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Sample records for pcr-based mst approach

  1. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

    Science.gov (United States)

    Smith, Cindy J; Osborn, A Mark

    2009-01-01

    Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

  2. PCR-based Approaches for the Detection of Clinical Methicillin-resistant Staphylococcus aureus

    Science.gov (United States)

    Liu, Ying; Zhang, Jiang; Ji, Yinduo

    2016-01-01

    Staphylococcus aureus is an important pathogen that can cause a variety of infections, including superficial and systematic infections, in humans and animals. The persistent emergence of multidrug resistant S. aureus, particularly methicillin-resistant S. aureus, has caused dramatically economic burden and concerns in the public health due to limited options of treatment of MRSA infections. In order to make a correct choice of treatment for physicians and understand the prevalence of MRSA, it is extremely critical to precisely and timely diagnose the pathogen that induces a specific infection of patients and to reveal the antibiotic resistant profile of the pathogen. In this review, we outlined different PCR-based approaches that have been successfully utilized for the rapid detection of S. aureus, including MRSA and MSSA, directly from various clinical specimens. The sensitivity and specificity of detections were pointed out. Both advantages and disadvantages of listed approaches were discussed. Importantly, an alternative approach is necessary to further confirm the detection results from the molecular diagnostic assays. PMID:27335617

  3. Heterologous Reconstitution of the Intact Geodin Gene Cluster in Aspergillus nidulans through a Simple and Versatile PCR Based Approach

    DEFF Research Database (Denmark)

    Nielsen, Morten Thrane; Nielsen, Jakob Blæsbjerg; Anyaogu, Dianna Chinyere

    2013-01-01

    was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to ransformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were...... of solid methodology for genetic manipulation of most species severely hampers pathway haracterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus...... successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC) encodes a polyketide synthase, ATEG_08453 (gedR) encodes a transcription factor...

  4. PCR-based approach to SINE isolation: simple and complex SINEs.

    Science.gov (United States)

    Borodulina, Olga R; Kramerov, Dmitri A

    2005-04-11

    Highly repeated copies of short interspersed elements (SINEs) occur in eukaryotic genomes. The distribution of each SINE family is usually restricted to some genera, families, or orders. SINEs have an RNA polymerase III internal promoter, which is composed of boxes A and B. Here we propose a method for isolation of novel SINE families based on genomic DNA PCR with oligonucleotide identical to box A as a primer. Cloning of the size-heterogeneous PCR-products and sequencing of their terminal regions allow determination of SINE structure. Using this approach, two novel SINE families, Rhin-1 and Das-1, from the genomes of great horseshoe bat (Rhinolophus ferrumequinum) and nine-banded armadillo (Dasypus novemcinctus), respectively, were isolated and studied. The distribution of Rhin-1 is restricted to two of six bat families tested. Copies of this SINE are characterized by frequent internal insertions and significant length (200-270 bp). Das-1 being only 90 bp in length is one of the shortest SINEs known. Most of Das-1 nucleotide sequences demonstrate significant similarity to alanine tRNA which appears to be an evolutionary progenitor of this SINE. Together with three other known SINEs (ID, Vic-1, and CYN), Das-1 constitutes a group of simple SINEs. Interestingly, three SINE families of this group are alanine tRNA-derived. Most probably, this tRNA gave rise to short and simple but successful SINEs several times during mammalian evolution.

  5. Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach.

    Directory of Open Access Journals (Sweden)

    Morten Thrane Nielsen

    Full Text Available Fungal natural products are a rich resource for bioactive molecules. To fully exploit this potential it is necessary to link genes to metabolites. Genetic information for numerous putative biosynthetic pathways has become available in recent years through genome sequencing. However, the lack of solid methodology for genetic manipulation of most species severely hampers pathway characterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to transformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC encodes a polyketide synthase, ATEG_08453 (gedR encodes a transcription factor responsible for activation of the geodin gene cluster and ATEG_08460 (gedL encodes a halogenase that catalyzes conversion of sulochrin to dihydrogeodin. We expect that our approach for transferring intact biosynthetic pathways to a fungus with a well developed genetic toolbox will be instrumental in characterizing the many exciting pathways for secondary metabolite production that are currently being uncovered by the fungal genome sequencing projects.

  6. A dual PCR-based sequencing approach for the identification and discrimination of Echinococcus and Taenia taxa.

    Science.gov (United States)

    Boubaker, Ghalia; Marinova, Irina; Gori, Francesca; Hizem, Amani; Müller, Norbert; Casulli, Adriano; Jerez Puebla, Luis Enrique; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

    2016-08-01

    Reliable and rapid molecular tools for the genetic identification and differentiation of Echinococcus species and/or genotypes are crucial for studying spatial and temporal transmission dynamics. Here, we describe a novel dual PCR targeting regions in the small (rrnS) and large (rrnL) subunits of mitochondrial ribosomal RNA (rRNA) genes, which enables (i) the specific identification of species and genotypes of Echinococcus (rrnS + L-PCR) and/or (ii) the identification of a range of taeniid cestodes, including different species of Echinococcus, Taenia and some others (17 species of diphyllidean helminths). This dual PCR approach was highly sensitive, with an analytical detection limit of 1 pg for genomic DNA of Echinococcus. Using concatenated sequence data derived from the two gene markers (1225 bp), we identified five unique and geographically informative single nucleotide polymorphisms (SNPs) that allowed genotypes (G1 and G3) of Echinococcus granulosus sensu stricto to be distinguished, and 25 SNPs that allowed differentiation within Echinococcus canadensis (G6/7/8/10). In conclusion, we propose that this dual PCR-based sequencing approach can be used for molecular epidemiological studies of Echinococcus and other taeniid cestodes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. A Molecular MST Approach to Investigate Fecal Indicator Bacteria in Bioaerosols, Bathing Water, Seaweed Wrack, and Sand at Recreational Beaches

    Science.gov (United States)

    Thoren, K. M.; Sinigalliano, C. D.

    2016-02-01

    Despite numerous cases of beach bacteria affecting millions of people worldwide, the persistence of the bacteria populations in coastal areas is still not well understood. The purpose of this study was to test the levels of persistence of Fecal Indicating Bacteria (FIB) of enterococci, Escherichia coli, and Human-source Bacteroidales, within the intertidal "swash zone" and the deeper waist zone in which people commonly bathe and play. In addition, the study sought to determine if these bacterial contaminants may also be found in aerosols at the beach. Measuring solar insolation in relation to bacterial persistence in seaweed wrack was used to determine if sunlight plays a role in modifying concentrations of FIB at the beach. Light intensity measured by a solar photometer and air quality measured by aerosol plate counts and qPCR Microbial Source Tracking (MST) was compared to varying locations where the beach samples were collected. Results from water samples demonstrate that bacteria measured using plate counts and qPCR were indeed higher within the swash zone than in the waist zone. This is in contrast with the way that the EPA currently measures and determines the public safety of beach waters. They commonly measure the waist zone, but disregard the swash zone. Results from beach bio-aerosol samples showed a wide variety of fungi and bacteria in the beach air, and qPCR MST analysis of these bio-aerosols showed the presence of FIBs such as enterococci on several of the aerosol collection plates. This emphasizes the need to collect samples from the entire beach instead of just measuring at an isolated area, and that exposure to microbial contaminants may include bathing water, beach sand, seaweed wrack, and bio-aerosols. Thus, the data reveals a potential way to identify harmful levels of bacteria and dangerous levels of poor air quality at recreational beaches. These results expound the need for broader assessment of potential beach contamination, not only the

  8. MST Filterability Tests

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Burket, P. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Duignan, M. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-03-12

    The Savannah River Site (SRS) is currently treating radioactive liquid waste with the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Extraction Unit (MCU). The low filter flux through the ARP has limited the rate at which radioactive liquid waste can be treated. Recent filter flux has averaged approximately 5 gallons per minute (gpm). Salt Batch 6 has had a lower processing rate and required frequent filter cleaning. Savannah River Remediation (SRR) has a desire to understand the causes of the low filter flux and to increase ARP/MCU throughput. In addition, at the time the testing started, SRR was assessing the impact of replacing the 0.1 micron filter with a 0.5 micron filter. This report describes testing of MST filterability to investigate the impact of filter pore size and MST particle size on filter flux and testing of filter enhancers to attempt to increase filter flux. The authors constructed a laboratory-scale crossflow filter apparatus with two crossflow filters operating in parallel. One filter was a 0.1 micron Mott sintered SS filter and the other was a 0.5 micron Mott sintered SS filter. The authors also constructed a dead-end filtration apparatus to conduct screening tests with potential filter aids and body feeds, referred to as filter enhancers. The original baseline for ARP was 5.6 M sodium salt solution with a free hydroxide concentration of approximately 1.7 M.3 ARP has been operating with a sodium concentration of approximately 6.4 M and a free hydroxide concentration of approximately 2.5 M. SRNL conducted tests varying the concentration of sodium and free hydroxide to determine whether those changes had a significant effect on filter flux. The feed slurries for the MST filterability tests were composed of simple salts (NaOH, NaNO2, and NaNO3) and MST (0.2 – 4.8 g/L). The feed slurry for the filter enhancer tests contained simulated salt batch 6 supernate, MST, and filter enhancers.

  9. RESULTS OF SUPPLEMENTAL MST STUDIES

    International Nuclear Information System (INIS)

    Peters, T; David Hobbs, D; Samuel Fink, S

    2006-01-01

    The current design of the Salt Waste Processing Facility (SWPF) includes an auxiliary facility, the Actinide Finishing Facility, which provides a second contact of monosodium titanate (MST) to remove soluble actinides and strontium from waste if needed. This treatment will occur after cesium removal by Caustic-Side Solvent Extraction (CSSX). Although the process changes and safety basis implications have not yet been analyzed, provisions also exist to recover the MST from this operation and return to the initial actinide removal step in the SWPF for an additional (third) contact with fresh waste. A U.S. Department of Energy (DOE) request identified the need to study the following issues involving this application of MST: Determine the effect of organics from the solvent extraction (CSSX) process on radionuclide sorption by MST; Determine the efficiency of re-using MST for multiple contacts; and Examine fissile loading on MST under conditions using a waste containing significantly elevated concentrations of plutonium, uranium, neptunium, and strontium. This report describes the results of three experimental studies conducted to address these needs: (1) Addition of high concentrations of entrained CSSX solvent had no noticeable effect, over a two week period, on the sorption of the actinides and strontium by MST in a direct comparison experiment. (2) Test results show that MST still retains appreciable capacity after being used once. For instance, reused MST--in the presence of entrained solvent--continued to sorb actinides and strontium. (3) A single batch of MST was used to sequentially contact five volumes of a simulant solution containing elevated concentrations of the radionuclides of interest. After the five contacts, we measured the following solution actinide loadings on the MST: plutonium: 0.884 ± 0.00539 wt % or (1.02 ± 0.0112) E+04 (micro)g/g MST, uranium: 12.1 ± 0.786 wt % or (1.40 ± 0.104) E+05 (micro)g/g MST, and neptunium: 0.426 ± 0.00406 wt % or

  10. Genetic deletion of Mst1 alters T cell function and protects against autoimmunity.

    Directory of Open Access Journals (Sweden)

    Konstantin V Salojin

    Full Text Available Mammalian sterile 20-like kinase 1 (Mst1 is a MAPK kinase kinase kinase which is involved in a wide range of cellular responses, including apoptosis, lymphocyte adhesion and trafficking. The contribution of Mst1 to Ag-specific immune responses and autoimmunity has not been well defined. In this study, we provide evidence for the essential role of Mst1 in T cell differentiation and autoimmunity, using both genetic and pharmacologic approaches. Absence of Mst1 in mice reduced T cell proliferation and IL-2 production in vitro, blocked cell cycle progression, and elevated activation-induced cell death in Th1 cells. Mst1 deficiency led to a CD4+ T cell development path that was biased toward Th2 and immunoregulatory cytokine production with suppressed Th1 responses. In addition, Mst1-/- B cells showed decreased stimulation to B cell mitogens in vitro and deficient Ag-specific Ig production in vivo. Consistent with altered lymphocyte function, deletion of Mst1 reduced the severity of experimental autoimmune encephalomyelitis (EAE and protected against collagen-induced arthritis development. Mst1-/- CD4+ T cells displayed an intrinsic defect in their ability to respond to encephalitogenic antigens and deletion of Mst1 in the CD4+ T cell compartment was sufficient to alleviate CNS inflammation during EAE. These findings have prompted the discovery of novel compounds that are potent inhibitors of Mst1 and exhibit desirable pharmacokinetic properties. In conclusion, this report implicates Mst1 as a critical regulator of adaptive immune responses, Th1/Th2-dependent cytokine production, and as a potential therapeutic target for immune disorders.

  11. PCR-Based EST Mapping in Wheat (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    J. PERRY GUSTAFSON

    2009-04-01

    Full Text Available Mapping expressed sequence tags (ESTs to hexaploid wheat is aimed to reveal the structure and function of the hexaploid wheat genome. Sixty eight ESTs representing 26 genes were mapped into all seven homologous chromosome groups of wheat (Triticum aestivum L using a polymerase chain reaction technique. The majority of the ESTs were mapped to homologous chromosome group 2, and the least were mapped to homologous chromosome group 6. Comparative analysis between the EST map from this study and the EST map based on RFLPs showed 14 genes that have been mapped by both approaches were mapped to the same arm of the same homologous chromosome, which indicated that using PCR-based ESTs was a reliable approach in mapping ESTs in hexaploid wheat.

  12. MST radar data-base management

    Science.gov (United States)

    Wickwar, V. B.

    1983-01-01

    Data management for Mesospheric-Stratospheric-Tropospheric, (MST) radars is addressed. An incoherent-scatter radar data base is discussed in terms of purpose, centralization, scope, and nature of the data base management system.

  13. MST - CEARÁ, 20 ANOS DE MARCHAS

    Directory of Open Access Journals (Sweden)

    Francisco Amaro Gomes de Alencar

    2010-01-01

    Full Text Available Este trabajo pretende hacer un rescate geográfi co e histórico de los veinte años del "Movimiento de los Trabajadores Rurales Sin Tierra" en Ceará (MST- CE, 1989 a 2009. Durante esos años, varias fueron las formas de luchas para que la espacialización y la territorialización del MST que sucedieron en Ceará. Algunas de esas formas de luchas fueron: los confl ictos; las ocupaciones de tierras, de los edifi cios públicos y de las avenidas; las marchas, la presencia de los militantes, en los asentamientos federal y estaduales, de los varios programas de reforma agraria. Para abordar esas marchas del MST-Ceará, este texto está estructurado en 4 partes. En la primera, la "Introducción", construimos una pequeña línea del tiempo de las luchas agrarias desde las indígenas hasta la primera ocupación de tierras realizada por el Movimiento. En la segunda, "Las acciones del MST-Ceará", describimos sus principales actividades tales como: caminadas, marchas, ocupaciones de inmuebles y edifi cios públicos en el Estado. En la tercera, "Territorialización del MST en Ceará", analizamos los caminos para tornarse presente, reconocido y respetado en Ceará.

  14. Rheology Of MonoSodium Titanate (MST) And Modified Mst (mMST) Mixtures Relevant To The Salt Waste Processing Facility

    Energy Technology Data Exchange (ETDEWEB)

    Koopman, D. C.; Martino, C. J.; Shehee, T. C.; Poirier, M. R.

    2013-07-31

    The Savannah River National Laboratory performed measurements of the rheology of suspensions and settled layers of treated material applicable to the Savannah River Site Salt Waste Processing Facility. Suspended solids mixtures included monosodium titanate (MST) or modified MST (mMST) at various solid concentrations and soluble ion concentrations with and without the inclusion of kaolin clay or simulated sludge. Layers of settled solids were MST/sludge or mMST/sludge mixtures, either with or without sorbed strontium, over a range of initial solids concentrations, soluble ion concentrations, and settling times.

  15. Rheology Of MonoSodium Titanate (MST) And Modified Mst (mMST) Mixtures Relevant To The Salt Waste Processing Facility

    International Nuclear Information System (INIS)

    Koopman, D. C.; Martino, C. J.; Shehee, T. C.; Poirier, M. R.

    2013-01-01

    The Savannah River National Laboratory performed measurements of the rheology of suspensions and settled layers of treated material applicable to the Savannah River Site Salt Waste Processing Facility. Suspended solids mixtures included monosodium titanate (MST) or modified MST (mMST) at various solid concentrations and soluble ion concentrations with and without the inclusion of kaolin clay or simulated sludge. Layers of settled solids were MST/sludge or mMST/sludge mixtures, either with or without sorbed strontium, over a range of initial solids concentrations, soluble ion concentrations, and settling times

  16. Meteor detection on ST (MST) radars

    International Nuclear Information System (INIS)

    Avery, S.K.

    1987-01-01

    The ability to detect radar echoes from backscatter due to turbulent irregularities of the radio refractive index in the clear atmosphere has lead to an increasing number of established mesosphere - stratosphere - troposphere (MST or ST) radars. Humidity and temperature variations are responsible for the echo in the troposphere and stratosphere and turbulence acting on electron density gradients provides the echo in the mesosphere. The MST radar and its smaller version, the ST radar, are pulsed Doppler radars operating in the VHF - UHF frequency range. These echoes can be used to determine upper atmosphere winds at little extra cost to the ST radar configuration. In addition, the meteor echoes can supplement mesospheric data from an MST radar. The detection techniques required on the ST radar for delineating meteor echo returns are described

  17. A Digital Signature Scheme Based on MST3 Cryptosystems

    Directory of Open Access Journals (Sweden)

    Haibo Hong

    2014-01-01

    Full Text Available As special types of factorization of finite groups, logarithmic signature and cover have been used as the main components of cryptographic keys for secret key cryptosystems such as PGM and public key cryptosystems like MST1, MST2, and MST3. Recently, Svaba et. al proposed a revised MST3 encryption scheme with greater security. Meanwhile, they put forward an idea of constructing signature schemes on the basis of logarithmic signatures and random covers. In this paper, we firstly design a secure digital signature scheme based on logarithmic signatures and random covers. In order to complete the task, we devise a new encryption scheme based on MST3 cryptosystems.

  18. MST e-News June 2016

    Energy Technology Data Exchange (ETDEWEB)

    Kippen, Karen Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-06-17

    This is Los Alamos National Laboratory's (LANL) June 2016 newsletter of the Materials Science and Technology Division. The following are major topics in this newsletter: MST-8 scientists guide national efforts to overcome nuclear energy technical challenges, first-ever scanning probe microscopy capabilities for plutonium, laboratory metallurgists make thorium targets for production of cancer-fighting isotopes, and a spotlight on Veronica Livescu.

  19. Effect of sludge solids to mono-sodium titanate (MST) ratio on MST-treated sludge

    International Nuclear Information System (INIS)

    Saito, H.H.

    1999-01-01

    The Salt Disposition Systems Engineering Team has selected two cesium removal technologies for further development to replace the In-Tank Precipitation process: small tank tetraphenylborate (TPB) precipitation and crystalline silicotitanate (CST) ion exchange. In the CST ion exchange process, incoming salt solution from storage tanks containing entrained sludge solids is pretreated with monosodium titanate (MST) to adsorb strontium and plutonium. The resulting slurry is filtered using a cross-flow filter, with the permeate sent forward to CST ion exchange columns for cesium removal prior to conversion into Class A grout at the Saltstone Facility. The MST and sludge solids are to be sent for vitrification at the Defense Waste Processing Facility (DWPF). The High Level Waste Division (HLWD) requested that the Waste Processing Technology Section (WPTS) study varying the insoluble sludge solids to MST ratio to determine the relative impact of sludge and MST on filter performance. The purpose of this study was not for an exhaustive comprehensive search for an optimized insoluble sludge solids to monosodium titanate (MST) ratio, but as a scoping study to identify any effects of having an excess of either material. This document reports the results obtained

  20. Testing and Characterization of Engineered Forms of Monosodium Titanate (MST)

    International Nuclear Information System (INIS)

    Taylor-Pashow, K.; Nash, C.; Hobbs, D.

    2012-01-01

    Engineered forms of MST and mMST were prepared at ORNL using an internal gelation process. Samples of these two materials were characterized at SRNL to examine particle size and morphology, peroxide content, tapped densities, and Na, Ti, and C content. Batch contact tests were also performed to examine the performance of the materials. The E mMST material was found to contain less than 10% of the peroxide found in a freshly prepared batch of mMST. This was also evidenced in batch contact testing with both simulated and actual waste, where little difference in performance was seen between the two engineered materials, E MST and E mMST. Based on these results, attempts were made to increase the peroxide content of the materials by post-treatment with hydrogen peroxide. The peroxide treatment resulted in a slight (∼10%) increase in peroxide content; however, the peroxide:Ti molar ratio was still much lower (∼0.1 X) than what is seen in a freshly prepared batch of mMST. Testing with simulated waste showed the performance of the peroxide treated materials was improved. Batch contact tests were also performed with an earlier (2003) prepared lot of E MST to examine the effect of ionic strength on the performance of the material. In general the results showed a decrease in removal performance with increasing ionic strength, which is consistent with previous testing with MST. A Sr loading isotherm was also determined, and the E MST material was found to reach a Sr loading as high as 13.2 wt % after 100 days of contact at a phase ratio of 20000 mL/g. At the typical MST phase ratio of 2500 mL/g (0.4 g/L), a Sr loading of 2.64 wt % was reached after 506 hours of contact. Samples of E MST and the post-peroxide treated E mMST were also tested in a column configuration using simulated waste solution. The breakthrough curves along with analysis of the sorbent beds at the conclusion of the experiments showed that the peroxide treated E mMST has a higher Sr and Np capacity, but

  1. TESTING AND CHARACTERIZATION OF ENGINEERED FORMS OF MONOSODIUM TITANATE (MST)

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K.; Nash, C.; Hobbs, D.

    2012-05-14

    Engineered forms of MST and mMST were prepared at ORNL using an internal gelation process. Samples of these two materials were characterized at SRNL to examine particle size and morphology, peroxide content, tapped densities, and Na, Ti, and C content. Batch contact tests were also performed to examine the performance of the materials. The {sup E}mMST material was found to contain less than 10% of the peroxide found in a freshly prepared batch of mMST. This was also evidenced in batch contact testing with both simulated and actual waste, where little difference in performance was seen between the two engineered materials, {sup E}MST and {sup E}mMST. Based on these results, attempts were made to increase the peroxide content of the materials by post-treatment with hydrogen peroxide. The peroxide treatment resulted in a slight ({approx}10%) increase in peroxide content; however, the peroxide:Ti molar ratio was still much lower ({approx}0.1 X) than what is seen in a freshly prepared batch of mMST. Testing with simulated waste showed the performance of the peroxide treated materials was improved. Batch contact tests were also performed with an earlier (2003) prepared lot of {sup E}MST to examine the effect of ionic strength on the performance of the material. In general the results showed a decrease in removal performance with increasing ionic strength, which is consistent with previous testing with MST. A Sr loading isotherm was also determined, and the {sup E}MST material was found to reach a Sr loading as high as 13.2 wt % after 100 days of contact at a phase ratio of 20000 mL/g. At the typical MST phase ratio of 2500 mL/g (0.4 g/L), a Sr loading of 2.64 wt % was reached after 506 hours of contact. Samples of {sup E}MST and the post-peroxide treated {sup E}mMST were also tested in a column configuration using simulated waste solution. The breakthrough curves along with analysis of the sorbent beds at the conclusion of the experiments showed that the peroxide treated

  2. Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme

    Directory of Open Access Journals (Sweden)

    Tatiana Rochat

    2017-09-01

    Full Text Available Flavobacterium psychrophilum is a devastating bacterial pathogen of salmonids reared in freshwater worldwide. So far, serological diversity between isolates has been described but the underlying molecular factors remain unknown. By combining complete genome sequence analysis and the serotyping method proposed by Lorenzen and Olesen (1997 for a set of 34 strains, we identified key molecular determinants of the serotypes. This knowledge allowed us to develop a robust multiplex PCR-based serotyping scheme, which was applied to 244 bacterial isolates. The results revealed a striking association between PCR-serotype and fish host species and illustrate the use of this approach as a simple and cost-effective method for the determination of F. psychrophilum serogroups. PCR-based serotyping could be a useful tool in a range of applications such as disease surveillance, selection of salmonids for bacterial coldwater disease resistance and future vaccine formulation.

  3. Robust MST-Based Clustering Algorithm.

    Science.gov (United States)

    Liu, Qidong; Zhang, Ruisheng; Zhao, Zhili; Wang, Zhenghai; Jiao, Mengyao; Wang, Guangjing

    2018-06-01

    Minimax similarity stresses the connectedness of points via mediating elements rather than favoring high mutual similarity. The grouping principle yields superior clustering results when mining arbitrarily-shaped clusters in data. However, it is not robust against noises and outliers in the data. There are two main problems with the grouping principle: first, a single object that is far away from all other objects defines a separate cluster, and second, two connected clusters would be regarded as two parts of one cluster. In order to solve such problems, we propose robust minimum spanning tree (MST)-based clustering algorithm in this letter. First, we separate the connected objects by applying a density-based coarsening phase, resulting in a low-rank matrix in which the element denotes the supernode by combining a set of nodes. Then a greedy method is presented to partition those supernodes through working on the low-rank matrix. Instead of removing the longest edges from MST, our algorithm groups the data set based on the minimax similarity. Finally, the assignment of all data points can be achieved through their corresponding supernodes. Experimental results on many synthetic and real-world data sets show that our algorithm consistently outperforms compared clustering algorithms.

  4. "Transit data"-based MST computation

    Directory of Open Access Journals (Sweden)

    Thodoris Karatasos

    2017-10-01

    Full Text Available In this work, we present an innovative image recognition technique which is based on the exploitation of transit-data in images or simple photographs of sites of interest. Our objective is to automatically transform real-world images to graphs and, then, compute Minimum Spanning Trees (MST in them.We apply this framework and present an application which automatically computes efficient construction plans (for escalator or low-emission hot spots for connecting all points of interest in cultural sites, i.e., archaeological sites, museums, galleries, etc, aiming to to facilitate global physical access to cultural heritage and artistic work and make it accessible to all groups of population.

  5. Veja o MST! - Um frame revelado

    Directory of Open Access Journals (Sweden)

    Adriana Maria Tenuta de Azevedo

    2005-01-01

    Full Text Available Esta é uma análise de duas reportagens jornalísticas publicadas em 3/04/2002, referentes a um único episódio: a invasão, liderada pelo Movimento dos Trabalhadores Sem-Terra (MST, da Fazenda Córrego da Ponte, situada em Buritis, Minas Gerais, de propriedade da família do então presidente Fernando Henrique Cardoso, ocorrida em 23/03/2002. Tal análise revela, no texto da Revista Veja (p. 46 a 50, a construção, principalmente através de recursos lexicais, de um determinado modelo cognitivo idealizado - frame - (Fauconnier, 1997 - subjacente à macro-estrutura do texto, o que não ocorre em relação à reportagem da Revista Isto é (p. 31 a 34. A existência de tal frame, compartilhada culturalmente por escritores e leitores, leva, por parte destes, a interpretações maniqueístas do evento sendo reportado.The present work is an analysis of two magazine reports referring to the episode of the invasion of Córrego da Ponte Farm, situated in Buritis, MG, which happened on March 23rd, 2002, led by the Landless Workers Movement (MST. Córrego da Ponte is property of the family of Fernando Henrique Cardoso (The president of Brazil at that time. The first of those reports (Veja Magazine, April 3rd, 2002, p. 46 to 50 is seen in details, since it presents elements of an idealized cognitive model - frame (Fauconnier, 1997 underlying the superstructure of the text. The existence of such frame, revealed by certain linguistic elements, especially the lexical choice, tends to raise dualistic interpretations of the socio-political event being reported. The second one (Isto é Magazine, edition 1696, April 03rd, 2002, p. 31 to 34 is taken as a differentiated parameter, for comparison to the analysis proposal for the first report.

