For RT, there are two steps. Step 1, the downscaling, original daily precipitation

The Reaumuria trigyna transcription factor RtWRKY1 confers tolerance to salt stress in transgenic Arabidopsis.

Science.gov (United States)

Du, Chao; Zhao, Pingping; Zhang, Huirong; Li, Ningning; Zheng, Linlin; Wang, Yingchun

2017-08-01

Reaumuria trigyna (R. trigyna) is an endangered small shrub endemic to the Eastern Alxa-Western Ordos area in Inner Mongolia, China. Based on R. trigyna transcriptome data, the Group I WRKY transcription factor gene RtWRKY1 was cloned from R. trigyna. The full-length RtWRKY1 gene was 2100bp, including a 1261-bp open reading frame (ORF) encoding 573 amino acids. RtWRKY1 was mainly expressed in the stem and was induced by salt, cold stress, and ABA treatment. Overexpression of RtWRKY1 in Arabidopsis significantly enhanced the chlorophyll content, root length, and fresh weight of the transgenic lines under salt stress. RtWRKY1 transgenic Arabidopsis exhibited higher proline content, GSH-PX, POD, SOD, and CAT activities, and lower MDA content, Na + content, and Na + /K + ratio than wild-type Arabidopsis under salt stress conditions. Salt stress affected the expression of ion transport, proline biosynthesis, and antioxidant related genes, including AtAPX1, AtCAT1, AtSOD1, AtP5CS1, AtP5CS2, AtPRODH1, AtPRODH2, and AtSOS1 in transgenic lines. RtWRKY1 confers tolerance to salt stress in transgenic Arabidopsis by regulating plant growth, osmotic balance, Na + /K + homeostasis, and the antioxidant system. Copyright © 2017 Elsevier GmbH. All rights reserved.

Development of duplex RT-PCR-ELISA for the simultaneous detection of hepatitis A virus and hepatitis E virus.

Science.gov (United States)

Tahk, Hongmin; Lee, Min Hwa; Lee, Kang Bum; Cheon, Doo-Sung; Choi, Changsun

2011-07-01

This study aimed to develop a specific and sensitive duplex reverse transcription polymerase chain reaction enzyme-linked immunosorbent assay (duplex RT-PCR-ELISA) for hepatitis A virus (HAV) and hepatitis E virus (HEV). Duplex RT-PCR-ELISA could detect and differentiate HAV and HEV with specific probes. When ELISA technique was used to detect probe-bound RT-PCR products, duplex RT-PCR-ELISA could detect as little as 0.1 ng/μL HAV and HEV from clinical samples. Human norovirus, enterovirus, poliovirus, murine norovirus and feline calicivirus were used for the specificity test; all were negative. Therefore duplex RT-PCR-ELISA can be used for the simultaneous detection of HAV and HEV in contaminated fecal samples. Copyright © 2011 Elsevier B.V. All rights reserved.

A collaborative framework for contributing DICOM RT PHI (Protected Health Information) to augment data mining in clinical decision support

Science.gov (United States)

Deshpande, Ruchi; Thuptimdang, Wanwara; DeMarco, John; Liu, Brent J.

2014-03-01

We have built a decision support system that provides recommendations for customizing radiation therapy treatment plans, based on patient models generated from a database of retrospective planning data. This database consists of relevant metadata and information derived from the following DICOM objects - CT images, RT Structure Set, RT Dose and RT Plan. The usefulness and accuracy of such patient models partly depends on the sample size of the learning data set. Our current goal is to increase this sample size by expanding our decision support system into a collaborative framework to include contributions from multiple collaborators. Potential collaborators are often reluctant to upload even anonymized patient files to repositories outside their local organizational network in order to avoid any conflicts with HIPAA Privacy and Security Rules. We have circumvented this problem by developing a tool that can parse DICOM files on the client's side and extract de-identified numeric and text data from DICOM RT headers for uploading to a centralized system. As a result, the DICOM files containing PHI remain local to the client side. This is a novel workflow that results in adding only relevant yet valuable data from DICOM files to the centralized decision support knowledge base in such a way that the DICOM files never leave the contributor's local workstation in a cloud-based environment. Such a workflow serves to encourage clinicians to contribute data for research endeavors by ensuring protection of electronic patient data.

Biomarker discovery for colon cancer using a 761 gene RT-PCR assay

Directory of Open Access Journals (Sweden)

Hackett James R

2007-08-01

Full Text Available Abstract Background Reverse transcription PCR (RT-PCR is widely recognized to be the gold standard method for quantifying gene expression. Studies using RT-PCR technology as a discovery tool have historically been limited to relatively small gene sets compared to other gene expression platforms such as microarrays. We have recently shown that TaqMan® RT-PCR can be scaled up to profile expression for 192 genes in fixed paraffin-embedded (FPE clinical study tumor specimens. This technology has also been used to develop and commercialize a widely used clinical test for breast cancer prognosis and prediction, the Onco typeDX™ assay. A similar need exists in colon cancer for a test that provides information on the likelihood of disease recurrence in colon cancer (prognosis and the likelihood of tumor response to standard chemotherapy regimens (prediction. We have now scaled our RT-PCR assay to efficiently screen 761 biomarkers across hundreds of patient samples and applied this process to biomarker discovery in colon cancer. This screening strategy remains attractive due to the inherent advantages of maintaining platform consistency from discovery through clinical application. Results RNA was extracted from formalin fixed paraffin embedded (FPE tissue, as old as 28 years, from 354 patients enrolled in NSABP C-01 and C-02 colon cancer studies. Multiplexed reverse transcription reactions were performed using a gene specific primer pool containing 761 unique primers. PCR was performed as independent TaqMan® reactions for each candidate gene. Hierarchal clustering demonstrates that genes expected to co-express form obvious, distinct and in certain cases very tightly correlated clusters, validating the reliability of this technical approach to biomarker discovery. Conclusion We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of

Detection of potato mop-top virus in soils and potato tubers using bait-plant bioassay, ELISA and RT-PCR.

Science.gov (United States)

Arif, Muhammad; Ali, Murad; Rehman, Anayatur; Fahim, Muhammad

2014-01-01

The hilly region of Northwest of Pakistan is leading seed potato producing areas of the country. Soil and plant samples were collected from the region and tested for PMTV using both conventional and molecular techniques. The bait plants exhibited PMTV-characteristic v-shaped yellow leaf markings in Nicotiana debneyi plants grown in putative viruliferious soils from 20/26 locations. The results were confirmed by back inoculation of sap from both roots and leaves of bait plant on indicator hosts (N. debneyi, Nicotiana benthamiana). The root samples of bait plants grown in soils of 25 locations and leaves of 24 locations reproduced systemic infection on indicator hosts upon back inoculation. The virus was identified in bait plants grown in soils from 25/26 locations using double antibody sandwich-enzyme linked immunosorbent assay (DAS)-ELISA and reverse transcription and polymerase chain reaction (RT-PCR) methods. The products of the 566bp were amplified from coat protein region of PMTV RNA 3 in both root and leaf samples of baited plants. The virus was detected in 10 potato cultivars commercially grown in the region using DAS-ELISA and RT-PCR. The virus was also detected in zoospores of Spongospora subterranea derived from the peels of selected scabby tubers using triple antibody sandwich (TAS)-ELISA. The results indicate that a bait plant bioassay, infectivity assay, ELISA and RT-PCR can detect PMTV in roots and leaves of baited plants, field samples, zoospores of S. subterranea and tubers of 10 potato cultivars commercially grown in the region. Copyright © 2013 Elsevier B.V. All rights reserved.

Pierādījumu vērtēšana kriminālprocesā

OpenAIRE

Griķe, Madara

2011-01-01

Pierādījumu vērtēšana ir viena no būtiskākajām valsts atzīto un aizsargāto cilvēka pamattiesību garantijām kriminālprocesā, tā nosaka tiesas nolēmuma tiesiskumu un pamatotību. Attiecībā uz pierādījumu vērtēšanu likumā nav konkrēta panta, ir reglamentēti pierādīšanas teorijas centrālie jēdzieni, principi un prasības, pēc kurām jāatbilst pierādījumiem un pēc kurām tie jāvērtē. Autore darbā pievēršas sastopamām problēmām praksē, kas saistītas ar pierādījumu vērtēšanu. Autore aktualizē jautājumu...

Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

Directory of Open Access Journals (Sweden)

Shiori Yabe

2018-03-01

Full Text Available To evaluate the potential of genomic selection (GS, a selection experiment with GS and phenotypic selection (PS was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench. To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.

Arvo Pärt ajas ja ajatuses / Igor Garšnek

Index Scriptorium Estoniae

Garšnek, Igor, 1958-

2010-01-01

Mõtteid Arvo Pärdi muusikast ajendatuna ETVs 2. septembril kavas olnud saadetest: "Arvo Pärt Istanbulis " ja "Arvo Pärdi autorikontsert Istanbulis", mis kajastasid 7. juunil Hagia Irene kirikus esiettekandel tulnud helilooja uusimat teost "Aadama itk"

Exogenous t-PA administration increases hippocampal mature BDNF levels. plasmin- or NMDA-dependent mechanism?

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Marion Rodier

Full Text Available Brain-derived neurotrophic factor (BDNF through TrkB activation is central for brain functioning. Since the demonstration that plasmin is able to process pro-BDNF to mature BDNF and that these two forms have opposite effects on neuronal survival and plasticity, a particular attention has been paid to the link between tissue plasminogen activator (tPA/plasmin system and BDNF metabolism. However, t-PA via its action on different N-methyl-D-aspartate (NMDA receptor subunits is also considered as a neuromodulator of glutamatergic transmission. In this context, the aim of our study was to investigate the effect of recombinant (rt-PA administration on brain BDNF metabolism in rats. In the hippocampus, we found that rt-PA (10 mg/kg administration induced a progressive increase in mature BDNF levels associated with TrkB activation. In order to delineate the mechanistic involved, plasmin activity was assessed and its inhibition was attempted using tranexamic acid (30 or 300 mg/kg, i.v. while NMDA receptors were antagonized with MK801 (0.3 or 3 mg/kg, i.p. in combination with rt-PA treatment. Our results showed that despite a rise in rt-PA activity, rt-PA administration failed to increase hippocampal plasmin activity suggesting that the plasminogen/plasmin system is not involved whereas MK801 abrogated the augmentation in mature BDNF levels observed after rt-PA administration. All together, our results show that rt-PA administration induces increase in hippocampal mature BDNF expression and suggests that rt-PA contributes to the control of brain BDNF synthesis through a plasmin-independent potentiation of NMDA receptors signaling.

Experimental study on the thermostable property of aramid fiber reinforced PE-RT pipes

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Guoquan Qi

2015-11-01

Full Text Available Flexible composite pipes are advantageous in ultra high strength, high modulus, pH and corrosion resistance and light weight, but there are still some hidden safety troubles because they are poorer in thermostable capacity. Therefore, test samples of flexible composite pipes were prepared with high-temperature polythene (PE-RT as the neck bush and aramid fiber as the reinforcement layer. Experimental study was conducted by using HPHT vessel and differential thermal scanner for different working conditions, different temperatures, whole-pipe pressure-bearing capacity and 1000 h viability. It is shown by the environmental compatibility test that high temperature has little effect on the weight, Vicat softening temperature, mechanical properties and structures of neck bush PE-RT, but exerts an obvious effect on the tensility and whole-pipe water pressure blasting of the reinforcement aramid fiber. Besides, the drop of whole-pipe pressure-bearing capacity is caused by deformation and breaking of aramid fibers when the reinforcement layer is under the force of internal pressure. Finally, disorientation and crystallization of molecular thermal motion occur with the rise of temperature, so amorphous orientation reduces, crystallinity factor and crystalline orientation factor increase gradually, thus, disorientation of macromolecular chains increases and tensile strength decreases. It is concluded that this type of flexible composite pipe can smoothly pass 1000 h viability test. And it is recommended that it be used in the situations with temperature not higher than 95 °C and internal pressure not higher than 4 MPa.

Propidium monoazide reverse transcription PCR and RT-qPCR for detecting infectious enterovirus and norovirus

Science.gov (United States)

Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the publ...

Investigations for a multi-marker RT-PCR to improve sensitivity of disseminated tumor cell detection.

NARCIS (Netherlands)

Vlems, F.A.; Diepstra, J.H.S.; Cornelissen, I.M.; Ligtenberg, M.J.L.; Wobbes, Th.; Punt, C.J.A.; Krieken, J.H.J.M. van; Ruers, T.J.M.; Muijen, G.N.P. van

2003-01-01

BACKGROUND: In order to develop a multi-marker RT-PCR, which as such may be more sensitive than a single marker assay for the detection of disseminated tumor cells, we evaluated six RT-PCR markers: cytokeratin 20 (CK20), carcinoembryonic antigen (CEA), guanylyl cyclase C (GCC), epidermal growth

Investigations for a multi-marker RT-PCR to improve sensitivity of disseminated tumor cell detection

NARCIS (Netherlands)

Vlems, F. A.; Diepstra, J. H. S.; Cornelissen, I. M. H. A.; Ligtenberg, M. J. L.; Wobbes, Th; Punt, C. J. A.; van Krieken, J. H. J. M.; Ruers, T. J. M.; van Muijen, G. N. P.

2003-01-01

In order to develop a multi-marker RT-PCR, which as such may be more sensitive than a single marker assay for the detection of disseminated tumor cells, we evaluated six RT-PCR markers: cytokeratin 20 (CK20), carcinoembryonic antigen (CEA), guanylyl cyclase C (GCC), epidermal growth factor receptor

Small Prizes Increased Plain Milk and Vegetable Selection by Elementary School Children without Adversely Affecting Total Milk Purchase

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Megan Emerson

2017-02-01

Full Text Available (1 Background: Pediatric obesity continues to be a major public health issue. Poor food selection in the school cafeteria is a risk factor. Chocolate or strawberry flavored milk is favored by the majority of elementary school students. Previous health promotion efforts have led to increased selection of plain milk, but may compromise total milk purchased. In our study, we examined the effectiveness of small prizes as incentives to improve healthy food and beverage selection by elementary school students; (2 Methods: In a small Midwestern school district, small prizes were given to elementary school students who selected a “Power Plate” (PP, the healthful combination of a plain milk, a fruit, a vegetable and an entrée with whole grain over two academic school years; (3 Results: PP selection increased from 0.05 per student to 0.19, a 271% increase (p < 0.001. All healthful foods had increased selection with plain milk having the greatest increase, 0.098 per student to 0.255, a 159% increase (p < 0.001; (4 Total milk purchased increased modestly from 0.916 to 0.956 per student (p = 0.000331. Conclusion: Giving small prizes as a reward for healthful food selection substantially improves healthful food selection and the effect is sustainable over two academic years.

Selective breeding for increased pheromone production in the boll weevil (Coleoptera: Curculionidae)

International Nuclear Information System (INIS)

McCoy, J.R.; Wright, J.E.

1990-01-01

The male boll weevil, Anthonomus grandis grandis Boheman, uses an aggregating pheromone to attract females, after which mating often occurs. Sterile boll weevil release programs depend upon this phenomenon to produce sterile matings with feral females. In an effort to increase the effectiveness of the individual sterile male and thereby reduce the number of sterile males required per hectare, a selective-breeding system was used to increase the total pheromone produced by individual male boll weevils. This breeding program increased the total pheromone production by individual male boll weevils to 4.5 times that of the parent population. After irradiation-induced sterilization, there remained 2.2 times more pheromone produced by the selected strain. Therefore, these sterile weevils should be about 2.2 times more attractive to feral females than the parent weevils now in use, and they have the potential to reduce the number of sterile males required in a sterile release program

Study of the thermal properties of selected PCMs for latent heat storage in buildings

Science.gov (United States)

Valentova, Katerina; Pechackova, Katerina; Prikryl, Radek; Ostry, Milan; Zmeskal, Oldrich

2017-07-01

The paper is focused on measurements of thermal properties of selected phase change materials (PCMs) which can be used for latent heat storage in building structures. The thermal properties were measured by the transient step-wise method and analyzed by the thermal spectroscopy. The results of three different materials (RT18HC, RT28HC, and RT35HC) and their thermal properties in solid, liquid, and phase change region were determined. They were correlated with the differential scanning calorimetry (DSC) measurement. The results will be used to determine the optimum ratio of components for the construction of drywall and plasters containing listed ingredients, respectively.

Dementia Population Risk Tool (DemPoRT): study protocol for a predictive algorithm assessing dementia risk in the community

OpenAIRE

Fisher, Stacey; Hsu, Amy; Mojaverian, Nassim; Taljaard, Monica; Huyer, Gregory; Manuel, Douglas G; Tanuseputro, Peter

2017-01-01

Introduction The burden of disease from dementia is a growing global concern as incidence increases dramatically with age, and average life expectancy has been increasing around the world. Planning for an ageing population requires reliable projections of dementia prevalence; however, existing population projections are simple and have poor predictive accuracy. The Dementia Population Risk Tool (DemPoRT) will predict incidence of dementia in the population setting using multivariable modellin...

Free cancer cell detection in peritoneal cavity in gastric cancer patients by RT-PCR for CEA

Energy Technology Data Exchange (ETDEWEB)

Lee, Jong Inn; Moon, Nan Mo; Paik, Nam Sun; Choi, Dong Wook; Bang, Ho Yun; Hong, Seok Il [Korea Cancer Center Hospital, Seoul (Korea, Republic of)

1997-12-01

Authors applied RT-PCR assay to detecting CEA expressing free cancer cells in peritoneal cavity of 114 gastric cancer patients to find an indication for prophylactic treatment to prevent peritoneal recurrence. Sixty-three of 114 cases were positive for RT-PCR, of which 16 cases were positive for cytologic examination and 47 cases were negative. Forty-nine of 51 cases who were negative for RT-PCR were negative for cytologic examination. Positivity for RT-PCR according to the depth of invasion were as follows : two (28.6 %) of seven cases whose cancer invaded mucosal or submucosal layer were positive. Ten (45.5 %) of 22 cases whose cancer invaded muscular or subserosal layer were positive. Forty-one (57.7 %) of 71 serosa involved cases were positive. Eleven (78.6 %) of cases who had grossly perioneal seedings were positive (p=0.026). However, all of 7 EGC cases, 19 of 22 cases whose cancer invaded to muscle layer or to subserosa were negative for cytologic examination, and eight of 13 cases who had had peritoneal seedings were positive. Positivity for RT-PCR according to cell differentiation were as follows: forty-two (61.8 %) of 68 cases who cancer were poorly differentiated type were positive. (p=0.163) Serum level of CEA of RT-PCR positive group and that of negative group were not statistically different. It was revealed that RT-PCR was more sensitive than cytologic examination in detecting free tumor cells, especially in pm, ss and serosa positive cancers, so if further study with more cases and longer follow-up is performed, its role as prognostic factor and an indication of prophylactic therapy will be clarified. (author). 22 refs., 5 tabs.

Free cancer cell detection in peritoneal cavity in gastric cancer patients by RT-PCR for CEA

International Nuclear Information System (INIS)

Lee, Jong Inn; Moon, Nan Mo; Paik, Nam Sun; Choi, Dong Wook; Bang, Ho Yun; Hong, Seok Il

1997-12-01

Authors applied RT-PCR assay to detecting CEA expressing free cancer cells in peritoneal cavity of 114 gastric cancer patients to find an indication for prophylactic treatment to prevent peritoneal recurrence. Sixty-three of 114 cases were positive for RT-PCR, of which 16 cases were positive for cytologic examination and 47 cases were negative. Forty-nine of 51 cases who were negative for RT-PCR were negative for cytologic examination. Positivity for RT-PCR according to the depth of invasion were as follows : two (28.6 %) of seven cases whose cancer invaded mucosal or submucosal layer were positive. Ten (45.5 %) of 22 cases whose cancer invaded muscular or subserosal layer were positive. Forty-one (57.7 %) of 71 serosa involved cases were positive. Eleven (78.6 %) of cases who had grossly perioneal seedings were positive (p=0.026). However, all of 7 EGC cases, 19 of 22 cases whose cancer invaded to muscle layer or to subserosa were negative for cytologic examination, and eight of 13 cases who had had peritoneal seedings were positive. Positivity for RT-PCR according to cell differentiation were as follows: forty-two (61.8 %) of 68 cases who cancer were poorly differentiated type were positive. (p=0.163) Serum level of CEA of RT-PCR positive group and that of negative group were not statistically different. It was revealed that RT-PCR was more sensitive than cytologic examination in detecting free tumor cells, especially in pm, ss and serosa positive cancers, so if further study with more cases and longer follow-up is performed, its role as prognostic factor and an indication of prophylactic therapy will be clarified. (author). 22 refs., 5 tabs

SPoRT Participation in the GOES-R and JPSS Proving Grounds

Science.gov (United States)

Jedlovec, Gary; Fuell, Kevin; Smith, Matthew

2013-01-01

For the last several years, the NASA Short-term Prediction Research and Transition (SPoRT) project at has been working with the various algorithm working groups and science teams to demonstrate the utility of future operational sensors for GOES-R and the suite of instruments for the JPSS observing platforms. For GOES-R, imagery and products have been developed from polar-orbiting sensors such as MODIS and geostationary observations from SEVIRI, simulated imagery, enhanced products derived from existing GOES satellites, and data from ground-based observing systems to generate pseudo or proxy products for the ABI and GLM instruments. The suite of products include GOES-POES basic and RGB hybrid imagery, total lightning flash products, quantitative precipitation estimates, and convective initiation products. SPoRT is using imagery and products from VIIRS, CrIS, ATMS, and OMPS to show the utility of data and products from their operational counterparts on JPSS. The products include VIIRS imagery in swath form, the GOES-POES hybrid, a suite of RGB products including the air mass RGB using water vapor and ozone channels from CrIS, and several DNB products. Over a dozen SPoRT collaborative WFOs and several National Centers are involved in an intensive evaluation of the operational utility of these products.

Radiographer-led plan selection for bladder cancer radiotherapy: initiating a training programme and maintaining competency.

Science.gov (United States)

McNair, H A; Hafeez, S; Taylor, H; Lalondrelle, S; McDonald, F; Hansen, V N; Huddart, R

2015-04-01

The implementation of plan of the day selection for patients receiving radiotherapy (RT) for bladder cancer requires efficient and confident decision-making. This article describes the development of a training programme and maintenance of competency. Cone beam CT (CBCT) images acquired on patients receiving RT for bladder cancer were assessed to establish baseline competency and training needs. A training programme was implemented, and observers were asked to select planning target volumes (PTVs) on two groups of 20 patients' images. After clinical implementation, the PTVs chosen were reviewed offline, and an audit performed after 3 years. A mean of 73% (range, 53-93%) concordance rate was achieved prior to training. Subsequent to training, the mean score decreased to 66% (Round 1), then increased to 76% (Round 2). Six radiographers and two clinicians successfully completed the training programme. An independent observer reviewed the images offline after clinical implementation, and a 91% (126/139) concordance rate was achieved. During the audit, 125 CBCT images from 13 patients were reviewed by a single observer and concordance was 92%. Radiographer-led selection of plan of the day was implemented successfully with the use of a training programme and continual assessment. Quality has been maintained over a period of 3 years. The training programme was successful in achieving and maintaining competency for a plan of the day technique.

A MIV-150/zinc acetate gel inhibits SHIV-RT infection in macaque vaginal explants.

Science.gov (United States)

Barnable, Patrick; Calenda, Giulia; Ouattara, Louise; Gettie, Agegnehu; Blanchard, James; Jean-Pierre, Ninochka; Kizima, Larisa; Rodríguez, Aixa; Abraham, Ciby; Menon, Radhika; Seidor, Samantha; Cooney, Michael L; Roberts, Kevin D; Sperling, Rhoda; Piatak, Michael; Lifson, Jeffrey D; Fernandez-Romero, Jose A; Zydowsky, Thomas M; Robbiani, Melissa; Teleshova, Natalia

2014-01-01

To extend our observations that single or repeated application of a gel containing the NNRTI MIV-150 (M) and zinc acetate dihydrate (ZA) in carrageenan (CG) (MZC) inhibits vaginal transmission of simian/human immunodeficiency virus (SHIV)-RT in macaques, we evaluated safety and anti-SHIV-RT activity of MZC and related gel formulations ex vivo in macaque mucosal explants. In addition, safety was further evaluated in human ectocervical explants. The gels did not induce mucosal toxicity. A single ex vivo exposure to diluted MZC (1∶30, 1∶100) and MC (1∶30, the only dilution tested), but not to ZC gel, up to 4 days prior to viral challenge, significantly inhibited SHIV-RT infection in macaque vaginal mucosa. MZC's activity was not affected by seminal plasma. The antiviral activity of unformulated MIV-150 was not enhanced in the presence of ZA, suggesting that the antiviral activity of MZC was mediated predominantly by MIV-150. In vivo administration of MZC and CG significantly inhibited ex vivo SHIV-RT infection (51-62% inhibition relative to baselines) of vaginal (but not cervical) mucosa collected 24 h post last gel exposure, indicating barrier effect of CG. Although the inhibitory effect of MZC (65-74%) did not significantly differ from CG (32-45%), it was within the range of protection (∼75%) against vaginal SHIV-RT challenge 24 h after gel dosing. Overall, the data suggest that evaluation of candidate microbicides in macaque explants can inform macaque efficacy and clinical studies design. The data support advancing MZC gel for clinical evaluation.

A MIV-150/zinc acetate gel inhibits SHIV-RT infection in macaque vaginal explants.

Directory of Open Access Journals (Sweden)

Patrick Barnable

Full Text Available To extend our observations that single or repeated application of a gel containing the NNRTI MIV-150 (M and zinc acetate dihydrate (ZA in carrageenan (CG (MZC inhibits vaginal transmission of simian/human immunodeficiency virus (SHIV-RT in macaques, we evaluated safety and anti-SHIV-RT activity of MZC and related gel formulations ex vivo in macaque mucosal explants. In addition, safety was further evaluated in human ectocervical explants. The gels did not induce mucosal toxicity. A single ex vivo exposure to diluted MZC (1∶30, 1∶100 and MC (1∶30, the only dilution tested, but not to ZC gel, up to 4 days prior to viral challenge, significantly inhibited SHIV-RT infection in macaque vaginal mucosa. MZC's activity was not affected by seminal plasma. The antiviral activity of unformulated MIV-150 was not enhanced in the presence of ZA, suggesting that the antiviral activity of MZC was mediated predominantly by MIV-150. In vivo administration of MZC and CG significantly inhibited ex vivo SHIV-RT infection (51-62% inhibition relative to baselines of vaginal (but not cervical mucosa collected 24 h post last gel exposure, indicating barrier effect of CG. Although the inhibitory effect of MZC (65-74% did not significantly differ from CG (32-45%, it was within the range of protection (∼75% against vaginal SHIV-RT challenge 24 h after gel dosing. Overall, the data suggest that evaluation of candidate microbicides in macaque explants can inform macaque efficacy and clinical studies design. The data support advancing MZC gel for clinical evaluation.

Increased Bleeding Risk With Concurrent Use of Selective Serotonin Reuptake inhibitors and Coumarins

NARCIS (Netherlands)

Schalekamp, Tom; Klungel, Olaf H; Souverein, Patrick C; de Boer, Anthonius

2008-01-01

BACKGROUND: Treatment with vitamin K antagonists (coumarins) is associated with an increased risk of bleeding. Because use of selective serotonin reuptake inhibitors (SSRIs) is also associated with an increased risk of bleeding, we assessed the odds ratio (OR) of abnormal bleeding associated with

ROS mediated selection for increased NADPH availability in Escherichia coli.

Science.gov (United States)

Reynolds, Thomas S; Courtney, Colleen M; Erickson, Keesha E; Wolfe, Lisa M; Chatterjee, Anushree; Nagpal, Prashant; Gill, Ryan T

2017-11-01

The economical production of chemicals and fuels by microbial processes remains an intense area of interest in biotechnology. A key limitation in such efforts concerns the availability of key co-factors, in this case NADPH, required for target pathways. Many of the strategies pursued for increasing NADPH availability in Escherichia coli involve manipulations to the central metabolism, which can create redox imbalances and overall growth defects. In this study we used a reactive oxygen species based selection to search for novel methods of increasing NADPH availability. We report a loss of function mutation in the gene hdfR appears to increase NADPH availability in E. coli. Additionally, we show this excess NADPH can be used to improve the production of 3HP in E. coli. © 2017 Wiley Periodicals, Inc.

Preoperative radiotherapy (RT) for prevention of heterotopic ossification (HO) after total hip replacement

International Nuclear Information System (INIS)

Heyd, R.; Schopohl, B.; Boettcher, H.D.; Kirchner, J.

1997-01-01

Preliminary results of a prospective study which investigates the efficacy of preoperative radiotherapy (RT) for prevention of heterotopic ossification (HO) after total hip arthroplasty are summarized. A total number of 20 hip joints (18 patients) were irradiated with a single dose of 6.0 Gy Brooker grade II). The functional outcome quantified with the Harris score was improved by an average of 37.9 points. The authors conclude that preoperative RT is an effective alternative for postoperative irradiation. (orig.) [de

Pärt, Arvo: De profundis. Missa Sillabica / Patric Wiklacz

Index Scriptorium Estoniae

Wiklacz, Patric

1997-01-01

Uuest heliplaadist "Pärt, Arvo: De profundis. Missa Sillabica. Solfeggio. And one of the Pharisees. Cantate Domino. Summa. 7 Antiennes du Magnificat. The Beautitudes. Magnificat. Christopher Bowers-Broadbent (org.), Daniel Kennedy (perc.). Theatre of Voices / Paul Hillier (bass)" Harmonia Mundi HMU907 182 F (CD:165F). 1996. TT:1h 16'06"

A Leu to Ile but not Leu to Val change at HIV-1 reverse transcriptase codon 74 in the background of K65R mutation leads to an increased processivity of K65R+L74I enzyme and a replication competent virus

Directory of Open Access Journals (Sweden)

Crumpacker Clyde S

2011-01-01

Full Text Available Abstract Background The major hurdle in the treatment of Human Immunodeficiency virus type 1 (HIV-1 includes the development of drug resistance-associated mutations in the target regions of the virus. Since reverse transcriptase (RT is essential for HIV-1 replication, several nucleoside analogues have been developed to target RT of the virus. Clinical studies have shown that mutations at RT codon 65 and 74 which are located in β3-β4 linkage group of finger sub-domain of RT are selected during treatment with several RT inhibitors, including didanosine, deoxycytidine, abacavir and tenofovir. Interestingly, the co-selection of K65R and L74V is rare in clinical settings. We have previously shown that K65R and L74V are incompatible and a R→K reversion occurs at codon 65 during replication of the virus. Analysis of the HIV resistance database has revealed that similar to K65R+L74V, the double mutant K65R+L74I is also rare. We sought to compare the impact of L→V versus L→I change at codon 74 in the background of K65R mutation, on the replication of doubly mutant viruses. Methods Proviral clones containing K65R, L74V, L74I, K65R+L74V and K65R+L74I RT mutations were created in pNL4-3 backbone and viruses were produced in 293T cells. Replication efficiencies of all the viruses were compared in peripheral blood mononuclear (PBM cells in the absence of selection pressure. Replication capacity (RC of mutant viruses in relation to wild type was calculated on the basis of antigen p24 production and RT activity, and paired analysis by student t-test was performed among RCs of doubly mutant viruses. Reversion at RT codons 65 and 74 was monitored during replication in PBM cells. In vitro processivity of mutant RTs was measured to analyze the impact of amino acid changes at RT codon 74. Results Replication kinetics plot showed that all of the mutant viruses were attenuated as compared to wild type (WT virus. Although attenuated in comparison to WT virus

Simultaneous Expression of GUS and Actin Genes by Using the Multiplex RT-PCR and Multiplex Gold Nanoparticle Probes.

Science.gov (United States)

Ghazi, Yaser; Vaseghi, Akbar; Ahmadi, Sepideh; Haddadi, Fatemeh

2018-04-23

Gene expression analysis is considered to be extremely important in many different biological researches. DNA-based diagnostic test, which contributes to DNA identification, has higher specificity, cost, and speed than some biochemical and molecular methods. In this study, we try to use the novel nano technology approach with Multiplex RT-PCR and Gold nano particular probes (GNPs-probes) in order to get gene expression in Curcumas melons. We used Agrobacterium tumefactions for gene transfer and GUS reporter gene as a reporter. After cDNA synthesis, Multiplex PCR and Multiplex RT-PCR techniques were used. Finally, probes were designed for RNA of GUS and Actin genes, and then the analysis of the gene expression using the probes attached to GNPs was carried out and the color changes in the GNPs were applied. In the following, probes hybridization was checked with DNA between 400 to 700 nm wavelengths and the highest rate was observed in the 550 to 650 nm. The results show that the simultaneous use of GNP-attached detectors and Multiplex RT-PCRcan reduce time and costmore considerably than somelaboratory methods for gene expiration investigation. Additionally, it can be seen thatthere is an increase in sensitivity and specificity of our investigation. Based on our findings, this can bea novel study doneusingMultiplex RT-PCRand unmodified AuNPs for gene transfer and expression detection to plants. We can claim that this assay has a remarkable advantage including rapid, cost-effectiveness, specificity and accuracy to detect transfer and expression genes in plants. Also,we can use this technique from other gene expressionsin many different biology samples.

Rooma põleb, kirjanik mängib viiulit / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

1996-01-01

Arvustus: Orwell, George. Valaskala kõhus. Tln.: Vagabund, 1995. Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 173-175

The effect of reverse triiodothyronine (rT3) treatment on the plasma levels of iodothyronines in growing Japanese quails

International Nuclear Information System (INIS)

Niezgoda, J.; Wronska-Fortuna, D.; Sechman, A.; Bobek, S.; Sowa, J.

1994-01-01

It has been established that 3.3',5-triiodothyronine (T 3 ) acts hipermetabolically, whereas 3'3.5'-triiodothyronine (reverse T 3 , rT 3 ) acts hypometabolically. The normal ratio of T 3 to rT 3 in domestic flows fluctuates around 10. Since the excess of T 3 may promote catabolic processes and lower weight gain, the aim of this experiment was to find the optimal ratio of T 3 :rT 3 in blood plasma which corresponds with the greatest weight gain in Japanese quail. Reverse T 3 was given in drinking water (1 μg rT 3 /ml) for 3, 10, 20 or 30 days. It has been found that T 3 /rT 3 ratio of about 5, after 20 days of rT 3 administration, stimulated the weight gain of Japanese quail of both sexes from 7 to 44% with more pronounced effect in female birds. (author). 26 refs, 4 figs, 1 tab

Intelligent software systems and SMiRT: Potentials, actual results, expectations, trends

International Nuclear Information System (INIS)

Jovanovic, A.

1993-01-01

The paper gives a survey of recent development trends in the area of knowledge-based systems, hypermedia, neural networks and other similar technologies which are on the baseline of modern 'intelligent' software systems, applied in the areas relevant for SMiRT: power plant operation, design and analysis of structural components, materials, and many others. The paper highlights the historical background of these trends, as well as the methodologies and technologies which made such a development possible ('enabling methodologies/technologies'). Examples from several, SMiRT characteristic application areas are mentioned, in order to give an illustration what the deployment of an intelligent software system can mean in practice. Finally, a summary of these result is made and future perspectives indicated. (author)

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

Science.gov (United States)

EPA Method 1615 measures enteroviruses and noroviruses present in environmental and drinking waters. The viral ribonucleic acid (RNA) from water sample concentrates is extracted and tested for enterovirus and norovirus RNA using reverse transcription-quantitative PCR (RT-qPCR). V...

DETECTION OF CLASSICAL SWINE FEVER VIRUS BY RT-PCR IN WEST BENGAL, INDIA

Directory of Open Access Journals (Sweden)

Sumit Chowdhury

2016-12-01

Full Text Available Classical swine fever is a deadly disease of swine, caused by a RNA virus. The present study has identified presence of the classical swine fever virus (CSFV in pigs of West Bengal by one step reverse transcriptase PCR (RT-PCR performed using 5’ NTR specific primers. Internal organs from clinically affected pigs were examined from three districts of West Bengal. RT-PCT has identified presence of CSFV in all the tissues examined confirming presence of CSFV in different parts of the state.

The role of pleural fluid MAGE RT-nested PCR in the diagnosis of malignant pleural effusion.

Science.gov (United States)

Jeon, Eun Ju; Park, Hye Kyeong; Jeon, Kyeongman; Koh, Won-Jung; Suh, Gee Young; Chung, Man Pyo; Kim, Hojoong; Kwon, O Jung; Ki, Chang-Seok; Kim, Jong-Won; Shim, Young Mog; Um, Sang-Won

2012-11-01

  Melanoma antigen (MAGE) genes are expressed in tumor cells, the testis and the placenta. The purpose of this prospective study was to investigate the sensitivity, specificity, and accuracy of the carcinoembryonic antigen (CEA), MAGE reverse transcriptase-nested polymerase chain reaction (RT-nested PCR), and cytology of pleural fluid in the diagnosis of malignant pleural effusion.   Patients in whom unilateral pleural effusion was identified on chest radiography from January to December 2009 were included in the study. MAGE genes were analyzed by RT-nested PCR using MAGE A1-6 common primers.   Of 81 enrolled patients, 46 were diagnosed as malignant pleural effusion, and 24 were diagnosed as benign pleural effusion. The diagnoses of 11 patients were not confirmed in this study. The diagnostic sensitivity, specificity, and accuracy of MAGE RT-nested PCR were 61.4%, 95.7%, and 73.1%, respectively. The diagnostic sensitivities of cytology and CEA (>5 ng/mL) were 61.4% and 75.0%, respectively. Among 17 patients with negative cytology who had malignant pleural effusion, 12 and 10 patients were positive for CEA (>5.0 ng/mL) and MAGE RT-nested PCR, respectively. However, of five patients with malignant pleural effusion that was not recognized by cytology and CEA, MAGE RT-nested PCR correctly predicted a malignant etiology in only one additional patient (20%).   MAGE RT-nested PCR seems to add little on the combination of conventional methods in the diagnosis of malignant effusion. © 2012 Tianjin Lung Cancer Institute and Wiley Publishing Asia Pty. Ltd.

Pärt: Fratres in sechs Versionen. Festina lente. Summa / C. S.

Index Scriptorium Estoniae

C. S.

1997-01-01

Uuest heliplaadist "Pärt: Fratres in sechs Versionen. Festina lente. Summa. Cantus in memoriam Benjamin Britten. Orchester der Ungarischen Staatsoper, Tamas Benedek". Naxos CD 8 553 750 (WD:79'06") DDD

Pärt, Arvo. Cantus in memory of Benjamin Britten / Andrew Achenbach

Index Scriptorium Estoniae

Achenbach, Andrew

1995-01-01

Uuest heliplaadist "Pärt, Arvo. Cantus in memory of Benjamin Britten. BBC Northern Symphony Orchestra / Norman del Mar; BBC Symphony Orchestra / Gennady Rozhdestvensky". BBC Radio Classics CD BBCRD 9129 (71 minutes)

The development and application of the two real-time RT-PCR assays to detect the pathogen of HFMD.

Directory of Open Access Journals (Sweden)

Aili Cui

Full Text Available Large-scale Hand, Foot, and Mouth Disease (HFMD outbreaks have frequently occurred in China since 2008, affecting more than one million children and causing several hundred children deaths every year. The pathogens of HFMD are mainly human enteroviruses (HEVs. Among them, human enterovirus 71 (HEV71 and coxsackievirus A16 (CVA16 are the most common pathogens of HFMD. However, other HEVs could also cause HFMD. To rapidly detect HEV71 and CVA16, and ensure detection of all HEVs causing HFMD, two real-time hybridization probe-based RT-PCR assays were developed in this study. One is a multiplex real-time RT-PCR assay, which was developed to detect and differentiate HEV71 specifically from CVA16 directly from clinical specimens within 1-2 h, and the other is a broad-spectrum real-time RT-PCR assay, which targeted almost all HEVs. The experiments confirmed that the two assays have high sensitivity and specificity, and the sensitivity was up to 0.1 TCID50/ml for detection of HEVs, HEV71, and CVA16, respectively. A total of 213 clinical specimens were simultaneously detected by three kinds of assays, including the two real-time RT-PCR assays, direct conventional RT-PCR assay, and virus isolation assay on human rhabdomyosarcoma cells (RD cells. The total positive rate of both HEV71 and CVA16 was 69.48% with real-time RT-PCR assay, 47.42% with RT-PCR assay, and 34.58% with virus isolation assay. One HFMD clinical specimen was positive for HEV, but negative for HEV71 or CVA16, which was identified as Echovirus 11 (Echo11 by virus isolation, RT-PCR, and sequencing for the VP1 gene. The two real-time RT-PCR assays had been applied in 31 provincial HFMD labs to detect the pathogens of HFMD, which has contributed to the rapid identification of the pathogens in the early stages of HFMD outbreaks, and helped to clarify the etiologic agents of HFMD in China.

Simultaneous detection of Plasmodium vivax and Plasmodium falciparum gametocytes in clinical isolates by multiplex-nested RT-PCR.

Science.gov (United States)

Kuamsab, Napaporn; Putaporntip, Chaturong; Pattanawong, Urassaya; Jongwutiwes, Somchai

2012-06-10

Gametocyte carriage is essential for malaria transmission and endemicity of disease; thereby it is a target for malaria control strategies. Malaria-infected individuals may harbour gametocytes below the microscopic detection threshold that can be detected by reverse transcription polymerase chain reaction (RT-PCR) targeting gametocyte-specific mRNA. To date, RT-PCR has mainly been applied to the diagnosis of Plasmodium falciparum gametocytes but very limited for that of Plasmodium vivax. A multiplex-nested RT-PCR targeting Pfs25 and Pvs25 mRNA specific to mature gametocytes of P. falciparum and P. vivax, respectively, was developed. The assay was evaluated using blood samples collected in rainy and dry seasons from febrile patients,in a malaria-endemic area in Thailand. Malaria diagnosis was performed by Giemsa-stained blood smears and 18S rRNA PCR. The multiplex-nested RT-PCR detected Pfs25 mRNA in 75 of 86 (87.2%) P. falciparum-infected individuals and Pvs25 mRNA in 82 of 90 (91.1%) P. vivax malaria patients diagnosed by 18S rRNA PCR. Gametocytes were detected in 38 (eight P. falciparum and 30 P. vivax) of 157 microscopy positive samples, implying that a large number of patients harbour sub-microscopic gametocytaemia. No seasonal differences in gametocyte carriage were observed for both malaria species diagnosed by multiplex-nested RT-PCR. With single-nested RT-PCR targeting Pfs25 or Pvs25 mRNA as standard, the multiplex-nested RT-PCR offered sensitivities of 97.4% and 98.9% and specificities of 100% and 98.8% for diagnosing mature gametocytes of P. falciparum and P. vivax, respectively. The minimum detection limit of the multiplex-nested PCR was 10 copies of templates. The multiplex-nested RT-PCR developed herein is useful for simultaneous assessment of both P. falciparum and P. vivax gametocyte carriage that is prevalent and generally sympatric in several malaria-endemic areas outside Africa.

Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures.

Science.gov (United States)

Ramos-Alemán, Fabiola; González-Jasso, Eva; Pless, Reynaldo C

2018-02-15

Several alkali chlorides were compared for their use in reverse transcription (RT) and PCR of different types of nucleic acid templates. On a test region of biological DNA incapable of forming G quadruplex (G4) structures, Taq DNA polymerase showed similar PCR performance with 50 mM KCl, CsCl, LiCl, and NaCl. In contrast, on a synthetic model polydeoxyribonucleotide prone to G4 formation, good PCR amplification was obtained with 50 mM CsCl, but little or none with LiCl or KCl. Similarly, in RT of a G4-prone model polyribonucleotide, MMLV reverse transcriptase produced a good yield with 50 mM CsCl, mediocre yields with LiCl or without added alkali chloride, and a poor yield with 50 mM KCl. The full RT-PCR assay starting from the G4-prone polyribonucleotide, showed good results with CsCl in both stages, poor results with LiCl, and no product formation with KCl. The model polynucleotides showed fast G quadruplex formation under PCR or RT conditions with 50 mM KCl, but not with CsCl or LiCl. The results argue for the use of CsCl instead of KCl for RT and PCR of G4-prone sequences. No advantage was observed when using the 7-deaza type nucleotide analog c 7 dGTP in PCR amplification of the G4-prone polydeoxyribonucleotide. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of genes for normalization of real-time RT-PCR data in breast carcinomas

DEFF Research Database (Denmark)

Lyng, Maria B; Laenkholm, Anne-Vibeke; Pallisgaard, Niels

2008-01-01

BACKGROUND: Quantitative real-time RT-PCR (RT-qPCR) has become a valuable molecular technique in basic and translational biomedical research, and is emerging as an equally valuable clinical tool. Correlation of inter-sample values requires data normalization, which can be accomplished by various...... means, the most common of which is normalization to internal, stably expressed, reference genes. Recently, such traditionally utilized reference genes as GAPDH and B2M have been found to be regulated in various circumstances in different tissues, emphasizing the need to identify genes independent...... of factors influencing the tissue, and that are stably expressed within the experimental milieu. In this study, we identified genes for normalization of RT-qPCR data for invasive breast cancer (IBC), with special emphasis on estrogen receptor positive (ER+) IBC, but also examined their applicability to ER...

Development of a new comprehensive and reliable endometrial receptivity map (ER Map/ER Grade) based on RT-qPCR gene expression analysis.

Science.gov (United States)

Enciso, M; Carrascosa, J P; Sarasa, J; Martínez-Ortiz, P A; Munné, S; Horcajadas, J A; Aizpurua, J

2018-02-01

Is it possible to determine the receptivity status of an endometrium by combined quantitative reverse transcription PCR (RT-qPCR) expression analysis of genes involved in endometrial proliferation and immunity? The new ER Map®/ER Grade® test can predict endometrial receptivity status by RT-qPCR using a new panel of genes involved in endometrial proliferation and the maternal immune response associated to embryonic implantation. The human endometrium reaches a receptive status adequate for embryonic implantation around Days 19-21 of the menstrual cycle. During this period, known as the window of implantation (WOI), the endometrium shows a specific gene expression profile suitable for endometrial function evaluation. The number of molecular diagnostic tools currently available to characterize this process is very limited. In this study, a new system for human endometrial receptivity evaluation was optimized and presented for the first time. ER Map®/ER Grade® validation was achieved on 312 endometrial samples including fertile women and patients undergoing fertility treatment between July 2014 and March 2016. Expression analyses of 184 genes involved in endometrial receptivity and immune response were performed. Samples were additionally tested with an independent endometrial receptivity test. A total of 96 fertile women and 120 assisted reproduction treatment (ART) patients participated in the study. Endometrial biopsy samples were obtained at LH + 2 and LH + 7 days in fertile subjects in a natural cycle and at the window of implantation (WOI) in patients in a hormone-replacement therapy (HRT) cycle. Total RNA was purified, quality-checked and reverse-transcribed. Gene expression was quantified by high-throughput RT-qPCR and statistically analyzed. Informative genes were selected and used to classify samples into four different groups of endometrial receptivity status. Significantly different gene expression levels were found in 85 out of 184 selected genes when

Simulating Rayleigh-Taylor (RT) instability using PPM hydrodynamics @scale on Roadrunner (u)

Energy Technology Data Exchange (ETDEWEB)

Woodward, Paul R [Los Alamos National Laboratory; Dimonte, Guy [Los Alamos National Laboratory; Rockefeller, Gabriel M [Los Alamos National Laboratory; Fryer, Christopher L [Los Alamos National Laboratory; Dimonte, Guy [Los Alamos National Laboratory; Dai, W [Los Alamos National Laboratory; Kares, R. J. [Los Alamos National Laboratory

2011-01-05

The effect of initial conditions on the self-similar growth of the RT instability is investigated using a hydrodynamics code based on the piecewise-parabolic-method (PPM). The PPM code was converted to the hybrid architecture of Roadrunner in order to perform the simulations at extremely high speed and spatial resolution. This paper describes the code conversion to the Cell processor, the scaling studies to 12 CU's on Roadrunner and results on the dependence of the RT growth rate on initial conditions. The relevance of the Roadrunner implementation of this PPM code to other existing and anticipated computer architectures is also discussed.

Clinical utility of RT-PCR in assessing HER 2 gene expression versus traditional IHC and FISH in breast cancer patients.

Science.gov (United States)

Suryavanshi, Moushumi; Mehta, Anurag; Jaipuria, Jiten; Kumar, Dushyant; Vishwakarma, Gayatri; Panigrahi, Manoj Kumar; Verma, Haristuti; Saifi, Mumtaz; Sharma, Sanjeev; Tandon, Simran; Doval, D C; Das, Bhudev C

2018-02-09

IHC and FISH are used for categorizing HER 2 status in breast cancer at the protein and DNA level, respectively. HER 2 expression at the RNA level is quantitative, cheaper, easier to standardize and free from interobserver variation. 115 consecutive patients were tested by IHC, FISH and RT-PCR (test cohort). Assuming FISH result to be the response variable, ROC curves for RT-PCR ratio were analyzed to label HER 2 negative, equivocal and positive cases as RT-PCR score 1, 2 and 3, respectively. Inter-relationships between RT-PCR, IHC and FISH were defined. 'Clinical benefit' of a test was defined as proportion of patients labeled unequivocally as HER 2 positive or negative. Population for 1 year was simulated constraint to previous reports of HER 2 positivity and IHC category distribution by a meta-analysis of previous studies that evaluated concordance between IHC and FISH to determine HER 2 status (simulation cohort). Four diagnostic pathways in the simulation cohort were defined-(1) initial IHC, followed by FISH (conventional pathway); (2) initial RT-PCR, followed by FISH; (3) initial IHC, followed by RT-PCR and then by FISH; (4) initial RT-PCR, followed by IHC and then by FISH. The clinical benefit of IHC and RT-PCR in the four pathways was analyzed and sensitivity analysis for incremental cost-effectiveness ratio and cost-benefit comapring RT-PCR against IHC, both as first-line tests and among those with IHC score 2 as a reflex second-line test was performed by the Monte Carlo technique. 115 patients comprised the study population. While none with IHC score of 0 or 1 was FISH positive for HER 2, all cases with IHC score of 3 were FISH positive. 43 cases were assigned IHC score of 2. Thus, 72 patients benefited from the initial IHC testing [clinical benefit 62.6%], with the overall concordance between IHC and FISH being 100% for those with IHC score of 0, 1 and 3 (conclusive IHC categories). For RT-PCR with 100% concordance, 15.7% (115-97 = 18) patients

Effects of selective breeding for increased wheel-running behavior on circadian timing of substrate oxidation and ingestive behavior.

Science.gov (United States)

Jónás, I; Vaanholt, L M; Doornbos, M; Garland, T; Scheurink, A J W; Nyakas, C; van Dijk, G

2010-04-19

Fluctuations in substrate preference and utilization across the circadian cycle may be influenced by the degree of physical activity and nutritional status. In the present study, we assessed these relationships in control mice and in mice from a line selectively bred for high voluntary wheel-running behavior, either when feeding a carbohydrate-rich/low-fat (LF) or a high-fat (HF) diet. Housed without wheels, selected mice, and in particular the females, exhibited higher cage activity than their non-selected controls during the dark phase and at the onset of the light phase, irrespective of diet. This was associated with increases in energy expenditure in both sexes of the selection line. In selected males, carbohydrate oxidation appeared to be increased compared to controls. In contrast, selected females had profound increases in fat oxidation above the levels in control females to cover the increased energy expenditure during the dark phase. This is remarkable in light of the finding that the selected mice, and in particular the females showed higher preference for the LF diet relative to controls. It is likely that hormonal and/or metabolic signals increase carbohydrate preference in the selected females, which may serve optimal maintenance of cellular metabolism in the presence of augmented fat oxidation. (c) 2010 Elsevier Inc. All rights reserved.

Análise de citocinas pela RT-PCR em pacientes com rinite alérgica RT-PCR cytokine study in patients with allergic rhinitis

Directory of Open Access Journals (Sweden)

Tarcimara Moreira da Silva

2009-02-01

knowing the cytokine expressions during this period. MATERIALS AND METHODS: Another prospective and transversal study was carried out, selecting 30 patients, 13 of these patients were pauci-symptomatic and 17 were non atopic. The groups were selected by means of a medical interview, an otolaryngologic clinical exam and allergy skin tests - Prick Test. The cytokines were investigated in fragments of the nasal mucosa, using RT-PCR - chosen because it has good reproducibility and specificity. RESULTS: IL-5, IL-8, IFN-gama cytokine values were kept homogeneous in relation to the control group. Only IL-4 presented significant statistic differences. CONCLUSION: Asymptomatic patients with allergic rhinitis presented with normalization of cytokine expression in the nasal mucosa, with exception of IL-4.