  6. Improvements to the MST Thomson Scattering Diagnostic

    Science.gov (United States)

    Adams, D. T.; Borchardt, M. T.; den Hartog, D. J.; Holly, D. J.; Kile, T.; Kubala, S. Z.; Jacobson, C. M.; Thomas, M. A.; Wallace, J. P.; Young, W. C.; MST Thomson Scattering Team

    2017-10-01

    Multiple upgrades to the MST Thomson Scattering diagnostic have been implemented to expand capabilities of the system. In the past, stray laser light prevented electron density measurements everywhere and temperature measurements for -z/a >0.75. To mitigate stray light, a new laser beamline is being commissioned that includes a longer entrance flight tube, close-fitting apertures, and baffles. A polarizer has been added to the collection optics to further reduce stray light. An absolute density calibration using Rayleigh scattering in argon will be performed. An insertable integrating sphere will provide a full-system spectral calibration as well as maps optical fibers to machine coordinates. Reduced transmission of the collection optics due to coatings from plasma-surface interactions is regularly monitored to inform timely replacements of the first lens. Long-wavelength filters have been installed to better characterize non-Maxwellian electron distribution features. Previous work has identified residual photons not described by a Maxwellian distribution during m =0 magnetic bursts. Further effort to characterize the distribution function will be described. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences program under Award No. DE-FC02-05ER54814.

  7. MST 1: Proceedings of a conference on the integration of mathematics, science and technology in precollege education

    Energy Technology Data Exchange (ETDEWEB)

    Swyler, K. [ed.

    1995-11-01

    Example MST activities examined here show: (1) an inquiry-driven learning stimulus, involving (2) the synthesis of concepts in math, science and technology, through (3) the application of the scientific method and engineering problem solving/test protocols, and provoking (4) a stimulus for further exploration. A semi-exploratory learning approach offered background aimed at enabling participants to take meaningful courses of investigation; this approach must be balanced by maintaining contact with framework content standards. On the whole, the philosophy underlying the MST learning approach--as envisioned in the draft NYS Framework, and embodied in the example activities--is strongly endorsed. This endorsement is broad-based: those represented include teachers of mathematics, science, and technology, and school district administrators--in roughly equal numbers. Discussion centers not on whether the MST approach should be pursued, but on what is involved in doing it. Teams of conference participants were given time to plan or extend MST initiatives in their own districts. Outlines of the initiatives proposed by ten of the teams are disseminated herein.

  8. A Ribeiroia spp. (Class: Trematoda) - Specific PCR-based diagnostic

    Science.gov (United States)

    Reinitz, David M.; Yoshino, T.P.; Cole, Rebecca A.

    2007-01-01

    Increased reporting of amphibian malformations in North America has been noted with concern in light of reports that amphibian numbers and species are declining worldwide. Ribeiroia ondatrae has been shown to cause a variety of types of malformations in amphibians. However, little is known about the prevalence of R. ondatrae in North America. To aid in conducting field studies of Ribeiroia spp., we have developed a polymerase chain reaction (PCR)-based diagnostic. Herein, we describe the development of an accurate, rapid, simple, and cost-effective diagnostic for detection of Ribeiroia spp. infection in snails (Planorbella trivolvis). Candidate oligonucleotide primers for PCR were designed via DNA sequence analyses of multiple ribosomal internal transcribed spacer-2 regions from Ribeiroia spp. and Echinostoma spp. Comparison of consensus sequences determined from both genera identified areas of sequence potentially unique to Ribeiroia spp. The PCR reliably produced a diagnostic 290-base pair (bp) product in the presence of a wide concentration range of snail or frog DNA. Sensitivity was examined with DNA extracted from single R. ondatrae cercaria. The single-tube PCR could routinely detect less than 1 cercariae equivalent, because DNA isolated from a single cercaria could be diluted at least 1:50 and still yield a positive result via gel electrophoresis. An even more sensitive nested PCR also was developed that routinely detected 100 fg of the 290-bp fragment. The assay did not detect furcocercous cercariae of certain Schistosomatidae, Echinostoma sp., or Sphaeridiotrema globulus nor adults of Clinostomum sp. or Cyathocotyle bushiensis. Field testing of 137 P. trivolvis identified 3 positives with no overt environmental cross-reactivity, and results concurred with microscopic examinations in all cases. ?? American Society of Parasitologists 2007.

  9. Assessment of performing an MST strike in Tank 21H

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, Michael R.

    2014-09-29

    Previous Savannah River National Laboratory (SRNL) tank mixing studies performed for the Small Column Ion Exchange (SCIX) project have shown that 3 Submersible Mixer Pumps (SMPs) installed in Tank 41 are sufficient to support actinide removal by MST sorption as well as subsequent resuspension and removal of settled solids. Savannah River Remediation (SRR) is pursuing MST addition into Tank 21 as part of the Large Tank Strike (LTS) project. The preliminary scope for LTS involves the use of three standard slurry pumps (installed in N, SE, and SW risers) in a Type IV tank. Due to the differences in tank size, internal interferences, and pump design, a separate mixing evaluation is required to determine if the proposed configuration will allow for MST suspension and strontium and actinide sorption. The author performed the analysis by reviewing drawings for Tank 21 [W231023] and determining the required cleaning radius or zone of influence for the pumps. This requirement was compared with previous pilot-scale MST suspension data collected for SCIX that determined the cleaning radius, or zone of influence, as a function of pump operating parameters. The author also reviewed a previous Tank 50 mixing analysis that examined the ability of standard slurry pumps to suspend sludge particles. Based on a review of the pilot-scale SCIX mixing tests and Tank 50 pump operating experience, three standard slurry pumps should be able to suspend sludge and MST to effectively sorb strontium and actinides onto the MST. Using the SCIX data requires an assumption about the impact of cooling coils on slurry pump mixing. The basis for this assumption is described in this report. Using the Tank 50 operating experience shows three standard slurry pumps should be able to suspend solids if the shear strength of the settled solids is less than 160 Pa. Because Tank 21 does not contain cooling coils, the shear strength could be larger.

  10. System aspects of the Indian MST radar facility

    Science.gov (United States)

    Viswanathan, G.

    1986-01-01

    One of the major objectives of the Indian Middle Atmosphere Program is to investigate the motions of the middle atmosphere on temporal and spatial scales and the interaction between the three height regions of the middle atmosphere. Realizing the fact that radar technique has proven to be a very powerful tool for the study of Earth atmosphere, the Indian Middle Atmosphere Program has recommended establishing a mesosphere-stratosphere-troposphere (MST) radar as a national facility for atmospheric research. The major landmarks in this attempt to setup the MST radar as a national facility are described.

  11. Overview of results from the MST reversed field pinch experiment

    International Nuclear Information System (INIS)

    Sarff, J.S.; Almagri, A.F.; Anderson, J.K.; Borchardt, M.; Carmody, D.; Caspary, K.; Chapman, B.E.; Den Hartog, D.J.; Duff, J.; Eilerman, S.; Falkowski, A.; Forest, C.B.; Goetz, J.A.; Holly, D.J.; Kim, J.-H.; King, J.; Ko, J.; Koliner, J.; Kumar, S.; Lee, J.D.

    2013-01-01

    An overview of recent results from the MST programme on physics important for the advancement of the reversed field pinch (RFP) as well as for improved understanding of toroidal magnetic confinement more generally is reported. Evidence for the classical confinement of ions in the RFP is provided by analysis of impurity ions and energetic ions created by 1 MW neutral beam injection (NBI). The first appearance of energetic-particle-driven modes by NBI in a RFP plasma is described. MST plasmas robustly access the quasi-single-helicity state that has commonalities to the stellarator and ‘snake’ formation in tokamaks. In MST the dominant mode grows to 8% of the axisymmetric field strength, while the remaining modes are reduced. Predictive capability for tearing mode behaviour has been improved through nonlinear, 3D, resistive magnetohydrodynamic computation using the measured resistivity profile and Lundquist number, which reproduces the sawtooth cycle dynamics. Experimental evidence and computational analysis indicates two-fluid effects, e.g., Hall physics and gyro-viscosity, are needed to understand the coupling of parallel momentum transport and current profile relaxation. Large Reynolds and Maxwell stresses, plus separately measured kinetic stress, indicate an intricate momentum balance and a possible origin for MST's intrinsic plasma rotation. Gyrokinetic analysis indicates that micro-tearing modes can be unstable at high beta, with a critical gradient for the electron temperature that is larger than for tokamak plasmas by roughly the aspect ratio. (paper)

  12. Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters.

    Science.gov (United States)

    Bergmann, I; Mundt, K; Sontag, M; Baumstark, I; Nettmann, E; Klocke, M

    2010-03-01

    Quantitative real-time PCR (Q-PCR) is commonly applied for the detection of certain microorganisms in environmental samples. However, some environments, like biomass-degrading biogas fermenters, are enriched with PCR-interfering substances. To study the impact of the DNA extraction protocol on the results of Q-PCR-based analysis of the methane-producing archaeal community in biogas fermenters, nine different protocols with varying cell disruption and DNA purification approaches were tested. Differences in the quantities of the isolated DNA and the purity parameters were found, with the best cell lysis efficiencies being obtained by a combined lysozyme/SDS-based lysis. When DNA was purified by sephacryl columns, the amount of DNA decreased by one log cycle but PCR inhibitors were eliminated sufficiently. In the case of detection of methanogenic Archaea, the chosen DNA isolation protocol strongly influenced the Q-PCR-based determination of 16S rDNA copy numbers. For example, with protocols including mechanical cell disruption, the 16S rDNA of Methanobacteriales were predominantly amplified (81-90% of the total 16S rDNA copy numbers), followed by the 16S rDNA of Methanomicrobiales (9-18%). In contrast, when a lysozyme/SDS-based cell lysis was applied, the 16S rDNA copy numbers determined for these two orders were the opposite (Methanomicrobiales 82-95%, Methanobacteriales 4-18%). In extreme cases, the DNA isolation method led to discrimination of some groups of methanogens (e.g. members of the Methanosaetaceae). In conclusion, for extraction of high amounts of microbial DNA with high purity from samples of biogas plants, a combined lysozyme/SDS-based cell lysis followed by a purification step with sephacryl columns is recommended. Copyright 2010 Elsevier GmbH. All rights reserved.

  13. Development and validation of a Q-PCR based TCID50 method for human herpesvirus 6

    Directory of Open Access Journals (Sweden)

    Gustafsson Rasmus K L

    2012-12-01

    Full Text Available Abstract Background For titer assessment of human herpesvirus 6 (HHV-6, IFA targeting viral proteins or a TCID50 method with ocular inspection for CPE can be used. These methods rely on the subjective decision of the assessor, obstructing the ability to obtain unanimous results. Findings We have developed and validated an alternative TCID50 read-out approach where infection in the titration culture plate is assessed by viral DNA load change by quantitative PCR. A ten time increase in viral DNA load was determined as cut point for infection since that yielded a maximum correlation with viral protein expression (93%. The average intra-assay CV was 9% for quantitative PCR read-out of TCID50 compared to 45% for ocular inspection read-out of TCID50, 14% for IFA read-out of TCID50, and 43% for an infectious units approach using IFA. The average inter-assay CV for quantitative PCR read-out of TCID50 was 73%, compared to 66%, 25% and 77% for the ocular inspection read-out for TCID50, IFA read-out of TCID50 and infectious unit approaches respectively. Conclusions The quantitative PCR based read-out of TCID50 proved to be more robust and easier to interpret than traditional TCID50 assessment approaches for HHV-6, and therefore it might be considered as an alternative method.

  14. Hypermethylation of MST1 in IgG4-related autoimmune pancreatitis and rheumatoid arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Fukuhara, Takataro; Tomiyama, Takashi [Division of Gastroenterology and Hepatology, The Third Department of Internal Medicine, JST CREST, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan); Yasuda, Kaneki [Department of Urology and Andrology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan); Ueda, Yoshihiro [Department of Molecular Genetics, Institute of Biomedical Science, and JST CREST, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan); Ozaki, Yoshio; Son, Yonsu; Nomura, Shosaku [Department of the First Department of Internal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan); Uchida, Kazushige; Okazaki, Kazuichi [Division of Gastroenterology and Hepatology, The Third Department of Internal Medicine, JST CREST, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan); Kinashi, Tatsuo, E-mail: kinashi@takii.kmu.ac.jp [Department of Molecular Genetics, Institute of Biomedical Science, and JST CREST, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010 (Japan)

    2015-08-07

    The serine/threonine kinase Mst1 plays important roles in the control of immune cell trafficking, proliferation, and differentiation. Previously, we reported that Mst1 was required for thymocyte selection and regulatory T-cell functions, thereby the prevention of autoimmunity in mice. In humans, MST1 null mutations cause T-cell immunodeficiency and hypergammaglobulinemia with autoantibody production. RASSF5C(RAPL) is an activator of MST1 and it is frequently methylated in some tumors. Herein, we investigated methylation of the promoter regions of MST1 and RASSF5C(RAPL) in leukocytes from patients with IgG4-related autoimmune pancreatitis (AIP) and rheumatoid arthritis (RA). Increased number of CpG methylation in the 5′ region of MST1 was detected in AIP patients with extrapancreatic lesions, whereas AIP patients without extrapancreatic lesions were similar to controls. In RA patients, we detected a slight increased CpG methylation in MST1, although the overall number of methylation sites was lower than that of AIP patients with extrapancreatic lesions. There were no significant changes of the methylation levels of the CpG islands in the 5′ region of RASSF5C(RAPL) in leukocytes from AIP and RA patients. Consistently, we found a significantly down-regulated expression of MST1 in regulatory T cells of AIP patients. Our results suggest that the decreased expression of MST1 in regulatory T cells due to hypermethylation of the promoter contributes to the pathogenesis of IgG4-related AIP. - Highlights: • Mst1 controls immune cells trafficking, cell proliferation and differentiation. • Autoimmune pancreatitis (AIP) is an idiopathic pancreatitis affecting multiple organs. • Decreased MST1 expression and increased CpG methylation of promoter of MST1 in AIP. • Slight increased CpG methylation of MST1 in rheumatoid arthritis patients. • MST1 contributes pathogenesis of IgG4-related AIP.

  15. Hypermethylation of MST1 in IgG4-related autoimmune pancreatitis and rheumatoid arthritis

    International Nuclear Information System (INIS)

    Fukuhara, Takataro; Tomiyama, Takashi; Yasuda, Kaneki; Ueda, Yoshihiro; Ozaki, Yoshio; Son, Yonsu; Nomura, Shosaku; Uchida, Kazushige; Okazaki, Kazuichi; Kinashi, Tatsuo

    2015-01-01

    The serine/threonine kinase Mst1 plays important roles in the control of immune cell trafficking, proliferation, and differentiation. Previously, we reported that Mst1 was required for thymocyte selection and regulatory T-cell functions, thereby the prevention of autoimmunity in mice. In humans, MST1 null mutations cause T-cell immunodeficiency and hypergammaglobulinemia with autoantibody production. RASSF5C(RAPL) is an activator of MST1 and it is frequently methylated in some tumors. Herein, we investigated methylation of the promoter regions of MST1 and RASSF5C(RAPL) in leukocytes from patients with IgG4-related autoimmune pancreatitis (AIP) and rheumatoid arthritis (RA). Increased number of CpG methylation in the 5′ region of MST1 was detected in AIP patients with extrapancreatic lesions, whereas AIP patients without extrapancreatic lesions were similar to controls. In RA patients, we detected a slight increased CpG methylation in MST1, although the overall number of methylation sites was lower than that of AIP patients with extrapancreatic lesions. There were no significant changes of the methylation levels of the CpG islands in the 5′ region of RASSF5C(RAPL) in leukocytes from AIP and RA patients. Consistently, we found a significantly down-regulated expression of MST1 in regulatory T cells of AIP patients. Our results suggest that the decreased expression of MST1 in regulatory T cells due to hypermethylation of the promoter contributes to the pathogenesis of IgG4-related AIP. - Highlights: • Mst1 controls immune cells trafficking, cell proliferation and differentiation. • Autoimmune pancreatitis (AIP) is an idiopathic pancreatitis affecting multiple organs. • Decreased MST1 expression and increased CpG methylation of promoter of MST1 in AIP. • Slight increased CpG methylation of MST1 in rheumatoid arthritis patients. • MST1 contributes pathogenesis of IgG4-related AIP

  16. Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis.

    Science.gov (United States)

    Waterfall, C M; Cobb, B D

    2001-12-01

    Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a 'matrix-based' optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.

  17. MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells

    International Nuclear Information System (INIS)

    Yu, Teng; Ji, Jiang; Guo, Yong-li

    2013-01-01

    Highlights: •Curcumin activates MST1 in melanoma cells. •MST1 mediates curcumin-induced apoptosis of melanoma cells. •ROS production is involved in curcumin-induced MST1 activation. •MST1 mediates curcumin-induced JNK activation in melanoma cells. •MST1 mediates curcumin-induced Foxo3a nuclear translocation and Bim expression. -- Abstract: Different groups including ours have shown that curcumin induces melanoma cell apoptosis, here we focused the role of mammalian Sterile 20-like kinase 1 (MST1) in it. We observed that curcumin activated MST1-dependent apoptosis in cultured melanoma cells. MST1 silencing by RNA interference (RNAi) suppressed curcumin-induced cell apoptosis, while MST1 over-expressing increased curcumin sensitivity. Meanwhile, curcumin induced reactive oxygen species (ROS) production in melanoma cells, and the ROS scavenger, N-acetyl-cysteine (NAC), almost blocked MST1 activation to suggest that ROS might be required for MST1 activation by curcumin. c-Jun N-terminal protein kinase (JNK) activation by curcumin was dependent on MST1, since MST1 inhibition by RNAi or NAC largely inhibited curcumin-induced JNK activation. Further, curcumin induced Foxo3 nuclear translocation and Bim-1 (Foxo3 target gene) expression in melanoma cells, such an effect by curcumin was inhibited by MST1 RNAi. In conclusion, we suggested that MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells

  18. MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Teng, E-mail: tengyu33@yahoo.com [Department of Dermatology, Shandong Ji-ning No. 1 People’s Hospital, Shandong Province 272011 (China); Ji, Jiang [Department of Dermatology, The Second Hospital Affiliated of Soochow University, SuZhou, Jiangsu Province 215000 (China); Guo, Yong-li [Department of Oncology, Shandong Ji-ning No. 1 People’s Hospital, Shandong Province 272011 (China)

    2013-11-08

    Highlights: •Curcumin activates MST1 in melanoma cells. •MST1 mediates curcumin-induced apoptosis of melanoma cells. •ROS production is involved in curcumin-induced MST1 activation. •MST1 mediates curcumin-induced JNK activation in melanoma cells. •MST1 mediates curcumin-induced Foxo3a nuclear translocation and Bim expression. -- Abstract: Different groups including ours have shown that curcumin induces melanoma cell apoptosis, here we focused the role of mammalian Sterile 20-like kinase 1 (MST1) in it. We observed that curcumin activated MST1-dependent apoptosis in cultured melanoma cells. MST1 silencing by RNA interference (RNAi) suppressed curcumin-induced cell apoptosis, while MST1 over-expressing increased curcumin sensitivity. Meanwhile, curcumin induced reactive oxygen species (ROS) production in melanoma cells, and the ROS scavenger, N-acetyl-cysteine (NAC), almost blocked MST1 activation to suggest that ROS might be required for MST1 activation by curcumin. c-Jun N-terminal protein kinase (JNK) activation by curcumin was dependent on MST1, since MST1 inhibition by RNAi or NAC largely inhibited curcumin-induced JNK activation. Further, curcumin induced Foxo3 nuclear translocation and Bim-1 (Foxo3 target gene) expression in melanoma cells, such an effect by curcumin was inhibited by MST1 RNAi. In conclusion, we suggested that MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells.

  19. Long-PCR based next generation sequencing of the whole mitochondrial genome of the peacock skate Pavoraja nitida (Elasmobranchii: Arhynchobatidae).

    Science.gov (United States)

    Yang, Lei; Naylor, Gavin J P

    2016-01-01

    We determined the complete mitochondrial genome sequence (16,760 bp) of the peacock skate Pavoraja nitida using a long-PCR based next generation sequencing method. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement. Primers, protocols, and procedures used to obtain this mitogenome are provided. We anticipate that this approach will facilitate rapid collection of mitogenome sequences for studies on phylogenetic relationships, population genetics, and conservation of cartilaginous fishes.

  20. Multiplex PCR-based assay for detection of Bordetella pertussis in nasopharyngeal swab specimens.

    Science.gov (United States)

    Wadowsky, R M; Michaels, R H; Libert, T; Kingsley, L A; Ehrlich, G D

    1996-11-01

    A multiplex PCR-based assay was developed for the detection of Bordetella pertussis in nasopharyngeal swab specimens. The assay simultaneously amplified two separate DNA targets (153 and 203 bp) within a B. pertussis repetitive element and a 438-bp target within the beta-actin gene of human DNA (PCR amplification control). PCR products were detected by a sensitive and specific liquid hybridization gel retardation assay. A total of 496 paired nasopharyngeal swab specimens were tested by both the PCR-based assay and culture. Although 30 (6%) of the specimens inhibited the amplification of the beta-actin target, in all 29 specimens studied, the inhibition disappeared on repeat testing or was easily overcome with a 1:8 dilution or less of specimen digest. Of the 495 specimen pairs yielding a final evaluable result by the PCR-based assay, 19.0% were positive by the PCR-based assay, whereas 13.9% were positive by culture (P < 0.0001). After resolving the PCR-positive, culture-negative results by testing an additional aliquot from these specimens by the multiplex PCR-based assay, the PCR-based assay had a sensitivity and specificity of 98.9 and 99.7%, respectively, compared with values of 73.4 and 100%, respectively, for culture. In comparison with patients with culture-confirmed pertussis, those with PCR-positive, culture-negative results were older and more likely to have had prolonged cough, immunization with pertussis vaccine, or treatment with erythromycin. This multiplex PCR-based assay is substantially more sensitive than culture and identifies specimens that contain inhibitors of PCR.

  1. Computerized adaptive and multistage testing with R using packages catR and mstR

    CERN Document Server

    Magis, David; von Davier, Alina A

    2017-01-01

    The goal of this guide and manual is to provide a practical and brief overview of the theory on computerized adaptive testing (CAT) and multistage testing (MST) and to illustrate the methodologies and applications using R open source language and several data examples.  Implementation relies on the R packages catR and mstR that have been already or are being developed by the first author (with the team) and that include some of the newest research algorithms on the topic. The book covers many topics along with the R-code: the basics of R, theoretical overview of CAT and MST, CAT designs, CAT assembly methodologies, CAT simulations, catR package, CAT applications, MST designs, IRT-based MST methodologies, tree-based MST methodologies, mstR package, and MST applications.  CAT has been used in many large-scale assessments over recent decades, and MST has become very popular in recent years.  R open source language also has become one of the most useful tools for applications in almost all fields, including b...

  2. Prospective IS-MST radar. Potential and diagnostic capabilities

    Directory of Open Access Journals (Sweden)

    Potekhin A.P.

    2016-09-01

    Full Text Available In the next few years, a new radar is planned to be built near Irkutsk. It should have capabilities of incoherent scatter (IS radars and mesosphere-stratosphere-troposphere (MST radars [Zherebtsov et al., 2011]. The IS-MST radar is a phased array of two separated antenna panels with a multichannel digital receiving system, which allows detailed space-time processing of backscattered signal. This paper describes characteristics, configuration, and capabilities of the antenna and transceiver systems of this radar. We estimate its potential in basic operating modes to study the ionosphere by the IS method at heights above 100 km and the atmosphere with the use of signals scattered from refractive index fluctuations, caused by turbulent mixing at heights below 100 km. The modeling shows that the radar will allow us to regularly measure neutral atmosphere parameters at heights up to 26 km as well as to observe mesosphere summer echoes at heights near 85 km in the presence of charged ice particles (an increase in Schmidt number and mesosphere winter echoes at heights near 65 km with increasing background electron density. Evaluation of radar resources at the IS mode in two height ranges 100–600 and 600–2000 km demonstrates that in the daytime and with the accumulation time of 10 min, the upper boundaries of electron density and ionospheric plasma temperature are ~1500 and ~1300 km respectively, with the standard deviation of no more than 10 %. The upper boundary of plasma drift velocity is ~1100 km with the standard deviation of 45 m/s. The estimation of interferometric capabilities of the MST radar shows that it has a high sensitivity to objects of angular size near 7.5 arc min, and its potential accuracy in determining target angles can reach 40 arc sec.

  3. Locked modes and magnetic field errors in MST

    International Nuclear Information System (INIS)

    Almagri, A.F.; Assadi, S.; Prager, S.C.; Sarff, J.S.; Kerst, D.W.

    1992-06-01

    In the MST reversed field pinch magnetic oscillations become stationary (locked) in the lab frame as a result of a process involving interactions between the modes, sawteeth, and field errors. Several helical modes become phase locked to each other to form a rotating localized disturbance, the disturbance locks to an impulsive field error generated at a sawtooth crash, the error fields grow monotonically after locking (perhaps due to an unstable interaction between the modes and field error), and over the tens of milliseconds of growth confinement degrades and the discharge eventually terminates. Field error control has been partially successful in eliminating locking

  4. MST4 kinase phosphorylates ACAP4 protein to orchestrate apical membrane remodeling during gastric acid secretion.

    Science.gov (United States)

    Yuan, Xiao; Yao, Phil Y; Jiang, Jiying; Zhang, Yin; Su, Zeqi; Yao, Wendy; Wang, Xueying; Gui, Ping; Mullen, McKay; Henry, Calmour; Ward, Tarsha; Wang, Wenwen; Brako, Larry; Tian, Ruijun; Zhao, Xuannv; Wang, Fengsong; Cao, Xinwang; Wang, Dongmei; Liu, Xing; Ding, Xia; Yao, Xuebiao

    2017-09-29

    Digestion in the stomach depends on acidification of the lumen. Histamine-elicited acid secretion is triggered by activation of the PKA cascade, which ultimately results in the insertion of gastric H,K-ATPases into the apical plasma membranes of parietal cells. Our recent study revealed the functional role of PKA-MST4-ezrin signaling axis in histamine-elicited acid secretion. However, it remains uncharacterized how the PKA-MST4-ezrin signaling axis operates the insertion of H,K-ATPases into the apical plasma membranes of gastric parietal cells. Here we show that MST4 phosphorylates ACAP4, an ARF6 GTPase-activating protein, at Thr 545 Histamine stimulation activates MST4 and promotes MST4 interaction with ACAP4. ACAP4 physically interacts with MST4 and is a cognate substrate of MST4 during parietal cell activation. The phosphorylation site of ACAP4 by MST4 was mapped to Thr 545 by mass spectrometric analyses. Importantly, phosphorylation of Thr 545 is essential for acid secretion in parietal cells because either suppression of ACAP4 or overexpression of non-phosphorylatable ACAP4 prevents the apical membrane reorganization and proton pump translocation elicited by histamine stimulation. In addition, persistent overexpression of MST4 phosphorylation-deficient ACAP4 results in inhibition of gastric acid secretion and blockage of tubulovesicle fusion to the apical membranes. Significantly, phosphorylation of Thr 545 enables ACAP4 to interact with ezrin. Given the location of Thr 545 between the GTPase-activating protein domain and the first ankyrin repeat, we reason that MST4 phosphorylation elicits a conformational change that enables ezrin-ACAP4 interaction. Taken together, these results define a novel molecular mechanism linking the PKA-MST4-ACAP4 signaling cascade to polarized acid secretion in gastric parietal cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Interlaboratory diagnostic accuracy of a Salmonella specific PCR-based method

    DEFF Research Database (Denmark)

    Malorny, B.; Hoorfar, Jeffrey; Hugas, M.