Novel embryo selection techniques to increase embryo implantation in IVF attempts.

Science.gov (United States)

Sigalos, George Α; Triantafyllidou, Olga; Vlahos, Nikos F

2016-11-01

The final success of an IVF attempt depends on several steps and decisions taken during the ovarian stimulation, the oocyte retrieval, the embryo culture and the embryo transfer. The final selection of the embryos most likely to implant is the final step in this process and the responsibility of the lab. Apart from strict morphologic criteria that historically have been used in embryo selection, additional information on genetic, metabolomic and morphokinetic characteristics of the embryo is recently combined to morphology to select the embryo most likely to produce a pregnancy. In this manuscript, we review the most recent information on the current methods used for embryo selection presenting the predictive capability of each one. A literature search was performed on Pubmed, Medline and Cochrane Database of Systematic Reviews for published studies using appropriate key words and phrases with no limits placed on time. It seems that the combination of morphologic criteria in conjunction to embryo kinetics as documented by time-lapse technology provides the most reliable information on embryo quality. Blastocyst biopsy with subsequent comprehensive chromosome analysis allows the selection of the euploid embryos with the higher implantation potential. Embryo time-lapse imaging and blastocyst biopsy combined to comprehensive chromosome analysis are the most promising technologies to increase pregnancy rates and reduce the possibility of multiple pregnancies. However, further studies will demonstrate the capability of routinely using these technologies to significantly improve IVF outcomes.

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

Science.gov (United States)

Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M; Zhao, Hui; Ma, Xiaoyue; Ellison, James A; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian; Li, Yu

2017-01-01

Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

Directory of Open Access Journals (Sweden)

Ashutosh Wadhwa

2017-01-01

Full Text Available Rabies, resulting from infection by Rabies virus (RABV and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses

Validation of reference genes for RT-qPCR analysis of CYP4T expression in crucian carp

Directory of Open Access Journals (Sweden)

Fei Mo

2014-09-01

Full Text Available Reference genes are commonly used for normalization of target gene expression during RT-qPCR analysis. However, no housekeeping genes or reference genes have been identified to be stable across different tissue types or under different experimental conditions. To identify the most suitable reference genes for RT-qPCR analysis of target gene expression in the hepatopancreas of crucian carp (Carassius auratus under various conditions (sex, age, water temperature, and drug treatments, seven reference genes, including beta actin (ACTB, beta-2 microglobulin (B2M, embryonic elongation factor-1 alpha (EEF1A, glyceraldehyde phosphate dehydrogenase (GAPDH, alpha tubulin (TUBA, ribosomal protein l8 (RPL8 and glucose-6-phosphate dehydrogenase (G6PDH, were evaluated in this study. The stability and ranking of gene expression were analyzed using three different statistical programs: GeNorm, Normfinder and Bestkeeper. The expression errors associated with selection of the genes were assessed by the relative quantity of CYP4T. The results indicated that all the seven genes exhibited variability under the experimental conditions of this research, and the combination of ACTB/TUBA/EEF1A or of ACTB/EEF1A was the best candidate that raised the accuracy of quantitative analysis of gene expression. The findings highlighted the importance of validation of housekeeping genes for research on gene expression under different conditions of experiment and species.

Enhancing the sensitivity of Dengue virus serotype detection by RT-PCR among infected children in India.

Science.gov (United States)

Ahamed, Syed Fazil; Vivek, Rosario; Kotabagi, Shalini; Nayak, Kaustuv; Chandele, Anmol; Kaja, Murali-Krishna; Shet, Anita

2017-06-01

Dengue surveillance relies on reverse transcription-polymerase chain reaction (RT-PCR), for confirmation of dengue virus (DENV) serotypes. We compared efficacies of published and modified primer sets targeting envelope (Env) and capsid-premembrane (C-prM) genes for detection of circulating DENV serotypes in southern India. Acute samples from children with clinically-diagnosed dengue were used for RT-PCR testing. All samples were also subjected to dengue serology (NS1 antigen and anti-dengue-IgM/IgG rapid immunochromatographic assay). Nested RT-PCR was performed on viral RNA using three methods targeting 654bp C-prM, 511bp C-prM and 641bp Env regions, respectively. RT-PCR-positive samples were validated by population sequencing. Among 171 children with suspected dengue, 121 were dengue serology-positive and 50 were dengue serology-negative. Among 121 serology-positives, RT-PCR detected 91 (75.2%) by CprM654, 72 (59.5%) by CprM511, and 74 (61.1%) by Env641. Among 50 serology-negatives, 10 (20.0%) were detected by CprM654, 12 (24.0%) by CprM511, and 11 (22.0%) by Env641. Overall detection rate using three methods sequentially was 82.6% (100/121) among serology-positive and 40.0% (20/50) among serology-negative samples; 6.6% (8/120) had co-infection with multiple DENV serotypes. We conclude that detection of acute dengue was enhanced by a modified RT-PCR method targeting the 654bp C-prM region, and further improved by using all three methods sequentially. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of canine distemper virus nucleoprotein gene by RT-PCR in urine of dogs with distemper clinical signs

International Nuclear Information System (INIS)

Gebara, C.M.S.; Wosiachi, S.R.; Negrao, F.J.; Oliveira, D.B. de; Beloni, S.N.E.; Alfieri, A.A.; Alfieri, A.F.

2004-01-01

The urine of 87 dogs with clinical signs suggestive of canine distemper was analyzed by RT-PCR for detection of canine distemper virus (CDV) nucleoprotein gene. The samples were allotted to the following groups: group A- with 41 dogs with systemic symptoms, group B- with 37 dogs with neurological signs, and group C- with 9 dogs with simultaneous systemic and neurological clinical signs. Group D (control) included 20 assymptomatic dogs. A c2 was used to test RT-PCR results according to clinical form and hematological characteristics. The RT-PCR was positive for CDV in 47% (41/87) of the urine samples from dogs with clinical signs. All samples from assymptomatic dogs were RT-PCR negatives. Positive samples were found in all groups of dogs with distemper symptoms according to the following propositions: 51.2% (21/41), 29% (11/37) and 100% (9/9) for groups A, B and C, respectively. In all clinical forms (groups A, B and C) leucocytosis was the most frequent observed hematological alteration. No relationship between RT-PCR results and hematological changes was observed. The results showed that independently of the clinical stage of the illness the RT-PCR based on urine sample can be applied for ante mortem diagnosis of CDV

Laboratory selection for increased longevity in Drosophila melanogaster reduces field performance

DEFF Research Database (Denmark)

Wit, Janneke; Kristensen, Torsten Nygaard; Sarup, Pernille

2013-01-01

, environmental temperature and longevity selection on performance in the fieldwas tested. Flies fromlongevity selected and control lines of different ages (2, 5, 10 and 15 days) were released in an environment free of natural food sources. Control flies were tested at low, intermediate and high temperatures......Drosophilamelanogaster is frequently used in ageing studies to elucidate whichmechanisms determine the onset and progress of senescence. Lines selected for increased longevity have often been shown to performaswell as or superior to control lines in life history, stress resistance and behavioural......,while longevity selected flieswere tested at the intermediate temperature only. The ability of flies to locate and reach a food sourcewas tested. Flies of intermediate agewere generally better at locating resources than both younger and older flies, where hot and cold environments accelerate the senescent decline...

From my Home: Dvarionas: Elegie; Pärt: Fratres / Patric Wiklacz

Index Scriptorium Estoniae

Wiklacz, Patric

1997-01-01

Uuest heliplaadist "From my Home: Dvarionas: Elegie; Pärt: Fratres; Barkauskas: Partita; Vasks: Musica Dolorosa; Pelecis: Concerto for Violin, Piano and String Orchestra, "Neverthless"; Plakidis: Two Grasshopper Dances; Tüür: Conversio. Deutsche Kammerphilharmonie, Gidon Kremer (violon), Vadim Sacharov (piano)" Teldec 0630-14654-2 (79 minutes:DDD)

Plant mortality and natural selection may increase biomass yield in switchgrass swards

Science.gov (United States)

Switchgrass (Panicum virgatum L.) is an important candidate for bioenergy feedstock production, prompting significant efforts to increase the number of breeding programs and the output of those programs. The objective of this experiment was to determine the potential utility of natural selection for...

Harsh corporal punishment is associated with increased T2 relaxation time in dopamine-rich regions.

Science.gov (United States)

Sheu, Yi-Shin; Polcari, Ann; Anderson, Carl M; Teicher, Martin H

2010-11-01

Harsh corporal punishment (HCP) was defined as frequent parental administration of corporal punishment (CP) for discipline, with occasional use of objects such as straps, or paddles. CP is linked to increased risk for depression and substance abuse. We examine whether long-term exposure to HCP acts as sub-traumatic stressor that contributes to brain alterations, particularly in dopaminergic pathways, which may mediate their increased vulnerability to drug and alcohol abuse. Nineteen young adults who experienced early HCP but no other forms of maltreatment and twenty-three comparable controls were studied. T2 relaxation time (T2-RT) measurements were performed with an echo planar imaging TE stepping technique and T2 maps were calculated and analyzed voxel-by-voxel to locate regional T2-RT differences between groups. Previous studies indicated that T2-RT provides an indirect index of resting cerebral blood volume. Region of interest (ROI) analyses were also conducted in caudate, putamen, nucleus accumbens, anterior cingulate cortex, dorsolateral prefrontal cortex, thalamus, globus pallidus and cerebellar hemispheres. Voxel-based relaxometry showed that HCP was associated with increased T2-RT in right caudate and putamen. ROI analyses also revealed increased T2-RT in dorsolateral prefrontal cortex, substantia nigra, thalamus and accumbens but not globus pallidus or cerebellum. There were significant associations between T2-RT measures in dopamine target regions and use of drugs and alcohol, and memory performance. Alteration in the paramagnetic or hemodynamic properties of dopaminergic cell body and projection regions were observed in subjects with HCP, and these findings may relate to their increased risk for drug and alcohol abuse. Copyright 2010 Elsevier Inc. All rights reserved.

Improvement of a real-time RT-PCR assay for the detection of enterovirus RNA

Directory of Open Access Journals (Sweden)

Bruynseels Peggy

2009-07-01

Full Text Available Abstract We describe an improvement of an earlier reported real-time RT-PCR assay for the detection of enterovirus RNA, based on the 5' exonuclease digestion of a dual-labeled fluorogenic probe by Taq DNA polymerase. A different extraction method, real-time RT-PCR instrument and primer set were evaluated. Our data show that the optimized assay yields a higher sensitivity and reproducibility and resulted in a significant reduced hands-on time per sample.

Experimentation of RT-LOTOS for a critical function of a power plant instrumentation and control system; Experimentation de RT-LOTOS pour une fonction critique d`un systeme de controle-commande en centrale

Energy Technology Data Exchange (ETDEWEB)

Andriantsiiferana, L.; Courtiat, J.P.; De Oliveira, R.C.

1996-01-01

This document is the final report of the contract between LAAS-CNRS and the EdF Direction of Researches and Studies about the experimentation of RT-LOTOS formal description technique on a critical function of a nuclear power plant instrumentation and control system. This report comprises 4 parts: part 1 describes the RT-LOTOS (Real Time-Language of Temporal Ordering Specifications) tutorial and its RTL tool environment, the different RT-LOTOS operators and semantics, and the RTL tool main functionalities; part 2 deals with the methodology and the global architecture for the specification and validation of the CCT (Central Calculator for Treatment); part 3 gives more details about the different processes identified in the specification architecture and presents the main results obtained for the validation of the nominal functioning; part 4 describes some exceptional situations and shows how some failures and their associated recovery mechanisms can be modelled. (J.S.). 6 refs., 53 figs., 5 tabs., 2 appends.

Request for regular monitoring of the symbiotic variable RT Cru

Science.gov (United States)

Waagen, Elizabeth O.

2014-08-01

Dr. Margarita Karovska (Harvard-Smithsonian Center for Astrophysics) and colleagues have requested AAVSO observer assistance in their campaign on the symbiotic variable RT Cru (member of a new class of hard X-ray emitting symbiotic binaries). Weekly or more frequent monitoring (B, V, and visual) beginning now is requested in support of upcoming Chandra observations still to be scheduled. "We plan Chandra observations of RT Cru in the near future that will help us understand the characteristics of the accretion onto the white dwarf in this sub-class of symbiotics. This is an important step for determining the precursor conditions for formation of a fraction of asymmetric Planetary Nebulae, and the potential of symbiotic systems as progenitors of at least a fraction of Type Ia supernovae." Finder charts with sequence may be created using the AAVSO Variable Star Plotter (http://www.aavso.org/vsp). Observations should be submitted to the AAVSO International Database. See full Alert Notice for more details and observations.

Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming.

Science.gov (United States)

Paten, A M; Pain, S J; Peterson, S W; Blair, H T; Kenyon, P R; Dearden, P K; Duncan, E J

2014-08-01

The mammary gland is a complex tissue consisting of multiple cell types which, over the lifetime of an animal, go through repeated cycles of development associated with pregnancy, lactation and involution. The mammary gland is also known to be sensitive to maternal programming by environmental stimuli such as nutrition. The molecular basis of these adaptations is of significant interest, but requires robust methods to measure gene expression. Reverse-transcription quantitative PCR (RT-qPCR) is commonly used to measure gene expression, and is currently the method of choice for validating genome-wide expression studies. RT-qPCR requires the selection of reference genes that are stably expressed over physiological states and treatments. In this study we identify suitable reference genes to normalize RT-qPCR data for the ovine mammary gland in two physiological states; late pregnancy and lactation. Biopsies were collected from offspring of ewes that had been subjected to different nutritional paradigms during pregnancy to examine effects of maternal programming on the mammary gland of the offspring. We evaluated eight candidate reference genes and found that two reference genes (PRPF3 and CUL1) are required for normalising RT-qPCR data from pooled RNA samples, but five reference genes are required for analyzing gene expression in individual animals (SENP2, EIF6, MRPL39, ATP1A1, CUL1). Using these stable reference genes, we showed that TET1, a key regulator of DNA methylation, is responsive to maternal programming and physiological state. The identification of these novel reference genes will be of utility to future studies of gene expression in the ovine mammary gland. Copyright © 2014 the American Physiological Society.

Sequential emergence and clinical implications of viral mutants with K70E and K65R mutation in reverse transcriptase during prolonged tenofovir monotherapy in rhesus macaques with chronic RT-SHIV infection

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Pedersen Niels C

2007-04-01

Full Text Available Abstract Background We reported previously on the emergence and clinical implications of simian immunodeficiency virus (SIVmac251 mutants with a K65R mutation in reverse transcriptase (RT, and the role of CD8+ cell-mediated immune responses in suppressing viremia during tenofovir therapy. Because of significant sequence differences between SIV and HIV-1 RT that affect drug susceptibilities and mutational patterns, it is unclear to what extent findings with SIV can be extrapolated to HIV-1 RT. Accordingly, to model HIV-1 RT responses, 12 macaques were inoculated with RT-SHIV, a chimeric SIV containing HIV-1 RT, and started on prolonged tenofovir therapy 5 months later. Results The early virologic response to tenofovir correlated with baseline viral RNA levels and expression of the MHC class I allele Mamu-A*01. For all animals, sensitive real-time PCR assays detected the transient emergence of K70E RT mutants within 4 weeks of therapy, which were then replaced by K65R mutants within 12 weeks of therapy. For most animals, the occurrence of these mutations preceded a partial rebound of plasma viremia to levels that remained on average 10-fold below baseline values. One animal eventually suppressed K65R viremia to undetectable levels for more than 4 years; sequential experiments using CD8+ cell depletion and tenofovir interruption demonstrated that both CD8+ cells and continued tenofovir therapy were required for sustained suppression of viremia. Conclusion This is the first evidence that tenofovir therapy can select directly for K70E viral mutants in vivo. The observations on the clinical implications of the K65R RT-SHIV mutants were consistent with those of SIVmac251, and suggest that for persons infected with K65R HIV-1 both immune-mediated and drug-dependent antiviral activities play a role in controlling viremia. These findings suggest also that even in the presence of K65R virus, continuation of tenofovir treatment as part of HAART may be

Screening Reliable Reference Genes for RT-qPCR Analysis of Gene Expression in Moringa oleifera.

Science.gov (United States)

Deng, Li-Ting; Wu, Yu-Ling; Li, Jun-Cheng; OuYang, Kun-Xi; Ding, Mei-Mei; Zhang, Jun-Jie; Li, Shu-Qi; Lin, Meng-Fei; Chen, Han-Bin; Hu, Xin-Sheng; Chen, Xiao-Yang

2016-01-01

Moringa oleifera is a promising plant species for oil and forage, but its genetic improvement is limited. Our current breeding program in this species focuses on exploiting the functional genes associated with important agronomical traits. Here, we screened reliable reference genes for accurately quantifying the expression of target genes using the technique of real-time quantitative polymerase chain reaction (RT-qPCR) in M. oleifera. Eighteen candidate reference genes were selected from a transcriptome database, and their expression stabilities were examined in 90 samples collected from the pods in different developmental stages, various tissues, and the roots and leaves under different conditions (low or high temperature, sodium chloride (NaCl)- or polyethyleneglycol (PEG)- simulated water stress). Analyses with geNorm, NormFinder and BestKeeper algorithms revealed that the reliable reference genes differed across sample designs and that ribosomal protein L1 (RPL1) and acyl carrier protein 2 (ACP2) were the most suitable reference genes in all tested samples. The experiment results demonstrated the significance of using the properly validated reference genes and suggested the use of more than one reference gene to achieve reliable expression profiles. In addition, we applied three isotypes of the superoxide dismutase (SOD) gene that are associated with plant adaptation to abiotic stress to confirm the efficacy of the validated reference genes under NaCl and PEG water stresses. Our results provide a valuable reference for future studies on identifying important functional genes from their transcriptional expressions via RT-qPCR technique in M. oleifera.

Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D

Science.gov (United States)

Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.

2013-01-01

A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.

Pärt: kultuurilis-diplomaatiline missioon Vatikanis täidetud / Valner Valme

Index Scriptorium Estoniae

Valme, Valner, 1970-

2011-01-01

23. augustil Katariina kirikus toimunud uue singli "Vater Unser" esitlusest. Selle pala kinkis A. Pärt paavstile 4. juulil Vatikanis. Esitlusel viibis ka president Toomas Hendrik Ilves. Pärdi päevade raames toimuvatest üritustest

IMPLEMENTASI PENGELOLAAN AIR MINUM RUMAH TANGGA (PAM RT DI JAWA BARAT DAN (NUSA TENGGARA TIMUR

Directory of Open Access Journals (Sweden)

Athena Anwar

2016-09-01

Full Text Available Abstract In order to reduce waterborne diseases, the current government and its partners are developing ahousehold water treatment and safety storage (HWTS. This article is part of a study on Development ofAn Evidence-Based Guidelines for Promotion of HWTS which is conducted in three pilot sites: Bandungcity, Bandung district (West Java and Sikka district (East Nusa Tenggara in 2008. The aim of this studywas to find out how the program was implemented and how is the public opinion about the management(processing and storage of drinking water. Data collection was done by interview through a questionnaire.Data source were health officers and partners (qualitative data and the community (quantitative data.Qualitative data processing was performed by the content and the domain method, while quantitative datawas processed through SPSS software. The results show that the government develop the HWTS alongwith its partner: Aman Tirta (Bandung City, Pelita Indonesia (Bandung District, and Dian Desa (SikkaDistrict. Activity of HWTS was done through several stages, such as preparation/dissemination,implementation, monitoring and evaluation. Every partner will have its own way in carrying out the stagesof activity. Not all health officers of district/city states involved in the implementation of the HWTSprogram. It was only Sikka District Health officer that claimed to have fully engaged in the implementationof HWTS in the region. The results of processing and data analysis showed that more than 80% ofrespondents said the HWTS methods were suitable with drinking water treatment for their region. In termsof increasing the water quality, price of materials/tools, and easyness in the water treatment; respondents'opinions very widely.Keywords: HWTS, drinking water, water treatment Abstrak Dalam upaya menurunkan penyakit yang ditularkan melalui air, saat ini pemerintah dan mitrasedang mengembangkan pengelolaan air minum rumah tangga (PAM RT atau household water

Rapid colorimetric detection of Zika virus from serum and urine specimens by reverse transcription loop-mediated isothermal amplification (RT-LAMP.

Directory of Open Access Journals (Sweden)

Amanda E Calvert

Full Text Available Zika virus (ZIKV has emerged as a major global public health concern in the last two years due to its link as a causative agent of human birth defects. Its rapid expansion into the Western Hemisphere as well as the ability to be transmitted from mother to fetus, through sexual transmission and possibly through blood transfusions has increased the need for a rapid and expansive public health response to this unprecedented epidemic. A non-invasive and rapid ZIKV diagnostic screening assay that can be performed in a clinical setting throughout pregnancy is vital for prenatal care of women living in areas of the world where exposure to the virus is possible. To meet this need we have developed a sensitive and specific reverse transcriptase loop-mediated isothermal amplification (RT-LAMP assay to detect ZIKV RNA in urine and serum with a simple visual detection. RT-LAMP results were shown to have a limit of detection 10-fold higher than qRT-PCR. As little as 1.2 RNA copies/μl was detected by RT-LAMP from a panel of 178 diagnostic specimens. The assay was shown to be highly specific for ZIKV RNA when tested with diagnostic specimens positive for dengue virus (DENV and chikungunya virus (CHIKV. The assay described here illustrates the potential for a fast, reliable, sensitive and specific assay for the detection of ZIKV from urine or serum that can be performed in a clinical or field setting with minimal equipment and technological expertise.

Pärt, Arvo: De profundis. Missa Sillabica. Solfeggio / Marc Rochester

Index Scriptorium Estoniae

Rochester, Marc

1997-01-01

Uuest heliplaadist "Pärt, Arvo: De profundis. Missa Sillabica. Solfeggio. And one of the Pharisees. Cantate Domino. Summa. Seven Magnificat Antiphons. The Beautitudes. Magnificat. Christopher Bowers-Broadbent (org.), Daniel Kennedy (perc.). Theatre of Voices / Paul Hillier (bass). Harmonia Mundi HMU40 7182; HMU90 7182 (76 minutes:DDD)"

Analysis of gene expression in small numbers of purified hemopoietic progenitor cells by RT-PCR.

Science.gov (United States)

Ziegler, B L; Lamping, C P; Thoma, S J; Fliedner, T M

1995-05-01

Primitive hemopoietic stem cells represent the most probable targets for genetic alterations due to exposure to ionizing irradiation or chemical carcinogens. We have applied a two-step protocol for the purification of CD34+HLA-DR-/low hemopoietic progenitor cells from cord blood (CB). CD34+ cells were isolated by monoclonal antibody (mAb) against CD34 (My10) and immunomagnetic beads. Beads were cleaved off the CD34+ cells by enzymatic treatment with chymopapain. Due to chymopapain-resistance of epitopes recognized by the used mAbs purity control of CD34+ cells and separation into CD34+HLA-DR-/low and CD34+HLA-DR+ subsets could be performed by using flow cytometry. Two miniaturized procedures were applied to isolate poly(A)+ mRNA for the reverse transcription polymerase chain reaction (RT-PCR) from small numbers of CD34+HLA-DR-/low cells. In five experiments, the mean purity of immunomagnetically isolated CD34+ cells was 93.8% +/- 3.9. Flow cytometry sorting of CD34+ cells resulted in pure CD34+HLA-DR-/low populations (purity > 98.8%; range 98.8% to 99.9%; viability > 96%) with an average yield of 2600 +/- 800 cells/5 x 10(7) low density CB cells. By RT-PCR using both poly(A)+ mRNA isolation procedures, sequences corresponding to CD34 and beta 2-microglobulin were amplified from as few as 20 cells. Furthermore, a sequence-independent RT-PCR (SIP-RT-PCR) was applied to amplify the cDNA derived from five erythroblasts isolated from a burst-forming unit-erythroid (BFU-E). Upon hybridization, full-length c-fos message was detected in the SIP-RT-PCR amplified material. Our data demonstrate that gene expression can be detected at the transcriptional level in small numbers of hemopoietic progenitor cells. In addition, the SIP-RT-PCR may allow the amplification of unique mRNA species when subtractive hybridization procedures are performed. The presented data should be useful to analyze gene expression in rare subsets of radiation-exposed immature hemopoietic stem

Applications of LANCE Data at SPoRT

Science.gov (United States)

Molthan, Andrew

2014-01-01

Short term Prediction Research and Transition (SPoRT) Center: Mission: Apply NASA and NOAA measurement systems and unique Earth science research to improve the accuracy of short term weather prediction at the regional/local scale. Goals: Evaluate and assess the utility of NASA and NOAA Earth science data and products and unique research capabilities to address operational weather forecast problems; Provide an environment which enables the development and testing of new capabilities to improve short term weather forecasts on a regional scale; Help ensure successful transition of new capabilities to operational weather entities for the benefit of society

SMAP Data Assimilation at NASA SPoRT

Science.gov (United States)

Blankenship, Clay B.; Case, Jonathan L.; Zavodsky, Bradley T.

2016-01-01

The NASA Short-Term Prediction Research and Transition (SPoRT) Center maintains a near-real- time run of the Noah Land Surface Model within the Land Information System (LIS) at 3-km resolution. Soil moisture products from this model are used by several NOAA/National Weather Service Weather Forecast Offices for flood and drought situational awareness. We have implemented assimilation of soil moisture retrievals from the Soil Moisture Ocean Salinity (SMOS) and Soil Moisture Active/ Passive (SMAP) satellites, and are now evaluating the SMAP assimilation. The SMAP-enhanced LIS product is planned for public release by October 2016.

Evaluation of reference genes for RT-qPCR study in abalone Haliotis discus hannai during heavy metal overload stress

Directory of Open Access Journals (Sweden)

Sang Yoon Lee

2016-06-01

Full Text Available Abstract Background The evaluation of suitable reference genes as normalization controls is a prerequisite requirement for launching quantitative reverse transcription-PCR (RT-qPCR-based expression study. In order to select the stable reference genes in abalone Haliotis discus hannai tissues (gill and hepatopancreas under heavy metal exposure conditions (Cu, Zn, and Cd, 12 potential candidate housekeeping genes were subjected to expression stability based on the comprehensive ranking while integrating four different statistical algorithms (geNorm, NormFinder, BestKeeper, and ΔCT method. Results Expression stability in the gill subset was determined as RPL7 > RPL8 > ACTB > RPL3 > PPIB > RPL7A > EF1A > RPL4 > GAPDH > RPL5 > UBE2 > B-TU. On the other hand, the ranking in the subset for hepatopancreas was RPL7 > RPL3 > RPL8 > ACTB > RPL4 > EF1A > RPL5 > RPL7A > B-TU > UBE2 > PPIB > GAPDH. The pairwise variation assessed by the geNorm program indicates that two reference genes could be sufficient for accurate normalization in both gill and hepatopancreas subsets. Overall, both gill and hepatopancreas subsets recommended ribosomal protein genes (particularly RPL7 as stable references, whereas traditional housekeepers such as β-tubulin (B-TU and glyceraldehyde-3-phosphate dehydrogenase (GAPDH genes were ranked as unstable genes. The validation of reference gene selection was confirmed with the quantitative assay of MT transcripts. Conclusions The present analysis showed the importance of validating reference genes with multiple algorithmic approaches to select genes that are truly stable. Our results indicate that expression stability of a given reference gene could not always have consensus across tissue types. The data from this study could be a good guide for the future design of RT-qPCR studies with respect to metal regulation/detoxification and other related

Cognition and Quality of Life After Chemotherapy Plus Radiotherapy (RT) vs. RT for Pure and Mixed Anaplastic Oligodendrogliomas: Radiation Therapy Oncology Group Trial 9402

International Nuclear Information System (INIS)

Wang Meihua; Cairncross, Gregory; Shaw, Edward

2010-01-01

Purpose: Radiation Therapy Oncology Group 9402 compared procarbazine, lomustine, and vincristine (PCV) chemotherapy plus radiation therapy (PCV + RT) vs. RT alone for anaplastic oligodendroglioma. Here we report longitudinal changes in cognition and quality of life, effects of patient factors and treatments on cognition, quality of life and survival, and prognostic implications of cognition and quality of life. Methods and Materials: Cognition was assessed by Mini Mental Status Examination (MMSE) and quality of life by Brain-Quality of Life (B-QOL). Scores were analyzed for survivors and within 5 years of death. Shared parameter models evaluated MMSE/B-QOL with survival. Results: For survivors, MMSE and B-QOL scores were similar longitudinally and between treatments. For those who died, MMSE scores remained stable initially, whereas B-QOL slowly declined; both declined rapidly in the last year of life and similarly between arms. In the aggregate, scores decreased over time (p = 0.0413 for MMSE; p = 0.0016 for B-QOL) and were superior with age <50 years (p < 0.001 for MMSE; p = 0.0554 for B-QOL) and Karnofsky Performance Score (KPS) 80-100 (p < 0.001). Younger age and higher KPS were associated with longer survival. After adjusting for patient factors and drop-out, survival was longer after PCV + RT (HR = 0.66, 95% CI = 0.49-0.9, p = 0.0084; HR = 0.74, 95% CI = 0.54-1.01, p = 0.0592) in models with MMSE and B-QOL. In addition, there were no differences in MMSE and B-QOL scores between arms (p = 0.4752 and p = 0.2767, respectively); higher scores predicted longer survival. Conclusion: MMSE and B-QOL scores held steady in the upper range in both arms for survivors. Younger, fitter patients had better MMSE and B-QOL and longer survival.

Selection for increased desiccation resistance in Drosophila melanogaster: Additive genetic control and correlated responses for other stresses

International Nuclear Information System (INIS)

Hoffmann, A.A.; Parsons, P.A.

1989-01-01

Previously we found that Drosophila melanogaster lines selected for increased desiccation resistance have lowered metabolic rate and behavioral activity levels, and show correlated responses for resistance to starvation and a toxic ethanol level. These results were consistent with a prediction that increased resistance to many environmental stresses may be genetically correlated because of a reduction in metabolic energy expenditure. Here we present experiments on the genetic basis of the selection response and extend the study of correlated responses to other stresses. The response to selection was not sex-specific and involved X-linked and autosomal genes acting additively. Activity differences contributed little to differences in desiccation resistance between selected and control lines. Selected lines had lower metabolic rates than controls in darkness when activity was inhibited. Adults from selected lines showed increased resistance to a heat shock, 60 Co-gamma-radiation, and acute ethanol and acetic acid stress. The desiccation, ethanol and starvation resistance of isofemale lines set up from the F2s of a cross between one of the selected and one of the control lines were correlated. Selected and control lines did not differ in ether-extractable lipid content or in resistance to acetone, ether or a cold shock

GSK-3β inhibitor TWS119 attenuates rtPA-induced hemorrhagic transformation and activates the Wnt/β-catenin signaling pathway after acute ischemic stroke in rats.

Science.gov (United States)

Wang, Wei; Li, Mingchang; Wang, Yuefei; Li, Qian; Deng, Gang; Wan, Jieru; Yang, Qingwu; Chen, Qianxue; Wang, Jian

2016-12-01

Hemorrhagic transformation (HT) is a devastating complication for patients with acute ischemic stroke who are treated with tissue plasminogen activator (tPA). It is associated with high morbidity and mortality, but no effective treatments are currently available to reduce HT risk. Therefore, methods to prevent HT are urgently needed. In this study, we used TWS119, an inhibitor of glycogen synthase kinase 3β (GSK-3β), to evaluate the role of the Wnt/β-catenin signaling pathway in recombinant tPA (rtPA)-induced HT. Sprague-Dawley rats were subjected to a middle cerebral artery occlusion (MCAO) model of ischemic stroke and then were administered rtPA, rtPA combined with TWS119, or vehicle at 4 h. The animals were sacrificed 24 h after infarct induction. Rats treated with rtPA showed evident HT, had more severe neurologic deficit, brain edema, and blood-brain barrier breakdown, and had larger infarction volume than did the vehicle group. Rats treated with TWS119 had significantly improved outcomes compared with those of rats treated with rtPA alone. In addition, Western blot analysis showed that TWS119 increased the protein expression of β-catenin, claudin-3, and ZO-1 while suppressing the expression of GSK-3β. These results suggest that TWS119 reduces rtPA-induced HT and attenuates blood-brain barrier disruption, possibly through activation of the Wnt/β-catenin signaling pathway. This study provides a potential therapeutic strategy to prevent tPA-induced HT after acute ischemic stroke.

Det retlige sprog som virkelighedsskabende - graviditetsvært kontra surrogatmoder

DEFF Research Database (Denmark)

Pedersen, Frank Høgholm

2018-01-01

I dag er det undtagelsen, at kvinden, der bærer graviditeten og føder barnet i et surrogati-arrangement, er genetisk relateret til barnet. I artiklen foreslås som en supplerende betegnelse til surrogatmoder derfor betegnelsen: graviditetsvært. Valget af en retlig betegnelse til beskrivelse af fak...

How feasible is remote 3D dosimetry for MR guided Radiation Therapy (MRgRT)?

International Nuclear Information System (INIS)

Mein, S; Miles, D; Juang, T; Fenoli, J; Oldham, M; Rankine, L; Cai, B; Curcuru, A; Mutic, S; Li, H; Adamovics, J

2017-01-01

To develop and apply a remote dosimetry protocol with PRESAGE® radiochromic plastic and optical-CT readout in the validation of MRI guided radiation therapy (MRgRT) treatments (MRIdian® by ViewRay®). Through multi-institutional collaboration we performed PRESAGE® dosimetry studies in 4ml cuvettes to investigate dose-response linearity, MR-compatibility, and energy-independence. An open calibration field and symmetrical 3-field plans were delivered to 10cm diameter PRESAGE® to examine percent depth dose and response uniformity under a magnetic field. Evidence of non-linear dose response led to a large volume PRESAGE® study where small corrections were developed for temporally- and spatially-dependent behaviors observed between irradiation and delayed readout. TG-119 plans were created in the MRIdian® TPS and then delivered to 14.5cm 2kg PRESAGE® dosimeters. Through the domestic investigation of an off-site MRgRT system, a refined 3D remote dosimetry protocol is presented capable of validation of advanced MRgRT radiation treatments. (paper)

How feasible is remote 3D dosimetry for MR guided Radiation Therapy (MRgRT)?

Science.gov (United States)

Mein, S.; Rankine, L.; Miles, D.; Juang, T.; Cai, B.; Curcuru, A.; Mutic, S.; Fenoli, J.; Adamovics, J.; Li, H.; Oldham, M.

2017-05-01

To develop and apply a remote dosimetry protocol with PRESAGE® radiochromic plastic and optical-CT readout in the validation of MRI guided radiation therapy (MRgRT) treatments (MRIdian® by ViewRay®). Through multi-institutional collaboration we performed PRESAGE® dosimetry studies in 4ml cuvettes to investigate dose-response linearity, MR-compatibility, and energy-independence. An open calibration field and symmetrical 3-field plans were delivered to 10cm diameter PRESAGE® to examine percent depth dose and response uniformity under a magnetic field. Evidence of non-linear dose response led to a large volume PRESAGE® study where small corrections were developed for temporally- and spatially-dependent behaviors observed between irradiation and delayed readout. TG-119 plans were created in the MRIdian® TPS and then delivered to 14.5cm 2kg PRESAGE® dosimeters. Through the domestic investigation of an off-site MRgRT system, a refined 3D remote dosimetry protocol is presented capable of validation of advanced MRgRT radiation treatments.

Real time RT-PCR assay for detection of different serotypes of FMDV in Egypt

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Laila El-Shehawy

Full Text Available Aim: The present study indicated that rRT-PCR could be provided for the detection of FMDV in infected, contact and carrier cattle and also provide a rapid sensitive tool aiming to aid in rapid disease detection and control. Foot and Mouth disease virus serotypes O and A still existing in Egypt. In January 2012, sever outbreaks struck the animal population in most Egyptian 1 governorates. The causative virus was identified as FMDV SAT2. Material and Methods: Five samples of tongue epithelium (ET and five oesophageal-pharyngeal (OP fluid samples were collected from FMD suspected cattle in infected farm at El-Fayoum and 20 OP samples from in-contact cattle at the same farm in addition to 30 OP samples from apparently healthy cattle at three different localities in El-Fayoum governorate (12 from Fayoum; 9 from Sinoras and 9 from Edsa in order to detect carrier cattle. All of these samples were collected during November and December 2011 and January 2012. Results: All the ET and OP samples were inoculated on BHK cell culture and baby mice. The obtained results were identified using complement fixation test in addition to real-time reverse transcriptase polymerase chain reaction (rRT-PCR. In the infected farm at El-Fayoum FMDV type SAT2 was detected in cattle which are considered as the first introduction of this type while FMDV type O and SAT2 were detected in the in-contact cattle in the same farm. The sensitivity of rRT-PCR was cleared in the in-contact cattle as 13 out of 20 OP samples were positive to FMDV by rRT-PCR while 11 out of 20 OP samples were positive to FMDV by CFT. The OP samples collected from apparently healthy cattle from Fayoum, Sinoras and Edsa localities in Fayoum governorate demonstrate the circulation of the FMDV type A, O and the recent SAT2 in carrier cattle which threaten cattle population in Fayoum governorate. Also the sensitivity of real time RT-PCR over the CFT in detection of FMDV carrier cattle was clearly noticed in

MINIX4RT: real-time interprocess communications facilities

OpenAIRE

Pessolani, Pablo Andrés

2006-01-01

MINIX4RT es una extensión del conocido Sistema Operativo MINIX que incorpora servicios de Tiempo Real Estricto en un nuevo microkernel pero manteniendo compatibilidad con las versiones anteriores del MINIX estándar. La Comunicación entre Procesos es un mecanismo que permite hacer extensible a un Sistema Operativo, pero debe estar libre de Inversión de Prioridades para ser utilizado en aplicaciones de Tiempo Real. Como las primitivas de MINIX no disponen de esta funcionalidad, se incorporar...

Selection and validation of a set of reliable reference genes for quantitative RT-PCR studies in the brain of the Cephalopod Mollusc Octopus vulgaris

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Biffali Elio

2009-07-01

Full Text Available Abstract Background Quantitative real-time polymerase chain reaction (RT-qPCR is valuable for studying the molecular events underlying physiological and behavioral phenomena. Normalization of real-time PCR data is critical for a reliable mRNA quantification. Here we identify reference genes to be utilized in RT-qPCR experiments to normalize and monitor the expression of target genes in the brain of the cephalopod mollusc Octopus vulgaris, an invertebrate. Such an approach is novel for this taxon and of advantage in future experiments given the complexity of the behavioral repertoire of this species when compared with its relatively simple neural organization. Results We chose 16S, and 18S rRNA, actB, EEF1A, tubA and ubi as candidate reference genes (housekeeping genes, HKG. The expression of 16S and 18S was highly variable and did not meet the requirements of candidate HKG. The expression of the other genes was almost stable and uniform among samples. We analyzed the expression of HKG into two different set of animals using tissues taken from the central nervous system (brain parts and mantle (here considered as control tissue by BestKeeper, geNorm and NormFinder. We found that HKG expressions differed considerably with respect to brain area and octopus samples in an HKG-specific manner. However, when the mantle is treated as control tissue and the entire central nervous system is considered, NormFinder revealed tubA and ubi as the most suitable HKG pair. These two genes were utilized to evaluate the relative expression of the genes FoxP, creb, dat and TH in O. vulgaris. Conclusion We analyzed the expression profiles of some genes here identified for O. vulgaris by applying RT-qPCR analysis for the first time in cephalopods. We validated candidate reference genes and found the expression of ubi and tubA to be the most appropriate to evaluate the expression of target genes in the brain of different octopuses. Our results also underline the

Avian metapneumovirus RT-nested-PCR: a novel false positive reducing inactivated control virus with potential applications to other RNA viruses and real time methods.

Science.gov (United States)

Falchieri, Marco; Brown, Paul A; Catelli, Elena; Naylor, Clive J

2012-12-01

Using reverse genetics, an avian metapneumovirus (AMPV) was modified for use as a positive control for validating all stages of a popular established RT-nested PCR, used in the detection of the two major AMPV subtypes (A and B). Resultant amplicons were of increased size and clearly distinguishable from those arising from unmodified virus, thus allowing false positive bands, due to control virus contamination of test samples, to be identified readily. Absorption of the control virus onto filter paper and subsequent microwave irradiation removed all infectivity while its function as an efficient RT-nested-PCR template was unaffected. Identical amplicons were produced after storage for one year. The modified virus is likely to have application as an internal standard as well as in real time methods. Additions to AMPV of RNA from other RNA viruses, including hazardous examples such HIV and influenza, are likely to yield similar safe RT-PCR controls. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project.

Science.gov (United States)

Letovanec, Igor; Finn, Stephen; Zygoura, Panagiota; Smyth, Paul; Soltermann, Alex; Bubendorf, Lukas; Speel, Ernst-Jan; Marchetti, Antonio; Nonaka, Daisuke; Monkhorst, Kim; Hager, Henrik; Martorell, Miguel; Sejda, Aleksandra; Cheney, Richard; Hernandez-Losa, Javier; Verbeken, Eric; Weder, Walter; Savic, Spasenija; Di Lorito, Alessia; Navarro, Atilio; Felip, Enriqueta; Warth, Arne; Baas, Paul; Meldgaard, Peter; Blackhall, Fiona; Dingemans, Anne-Marie; Dienemann, Hendrik; Dziadziuszko, Rafal; Vansteenkiste, Johan; O'Brien, Cathal; Geiger, Thomas; Sherlock, Jon; Schageman, Jeoffrey; Dafni, Urania; Kammler, Roswitha; Kerr, Keith; Thunnissen, Erik; Stahel, Rolf; Peters, Solange

2018-03-01

The reported prevalence of ALK receptor tyrosine kinase gene (ALK) rearrangement in NSCLC ranges from 2% to 7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proved to be a reproducible and sensitive technique. Reverse-transcriptase polymerase chain reaction (RT-PCR) has also been advocated, and most recently, the advent of targeted next-generation sequencing (NGS) for ALK and other fusions has become possible. This study compares anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape cohort. A total of 96 cases from the European Thoracic Oncology Platform Lungscape iBiobank, with any ALK immunoreactivity were examined by FISH, central RT-PCR, and NGS. An H-score higher than 120 defines IHC positivity. RNA was extracted from the same formalin-fixed, paraffin-embedded tissues. For RT-PCR, primers covered the most frequent ALK translocations. For NGS, the Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific, Waltham, MA) was used. The concordance was assessed using the Cohen κ coefficient (two-sided α ≤ 5%). NGS provided results for 77 of the 95 cases tested (81.1%), whereas RT-PCR provided results for 77 of 96 (80.2%). Concordance occurred in 55 cases of the 60 cases tested with all four methods (43 ALK negative and 12 ALK positive). Using ALK copositivity for IHC and FISH as the criterion standard, we derived a sensitivity for RT-PCR/NGS of 70.0%/85.0%, with a specificity of 87.1%/79.0%. When either RT-PCR or NGS was combined with IHC, the sensitivity remained the same, whereas the specificity increased to 88.7% and 83.9% respectively. NGS evaluation with the Oncomine Solid Tumour Fusion transcript kit and RT-PCR proved to have high sensitivity and specificity, advocating their use in routine practice. For maximal sensitivity and specificity, ALK status should be

Detection of canine distemper virus nucleocapsid protein gene in canine peripheral blood mononuclear cells by RT-PCR.

Science.gov (United States)

Shin, Y; Mori, T; Okita, M; Gemma, T; Kai, C; Mikami, T

1995-06-01

For a rapid diagnosis of canine distemper virus (CDV) infection, the reverse transcription-PCR (RT-PCR) was carried out to detect CDV nucleoprotein (NP) gene from canine peripheral blood mononuclear cells (PBMCs). Two sets of primers were targeted to two regions of NP gene of CDV Onderstepoort strain. The NP gene fragments were well amplified by the RT-PCR in each of the RNA extracts from Vero cells infected with 6 laboratory strains of CDV including Onderstepoort strain, and from PBMCs of a dog experimentally infected with CDV. The amplified NP gene was detected in 17 of 32 samples from dogs which were clinically suspected for CDV infection at veterinary hospitals. No RT-PCR product was found in 52 samples from healthy dogs including 40 specific pathogen free beagles vaccinated with an attenuated live virus-vaccine for CDV and 12 stray dogs. The RT-PCR provides a fast, sensitive, and supplementary method for the diagnosis of CDV infection in dogs.

Selective attention increases choice certainty in human decision making.

Science.gov (United States)

Zizlsperger, Leopold; Sauvigny, Thomas; Haarmeier, Thomas

2012-01-01

Choice certainty is a probabilistic estimate of past performance and expected outcome. In perceptual decisions the degree of confidence correlates closely with choice accuracy and reaction times, suggesting an intimate relationship to objective performance. Here we show that spatial and feature-based attention increase human subjects' certainty more than accuracy in visual motion discrimination tasks. Our findings demonstrate for the first time a dissociation of choice accuracy and certainty with a significantly stronger influence of voluntary top-down attention on subjective performance measures than on objective performance. These results reveal a so far unknown mechanism of the selection process implemented by attention and suggest a unique biological valence of choice certainty beyond a faithful reflection of the decision process.

Using the SPoRT POES/GOES Hybrid Product in OCONUS Forecasting

Science.gov (United States)

Smith, Matt; Fuell, Kevin; Nelson, Jim

2014-01-01

The SPoRT (Short-term Prediction and Research Transition) Program at the NASA/Marshall Space Flight Center has been providing unique NASA and NOAA data and techniques to partner Weather Forecast Offices (WFOs) for ten years. Data are provided in the Decision Support System used by WFO forecasters: AWIPS. For the last couple of years, SPoRT has been producing the POES/GOES Hybrid. This suite of products combines the strength ofl5- minute animations of GOES imagery - providing temporal continuity, with the higher resolution, relatively random availability, of polar orbiting (POES) imagery data. The product was first introduced with only MODIS data from NASA's Terra and Aqua satellites, but recently the VIIRS instrument onboard the Suomi-NPP satellite was added, providing better high-resolution coverage. These products represent SPoRT's efforts to prepare for higher resolution, higher frequency GOES-R imagery - as well as helping to move VIIRS (JPSS) data into the mainstream of weather forecasting. SPoRT generates 5 products for this dataset: Visible, Longwave Infrared (11 micrometers), Shortwave IR (3.7 micrometers), Water Vapor (6.7 micrometers), and Fog (Difference of 11 micrometer and 3.7 micrometer channels). The Water Vapor hybrid product has a Red-Blue-Green image from MODIS inlaid, since it provides even more qualitative information than water vapor alone. Animated examples of the products will be shown in this presentation. While the resolution at nadir of GOES imagery is nominally Han (4km for IR channels), the inlaid polar orbiter imagery has a resolution of 250m (lkm for IR channels). This has tremendous application in the continental US. However, in high latitudes, since the usefulness of GOES degrades poleward rapidly, the contrast of GOES and POES data is stark. The consistent temporal nature of GOES, even though at a reduced resolution at high latitudes, provides basic situational awareness, but the introduction of polar data is very helpful in seeing

Transuranics and fission products release from PWR fuels in severe accident conditions. Lessons learnt from VERCORS RT3 and RT4 tests

International Nuclear Information System (INIS)

Pontillon, Y.; Ducros, G.; Van Winckel, S.; Christiansen, B.; Kissane, M.P.; Dubourg, R.; Dutheillet, Y.; Andreo, F.

2006-01-01

), chemical analysis of the filter deposits and other surface deposits downstream were performed in some specific cases, in order to extend the result to non gamma-active isotopes and confirm the gamma-spectroscopy results; this, in turn, will help to close the mass balance of the fission products and transuranic elements. In the present case, VERCORS RT3 and RT4 samples were sent to ITU in order to be analysed by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS) after dissolution. The present communication gives a general overview of the VERCORS program and presents in more detail the main findings regarding RT3 and RT4 with, on the one hand, the general FP behaviour including the comparison between gamma-spectrometry and ICP-MS results and, on the other hand, the significant release - up to ∼10 % of the initial inventory - of uranium in oxidizing conditions. (author)

Changes in Plasma Prolactin and Growth Hormone Level and Visual Problem after radiation Therapy(RT) of Pituitary Adenoma

International Nuclear Information System (INIS)

Yoon, Sei Chul; Kwon, Hyung Chul; Oh, Yoon Kyeong; Bahk, Yong Whee; Son, Ho Young; Kang, Joon Ki; Song, Jin Un

1985-01-01

Twenty-four cases of pituitary adenoma, 13 males and 11 females with the age ranging from 11 to 65 years, received radiation therapy(RT) on the pituitary area with 6MV linear accelerator during past 25 months at the Division of Radiation Therapy, Kangnam St. Mary Hospital, Catholic Medical College. Of 24 case of RT, 20 were postoperative and 4 primary. To evaluate the effect of RT, we analyzed the alteration of the endocrinological tests, neurologic abnormalities, major clinical symptoms, endocrinological changes and improvement in visual problems after RT. The results were as follows ; 1. Major clinical symptoms were headache, visual defects, diabetes insipidus, hypogonadisms and general weakness in decreasing order of frequency. 2. All but the one with Nelson syndrome showed abnormal neuroradiologic changes in the sella turcica with an invasive tumor mass around supra and para-sellar area. 3. Endocrinological classifications of the patient were 11 prolactinoma, 4 growth hormonesecreting tumors, 3 ACTH-secreting tumors consisting of one Cushing disease and two Nelson syndrome, and 6 nonfunctioning tumors. 4. Eleven of 14 patients, visual problems were improved after treatment but remaining 3 were unchanged. 5. Seven of 11 prolactinomas returned to normal hormonal level after postoperative and primary RT and 3 patients are being treated with bromocriptine (BMCP) but on lost case. 6. Two of 4 growth hormone-secreting tumor returned to normal level after RT but the remaining 2 are being treated with BMCP, as well

Increased lymphangiogenesis in Riedel thyroiditis (Immunoglobulin G4-related thyroid disease).

Science.gov (United States)

Cameselle-Teijeiro, José; Ladra, María Jesús; Abdulkader, Ihab; Eloy, Catarina; Soares, Paula; Barreiro, Francisco; Sobrinho-Simões, Manuel; Beiras-Iglesias, Andrés

2014-09-01

The present study describes in depth a case of Riedel thyroiditis (RT) to clarify its pathogenesis and its putative inclusion in the spectrum of IgG4-related disease. We report the clinicopathological, immunohistochemical, and ultrastructural features of a case of RT in a 39-year-old white Spanish woman, admitted with a hard goiter and cold nodule in the left thyroid lobe. This case represents 0.05 % of a series of 1,973 consecutive thyroidectomies performed in our hospital. More than 80 % of the left thyroid lobe was effaced by fibrosis and inflammation (lymphocytes, 57 IgG4+ plasma cells per 1 high-power field, an IgG4/IgG ratio of 0.67, and eosinophils) with extension into the surrounding tissues and occlusive phlebitis. Immunostaining for podoplanin (D2-40) detected signs of increased lymphangiogenesis in the fibroinflammatory areas that were confirmed by electron microscopy. A strong, diffuse stain for podoplanin and transforming growth factor ß1 was also detected in the same areas. The increased number of lymphatic vessels in RT is reported for the first time. Our findings support the inclusion of RT within the spectrum of IgG4-related thyroid disease (IgG4-RTD). Although the etiology and physiopathology of IgG4-RTD still remain elusive, the results obtained in the present case suggest the participation of lymphatic vessels in the pathogenesis of RT.

A simple RT-PCR-based strategy for screening connexin identity

Directory of Open Access Journals (Sweden)

M. Urban

1999-08-01

Full Text Available Vertebrate gap junctions are aggregates of transmembrane channels which are composed of connexin (Cx proteins encoded by at least fourteen distinct genes in mammals. Since the same Cx type can be expressed in different tissues and more than one Cx type can be expressed by the same cell, the thorough identification of which connexin is in which cell type and how connexin expression changes after experimental manipulation has become quite laborious. Here we describe an efficient, rapid and simple method by which connexin type(s can be identified in mammalian tissue and cultured cells using endonuclease cleavage of RT-PCR products generated from "multi primers" (sense primer, degenerate oligonucleotide corresponding to a region of the first extracellular domain; antisense primer, degenerate oligonucleotide complementary to the second extracellular domain that amplify the cytoplasmic loop regions of all known connexins except Cx36. In addition, we provide sequence information on RT-PCR primers used in our laboratory to screen individual connexins and predictions of extension of the "multi primer" method to several human connexins.

CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

OpenAIRE

Zhu, Houxiang; Richmond, Emily; Liang, Chun

2017-01-01

CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model org...

Shielding of the Hip Prosthesis During Radiation Therapy for Heterotopic Ossification is Associated with Increased Failure of Prophylaxis

International Nuclear Information System (INIS)

Balboni, Tracy A.; Gaccione, Peter; Gobezie, Reuben; Mamon, Harvey J.