    2003-01-01

    A collaborative study involving four European laboratories was conducted to investigate the diagnostic accuracy of a Salmonella specific PCR-based method, which was evaluated within the European FOOD-PCR project (http://www.pcr.dk). Each laboratory analysed by the PCR a set of independent obtained...... presumably naturally contaminated samples and compared the results with the microbiological culture method. The PCR-based method comprised a preenrichment step in buffered peptone water followed by a thermal cell lysis using a closed tube resin-based method. Artificially contaminated minced beef and whole......-based diagnostic methods and is currently proposed as international standard document....

  6. A novel non-canonical mechanism of regulation of MST3 (mammalian Sterile20-related kinase 3).

    Science.gov (United States)

    Fuller, Stephen J; McGuffin, Liam J; Marshall, Andrew K; Giraldo, Alejandro; Pikkarainen, Sampsa; Clerk, Angela; Sugden, Peter H

    2012-03-15

    The canonical pathway of regulation of the GCK (germinal centre kinase) III subgroup member, MST3 (mammalian Sterile20-related kinase 3), involves a caspase-mediated cleavage between N-terminal catalytic and C-terminal regulatory domains with possible concurrent autophosphorylation of the activation loop MST3(Thr(178)), induction of serine/threonine protein kinase activity and nuclear localization. We identified an alternative 'non-canonical' pathway of MST3 activation (regulated primarily through dephosphorylation) which may also be applicable to other GCKIII (and GCKVI) subgroup members. In the basal state, inactive MST3 co-immunoprecipitated with the Golgi protein GOLGA2/gm130 (golgin A2/Golgi matrix protein 130). Activation of MST3 by calyculin A (a protein serine/threonine phosphatase 1/2A inhibitor) stimulated (auto)phosphorylation of MST3(Thr(178)) in the catalytic domain with essentially simultaneous cis-autophosphorylation of MST3(Thr(328)) in the regulatory domain, an event also requiring the MST3(341-376) sequence which acts as a putative docking domain. MST3(Thr(178)) phosphorylation increased MST3 kinase activity, but this activity was independent of MST3(Thr(328)) phosphorylation. Interestingly, MST3(Thr(328)) lies immediately C-terminal to a STRAD (Sterile20-related adaptor) pseudokinase-like site identified recently as being involved in binding of GCKIII/GCKVI members to MO25 scaffolding proteins. MST3(Thr(178)/Thr(328)) phosphorylation was concurrent with dissociation of MST3 from GOLGA2/gm130 and association of MST3 with MO25, and MST3(Thr(328)) phosphorylation was necessary for formation of the activated MST3-MO25 holocomplex.

  7. The Campus take over – the MST under graduate students Ocupando o campus - uma análise sobre os universitários do MST

    Directory of Open Access Journals (Sweden)

    Emerson Dias

    2007-05-01

    Full Text Available This is an analysis how the historical and sociological influences that belong to the (Movement of the No Land Rural Workers MST are understood by the under graduate student of the movement. He is a new sociological character who arises as a resistance test to testify the capacity of reorganizing and mobilizing the country. Keywords: Rural social movements. Education. MST. O artigo analisa como as influências históricas e sociológicas que permeiam os ideais das lideranças do Movimento dos Trabalhadores Rurais Sem-Terra (MST são compreendidas pelo universitário sem-terra, este novo personagem sociológico que desponta como prova da resistência e da capacidade de reorganização das mobilizações do campo. Palavras-chave: Movimentos sociais rurais. Educação. MST.

  8. Pervanadate induces Mammalian Ste20 Kinase 3 (MST3) tyrosine phosphorylation but not activation.

    Science.gov (United States)

    Kan, Wei-Chih; Lu, Te-Ling; Ling, Pin; Lee, Te-Hsiu; Cho, Chien-Yu; Huang, Chi-Ying F; Jeng, Wen-Yih; Weng, Yui-Ping; Chiang, Chun-Yen; Wu, Jin Bin; Lu, Te-Jung

    2016-07-01

    The yeast Ste20 (sterile) protein kinase, which is a serine/threonine kinase, responds to the stimulation of the G proteincoupled receptor (GPCR) pheromone receptor. Ste20 protein kinase serves as the critical component that links signaling from the GPCR/G proteins to the mitogen-activated protein kinase (MAPK) cascade in yeast. The yeast Ste20p functions as a MAP kinase kinase kinase kinase (MAP4K) in the pheromone response. Ste20-like kinases are structurally conserved from yeast to mammals. The mechanism by which MAP4K links GPCR to the MAPK pathway is less clearly defined in vertebrates. In addition to MAP4K, the tyrosine kinase cascade bridges G proteins and the MAPK pathway in vertebrate cells. Mammalian Ste20 Kinase 3 (MST3) has been categorized into the Ste20 family and has been reported to function in the regulation of cell polarity and migration. However, whether MST3 tyrosine phosphorylation regulates diverse signaling pathways is unknown. In this study, the tyrosine phosphatase inhibitor pervanadate was found to induce MST3 tyrosine phosphorylation in intact cells, and the activity of tyrosine-phosphorylated MST3 was measured. This tyrosine-directed phosphorylation was independent of MST3 activity. Parameters including protein conformation, Triton concentration and ionic concentration influenced the sensitivity of MST3 activity. Taken together, our data suggests that the serine/threonine kinase MST3 undergoes tyrosinedirected phosphorylation. The tyrosine-phosphorylated MST3 may create a docking site for the structurally conserved SH2/SH3 (Src Homology 2 and 3) domains within the Src oncoprotein. The unusual tyrosinephosphorylated MST3 may recruit MST3 to various signaling components. Copyright © 2016. Published by Elsevier Inc.

  9. MST radar and polarization lidar observations of tropical cirrus

    Directory of Open Access Journals (Sweden)

    Y. Bhavani Kumar

    2001-08-01

    Full Text Available Significant gaps in our understanding of global cirrus effects on the climate system involve the role of frequently occurring tropical cirrus. Much of the cirrus in the atmosphere is largely due to frequent cumulus and convective activity in the tropics. In the Indian sub-tropical region, the deep convective activity is very prominent from April to December, which is a favorable period for the formation of deep cumulus clouds. The fibrous anvils of these clouds, laden with ice crystals, are one of the source mechanisms for much of the cirrus in the atmosphere. In the present study, several passages of tropical cirrus were investigated by simultaneously operating MST radar and a co-located polarization lidar at the National MST Radar Facility (NMRF, Gadanki (13.45° N, 79.18° E, India to understand its structure, the background wind field and the microphysics at the cloud boundaries. The lidar system used is capable of measuring the degree of depolarization in the laser backscatter. It has identified several different cirrus structures with a peak linear depolarization ratio (LDR in the range of 0.1 to 0.32. Simultaneous observations of tropical cirrus by the VHF Doppler radar indicated a clear enhancement of reflectivity detected in the vicinity of the cloud boundaries, as revealed by the lidar and are strongly dependent on observed cloud LDR. An inter-comparison of radar reflectivity observed for vertical and oblique beams reveals that the radar-enhanced reflectivity at the cloud boundaries is also accompanied by significant aspect sensitivity. These observations indicate the presence of anisotropic turbulence at the cloud boundaries. Radar velocity measurements show that boundaries of cirrus are associated with enhanced horizontal winds, significant vertical shear in the horizontal winds and reduced vertical velocity. Therefore, these measurements indicate that a circulation at the cloud boundaries suggest an entrainment taking place close to

  10. MST radar and polarization lidar observations of tropical cirrus

    Directory of Open Access Journals (Sweden)

    Y. Bhavani Kumar

    Full Text Available Significant gaps in our understanding of global cirrus effects on the climate system involve the role of frequently occurring tropical cirrus. Much of the cirrus in the atmosphere is largely due to frequent cumulus and convective activity in the tropics. In the Indian sub-tropical region, the deep convective activity is very prominent from April to December, which is a favorable period for the formation of deep cumulus clouds. The fibrous anvils of these clouds, laden with ice crystals, are one of the source mechanisms for much of the cirrus in the atmosphere. In the present study, several passages of tropical cirrus were investigated by simultaneously operating MST radar and a co-located polarization lidar at the National MST Radar Facility (NMRF, Gadanki (13.45° N, 79.18° E, India to understand its structure, the background wind field and the microphysics at the cloud boundaries. The lidar system used is capable of measuring the degree of depolarization in the laser backscatter. It has identified several different cirrus structures with a peak linear depolarization ratio (LDR in the range of 0.1 to 0.32. Simultaneous observations of tropical cirrus by the VHF Doppler radar indicated a clear enhancement of reflectivity detected in the vicinity of the cloud boundaries, as revealed by the lidar and are strongly dependent on observed cloud LDR. An inter-comparison of radar reflectivity observed for vertical and oblique beams reveals that the radar-enhanced reflectivity at the cloud boundaries is also accompanied by significant aspect sensitivity. These observations indicate the presence of anisotropic turbulence at the cloud boundaries. Radar velocity measurements show that boundaries of cirrus are associated with enhanced horizontal winds, significant vertical shear in the horizontal winds and reduced vertical velocity. Therefore, these measurements indicate that a circulation at the cloud boundaries suggest an entrainment taking place close to

  11. Turbulent transport in the MST reversed-field pinch

    International Nuclear Information System (INIS)

    Rempel, T.D.; Almagri, A.F.; Assadi, S.; Den Hartog, D.J.; Hokin, S.A.; Prager, S.C.; Sarff, J.S.; Shen, W.; Sidikman, K.L.; Spragins, C.W.; Sprott, J.C.; Stoneking, M.R.; Zita, E.J.

    1991-11-01

    Measurements of edge turbulence and the associated transport are ongoing in the Madison Symmetric Torus (R = 1.5 m, a = 0.52 m) reversed-field pinch using magnetic and electrostatic probes. Magnetic fluctuations are dominated by m = 1 and n ∼ 2R/a tearing modes. Particle losses induced by magnetic field fluctuations have been found to be ambipolar ( parallel B r > = O). Electrostatic fluctuations are broadband and turbulent, with mode widths δm ∼ 3--7 and δn ∼70--150. Particle, parallel current, and energy transport arising from coherent motion with the fluctuating ExB drift has been measured. Particle transport via this channel is comparable to the total particle loss from MST. Energy transport (from phi >/B o ) due to electrostatic fluctuations is relatively small, and parallel current transport (from parallel E chi >/B o ) may be small as well

  12. 20 ANOS EM MOVIMENTO. 20 ANOS DE EZLN E MST

    Directory of Open Access Journals (Sweden)

    Jorge Ramon Montenegro Gómez

    2012-04-01

    Full Text Available Ao longo dos meses de abril e maio, aconteceu na FCT/UNESP, campus de Presidente Prudente, uma série de atividades, organizadas pelo Centro de Estudos de Geografia do Trabalho – CEGeT, pelo Centro de Memória e Hemeroteca Sindical “Florestan Fernandes” – CEMOSi e pelo Núcleo de Estudos, Pesquisas e Projetos de Reforma Agrária – NERA, apresentando as lutas e resistências dos dois movimentos sociais com maior visibilidade e reconhecimento na América Latina (e, seguramente, no mundo: O Exército Zapatista de Libertação Nacional – EZLN e o Movimento dos Trabalhadores Rurais Sem Terra – MST.

  13. Diagnosis of clinical samples spotted on FTA cards using PCR-based methods.

    Science.gov (United States)

    Jamjoom, Manal; Sultan, Amal H

    2009-04-01

    The broad clinical presentation of Leishmaniasis makes the diagnosis of current and past cases of this disease rather difficult. Differential diagnosis is important because diseases caused by other aetiologies and a clinical spectrum similar to that of leishmaniasis (e.g. leprosy, skin cancers and tuberculosis for CL; malaria and schistosomiasis for VL) are often present in endemic areas of endemicity. Presently, a variety of methods have been developed and tested to aid the identification and diagnosis of Leishmania. The advent of the PCR technology has opened new channels for the diagnosis of leishmaniasis in a variety of clinical materials. PCR is a simple, rapid procedure that has been adapted for diagnosis of leishmaniasis. A range of tools is currently available for the diagnosis and identification of leishmaniasis and Leishmania species, respectively. However, none of these diagnostic tools are examined and tested using samples spotted on FTA cards. Three different PCR-based approaches were examined including: kDNA minicircle, Leishmania 18S rRNA gene and PCR-RFLP of Intergenic region of ribosomal protein. PCR primers were designed that sit within the coding sequences of genes (relatively well conserved) but which amplify across the intervening intergenic sequence (relatively variable). These were used in PCR-RFLP on reference isolates of 10 of the most important Leishmania species: L. donovani, L. infantum, L. major & L. tropica. Digestion of PCR products with restriction enzymes produced species-specific restriction patterns allowed discrimination of reference isolates. The kDNA minicircle primers are highly sensitive in diagnosis of both bone marrow and skin smears from FTA cards. Leishmania 18S rRNA gene conserved region is sensitive in identification of bone marrow smear but less sensitive in diagnosing skin smears. The intergenic nested PCR-RFLP using P5 & P6 as well as P1 & P2 newly designed primers showed high level of reproducibility and sensitivity

  14. Development and evaluation of new primers for PCR-based identification of Prevotella intermedia.

    Science.gov (United States)

    Zhou, Yanbin; Liu, Dali; Wang, Yiwei; Zhu, Cailian; Liang, Jingping; Shu, Rong

    2014-08-01

    The aim of this study was to develop new Prevotella intermedia-specific PCR primers based on the 16S rRNA. The new primer set, Pi-192 and Pi-468, increased the accuracy of PCR-based P. intermedia identification and could be useful in the detection of P. intermedia as well as epidemiological studies on periodontal disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Pyrosequencing for classification of human FcγRIIIA allotypes: a comparison with PCR-based techniques.

    Science.gov (United States)

    Matlawska-Wasowska, Ksenia; Gale, James M; Nickl, Christian K; Khalili, Parisa; Shirley, Brian; Wilson, Bridget S; Vasef, Mohammad A; Winter, Stuart S

    2014-12-01

    Surface-specific antigens expressed by hematopoietic cells are attractive targets for antibody-mediated immunotherapy. Monoclonal antibodies (mAbs) involve various mechanisms to eliminate target cells, including antibody-dependent cellular cytotoxicity (ADCC)- and phagocytosis (ADCP)-mediated killing through natural killer (NK) and macrophage effector cells bearing FcγRIIIA (CD16). The clinical efficacy of ADCC is particularly impacted by a single nucleotide polymorphism (SNP) found in the gene encoding FcγRIIIA (FCGR3A), which generates a variable distribution of the 158 V/V, F/V or F/F CD16 allotypes (F = phenylalanine, V = valine) in the normal human population. Currently, most patients are not screened for CD16 allotypes, creating the potential to include in their treatment a mAb-based therapy that may have limited benefit. Therefore, it is important to identify CD16 allotypes when considering mAb therapies that require ADCC/ADCP. The objective of this study was to develop a reliable PCR-based assay for classification of human FcγRIIIA allotypes. We studied 42 normal human subjects for the incidence of FcγRIIIA-158 polymorphisms using comparative molecular approaches. The results of our study showed 100% accuracy in genotyping by pyrosequencing. In contrast, nested PCR-based allele-specific restriction assay and quantitative PCR techniques proved to be relatively less sensitive and less specific in distinguishing variant genotypes. Since the efficacy of the mAb-based targeted immunotherapy may be highly dependent upon the CD16 polymorphism in a given individual, we recommend pyrosequencing for CD16 allotype testing.

  16. A rapid PCR-based approach for molecular identification of filamentous fungi.

    Science.gov (United States)

    Chen, Yuanyuan; Prior, Bernard A; Shi, Guiyang; Wang, Zhengxiang

    2011-08-01

    In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal with a large number of filamentous fungal isolates in the same batch, was established. The filamentous fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted DNA also can be used to amplify other protein-coding genes for fungal identification. This method can be used for rapid systematic identification of filamentous fungal isolates.

  17. Overcoming the hurdles of multi-step targeting (MST) for effective radioimmunotherapy of solid tumors

    International Nuclear Information System (INIS)

    Larson, Steven M.; Cheung, Nai-Kong

    2009-01-01

    The 4 specific aims of this project are: (1) Optimization of MST to increase tumor uptake; (2) Antigen heterogeneity; (3) Characterization and reduction of renal uptake; and (4) Validation in vivo of optimized MST targeted therapy. This proposal focussed upon optimizing multistep immune targeting strategies for the treatment of cancer. Two multi-step targeting constructs were explored during this funding period: (1) anti-Tag-72 and (2) anti-GD2.

  18. EL MST Y LAS DISPUTAS POR LAS ALTERNATIVAS EN BRASIL

    Directory of Open Access Journals (Sweden)

    João Pedro Stédile

    2012-04-01

    Full Text Available La victoria del presidente Lulaen las últimas elecciones cambió la correlaciónde fuerzas de la lucha por la reforma agraria enBrasil. Por los compromisos históricos del PT,su liderazgo y como partido de izquierda,tenemos ahora un gobierno federal que apoyala reforma agraria, al contrario de lo que fue elgobierno de Fernando Henrique Cardoso. Porlo tanto, la disputa se sitúa en otro nivel. Sinembargo, hay otras fuerzas poderosas que seoponen a la reforma agraria como lo son ellatifundio, el modelo neoliberal del agro-negocio, la clase dominante como un todo, elEstado burgués brasileño y los medios decomunicación que actúan como un espacio delucha ideológica que disputa la hegemonía en lasociedad contra nosotros. En este nuevocontexto, el MST evalúa que ahora sí se puedeavanzar en la reforma agraria, pero que es unmomento de acumulación de fuerzas y no degrandes definiciones que consoliden la reformaagraria de nuevo tipo que nosotrosdefendemos. Es decir, estamos acumulandopara el futuro.

  19. Specific PCR-based detection of Alternaria helianthi

    DEFF Research Database (Denmark)

    Udayashankar, A.C.; Nayaka, S. Chandra; Archana, B.

    2012-01-01

    Alternaria helianthi is an important seed-borne pathogenic fungus responsible for blight disease in sunflower. The current detection methods, which are based on culture and morphological identification, are time-consuming, laborious and are not always reliable. A PCR-based diagnostic method...... tested. The detection limit of the PCR method was of 10 pg from template DNA. The primers could also detect the pathogen in infected sunflower seed. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification...

  20. A PCR-based protocol to accurately size C9orf72 intermediate-length alleles.

    Science.gov (United States)

    Biasiotto, Giorgio; Archetti, Silvana; Di Lorenzo, Diego; Merola, Francesca; Paiardi, Giulia; Borroni, Barbara; Alberici, Antonella; Padovani, Alessandro; Filosto, Massimiliano; Bonvicini, Cristian; Caimi, Luigi; Zanella, Isabella

    2017-04-01

    Although large expansions of the non-coding GGGGCC repeat in C9orf72 gene are clearly defined as pathogenic for Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD), intermediate-length expansions have also been associated with those and other neurodegenerative diseases. Intermediate-length allele sizing is complicated by intrinsic properties of current PCR-based methodologies, in that somatic mosaicism could be suspected. We designed a protocol that allows the exact sizing of intermediate-length alleles, as well as the identification of large expansions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Evaluation of DNA Extraction Methods Suitable for PCR-based Detection and Genotyping of Clostridium botulinum

    DEFF Research Database (Denmark)

    Auricchio, Bruna; Anniballi, Fabrizio; Fiore, Alfonsina

    2013-01-01

    in terms of cost, time, labor, and supplies. Eleven botulinum toxin–producing clostridia strains and 25 samples (10 food, 13 clinical, and 2 environmental samples) naturally contaminated with botulinum toxin–producing clostridia were used to compare 4 DNA extraction procedures: Chelex® 100 matrix, Phenol......Sufficient quality and quantity of extracted DNA is critical to detecting and performing genotyping of Clostridium botulinum by means of PCR-based methods. An ideal extraction method has to optimize DNA yield, minimize DNA degradation, allow multiple samples to be extracted, and be efficient...

  2. The Telomerase Inhibitor MST-312 Interferes with Multiple Steps in the Herpes Simplex Virus Life Cycle.

    Science.gov (United States)

    Haberichter, Jarod; Roberts, Scott; Abbasi, Imran; Dedthanou, Phonphanh; Pradhan, Prajakta; Nguyen, Marie L

    2015-10-01

    The life cycle of herpes simplex virus (HSV) has the potential to be further manipulated to yield novel, more effective therapeutic treatments. Recent research has demonstrated that HSV-1 can increase telomerase activity and that expression of the catalytic component of telomerase, telomerase reverse transcriptase (TERT), alters sensitivity to HSV-dependent apoptosis. Telomerase is a cellular enzyme that synthesizes nucleotide repeats at the ends of chromosomes (telomeres), which prevents shortening of the 3' ends of DNA with each cell division. Once telomeres reach a critical length, cells undergo senescence and apoptosis. Here, we used a cell-permeable, reversible inhibitor of the telomerase enzyme, MST-312, to investigate telomerase activity during HSV infection. Human mammary epithelial cells immortalized through TERT expression and human carcinoma HEp-2 cells were infected with the KOS1.1 strain of HSV-1 in the presence of MST-312. MST-312 treatment reduced the number of cells displaying a cytopathic effect and the accumulation of immediate early and late viral proteins. Moreover, the presence of 20 μM to 100 μM MST-312 during infection led to a 2.5- to 5.5-log10 decrease in viral titers. MST-312 also inhibited the replication of HSV-2 and a recent clinical isolate of HSV-1. Additionally, we determined that MST-312 has the largest impact on viral events that take place prior to 5 h postinfection (hpi). Furthermore, MST-312 treatment inhibited virus replication, as measured by adsorption assays and quantification of genome replication. Together, these findings demonstrate that MST-312 interferes with the HSV life cycle. Further investigation into the mechanism for MST-312 is warranted and may provide novel targets for HSV therapies. Herpes simplex virus (HSV) infections can lead to cold sores, blindness, and brain damage. Identification of host factors that are important for the virus life cycle may provide novel targets for HSV antivirals. One such factor

  3. Do essencialismo ao não essencialismo? reflexões sobre a identidade cultural do MST From essentialism to non essentialism? reflections about cultural identity of MST

    Directory of Open Access Journals (Sweden)

    Fábio Souza da Cruz

    2010-01-01

    Full Text Available O trabalho apresenta um estudo envolvendo um movimento social, o MST (Movimento dos Trabalhadores Rurais Sem-Terra, e as noções de identidade cultural. A investigação desenvolve um breve exercício de contextualização do movimento através de sua história, seu relacionamento com o poder e sua estrutura nos dias atuais. Com relação aos marcos teórico-metodológicos, a pesquisa adota os pressupostos de Kathryn Woodward (2000, Stuart Hall (2002 e Zygmunt Bauman (2005 e os discursos dos integrantes do movimento retirados do estudo de recepção realizado por Cruz (2006. Como discussão central, pretende-se analisar os desafios do MST em tempos de globalização.The work presents a study involving a social movement, the MST (Portuguese acronym for Movement of the Agricultural Landless Workers, and the slight knowledge of cultural identity. The inquiry develops a brief exercise combining the meaning of the movement through its history, its relationship with the power and its structure in the current days. In regard to theoretical-methodological landmarks, the research adopts pressupositions of Kathryn Woodward (2000, Stuart Hall (2002 e Zygmunt Bauman (2005 and speeches of people from the movement, taken from Cruz' study of reception (2006. As central quarrel, it is intended to analyze the challenges of the MST in globalization times.

  4. Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

    Energy Technology Data Exchange (ETDEWEB)

    Purandare, S.M.; Viskochil, D.H.; Cawthon, R. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

    1996-07-01

    Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

  5. A novel, non-canonical mechanism of regulation of MST3 (mammalian Sterile20-related kinase 3)

    OpenAIRE

    Fuller, Stephen J; McGuffin, Liam J; Marshall, Andrew K; Giraldo, Alejandro; Pikkarainen, Sampsa; Clerk, Angela; Sugden, Peter

    2012-01-01

    The canonical pathway of regulation of the GCK (germinal centre kinase) III subgroup member, MST3 (mammalian Sterile20-related kinase 3), involves a caspase-mediated cleavage between N-terminal catalytic and C-terminal regulatory domains with possible concurrent autophosphorylation of the activation loop MST3(Thr178), induction of serine/threonine protein kinase activity and nuclear localization. We identified an alternative ‘non-canonical’ pathway of MST3 activation (regulated primarily thro...

  6. MstApp, a rich client control applications framework at DESY

    International Nuclear Information System (INIS)

    Kirsten Hinsch, Winfried Schuette

    2012-01-01

    The control systems for PETRA 3 (a dedicated synchrotron machine) and its pre-accelerators extensively use rich clients for the control room and the servers. Most of them are written with the help of a rich client Java framework: MstApp. They totalize 106 different consoles and 158 individual server applications. MstApp takes care of many common control system application aspects beyond communication. MstApp provides a common look and feel: core menu items, a colour scheme for standard states of hardware components and predefined standardized screen sizes/locations. It interfaces our console application manager (CAM) and displays on demand our communication link diagnostics tools. MstApp supplies an accelerator context for each application; it handles printing, logging, re-sizing and unexpected application crashes. Due to our standardized deploy process MstApp applications know their individual developers and can even send them - on button press of the users - E-mails. Further a concept of different operation modes is implemented: view only, operating and expert use. Administration of the corresponding rights is done via web access of a database server. Initialization files on a web server are instantiated as JAVA objects with the help of the Java SE XML-Decoder. Data tables are read with the same mechanism. New MstApp applications can easily be created with in house wizards like the NewProjectWizard or the DeviceServerWizard. MstApp improves the operator experience, application developer productivity and delivered software quality. (authors)

  7. Neurons in cortical area MST remap the memory trace of visual motion across saccadic eye movements.

    Science.gov (United States)

    Inaba, Naoko; Kawano, Kenji

    2014-05-27

    Perception of a stable visual world despite eye motion requires integration of visual information across saccadic eye movements. To investigate how the visual system deals with localization of moving visual stimuli across saccades, we observed spatiotemporal changes of receptive fields (RFs) of motion-sensitive neurons across periods of saccades in the middle temporal (MT) and medial superior temporal (MST) areas. We found that the location of the RFs moved with shifts of eye position due to saccades, indicating that motion-sensitive neurons in both areas have retinotopic RFs across saccades. Different characteristic responses emerged when the moving visual stimulus was turned off before the saccades. For MT neurons, virtually no response was observed after the saccade, suggesting that the responses of these neurons simply reflect the reafferent visual information. In contrast, most MST neurons increased their firing rates when a saccade brought the location of the visual stimulus into their RFs, where the visual stimulus itself no longer existed. These findings suggest that the responses of such MST neurons after saccades were evoked by a memory of the stimulus that had preexisted in the postsaccadic RFs ("memory remapping"). A delayed-saccade paradigm further revealed that memory remapping in MST was linked to the saccade itself, rather than to a shift in attention. Thus, the visual motion information across saccades was integrated in spatiotopic coordinates and represented in the activity of MST neurons. This is likely to contribute to the perception of a stable visual world in the presence of eye movements.