2007-01-01

Purpose: Radiation therapy (RT) is frequently administered to prevent heterotopic ossification (HO) after total hip arthroplasty (THA). The purpose of this study was to determine if there is an increased risk of HO after RT prophylaxis with shielding of the THA components. Methods and Materials: This is a retrospective analysis of THA patients undergoing RT prophylaxis of HO at Brigham and Women's Hospital between June 1994 and February 2004. Univariate and multivariate logistic regressions were used to assess the relationships of all variables to failure of RT prophylaxis. Results: A total of 137 patients were identified and 84 were eligible for analysis (61%). The median RT dose was 750 cGy in one fraction, and the median follow-up was 24 months. Eight of 40 unshielded patients (20%) developed any progression of HO compared with 21 of 44 shielded patients (48%) (p = 0.009). Brooker Grade III-IV HO developed in 5% of unshielded and 18% of shielded patients (p 0.08). Multivariate analysis revealed shielding (p = 0.02) and THA for prosthesis infection (p = 0.03) to be significant predictors of RT failure, with a trend toward an increasing risk of HO progression with age (p = 0.07). There was no significant difference in the prosthesis failure rates between shielded and unshielded patients. Conclusions: A significantly increased risk of failure of RT prophylaxis for HO was noted in those receiving shielding of the hip prosthesis. Shielding did not appear to reduce the risk of prosthesis failure

The SPoRT concept of bracing for idiopathic scoliosis.

Science.gov (United States)

Zaina, Fabio; Fusco, Claudia; Atanasio, Salvatore; Negrini, Stefano

2011-01-01

The SPoRT (acronym: Symmetrical, Patient-oriented, Rigid, Three-dimensional, active) concept of bracing is a new way to build braces based on our 20 years of experience and the biomechanical principles of scoliosis correction, inclusive of the Sibilla and Sforzesco braces. The concept always requires a custom brace, which is made according to the patient's individual requirements. New technologies such as CAD-CAM can be applied, and often for better results, without the customary use of prebuilt forms whose measurements are stored in databases. Once the initial draft brace is completed, a final test must be made on the patient to modify and adapt it, depending on his or her real interaction between the body and the brace. The results that are today available on the SPoRT concept relate to the Sforzesco brace and are necessarily short-term, because the first treated patients are now reaching the fourth-year follow-up examination and haven't yet completed their treatments. On the basis of the initial evaluations, we can state that the Sforzesco brace is more effective than the Lyon brace after 6 months of treatment and that the Sforzesco brace is equally effective as the Risser Plast brace.

Märt Sultsi kavandatud kasiinosaar vajab 300 miljonit krooni laenu / Kertu Kalmus

Index Scriptorium Estoniae

Kalmus, Kertu

2008-01-01

Tallinna linnavolikogu liige Märt Sults palub linnavalitsused toetada ja aktsepteerida SA Kasiinosaar laenu taotlemist Saksamaalt 300 mln. krooni ulatuses. Tema ideekavandi järgi kerkiksid Tallinnas Paljassaare lahte tehissaared: lastesaar, kultuurisaar ja kasiinosaar

Searching for the best real-time RT-PCRs to detect Zika virus infections: the importance of comparing several protocols

Directory of Open Access Journals (Sweden)

F.M. de Moraes

2018-05-01

Full Text Available Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.

Epidemiology of Human Parechovirus Type1 in Clinical Samples from Children with Gastroenteritis Using RT-PCR

Directory of Open Access Journals (Sweden)

Dabirmanesh B

2011-03-01

Full Text Available Background and Objectives: Human parechovirus type-1 (HPeV-1 is a genus of picornaviridea with a single stranded positive sense RNA genome. In general it seems to be responsible for more gastrointestinal and respiratory syndromes and less responsible for central nervous system (CNS symptoms. Since there is no accurate information about diagnosis and epidemiology of HPeV-1 in Iran and it is very important to distinguish between viral and bacterial diarrhea to decrease the unnecessary use of antibiotics, this study aimed at rapid detection and epidemiology of HPeV-1 in stool samples from children with gastroenteritis using specific RT-PCR. Methods: Viral RNA was isolated from 472 stool samples from children (under 4 years old with diarrhea; CDNA was prepared and amplified using specific primers from 5′untranslated region (5′ UTR of HPeV-1 genome by nested RT-PCR. Amplified DNA product was electrophoresed on 1% agarose gel and a single band of 265 bp was obtained. Data were analyzed by SPSS software. We also performed a comparison between the cell culture (Vero and RT-PCR method for HPeV1 detection.Results: Out of 472 samples examined during two years, 112 samples were HpeV-1 positive (23.7%. The results showed that the prevalence of this virus was in children under one year (6-12 months old with diarrhea (p=0.036 in spring and autumn (p<0.001. Boys had more positive cases than the girls (p<0.001. Out of 20 samples which were found positive by HPeV1 RT-PCR only three of them showed CPE on Vero Cells after a week.Conclusion: The results revealed that RT-PCR is a more practical and sensitive technique for HPeV-1 detection directly from clinical samples, which is valuable for epidemiology. Also, the rapid detection of HPeV1 by RT-PCR can decrease both the unnecessary use of antibiotics and the costs in clinical practice

Development of single-step multiplex real-time RT-PCR assays for rapid diagnosis of enterovirus 71, coxsackievirus A6, and A16 in patients with hand, foot, and mouth disease.

Science.gov (United States)

Puenpa, Jiratchaya; Suwannakarn, Kamol; Chansaenroj, Jira; Vongpunsawad, Sompong; Poovorawan, Yong

2017-10-01

Real-time reverse-transcription polymerase chain reaction (rRT-PCR) to detect enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) has facilitated the rapid and accurate identification of the two most common etiological agents underlying hand, foot, and mouth disease (HFMD). However, the worldwide emergence of CV-A6 infection in HFMD necessitates development of an improved multiplex rRT-PCR method. To rapidly determine the etiology of HFMD, two rRT-PCR assays using TaqMan probes were developed to differentiate among three selected common enteroviruses (EV-A71, CV-A16 and CV-A6) and to enable broad detection of enteroviruses (pan-enterovirus assay). No cross-reactions were observed with other RNA viruses examined. The detection limits of both assays were 10 copies per microliter for EV-A71, CV-A6 and CV-A16, and pan-enterovirus. The methods showed high accuracy (EV-A71, 90.6%; CV-A6, 92.0%; CV-A16, 100%), sensitivity (EV-A71, 96.5%; CV-A6, 95.8%; CV-A16, 99.0%), and specificity (EV-A71, 100%; CV-A6, 99.9%; CV-A16, 99.9%) in testing clinical specimens (n=1049) during 2014-2016, superior to those of conventional RT-PCR. Overall, the multiplex rRT-PCR assays enabled highly sensitive detection and rapid simultaneous typing of EV-A71, CV-A6 and CV-A16, and enteroviruses, rendering them feasible and attractive methods for large-scale surveillance of enteroviruses associated with HFMD outbreaks. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamo transformation of the collisional R-T in a weakly ionized ...

Indian Academy of Sciences (India)

where the interstellar neutrals undergo charge exchange collisions with ions in the solar wind [1]. ... regime of magnetically confined torroidal plasma. The author refutes their ... rate ´7К-М µ for the usual collisional R-T is given as. 7К-М g v Дp.

Sex in murky waters: algal-induced turbidity increases sexual selection in pipefish.

Science.gov (United States)

Sundin, Josefin; Aronsen, Tonje; Rosenqvist, Gunilla; Berglund, Anders

2017-01-01

Algal-induced turbidity has been shown to alter several important aspects of reproduction and sexual selection. However, while turbidity has been shown to negatively affect reproduction and sexually selected traits in some species, it may instead enhance reproductive success in others, implying that the impact of eutrophication is far more complex than originally believed. In this study, we aimed to provide more insight into these inconsistent findings. We used molecular tools to investigate the impact of algal turbidity on reproductive success and sexual selection on males in controlled laboratory experiments, allowing mate choice, mating competition, and mate encounter rates to affect reproduction. As study species, we used the broad-nosed pipefish, Syngnathus typhle , a species practicing male pregnancy and where we have previously shown that male mate choice is impaired by turbidity. Here, turbidity instead enhanced sexual selection on male size and mating success as well as reproductive success. Effects from mating competition and mate encounter rates may thus override effects from mate choice based on visual cues, producing an overall stronger sexual selection in turbid waters. Hence, seemingly inconsistent effects of turbidity on sexual selection may depend on which mechanisms of sexual selection that have been under study. Algal blooms are becoming increasingly more common due to eutrophication of freshwater and marine environments. The high density of algae lowers water transparency and reduces the possibility for fish and other aquatic animals to perform behaviors dependent on vision. We have previously shown that pipefish are unable to select the best partner in mate choice trials when water transparency was reduced. However, fish might use other senses than vision to compensate for the reduction in water transparency. In this study, we found that when fish were allowed to freely interact, thereby allowing competition between partners and direct contact

Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

International Nuclear Information System (INIS)

Rosa, Fabíola E; Silveira, Sara M; Silveira, Cássia GT; Bérgamo, Nádia A; Neto, Francisco A Moraes; Domingues, Maria AC; Soares, Fernando A; Caldeira, José RF; Rogatto, Silvia R

2009-01-01

HER-2 gene testing has become an integral part of breast cancer patient diagnosis. The most commonly used assay in the clinical setting for evaluating HER-2 status is immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). These procedures permit correlation between HER-2 expression and morphological features. However, FISH signals are labile and fade over time, making post-revision of the tumor difficult. CISH (chromogenic in situ hybridization) is an alternative procedure, with certain advantages, although still limited as a diagnostic tool in breast carcinomas. To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR) and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. The concordance rate between IHC and qRT-PCR results was 78.9%, and 94.6% for qRT-PCR and CISH. Intratumoral heterogeneity of HER-2 status was identified in three cases by CISH. The results of the three procedures were compared and showed a concordance rate of 83.8%; higher discordances were observed in 0 or 1+ immunostaining cases, which showed high-level amplification (15.4%) and HER-2 transcript overexpression (20%). Moreover, 2+ immunostaining cases presented nonamplified status (50%) by CISH and HER-2 downexpression (38.5%) by qRT-PCR. In general, concordance occurred between qRT-PCR and CISH results. A high concordance was observed between CISH/qRT-PCR and FISH. Comparisons with clinicopathological data revealed a significant association between HER-2 downexpression and the involvement of less than four lymph nodes (P = 0.0350). Based on these findings, qRT-PCR was more precise and reproducible than IHC. Furthermore, CISH was revealed as an alternative and useful procedure for investigating amplifications involving the HER-2 gene

Selective Inhibition and Naming Performance in Semantic Blocking, Picture-Word Interference, and Color-Word Stroop Tasks

Science.gov (United States)

Shao, Zeshu; Roelofs, Ardi; Martin, Randi C.; Meyer, Antje S.

2015-01-01

In 2 studies, we examined whether explicit distractors are necessary and sufficient to evoke selective inhibition in 3 naming tasks: the semantic blocking, picture-word interference, and color-word Stroop task. Delta plots were used to quantify the size of the interference effects as a function of reaction time (RT). Selective inhibition was…

Elu on väärt riskideski / Juta Üts

Index Scriptorium Estoniae

Üts, Juta, 1934-

2004-01-01

Tallinna Noorte Naiste ja Noorte Meeste Kristlik Ühing aitab läbi projektide "Terve Eesti laps" ja "Elu on väärt ka riskides" õpetada astma- ja suhkruhaigetele lastele toimetulekut oma haigusega. Projekte tutvustavad Tallinna NNKÜ ja NMKÜ peasekretär Katrin Ohno, Tallinna Kesklinna Lastepolikliiniku päevastatsionaari töötaja Viive Sirge ning endokrinoloog dr. Riina Shor

Assessment of brain reference genes for RT-qPCR studies in neurodegenerative diseases.

Science.gov (United States)

Rydbirk, Rasmus; Folke, Jonas; Winge, Kristian; Aznar, Susana; Pakkenberg, Bente; Brudek, Tomasz

2016-11-17

Evaluation of gene expression levels by reverse transcription quantitative real-time PCR (RT-qPCR) has for many years been the favourite approach for discovering disease-associated alterations. Normalization of results to stably expressed reference genes (RGs) is pivotal to obtain reliable results. This is especially important in relation to neurodegenerative diseases where disease-related structural changes may affect the most commonly used RGs. We analysed 15 candidate RGs in 98 brain samples from two brain regions from Alzheimer's disease (AD), Parkinson's disease (PD), Multiple System Atrophy, and Progressive Supranuclear Palsy patients. Using RefFinder, a web-based tool for evaluating RG stability, we identified the most stable RGs to be UBE2D2, CYC1, and RPL13 which we recommend for future RT-qPCR studies on human brain tissue from these patients. None of the investigated genes were affected by experimental variables such as RIN, PMI, or age. Findings were further validated by expression analyses of a target gene GSK3B, known to be affected by AD and PD. We obtained high variations in GSK3B levels when contrasting the results using different sets of common RG underlining the importance of a priori validation of RGs for RT-qPCR studies.

Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas - A biodiesel plant.

Science.gov (United States)

Karuppaiya, Palaniyandi; Yan, Xiao-Xue; Liao, Wang; Wu, Jun; Chen, Fang; Tang, Lin

2017-01-01

Physic nut (Jatropha curcas L) seed oil is a natural resource for the alternative production of fossil fuel. Seed oil production is mainly depended on seed yield, which was restricted by the low ratio of staminate flowers to pistillate flowers. Further, the mechanism of physic nut flower sex differentiation has not been fully understood yet. Quantitative Real Time-Polymerase Chain Reaction is a reliable and widely used technique to quantify the gene expression pattern in biological samples. However, for accuracy of qRT-PCR, appropriate reference gene is highly desirable to quantify the target gene level. Hence, the present study was aimed to identify the stable reference genes in staminate and pistillate flowers of J. curcas. In this study, 10 candidate reference genes were selected and evaluated for their expression stability in staminate and pistillate flowers, and their stability was validated by five different algorithms (ΔCt, BestKeeper, NormFinder, GeNorm and RefFinder). Resulting, TUB and EF found to be the two most stably expressed reference for staminate flower; while GAPDH1 and EF found to be the most stably expressed reference gene for pistillate flowers. Finally, RT-qPCR assays of target gene AGAMOUS using the identified most stable reference genes confirmed the reliability of selected reference genes in different stages of flower development. AGAMOUS gene expression levels at different stages were further proved by gene copy number analysis. Therefore, the present study provides guidance for selecting appropriate reference genes for analyzing the expression pattern of floral developmental genes in staminate and pistillate flowers of J. curcas.

Voldemar Panso preemia said kaksikvennad Priit ja Märt Pius / Tiiu Laks

Index Scriptorium Estoniae

Laks, Tiiu, 1984-

2010-01-01

Lavakunstikooli 25. lennu üliõpilased Priit ja Märt Pius pälvisid Voldemar Panso nimelise preemia. Terve kursuse esimene bakalaureuselavastus "Jumala Narride Vennaskond" esietendub 4. detsembril Tallinna Linnateatri Põrgulaval. Lavastas kursuse juhendaja Elmo Nüganen

Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR

Science.gov (United States)

2014-01-01

Background Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars. Results A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual. Conclusions The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level

A methodology for improving the SIS-RT in analyzing the traceability of the documents written in Korean language

International Nuclear Information System (INIS)

Yoo, Yeong Jae; Kim, Man Cheol; Seong, Poong Hyun

2002-01-01

Inspection is widely believed to be an effective software verification and validation (V and V) method. However, software inspection is labor-intensive. This labor-intensive nature is compounded by a view that since software inspection uses little technology, they do not fit in well with a more technology-oriented development environment. Nevertheless, software inspection is gaining in popularity. The researchers of KAIST I and C laboratory developed the software tool managing and supporting inspection tasks, named SIS-RT. SIS-RT is designed to partially automate the software inspection processes. SIS-RT supports the analyses of traceability between the spec documents. To make SIS-RT prepared for the spec document written in Korean language, certain techniques in natural language processing have been reviewed. Among those, the case grammar is most suitable for the analyses of Korean language. In this paper, the methodology for analyzing the traceability between spec documents written in Korean language will be proposed based on the case grammar

Evaluation of NASA SPoRT's Pseudo-Geostationary Lightning Mapper Products in the 2011 Spring Program

Science.gov (United States)

Stano, Geoffrey T.; Carcione, Brian; Siewert, Christopher; Kuhlman, Kristin M.

2012-01-01

NASA's Short-term Prediction Research and Transition (SPoRT) program is a contributing partner with the GOES-R Proving Ground (PG) preparing forecasters to understand and utilize the unique products that will be available in the GOES-R era. This presentation emphasizes SPoRT s actions to prepare the end user community for the Geostationary Lightning Mapper (GLM). This preparation is a collaborative effort with SPoRT's National Weather Service partners, the National Severe Storms Laboratory (NSSL), and the Hazardous Weather Testbed s Spring Program. SPoRT continues to use its effective paradigm of matching capabilities to forecast problems through collaborations with our end users and working with the developers at NSSL to create effective evaluations and visualizations. Furthermore, SPoRT continues to develop software plug-ins so that these products will be available to forecasters in their own decision support system, AWIPS and eventually AWIPS II. In 2009, the SPoRT program developed the original pseudo geostationary lightning mapper (PGLM) flash extent product to demonstrate what forecasters may see with GLM. The PGLM replaced the previous GLM product and serves as a stepping-stone until the AWG s official GLM proxy is ready. The PGLM algorithm is simple and can be applied to any ground-based total lightning network. For 2011, the PGLM used observations from four ground-based networks (North Alabama, Kennedy Space Center, Oklahoma, and Washington D.C.). While the PGLM is not a true proxy product, it is intended as a tool to train forecasters about total lightning as well as foster discussions on product visualizations and incorporating GLM-resolution data into forecast operations. The PGLM has been used in 2010 and 2011 and is likely to remain the primary lightning training tool for the GOES-R program for the near future. This presentation will emphasize the feedback received during the 2011 Spring Program. This will discuss several topics. Based on feedback

One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples

Science.gov (United States)

Mijatovic-Rustempasic, Slavica; Esona, Mathew D.; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D.

2016-01-01

Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8�

The role of magnetic resonance imaging to select patients for preoperative treatment in rectal cancer

International Nuclear Information System (INIS)

Roedel, Claus; Sauer, Rolf; Fietkau, Rainer

2009-01-01

Background: Traditionally, the decision to apply preoperative treatment for rectal cancer patients has been based on the T- and N-category. Recently, the radial distance of the tumor to the circumferential resection margin (CRM) has been identified as an important risk factor for local failure. By magnetic resonance imaging (MRI) this distance can be measured preoperatively with high reliability. Thus, selected groups have started to limit the indication for preoperative therapy to tumors extending to - or growing within 1 mm from - the mesorectal fascia (CRM+). Methods: Pros and cons of this selected approach for preoperative treatment and first clinical results are presented. Prerequisites are the availability of modern high-resolution thin-section MRI technology as well as strict quality control of MRI and surgical quality of total mesorectal excision (TME). Results: By selecting patients with CRM-positive tumors on MRI for preoperative therapy, only approximately 35% patients will require preoperative radiotherapy (RT) or radiochemotherapy (RCT). However, with histopathologic work-up of the resected specimen after primary surgery, the indication for postoperative RCT is given for a rather large percentage of patients, i.e., for pCRM+ (5-10%), intramesorectal or intramural excision (30-40%), pN+ (30-40%). Postoperative RCT, however, is significantly less effective and more toxic than preoperative RCT. A further point of concern is the assertion that patients, in whom a CRM-negative status is achieved by surgery alone, do not benefit from additional RT. Data of the Dutch TME trial and the British MRC (Medical Research Council) CR07 trial, however, suggest the reverse. Conclusion: To omit preoperative RT/RCT for CRM-negative tumors on MRI needs to be further investigated in prospective clinical trials. The German guidelines for the treatment of colorectal cancer 2008 continue to indicate preoperative RT/RCT based on the T- and N-category. (orig.)

[The role of magnetic resonance imaging to select patients for preoperative treatment in rectal cancer].

Science.gov (United States)

Rödel, Claus; Sauer, Rolf; Fietkau, Rainer

2009-08-01

Traditionally, the decision to apply preoperative treatment for rectal cancer patients has been based on the T- and N-category. Recently, the radial distance of the tumor to the circumferential resection margin (CRM) has been identified as an important risk factor for local failure. By magnetic resonance imaging (MRI) this distance can be measured preoperatively with high reliability. Thus, selected groups have started to limit the indication for preoperative therapy to tumors extending to - or growing within 1 mm from - the mesorectal fascia (CRM+). Pros and cons of this selected approach for preoperative treatment and first clinical results are presented. Prerequisites are the availability of modern high-resolution thin-section MRI technology as well as strict quality control of MRI and surgical quality of total mesorectal excision (TME). By selecting patients with CRM-positive tumors on MRI for preoperative therapy, only approximately 35% patients will require preoperative radiotherapy (RT) or radiochemotherapy (RCT). However, with histopathologic work-up of the resected specimen after primary surgery, the indication for postoperative RCT is given for a rather large percentage of patients, i.e., for pCRM+ (5-10%), intramesorectal or intramural excision (30-40%), pN+ (30-40%). Postoperative RCT, however, is significantly less effective and more toxic than preoperative RCT. A further point of concern is the assertion that patients, in whom a CRM-negative status is achieved by surgery alone, do not benefit from additional RT. Data of the Dutch TME trial and the British MRC (Medical Research Council) CR07 trial, however, suggest the reverse. To omit preoperative RT/RCT for CRM-negative tumors on MRI needs to be further investigated in prospective clinical trials. The German guidelines for the treatment of colorectal cancer 2008 continue to indicate preoperative RT/RCT based on the T- and N-category.

Detection of Cucurbit chlorotic yellows virus from Bemisia tabaci captured on sticky traps using reverse transcription loop-mediated isothermal amplification (RT-LAMP) and simple template preparation.

Science.gov (United States)

Okuda, Mitsuru; Okuda, Shiori; Iwai, Hisashi

2015-09-01

Cucurbit chlorotic yellows virus (CCYV) of the genus Crinivirus within the family Closteroviridae is an emerging infectious agent of cucurbits leading to severe disease and significant economic losses. Effective detection and identification methods for this virus are urgently required. In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect CCYV from its vector Bemisia tabaci. LAMP primer sets to detect CCYV were evaluated for their sensitivity and specificity, and a primer set designed from the HSP70h gene with corresponding loop primers were selected. The RT-LAMP assay was applied to detect CCYV from viruliferous B. tabaci trapped on sticky traps. A simple extraction procedure using RNAsecure™ was developed for template preparation. CCYV was detected in all of the B. tabaci 0, 1, 7 and 14 days after they were trapped. Although the rise of turbidity was delayed in reactions using RNA from B. tabaci trapped for 7 and 14 days compared with those from 0 and 1 day, the DNA amplification was sufficient to detect CCYV in all of the samples. These findings therefore present a simple template preparation method and an effective RT-LAMP assay, which can be easily and rapidly performed to monitor CCYV-viruliferous B. tabaci in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Selecting PCR for the Diagnosis of Intestinal Parasitosis

DEFF Research Database (Denmark)

Hartmeyer, G. N.; Hoegh, S. V.; Skov, M. N.

2017-01-01

Microscopy of stool samples is a labour-intensive and inaccurate technique for detection of intestinal parasites causing diarrhoea and replacement by PCR is attractive. Almost all cases of diarrhoea induced by parasites over a nine-year period in our laboratory were due to Giardia lamblia......, Cryptosporidium species, or Entamoeba histolytica detected by microscopy. We evaluated and selected in-house singleplex real-time PCR (RT-PCR) assays for these pathogens in 99 stool samples from patients suspected of having intestinal parasitosis tested by microscopy. The strategy included a genus-specific PCR...... assay for C. parvum and C. hominis, with subsequent identification by a PCR that distinguishes between the two species. G. lamblia was detected in five and C. parvum in one out of 68 microscopy-negative samples. The performance of the in-house RT-PCR assays was compared to three commercially available...

Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

Science.gov (United States)

Lehermeier, Christina; Teyssèdre, Simon; Schön, Chris-Carolin

2017-12-01

A crucial step in plant breeding is the selection and combination of parents to form new crosses. Genome-based prediction guides the selection of high-performing parental lines in many crop breeding programs which ensures a high mean performance of progeny. To warrant maximum selection progress, a new cross should also provide a large progeny variance. The usefulness concept as measure of the gain that can be obtained from a specific cross accounts for variation in progeny variance. Here, it is shown that genetic gain can be considerably increased when crosses are selected based on their genomic usefulness criterion compared to selection based on mean genomic estimated breeding values. An efficient and improved method to predict the genetic variance of a cross based on Markov chain Monte Carlo samples of marker effects from a whole-genome regression model is suggested. In simulations representing selection procedures in crop breeding programs, the performance of this novel approach is compared with existing methods, like selection based on mean genomic estimated breeding values and optimal haploid values. In all cases, higher genetic gain was obtained compared with previously suggested methods. When 1% of progenies per cross were selected, the genetic gain based on the estimated usefulness criterion increased by 0.14 genetic standard deviation compared to a selection based on mean genomic estimated breeding values. Analytical derivations of the progeny genotypic variance-covariance matrix based on parental genotypes and genetic map information make simulations of progeny dispensable, and allow fast implementation in large-scale breeding programs. Copyright © 2017 by the Genetics Society of America.

Läheneb Vikerkaare 75. aastapäev / Märt Väljataga

Index Scriptorium Estoniae

Väljataga, Märt, 1965-

1997-01-01

Vastukaja : Haug, Toomas. Kultuurilooline õppetund peatoimetaja Väljatagale. // Eesti Ekspress (1997) 18. apr., lk. B6. (Poleemika); Väljataga, Märt. Vikerkaart nähti juba Sumeris!. // Eesti Ekspress (1997) 25. apr., lk. B7; Haug, Toomas. Ei soovi vasikaga võidu joosta. // Eesti Ekspress (1997) 2. mai, lk. B7

Mesing Kirke:Opmålinger og undersøgelser af Mesing Kirke udført 1978

OpenAIRE

Bock, Lars Nicolai; Longmose Jakobsen, Bendt; Nielsen, Ole

1989-01-01

Detaljerede opmålinger og bygningsarkæologiske undersøgelser udført i Mesing Kirke i efteråret 1978. Arbejdet er udført i samarbejde med Bendt Longmose Jakobsen og Ole Nielsen. Det samlede arbejde indgår i Nationalmuseets værk Danmarks Kirker, XVI, bind 6 (1988-89) Side: 3123 - 3147. Afsnittet om Mesing Kirke er skrevet og redigeret af dr. arkitekt maa Kjeld de Fine Licht

Simultaneous VENTANA IHC and RT-PCR testing of ALK status in Chinese non-small cell lung cancer patients and response to crizotinib.

Science.gov (United States)

Xu, Chun-Wei; Wang, Wen-Xian; Chen, Yan-Ping; Chen, Yu; Liu, Wei; Zhong, Li-Hua; Chen, Fang-Fang; Zhuang, Wu; Song, Zheng-Bo; Chen, Xiao-Hui; Huang, Yun-Jian; Guan, Yan-Fang; Yi, Xin; Lv, Tang-Feng; Zhu, Wei-Feng; Lu, Jian-Ping; Wang, Xiao-Jiang; Shi, Yi; Lin, Xian-Dong; Chen, Gang; Song, Yong

2018-04-11

ALK rearrangement-advanced NSCLC patients respond to crizotinib. ALK rearrangement is currently determined with RT-PCR. VENTANA IHC is a standard method to identify ALK protein overexpression in NSCLC; however, VENTANA IHC has rarely been used to determine the response to crizotinib in Chinese patients with NSCLC and ALK overexpression. To better clarify the clinical implication of VENTANA IHC to detect ALK rearrangements, we conducted this study to analyze VENTANA IHC and RT-PCR in a large cohort of Chinese patients with NSCLC undergoing screening for ALK rearrangements. A total of 1720 patients with NSCLC who had ALK rearrangements detected by VENTANA IHC and/or RT-PCR were included in this analysis. We compared the efficacy and survival of ALK-positive patients detected by VENTANA IHC and RT-PCR. We used NGS to identify patients in whom the two methods were inconsistent. Among 1720 patients, 187 (10.87%) were shown to be ALK-positive by VENTANA IHC and/or RT-PCR, and 66 received crizotinib treatment. We identified 10.27% (172/1674) of patients as ALK-positive by the VENTANA IHC method, and 12.73% (41/322) of patients had ALK rearrangements by the RT-PCR method. Twenty-nine of 276 (10.51%) ALK-positive patients were simultaneously analyzed using VENTANA IHC and RT-PCR. The overall response rates were 65.90% (29/44) by VENTANA IHC and 55.88% (19/34) by RT-PCR. The disease control rates were 86.36% (38/44) by VENTANA IHC and 76.47% (26/34) by RT-PCR. In contrast, the median progression-free survival for VENTANA IHC and RT-PCR was 8.5 and 9.2 months, respectively. The VENTANA IHC and RT-PCR results obtained for 6 of 17 ALK-positive patients were inconsistent based on NGS; specifically, 4 patients had EML4-ALK fusions, 2 patients had non EML4-ALK fusions, 1 patient had a KCL1-ALK fusion, and one patient had a FBXO36-ALK fusion. VENTANA IHC is a reliable and rapid screening tool used in routine pathologic laboratories for the identification of suitable candidates for

Diagnostic evaluation of a multiplexed RT-PCR microsphere array assay for the detection of foot-and-mouth disease virus and look-alike disease viruses

Energy Technology Data Exchange (ETDEWEB)

Hindson, B J; Reid, S M; Baker, B R; Ebert, K; Ferris, N P; Bentley Tammero, L F; Lenhoff, R J; Naraghi-Arani, P; Vitalis, E A; Slezak, T R; Hullinger, P J; King, D P

2007-07-26

A high-throughput multiplexed assay was developed for the differential laboratory diagnosis of foot-and-mouth disease virus (FMDV) from viruses which cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses using multiplexed reverse transcription PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the seventeen primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR was evaluated using 287 field samples, including 248 (true positive n= 213, true negative n=34) from suspect cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true negative samples collected from healthy animals. The mRT-PCR assay results were compared with two singleplex rRT-PCR assays, using virus isolation with antigen-ELISA as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% [95% C.I. 89.8-96.4%], compared to 98.1% [95% C.I. 95.3-99.3%] for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n=2) and bovine viral diarrhea virus (n=2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized using focused single-target rRT-PCR assays.

A Novel Leu92 Mutant of HIV-1 Reverse Transcriptase with a Selective Deficiency in Strand Transfer Causes a Loss of Viral Replication.

Science.gov (United States)

Herzig, Eytan; Voronin, Nickolay; Kucherenko, Nataly; Hizi, Amnon

2015-08-01

The process of reverse transcription (RTN) in retroviruses is essential to the viral life cycle. This key process is catalyzed exclusively by the viral reverse transcriptase (RT) that copies the viral RNA into DNA by its DNA polymerase activity, while concomitantly removing the original RNA template by its RNase H activity. During RTN, the combination between DNA synthesis and RNA hydrolysis leads to strand transfers (or template switches) that are critical for the completion of RTN. The balance between these RT-driven activities was considered to be the sole reason for strand transfers. Nevertheless, we show here that a specific mutation in HIV-1 RT (L92P) that does not affect the DNA polymerase and RNase H activities abolishes strand transfer. There is also a good correlation between this complete loss of the RT's strand transfer to the loss of the DNA clamp activity of the RT, discovered recently by us. This finding indicates a mechanistic linkage between these two functions and that they are both direct and unique functions of the RT (apart from DNA synthesis and RNA degradation). Furthermore, when the RT's L92P mutant was introduced into an infectious HIV-1 clone, it lost viral replication, due to inefficient intracellular strand transfers during RTN, thus supporting the in vitro data. As far as we know, this is the first report on RT mutants that specifically and directly impair RT-associated strand transfers. Therefore, targeting residue Leu92 may be helpful in selectively blocking this RT activity and consequently HIV-1 infectivity and pathogenesis. Reverse transcription in retroviruses is essential for the viral life cycle. This multistep process is catalyzed by viral reverse transcriptase, which copies the viral RNA into DNA by its DNA polymerase activity (while concomitantly removing the RNA template by its RNase H activity). The combination and balance between synthesis and hydrolysis lead to strand transfers that are critical for reverse transcription

NASA SPoRT Initialization Datasets for Local Model Runs in the Environmental Modeling System

Science.gov (United States)

Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Carcione, Brian; Wood, Lance; Maloney, Joseph; Estupinan, Jeral; Medlin, Jeffrey M.; Blottman, Peter; Rozumalski, Robert A.

2011-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its National Weather Service (NWS) partners that can be used to initialize local model runs within the Weather Research and Forecasting (WRF) Environmental Modeling System (EMS). These real-time datasets consist of surface-based information updated at least once per day, and produced in a composite or gridded product that is easily incorporated into the WRF EMS. The primary goal for making these NASA datasets available to the WRF EMS community is to provide timely and high-quality information at a spatial resolution comparable to that used in the local model configurations (i.e., convection-allowing scales). The current suite of SPoRT products supported in the WRF EMS include a Sea Surface Temperature (SST) composite, a Great Lakes sea-ice extent, a Greenness Vegetation Fraction (GVF) composite, and Land Information System (LIS) gridded output. The SPoRT SST composite is a blend of primarily the Moderate Resolution Imaging Spectroradiometer (MODIS) infrared and Advanced Microwave Scanning Radiometer for Earth Observing System data for non-precipitation coverage over the oceans at 2-km resolution. The composite includes a special lake surface temperature analysis over the Great Lakes using contributions from the Remote Sensing Systems temperature data. The Great Lakes Environmental Research Laboratory Ice Percentage product is used to create a sea-ice mask in the SPoRT SST composite. The sea-ice mask is produced daily (in-season) at 1.8-km resolution and identifies ice percentage from 0 100% in 10% increments, with values above 90% flagged as ice.

RT-qPCR work-flow for single-cell data analysis

Czech Academy of Sciences Publication Activity Database

Stahlberg, A.; Rusňáková, Vendula; Forootan, A.; Anděrová, Miroslava; Kubista, Mikael

2013-01-01

Roč. 59, č. 1 (2013), s. 80-88 ISSN 1046-2023 R&D Projects: GA MŠk(CZ) ME10052; GA ČR GAP303/10/1338 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:68378041 Keywords : RT-qPCR * Single-cell biology * Single-cell data analysis Subject RIV: EB - Genetics ; Molecular Biology; FH - Neurology (UEM-P) Impact factor: 3.221, year: 2013

Identification of Suitable Endogenous Normalizers for qRT- PCR Analysis of Plasma microRNA Expression in Essential Hypertension

Science.gov (United States)

Solayman, Mohamed Hassan M.; Langaee, Taimour; Patel, Archanakumari; El-Wakeel, Lamia; El-Hamamsy, Manal; Badary, Osama; Johnson, Julie A.

2016-01-01

Circulating microRNAs (miRNAs) are promising biomarkers for many diseases. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a gold standard for miRNA expression profiling that requires proper data normalization. Since there is no universal normalizer, it is recommended to evaluate normalizers under every experimental condition. This study describes the identification of suitable endogenous normalizer(s) (ENs) for plasma miRNA expression in essential hypertension. Expression levels of 5 candidate ENs and 2 plasma quality markers were determined by qRT-PCR in plasma samples from 18 hypertensive patients and 10 healthy controls. NormFinder, GeNorm, and DataAssist software programs were used to select the best EN(s). Expression levels of the 5 candidate ENs were also analyzed in urine samples from hypertensive patients and compared to the plasma samples of the hypertensive patients. Among the analyzed candidates, hsa-miR-92a-3p was identified as the best EN, and hsa-miR-21-5p and hsa-miR-16-5p as next best. Moreover, hsa-miR-92a-3p showed the most consistent expression between plasma and urine In conclusion, this study showed that hsa-miR-92a-3p, hsa-miR-21-5p, and hsa-miR-16-5p may be used as normalizers for plasma miRNA expression data in essential hypertension studies. PMID:26798072

Romantiline mässaja või irooniline intellektuaal? / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

2005-01-01

Arvustus: Camus, Albert. Pagendus ja kuningriik : kogutud lühiproosa / prantsuse keelest tõlkinud Triinu Tamm, Krista Vogelberg, Tanel Lepsoo, Henno Rajandi. Tallinn : Varrak, 2004. Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 200-202, pealk. Must päike ja igaviku helk

Mixed signals: The effect of conflicting reward- and goal-driven biases on selective attention

OpenAIRE

Preciado, Daniel; Munneke, Jaap; Theeuwes, Jan

2017-01-01

Attentional selection depends on the interaction between exogenous (stimulus-driven), endogenous (goal-driven), and selection history (experience-driven) factors. While endogenous and exogenous biases have been widely investigated, less is known about their interplay with value-driven attention. The present study investigated the interaction between reward-history and goal-driven biases on perceptual sensitivity (d?) and response time (RT) in a modified cueing paradigm presenting two coloured...

Comparison of ELISA and dual stage real time RT-PCR to differentiate Sabin like and non-Sabin like poliovirus isolates.

Science.gov (United States)

Kaundal, Nirmal; Sarkate, Purva; Prakash, Charu; Rishi, Narayan

2017-06-01

Environmental surveillance of polioviruses has been used as an important tool in monitoring circulation of wild polioviruses and/or Vaccine derived polioviruses in sewage samples. It is important to distinguish Sabin like isolates from non-Sabin like; ELISA & dual stage real time RT-PCR have been used for the same. Current study was carried out on sewage isolates to compare ELISA & RT-PCR with sequencing to distinguish Sabin like from non-Sabin like. Out of 468 sewage specimens, 91 (19.44%) were non-polio enteroviruses positive and 377 (80.56%) were polio positive by virus isolation method. A total of 488 polio virus isolates were detected by L20B and RD route which were further subjected to ELISA and RT-PCR. The results were compared with sequencing. On comparison, the specificity of ELISA was only 66.67% in spite of very low sensitivity (3.43%). The sensitivity of RT-PCR was 97.71% which makes it a good primary screening test for detection of non-Sabin like viruses. However, the specificity was only 33.33%. RT-PCR appears to be a sensitive tool for detecting non-Sabin like viruses however; the isolates which are non-Sabin like by RT-PCR may not necessarily be mutated viruses. ELISA cannot be used for differentiation of Sabin likes from non-Sabin likes due to low sensitivity.

Strategy for the maximization of clinically relevant information from hepatitis C virus, RT-PCR quantification.

LENUS (Irish Health Repository)

Levis, J

2012-02-03

BACKGROUND: The increasing clinical application of viral load assays for monitoring viral infections has been an incentive for the development of standardized tests for the hepatitis C virus. OBJECTIVE: To develop a simple model for the prediction of baseline viral load in individuals infected with the hepatitis C virus. METHODOLOGY: Viral load quantification of each patient\\'s first sample was assessed by RT-PCR-ELISA using the Roche MONITOR assay in triplicate. Genotype of the infecting virus was identified by reverse line probe hybridization, using amplicons resulting from the qualitative HCV Roche AMPLICOR assay. RESULTS: Retrospective evaluation of first quantitative values suggested that 82.4% (n=168\\/204) of individuals had a viral load between 4.3 and 6.7 log(10) viral copies per ml. A few patients (3.4%; n=7\\/204) have a serum viremia less than the lower limit of the linear range of the RT-PCR assay. Subsequent, prospective evaluation of hepatitis C viral load of all new patients using a model based on the dynamic range of viral load in the retrospective group correctly predicted the dynamic range in 75.9% (n=33\\/54). CONCLUSION: The dynamic range of hepatitis C viremia extends beyond the linear range of the Roche MONITOR assay. Accurate determination of serum viremia is substantially improved by dilution of specimens prior to quantification.

Searching for Roots. Pärt: Symphony No. 1, "Polyphonic" / Guy S. Rickards

Index Scriptorium Estoniae

Rickards, Guy S.

1997-01-01

Uuest heliplaadist "Searching for Roots. Pärt: Symphony No. 1, "Polyphonic". Nekrolog, Op. 3; Tubin: Symphony No. 11; Tüür: Searching for Roots. Insula deserta. Zeitraum. Royal Stockholm Philharmonic Orchestra / Paavo Järvi. Virgin Classics VC5 45212-2 (72 min.:DDD)

Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

Directory of Open Access Journals (Sweden)

Aditi Gupta

2016-03-01

Full Text Available Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1 using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing

Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

Directory of Open Access Journals (Sweden)

Soares Fernando A

2009-03-01

Full Text Available Abstract Background HER-2 gene testing has become an integral part of breast cancer patient diagnosis. The most commonly used assay in the clinical setting for evaluating HER-2 status is immunohistochemistry (IHC and fluorescence in situ hybridization (FISH. These procedures permit correlation between HER-2 expression and morphological features. However, FISH signals are labile and fade over time, making post-revision of the tumor difficult. CISH (chromogenic in situ hybridization is an alternative procedure, with certain advantages, although still limited as a diagnostic tool in breast carcinomas. Methods To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. Results The concordance rate between IHC and qRT-PCR results was 78.9%, and 94.6% for qRT-PCR and CISH. Intratumoral heterogeneity of HER-2 status was identified in three cases by CISH. The results of the three procedures were compared and showed a concordance rate of 83.8%; higher discordances were observed in 0 or 1+ immunostaining cases, which showed high-level amplification (15.4% and HER-2 transcript overexpression (20%. Moreover, 2+ immunostaining cases presented nonamplified status (50% by CISH and HER-2 downexpression (38.5% by qRT-PCR. In general, concordance occurred between qRT-PCR and CISH results. A high concordance was observed between CISH/qRT-PCR and FISH. Comparisons with clinicopathological data revealed a significant association between HER-2 downexpression and the involvement of less than four lymph nodes (P = 0.0350. Conclusion Based on these findings, qRT-PCR was more precise and reproducible than IHC. Furthermore, CISH was revealed as an alternative and useful procedure for investigating amplifications involving the HER-2 gene.

Use of fluorescent-metal intensifying screens with RT-type films for X-ray radiography using pulse devices

International Nuclear Information System (INIS)

Morgovskij, L.Ya.; Khakim'yanov, R.R.

1985-01-01

A study was made on characteristics of combination of fluorescent-metal Kyokko SMP-308 (Japan) and RCF (Agfa-Gevert) screens with domestic X-ray RT-1, RT-2, RT-5 films. Pulse X-ray MIRA-3D and NORA devices at 200 kV voltage amplitude in X-ray tube were used as radiation source. Testing was conducted for steel samples of 5-40 mm thickness. Comparative exposures for various film combinations with fluorescent-metal screens, fluorescent VP-2 screens and lead foils of 27 μm thickness were determined at that. It is shown that fluorescent-metal screens can be successfully applied with domestic X-ray technical films. They enable to decrease exposure by one order with insignificant deterioration of sensitivity. It is important for testing of pipeline welds

A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries.

Science.gov (United States)

Dobhal, Shefali; Olson, Jennifer D; Arif, Mohammad; Garcia Suarez, Johnny A; Ochoa-Corona, Francisco M

2016-06-01

Rose rosette disease is a disorder associated with infection by Rose rosette virus (RRV), a pathogen of roses that causes devastating effects on most garden cultivated varieties, and the wild invasive rose especially Rosa multiflora. Reliable and sensitive detection of this disease in early phases is needed to implement proper control measures. This study assesses a single primer-set based detection method for RRV and demonstrates its application in three different chemistries: Endpoint RT-PCR, TaqMan-quantitative RT-PCR (RT-qPCR) and SYBR Green RT-qPCR with High Resolution Melting analyses. A primer set (RRV2F/2R) was designed from consensus sequences of the nucleocapsid protein gene p3 located in the RNA 3 region of RRV. The specificity of primer set RRV2F/2R was validated in silico against published GenBank sequences and in-vitro against infected plant samples and an exclusivity panel of near-neighbor and other viruses that commonly infect Rosa spp. The developed assay is sensitive with a detection limit of 1fg from infected plant tissue. Thirty rose samples from 8 different states of the United States were tested using the developed methods. The developed methods are sensitive and reliable, and can be used by diagnostic laboratories for routine testing and disease management decisions. Copyright © 2016 Elsevier B.V. All rights reserved.

Hydrogen-bond-driven electrophilic activation for selectivity control: scope and limitations of fluorous alcohol-promoted selective formation of 1,2-disubstituted benzimidazoles and mechanistic insight for rationale of selectivity.

Science.gov (United States)

Chebolu, Rajesh; Kommi, Damodara N; Kumar, Dinesh; Bollineni, Narendra; Chakraborti, Asit K

2012-11-16

Hydrogen-bond-driven electrophilic activation for selectivity control during competitive formation of 1,2-disubstituted and 2-substituted benzimidazoles from o-phenylenediamine and aldehydes is reported. The fluorous alcohols trifluoroethanol and hexafluoro-2-propanol efficiently promote the cyclocondensation of o-phenylenediamine with aldehydes to afford selectively the 1,2-disubstituted benzimidazoles at rt in short times. A mechanistic insight is invoked by NMR, mass spectrometry, and chemical studies to rationalize the selectivity. The ability of the fluorous alcohols in promoting the reaction and controlling the selectivity can be envisaged from their better hydrogen bond donor (HBD) abilities compared to that of the other organic solvents as well as of water. Due to the better HBD values, the fluorous alcohols efficiently promote the initial bisimine formation by electrophilic activation of the aldehyde carbonyl. Subsequently the hydrogen-bond-mediated activation of the in situ-formed bisimine triggers the rearrangement via 1,3-hydride shift to form the 1,2-disubstituted benzimidazoles.

Radiotherapy did not increase thyroid cancer risk among women with breast cancer: A nationwide population-based cohort study.

Science.gov (United States)

Sun, Li-Min; Lin, Cheng-Li; Liang, Ji-An; Huang, Wen-Sheng; Kao, Chia-Hung

2015-12-15

The aim of this study was to evaluate whether an increased risk of thyroid cancer exists among women with breast cancer in Taiwan, particularly among those receiving RT. We used data from the National Health Insurance system of Taiwan for the investigation. The breast cancer cohort contained 55,318 women (including 28,187 who received RT and 27,131 who received no RT), each of whom was randomly frequency matched according to age and index year with three women without breast cancer from the general population. Cox's proportion hazards regression analysis was conducted to estimate the effects of breast cancer with or without RT treatment on subsequent thyroid cancer risk. We found that women with breast cancer exhibited a significantly higher risk of subsequent thyroid cancer (adjusted hazard ratio [aHR] = 1.98, 95% confidence interval [CI] = 1.60-2.44). The two groups (with or without RT) in the breast cancer cohort exhibited significantly increased risks. However, in the breast cancer cohort, the risk of thyroid cancer among women who received RT was not significantly higher than that of women who received no RT (aHR = 1.28, 95% CI = 0.90-1.83). Stratified analysis according to age revealed that only younger women with breast cancer (20-54 y) had a significantly higher risk of developing thyroid cancer. This study determined that Taiwanese women with breast cancer had a higher risk of developing thyroid cancer; however, RT seems to not play a crucial role in this possible relationship. © 2015 UICC.

Selection of progenitors for increase in oil content in soybean

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Josiane Isabela da Silva Rodrigues

Full Text Available ABSTRACT The low genetic diversity brings limitation to breeding, because genetically similar genotypes share alleles in common, causing little complementarity and low vigor due to the low levels of heterozygosity in crosses. The objective of this work was to analyze the oil content and genetic diversity of soybean genotypes (Glycine max (L. Merrill based on QTL regions of this trait for choice of progenitors for increase in oil content. Twenty-two genotypes with wide variation in oil content, including cultivars with high oil contents, were cultivated in different Brazilian conditions and the oil content of the grains was quantified by infrared spectrometry. Microsatellite markers selected based on QTL regions for oil content in soybean were analyzed to estimate the genetic diversity. In these studies, a wide variation in oil content (17.28-23.01% and a reasonable diversity among the genotypes were observed, being PI181544 the most divergent genotype, followed by Suprema. The genotypes PI371610/Suprema and Suprema/CD01RR8384 showed genetic distance and higher oil contents in the grains, while the cultivars Suprema and CD01RR8384 had the highest oil contents and proved to be little genetically related. These genotypes are promising progenitors for selection of high oil content in soybean.

Selma Lagerlöf kui ülima õiguse eestkostja / Kärt Hellerma

Index Scriptorium Estoniae

Hellerma, Kärt, 1956-

1998-01-01

Arvustus: Lagerlöf, Selma. Portugali keiser; Surmakutsar; Liljecrona kodu / tlk. Tõnu Arnover. Tallinn : Eesti Raamat, 1998. (Nobeli laureaat). Ilmunud ka kogumikus: Hellerma, Kärt. Kohanenud kirjandus : valik kirjanduskriitikat 1987-2006. Eesti Keele Sihtasutus : Tallinn, 2006. Lk. 155-157, pealk. Ülima õiguse eestkostja

The AMI speaker diarization system for NIST RT06s meeting data

NARCIS (Netherlands)

Leeuwen, D.A. van; Huijbregts, Marijn

2006-01-01

We describe the systems submitted to the NIST RT06s evaluation for the Speech Activity Detection (SAD) and Speaker Diarization (SPKR) tasks. For speech activity detection, a new analysis methodology is presented that generalizes the Detection Erorr Tradeoff analysis commonly used in speaker

The AMI speaker diarization system for NIST RT06s meeting data

NARCIS (Netherlands)

van Leeuwen, David A.; Huijbregts, M.A.H.

2007-01-01

We describe the systems submitted to the NIST RT06s evaluation for the Speech Activity Detection (SAD) and Speaker Diarization (SPKR) tasks. For speech activity detection, a new analysis methodology is presented that generalizes the Detection Erorr Tradeoff analysis commonly used in speaker detection

One-step cross-genogroup multiplex RT-qPCR with an internal control system for the detection of infectious pancreatic necrosis virus (IPNV).

Science.gov (United States)

Hoferer, Marc; Braun, Anne; Skrypski, Julia; Bock, Sabine; Thalheim, Sabine; Sting, Reinhard

2017-09-01

Infectious pancreatic necrosis virus (IPNV) causes great losses in fish hatcheries world-wide. The detection of IPNV can be challenging in certain circumstances, particularly due to low viral load and the genetic variability of this RNA virus. For the first time, this project created a quantitative triplex real-time reverse transcription PCR (RT-qPCR), including an endogenous control system, for specific, sensitive and rapid detection of IPNV in routine diagnostics. Multiple sequence alignment of 46 nucleotide sequences of the segment A genome obtained from the NCBI database allowed the design of two RT-qPCR systems covering the IPNV genogroup 1 and genogroups 2-5, respectively. The completed triplex RT-qPCR including a salmonid-specific endogenous control showed high specificity and an analytical sensitivity of 20-40 oligonucleotide copies. Testing of dilution series of virus-loaded cell culture suspensions proved equality of the triplex RT-qPCR with virus detection in cell culture and a higher sensitivity than conventional RT-PCR in field samples. In comparative studies of a total of 77 field samples tested, 51 showed identical positive and 19 identical negative results in cell culture and the triplex RT-qPCR. However, seven other samples yielded positive results in the triplex RT-qPCR, but negative results in cell culture. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of ALK gene rearrangement in central nervous system metastases of non-small-cell lung cancer using two-step RT-PCR technique.

Science.gov (United States)

Nicoś, M; Krawczyk, P; Wojas-Krawczyk, K; Bożyk, A; Jarosz, B; Sawicki, M; Trojanowski, T; Milanowski, J

2017-12-01

RT-PCR technique has showed a promising value as pre-screening method for detection of mRNA containing abnormal ALK sequences, but its sensitivity and specificity is still discussable. Previously, we determined the incidence of ALK rearrangement in CNS metastases of NSCLC using IHC and FISH methods. We evaluated ALK gene rearrangement using two-step RT-PCR method with EML4-ALK Fusion Gene Detection Kit (Entrogen, USA). The studied group included 145 patients (45 females, 100 males) with CNS metastases of NSCLC and was heterogeneous in terms of histology and smoking status. 21% of CNS metastases of NSCLC (30/145) showed presence of mRNA containing abnormal ALK sequences. FISH and IHC tests confirmed the presence of ALK gene rearrangement and expression of ALK abnormal protein in seven patients with positive result of RT-PCR analysis (4.8% of all patients, 20% of RT-PCR positive patients). RT-PCR method compared to FISH analysis achieved 100% of sensitivity and only 82.7% of specificity. IHC method compared to FISH method indicated 100% of sensitivity and 97.8% of specificity. In comparison to IHC, RT-PCR showed identical sensitivity with high number of false positive results. Utility of RT-PCR technique in screening of ALK abnormalities and in qualification patients for molecularly targeted therapies needs further validation.