  8. A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition.

    Directory of Open Access Journals (Sweden)

    Huiling Qiu

    Full Text Available DNA vector-encoded Tough Decoy (TuD miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer, which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD vector in which only two sets of shorter oligonucleotides (< 60 mer were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324 were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.

  9. Detection of Hepatitis B and C Viruses in Almost All Hepatocytes by Modified PCR-Based In Situ Hybridization▿

    Science.gov (United States)

    Nuriya, Hideko; Inoue, Kazuaki; Tanaka, Takeshi; Hayashi, Yukiko; Hishima, Tsunekazu; Funata, Nobuaki; Kaji, Kyosuke; Hayashi, Seishu; Kaneko, Shuichi; Kohara, Michinori

    2010-01-01

    Although PCR-based in situ hybridization (PCR-ISH) can be used to determine the distribution and localization of pathogens in tissues, this approach is hampered by its low specificity. Therefore, we used a highly specific and sensitive PCR-ISH method to reveal the lobular distribution and intracellular localization of hepatitis B virus (HBV) and HCV in chronic liver disease and to clarify the state of persistent HBV and HCV infection in the liver. HBV genomic DNA was detected in almost all hepatocytes, whereas HBV RNA or protein was differentially distributed only in a subset of the HBV DNA-positive region. Further, HCV genomic RNA was detected in almost all hepatocytes and was localized to the cytoplasm. HCV RNA was also detected in the epithelium of the large bile duct but not in endothelial cells, portal tracts, or sinusoidal lymphocytes. In patients with HBV and HCV coinfection, HCV RNA was localized to the noncancerous tissue, whereas HBV DNA was found only in the cancerous tissue. Using this novel PCR-ISH method, we could visualize the staining pattern of HBV and HCV in liver sections, and we obtained results consistent with those of real-time detection (RTD)-PCR analysis. In conclusion, almost all hepatocytes are infected with HBV or HCV in chronic liver disease; this finding implies that the viruses spreads throughout the liver in the chronic stage. PMID:20739486

  10. Internal quality control of PCR-based genotyping methods in research studies and patient diagnostics

    DEFF Research Database (Denmark)

    Bladbjerg, Else-Marie; Gram, Jørgen; Jespersen, Jørgen

    2002-01-01

    Genetic analyses are increasingly integrated in the clinical laboratory, and internal quality control programmes are needed. We have focused on quality control aspects of selected polymorphism analyses used in thrombosis research. DNA was isolated from EDTA-blood (n = 500) by ammonium acetate....... Control of data handling revealed 0.1% reading mistakes and 0.5% entry mistakes. Based on our experiences we propose an internal quality control programme for widely used PCR-based haemostasis polymorphism analyses.......-isolation (pre-analytical factors), DNA-amplification, digestion with restriction enzymes, electrophoresis (analytical factors), result reading and entry into a database (post-analytical factors). Furthermore, we evaluated a procedure for result confirmation. Isolated DNA was of good quality (42 microg/ml blood...

  11. PCR-based detection of a rare linear DNA in cell culture

    Directory of Open Access Journals (Sweden)

    Saveliev Sergei V.

    2002-01-01

    Full Text Available The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

  12. PCR-based detection of a rare linear DNA in cell culture.

    Science.gov (United States)

    Saveliev, Sergei V.

    2002-11-11

    The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

  13. Multicenter validation of PCR-based method for detection of Salmonella in chicken and pig samples

    DEFF Research Database (Denmark)

    Malorny, B.; Cook, N.; D'Agostino, M.

    2004-01-01

    As part of a standardization project, an interlaboratory trial including 15 laboratories from 13 European countries was conducted to evaluate the performance of a noproprietary polymerase chain reaction (PCR)-based method for the detection of Salmonella on artificially contaminated chicken rinse...... or positive. Outlier results caused, for example, by gross departures from the experimental protocol, were omitted from the analysis. For both the chicken rinse and the pig swab samples, the diagnostic sensitivity was 100%, with 100% accordance (repeatability) and concordance (reproducibility). The diagnostic...... specificity was 80.1% (with 85.7% accordance and 67.5% concordance) for chicken rinse, and 91.7% (with 100% accordance and 83.3% concordance) for pig swab. Thus, the interlaboratory variation due to personnel, reagents, thermal cyclers, etc., did not affect the performance of the method, which...

  14. PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in Escherichia coli

    DEFF Research Database (Denmark)

    Liu, Yilan; Yang, Maohua; Yan, Daojiang

    2016-01-01

    Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double...... for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision...... of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli....

  15. Eye position effects on the remapped memory trace of visual motion in cortical area MST.

    Science.gov (United States)

    Inaba, Naoko; Kawano, Kenji

    2016-02-23

    After a saccade, most MST neurons respond to moving visual stimuli that had existed in their post-saccadic receptive fields and turned off before the saccade ("trans-saccadic memory remapping"). Neuronal responses in higher visual processing areas are known to be modulated in relation to gaze angle to represent image location in spatiotopic coordinates. In the present study, we investigated the eye position effects after saccades and found that the gaze angle modulated the visual sensitivity of MST neurons after saccades both to the actually existing visual stimuli and to the visual memory traces remapped by the saccades. We suggest that two mechanisms, trans-saccadic memory remapping and gaze modulation, work cooperatively in individual MST neurons to represent a continuous visual world.

  16. INVESTIGATING SUSPENSION OF MST, CST, AND SIMULATED SLUDGE SLURRIES IN A PILOT-SCALE WASTE TANK

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M.; Qureshi, Z.; Restivo, M.; Steeper, T.; Williams, M.

    2011-05-24

    The Small Column Ion Exchange (SCIX) process is being developed to remove cesium, strontium, and actinides from Savannah River Site (SRS) Liquid Waste using an existing waste tank (i.e., Tank 41H) to house the process. Savannah River National Laboratory (SRNL) is conducting pilot-scale mixing tests to determine the pump requirements for suspending and resuspending monosodium titanate (MST), crystalline silicotitanate (CST), and simulated sludge. The purpose of this pilot scale testing is for the pumps to resuspend the MST, CST, and simulated sludge particles so that they can be removed from the tank, and to suspend the MST so it can contact strontium and actinides. The pilot-scale tank is a 1/10.85 linear scaled model of Tank 41H. The tank diameter, tank liquid level, pump nozzle diameter, pump elevation, and cooling coil diameter are all 1/10.85 of their dimensions in Tank 41H. The pump locations correspond to the proposed locations in Tank 41H by the SCIX program (Risers B5, B3, and B1). Previous testing showed that three Submersible Mixer Pumps (SMPs) will provide sufficient power to initially suspend MST in an SRS waste tank, and to resuspend MST that has settled in a waste tank at nominal 45 C for four weeks. The conclusions from this analysis are: (1) Three SMPs will be able to resuspend more than 99.9% of the MST and CST that has settled for four weeks at nominal 45 C. The testing shows the required pump discharge velocity is 84% of the maximum discharge velocity of the pump. (2) Three SMPs will be able to resuspend more than 99.9% of the MST, CST, and simulated sludge that has settled for four weeks at nominal 45 C. The testing shows the required pump discharge velocity is 82% of the maximum discharge velocity of the pump. (3) A contact time of 6-12 hours is needed for strontium sorption by MST in a jet mixed tank with cooling coils, which is consistent with bench-scale testing and actinide removal process (ARP) operation.

  17. STRONTIUM AND ACTINIDE SORPTION BY MST AND MMST UNDER CONDITIONS REVELANT TO THE SMALL COLUMN ION-EXCHANGE PROCESS

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K.; Hobbs, D.; Poirier, M.

    2011-05-06

    A series of tests were performed to examine the kinetics of Sr and actinide removal by monosodium titanate (MST) and modified monosodium titanate (mMST) under mixing conditions similar to what will be provided in the Small Column Ion Exchange (SCIX) Program. Similar removal kinetics were seen for two different mixing energies, indicating that under these conditions bulk solution transport is not the rate limiting step for Sr and actinide removal. Sr removal was found to be rapid for both MST and mMST, reaching steady-state conditions within six hours. In contrast, at least six weeks is necessary to reach steady-state conditions for Pu with MST. For mMST, steady-state conditions for Pu were achieved within two weeks. The actual contact time required for the SCIX process will depend on starting sorbate concentrations as well as the requirements for the decontaminated salt solution. During testing leaks occurred in both the MST and mMST tests and evidence of potential desorption was observed. The desorption likely occurred as a result of the change in solids to liquid phase ratio that occurred due to the loss of solution. Based on these results, Savannah River National Laboratory (SRNL) recommended additional testing to further study the effect of changing phase ratios on desorption. This testing is currently in progress and results will be documented in a separate report.

  18. Changes in maternal depression are associated with MST outcomes for adolescents with co-occurring externalizing and internalizing problems

    NARCIS (Netherlands)

    Grimbos, T.; Granic, I.

    2010-01-01

    he efficacy of Multisystemic therapy (MST) in treating adolescent aggression has been established, however, not all youth and their families benefit from MST. One reason for this treatment variability could be the failure to distinguish between different aggressive Subtypes with different risk

  19. Changes in Maternal Depression Are Associated with MST Outcomes for Adolescents with Co-Occurring Externalizing and Internalizing Problems

    Science.gov (United States)

    Grimbos, Teresa; Granic, Isabela

    2009-01-01

    The efficacy of Multisystemic therapy (MST) in treating adolescent aggression has been established, however, not all youth and their families benefit from MST. One reason for this treatment variability could be the failure to distinguish between different aggressive subtypes with different risk factors, developmental prognoses and treatment needs.…

  20. Evaluation of PCR-based preimplantation genetic diagnosis applied to monogenic diseases: a collaborative ESHRE PGD consortium study

    Science.gov (United States)

    Dreesen, Jos; Destouni, Aspasia; Kourlaba, Georgia; Degn, Birte; Mette, Wulf Christensen; Carvalho, Filipa; Moutou, Celine; Sengupta, Sioban; Dhanjal, Seema; Renwick, Pamela; Davies, Steven; Kanavakis, Emmanouel; Harton, Gary; Traeger-Synodinos, Joanne

    2014-01-01

    Preimplantation genetic diagnosis (PGD) for monogenic disorders currently involves polymerase chain reaction (PCR)-based methods, which must be robust, sensitive and highly accurate, precluding misdiagnosis. Twelve adverse misdiagnoses reported to the ESHRE PGD-Consortium are likely an underestimate. This retrospective study, involving six PGD centres, assessed the validity of PCR-based PGD through reanalysis of untransferred embryos from monogenic-PGD cycles. Data were collected on the genotype concordance at PGD and follow-up from 940 untransferred embryos, including details on the parameters of PGD cycles: category of monogenic disease, embryo morphology, embryo biopsy and genotype assay strategy. To determine the validity of PCR-based PGD, the sensitivity (Se), specificity (Sp) and diagnostic accuracy were calculated. Stratified analyses were also conducted to assess the influence of the parameters above on the validity of PCR-based PGD. The analysis of overall data showed that 93.7% of embryos had been correctly classified at the time of PGD, with Se of 99.2% and Sp of 80.9%. The stratified analyses found that diagnostic accuracy is statistically significantly higher when PGD is performed on two cells versus one cell (P=0.001). Se was significantly higher when multiplex protocols versus singleplex protocols were applied (P=0.005), as well as for PGD applied on cells from good compared with poor morphology embryos (P=0.032). Morphology, however, did not affect diagnostic accuracy. Multiplex PCR-based methods on one cell, are as robust as those on two cells regarding false negative rate, which is the most important criteria for clinical PGD applications. Overall, this study demonstrates the validity, robustness and high diagnostic value of PCR-based PGD. PMID:24301057

  1. Em busca da visibilidade: apropriações e produções de audiovisuais pelo MST * Searching for visibility: appropriations and audiovisual producions by MST

    Directory of Open Access Journals (Sweden)

    FERNANDO PERLI

    2013-12-01

    Full Text Available Resumo: A formação do Movimento dos Trabalhadores Rurais Sem Terra (MST marcou-se pelo envolvimento de entidades civis e religiosas na produção de diversos meios de comunicação. Dentre a variedade, os audiovisuais tornaram-se instrumentos cada vez mais recorrentes para a capacitação de quadros e a visibilidade social do MST. Na década de 1990, as coberturas dadas pela mídia e a ampliação dos mecanismos de divulgação do movimento social contribuíram para o desenvolvimento de projetos que incentivaram a produção de vídeos-documentários pelos sem-terra. O presente artigo suscita a análise das apropriações e produções de audiovisuais na organização do MST, considerando o sentido político do reconhecimento de audiovisuais para a divulgação do movimento social e o debate sobre o lugar ocupado por diferentes mecanismos de difusão de representações na luta pela reforma agrária.Palavras-chave: Audiovisuais – Movimentos sociais – Movimento dos Trabalhadores Rurais Sem-Terra. Abstract: The formation of the Landless Rural Workers Movement (MST was marked by the participation of civil and religious authorities in the production of various media. Among them, the audiovisual production became an increasingly recurrent instrument to train its cadre and to enable social visibility to the organization. In the 1990s, the media coverage and the expansion of dissemination mechanisms have contributed to the development of projects that stimulated the production of documentaries by the landless rural workers. This paper raises the analysis of appropriations and audiovisual productions within MST, considering the political sense of acknowledging the audiovisual as a means to disseminate the social movement as well as the debate on the place occupied by different diffusion mechanisms of representations in the struggle for agrarian reform.Keywords: Audiovisual – Social movement – Landless Rural Workers Movement.

  2. PCR-based clonality analysis of B-cell lymphomas in paraffin-embedded tissues: diagnostic value of immunoglobulin kappa and lambda light chain gene rearrangement investigation.

    Science.gov (United States)

    Amara, Khaled; Trimeche, Mounir; Ziadi, Sonia; Sriha, Badreddine; Mokni, Moncef; Korbi, Sadok

    2006-01-01

    Polymerase chain reaction (PCR)-based analysis, employed for detecting immunoglobulin heavy chain (IgH) gene rearrangements, has become a diagnostic tool widely used in the investigation of B-cell lymphomas, but the overall sensitivity of these methods does not exceed 80%, notably in germinal center (GC) and post-GC B-cell origin lymphomas. Many PCR strategies devised for detecting immunoglobulin light chain (IgL) gene rearrangements have been developed to enhance the clonality detection rates. However, the feasibility of these methods in routine clinical diagnosis using paraffin-embedded tissues has not yet been investigated sufficiently. We studied a large series of 108 cases of B-cell lymphomas, as well as 20 reactive lymphoid tissues using degenerate primers to amplify immunoglobulin kappa (Igkappa) and lambda (Iglambda) light chain genes. B-cell clonality was further investigated using semi-nested PCR for IgH gene rearrangements. B-cell clonality was detected in 74%, 56.5%, and 43.5% of cases using IgH, Igkappa, and Iglambda PCR, respectively. By combining these methods, the clonality detection rate increased to 93.5%. Only polyclonal patterns were noted in reactive lymphoid samples. We concluded that in addition to the established methods for IgH analysis, a PCR-based approach for IgL gene rearrangements analysis improves the clonality detection rate in over 90% of B-cell lymphoma cases using routine histological specimens with poor preservation of the genomic DNA.

  3. Diagnosis of Giardia infections by PCR-based methods in children of an endemic area

    Directory of Open Access Journals (Sweden)

    EB David

    2011-01-01

    Full Text Available The present study was designed to estimate the prevalence of Giardia infection in preschool- and school-aged children living in an endemic area. Fecal samples from 573 children were processed by zinc sulfate centrifugal flotation, centrifugal sedimentation (using a commercial device for fecal concentration - TF-Test kit® and polymerase chain reaction (PCR-based methods. Of the stool samples assessed, 277 (48.3% were positive for intestinal parasites and/or commensal protozoa. Centrifugal flotation presented the highest diagnostic sensitivity for Giardia infections. The kappa index revealed that both coproparasitological techniques closely agreed on the Giardia diagnosis (86% versus satisfactory (72% and poor (35% concordances for commensal protozoan and helminth infections, respectively. Concerning Giardia molecular diagnosis, from the 71 microscopy-positive samples, specific amplification of gdh and tpi fragments was noted in 68 (95.7% and 64 (90% samples, respectively. Amplification of gdh and tpi genes was observed, respectively, in 95.7% and 90% of microscopy-positive Giardia samples. For 144 microscopy-negative samples, gdh and tpi gene amplification products were obtained from 8.3% and 35.9% samples, respectively. The agreement between these genes was about 40%. The centrifuge-flotation based method was the most suitable means of Giardia diagnosis assessed in the present study by combining accuracy and low cost.

  4. PCR-based detection of gene transfer vectors: application to gene doping surveillance.

    Science.gov (United States)

    Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

    2013-12-01

    Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.

  5. Effective PCR-based detection of Naegleria fowleri from cultured sample and PAM-developed mouse.

    Science.gov (United States)

    Kang, Heekyoung; Seong, Gi-Sang; Sohn, Hae-Jin; Kim, Jong-Hyun; Lee, Sang-Eun; Park, Mi Yeoun; Lee, Won-Ja; Shin, Ho-Joon

    2015-10-01

    Increasing numbers of Primary Amoebic Meningoencephalitis (PAM) cases due to Naegleria fowleri are becoming a serious issue in subtropical and tropical countries as a Neglected Tropical Disease (NTD). To establish a rapid and effective diagnostic tool, a PCR-based detection technique was developed based on previous PCR methods. Four kinds of primer pairs, Nfa1, Nae3, Nf-ITS, and Naegl, were employed in the cultured amoebic trophozoites and a mouse with PAM experimentally developed by N. fowleri inoculation (PAM-mouse). For the extraction of genomic DNA from N. fowleri trophozoites (1×10(6)), simple boiling with 10μl of PBS (pH 7.4) at 100°C for 30min was found to be the most rapid and efficient procedure, allowing amplification of 2.5×10(2) trophozoites using the Nfa-1 primer. The primers Nfa1 and Nae3 amplified only N. fowleri DNA, whereas the ITS primer detected N. fowleri and N. gruberi DNA. Using the PAM-mouse brain tissue, the Nfa1 primer was able to amplify the N. fowleri DNA 4 days post infection with 1ng/μl of genomic DNA being detectable. Using the PAM-mouse CSF, amplification of the N. fowleri DNA with the Nae3 primer was possible 5 days post infection showing a better performance than the Nfa1 primer at day 6. Copyright © 2015 Elsevier GmbH. All rights reserved.

  6. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  7. Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment.

    Directory of Open Access Journals (Sweden)

    Zhenming Yu

    Full Text Available Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.

  8. Design and development of a lower-hybrid antenna for the MST reversed field pinch

    International Nuclear Information System (INIS)

    Thomas, M.; Cekic, M.; Lovell, T.W.; Prager, S.C.; Sarff, J.S.; Uchimoto, E.

    1995-01-01

    Recent theoretical studies strongly motivated the development of a radio-frequency current drive scheme for current density gradient reduction in the outer region of a reversed field pinch. The preliminary experiments using inductive current drive indicate that such current density profile modification reduces the magnetic fluctuation amplitude and related energy and particle losses. To test the theoretical predictions and to further improve confinement in the MST, the authors are planning a series of lower-hybrid wave experiments. The initial phase is the design and optimization of a low-power antenna to study slow wave propagation in a frequency range 2--3 f LH (200--300 MHz) with parallel index of refraction n parallel ∼10. Ray-tracing calculations, for typical MST plasma parameters, indicate that such a wave will spiral radially into a target zone inside the reversal layer. The antenna consists of an array of tunable loops arranged in the poloidal direction. The design is compatible with the existing box-port openings in the MST conductive shell to prevent additional magnetic field errors associated with large portholes. Antenna vacuum characteristics are studied on a test-stand designed to approximate the geometry of the MST shell. For the initial measurements of plasma response and antenna loading, the authors designed a reduced, easily insertable, vacuum antenna structure. The results of plasma impedance measurements will be compared with the numerical modeling results and incorporated in the optimized design of the antenna for wave propagation experiments

  9. The Politics of the MST Autonomous Rural Communities, the State, and Electoral Politics

    NARCIS (Netherlands)

    Vergara Camus, Leandro

    Examination of the politicization of landless people in the encampments and settlements of the Movimento dos Trabalhadores Rurais Sem-Terra (Landless Rural Workers' Movement-MST) in Brazil suggests that the movement's success rest on the fact that it generates relatively autonomous rural communities

  10. Edge fluctuations in the MST [Madison Symmetric Torus] reversed field pinch

    International Nuclear Information System (INIS)

    Almagri, A.; Assadi, S.; Beckstead, J.; Chartas, G.; Crocker, N.; Den Hartog, D.; Dexter, R.; Hokin, S.; Holly, D.; Nilles, E.; Prager, S.; Rempel, T.; Sarff, J.; Scime, E.; Shen, W.; Spragins, C.; Sprott, J.; Starr, G.; Stoneking, M.; Watts, C.

    1990-10-01

    Edge magnetic and electrostatic fluctuations are measured in the Madison Symmetric Torus (MST) reversed field pinch. At low frequency ( e > p e /p e where φ and p e are the fluctuating potential and pressure, respectively). From measurements of the fluctuating density, temperature, and potential we infer that the electrostatic fluctuation induced transport of particles and energy can be substantial. 13 refs., 11 figs

  11. PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at the inhibitory site

    International Nuclear Information System (INIS)

    Jung, Sujin; Kang, Jeong Gu; Lee, Ju Hee; Song, Kyoung Jin; Ko, Jeong-Heon; Kim, Yong-Sam

    2014-01-01

    Highlights: • PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at Thr 387 . • Overexpression of PHLPP1 sensitizes contact inhibition. • Tumor cells with suppressed PHLPP1 expression are refractory to apoptosis and highly proliferative. • Loss or down-regulation of PHLPP1 may drive tumor development and progression. - Abstract: Contact inhibition has been largely elusive despite that a loss of contact inhibition is a critical event for cancer development and progression. Here, we report that PHLPP1 is a binding protein for Mst1 and it modulates the Hippo pathway by dephosphorylating Mst1 at the inhibitory Thr 387 of Mst1. Yap1 was localized predominantly in the nucleus but marginally in the cytoplasm in HeLa cells under sparse conditions, whereas the functional protein was more directed to sequestration in the cytoplasm under dense environments. Furthermore, loss of PHLPP1 resulted in a failure of the apoptotic control. It is interesting that down-regulated expression of PHLPP1 appears to mimic the loss of contact inhibition, a hallmark of cancer

  12. PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at the inhibitory site

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Sujin; Kang, Jeong Gu [Targeted Gene Regulation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Deajeon (Korea, Republic of); Lee, Ju Hee [Targeted Gene Regulation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Deajeon (Korea, Republic of); Department of Biomolecular Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon (Korea, Republic of); Song, Kyoung Jin [Targeted Gene Regulation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Deajeon (Korea, Republic of); Ko, Jeong-Heon [Targeted Gene Regulation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Deajeon (Korea, Republic of); Department of Biomolecular Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon (Korea, Republic of); Kim, Yong-Sam, E-mail: omsys1@kribb.re.kr [Targeted Gene Regulation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Deajeon (Korea, Republic of); Department of Biomolecular Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon (Korea, Republic of)

    2014-01-24

    Highlights: • PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at Thr{sup 387}. • Overexpression of PHLPP1 sensitizes contact inhibition. • Tumor cells with suppressed PHLPP1 expression are refractory to apoptosis and highly proliferative. • Loss or down-regulation of PHLPP1 may drive tumor development and progression. - Abstract: Contact inhibition has been largely elusive despite that a loss of contact inhibition is a critical event for cancer development and progression. Here, we report that PHLPP1 is a binding protein for Mst1 and it modulates the Hippo pathway by dephosphorylating Mst1 at the inhibitory Thr{sup 387} of Mst1. Yap1 was localized predominantly in the nucleus but marginally in the cytoplasm in HeLa cells under sparse conditions, whereas the functional protein was more directed to sequestration in the cytoplasm under dense environments. Furthermore, loss of PHLPP1 resulted in a failure of the apoptotic control. It is interesting that down-regulated expression of PHLPP1 appears to mimic the loss of contact inhibition, a hallmark of cancer.

  13. '"My Land, Your Social Transformation": Conflicts within the Landless People Movement (MST), Rio De Janeiro, Brazil

    Science.gov (United States)

    Caldeira, Rute

    2008-01-01

    The Brazilian "Movimento dos Trabalhadores Rurais Sem-Terra" (MST) is one of the best-known and most prominent rural social movements. The unequal distribution of land in Brazil, and the neglect of this problem by successive Brazilian governments contributed greatly to the organisation of rural movements striving for the implementation…

  14. Reframing the Public in Public Education: The Landless Workers Movement (MST) and Adult Education in Brazil

    Science.gov (United States)

    Thapliyal, Nisha

    2013-01-01

    Education for rural Brazilians has historically been dominated by two imperatives: human capital and political patronage. For the last four decades, the Landless Workers Movement (MST) have maintained a struggle to democratise public education and democracy itself. In this article, I make a situated analysis of the educational politics of the MST…

  15. Evaluation of no-MST operations in the SRS ARP for Hanford LAWPS

    Energy Technology Data Exchange (ETDEWEB)

    Herman, D. [Savannah River Site (SRS), Aiken, SC (United States)

    2016-11-14

    The Savannah River Site (SRS) Actinide Removal Process has been processing salt waste since 2008. This process includes a filtration step in the 512-S facility. Initial operations included the addition, or strike, of monosodium titanate (MST) to remove soluble actinides and strontium. The added MST and any entrained sludge solids were then separated from the supernate by cross flow filtration. During this time, the filter operations have, on many occasions, been the bottleneck process limiting the rate of salt processing. Recently, 512-S- has started operations utilizing “No-MST” where the MST actinide removal strike was not performed and the supernate was simply pre-filtered prior to Cs removal processing. Direct filtration of decanted tank supernate, as demonstrated in 512-S, is the proposed method of operation for the Hanford Low Activity Waste Pretreatment System (LAWPS) facility. Processing decanted supernate without MST solids has been demonstrated for cross flow filtration to provide a significant improvement in production with the SRS Salt Batches 8 and 9 feed chemistries. The average filtration rate for the first 512-S batch processing cycle using No-MST has increased filtrate production by over 35% of the historical average. The increase was sustained for more than double the amount of filtrate batches processed before cleaning of the filter was necessary. While there are differences in the design of the 512-S and Hanford filter systems, the 512-S system should provide a reasonable indication of LAWPS filter performance with similar feed properties. Based on the data from the 512-S facility and with favorable feed properties, the LAWPS filter, as currently sized at over twice the size of the 512-S filter (532 square feet filtration area versus 235 square feet), has the potential to provide sustained filtrate production at the upper range of the planned LAWPS production rate of 17 gpm.

  16. A PCR-based method for identification of bifidobacteria from the human alimentary tract at the species level

    NARCIS (Netherlands)

    Venema, K.; Maathuis, A.J.H.