Selection of scFvs specific for the HepG2 cell line using ribosome ...

Indian Academy of Sciences (India)

Madhsudhan

the important advantage of requiring no prior knowledge of ... were amplified separately by RT-PCR, and an anti-HepG2 VH/k chain ribosome display library was constructed ..... Engert A, Hudson P R and Power B E 2007 Selection of human.

Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

Science.gov (United States)

Case, Jonathan L.; Lafontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its NOAA/National Weather Service (NWS) partners that can initialize specific fields for local model runs within the NOAA/NWS Science and Training Resource Center Environmental Modeling System (EMS). The suite of SPoRT products for use in the EMS consists of a Sea Surface Temperature (SST) composite that includes a Lake Surface Temperature (LST) analysis over the Great Lakes, a Great Lakes sea-ice extent within the SST composite, a real-time Green Vegetation Fraction (GVF) composite, and NASA Land Information System (LIS) gridded output. This paper and companion poster describe each dataset and provide recent upgrades made to the SST, Great Lakes LST, GVF composites, and the real-time LIS runs.

Lethal outcome after pelvic salvage radiotherapy in a patient with prostate cancer due to increased radiosensitivity. Case report and literature review

International Nuclear Information System (INIS)

Fahrig, Antje; Koch, T.; Lenhart, M.; Rieckmann, P.; Fietkau, R.; Distel, Luitpold; Schuster, B.

2018-01-01

In general, late side effects after salvage radiotherapy (RT) for prostate cancer are below 10%. Patients with impaired DNA repair ability and genetic instability can have significantly increased reactions after RT. We present a patient who experienced severe side effects after additive RT for prostate cancer and died from the complications 25 months after RT. Imaging (MR) is shown as well as three-color fluorescence in situ hybridization. The blood sample testing revealed that radiosensitivity was increased by 35-55%. We undertook a review of the literature to give an overview over the tests established that are currently considered useful. This case highlights that the identification of patients with increased radiosensitivity is an important task in radiation protection. Groups of patients who should be screened have to be found and corresponding research facilities have to be set up. (orig.) [de

RT-CaCCO process: an improved CaCCO process for rice straw by its incorporation with a step of lime pretreatment at room temperature.

Science.gov (United States)

Shiroma, Riki; Park, Jeung-yil; Al-Haq, Muhammad Imran; Arakane, Mitsuhiro; Ike, Masakazu; Tokuyasu, Ken

2011-02-01

We improved the CaCCO process for rice straw by its incorporation with a step of lime pretreatment at room temperature (RT). We firstly optimized the RT-lime pretreatment for the lignocellulosic part. When the ratio of lime/dry-biomass was 0.2 (w/w), the RT lime-pretreatment for 7-d resulted in an effect on the enzymatic saccharification of cellulose and xylan equivalent to that of the pretreatment at 120°C for 1h. Sucrose, starch and β-1,3-1,4-glucan, which could be often detected in rice straw, were mostly stable under the RT-lime pretreatment condition. Then, the pretreatment condition in the conventional CaCCO process was modified by the adaptation of the optimized RT lime-pretreatment, resulting in significantly better carbohydrate recoveries via enzymatic saccharification than those of the CaCCO process (120°C for 1 h). Thus, the improved CaCCO process (the RT-CaCCO process) could preserve/pretreat the feedstock at RT in a wet form with minimum loss of carbohydrates. Copyright © 2010 Elsevier Ltd. All rights reserved.

High sensitive RNA detection by one-step RT-PCR using the genetically engineered variant of DNA polymerase with reverse transcriptase activity from hyperthermophilies.

Science.gov (United States)

Okano, Hiroyuki; Baba, Misato; Kawato, Katsuhiro; Hidese, Ryota; Yanagihara, Itaru; Kojima, Kenji; Takita, Teisuke; Fujiwara, Shinsuke; Yasukawa, Kiyoshi

2018-03-01

One-step RT-PCR has not been widely used even though some thermostable DNA polymerases with reverse transcriptase (RT) activity were developed from bacterial and archaeal polymerases, which is owing to low cDNA synthesis activity from RNA. In the present study, we developed highly-sensitive one-step RT-PCR using the single variant of family A DNA polymerase with RT activity, K4pol L329A (L329A), from the hyperthermophilic bacterium Thermotoga petrophila K4 or the 16-tuple variant of family B DNA polymerase with RT activity, RTX, from the hyperthermophilic archaeon Thermococcus kodakarensis. Optimization of reaction condition revealed that the activities for cDNA synthesis and PCR of K4pol L329A and RTX were highly affected by the concentrations of MgCl 2 and Mn(OCOCH 3 ) 2 as well as those of K4pol L329A or RTX. Under the optimized condition, 300 copies/μl of target RNA in 10 μl reaction volumes were successfully detected by the one-step RT-PCR with K4pol L329A or RTX, which was almost equally sensitive enough compared with the current RT-PCR condition using retroviral RT and thermostable DNA polymerase. Considering that K4pol L329A and RTX are stable even at 90-100°C, our results suggest that the one-step RT-PCR with K4pol L329A or RTX is more advantageous than the current one. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Localisation of Abundant and Organ-Specific Genes Expressed in Rosa hybrida Leaves and Flower Buds by Direct In Situ RT-PCR

Directory of Open Access Journals (Sweden)

Agata Jedrzejuk

2012-01-01

Full Text Available In situ PCR is a technique that allows specific nucleic acid sequences to be detected in individual cells and tissues. In situ PCR and IS-RT-PCR are elegant techniques that can increase both sensitivity and throughput, but they are, at best, only semiquantitative; therefore, it is desirable first to ascertain the expression pattern by conventional means to establish the suitable conditions for each probe. In plants, in situ RT-PCR is widely used in the expression localisation of specific genes, including MADS-box and other function-specific genes or housekeeping genes in floral buds and other organs. This method is especially useful in small organs or during early developmental stages when the separation of particular parts is impossible. In this paper, we compared three different labelling and immunodetection methods by using in situ RT-PCR in Rosa hybrida flower buds and leaves. As target genes, we used the abundant β-actin and RhFUL gene, which is expressed only in the leaves and petals/sepals of flower buds. We used digoxygenin-11-dUTP, biotin-11-dUTP, and fluorescein-12-dUTP-labelled nucleotides and antidig-AP/ streptavidin-fluorescein-labelled antibodies. All of the used methods gave strong, specific signal and all of them may be used in localization of gene expression on tissue level in rose organs.

Complete nucleotide sequence of the self-transmissible TOL plasmid pD2RT provides new insight into arrangement of toluene catabolic plasmids

DEFF Research Database (Denmark)

Jutkina, Jekaterina; Hansen, Lars Hestbjerg; Li, Lili

2013-01-01

In the present study we report the complete nucleotide sequence of the toluene catabolic plasmid pD2RT of Pseudomonas migulae strain D2RT isolated from Baltic Sea water. The pD2RT is 129,894 base pairs in size with an average G+ C content of 53.75%. A total of 135 open reading frames (ORFs) were ...

Sodium sulphite inhibition of potato and cherry polyphenolics in nucleic acid extraction for virus detection by RT-PCR.

Science.gov (United States)

Singh, R P; Nie, X; Singh, M; Coffin, R; Duplessis, P

2002-01-01

Phenolic compounds from plant tissues inhibit reverse transcription-polymerase chain reaction (RT-PCR). Multiple-step protocols using several additives to inhibit polyphenolic compounds during nucleic acid extraction are common, but time consuming and laborious. The current research highlights that the inclusion of 0.65 to 0.70% of sodium sulphite in the extraction buffer minimizes the pigmentation of nucleic acid extracts and improves the RT-PCR detection of Potato virus Y (PVY) and Potato leafroll virus (PLRV) in potato (Solanum tuberosum) tubers and Prune dwarf virus (PDV) and Prunus necrotic ringspot virus (PNRSV) in leaves and bark in the sweet cherry (Prunus avium) tree. Substituting sodium sulphite in the nucleic acid extraction buffer eliminated the use of proteinase K during extraction. Reagents phosphate buffered saline (PBS)-Tween 20 and polyvinylpyrrolidone (PVP) were also no longer required during RT or PCR phase. The resultant nucleic acid extracts were suitable for both duplex and multiplex RT-PCR. This simple and less expensive nucleic acid extraction protocol has proved very effective for potato cv. Russet Norkotah, which contains a high amount of polyphenolics. Comparing commercially available RNA extraction kits (Catrimox and RNeasy), the sodium sulphite based extraction protocol yielded two to three times higher amounts of RNA, while maintaining comparable virus detection by RT-PCR. The sodium sulphite based extraction protocol was equally effective in potato tubers, and in leaves and bark from the cherry tree.

Thrombolysis with Intravenous Tissue Plasminogen Activator (rt-PA) Predicts Favorable Discharge Disposition in Patients with Acute Ischemic Stroke

Science.gov (United States)

Ifejika-Jones, Nneka L.; Harun, Nusrat; Mohammed-Rajput, Nareesa A.; Noser, Elizabeth A.; Grotta, James C.

2011-01-01

Background and Purpose Acute ischemic stroke patients receiving IV tissue plasminogen activator (rt-PA) within 3 hours of symptom onset are 30% more likely to have minimal disability at three months. During hospitalization, short-term disability is subjectively measured by discharge disposition, whether to home, Inpatient Rehabilitation (IR), Skilled Nursing Facility (SNF) or Subacute Care (Sub). There are no studies assessing the role of rt-PA use as a predictor of post-stroke disposition. Methods Retrospective analysis of all ischemic stroke patients admitted to the University of Texas Houston Medical School (UTHMS) Stroke Service between Jan 2004 and Oct 2009. Baseline demographics and National Institute of Health Stroke Scale (NIHSS) score were collected. Cerebrovascular disease risk factors were used for risk stratification. Results Home vs. IR, SNF, Sub Of 2225 acute ischemic stroke patients, 1019 were discharged home, 1206 to another level of care. Patients who received rt-PA therapy were 1.9 times more likely to be discharged home (P = stroke patients, 719 patients were discharged to acute IR, 371 were discharged to SNF, 116 to Sub. There were no differences in disposition between patients who received rt-PA therapy. Conclusions Stroke patients who receive IV rt-PA for acute ischemic stroke are more 1.9 times more likely to be discharged directly home after hospitalization. This study is limited by its retrospective nature and the undetermined role of psychosocial factors related to discharge. PMID:21293014

Experimentation of RT-LOTOS for a critical function of a power plant instrumentation and control system

International Nuclear Information System (INIS)

Andriantsiiferana, L.; Courtiat, J.P.; De Oliveira, R.C.

1996-01-01

This document is the final report of the contract between LAAS-CNRS and the EdF Direction of Researches and Studies about the experimentation of RT-LOTOS formal description technique on a critical function of a nuclear power plant instrumentation and control system. This report comprises 4 parts: part 1 describes the RT-LOTOS (Real Time-Language of Temporal Ordering Specifications) tutorial and its RTL tool environment, the different RT-LOTOS operators and semantics, and the RTL tool main functionalities; part 2 deals with the methodology and the global architecture for the specification and validation of the CCT (Central Calculator for Treatment); part 3 gives more details about the different processes identified in the specification architecture and presents the main results obtained for the validation of the nominal functioning; part 4 describes some exceptional situations and shows how some failures and their associated recovery mechanisms can be modelled. (J.S.). 6 refs., 53 figs., 5 tabs., 2 appends

Neural congruency effects in the multi-source interference task vanish in healthy youth after controlling for conditional differences in mean RT.

Directory of Open Access Journals (Sweden)

Kamin Kim

Full Text Available According to the conflict monitoring model of cognitive control, reaction time (RT in distracter interference tasks (e.g., the Stroop task is a more precise index of response conflict than stimulus congruency (incongruent vs. congruent. The model therefore predicts that RT should be a reliable predictor of activity in regions of the posterior medial frontal cortex (pMFC that are posited to detect response conflict. In particular, pMFC activity should be (a greater in slow-RT than in fast-RT trials within a given task condition (e.g., congruent and (b equivalent in RT-matched trials from different conditions (i.e., congruent and incongruent trials. Both of these effects have been observed in functional magnetic resonance imaging (MRI studies of adults. However, neither effect was observed in a recent study of healthy youth, suggesting that (a the model does not accurately describe the relationship between RT and pMFC activity in this population or (b the recent study was characterized by high variability due to a relatively small sample size. To distinguish between these possibilities, we asked a relatively large group of healthy youth (n = 28 to perform a distracter interference task - the multi-source interference task (MSIT - while we recorded their brain activity with functional MRI. In this relatively large sample, both of the model's predictions were confirmed. We conclude that the model accurately describes the relationship between pMFC activity and RT in healthy youth, but that additional research is needed to determine whether processes unrelated to response conflict contribute to this relationship.

PAM50 Breast Cancer Subtyping by RT-qPCR and Concordance with Standard Clinical Molecular Markers

Directory of Open Access Journals (Sweden)

Bastien Roy RL

2012-10-01

Full Text Available Abstract Background Many methodologies have been used in research to identify the “intrinsic” subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E and Basal-like. The PAM50 gene set is often used for gene expression-based subtyping; however, surrogate subtyping using panels of immunohistochemical (IHC markers are still widely used clinically. Discrepancies between these methods may lead to different treatment decisions. Methods We used the PAM50 RT-qPCR assay to expression profile 814 tumors from the GEICAM/9906 phase III clinical trial that enrolled women with locally advanced primary invasive breast cancer. All samples were scored at a single site by IHC for estrogen receptor (ER, progesterone receptor (PR, and Her2/neu (HER2 protein expression. Equivocal HER2 cases were confirmed by chromogenic in situ hybridization (CISH. Single gene scores by IHC/CISH were compared with RT-qPCR continuous gene expression values and “intrinsic” subtype assignment by the PAM50. High, medium, and low expression for ESR1, PGR, ERBB2, and proliferation were selected using quartile cut-points from the continuous RT-qPCR data across the PAM50 subtype assignments. Results ESR1, PGR, and ERBB2 gene expression had high agreement with established binary IHC cut-points (area under the curve (AUC ≥ 0.9. Estrogen receptor positivity by IHC was strongly associated with Luminal (A and B subtypes (92%, but only 75% of ER negative tumors were classified into the HER2-E and Basal-like subtypes. Luminal A tumors more frequently expressed PR than Luminal B (94% vs 74% and Luminal A tumors were less likely to have high proliferation (11% vs 77%. Seventy-seven percent (30/39 of ER-/HER2+ tumors by IHC were classified as the HER2-E subtype. Triple negative tumors were mainly comprised of Basal-like (57% and HER2-E (30% subtypes. Single gene scoring for ESR1, PGR, and ERBB2 was more prognostic than the corresponding IHC markers as

Evaluating the Impact of AIRS Observations on Regional Forecasts at the SPoRT Center

Science.gov (United States)

Zavodsky, Bradley

2011-01-01

NASA Short-term Prediction Research and Transition (SPoRT) Center collaborates with operational partners of different sizes and operational goals to improve forecasts using targeted projects and data sets. Modeling and DA activities focus on demonstrating utility of NASA data sets and capabilities within operational systems. SPoRT has successfully assimilated the Atmospheric Infrared Sounder (AIRS) radiance and profile data. A collaborative project is underway with the Joint Center for Satellite Data Assimilation (JCSDA) to use AIRS profiles to better understand the impact of AIRS radiances assimilated within Gridpoint Statistical Interpolation (GSI) in hopes of engaging the operational DA community in a reassessment of assimilation methodologies to more effectively assimilate hyperspectral radiances.

Briti peaminister Tony Blair tuleb hiiobisõnumiga / Andris Feldmanis, Märt Kivine

Index Scriptorium Estoniae

Feldmanis, Andris, 1982-

2005-01-01

Eestisse visiidile saabuv Suurbritannia peaminister Tony Blair soovib toetust EL-i eelarveprojektile, mis säilitaks Suurbritannia tagasimakse EL-i eelarvest ning vähendaks uute liikmesriikide toetusi. Kommenteerib Andrus Ansip. Vt. samas intervjuud Toomas Hendrik Ilvesega; Märt Kivine. Vajalik täpsustus: saagem mandri-eurooplasteks!

Emulating a crowded intracellular environment in vitro dramatically improves RT-PCR performance

International Nuclear Information System (INIS)

Lareu, Ricky R.; Harve, Karthik S.; Raghunath, Michael

2007-01-01

The polymerase chain reaction's (PCR) phenomenal success in advancing fields as diverse as Medicine, Agriculture, Conservation, or Paleontology is based on the ability of using isolated prokaryotic thermostable DNA polymerases in vitro to copy DNA irrespective of origin. This process occurs intracellularly and has evolved to function efficiently under crowded conditions, namely in an environment packed with macromolecules. However, current in vitro practice ignores this important biophysical parameter of life. In order to more closely emulate conditions of intracellular biochemistry in vitro we added inert macromolecules into reverse transcription (RT) and PCR. We show dramatic improvements in all parameters of RT-PCR including 8- to 10-fold greater sensitivity, enhanced polymerase processivity, higher specific amplicon yield, greater primer annealing and specificity, and enhanced DNA polymerase thermal stability. The faster and more efficient reaction kinetics was a consequence of the cumulative molecular and thermodynamic effects of the excluded volume effect created by macromolecular crowding

Highly Specific Detection of Five Exotic Quarantine Plant Viruses using RT-PCR

Directory of Open Access Journals (Sweden)

Hoseong Choi

2013-03-01

Full Text Available To detect five plant viruses (Beet black scorch virus, Beet necrotic yellow vein virus, Eggplant mottled dwarf virus, Pelargonium zonate spot virus, and Rice yellow mottle virus for quarantine purposes, we designed 15 RT-PCR primer sets. Primer design was based on the nucleotide sequence of the coat protein gene, which is highly conserved within species. All but one primer set successfully amplified the targets, and gradient PCRs indicated that the optimal temperature for the 14 useful primer sets was 51.9°C. Some primer sets worked well regardless of annealing temperature while others required a very specific annealing temperature. A primer specificity test using plant total RNAs and cDNAs of other plant virus-infected samples demonstrated that the designed primer sets were highly specific and generated reproducible results. The newly developed RT-PCR primer sets would be useful for quarantine inspections aimed at preventing the entry of exotic plant viruses into Korea.

Validation of putative reference genes for normalization of Q-RT-PCR data from paraffin-embedded lymphoid tissue

DEFF Research Database (Denmark)

Green, Tina Marie; de Stricker, Karin; Møller, Michael Boe

2009-01-01

Normalization of quantitative reverse transcription-PCR (Q-RT-PCR) data to appropriate tissue-specific reference genes is an essential part of interpreting the results. This study aimed to determine the most appropriate reference genes for normalizing gene expressions in lymphatic tissue...... was 0.93 (Pnormalization with the appropriate reference genes. Thus, we show that formalin-fixed, paraffin-embedded lymphoid samples are suitable for Q-RT-PCR when using thoroughly validated reference genes....

A validation of carbon fiber imaging couch top modeling in two radiation therapy treatment planning systems: Philips Pinnacle3 and BrainLAB iPlan RT Dose

International Nuclear Information System (INIS)

Njeh, Christopher F; Parker, Jason; Spurgin, Joseph; Rhoe, Elizabeth

2012-01-01

Carbon fiber (CF) is now the material of choice for radiation therapy couch tops. Initial designs included side metal bars for rigidity; however, with the advent of IGRT, involving on board imaging, new thicker CF couch tops without metal bars have been developed. The new design allows for excellent imaging at the expense of potentially unacceptable dose attenuation and perturbation. We set out to model the BrainLAB imaging couch top (ICT) in Philips Pinnacle 3 treatment planning system (TPS), to validate the already modeled ICT in BrainLAB iPlan RT Dose treatment planning system and to compute the magnitude of the loss in skin sparing. Using CF density of 0.55 g/cm 3 and foam density of 0.03 g/cm 3 , we demonstrated an excellent agreement between measured dose and Pinnacle 3 TPS computed dose using 6 MV beam. The agreement was within 1% for all gantry angle measured except for 120 o , which was 1.8%. The measured and iPlan RT Dose TPS computed dose agreed to within 1% for all gantry angles and field sizes measured except for 100 o where the agreement was 1.4% for 10 cm × 10 cm field size. Predicted attenuation through the couch by iPlan RT Dose TPS (3.4% - 9.5%) and Pinnacle 3 TPS (2% - 6.6%) were within the same magnitude and similar to previously reported in the literature. Pinnacle 3 TPS estimated an 8% to 20% increase in skin dose with increase in field size. With the introduction of the CF couch top, it estimated an increase in skin dose by approximately 46 - 90%. The clinical impact of omitting the couch in treatment planning will be dependent on the beam arrangement, the percentage of the beams intersecting the couch and their angles of incidence. We have successfully modeled the ICT in Pinnacle 3 TPS and validated the modeled ICT in iPlan RT Dose. It is recommended that the ICT be included in treatment planning for all treatments that involve posteriors beams. There is a significant increase in skin dose that is dependent on the percentage of the beam

Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.

Science.gov (United States)

Kierczak, Marcin; Dramiński, Michał; Koronacki, Jacek; Komorowski, Jan

2010-12-12

Despite more than two decades of research, HIV resistance to drugs remains a serious obstacle in developing efficient AIDS treatments. Several computational methods have been developed to predict resistance level from the sequence of viral proteins such as reverse transcriptase (RT) or protease. These methods, while powerful and accurate, give very little insight into the molecular interactions that underly acquisition of drug resistance/hypersusceptibility. Here, we attempt at filling this gap by using our Monte Carlo feature selection and interdependency discovery method (MCFS-ID) to elucidate molecular interaction networks that characterize viral strains with altered drug resistance levels. We analyzed a number of HIV-1 RT sequences annotated with drug resistance level using the MCFS-ID method. This let us expound interdependency networks that characterize change of drug resistance to six selected RT inhibitors: Abacavir, Lamivudine, Stavudine, Zidovudine, Tenofovir and Nevirapine. The networks consider interdependencies at the level of physicochemical properties of mutating amino acids, eg,: polarity. We mapped each network on the 3D structure of RT in attempt to understand the molecular meaning of interacting pairs. The discovered interactions describe several known drug resistance mechanisms and, importantly, some previously unidentified ones. Our approach can be easily applied to a whole range of problems from the domain of protein engineering. A portable Java implementation of our MCFS-ID method is freely available for academic users and can be obtained at: http://www.ipipan.eu/staff/m.draminski/software.htm.

Epidemiology of Human Parechovirus Type1 in Clinical Samples from Children with Gastroenteritis Using RT-PCR

Directory of Open Access Journals (Sweden)

F Ghazi

2012-05-01

Full Text Available

Background and Objectives: Human parechovirus type-1 (HPeV-1 is a genus of picornaviridea with a single stranded positive sense RNA genome. In general it seems to be responsible for more gastrointestinal and respiratory syndromes and less responsible for central nervous system (CNS symptoms. Since there is no accurate information about diagnosis and epidemiology of HPeV-1 in Iran and it is very important to distinguish between viral and bacterial diarrhea to decrease the unnecessary use of antibiotics, this study aimed at rapid detection and epidemiology of HPeV-1 in stool samples from children with gastroenteritis using specific RT-PCR.

Methods: Viral RNA was isolated from 472 stool samples from children (under 4 years old with diarrhea; CDNA was prepared and amplified using specific primers from 5^′untranslated region (5^′ UTR of HPeV-1 genome by nested RT-PCR. Amplified DNA product was electrophoresed on 1% agarose gel and a single band of 265 bp was obtained. Data were analyzed by SPSS software. We also performed a comparison between the cell culture (Vero and RT-PCR method for HPeV1 detection.

Results: Out of 472 samples examined during two years, 112 samples were HpeV-1 positive (23.7%. The results showed that the prevalence of this virus was in children under one year (6-12 months old with diarrhea (p=0.036 in spring and autumn (p<0.001. Boys had more positive cases than the girls (p<0.001. Out of 20 samples which were found positive by HPeV1 RT-PCR only three of them showed CPE on Vero Cells after a week.

Conclusion: The results revealed that RT-PCR is a more practical and sensitive technique for HPeV-1 detection directly from clinical samples, which is valuable for epidemiology. Also, the rapid

Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler's murine encephalomyelitis virus and rat theilovirus.

Science.gov (United States)

Yuan, Wen; Wang, Jing; Xu, Fengjiao; Huang, Bihong; Lian, Yuexiao; Rao, Dan; Yin, Xueqin; Wu, Miaoli; Zhu, Yujun; Zhang, Yu; Huang, Ren; Guo, Pengju

2016-10-01

Theiler's murine encephalomyelitis virus (TMEV) and rat theilovirus (RTV), the member of the genus Cardiovirus, are widespread in laboratory mice and rats, and are potential contaminants of biological materials. Cardioviruses infection may cause serious complications in biomedical research. To improve the efficiency of routine screening for Cardioviruses infection, a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection and differentiation of TMEV and RTV. The duplex assay was specific for reference strains of TMEV and RTV, and no cross-reaction was found with seven other rodent viruses. The limits of detection of both TMEV and RTV were 4×10(1) copies RNA/reaction. Reproducibility was estimated using standard dilutions, with coefficients of variation duplex real-time RT-PCR and conventional RT-PCR. For 439 clinical samples，95 samples were positive for TMEV and 72 samples were positive for RTV using duplex real-time RT-PCR approach, whereas only 77 samples were positive for TMEV and 66 samples were positive for RTV when conventional RT-PCR was applied. Mixed infections were found in 20 samples when analyzed by conventional RT-PCR whereas 30 samples were found to be mixed infection when duplex real-time RT-PCR was applied. This duplex assay provides a useful tool for routine health monitoring and screening of contaminated biological materials of these two viruses. Copyright © 2016 Elsevier B.V. All rights reserved.

AmbientRT - real time system software support for data centric sensor networks

NARCIS (Netherlands)

Hofmeijer, T.J.; Dulman, S.O.; Jansen, P.G.; Havinga, Paul J.M.

We present the architecture and design of a real time operating system for mobile wireless sensor networks. AmbientRT is being developed for environments with very limited resources in order to relieve the burden of the developer and to efficiently use the resources of the node. This paper presents

AmbientRT - real time system software support for data centric sensor networks

NARCIS (Netherlands)

Hofmeijer, T.J.; Dulman, S.O.; Jansen, P.G.; Havinga, Paul J.M.