    2003-01-01

    A polymerase chain reaction (PCR)-based method was developed for the identification of isolates of Bifidobacterium at the species level. Using two Bifidobacterium-specific primers directed against the 16S ribosomal gene (Bif164 and Bif662), a PCR product was obtained from the type strains of 12

  17. Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

    Science.gov (United States)

    A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing. Here, we evaluated ten of these methods (BacH, BacHum-UCD, B. thetaiotaomic...

  18. Development of PCR-based detection methods for the quarantine phytopathogen Synchytrium endobioticum, causal agent of wart disease

    NARCIS (Netherlands)

    Boogert, van den P.H.J.F.; Gent-Pelzer, van M.P.E.; Bonants, P.J.M.; Boer, de S.H.; Wander, J.G.N.; Lévesque, C.A.; Leeuwen, van G.C.M.; Baayen, R.P.

    2005-01-01

    Abstract PCR-based methods were developed for the detection and quantification of the potato pathogen Synchytrium endobioticum in soil extracts and in planta. PCR primers, based on the internal transcribed spacer region of the multi-copy gene rDNA were tested for specificity, sensitivity and

  19. Shikonin regulates C-MYC and GLUT1 expression through the MST1-YAP1-TEAD1 axis

    Energy Technology Data Exchange (ETDEWEB)

    Vališ, Karel, E-mail: karel.valis@biomed.cas.cz [Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Prague (Czech Republic); Faculty of Science, Charles University, Prague (Czech Republic); Talacko, Pavel; Grobárová, Valéria [Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Prague (Czech Republic); Faculty of Science, Charles University, Prague (Czech Republic); Černý, Jan [Faculty of Science, Charles University, Prague (Czech Republic); Novák, Petr, E-mail: pnovak@biomed.cas.cz [Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Prague (Czech Republic); Faculty of Science, Charles University, Prague (Czech Republic)

    2016-12-10

    The general mechanism underlying the tumor suppressor activity of the Hippo signaling pathway remains unclear. In this study, we explore the molecular mechanisms connecting the Hippo signaling pathway with glucose metabolism. We have found that two key regulators of glycolysis, C-MYC and GLUT1, are targets of the Hippo signaling pathway in human leukemia cells. Our results revealed that activation of MST1 by the natural compound shikonin inhibited the expression of GLUT1 and C-MYC. Furthermore, RNAi experiments confirmed the regulation of GLUT1 and C-MYC expression via the MST1-YAP1-TEAD1 axis. Surprisingly, YAP1 was found to positively regulate C-MYC mRNA levels in complex with TEAD1, while it negatively regulates C-MYC levels in cooperation with MST1. Hence, YAP1 serves as a rheostat for C-MYC, which is regulated by MST1. In addition, depletion of MST1 stimulates lactate production, whereas the specific depletion of TEAD1 has an opposite effect. The inhibition of lactate production and cellular proliferation induced by shikonin also depends on the Hippo pathway activity. Finally, a bioinformatic analysis revealed conserved TEAD-binding motifs in the C-MYC and GLUT1 promoters providing another molecular data supporting our observations. In summary, regulation of glucose metabolism could serve as a new tumor suppressor mechanism orchestrated by the Hippo signaling pathway. - Highlights: • Shikonin inhibits C-MYC and GLUT1 expression in MST1 and YAP1 dependent manner. • YAP1-TEAD1 interaction activates C-MYC and GLUT1 expression. • MST1 in cooperation with YAP1 inhibits C-MYC and GLUT1 expression. • MST1-YAP1-TEAD1 axis regulates lactate production by leukemic cells. • MST1 and YAP1 proteins block proliferation of leukemic cells.

  20. Clinical Assessment of a Nocardia PCR-Based Assay for Diagnosis of Nocardiosis.

    Science.gov (United States)

    Rouzaud, Claire; Rodriguez-Nava, Véronica; Catherinot, Emilie; Méchaï, Frédéric; Bergeron, Emmanuelle; Farfour, Eric; Scemla, Anne; Poirée, Sylvain; Delavaud, Christophe; Mathieu, Daniel; Durupt, Stéphane; Larosa, Fabrice; Lengelé, Jean-Philippe; Christophe, Jean-Louis; Suarez, Felipe; Lortholary, Olivier; Lebeaux, David

    2018-06-01

    The diagnosis of nocardiosis, a severe opportunistic infection, is challenging. We assessed the specificity and sensitivity of a 16S rRNA Nocardia PCR-based assay performed on clinical samples. In this multicenter study (January 2014 to April 2015), patients who were admitted to three hospitals and had an underlying condition favoring nocardiosis, clinical and radiological signs consistent with nocardiosis, and a Nocardia PCR assay result for a clinical sample were included. Patients were classified as negative control (NC) (negative Nocardia culture results and proven alternative diagnosis or improvement at 6 months without anti- Nocardia treatment), positive control (PC) (positive Nocardia culture results), or probable nocardiosis (positive Nocardia PCR results, negative Nocardia culture results, and no alternative diagnosis). Sixty-eight patients were included; 47 were classified as NC, 8 as PC, and 13 as probable nocardiosis. PCR results were negative for 35/47 NC patients (74%). For the 12 NC patients with positive PCR results, the PCR assay had been performed with respiratory samples. These NC patients had chronic bronchopulmonary disease more frequently than did the NC patients with negative PCR results (8/12 patients [67%] versus 11/35 patients [31%]; P = 0.044). PCR results were positive for 7/8 PC patients (88%). There were 13 cases of probable nocardiosis, diagnosed solely using the PCR results; 9 of those patients (69%) had lung involvement (consolidation or nodule). Nocardia PCR testing had a specificity of 74% and a sensitivity of 88% for the diagnosis of nocardiosis. Nocardia PCR testing may be helpful for the diagnosis of nocardiosis in immunocompromised patients but interpretation of PCR results from respiratory samples is difficult, because the PCR assay may also detect colonization. Copyright © 2018 American Society for Microbiology.

  1. PCR-based techniques for leprosy diagnosis: from the laboratory to the clinic.

    Directory of Open Access Journals (Sweden)

    Alejandra Nóbrega Martinez

    2014-04-01

    Full Text Available In leprosy, classic diagnostic tools based on bacillary counts and histopathology have been facing hurdles, especially in distinguishing latent infection from active disease and diagnosing paucibacillary clinical forms. Serological tests and IFN-gamma releasing assays (IGRA that employ humoral and cellular immune parameters, respectively, are also being used, but recent results indicate that quantitative PCR (qPCR is a key technique due to its higher sensitivity and specificity. In fact, advances concerning the structure and function of the Mycobacterium leprae genome led to the development of specific PCR-based gene amplification assays for leprosy diagnosis and monitoring of household contacts. Also, based on the validation of point-of-care technologies for M. tuberculosis DNA detection, it is clear that the same advantages of rapid DNA detection could be observed in respect to leprosy. So far, PCR has proven useful in the determination of transmission routes, M. leprae viability, and drug resistance in leprosy. However, PCR has been ascertained to be especially valuable in diagnosing difficult cases like pure neural leprosy (PNL, paucibacillary (PB, and patients with atypical clinical presentation and histopathological features compatible with leprosy. Also, the detection of M. leprae DNA in different samples of the household contacts of leprosy patients is very promising. Although a positive PCR result is not sufficient to establish a causal relationship with disease outcome, quantitation provided by qPCR is clearly capable of indicating increased risk of developing the disease and could alert clinicians to follow these contacts more closely or even define rules for chemoprophylaxis.

  2. Jornadas de trabalho de mulheres e homens em um assentamento do MST Workdays of men and women in a collective settlement of the landless movement (MST

    Directory of Open Access Journals (Sweden)

    Giovana Ilka Jacinto Salvaro

    2004-04-01

    Full Text Available Este texto busca discutir a divisão do trabalho em um assentamento coletivo do Movimento dos Trabalhadores Rurais Sem Terra (MST, em Santa Catarina, marcado pela proposta de coletivização da terra e dos meios de produção. Nessa forma de organização, busca-se, seguindo as diretrizes estabelecidas pelo MST, a transformação igualitária e solidária da sociedade, incluindo a construção de novas relações de gênero. O que se observou é que, no cotidiano, mulheres e homens, sujeitos históricos e culturais, apropriam-se desses discursos de gênero, ao mesmo tempo que buscam lidar com as contradições que se apresentam. Entre estas, colocam-se as diferentes jornadas de trabalho que, apoiadas em padrões relacionais fixos, determinam oito horas diárias para os homens na produção e quatro para as mulheres, em função do trabalho doméstico e do cuidado das crianças.This text presents a discussion on the division of labor in a collective settlement of the Landless Movement (Movimento dos Trabalhadores Rurais Sem Terra - MST in Santa Catarina, characterized by the collectivization of land and of all means of production. Within this form of organization and according to the directives established by the MST, an equalitarian and solidarious transformation of society, including the construction of new genre relations, is sought for. What has been noted, throughout the daily routine, is that men and women alike, both historical and cultural subjects, appropriate this discourse at the same time in which they try to deal with upcoming contradictions. Within the latter, and based on fixed relational standards, different work hours are thus established. Men are determined to work on a daily eight hour basis in production whereas women, due to domestic work and child rearing, are granted a four hour schedule.

  3. Development and Validation of a Multiplex PCR-Based Assay for the Upper Respiratory Tract Bacterial Pathogens Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis.

    Science.gov (United States)

    Post; White; Aul; Zavoral; Wadowsky; Zhang; Preston; Ehrlich

    1996-06-01

    Background: Conventional simplex polymerase chain reaction (PCR)-based assays are limited in that they only provide for the detection of a single infectious agent. Many clinical diseases, however, present in a nonspecific, or syndromic, fashion, thereby necessitating the simultaneous assessment of multiple pathogens. Panel-based molecular diagnostic testing can be accomplished by the development of multiplex PCR-based assays, which can detect, individually or severally, different pathogens that are associated with syndromic illness. As part of a larger program of panel development, an assay that can simultaneously detect Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis was developed. These organisms were chosen as they are the most common bacterial pathogens associated with both the acute and chronic forms of otitis media; they are also responsible for a high percentage of sinus infections in both children and adults. In addition, H. influenzae and S. pneumoniae are commonly associated with septic meningitits. Methods and Results: Multiple individual PCR-based assays were developed for each of the three target organisms which were then evaluated for sensitivity and specificity. Utilizing the simplex assays that met our designated performance criteria, a matrix style approach was used to develop a duplex H. influenzae-S. pneumoniae assay. The duplex assay was then used as a single component in the development of a triplex assay, wherein the various M. catarrhalis primer-probe sets were tested for compatibility with the existing assay. A single-step PCR protocol, with species-specific primers for each of the three target organisms and a liquid hybridization-gel retardation amplimer detection system, was developed, which amplifies and then discriminates among each of the amplification products according to size. This assay is able to detect all three organisms in a specific manner, either individually or severally. Dilutional experiments

  4. Screening for methicillin-resistant Staphylococcus aureus in clinical swabs using a high-throughput real-time PCR-based method

    DEFF Research Database (Denmark)

    Ornskov, D; Kolmos, B; Bendix Horn, P

    2008-01-01

    2005, all patients and healthcare personnel have been screened for MRSA colonisation, involving analysis of 300-400 samples daily. To deal with this number of samples, a PCR-based method customised for high-throughput analysis and a system for fast reporting of MRSA carrier status were developed. Swab...... samples were incubated overnight in a selective tryptone soya broth and were analysed by PCR the following day. Using this strategy, non-colonised individuals were identified within 24 h, while MRSA-positive samples were analysed further by traditional microbiological methods to determine the resistance...... pattern. This is a cost-effective approach, as the greatest expense in hospitals involves the isolation of patients of unknown MRSA status. The method was evaluated by testing 2194 clinical samples, with a sensitivity and specificity of 100% and 94%, respectively. The analytical sensitivity was 97...

  5. Music-supported therapy (MST) in improving post-stroke patients' upper-limb motor function: a randomised controlled pilot study.

    Science.gov (United States)

    Tong, Yanna; Forreider, Brian; Sun, Xinting; Geng, Xiaokun; Zhang, Weidong; Du, Huishan; Zhang, Tong; Ding, Yuchuan

    2015-05-01

    Music-supported therapy (MST) is a new approach for motor rehabilitation of stroke patients. Recently, many studies have demonstrated that MST improved the motor functions of post-stroke patients. However, the underlying mechanism for this effect is still unclear. It may result from repeated practice or repeated practice combined with musical stimulation. Currently, few studies have been designed to clarify this discrepancy. In this study, the application of "mute" musical instruments allowed for the study of music as an independent factor. Thirty-three post-stroke patients with no substantial previous musical training were included. Participants were assigned to either audible music group (MG) or mute music group (CG), permitting observation of music's independent effect. All subjects received the conventional rehabilitation treatments. Patients in MG (n = 15) received 20 extra sessions of audible musical instrument training over 4 weeks. Patients in CG (n = 18) received "mute" musical instrument training of the same protocol as that of MG. Wolf motor function test (WMFT) and Fugl-Meyer assessment (FMA) for upper limbs were utilised to evaluate motor functions of patients in both groups before and after the treatment. Three patients in CG dropped out. All participants in both groups showed significant improvements in motor functions of upper limbs after 4  weeks' treatment. However, significant differences in the WMFT were found between the two groups (WMFT-quality: P = 0.025; WMFT-time: P = 0.037), but not in the FMA (P = 0.448). In short, all participants showed significant improvement after 4 weeks' treatment, but subjects in MG demonstrated greater improvement than those in CG. This study supports that MST, when combined with conventional treatment, is effective for the recovery of motor skills in post-stroke patients. Additionally, it suggests that apart from the repetitive practices of MST, music may play a unique role in improving

  6. PCR Based Microbial Monitor for Analysis of Recycled Water Aboard the ISSA: Issues and Prospects

    Science.gov (United States)

    Cassell, Gail H.; Lefkowitz, Elliot J.; Glass, John I.

    1995-01-01

    The monitoring of spacecraft life support systems for the presence of health threatening microorganisms is paramount for crew well being and successful completion of missions. Development of technology to monitor spacecraft recycled water based on detection and identification of the genetic material of contaminating microorganisms and viruses would be a substantial improvement over current NASA plans to monitor recycled water samples that call for the use of conventional microbiology techniques which are slow, insensitive, and labor intensive. The union of the molecular biology techniques of DNA probe hybridization and polymerase chain reaction (PCR) offers a powerful method for the detection, identification, and quantification of microorganisms and viruses. This technology is theoretically capable of assaying samples in as little as two hours with specificity and sensitivity unmatched by any other method. A major advance in probe-hybridization/PCR has come about in a technology called TaqMan(TM), which was invented by Perkin Elmer. Instrumentation using TaqMan concepts is evolving towards devices that could meet NASA's needs of size, low power use, and simplicity of operation. The chemistry and molecular biology needed to utilize these probe-hybridization/PCR instruments must evolve in parallel with the hardware. The following issues of chemistry and biology must be addressed in developing a monitor: Early in the development of a PCR-based microbial monitor it will be necessary to decide how many and which organisms does the system need the capacity to detect. We propose a set of 17 different tests that would detect groups of bacteria and fungus, as well as specific eukaryotic parasites and viruses; In order to use the great sensitivity of PCR it will be necessary to concentrate water samples using filtration. If a lower limit of detection of 1 microorganism per 100 ml is required then the microbes in a 100 ml sample must be concentrated into a volume that can be

  7. Development of Ethernet Based Remote Monitoring and Controlling of MST Radar Transmitters using ARM Cortex Microcontroller

    Directory of Open Access Journals (Sweden)

    Lakshmi Narayana ROSHANNA

    2013-01-01

    Full Text Available The recently emerging Web Services technology has provided a new and excellent solution to Industrial Automation in online control and remote monitoring. In this paper, a Web Service Based Remote Monitoring & Controlling of Radar Transmitters for safety management (WMCT developed for MST Radar is described. It achieved the MST radar transmitters’ remote supervisory, data logging and controlling activities. The system is developed using an ARM Cortex M3 processor to monitor and control the 32 triode-based transmitters of the 53-MHz Radar. The system controls transmitters via the internet using an Ethernet client server and store health status in the Database for radar performance analysis. The system enables scientists to operate and control the radar transmitters from a remote client machine Webpage.

  8. B4C solid target boronization of the MST reversed-field pinch

    International Nuclear Information System (INIS)

    Den Hartog, D.J.; Cekic, M.; Fiksel, G.; Hokin, S.A.; Kendrick, R.D.; Prager, S.C.; Stoneking, M.R.

    1992-10-01

    A solid rod of hot-pressed boron carbide is being used as the source of boron during boronization of MST. The most striking result of this procedure is the reduction in oxygen contamination of the plasma (O III radiation, characteristic of oxygen at the edge, falls by about a factor of 3 after boronization.). The radiated power fraction drops to about half its initial value. Particle reflux from the wall is also lowered, making density control simpler. The rod (12.7 mm diameter) is inserted into the edge plasma of normal high-power RFP discharges. B 4 C is ablated from the surface of the rod and deposited in a thin film (a-B/C:H) on the walls and limiters. The energy flux carried by ''superthermal'' (not ''runaway'') electrons at the edge of MST appears to enhance the efficient, non-destructive ablation of the boron carbide rod

  9. Increase in MST activity correlates with visual motion learning: A functional MRI study of perceptual learning.

    Science.gov (United States)

    Larcombe, Stephanie J; Kennard, Chris; Bridge, Holly

    2018-01-01

    Repeated practice of a specific task can improve visual performance, but the neural mechanisms underlying this improvement in performance are not yet well understood. Here we trained healthy participants on a visual motion task daily for 5 days in one visual hemifield. Before and after training, we used functional magnetic resonance imaging (fMRI) to measure the change in neural activity. We also imaged a control group of participants on two occasions who did not receive any task training. While in the MRI scanner, all participants completed the motion task in the trained and untrained visual hemifields separately. Following training, participants improved their ability to discriminate motion direction in the trained hemifield and, to a lesser extent, in the untrained hemifield. The amount of task learning correlated positively with the change in activity in the medial superior temporal (MST) area. MST is the anterior portion of the human motion complex (hMT+). MST changes were localized to the hemisphere contralateral to the region of the visual field, where perceptual training was delivered. Visual areas V2 and V3a showed an increase in activity between the first and second scan in the training group, but this was not correlated with performance. The contralateral anterior hippocampus and bilateral dorsolateral prefrontal cortex (DLPFC) and frontal pole showed changes in neural activity that also correlated with the amount of task learning. These findings emphasize the importance of MST in perceptual learning of a visual motion task. Hum Brain Mapp 39:145-156, 2018. © 2017 Wiley Periodicals, Inc. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

  10. Application of PCR-based DNA sequencing technique for the detection of Leptospira in peripheral blood of septicemia patients

    OpenAIRE

    Ram, S.; Vimalin, J.M.; Jambulingam, M.; Tiru, V.; Gopalakrishnan, R.K.; Madhavan, H.N.

    2012-01-01

    Aim: Isolation, dark field detection and microscopic agglutination test (MAT) are considered ―gold standard‖ tests for diagnosis of Leptospirosis. Several PCR assays are reported but very few have been evaluated for detection of Leptospirosis. Therefore, this study was undertaken. This study aims to design and standardize polymerase chain reaction (PCR) - based DNA sequencing technique for the detection of pathogenic Leptospira from peripheral blood of patients clinically diagnosed with septi...

  11. Validation of a PCR-based method for detection of food-borne thermotolerant Campylobacters in a multicenter collaborative trial

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Cook, N.; D'Agostino, M.

    2004-01-01

    A PCR-based method for rapid detection of food-borne thermotolerant campylobacters was evaluated through a collaborative trial with 12 laboratories testing spiked carcass rinse samples. The method showed an interlaboratory diagnostic sensitivity of 96.7% and a diagnostic specificity of 100% for c......% for chicken samples, while these values were 94.2 and 83.3%, respectively, for pig samples....

  12. Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

    OpenAIRE

    Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

    1999-01-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy pr...

  13. Inherited MST1 deficiency underlies susceptibility to EV-HPV infections.

    Directory of Open Access Journals (Sweden)

    Amandine Crequer

    Full Text Available Epidermodysplasia verruciformis (EV is characterized by persistent cutaneous lesions caused by a specific group of related human papillomavirus genotypes (EV-HPVs in otherwise healthy individuals. Autosomal recessive (AR EVER1 and EVER2 deficiencies account for two thirds of known cases of EV. AR RHOH deficiency has recently been described in two siblings with EV-HPV infections as well as other infectious and tumoral manifestations. We report here the whole-exome based discovery of AR MST1 deficiency in a 19-year-old patient with a T-cell deficiency associated with EV-HPV, bacterial and fungal infections. MST1 deficiency has recently been described in seven patients from three unrelated kindreds with profound T-cell deficiency and various viral and bacterial infections. The patient was also homozygous for a rare ERCC3 variation. Our findings broaden the clinical range of infections seen in MST1 deficiency and provide a new genetic etiology of susceptibility to EV-HPV infections. Together with the recent discovery of RHOH deficiency, they suggest that T cells are involved in the control of EV-HPVs, at least in some individuals.

  14. INVESTIGATING SUSPENSION OF MST SLURRIES IN A PILOT-SCALE WASTE TANK

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M.; Restivo, M.; Steeper, T.; Williams, M.; Qureshi, Z.

    2011-01-24

    The Small Column Ion Exchange (SCIX) process is being developed to remove cesium, strontium, and actinides from Savannah River Site (SRS) Liquid Waste using an existing waste tank (i.e., Tank 41H) to house the process. Savannah River National Laboratory (SRNL) is conducting pilot-scale mixing tests to determine the pump requirements for suspending monosodium titanate (MST), crystalline silicotitanate (CST), and simulated sludge. The purpose of this pilot scale testing is for the pumps to suspend the MST particles so that MST can be removed from the tank. The pilot-scale tank is a 1/10.85 linear scaled model of Tank 41H. The tank diameter, tank liquid level, pump nozzle diameter, pump elevation, and cooling coil diameter are all 1/10.85 of their dimensions in Tank 41H. The pump locations correspond to the proposed locations in Tank 41H by the SCIX program (Risers B5 and B2 for two pump configurations and Risers B5, B3, and B1 for three pump configurations).

  15. PCR-based identification of eight Lactobacillus species and 18 hr-HPV genotypes in fixed cervical samples of South African women at risk of HIV and BV.

    NARCIS (Netherlands)

    Dols, J.A.M.; Reid, G.; Kort, R.; Schuren, F.H.J.; Tempelman, H.; Bontekoe, T.R.; Korporaal, H.; van der Veer, E.M.; Smit, P.W,; Boon, M.E.

    2012-01-01

    Vaginal lactobacilli assessed by PCR-based microarray and PCR-based genotyping of HPV in South African women at risk for HIV and BV. Vaginal lactobacilli can be defined by microarray techniques in fixed cervical samples of South African women. Cervical brush samples suspended in the coagulant

  16. PCR-based identification of eight lactobacillus species and 18 hr-HPV genotypes in fixed cervical samples of south african women at risk of HIV and BV

    NARCIS (Netherlands)

    Dols, J.A.M.; Reid, G.; Kort, R.; Schuren, F.H.J.; Tempelman, H.; Bontekoe, T.R.; Korporaal, H.; Veer, E.M. van der; Smit, P.W.; Boon, M.E.

    2012-01-01

    Vaginal lactobacilli assessed by PCR-based microarray and PCR-based genotyping of HPV in South African women at risk for HIV and BV. Vaginal lactobacilli can be defined by microarray techniques in fixed cervical samples of South African women. Cervical brush samples suspended in the coagulant

  17. Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA.

    Science.gov (United States)

    Kim, Sung-Su; Choi, Hyun-Jeung; Kim, Jin Ju; Kim, M Sun; Lee, In-Seon; Byun, Bohyun; Jia, Lina; Oh, Myung Ryurl; Moon, Youngho; Park, Sarah; Choi, Joon-Seok; Chae, Seoung Wan; Nam, Byung-Ho; Kim, Jin-Soo; Kim, Jihun; Min, Byung Soh; Lee, Jae Seok; Won, Jae-Kyung; Cho, Soo Youn; Choi, Yoon-La; Shin, Young Kee

    2018-01-11

    In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an 'internal quality control (iQC) index' as a criterion for judging the minimum quality of DNA for PCR-based analyses. In a pre-clinical study comparing the results from droplet digital PCR-based EGFR mutation test (ddEGFR test) and qPCR-based EGFR mutation test (cobas EGFR test), iQC index ≥ 0.5 (iQC copies ≥ 500, using 3.3 ng of FFPET-DNA [1,000 genome equivalents]) was established, indicating that more than half of the input DNA was amplifiable. Using this criterion, we conducted a retrospective comparative clinical study of the ddEGFR and cobas EGFR tests for the detection of EGFR mutations in non-small cell lung cancer (NSCLC) FFPET-DNA samples. Compared with the cobas EGFR test, the ddEGFR test exhibited superior analytical performance and equivalent or higher clinical performance. Furthermore, iQC index is a reliable indicator of the quality of FFPET-DNA and could be used to prevent incorrect diagnoses arising from low-quality samples.

  18. First mesospheric turbulence study using coordinated rocket and MST radar measurements over Indian low latitude region

    Directory of Open Access Journals (Sweden)

    H. Chandra

    2008-09-01

    Full Text Available A campaign to study turbulence in the mesosphere, over low latitudes in India, using rocket-borne measurements and Indian MST radar, was conducted during July 2004. A rocket-borne Langmuir probe detected a spectrum of electron density irregularities, with scale sizes in the range of about 1 m to 1 km, in 67.5–78.0 km and 84–89 km altitude regions over a low latitude station Sriharikota (13.6° N, 80.2° E. A rocket-borne chaff experiment measured zonal and meridional winds about 30 min after the Langmuir probe flight. The MST radar located at Gadanki (13.5° N, 79.2° E, which is about 100 km west of Sriharikota, also detected the presence of a strong scattering layer in 73.5–77.5 km region from which radar echoes corresponding to 3 m irregularities were received. Based on the region of occurrence of irregularities, which was highly collisional, presence of significant shears in zonal and meridional components of wind measured by the chaff experiment, 10 min periodicity in zonal and meridional winds obtained by the MST radar and the nature of wave number spectra of the irregularities, it is suggested that the observed irregularities were produced through the neutral turbulence mechanism. The percentage amplitude of fluctuations across the entire scale size range showed that the strength of turbulence was stronger in the lower altitude regions and decreased with increasing altitude. It was also found that the amplitude of fluctuations was large in regions of steeper electron density gradients. MST radar observations showed that at smaller scales of turbulence such as 3 m, (a the thickness of the turbulent layer was between 2 and 3 km and (b and fine structures, with layer thicknesses of about a km or less were also embedded in these layers. Rocket also detected 3-m fluctuations, which were very strong (a few percent in lower altitudes (67.5 to 71.0 km and small but clearly well above the noise floor at higher altitudes. Rocket and radar

  19. First mesospheric turbulence study using coordinated rocket and MST radar measurements over Indian low latitude region

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, H.; Sinha, H.S.S.; Das, U.; Misra, R.N.; Das, S.R. [Physical Research Lab., Ahmedabad (India); Datta, J.; Chakravarty, S.C. [ISRO Headquarters, Bangalore (India); Patra, A.K.; Vekateswara Rao, N.; Narayana Rao, D. [National Atmospheric Research Lab., Tirupati (India)

    2008-07-01

    A campaign to study turbulence in the mesosphere, over low latitudes in India, using rocket-borne measurements and Indian MST radar, was conducted during July 2004. A rocket-borne Langmuir probe detected a spectrum of electron density irregularities, with scale sizes in the range of about 1 m to 1 km, in 67.5-78.0 km and 84-89 km altitude regions over a low latitude station Sriharikota (13.6 N, 80.2 E). A rocket-borne chaff experiment measured zonal and meridional winds about 30 min after the Langmuir probe flight. The MST radar located at Gadanki (13.5 N, 79.2 E), which is about 100 km west of Sriharikota, also detected the presence of a strong scattering layer in 73.5-77.5 km region from which radar echoes corresponding to 3 m irregularities were received. Based on the region of occurrence of irregularities, which was highly collisional, presence of significant shears in zonal and meridional components of wind measured by the chaff experiment, 10 min periodicity in zonal and meridional winds obtained by the MST radar and the nature of wave number spectra of the irregularities, it is suggested that the observed irregularities were produced through the neutral turbulence mechanism. The percentage amplitude of fluctuations across the entire scale size range showed that the strength of turbulence was stronger in the lower altitude regions and decreased with increasing altitude. It was also found that the amplitude of fluctuations was large in regions of steeper electron density gradients. MST radar observations showed that at smaller scales of turbulence such as 3 m, (a) the thickness of the turbulent layer was between 2 and 3 km and (b) and fine structures, with layer thicknesses of about a km or less were also embedded in these layers. Rocket also detected 3-m fluctuations, which were very strong (a few percent) in lower altitudes (67.5 to 71.0 km) and small but clearly well above the noise floor at higher altitudes. Rocket and radar results also point to the

  20. European validation of a real-time PCR-based method for detection of Listeria monocytogenes in soft cheese.

    Science.gov (United States)

    Gianfranceschi, Monica Virginia; Rodriguez-Lazaro, David; Hernandez, Marta; González-García, Patricia; Comin, Damiano; Gattuso, Antonietta; Delibato, Elisabetta; Sonnessa, Michele; Pasquali, Frederique; Prencipe, Vincenza; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Kozačinski, Lidija; Tomic, Danijela Horvatek; Zdolec, Nevijo; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John Elmerdahl; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Paiusco, Antonella; De Cesare, Alessandra; Manfreda, Gerardo; De Medici, Dario

    2014-08-01

    The classical microbiological method for detection of Listeria monocytogenes requires around 7 days for final confirmation, and due to perishable nature of RTE food products, there is a clear need for an alternative methodology for detection of this pathogen. This study presents an international (at European level) ISO 16140-based validation trial of a non-proprietary real-time PCR-based methodology that can generate final results in the following day of the analysis. This methodology is based on an ISO compatible enrichment coupled to a bacterial DNA extraction and a consolidated real-time PCR assay. Twelve laboratories from six European countries participated in this trial, and soft cheese was selected as food model since it can represent a difficult matrix for the bacterial DNA extraction and real-time PCR amplification. The limit of detection observed was down to 10 CFU per 25 of sample, showing excellent concordance and accordance values between samples and laboratories (>75%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (82.75%, 96.70% and 97.62%, respectively) when the results obtained for the real-time PCR-based methods were compared to those of the ISO 11290-1 standard method. An interesting observation was that the L. monocytogenes detection by the real-time PCR method was less affected in the presence of Listeria innocua in the contaminated samples, proving therefore to be more reliable than the reference method. The results of this international trial demonstrate that the evaluated real-time PCR-based method represents an excellent alterative to the ISO standard since it shows a higher performance as well as reduce the extent of the analytical process, and can be easily implemented routinely by the competent authorities and food industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. A Sensitive and Specific PCR Based Method for Identification of Cryptosporidium Sp. Using New Primers from 18S Ribosomal RNA

    Directory of Open Access Journals (Sweden)

    M Heydarnezhadi

    2011-09-01

    Full Text Available Background: The main goal of the present study was to develop a new sensitive and specific PCR based method for Identification of Cryptosporidium sp. using novel primers from 18S ribosomal RNA. Cryptosporidi­osis in high-risk host groups particularly in neonates and immuno-compromised individuals may result in death. To the best of our knowledge this is the first study regarding develop a new PCR based method to diagnose the cryptosporidiosis in Iran.Methods: A total of 850 human fecal samples from patients clinically suspected to cryptosporidiosis and 100 healthy and diarrheic cattle stool specimens were collected. The simplified formol-ether concentration method was carried out for all samples. They were then examined microscopically by modified Ziehl-Neel­sen staining method. Total DNA was extracted by QIA amp DNA stool mini kit was carried out by using designed prim­ers.Results: Twenty nine cases of cryptosporidiosis infection in human and 30 samples from cattle microscopi­cally were posi­tive. The described primary and nested PCR method could detect all Cryptospori­dium positive samples from human and cattle. Regards to suspected negative samples in pri­mary PCR examination, the Nested PCR could ap­prove two more positive results. Furthermore, Nested PCR analysis was able to detect one more case which was nega­tive in both microscopically examination and primary PCR. Specificity of the test was 100%. Sensitivity of Nested PCR in comparison to our gold standard; microscopy after Ridley concentration modified ziehl-Neelsen, was 100 %.Conclusion: Our developed PCR based method by using new primers devised from 18S ribosomal RNA revealed the ability for identification of the Cryptosporidium species such as C. parvum and C. huminis with high specificity and sensitivity.

  2. Studying small molecule-aptamer interactions using MicroScale Thermophoresis (MST).

    Science.gov (United States)

    Entzian, Clemens; Schubert, Thomas

    2016-03-15

    Aptamers are potent and versatile binding molecules recognizing various classes of target molecules. Even challenging targets such as small molecules can be identified and bound by aptamers. Studying the interaction between aptamers and drugs, antibiotics or metabolites in detail is however difficult due to the lack of sophisticated analysis methods. Basic binding parameters of these small molecule-aptamer interactions such as binding affinity, stoichiometry and thermodynamics are elaborately to access using the state of the art technologies. The innovative MicroScale Thermophoresis (MST) is a novel, rapid and precise method to characterize these small molecule-aptamer interactions in solution at microliter scale. The technology is based on the movement of molecules through temperature gradients, a physical effect referred to as thermophoresis. The thermophoretic movement of a molecule depends - besides on its size - on charge and hydration shell. Upon the interaction of a small molecule and an aptamer, at least one of these parameters is altered, leading to a change in the movement behavior, which can be used to quantify molecular interactions independent of the size of the target molecule. The MST offers free choice of buffers, even measurements in complex bioliquids are possible. The dynamic affinity range covers the pM to mM range and is therefore perfectly suited to analyze small molecule-aptamer interactions. This section describes a protocol how quantitative binding parameters for aptamer-small molecule interactions can be obtained by MST. This is demonstrated by mapping down the binding site of the well-known ATP aptamer DH25.42 to a specific region at the adenine of the ATP molecule. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Fluctuation reduction and enhanced confinement in the MST reversed-field pinch

    International Nuclear Information System (INIS)

    Chapman, B.E.

    1997-10-01

    Plasmas with a factor of ≥3 improvement in energy confinement have been achieved in the MST reversed-field pinch (RFP). These plasmas occur spontaneously, following sawtooth crashes, subject to constraints on, eg, toroidal magnetic field reversal and wall conditioning. Possible contributors to the improved confinement include a reduction of core-resonant, global magnetic fluctuations and a reduction of electrostatic fluctuations over the entire plasma edge. One feature of these plasmas is a region of strong ExB flow shear in the edge. Never before observed in conjunction with enhanced confinement in the RFP, such shear is common in enhanced confinement discharges in tokamaks and stellarators. Another feature of these plasmas is a new type of discrete dynamo event. Like sawtooth crashes, a common form of discrete dynamo, these events correspond to bursts of edge parallel current. The reduction of electrostatic fluctuations in these plasmas occurs within and beyond the region of strong ExB flow shear, similar to what is observed in tokamaks and stellarators. However, the reductions in the MST include fluctuations whose correlation lengths are larger than the width of the shear region. The reduction of the global magnetic fluctuations is most likely due to flattening of the μ=μ 0 rvec J· rvec B/B 2 profile. Flattening can occur, eg, due to the new type of discrete dynamo event and reduced edge resistivity. Enhanced confinement plasmas are also achieved in the MST when auxiliary current is applied to flatten the μ profile and reduce magnetic fluctuations. Unexpectedly, these plasmas also exhibit a region (broader than in the case above) of strong ExB flow shear in the edge, an edge-wide reduction of electrostatic fluctuations, and the new type of discrete dynamo event. Auxiliary current drive has historically been viewed as the principal route to fusion reactor viability for the RFP

  4. An overview of data acquisition, signal coding and data analysis techniques for MST radars

    Science.gov (United States)

    Rastogi, P. K.

    1986-01-01

    An overview is given of the data acquisition, signal processing, and data analysis techniques that are currently in use with high power MST/ST (mesosphere stratosphere troposphere/stratosphere troposphere) radars. This review supplements the works of Rastogi (1983) and Farley (1984) presented at previous MAP workshops. A general description is given of data acquisition and signal processing operations and they are characterized on the basis of their disparate time scales. Then signal coding, a brief description of frequently used codes, and their limitations are discussed, and finally, several aspects of statistical data processing such as signal statistics, power spectrum and autocovariance analysis, outlier removal techniques are discussed.

  5. (Re politicizing the concept of gender: the political participation of the women in the MST

    Directory of Open Access Journals (Sweden)

    Renata Gonçalves

    2009-12-01

    Full Text Available In this article we examine the complex and contradictory construction of the Gender Sector as a part of the organizational structure of the Movement of Landless Rural Workers (MST. The background is formed by the tensions surrounding the political participation of women in the struggle for land, in which the initial emphasis given to the category woman is substituted by the concept of gender. More than a simple alteration in terminology, this change involves the challenge of understanding theoretically and constructing in political practice new gender relations.

  6. Analysis of the water dynamics for the MSE-COIL and theMST-COIL

    CERN Document Server

    Massidda, L; Kadi, Y; Balhan, B

    2005-01-01

    In this report, we present the technical specification for the numerical model and the study of the acoustic wave propagation in the water tubes of the extraction septum magnet (MSE) and the thin magnetic septum (MST) in the event of an asynchronous firing of the extraction kickers (MKE). The deposited energy densities, estimated by the high-energy particle transport code FLUKA, were converted to internal heat generation rates according to the time dependence of the extracted beam. The transient response to this thermal load was obtained by simulating power deposition and acoustic wave propagation by the spectral-element code ELSE.

  7. A brief history of the development of wind-profiling or MST radars

    Directory of Open Access Journals (Sweden)

    T. E. Van Zandt

    Full Text Available The history of the development of the wind-profiling or MST radar technique is reviewed from its inception in the late 1960s to the present. Extensions of the technique by the development of boundary-layer radars and the radio-acoustic sounding system (RASS technique to measure temperature are documented. Applications are described briefly, particularly practical applications to weather forecasting, with data from networks of radars, and scientific applications to the study of rapidly varying atmospheric phenomena such as gravity waves and turbulence.

    Key words: Meteorology and atmospheric dynamics (instruments and techniques · Radio science (remote sensing; instruments and techniques

  8. A brief history of the development of wind-profiling or MST radars

    Directory of Open Access Journals (Sweden)

    T. E. Van Zandt

    2000-07-01

    Full Text Available The history of the development of the wind-profiling or MST radar technique is reviewed from its inception in the late 1960s to the present. Extensions of the technique by the development of boundary-layer radars and the radio-acoustic sounding system (RASS technique to measure temperature are documented. Applications are described briefly, particularly practical applications to weather forecasting, with data from networks of radars, and scientific applications to the study of rapidly varying atmospheric phenomena such as gravity waves and turbulence.Key words: Meteorology and atmospheric dynamics (instruments and techniques · Radio science (remote sensing; instruments and techniques

  9. Magnetic fluctuation induced transport and edge dynamo measurements in the MST reversed-field pinch

    International Nuclear Information System (INIS)

    Hokin, S.; Fiksel, G.; Ji, H.

    1994-09-01

    Probe measurements in MST indicate that RFP particle and energy loss is governed by magnetic fluctuations inside r/a = 0.8, with energy carried out convectively by superthermal electrons. The radial loss rate is lower than the Rechester-Rosenbluth level, presumably due to the establishment of a restraining ambipolar potential. Several aspects of these measurements contradict the Kinetic Dynamo Theory, while the MHD dynamo EMF is measured to be large enough to drive the edge current carried by these superthermal electrons

  10. Detection of cyclospora in captive chimpanzees and macaques by a quantitative PCR-based mutation scanning approach

    OpenAIRE

    Marangi, M.; Koehler, A.V.; Zanzani, S.A.; Manfredi, M.T.; Brianti, E.; Giangaspero, A.; Gasser, R.B.

    2015-01-01

    Background Cyclospora is a protistan parasite that causes enteritis in several species of animals including humans. The aim of this study was to investigate the presence of Cyclospora in captive non-human primates. Methods A total of 119 faecal samples from Pan troglodytes, Macaca sylvanus, Cercopithecus cephus, Erythrocebus patas, Chlorocebus aethiops and Macaca fascicularis from a wildlife animal rescue center as well as from Macaca fascicularis from an experimental primate research center ...

  11. A new PCR-based approach indicates the range of Clonorchis sinensis now extends to Central Thailand.

    Directory of Open Access Journals (Sweden)

    Rebecca J Traub

    Full Text Available Differentiation of the fish-borne trematodes belonging to the Opisthorchiidae, Heterophyidae and Lecithodendriidae is important from a clinical and epidemiological perspective, yet it is impossible to do using conventional coprological techniques, as the eggs are morphologically similar. Epidemiological investigation therefore currently relies on morphological examination of adult worms following expulsion chemotherapy. A PCR test capable of amplifying a segment of the internal transcribed spacer region of ribosomal DNA for the opisthorchiid and heterophyid flukes eggs taken directly from faeces was developed and evaluated in a rural community in central Thailand. The lowest quantity of DNA that could be amplified from individual adults of Opisthorchis viverrini, Clonorchis sinensis and Haplorchis taichui was estimated at 0.6 pg, 0.8 pg and 3 pg, respectively. The PCR was capable of detecting mixed infection with the aforementioned species of flukes under experimental conditions. A total of 11.6% of individuals in rural communities in Sanamchaikaet district, central Thailand, were positive for 'Opisthorchis-like' eggs in their faeces using conventional parasitological detection techniques. In comparison to microscopy, the PCR yielded a sensitivity and specificity of 71.0% and 76.7%, respectively. Analysis of the microscopy-positive PCR products revealed 64% and 23% of individuals to be infected with O. viverrini and C. sinensis, respectively. The remaining 13% (three individuals were identified as eggs of Didymozoidae, presumably being passed mechanically in the faeces following the ingestion of infected fishes. An immediate finding of this study is the identification and first report of a C. sinensis-endemic community in central Thailand. This extends the known range of this liver fluke in Southeast Asia. The PCR developed herein provides an important tool for the specific identification of liver and intestinal fluke species for future epidemiological surveys.

  12. Introducing GUt Low-Density Array (GULDA) - a validated approach for qPCR-based intestinal microbial community analysis

    DEFF Research Database (Denmark)

    Bergström, Anders; Licht, Tine Rask; Wilcks, Andrea

    2012-01-01

    obtained from individuals at various points in time. The target genes represent important phyla, genera, species, or other taxonomic groups within the five predominant bacterial phyla of the gut, Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia and also Euryarchaeota...

  13. A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

    Science.gov (United States)

    Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

    2011-06-30

    Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms

    Directory of Open Access Journals (Sweden)

    Manuel Ares-Arroyo

    2018-03-01

    Full Text Available ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants. From this exhaustive computational analysis we developed a new PCR-based technique, targeting a specific sequence in the conserved region, for the screening, capture and sequencing of these small plasmids, either specific for Enterobacteriaceae or specific for Pasteurellaceae. To validate this PCR-based system, we tested various collections of isolates from both bacterial families, finding that ColE1 replicons were not only highly prevalent in antibiotic-resistant isolates, but also present in susceptible bacteria. In Pasteurellaceae, ColE1 plasmids carried almost exclusively antibiotic resistance genes. In Enterobacteriaceae, these plasmids encoded a large range of traits, including not only antibiotic resistance determinants, but also a wide variety of genes, showing the huge genetic plasticity of these small replicons. Finally, we also used a metagenomic approach in order to validate this technique, performing this PCR system using total DNA extractions from fecal samples from poultry, turkeys, pigs and humans. Using Illumina sequencing of the PCR products we identified a great diversity of genes encoded by ColE1 replicons, including different antibiotic resistance

  15. Prediction Models for Plutonium, Strontium, Uranium and Neptunium Loading onto Monosodium Titanate (MST)

    International Nuclear Information System (INIS)

    Fondeur, F. F.; Hobbs, D. T.; Barnes, M. J.; Peters, T. B.; Fink, S. D.

    2005-01-01

    The DA isotherm parameters for U, Pu, Sr and Np have been updated to include additional data obtained since the original derivation. The DA isotherms were modified to include a kinetic function derived by Rahn to describe sorbate loading from the beginning of sorption up to equilibrium. The final functions describe both kinetic and thermodynamic sorption. We selected the Rahn function to describe radionuclide sorption because it originates from diffusion and absorption controlled sorption. An investigation of the thermal behavior of radionuclide sorption on MST as shown by this data revealed the sorption process is diffusion (or transport) controlled (in solution). Transport in solution can in theory be accelerated by vigorous mixing but the range of available mixing speed in the facility design will probably not be sufficient to markedly increase radionuclide sorption rate on MST from diffusion-controlled sorption. The laboratory studies included mixing energies hydraulically-scaled to match those of the Actinide Removal Process and these likely approximate the range of energies available in the Salt Waste Processing Facility

  16. First Absolutely Calibrated Localized Measurements of Ion Velocity in the MST in Locked and Rotating Plasmas

    Science.gov (United States)

    Baltzer, M.; Craig, D.; den Hartog, D. J.; Nornberg, M. D.; Munaretto, S.

    2015-11-01

    An Ion Doppler Spectrometer (IDS) is used on MST for high time-resolution passive and active measurements of impurity ion emission. Absolutely calibrated measurements of flow are difficult because the spectrometer records data within 0.3 nm of the C+5 line of interest, and commercial calibration lamps do not produce lines in this narrow range . A novel optical system was designed to absolutely calibrate the IDS. The device uses an UV LED to produce a broad emission curve in the desired region. A Fabry-Perot etalon filters this light, cutting transmittance peaks into the pattern of the LED emission. An optical train of fused silica lenses focuses the light into the IDS with f/4. A holographic diffuser blurs the light cone to increase homogeneity. Using this light source, the absolute Doppler shift of ion emissions can be measured in MST plasmas. In combination with charge exchange recombination spectroscopy, localized ion velocities can now be measured. Previously, a time-averaged measurement along the chord bisecting the poloidal plane was used to calibrate the IDS; the quality of these central chord calibrations can be characterized with our absolute calibration. Calibration errors may also be quantified and minimized by optimizing the curve-fitting process. Preliminary measurements of toroidal velocity in locked and rotating plasmas will be shown. This work has been supported by the US DOE.

  17. Development of radio acoustic sounding system (RASS with Gadanki MST radar – first results

    Directory of Open Access Journals (Sweden)

    T. Tsuda

    2008-09-01

    Full Text Available A high-power acoustic exciter was designed and developed for the Gadanki MST Radar to facilitate observations in the Radio Acoustic Sounding System (RASS mode. Sweep range of acoustic signal frequencies was set to 94–125 Hz so as to satisfy Bragg matching condition for temperature range of −90°–40°C between surface and the tropopause (about 17 km. Raytracing of acoustic wave propagation was used to predict the antenna beam directions along which optimum RASS echoes could be obtained. During the RASS observation period of about 18 h on 23–24 July 2006 height profiles of atmospheric virtual temperature were obtained between 1.5 km and 10 km and occasionally up to 14 km. In comparison with the three simultaneous radiosonde launches, RASS derived temperature profiles had the r.m.s. discrepancy of about 1 K, although deviation of the RASS results sometimes appeared when the radial wind velocity was not fully available for the correction of apparent sound speed. This study has successfully demonstrated capability of the RASS application with the Gadanki MST radar, which will be used for continuous monitoring of the temperature profiles in the troposphere and lower stratosphere region in the tropics.

  18. Absolute brightness modeling for improved measurement of electron temperature from soft x-rays on MST

    Science.gov (United States)

    Reusch, L. M.; Franz, P.; Goetz, J. A.; den Hartog, D. J.; Nornberg, M. D.; van Meter, P.

    2017-10-01

    The two-color soft x-ray tomography (SXT) diagnostic on MST is now capable of Te measurement down to 500 eV. The previous lower limit was 1 keV, due to the presence of SXR emission lines from Al sputtered from the MST wall. The two-color technique uses two filters of different thickness to form a coarse spectrometer to estimate the slope of the continuum x-ray spectrum, which depends on Te. The 1.6 - 2.0 keV Al emission lines were previously filtered out by using thick Be filters (400 µm and 800 µm), thus restricting the range of the SXT diagnostic to Te >= 1 keV. Absolute brightness modeling explicitly includes several sources of radiation in the analysis model, enabling the use of thinner filters and measurement of much lower Te. Models based on the atomic database and analysis structure (ADAS) agree very well with our experimental SXR measurements. We used ADAS to assess the effect of bremsstrahlung, recombination, dielectronic recombination, and line emission on the inferred Te. This assessment informed the choice of the optimum filter pair to extend the Te range of the SXT diagnostic. This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences program under Award Numbers DE-FC02-05ER54814 and DE-SC0015474.

  19. Molecular cloning, functional characterization and expression analysis of a novel monosaccharide transporter gene OsMST6 from rice (Oryza sativa L.)

    NARCIS (Netherlands)

    Wang, Y.; Xiao, Y.; Zhang, Y.; Chai, C.; Wei, G.; Wei, X.; Xu, H.; Wang, M.; Ouwerkerk, P.B.F.; Zhu, Z.

    2008-01-01

    Monosaccharides transporters play important roles in assimilate supply for sink tissue development. In this study, a new monosaccharide transporter gene OsMST6 was identified from rice (Oryza sativa L.). The predicted OsMST6 protein shows typical features of sugar transporters and shares 79.6%

  20. High performance of a new PCR-based urine assay for HPV-DNA detection and genotyping.

    Science.gov (United States)

    Tanzi, Elisabetta; Bianchi, Silvia; Fasolo, Maria Michela; Frati, Elena R; Mazza, Francesca; Martinelli, Marianna; Colzani, Daniela; Beretta, Rosangela; Zappa, Alessandra; Orlando, Giovanna

    2013-01-01

    Human papillomavirus (HPV) testing has been proposed as a means of replacing or supporting conventional cervical screening (Pap test). However, both methods require the collection of cervical samples. Urine sample is easier and more acceptable to collect and could be helpful in facilitating cervical cancer screening. The aim of this study was to evaluate the sensitivity and specificity of urine testing compared to conventional cervical smear testing using a PCR-based method with a new, designed specifically primer set. Paired cervical and first voided urine samples collected from 107 women infected with HIV were subjected to HPV-DNA detection and genotyping using a PCR-based assay and a restriction fragment length polymorphism method. Sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated using the McNemar's test for differences. Concordance between tests was assessed using the Cohen's unweighted Kappa (k). HPV DNA was detected in 64.5% (95% CI: 55.1-73.1%) of both cytobrush and urine samples. High concordance rates of HPV-DNA detection (k = 0.96; 95% CI: 0.90-1.0) and of high risk-clade and low-risk genotyping in paired samples (k = 0.80; 95% CI: 0.67-0.92 and k = 0.74; 95% CI: 0.60-0.88, respectively) were observed. HPV-DNA detection in urine versus cervix testing revealed a sensitivity of 98.6% (95% CI: 93.1-99.9%) and a specificity of 97.4% (95% CI: 87.7-99.9%), with a very high NPV (97.4%; 95% CI: 87.7-99.9%). The PCR-based assay utilized in this study proved highly sensitive and specific for HPV-DNA detection and genotyping in urine samples. These data suggest that a urine-based assay would be a suitable and effective tool for epidemiological surveillance and, most of all, screening programs. Copyright © 2012 Wiley Periodicals, Inc.

  1. PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

    Science.gov (United States)

    Singh, Om P; Bali, Prerna; Hemingway, Janet; Subbarao, Sarala K; Dash, Aditya P; Adak, Tridibes

    2009-01-01

    Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr) is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F) in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F) in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR), an Amplification Refractory Mutation System (ARMS) and Primer Introduced Restriction Analysis-PCR (PIRA-PCR) were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method was refractory to non

  2. PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

    Directory of Open Access Journals (Sweden)

    Dash Aditya P

    2009-07-01

    Full Text Available Abstract Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR, an Amplification Refractory Mutation System (ARMS and Primer Introduced Restriction Analysis-PCR (PIRA-PCR were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method

  3. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    International Nuclear Information System (INIS)

    Jackson, Christopher B.; Gallati, Sabina; Schaller, André

    2012-01-01

    Highlights: ► Serial qPCR accurately determines fragmentation state of any given DNA sample. ► Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. ► Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. ► Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze–thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λ nDNA ) and mtDNA (λ mtDNA ) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two

  4. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

  5. Rust resistance evaluation of advanced wheat (triticum aestivum l.) genotypes using pcr-based dna markers

    International Nuclear Information System (INIS)

    Rahman, S.U.; Younis, M.; Iqbal, M.Z.; Nawaz, M.

    2014-01-01

    The most effective and environmental friendly approach for the control of wheat rust disease is the use of resistant genotypes. The present study was conducted to explore rust resistance potential of 85 elite wheat genotypes (36 varieties and 49 advanced lines) using various types of DNA markers like STS, SCAR and SSR. DNA markers linked with different genes conferring resistance to rusts (Leaf rust=Lr, Yellow rust=Yr and Stem rust=Sr) were employed in this study. A total of 18 genes, consisting of eleven Lr (lr1, lr10, lr19, lr21, lr28, lr34, lr39, lr46, lr47, lr51 and lr52), four Yr (yr5, yr18, yr26 and yr29) and three Sr genes (sr2, sr29, and sr36) were studied through linked DNA markers. Maximum number of Lr genes was found in 17 advanced lines and 9 varieties, Yr genes in 26 advanced lines and 20 wheat varieties, and Sr genes in 43 advanced lines and 27 varieties. Minimum number of Lr genes was found in advanced line D-97 and variety Kohinoor-83, Yr genes in wheat variety Bwp-97 and Sr genes in 6 advanced lines and 8 varieties. Molecular data revealed that genotypes having same origin, from a specified area showed resistance for similar type of genes. In this study, an average similarity of 84% was recorded among wheat genotypes. Out of 18 loci, 15 were found to be polymorphic. (author)

  6. Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

    Science.gov (United States)

    Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

    1999-01-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412T, which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains. PMID:10508059

  7. Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis.

    Science.gov (United States)

    Torriani, S; Zapparoli, G; Dellaglio, F

    1999-10-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412(T), which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

  8. Molecular analysis of commercial date palm cultivars in Lybia using ISSR and SRAP PCR-based markers

    Directory of Open Access Journals (Sweden)

    Khalifa Noha S.