2004-01-01

We present the architecture and design of a real time operating system for mobile wireless sensor networks. AmbientRT is being developed for environments with very limited resources in order to relieve the burden of the developer and to efficiently use the resources of the node. This paper presents

Effect of panax notoginseng saponins on efficacy and hemorrhagic transformation of rt-PA intravenous thrombolysis in patients with acute ischemic stroke

Directory of Open Access Journals (Sweden)

Chun-sheng LI

2016-11-01

Full Text Available Objective To study the effect of panax notoginseng saponins (PNS on the efficacy and hemorrhagic transformation (HT of recombinant tissue-type plasminogen activator (rt-PA intravenous thrombolysis in patients with acute ischemic stroke.  Methods A total of 200 patients with early acute ischemic stroke (the length of time between attack and hospital admission < 4.50 h were divided into 2 groups according to random number table method: treatment group (N = 100 and control group (N = 100. The control group was treated with routine rt-PA intravenous thrombolysis treatment, and the treatment group was treated with rt-PA intravenous thrombolysis plus PNS injection. The ischemia-reperfusion injury index [malondialdehyde (MDA and superoxide dismutase (SOD], hemorrhagic transformation prediction index [matrix metalloproteinase-9 (MMP-9 and fibronectin (FN] and nerve function index [National Institutes of Health Stroke Scale (NIHSS and Barthel Index (BI] were measured and compared before treatment, 24 h after thrombolysis and 14 d after thrombolysis. Adverse drug reactions and hemorrhagic transformation rate were observed 14 d after thrombolysis, and the prognosis (mortality and BI was evaluated 12 months after thrombolysis.  Results Compared with control group, serum SOD (P = 0.000 and BI (P = 0.000 in treatment group were significantly higher, while serum MDA (P = 0.001, MMP-9 (P = 0.001, plasma FN (P = 0.000 and NIHSS score (P = 0.006 were significantly lower. In treatment group, 24 h after rt-PA intravenous thrombolysis plus PNS injection, serum MDA (P = 0.000, MMP-9 (P = 0.000 and BI (P = 0.000 were significantly increased, while NIHSS score (P = 0.000 was significantly decreased; 14 d after treatment, serum MDA (P = 0.000 and MMP-9 (P = 0.000 were decreased, serum SOD (P = 0.000 and BI (P = 0.000 were continuously increased, plasma FN (P = 0.000 and NIHSS score (P = 0.000 were continuously decreased. On the 14th day after thrombolysis

Matsalu festival - aina parem / Ingmar Muusikus ; kommenteerinud Ulvar Käärt

Index Scriptorium Estoniae

Muusikus, Ingmar, 1971-

2011-01-01

Lihulas toimunud 9. Matsalu loodusfilmide festivali fotoprogrammist. Remo Savisaare näitusest "Imelised linnud". Tiit Leito näitusest "Minevikumälestused". Mark Soosaare näitusest "Kihnukielsed ljõnnud". Jarek Jõepera ja Jaan Künnapi näitustest. Näitusest "Meil on elu keset metsa" (Veiko Belials jt.). Ulvar Käärt peapreemia saanud Oliver Götzli filmist "Skandinaavia loodus - Soome" (Saksamaa)

Concurrent deployment of visual attention and response selection bottleneck in a dual-task: Electrophysiological and behavioural evidence.

Science.gov (United States)

Reimer, Christina B; Strobach, Tilo; Schubert, Torsten

2017-12-01

Visual attention and response selection are limited in capacity. Here, we investigated whether visual attention requires the same bottleneck mechanism as response selection in a dual-task of the psychological refractory period (PRP) paradigm. The dual-task consisted of an auditory two-choice discrimination Task 1 and a conjunction search Task 2, which were presented at variable temporal intervals (stimulus onset asynchrony, SOA). In conjunction search, visual attention is required to select items and to bind their features resulting in a serial search process around the items in the search display (i.e., set size). We measured the reaction time of the visual search task (RT2) and the N2pc, an event-related potential (ERP), which reflects lateralized visual attention processes. If the response selection processes in Task 1 influence the visual attention processes in Task 2, N2pc latency and amplitude would be delayed and attenuated at short SOA compared to long SOA. The results, however, showed that latency and amplitude were independent of SOA, indicating that visual attention was concurrently deployed to response selection. Moreover, the RT2 analysis revealed an underadditive interaction of SOA and set size. We concluded that visual attention does not require the same bottleneck mechanism as response selection in dual-tasks.

Simple, specific molecular typing of dengue virus isolates using one-step RT-PCR and restriction fragment length polymorphism.

Science.gov (United States)

Ortiz, Alma; Capitan, Zeuz; Mendoza, Yaxelis; Cisneros, Julio; Moreno, Brechla; Zaldivar, Yamitzel; Garcia, Mariana; Smith, Rebecca E; Motta, Jorge; Pascale, Juan Miguel

2012-10-01

A one-step RT-PCR and one-enzyme RFLP was used to detect and distinguish among flaviviruses, including the four serotypes of dengue and the St. Louis Encephalitis, West Nile and Yellow Fever viruses in cultured virus samples or acute-phase human serum. Using a previously described RT-PCR, but novel RFLP procedure, results are obtained in 24 h with basic PCR and electrophoresis equipment. There is 95% agreement between RT-PCR/RFLP results and those achieved by indirect immunofluorescence assays, and 100% agreement between RT-PCR/RFLP results and gene sequencing. This method is more rapid than tests of cytopathic effect based on virus isolation in tissue culture, and simpler than real-time PCR. It does not require specialized equipment, radioisotopes or computer analysis and is a method that can be applied widely in the developing world. It allows for prompt determination of whether a flavivirus is the cause of illness in a febrile patient, rapid identification of dengue serotypes in circulation, and improved patient management in cases where prior dengue exposure make dengue hemorrhagic fever or dengue shock syndrome a risk. Copyright © 2012 Elsevier B.V. All rights reserved.

Technique for Increasing the Selectivity of the Method of Laser Fragmentation/Laser-Induced Fluorescence

Science.gov (United States)

Bobrovnikov, S. M.; Gorlov, E. V.; Zharkov, V. I.

2018-05-01

A technique for increasing the selectivity of the method of detecting high-energy materials (HEMs) based on laser fragmentation of HEM molecules with subsequent laser excitation of fluorescence of the characteristic NO fragments from the first vibrational level of the ground state is suggested.

Detection of enteroviruses and hepatitis a virus in water by consensus primer multiplex RT-PCR

Science.gov (United States)

Li, Jun-Wen; Wang, Xin-Wei; Yuan, Chang-Qing; Zheng, Jin-Lai; Jin, Min; Song, Nong; Shi, Xiu-Quan; Chao, Fu-Huan

2002-01-01

AIM: To develop a rapid detection method of enteroviruses and Hepatitis A virus (HAV). METHODS: A one-step, single-tube consensus primers multiplex RT-PCR was developed to simultaneously detect Poliovirus, Coxsackie virus, Echovirus and HAV. A general upstream primer and a HAV primer and four different sets of primers (5 primers) specific for Poliovirus, Coxsacki evirus, Echovirus and HAV cDNA were mixed in the PCR mixture to reverse transcript and amplify the target DNA. Four distinct amplified DNA segments representing Poliovirus, Coxsackie virus, Echovirus and HAV were identified by gel electrophoresis as 589-, 671-, 1084-, and 1128 bp sequences, respectively. Semi-nested PCR was used to confirm the amplified products for each enterovirus and HAV. RESULTS: All four kinds of viral genome RNA were detected, and producing four bands which could be differentiated by the band size on the gel. To confirm the specificity of the multiplex PCR products, semi-nested PCR was performed. For all the four strains tested gave positive results. The detection sensitivity of multiplex PCR was similar to that of monoplex RT-PCR which was 24 PFU for Poliovrus, 21 PFU for Coxsackie virus, 60 PFU for Echovirus and 105 TCID50 for HAV. The minimum amount of enteric viral RNA detected by semi-nested PCR was equivalent to 2.4 PFU for Poliovrus, 2.1 PFU for Coxsackie virus, 6.0 PFU for Echovirus and 10.5 TCID50 for HAV. CONCLUSION: The consensus primers multiplex RT-PCR has more advantages over monoplex RT-PCR for enteric viruses detection, namely, the rapid turnaround time and cost effectiveness. PMID:12174381

Evaluation of RIDA®GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis.

Science.gov (United States)

Kanwar, N; Hassan, F; Barclay, L; Langley, C; Vinjé, J; Bryant, P W; George, K St; Mosher, L; Matthews-Greer, J M; Rocha, M A; Beenhouwer, D O; Harrison, C J; Moffatt, M; Shastri, N; Selvarangan, R

2018-04-10

Norovirus is the leading cause of epidemic and sporadic acute gastroenteritis (AGE) in the United States. Widespread prevalence necessitates implementation of accurate norovirus detection assays in clinical diagnostic laboratories. To evaluate RIDA ® GENE norovirus GI/GII real-time RT-PCR assay (RGN RT-PCR) using stool samples from patients with sporadic AGE. Patients between 14 days to 101 years of age with symptoms of AGE were enrolled prospectively at four sites across the United States during 2014-2015. Stool specimens were screened for the presence of norovirus RNA by the RGN RT-PCR assay. Results were compared with a reference method that included conventional RT-PCR and sequencing of a partial region of the 5'end of the norovirus ORF2 gene. A total of 259 (36.0%) of 719 specimens tested positive for norovirus by the reference method. The RGN RT-PCR assay detected norovirus in 244 (94%) of these 259 norovirus positive specimens. The sensitivity and specificity (95% confidence interval) of the RGN RT-PCR assay for detecting norovirus genogroup (G) I was 82.8% (63.5-93.5) and 99.1% (98.0-99.6) and for GII was 94.8% (90.8-97.2) and 98.6% (96.9-99.4), respectively. Seven specimens tested positive by the RGN-RT PCR that were negative by the reference method. The fifteen false negative samples were typed as GII.4 Sydney, GII.13, GI.3, GI.5, GI.2, GII.1, and GII.3 in the reference method. The RGN RT-PCR assay had a high sensitivity and specificity for the detection of norovirus in stool specimens from patients with sporadic AGE. Copyright © 2018. Published by Elsevier B.V.

Simultaneous detection of three pome fruit tree viruses by one-step multiplex quantitative RT-PCR.

Science.gov (United States)

Malandraki, Ioanna; Beris, Despoina; Isaioglou, Ioannis; Olmos, Antonio; Varveri, Christina; Vassilakos, Nikon

2017-01-01

A one-step multiplex real-time reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan probes was developed for the simultaneous detection of Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in total RNA of pome trees extracted with a CTAB method. The sensitivity of the method was established using in vitro synthesized viral transcripts serially diluted in RNA from healthy, virus-tested (negative) pome trees. The three viruses were simultaneously detected up to a 10-4 dilution of total RNA from a naturally triple-infected apple tree prepared in total RNA of healthy apple tissue. The newly developed RT-qPCR assay was at least one hundred times more sensitive than conventional single RT-PCRs. The assay was validated with 36 field samples for which nine triple and 11 double infections were detected. All viruses were detected simultaneously in composite samples at least up to the ratio of 1:150 triple-infected to healthy pear tissue, suggesting the assay has the capacity to examine rapidly a large number of samples in pome tree certification programs and surveys for virus presence.

Applications of NASA and NOAA Satellite Observations by NASA's Short-term Prediction Research and Transition (SPoRT) Center in Response to Natural Disasters

Science.gov (United States)

Molthan, Andrew L.; Burks, Jason E.; McGrath, Kevin M.; Jedlovec, Gary J.

2012-01-01

NASA s Short-term Prediction Research and Transition (SPoRT) Center supports the transition of unique NASA and NOAA research activities to the operational weather forecasting community. SPoRT emphasizes real-time analysis and prediction out to 48 hours. SPoRT partners with NOAA s National Weather Service (NWS) Weather Forecast Offices (WFOs) and National Centers to improve current products, demonstrate future satellite capabilities and explore new data assimilation techniques. Recently, the SPoRT Center has been involved in several activities related to disaster response, in collaboration with NOAA s National Weather Service, NASA s Applied Sciences Disasters Program, and other partners.

Management and Development of the RT Research Facilities and Infrastructures

International Nuclear Information System (INIS)

Kim, Won Ho; Nho, Young Chang; Kim, Jae Sung

2009-01-01

The purpose of this project are to operate the core facilities of the research for the Radiation Technology in stable and to assist the research activities efficiently in the industry, academic, and research laboratory. By developing the infrastructure of the national radio technology industry, we can activate the researching area of the RT and the related industry, and obtain the primary and original technology. The key point in the study of the RT and the assistance of the industry, academic, and research laboratory for the RT area smoothly, is managing the various of unique radiation facilities in our country. The gamma Phytotron and Gene Bank are essential in the agribiology because these facilities are used to preserve and utilize the genes and to provide an experimental field for the environment and biotechnology. The Radiation Fusion Technology research supporting facilities are the core support facilities, and are used to develop the high-tech fusion areas. In addition, the most advanced analytical instruments, whose costs are very high, should be managed in stable and be utilized in supporting works, and the experimental animal supporting laboratory and Gamma Cell have to be maintained in high level and managed in stable also. The ARTI have been developed the 30MeV cyclotron during 2005∼2006, aimed to produce radioisotopes and to research the beam applications as a result of the project, 'Establishment of the Infrastructure for the Atomic Energy Research Expansion', collaborated with the Korea Institute of Radiological and Medical Sciences. In addition, the ARTI is in the progress of establishing cyclotron integrated complex as a core research facility, using a proton beam to produce radioisotopes and to support a various research areas. The measurement and evaluation of the irradiation dose, and irradiation supporting technology of the Good Irradiation Practice(GIP) are essential in various researching areas. One thing to remember is that the publicity

Når det er svært at være ung i DK

DEFF Research Database (Denmark)

Nielsen, Jens Christian; Sørensen, Niels Ulrik; Grubb, Ane

I rapporten Når det er svært at være ung i DK – unges beretninger om mistrivsel og ungdomsliv præsenteres resultaterne af et kvalitativt studie af mistrivsel og ungdomsliv blandt 15-24-årige unge i Danmark. Studiet bygger på dybdegående interviews med 33 unge fra forskellige dele af landet, der...... fortæller om deres erfaringer med diverse mistrivselsformer, som ensomhed, selvskadende adfærd og mobning, og om deres besvær med at håndtere de krav, udfordringer og muligheder, der i øvrigt præger det moderne ungdomsliv. Studiet indgår i det treårige forskningsprojekt Når det er svært at være ung i DK...

Using Negative Reinforcement to Increase Self-Feeding in a Child with Food Selectivity

Science.gov (United States)

Vaz, Petula C. M.; Volkert, Valerie M.; Piazza, Cathleen C.

2011-01-01

We examined the effects of a negative reinforcement-based treatment on the self-feeding of 1 child with food selectivity by type and texture. Self-feeding increased when the child could choose to either self-feed 1 bite of a target food or be fed 1 bite of the target food and 5 bites of another food. Possible mechanisms that underlie the…

Märt Agu käib isa Mait Agu jälgedes / Heili Sibrits

Index Scriptorium Estoniae

Sibrits, Heili, 1977-

2001-01-01

Koreograafi ja tantsupedagoogi Mait Agu poeg Märt Agu on Eesti Tantsuagentuuri tantsija ja Pedagoogilise Instituudi tantsujuhtimise viimase kursuse üliõpilane, kes esineb revüüteatris "Bel-⁹tage"

A Prolonged Time Interval Between Trauma and Prophylactic Radiation Therapy Significantly Increases the Risk of Heterotopic Ossification

Energy Technology Data Exchange (ETDEWEB)

Mourad, Waleed F., E-mail: Waleed246@gmail.com [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS (United States); Department of Radiation Oncology, Beth Israel Medical Center, New York, NY (Israel); Packianathan, Satyaseelan [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS (United States); Shourbaji, Rania A. [Department of Epidemiology and Biostatistics, Jackson State University, Jackson, MS (United States); Zhang Zhen; Graves, Mathew [Department of Orthopedic Surgery, University of Mississippi Medical Center, Jackson, MS (United States); Khan, Majid A. [Department of Radiology, University of Mississippi Medical Center, Jackson, MS (United States); Baird, Michael C. [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS (United States); Russell, George [Department of Orthopedic Surgery, University of Mississippi Medical Center, Jackson, MS (United States); Vijayakumar, Srinivasan [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS (United States)

2012-03-01

Purpose: To ascertain whether the time from injury to prophylactic radiation therapy (RT) influences the rate of heterotopic ossification (HO) after operative treatment of displaced acetabular fractures. Methods and Materials: This is a single-institution, retrospective analysis of patients referred for RT for the prevention of HO. Between January 2000 and January 2009, 585 patients with displaced acetabular fractures were treated surgically followed by RT for HO prevention. We analyzed the effect of time from injury on prevention of HO by RT. In all patients, 700 cGy was prescribed in a single fraction and delivered within 72 hours postsurgery. The patients were stratified into five groups according to time interval (in days) from the date of their accident to the date of RT: Groups A {<=}3, B {<=}7, C {<=}14, D {<=}21, and E >21days. Results: Of the 585 patients with displaced acetabular fractures treated with RT, (18%) 106 patients developed HO within the irradiated field. The risk of HO after RT increased from 10% for RT delivered {<=}3 days to 92% for treatment delivered >21 days after the initial injury. Wilcoxon test showed a significant correlation between the risk of HO and the length of time from injury to RT (p < 0.0001). Chi-square test and multiple logistic regression analysis showed no significant association between all other factors and the risk of HO (race, gender, cause and type of fracture, surgical approach, or the use of indomethacin). Conclusions: Our data suggest that there is higher incidence and risk of HO if prophylactic RT is significantly delayed after a displaced acetabular fracture. Thus, RT should be administered as early as clinically possible after the trauma. Patients undergoing RT >3 weeks from their displaced acetabular fracture should be informed of the higher risk (>90%) of developing HO despite prophylaxis.

Development and validation of sensitive real-time RT-PCR assay for broad detection of rabies virus.

Science.gov (United States)

Faye, Martin; Dacheux, Laurent; Weidmann, Manfred; Diop, Sylvie Audrey; Loucoubar, Cheikh; Bourhy, Hervé; Sall, Amadou Alpha; Faye, Ousmane

2017-05-01

Rabies virus (RABV) remains one of the most important global zoonotic pathogens. RABV causes rabies, an acute encephalomyelitis associated with a high rate of mortality in humans and animals and affecting different parts of the world, particularly in Asia and Africa. Confirmation of rabies diagnosis relies on laboratory diagnosis, in which molecular techniques such as detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) are increasingly being used. In this study, two real-time quantitative RT-PCR assays were developed for large-spectrum detection of RABV, with a focus on African isolates. The primer and probe sets were targeted highly conserved regions of the nucleoprotein (N) and polymerase (L) genes. The results indicated the absence of non-specific amplification and cross-reaction with a range of other viruses belonging to the same taxonomic family, i.e. Rhabdoviridae, as well as negative brain tissues from various host species. Analytical sensitivity ranged between 100 to 10 standard RNA copies detected per reaction for N-gene and L-gene assays, respectively. Effective detection and high sensitivity of these assays on African isolates showed that they can be successfully applied in general research and used in diagnostic process and epizootic surveillance in Africa using a double-check strategy. Copyright © 2017 Elsevier B.V. All rights reserved.

Classic debates in selective attention: early vs late, perceptual load vs dilution, mean RT vs measures of capacity.

Science.gov (United States)

Nelson, Michael D; Crisostomo, Marisa; Khericha, Alifiya; Russo, Francis; Thorne, Gary L

2012-01-01

We briefly summarize two important debates regarding selective attention (early vs late selection; perceptual load vs distractor dilution). Also, we report the results of an attempt to replicate Lavie (1995, Journal of Experimental Psychology: Human Perception and Performance 21 451-468). We suggest that measures capable of characterizing the capacity of information processing systems (compared to reporting only mean reaction time) could add great clarity to this literature.

MINIX4RT: a real-time operating system based on MINIX

OpenAIRE

Pessolani, Pablo Andrés

2006-01-01

Tanenbaum's MINIX Operating System was extended with a Real-Time microkernel and services to conform MINIX4RT, a Real-Time Operating System for academic uses that includes more flexible Interprocess Communications facilities supporting basic priority inheritance protocol, a fixed priority scheduler, timer and event driven interrupt management, statistics and Real-Time metrics gathering keeping backward compatibility with standard MINIX versions. Facultad de Informática

WE-G-17A-03: MRIgRT: Quantification of Organ Motion

International Nuclear Information System (INIS)

Stanescu, T; Tadic, T; Jaffray, D

2014-01-01

Purpose: To develop an MRI-based methodology and tools required for the quantification of organ motion on a dedicated MRI-guided radiotherapy system. A three-room facility, consisting of a TrueBeam 6X linac vault, a 1.5T MR suite and a brachytherapy interventional room, is currently under commissioning at our institution. The MR scanner can move and image in either room for diagnostic and treatment guidance purposes. Methods: A multi-imaging modality (MR, kV) phantom, featuring programmable 3D simple and complex motion trajectories, was used for the validation of several image sorting algorithms. The testing was performed on MRI (e.g. TrueFISP, TurboFLASH), 4D CT and 4D CBCT. The image sorting techniques were based on a) direct image pixel manipulation into columns or rows, b) single and aggregated pixel data tracking and c) using computer vision techniques for global pixel analysis. Subsequently, the motion phantom and sorting algorithms were utilized for commissioning of MR fast imaging techniques for 2D-cine and 4D data rendering. MR imaging protocols were optimized (e.g. readout gradient strength vs. SNR) to minimize the presence of susceptibility-induced distortions, which were reported through phantom experiments and numerical simulations. The system-related distortions were also quantified (dedicated field phantom) and treated as systematic shifts where relevant. Results: Image sorting algorithms were validated for specific MR-based applications such as quantification of organ motion, local data sampling, and 4D MRI for pre-RT delivery with accuracy better than the raw image pixel size (e.g. 1 mm). MR fast imaging sequences were commissioning and imaging strategies were developed to mitigate spatial artifacts with minimal penalty on the image spatial and temporal sampling. Workflows (e.g. liver) were optimized to include the new motion quantification tools for RT planning and daily patient setup verification. Conclusion: Comprehensive methods were developed

Resistance training and hormone replacement increase MMP-2 activity, quality and quantity of bone in ovariectomized rats

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Markus V.C Souza

2017-12-01

Full Text Available Abstract AIMS The aim of the present study was to investigate the influence of resistance training (RT and hormone replacement (HR on MMP-2 activity, biomechanical and physical properties bone of ovariectomized (OVX rats. METHODS Sprague-Dawley female rats were grouped into six experimental groups (n = 11 per group: sham-operated sedentary (SHAM Sed, ovariectomized sedentary (OVX Sed, sham-operated resistance training (SHAM RT, ovariectomized resistance training (OVX RT, ovariectomized sedentary hormone replacement (OVX Sed-HR, and ovariectomized resistance training hormone replacement (OVX RT-HR. HR groups received implanted silastic capsules with a 5% solution of 17β-estradiol (50 mg 17β-estradiol/ml of sunflower oil. In a 12-week RT period (27 sessions; 4-9 climbs the animals climbed a 1.1 m vertical ladder with weights attached to their tails. Biomechanical and physical bone analyses were performed using a universal testing machine, and MMP-2 activity analysis was done by zymography. RESULTS Bone density and bone mineral content was higher in the RT and HR groups. The MMP-2 activity was higher in the RT and HR groups. The biomechanical analysis (stiffness, fracture load and maximum load demonstrated better bone tissue quality in the RT associated with HR. CONCLUSION The RT alone as well as when it is associated with HR was efficient in increasing MMP-2 activity, biomechanical and biophysical properties bone of ovariectomized rats.

Quantitation of TGF-beta1 mRNA in porcine mesangial cells by comparative kinetic RT/PCR: comparison with ribonuclease protection assay and in situ hybridization.

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Ceol, M; Forino, M; Gambaro, G; Sauer, U; Schleicher, E D; D'Angelo, A; Anglani, F

2001-01-01

Gene expression can be examined with different techniques including ribonuclease protection assay (RPA), in situ hybridisation (ISH), and quantitative reverse transcription-polymerase chain reaction (RT/PCR). These methods differ considerably in their sensitivity and precision in detecting and quantifying low abundance mRNA. Although there is evidence that RT/PCR can be performed in a quantitative manner, the quantitative capacity of this method is generally underestimated. To demonstrate that the comparative kinetic RT/PCR strategy-which uses a housekeeping gene as internal standard-is a quantitative method to detect significant differences in mRNA levels between different samples, the inhibitory effect of heparin on phorbol 12-myristate 13-acetate (PMA)-induced-TGF-beta1 mRNA expression was evaluated by RT/PCR and RPA, the standard method of mRNA quantification, and the results were compared. The reproducibility of RT/PCR amplification was calculated by comparing the quantity of G3PDH and TGF-beta1 PCR products, generated during the exponential phases, estimated from two different RT/PCR (G3PDH, r = 0.968, P = 0.0000; TGF-beta1, r = 0.966, P = 0.0000). The quantitative capacity of comparative kinetic RT/PCR was demonstrated by comparing the results obtained from RPA and RT/PCR using linear regression analysis. Starting from the same RNA extraction, but using only 1% of the RNA for the RT/PCR compared to RPA, significant correlation was observed (r = 0.984, P = 0.0004). Moreover the morphometric analysis of ISH signal was applied for the semi-quantitative evaluation of the expression and localisation of TGF-beta1 mRNA in the entire cell population. Our results demonstrate the close similarity of the RT/PCR and RPA methods in giving quantitative information on mRNA expression and indicate the possibility to adopt the comparative kinetic RT/PCR as reliable quantitative method of mRNA analysis. Copyright 2001 Wiley-Liss, Inc.

Comparison of ELISA and RT-PCR for the detection of Prunus necrotic ring spot virus and prune dwarf virus in almond (Prunus dulcis).

Science.gov (United States)

Mekuria, Genet; Ramesh, Sunita A; Alberts, Evita; Bertozzi, Terry; Wirthensohn, Michelle; Collins, Graham; Sedgley, Margaret

2003-12-01

A technique based on the reverse transcriptase-polymerase chain reaction (RT-PCR) has been developed to detect the presence of Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV) simultaneously in almond. This paper presents the results of a 3-year study comparing both enzyme-linked immunosorbent assay (ELISA) and RT-PCR for the detection of PNRSV and PDV using 175 almond leaf samples. Multiplex RT-PCR was found to be more sensitive than ELISA, especially when followed by nested PCR for the detection of PDV. The RT-PCR technique has the added advantage that plant material can be tested at any time throughout the growing season.