    2016-01-01

    Full Text Available Little is known about the molecular structure of the date palm (Phoenix dactylifera L. despite its importance as invaluable drought tolerant crop. Intervarietal variation and cultivar identification are crucial for breeding and gene bank conservation of this plant worldwide. In this work, two PCR based marker systems (ISSR and SRAP were applied on top quality eight commercial cultivars in Libya (Umfetity, Bekrary, Alhamraya, Sufeer Genab, Alsaeedy Show, Farag Barameel, Majhool Alheelo and Alkhadraya. DNA variations were explored using eleven ISSR and nine combinations of SRAP markers. All markers used generated polymorphic bands among the different cultivars that can be used as molecular markers for their differentiation. The genetic distance between cultivars was also estimated from banding patterns. Our results indicate that ISSR and SRAP systems can efficiently identify and differentiate between the selected cultivars. This work can be used as a model to establish a road map for all date palm cultivars worldwide.

  9. Real-Time PCR-Based Quantitation Method for the Genetically Modified Soybean Line GTS 40-3-2.

    Science.gov (United States)

    Kitta, Kazumi; Takabatake, Reona; Mano, Junichi

    2016-01-01

    This chapter describes a real-time PCR-based method for quantitation of the relative amount of genetically modified (GM) soybean line GTS 40-3-2 [Roundup Ready(®) soybean (RRS)] contained in a batch. The method targets a taxon-specific soybean gene (lectin gene, Le1) and the specific DNA construct junction region between the Petunia hybrida chloroplast transit peptide sequence and the Agrobacterium 5-enolpyruvylshikimate-3-phosphate synthase gene (epsps) sequence present in GTS 40-3-2. The method employs plasmid pMulSL2 as a reference material in order to quantify the relative amount of GTS 40-3-2 in soybean samples using a conversion factor (Cf) equal to the ratio of the RRS-specific DNA to the taxon-specific DNA in representative genuine GTS 40-3-2 seeds.

  10. In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences

    DEFF Research Database (Denmark)

    Ågren, Joakim; Hamidjaja, Raditijo A.; Hansen, Trine

    2013-01-01

    Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely...... on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S...... targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European...

  11. PCR-based karyotyping of Anopheles gambiae inversion 2Rj identifies the BAMAKO chromosomal form

    Directory of Open Access Journals (Sweden)

    Conway David J

    2007-10-01

    Full Text Available Abstract Background The malaria vector Anopheles gambiae is polymorphic for chromosomal inversions on the right arm of chromosome 2 that segregate nonrandomly between assortatively mating populations in West Africa. One such inversion, 2Rj, is associated with the BAMAKO chromosomal form endemic to southern Mali and northern Guinea Conakry near the Niger River. Although it exploits a unique ecology and both molecular and chromosomal data suggest reduced gene flow between BAMAKO and other A. gambiae populations, no molecular markers exist to identify this form. Methods To facilitate study of the BAMAKO form, a PCR assay for molecular karyotyping of 2Rj was developed based on sequences at the breakpoint junctions. The assay was extensively validated using more than 700 field specimens whose karyotypes were determined in parallel by cytogenetic and molecular methods. As inversion 2Rj also occurs in SAVANNA populations outside the geographic range of BAMAKO, samples were tested from Senegal, Cameroon and western Guinea Conakry as well as from Mali. Results In southern Mali, where 2Rj polymorphism in SAVANNA populations was very low and most of the 2Rj homozygotes were found in BAMAKO karyotypes, the molecular and cytogenetic methods were almost perfectly congruent. Elsewhere agreement between the methods was much poorer, as the molecular assay frequently misclassified 2Rj heterozygotes as 2R+j standard homozygotes. Conclusion Molecular karyotyping of 2Rj is robust and accurate on 2R+j standard and 2Rj inverted homozygotes. Therefore, the proposed approach overcomes the lack of a rapid tool for identifying the BAMAKO form across developmental stages and sexes, and opens new perspectives for the study of BAMAKO ecology and behaviour. On the other hand, the method should not be applied for molecular karyotyping of j-carriers within the SAVANNA chromosomal form.

  12. An Ecological System Curriculum: An Integrated MST Approach to Environmental Science Education.

    Science.gov (United States)

    Leonhardt, Nina A.

    This paper describes an inquiry-based, student-centered mathematics, science, and technology curriculum guide. It features activities addressing such environmental science topics as groundwater modeling, water filtration, soil permeability and porosity, water temperature and salinity, and quadrant studies. Activities are organized so that the…

  13. The lack of cross-national equivalence of a therapist adherence measure (TAM-R) in multisystemic therapy (MST)

    NARCIS (Netherlands)

    Lange, A.M.C.; Scholte, R.H.J.; Geffen, W. van; Timman, R.; Busschbach, J.J.V. van; Rijken, R.E.A. van der

    2016-01-01

    This two-study report investigates the equivalence of the Dutch Therapist Adherence Measure Revised (TAM-R) to the US original. The TAM-R is a questionnaire measuring therapist adherence to the treatment model of Multisystemic Therapy (MST). Monitoring of therapist adherence is essential for

  14. Gaseous signalling molecule SO2 via Hippo‑MST pathway to improve myocardial fibrosis of diabetic rats.

    Science.gov (United States)

    Liu, Maojun; Liu, Shengquan; Tan, Wenting; Tang, Fen; Long, Junrong; Li, Zining; Liang, Biao; Chu, Chun; Yang, Jun

    2017-12-01

    Recent studies have indicated the existence of an endogenous sulfur dioxide (SO2)‑generating system in the cardiovascular system. The present study aimed to discuss the function and regulatory mechanism of gaseous signal molecule SO2 in inhibiting apoptosis and endoplasmic reticulum stress (ERS) via the Hippo‑MST signaling pathway to improve myocardial fibrosis of diabetic rats. A total of 40 male Sprague‑Dawley rats were randomly divided into four groups (10 rats per group): Normal control group (control group), diabetic rats group [streptozotocin (STZ) group], SO2 intervention group (STZ+SO2 group) and diabetes mellitus rats treated with L‑Aspartic acid β‑hydroxamate (HDX) group (HDX group). Diabetic rats models were established by intra‑peritoneal injection of STZ (40 mg/kg) Following model establishment, intra‑peritoneal injection of Na2SO3/NaHSO3 solution (0.54 mmol/kg) was administered in the STZ+SO2 group, and HDX solution (25 mg/kg/week) was administered in the HDX group. A total of 4 weeks later, echocardiography was performed to evaluate rats' cardiac function; Masson staining, terminal deoxynucleotidyl transferase dUTP nick end labeling staining and transmission electron microscopy examinations were performed to observe myocardial morphological changes. ELISA was employed to determine the SO2 content. Western blot analysis was performed to detect the expression of proteins associated with apoptosis, ERS and the Hippo‑MST signalling pathway. Compared with the control group, the STZ group and HDX group had a disordered arrangement of myocardial cells with apparent myocardial fibrosis, and echocardiography indicated that the cardiac function was lowered, there was an obvious increase of apoptosis in myocardial tissue, the expression levels of apoptosis‑associated protein B‑cell lymphoma associated protein X, caspase‑3 and caspase‑9 were upregulated, and Bcl‑2 expression was downregulated. The expression of ERS and Hippo‑MST

  15. Confinement and fluctuations in the MST [Madison Symmetric Torus] reversed field pinch

    International Nuclear Information System (INIS)

    Sprott, J.C.; Almagri, A.F.; Assadi, S.; Beckstead, J.A.; Chartas, G.; Dexter, N.; Den Hartog, D.J.; Hokin, S.A.; Holly, D.J.; Prager, S.C.; Rempel, T.D.; Sarff, J.S.; Scime, E.; Shen, W.; Spragins, C.W.; Watts, C.

    1990-09-01

    MST is a large (R 0 /a = 1.5/0.52 m) RFP which to date has obtained 80 ms discharges at a peak plasma current of 0.6 MA. Low loop voltages (15 volts) and modest temperatures (T e /T i ∼ 350/250 eV) are routinely obtained giving estimated unoptimized energy confinement times of about 1 ms. Loop voltage and ion temperature are anomalous. Magnetic fluctuations are typically 0.5% with most of the power at frequencies below 30 kHz and mode numbers in agreement with MHD prediction for tearing modes. Electrostatic fluctuations are typically 10 to 20% with a spectrum that decreases with frequency. 5 refs., 2 figs

  16. 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

  17. Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform.

    Science.gov (United States)

    Opota, Onya; Brouillet, René; Greub, Gilbert; Jaton, Katia

    2017-01-01

    The advances in molecular biology of the last decades have dramatically improved the field of diagnostic bacteriology. In particular, PCR-based technologies have impacted the diagnosis of infections caused by obligate intracellular bacteria such as pathogens from the Chlamydiacae family. Here, we describe a real-time PCR-based method using the Taqman technology for the diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus infection. The method presented here can be applied to various clinical samples and can be adapted on opened molecular diagnostic platforms.

  18. Inhibition of PCR-based assay for Bordetella pertussis by using calcium alginate fiber and aluminum shaft components of a nasopharyngeal swab.

    Science.gov (United States)

    Wadowsky, R M; Laus, S; Libert, T; States, S J; Ehrlich, G D

    1994-04-01

    A PCR-based assay for Bordetella pertussis was inhibited by using a calcium alginate fiber-tipped swab with an aluminum shaft but not by using a Dacron fiber-tipped swab with a plastic shaft. The calcium alginate fiber component inhibited the assay following storage for less than 1 min in a suspension of 10(3) CFU of B. pertussis per ml, whereas the aluminum shaft component required storage for at least 48 h in order to cause inhibition. We recommend the Dacron swab over the calcium alginate swab for collecting specimens for testing in PCR-based assays.

  19. Real-time PCR-based method for rapid detection of Aspergillus niger and Aspergillus welwitschiae isolated from coffee.

    Science.gov (United States)

    von Hertwig, Aline Morgan; Sant'Ana, Anderson S; Sartori, Daniele; da Silva, Josué José; Nascimento, Maristela S; Iamanaka, Beatriz Thie; Pelegrinelli Fungaro, Maria Helena; Taniwaki, Marta Hiromi

    2018-05-01

    Some species from Aspergillus section Nigri are morphologically very similar and altogether have been called A. niger aggregate. Although the species included in this group are morphologically very similar, they differ in their ability to produce mycotoxins and other metabolites and their taxonomical status has evolved continuously. Among them, A. niger and A. welwitschiae are ochratoxin A and fumonisin B 2 producers and their detection and/or identification is of crucial importance for food safety. The aim of this study was the development of a real-time PCR-based method for simultaneous discrimination of A. niger and A. welwitschiae from other species of the A. niger aggregate isolated from coffee beans. One primer pair and a hybridization probe specific for detection of A. niger and A. welwitschiae strains were designed based on the BenA gene sequences, and used in a Real-time PCR assay for the rapid discrimination between both these species from all others of the A. niger aggregate. The Real-time PCR assay was shown to be 100% efficient in discriminating the 73 isolates of A. niger/A. welwitschiae from the other A. niger aggregate species analyzed as a negative control. This result testifies to the use of this technique as a good tool in the rapid detection of these important toxigenic species. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. A multiplex PCR-based method for the detection and early identification of wood rotting fungi in standing trees.

    Science.gov (United States)

    Guglielmo, F; Bergemann, S E; Gonthier, P; Nicolotti, G; Garbelotto, M

    2007-11-01

    The goal of this research was the development of a PCR-based assay to identify important decay fungi from wood of hardwood tree species in northern temperate regions. Eleven taxon-specific primers were designed for PCR amplification of either nuclear or mitochondrial ribosomal DNA regions of Armillaria spp., Ganoderma spp., Hericium spp., Hypoxylon thouarsianum var. thouarsianum, Inonotus/Phellinus-group, Laetiporus spp., Perenniporia fraxinea, Pleurotus spp., Schizophyllum spp., Stereum spp. and Trametes spp. Multiplex PCR reactions were developed and optimized to detect fungal DNA and identify each taxon with a sensitivity of at least 1 pg of target DNA in the template. This assay correctly identified the agents of decay in 82% of tested wood samples. The development and optimization of multiplex PCRs allowed for reliable identification of wood rotting fungi directly from wood. Early detection of wood decay fungi is crucial for assessment of tree stability in urban landscapes. Furthermore, this method may prove useful for prediction of the severity and the evolution of decay in standing trees.

  1. Neutralization Assay for Zika and Dengue Viruses by Use of Real-Time-PCR-Based Endpoint Assessment.

    Science.gov (United States)

    Wilson, Heather L; Tran, Thomas; Druce, Julian; Dupont-Rouzeyrol, Myrielle; Catton, Michael

    2017-10-01

    The global spread and infective complications of Zika virus (ZKV) and dengue virus (DENV) have made them flaviviruses of public health concern. Serological diagnosis can be challenging due to antibody cross-reactivity, particularly in secondary flavivirus infections or when there is a history of flavivirus vaccination. The virus neutralization assay is considered to be the most specific assay for measurement of anti-flavivirus antibodies. This study describes an assay where the neutralization endpoint is measured by real-time PCR, providing results within 72 h. It demonstrated 100% sensitivity (24/24 ZKV and 15/15 DENV) and 100% specificity (11/11 specimens) when testing well-characterized sera. In addition, the assay was able to determine the correct DENV serotype in 91.7% of cases. The high sensitivity and specificity of the real-time PCR neutralization assay makes it suitable to use as a confirmatory test for sera that are reactive in commercial IgM/IgG enzyme immunoassays. Results are objective and the PCR-based measurement of the neutralization endpoint lends itself to automation so that throughput may be increased in times of high demand. Copyright © 2017 American Society for Microbiology.

  2. Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid

    Directory of Open Access Journals (Sweden)

    Johnson Sandra

    2010-10-01

    Full Text Available Abstract Background Detection of bacterial nucleic acids in synovial fluid following total joint arthroplasty with suspected infection can be difficult; among other technical challenges, inhibitors in the specimens require extensive sample preparation and can diminish assay sensitivity even using polymerase chain reaction (PCR-based methods. To address this problem a simple protocol for prior use of multiple displacement amplification (MDA as an adjunct to PCR was established and tested on both purified S. aureus DNA as well as on clinical samples known to contain S. aureus nucleic acids. Findings A single round of MDA on purified nucleic acids resulted in a > 300 thousand-fold increase in template DNA on subsequent quantitative PCR (qPCR analysis. MDA use on clinical samples resulted in at least a 100-fold increase in sensitivity on subsequent qPCR and required no sample preparation other than a simple alkali/heat lysis step. Mixed samples of S. aureus DNA with a 103 - 104-fold excess of human genomic DNA still allowed for MDA amplification of the minor bacterial component to the threshold of detectability. Conclusion MDA is a promising technique that may serve to significantly enhance the sensitivity of molecular assays in cases of suspected joint infection while simultaneously reducing the specimen handling required.

  3. A PCR based method to detect Russula spp. in soil samples and Limodorum abortivum roots in Mediterranean environments

    Directory of Open Access Journals (Sweden)

    Eduardo Larriba

    2015-04-01

    Full Text Available Aim of study: Orchidaceaehas the largest number of species of any family in the plant kingdom. This family is subject to a high risk of extinction in natural environments, such as natural parks and protected areas. Recent studies have shown the prevalence of many species of orchids to be linked to fungal soil diversity, due to their myco-heterotrophic behaviour. Plant communities determine fungal soil diversity, and both generate optimal conditions for orchid development. Area of study: The work was carried out in n the two most important natural parks in Alicante (Font Roja and Sierra Mariola, in South-eastern of Spain. Material and Methods: We designed a molecular tool to monitor the presence of Russula spp. in soil and orchids roots, combined with phytosociological methods. Main results: Using a PCR-based method, we detected the presence in the soil and Limodorum abortivum orchid roots of the mycorrhizal fungi Russula spp. The species with highest coverage was Quercus rotundifolia in areas where the orchid was present. Research highlights: We present a useful tool based on PCR to detect the presence of Russula spp. in a natural environment. These results are consistent with those obtained in different studies that linked the presence of the mycorrhizal fungi Russula spp. in roots of the species Limodorum and the interaction between these fungal species and Quercus ilex trees in Mediterranean forest environments.

  4. A novel PCR-based marker for identifying Ns chromosomes in wheat-Psathyrostachys huashanica Keng derivative lines

    Directory of Open Access Journals (Sweden)

    J. Wang

    2013-10-01

    Full Text Available Psathyrostachys huashanica Keng is an endangered species that is endemic to China, which provides an important gene pool for wheat improvement. We developed a quick and reliable PCR-based diagnostic assay to accurately and efficiently detect P. huashanica DNA sequences from introgression lines, which was based on a species-specific marker derived from genomic DNA. The 900-bp PCR-amplified band used as a P. huashanica-specific RAPD marker was tested with 21 different plant species and was converted into a sequence-characterized amplified region (SCAR marker by cloning and sequencing the selected fragments (pHs11. This SCAR marker, which was designated as RHS23, could clearly distinguish the presence of P. huashanica DNA repetitive sequences in wheat-P. huashanica derivative lines. The specificity of the marker was validated using 21 different plant species and a complete set of wheat-P. huashanica disomic addition lines (1Ns–7Ns, 2n=44=22II. This specific sequence targeted the Ns genome of P. huashanica and it was present in all the seven P. huashanica chromosomes. Therefore, this SCAR marker is specific for P. huashanica chromosomes and may be used in the identification of alien repetitive sequences in large gene pools. This diagnostic PCR assay for screening the target genetic material may play a key role in marker-assisted selective breeding programs.

  5. Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism.

    Science.gov (United States)

    Huang, Suzhen; Xue, Tingli; Wang, Zhiquan; Ma, Yuanyuan; He, Xueting; Hong, Jiefang; Zou, Shaolan; Song, Hao; Zhang, Minhua

    2018-04-01

    Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.

  6. A novel PCR-based system for the detection of four species of human malaria parasites and Plasmodium knowlesi.

    Directory of Open Access Journals (Sweden)

    Kanako Komaki-Yasuda

    Full Text Available A microscopy-based diagnosis is the gold standard for the detection and identification of malaria parasites in a patient's blood. However, the detection of cases involving a low number of parasites and the differentiation of species sometimes requires a skilled microscopist. Although PCR-based diagnostic methods are already known to be very powerful tools, the time required to apply such methods is still much longer in comparison to traditional microscopic observation. Thus, improvements to PCR systems are sought to facilitate the more rapid and accurate detection of human malaria parasites Plasmodium falciparum, P. vivax, P. ovale, and P. malariae, as well as P. knowlesi, which is a simian malaria parasite that is currently widely distributed in Southeast Asia. A nested PCR that targets the small subunit ribosomal RNA genes of malaria parasites was performed using a "fast PCR enzyme". In the first PCR, universal primers for all parasite species were used. In the second PCR, inner-specific primers, which targeted sequences from P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, were used. The PCR reaction time was reduced with the use of the "fast PCR enzyme", with only 65 minutes required to perform the first and second PCRs. The specific primers only reacted with the sequences of their targeted parasite species and never cross-reacted with sequences from other species under the defined PCR conditions. The diagnoses of 36 clinical samples that were obtained using this new PCR system were highly consistent with the microscopic diagnoses.

  7. Effect of Mst1 on Endometriosis Apoptosis and Migration: Role of Drp1-Related Mitochondrial Fission and Parkin-Required Mitophagy.

    Science.gov (United States)

    Zhao, Qingdong; Ye, Mingxia; Yang, Wen; Wang, Min; Li, Mingxia; Gu, Chenglei; Zhao, Luyang; Zhang, Zhe; Han, Weidong; Fan, Wensheng; Meng, Yuanguang

    2018-01-01

    Mitochondrial homeostasis is implicated in the development and progression of endometriosis through poorly defined mechanisms. Mst1 is the major growth suppressor related to cancer migration, apoptosis and proliferation. However, whether Mst1 is involved in endometriosis apoptosis and migration via regulating the mitochondrial function remains to be elucidated. Expression of Mst1 in endometriosis was examined via western blots. Cellular apoptosis was detected via MTT and TUNEL assay. Gain of function assay about Mst1 was conducted via adenovirus over-expression. Mitochondrial functions were evaluated via mitochondrial membrane potential JC-1 staining, ROS flow cytometry analysis, mPTP opening assessment and immunofluorescence of HtrA2/Omi. The mitophagy activity were examined via western blots and immunofluorescence. First, we found that Mst1 was significantly downregulated in the ectopic endometrium of endometriosis compared to the normal endometrium. However, the recovery of Mst1 function was closely associated with the inability of endometrial stromal cells (ESCs) to migrate and survive. A functional study indicated that regaining Mst1 enhanced Drp1 post-transcriptional phosphorylation at Ser616 and repressed Parkin transcription activity via p53, leading to mitochondrial fission activation and mitophagy inhibition. Excessive Drp1-related fission forced the mitochondria to liberate HtrA2/Omi into the cytoplasm. Moreover, Mst1-induced defective mitophagy evoked cellular oxidative stress, energy metabolism and calcium overload. Through excessive mitochondrial fission and aberrant mitophagy, Mst1 launched caspase 9-related mitochondrial apoptosis and abrogated F-actin/lamellipodium-dependent cellular migration. Notably, we also defined NR4A/miR181c as the upstream signal for Mst1 dysfunction in endometriosis. Collectively, our results comprehensively described the important role of the NR4A-miR181c-Mst1 pathway in endometriosis, which handled mitochondrial

  8. Identification and mitigation of stray laser light in the Thomson scattering system on the Madison Symmetric Torus (MST)

    International Nuclear Information System (INIS)

    Jacobson, C. M.; Borchardt, M. T.; Den Hartog, D. J.; Falkowski, A. F.; Morton, L. A.; Thomas, M. A.

    2016-01-01

    The Thomson scattering diagnostic on the Madison Symmetric Torus (MST) records excessive levels of stray Nd:YAG laser light. Stray light saturates the 1064 nm spectral channel in all polychromators, which prevents absolute electron density measurements via Rayleigh scattering calibration. Furthermore, stray light contaminates adjacent spectral channels for r/a ≥ 0.75, which renders the diagnostic unable to make electron temperature measurements at these radii. In situ measurements of stray light levels during a vacuum vessel vent are used to identify stray light sources and strategies for reduction of stray light levels. Numerical modeling using Zemax OpticStudio supports these measurements. The model of the vacuum vessel and diagnostic includes synthetic collection optics to enable direct comparison of measured and simulated stray light levels. Modeling produces qualitatively similar stray light distributions to MST measurements, and quantifies the mitigation effects of stray light mitigation strategies prior to implementation.

  9. Identification and mitigation of stray laser light in the Thomson scattering system on the Madison Symmetric Torus (MST)

    Energy Technology Data Exchange (ETDEWEB)

    Jacobson, C. M., E-mail: cjacobson@wisc.edu; Borchardt, M. T.; Den Hartog, D. J.; Falkowski, A. F.; Morton, L. A.; Thomas, M. A. [Department of Physics, University of Wisconsin–Madison, 1150 University Avenue, Madison, Wisconsin 53706 (United States)

    2016-11-15

    The Thomson scattering diagnostic on the Madison Symmetric Torus (MST) records excessive levels of stray Nd:YAG laser light. Stray light saturates the 1064 nm spectral channel in all polychromators, which prevents absolute electron density measurements via Rayleigh scattering calibration. Furthermore, stray light contaminates adjacent spectral channels for r/a ≥ 0.75, which renders the diagnostic unable to make electron temperature measurements at these radii. In situ measurements of stray light levels during a vacuum vessel vent are used to identify stray light sources and strategies for reduction of stray light levels. Numerical modeling using Zemax OpticStudio supports these measurements. The model of the vacuum vessel and diagnostic includes synthetic collection optics to enable direct comparison of measured and simulated stray light levels. Modeling produces qualitatively similar stray light distributions to MST measurements, and quantifies the mitigation effects of stray light mitigation strategies prior to implementation.

  10. A novel PCR-based system for the detection of four species of human malaria parasites and Plasmodium knowlesi

    Science.gov (United States)

    Komaki-Yasuda, Kanako; Vincent, Jeanne Perpétue; Nakatsu, Masami; Kato, Yasuyuki; Ohmagari, Norio

    2018-01-01

    A microscopy-based diagnosis is the gold standard for the detection and identification of malaria parasites in a patient’s blood. However, the detection of cases involving a low number of parasites and the differentiation of species sometimes requires a skilled microscopist. Although PCR-based diagnostic methods are already known to be very powerful tools, the time required to apply such methods is still much longer in comparison to traditional microscopic observation. Thus, improvements to PCR systems are sought to facilitate the more rapid and accurate detection of human malaria parasites Plasmodium falciparum, P. vivax, P. ovale, and P. malariae, as well as P. knowlesi, which is a simian malaria parasite that is currently widely distributed in Southeast Asia. A nested PCR that targets the small subunit ribosomal RNA genes of malaria parasites was performed using a “fast PCR enzyme”. In the first PCR, universal primers for all parasite species were used. In the second PCR, inner-specific primers, which targeted sequences from P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, were used. The PCR reaction time was reduced with the use of the “fast PCR enzyme”, with only 65 minutes required to perform the first and second PCRs. The specific primers only reacted with the sequences of their targeted parasite species and never cross-reacted with sequences from other species under the defined PCR conditions. The diagnoses of 36 clinical samples that were obtained using this new PCR system were highly consistent with the microscopic diagnoses. PMID:29370297

  11. Application of PCR-based DNA sequencing technique for the detection of Leptospira in peripheral blood of septicemia patients

    Directory of Open Access Journals (Sweden)

    Ram, S.

    2012-01-01

    Full Text Available Aim: Isolation, dark field detection and microscopic agglutination test (MAT are considered ―gold standard‖ tests for diagnosis of Leptospirosis. Several PCR assays are reported but very few have been evaluated for detection of Leptospirosis. Therefore, this study was undertaken. This study aims to design and standardize polymerase chain reaction (PCR - based DNA sequencing technique for the detection of pathogenic Leptospira from peripheral blood of patients clinically diagnosed with septicemia. Methodology and Results: Two hundred and seven (207 blood samples from patients were diagnosed with septicemia which includes 100 bacterial (other than Leptospira culture positive and 107 bacterial culture negative samples were studied. Primers for Nested PCR targeting LipL32 gene of Leptospira interrogans were designed and the specificity of primers was tested against serum samples positive/negative by either MAT or dark field microscopy. PCR amplified products were further confirmed by DNA sequencing. The standardized nPCR was sensitive and specific to Leptospira interrogans. Twenty-one (21% out of 100 culture positive blood samples, three (2.8% out of 107 culture negative samples showed nPCR positivity and were confirmed as Leptospira interrogans by DNA sequencing (p<0.001. A sensitive nPCR specific to Leptospira interrogans was developed. Conclusion, significance and impact of study: The p value (<0.001 signifies that Leptospira is commonly associated with other bacteria circulating in blood indicating that a decreased immune status is created primarily by a bacterium with enhanced possibility of development of Leptospiral infection probably be of an endogenous origin.

  12. Comparison of a PCR-Based Method with Culture and Direct Examination for Diagnosis of Acanthamoeba keratitis

    Directory of Open Access Journals (Sweden)

    S Farnia

    2009-05-01

    Full Text Available "nBackground: The aim was to compare three different methods (direct examination, culture and PCR meth­ods for the diagnosis of Acanthamoeba keratitis (AK in corneal scrapes."nMethods: Twenty eight corneal scrapes and contact lenses were collected from keratitis patients and re­ferred to the De­partment of Medical Parasitology and Mycology, School of Public Health, Tehran Univer­sity of Medical Sci­ences. Corneal scrapes were divided in three parts for direct examination, culture on non-nutrient agar and PCR analysis. PCR analysis was also performed using a 18S rRNA gene primer pair (DF3 region. DF3 (Diagnostic frag­ment 3 is a region of the nuclear small subunit ribosomal RNA gene which is specific for detecting Acan­thamoeba strains."nResults:  Acanthamoeba was the causative agent of keratitis in 50% of the patients. Direct smear of all pre­pared corneal scrapes in AK patients was negative and culture was positive in only 14.3% of the isolates. PCR analysis was positive in 71.4% of AK patients. These three methods were negative in corneal scrapes of non-AK patients. The sensitivity and specificity of PCR technique for the detection of Acanthamoeba sp. were calculated as 71.4% and 100%, respectively."nConclusion: According to high sensitivity and specificity of PCR-based method, this study confirmed that PCR using 18S rRNA gene primers (DF3 region is more useful for detecting AK cases compare to culture and direct microscopy methods.

  13. PILOT-SCALE TESTING OF THE SUSPENSION OF MST, CST, AND SIMULATED SLUDGE SLURRIES IN A SLUDGE TANK

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M.; Qureshi, Z.; Restivo, M.; Steeper, T.; Williams, M.; Herman, D.

    2011-08-02

    The Small Column Ion Exchange (SCIX) process is being developed to remove cesium, strontium, and actinides from Savannah River Site (SRS) Liquid Waste using an existing waste tank (i.e., Tank 41H) to house the process. Following strontium, actinide, and cesium removal, the concentrated solids will be transported to a sludge tank (i.e., monosodium titanate (MST)/sludge solids to Tank 42H or Tank 51H and crystalline silicotitanate (CST) to Tank 40H) for eventual transfer to the Defense Waste Processing Facility (DWPF). Savannah River National Laboratory (SRNL) is conducting pilot-scale mixing tests to determine the pump requirements for mixing MST, CST, and simulated sludge. The purpose of this pilot scale testing is to determine the pump requirements for mixing MST and CST with sludge in a sludge tank and to determine whether segregation of particles occurs during settling. Tank 40H and Tank 51H have four Quad Volute pumps; Tank 42H has four standard pumps. The pilot-scale tank is a 1/10.85 linear scaled model of Tank 40H. The tank diameter, tank liquid level, pump nozzle diameter, pump elevation, and cooling coil diameter are all 1/10.85 of their dimensions in Tank 40H. The pump locations correspond to the current locations in Tank 40H (Risers B2, H, B6, and G). The pumps are pilot-scale Quad Volute pumps. Additional settling tests were conducted in a 30 foot tall, 4 inch inner diameter clear column to investigate segregation of MST, CST, and simulated sludge particles during settling.

  14. An Alternative to Optimize the Indonesian’s Airport Network Design: An Application of Minimum Spanning Tree (MST Technique

    Directory of Open Access Journals (Sweden)

    Luluk Lusiantoro

    2012-09-01

    Full Text Available Using minimum spanning tree technique (MST, this exploratory research was done to optimize the interrelation and hierarchical network design of Indonesian’s airports. This research also identifies the position of the Indonesian’s airports regionally based on the ASEAN Open Sky Policy 2015. The secondary data containing distance between airports (both in Indonesia and in ASEAN, flight frequency, and correlation of Gross Domestic Regional Product (GDRP for each region in Indonesia are used as inputs to form MST networks. The result analysis is done by comparing the MST networks with the existing network in Indonesia. This research found that the existing airport network in Indonesia does not depict the optimal network connecting all airports with the shortest distance and maximizing the correlation of regional economic potential in the country. This research then suggests the optimal networks and identifies the airports and regions as hubs and spokes formed by the networks. Lastly, this research indicates that the Indonesian airports have no strategic position in the ASEAN Open Sky network, but they have an opportunity to get strategic positions if 33 airports in 33 regions in Indonesia are included in the network.

  15. Morin impedes Yap nuclear translocation and fosters apoptosis through suppression of Wnt/β-catenin and NF-κB signaling in Mst1 overexpressed HepG2 cells

    Energy Technology Data Exchange (ETDEWEB)

    Perumal, NaveenKumar [Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu (India); Perumal, MadanKumar [Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu (India); Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 (United States); Kannan, Anbarasu [Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas (United States); Subramani, Kumar [Centre for Biotechnology, Anna University, Chennai 600025, Tamil Nadu (India); Halagowder, Devaraj [Department of Zoology, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu (India); Sivasithamparam, NiranjaliDevaraj, E-mail: profniranjali@gmail.com [Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu (India)

    2017-06-15

    Recent clinical and experimental evidences strongly acclaim Yes-associated protein (Yap), a key oncogenic driver in liver carcinogenesis, as a therapeutic target. Of the known multiple schemes to inhibit Yap activity, activation of Mammalian Sterile 20-like Kinase 1 (Mst1), an upstream regulator of Yap, appears to be a promising one. In this study, we hypothesize that morin, a bioflavonoid, mediates its anti-cancer effect through the activation of Mst1/hippo signaling in liver cancer cells. To test this hypothesis, both full length Mst1 (F-Mst1) and kinase active N-terminal Mst1 (N-Mst1)-overexpressed HepG2 cells were used. Exposure of F-Mst1 overexpressed HepG2 cells to morin activated Mst1 by caspase-3 cleavage and thereby inhibited Yap nuclear translocation and fostered apoptosis. Morin suppressed NF-κB p65 and Wnt/β-catenin signaling through Mst1 activation via cleavage and phosphorylation, leading to cell death. Annexin-V/PI staining further confirmed the induction of apoptosis in morin treated F-Mst1 overexpressed cells. The present study shows that morin targets cell survival molecules such as NF-κB p65 and β-catenin through activation of hippo signaling. Therefore, morin could be considered as a potential anti-cancer agent against liver cancer. - Highlights: • Morin induced cytotoxicity in cultured HepG2 cells. • Morin activated hippo pathway via Mst1 activation in transfected HepG2 cells. • Morin suppressed Wnt/β-catenin signaling and induced G0/G1 cell cycle arrest. • Morin inhibited NF-κB signaling through Mst1 activation in transfected HepG2 cells. • Morin potentiates apoptosis through Mst1-JNK-caspase mediated mechanism in HepG2 cells.

  16. Morin impedes Yap nuclear translocation and fosters apoptosis through suppression of Wnt/β-catenin and NF-κB signaling in Mst1 overexpressed HepG2 cells

    International Nuclear Information System (INIS)

    Perumal, NaveenKumar; Perumal, MadanKumar; Kannan, Anbarasu; Subramani, Kumar; Halagowder, Devaraj; Sivasithamparam, NiranjaliDevaraj

    2017-01-01

    Recent clinical and experimental evidences strongly acclaim Yes-associated protein (Yap), a key oncogenic driver in liver carcinogenesis, as a therapeutic target. Of the known multiple schemes to inhibit Yap activity, activation of Mammalian Sterile 20-like Kinase 1 (Mst1), an upstream regulator of Yap, appears to be a promising one. In this study, we hypothesize that morin, a bioflavonoid, mediates its anti-cancer effect through the activation of Mst1/hippo signaling in liver cancer cells. To test this hypothesis, both full length Mst1 (F-Mst1) and kinase active N-terminal Mst1 (N-Mst1)-overexpressed HepG2 cells were used. Exposure of F-Mst1 overexpressed HepG2 cells to morin activated Mst1 by caspase-3 cleavage and thereby inhibited Yap nuclear translocation and fostered apoptosis. Morin suppressed NF-κB p65 and Wnt/β-catenin signaling through Mst1 activation via cleavage and phosphorylation, leading to cell death. Annexin-V/PI staining further confirmed the induction of apoptosis in morin treated F-Mst1 overexpressed cells. The present study shows that morin targets cell survival molecules such as NF-κB p65 and β-catenin through activation of hippo signaling. Therefore, morin could be considered as a potential anti-cancer agent against liver cancer. - Highlights: • Morin induced cytotoxicity in cultured HepG2 cells. • Morin activated hippo pathway via Mst1 activation in transfected HepG2 cells. • Morin suppressed Wnt/β-catenin signaling and induced G0/G1 cell cycle arrest. • Morin inhibited NF-κB signaling through Mst1 activation in transfected HepG2 cells. • Morin potentiates apoptosis through Mst1-JNK-caspase mediated mechanism in HepG2 cells.

  17. SUT sucrose and MST monosaccharide transporter inventory of the Selaginella genome

    Directory of Open Access Journals (Sweden)

    Sylvie eLalonde

    2012-02-01

    Full Text Available While most metazoa mainly use hexose transporters to acquire hexoses from their diet and as a transport form for distributing carbon and energy within their bodies, insects use trehalose and plants use sucrose as their major form for translocation. Plant genomes contain at least three families of mono- and disaccharide transporters: monosaccharide/polyol transporters that are evolutionary closely related to the yeast and human glucose transporters, sucrose transporters of the SUT family, which similar to the hexose transporters belong to the major facilitator superfamily (MFS, but share only minimal amino acid sequence homology to the hexose transporters, and the family of SWEET sugar transporters conserved between animals and plants. Recently, the genome sequence of the spikemoss Selaginella has been determined. In order to study the evolution of sugar transport in plants, we carried out a careful annotation of the complement of sugar transporters in Selaginella. We review what is known about sugar transport in spikemoss and provide phylogenetic analyses of the complement of MST and SUT homologs in Selaginella.

  18. Control of the wax moth Galleria mellonella L. (Lepidoptera: Pyralidae by the male sterile technique (MST

    Directory of Open Access Journals (Sweden)

    Jafari Reza

    2010-01-01

    Full Text Available In this study we examined the control of wax moth using the male sterile technique (MST with gamma-rays. To determine the safe and effective dosage of gamma-rays capable of sterilizing male pupae of the wax moth, male pupae were exposed to increasing single doses of gamma-rays (250, 300, 350 and 400 Gy. The release ratio of sterile to normal males was also studied in a similar experiment. Treatments included sterile males, normal males and virgin females at the following ratios: 1:1:1, 2:1:1, 3:1:1, 4:1:1 and 5:1:1. Possible parthenogenetic reproduction of this pest was also examined. The results showed that 350 Gy was the most effective dose capable of sterilizing the male pupae of the wax moth. The best release ratio was established at four sterile males, one normal male for each normal female (4:1:1. Also females were incapable of producing offspring without males.

  19. New methods of minimally invasive brain modulation as therapies in psychiatry: TMS, MST, VNS and DBS.

    Science.gov (United States)

    George, Mark S

    2002-08-01

    Over the past 20 years, new methods have been developed that have allowed scientists to visualize the human brain in action. Initially positron emission tomography (PET) and now functional magnetic resonance imaging (fMRI) are causing a paradigm shift in psychiatry and the neurosciences. Psychiatry is abandoning the pharmacological model of 'brain as soup', used for much of the past 20 years. Instead, there is new realization that both normal and abnormal behavior arise from chemical processes that occur within parallel distributed networks in specific brain regions. Many of these pathological circuits are becoming well characterized, in disorders ranging from Parkinson's disease, to obsessive-compulsive disorder, to depression. Most recently, there has been an explosion of new techniques that allow for direct stimulation of these brain circuits, without the need for open craniotomy and neurosurgical ablation. The techniques include transcranial magnetic stimulation (TMS), magnetic seizure therapy (MST), vagus nerve stimulation (VNS), and deep brain stimulation (DBS). This review will describe these new tools, and overview their current and future potential for research and clinical neuropsychiatric use. The psychiatry of the future will be better grounded in a firm understanding of neuroanatomy and neurophysiology (as well as pharmacology). These brain stimulation tools, or their next iterations, will play an ever-larger role in clinical neuropsychiatric practice.

  20. Characterization of beam-driven instabilities and current redistribution in MST plasmas

    Science.gov (United States)

    Parke, E.

    2015-11-01

    A unique, high-rep-rate (>10 kHz) Thomson scattering diagnostic and a high-bandwidth FIR interferometer-polarimeter on MST have enabled characterization of beam-driven instabilities and magnetic equilibrium changes observed during high power (1 MW) neutral beam injection (NBI). While NBI leads to negligible net current drive, an increase in on-axis current density observed through Faraday rotation is offset by a reduction in mid-radius current. Identification of the phase flip in temperature fluctuations associated with tearing modes provides a sensitive measure of rational surface locations. This technique strongly constrains the safety factor for equilibrium reconstruction and provides a powerful new tool for measuring the equilibrium magnetic field. For example, the n = 6 temperature structure is observed to shift inward 1.1 +/- 0.6 cm, with an estimated reduction of q0 by 5%. This is consistent with a mid-radius reduction in current, and together the Faraday rotation and Thomson scattering measurements corroborate an inductive redistribution of current that compares well with TRANSP/MSTFit predictions. Interpreting tearing mode temperature structures in the RFP remains challenging; the effects of multiple, closely-spaced tearing modes on the mode phase measurement require further verification. In addition to equilibrium changes, previous work has shown that the large fast ion population drives instabilities at higher frequencies near the Alfvén continuum. Recent observations reveal a new instability at much lower frequency (~7 kHz) with strongly chirping behavior. It participates in extensive avalanches of the higher frequency energetic particle and Alfvénic modes to drive enhanced fast ion transport. Internal structures measured from Te and ne fluctuations, their dependence on the safety factor, as well as frequency scaling motivate speculation about mode identity. Work supported by U.S. DOE.

  1. Momentum transport during reconnection events in the MST reversed field pinch

    Science.gov (United States)

    Kuritsyn, Alexey

    2008-11-01

    During reconnection events in the MST reversed field pinch momentum parallel to the magnetic field is observed to be suddenly transported from the core to the edge. This occurs simultaneous with a surge in multiple resistive tearing instabilities. From measurements of the plasma flow and the forces arising from tearing instability (Maxwell and Reynolds stresses) we have established that tearing instabilities induce strong momentum transport. Comparison with nonlinear MHD computation of tearing fluctuations supports this conclusion, although it also indicates that effects beyond single-fluid MHD are likely to be important. The radial profile of the parallel velocity is reconstructed from a combination of diagnostics: Rutherford scattering of injected neutral atoms (for majority ions), charge exchange recombination spectroscopy (for minority ions), and Mach probes (for edge majority ion flow). Maxwell stress has been measured previously in the core by laser Faraday rotation, and both stresses are measured in the edge with probes. A surprising observation is that both the Maxwell and Reynolds stresses are each ten times larger than needed to account for the observed momentum transport (i.e., larger than the inertial and viscous terms in the momentum balance equation). However, they are oppositely directed such that their difference is approximately equal to the rate of change of plasma momentum. The large magnitude of the individual stresses is not predicted by MHD theory; the Maxwell stress also produces a Hall dynamo effect, implying that a two-fluid theory might be necessary for a complete description of momentum transport. To test further the relation between momentum transport and tearing fluctuations, momentum transport was measured perturbatively, by altering plasma rotation with inserted biased electrodes. Biasing is applied in plasmas with large tearing activity and improved confinement plasmas in which tearing activity is reduced by inductive current profile

  2. Spectroscopic measurement of the MHD dynamo in the MST reversed field pinch

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, James Tharp [Univ. of Wisconsin, Madison, WI (United States)

    1998-09-01

    The author has directly observed the coupling of ion velocity fluctuations and magnetic field fluctuations to produce an MHD dynamo electric field in the interior of the MST reversed field pinch. Chord averaged ion velocity fluctuations were measured with a fast spectroscopic diagnostic which collects line radiation from intrinsic carbon impurities simultaneously along two lines of sight. The chords employed for the measurements resolved long wavelength velocity fluctuations of several km/s at 8-20 kHz as tiny, fast Doppler shifts in the emitted line profile. During discrete dynamo events the velocity fluctuations, like the magnetic fluctuations, increase dramatically. The toroidal and poloidal chords with impact parameters of 0.3 a and 0.6 a respectively, resolved fluctuation wavenumbers with resonance surfaces near or along the lines of sight indicating a radial velocity fluctuation width for each mode which spans only a fraction of the plasma radius. The phase between the measured toroidal velocity fluctuations and the magnetic fluctuations matches the predictions of resistive MHD while the poloidal velocity fluctuations exhibit a phase consistent with the superposition of MHD effects and the advection of a mean flow gradient past the poloidal line of sight. Radial velocity fluctuations resolved by a chord through the center of the plasma were small compared to the poloidal and toroidal fluctuations and exhibited low coherence with the magnetic fluctuations. The ensembled nonlinear product of the ion velocity fluctuations and fluctuations in the magnetic field indicates a substantial dynamo electric field which peaks during the periods of spontaneous flux generation.

  3. Spectroscopic measurement of the MHD dynamo in the MST reversed field pinch

    International Nuclear Information System (INIS)

    Chapman, J.T.

    1998-09-01

    The author has directly observed the coupling of ion velocity fluctuations and magnetic field fluctuations to produce an MHD dynamo electric field in the interior of the MST reversed field pinch. Chord averaged ion velocity fluctuations were measured with a fast spectroscopic diagnostic which collects line radiation from intrinsic carbon impurities simultaneously along two lines of sight. The chords employed for the measurements resolved long wavelength velocity fluctuations of several km/s at 8--20 kHz as tiny, fast Doppler shifts in the emitted line profile. During discrete dynamo events the velocity fluctuations, like the magnetic fluctuations, increase dramatically. The toroidal and poloidal chords with impact parameters of 0.3 a and 0.6 a respectively, resolved fluctuation wavenumbers with resonance surfaces near or along the lines of sight indicating a radial velocity fluctuation width for each mode which spans only a fraction of the plasma radius. The phase between the measured toroidal velocity fluctuations and the magnetic fluctuations matches the predictions of resistive MHD while the poloidal velocity fluctuations exhibit a phase consistent with the superposition of MHD effects and the advection of a mean flow gradient past the poloidal line of sight. Radial velocity fluctuations resolved by a chord through the center of the plasma were small compared to the poloidal and toroidal fluctuations and exhibited low coherence with the magnetic fluctuations. The ensembled nonlinear product of the ion velocity fluctuations and fluctuations in the magnetic field indicates a substantial dynamo electric field which peaks during the periods of spontaneous flux generation

  4. Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.

    Science.gov (United States)

    Teixeira, Andreia Sofia; Monteiro, Pedro T; Carriço, João A; Ramirez, Mário; Francisco, Alexandre P

    2015-01-01

    Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by introducing a new edge betweenness metric for undirected and weighted graphs. This spanning edge betweenness metric is defined as the fraction of equivalent MSTs where a given edge is present. The metric provides a per edge statistic that is similar to that of the bootstrap approach frequently used in phylogenetics to support the grouping of taxa. We provide methods for the exact computation of this metric based on the well known Kirchhoff's matrix tree theorem. Moreover, we implement and make available a module for the PHYLOViZ software and evaluate the proposed metric concerning both effectiveness and computational performance. Analysis of trees generated using multilocus sequence typing data (MLST) and the goeBURST algorithm revealed that the space of possible MSTs in real data sets is extremely large. Selection of the edge to be represented using bootstrap could lead to unreliable results since alternative edges are present in the same fraction of equivalent MSTs. The choice of the MST to be presented, results from criteria implemented in the algorithm that must be based in biologically plausible models.

  5. A PCR-based genotyping method to distinguish between wild-type and ornamental varieties of Imperata cylindrica.

    Science.gov (United States)

    Cseke, Leland J; Talley, Sharon M

    2012-02-20

    viable wind-dispersed seeds that spread cogongrass over wide distances(5-7). JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass(8-10), and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential(3,7,11). The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert.

  6. Reducing and measuring fluctuations in the MST RFP: Enhancement of energy confinement and measurement of the MHD dynamo

    International Nuclear Information System (INIS)

    Den Hartog, D.J.; Almagri, A.F.

    1996-09-01

    A three- to five-fold enhancement of the energy confinement time in a reversed-field pinch (RFP) has been achieved in the Madison Symmetric Torus (MST) by reducing the amplitude of tearing mode fluctuations responsible for anomalous transport in the core of the RFP. By applying a transient poloidal inductive electric field to flatten the current density profile, the fluctuation amplitude b/B decreases from 1.5% to 0.8%, the electron temperature T e0 increases from 250 eV to 370 eV, the ohmic input power decreases from 4.5 MW to approximately 1.5 MW, the poloidal beta β 0 increases from 6% to 9%, and the energy confinement time τ E increases from 1 ms to ∼5 ms in I φ = 340 kA plasmas with density n = 1 x 10 19 m -3 . Current profile control methods are being developed for the RFP in a program to eliminate transport associated with these current-gradient-driven fluctuations. In addition to controlling the amplitude of the tearing modes, we are vigorously pursuing an understanding of the physics of these fluctuations. In particular, plasma flow, both equilibrium and fluctuating, plays a critical role in a diversity of physical phenomena in MST. The key results: 1) Edge probe measurements show that the MHD dynamo is active in low collisionality plasmas, while at high collisionality a new mechanism, the 'electron diamagnetic dynamo,' is observed. 2) Core spectroscopic measurements show that the toroidal velocity fluctuations of the plasma are coherent with the large-scale magnetic tearing modes; the scalar product of these two fluctuating quantities is similar to that expected for the MHD dynamo electromotive force. 3) Toroidal plasma flow in MST exhibits large radial shear and can be actively controlled, including unlocking locked discharges, by modifying E r with a robust biased probe. 24 refs

  7. A biblioteca na página eletrônica do MST: heterogeneidade e memória The library in the electronic site of MST: heterogeneity and memory

    Directory of Open Access Journals (Sweden)

    Lucília Maria Sousa Romão

    2007-12-01

    Full Text Available Esse trabalho busca, à luz da teoria do discurso, investigar como a heterogeneidade é manifesta em uma biblioteca virtual, a saber, a Biblioteca inscrita dentro do site do Movimento dos Trabalhadores Rurais Sem Terra (MST. Interessa-nos perceber como há uma memória sustentadora dos atos de linguagem e como há uma inscrição histórica dos sentidos no verbal e no imagético, que possibilitam a construção de vários gestos de leitura. Por fim, julgamos ser produtivo analisar a biblioteca como o espaço polifônico em que várias vozes estão inscritas, marcando o movimento dos sujeitos, dos sentidos, enfim, dos discursos.This work searches, at the light of the theory of speech, to investigate as the heterogeneity is obvious in a virtual library, in this case, the library in the site of the Rural Workers Movement (MST. It is interesting to know that there is a supporting memory of the language actions and a historical registration of verbal and no-verbal senses, that allow the construction of several reading gestures. Finally, we considered important to analyze the library as a polyphonic space where several voices are enrolled, marking the movement of the subjects, of the senses, that is, of the speech.

  8. Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter

    DEFF Research Database (Denmark)

    Jørgensen, Thomas R; vanKuyk, Patricia A; Poulsen, Bjarne R

    2007-01-01

    This is a study of high-affinity glucose uptake in Aspergillus niger and the effect of disruption of a high-affinity monosaccharide-transporter gene, mstA. The substrate saturation constant (K(s)) of a reference strain was about 15 microM in glucose-limited chemostat culture. Disruption of mst......-affinity uptake system of A. niger. The mstA disruptant and a reference strain were cultivated in glucose-limited chemostat cultures at low, intermediate and high dilution rate (D=0.07 h(-1), 0.14 h(-1) and 0.20 h(-1)). Mycelium harvested from steady-state cultures was subjected to glucose uptake assays...

  9. PCR-based isolation and identification of full-length low-molecular-weight glutenin subunit genes in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Zhang, Xiaofei; Liu, Dongcheng; Jiang, Wei; Guo, Xiaoli; Yang, Wenlong; Sun, Jiazhu; Ling, Hongqing; Zhang, Aimin

    2011-12-01

    Low-molecular-weight glutenin subunits (LMW-GSs) are encoded by a multi-gene family and are essential for determining the quality of wheat flour products, such as bread and noodles. However, the exact role or contribution of individual LMW-GS genes to wheat quality remains unclear. This is, at least in part, due to the difficulty in characterizing complete sequences of all LMW-GS gene family members in bread wheat. To identify full-length LMW-GS genes, a polymerase chain reaction (PCR)-based method was established, consisting of newly designed conserved primers and the previously developed LMW-GS gene molecular marker system. Using the PCR-based method, 17 LMW-GS genes were identified and characterized in Xiaoyan 54, of which 12 contained full-length sequences. Sequence alignments showed that 13 LMW-GS genes were identical to those found in Xiaoyan 54 using the genomic DNA library screening, and the other four full-length LMW-GS genes were first isolated from Xiaoyan 54. In Chinese Spring, 16 unique LMW-GS genes were isolated, and 13 of them contained full-length coding sequences. Additionally, 16 and 17 LMW-GS genes in Dongnong 101 and Lvhan 328 (chosen from the micro-core collections of Chinese germplasm), respectively, were also identified. Sequence alignments revealed that at least 15 LMW-GS genes were common in the four wheat varieties, and allelic variants of each gene shared high sequence identities (>95%) but exhibited length polymorphism in repetitive regions. This study provides a PCR-based method for efficiently identifying LMW-GS genes in bread wheat, which will improve the characterization of complex members of the LMW-GS gene family and facilitate the understanding of their contributions to wheat quality.

  10. Inhibition of PCR-based assay for Bordetella pertussis by using calcium alginate fiber and aluminum shaft components of a nasopharyngeal swab.

    OpenAIRE

    Wadowsky, R M; Laus, S; Libert, T; States, S J; Ehrlich, G D

    1994-01-01

    A PCR-based assay for Bordetella pertussis was inhibited by using a calcium alginate fiber-tipped swab with an aluminum shaft but not by using a Dacron fiber-tipped swab with a plastic shaft. The calcium alginate fiber component inhibited the assay following storage for less than 1 min in a suspension of 10(3) CFU of B. pertussis per ml, whereas the aluminum shaft component required storage for at least 48 h in order to cause inhibition. We recommend the Dacron swab over the calcium alginate ...

  11. Analysis of performance of a PCR-based assay to detect DNA of Aspergillus fumigatus in whole blood and serum: a comparative study with clinical samples.

    Science.gov (United States)

    Bernal-Martínez, Leticia; Gago, Sara; Buitrago, María J; Gomez-Lopez, Alicia; Rodríguez-Tudela, Juan L; Cuenca-Estrella, Manuel

    2011-10-01

    The performance of a real-time PCR-based assay was retrospectively analyzed (according to European Organization for Research and Treatment of Cancer/Mycosis Study Group criteria) in the samples of patients with invasive aspergillosis. A total of 711 serial samples (356 whole-blood and 355 serum samples) from 38 adult patients were analyzed. The Aspergillus fumigatus PCR assay results were positive for 89 of 356 (25%) whole-blood samples and 90 of 355 (25.35%) serum samples. Positive PCR results were seen in 29 of 31 (93.5%) patients for which serum was analyzed and in 31 of 33 (93.9%) cases with whole-blood specimens. Both blood and serum samples were available in 26 cases, and significant differences were not observed in this subgroup of cases. The average number of threshold cycles (C(T)) for positive blood samples was 37.6, and the average C(T) for serum was 37.4. The DNA concentration ranged between 2 and 50 fg per μl of sample, with average DNA concentrations of 10.2 and 11.7 fg in positive blood and serum samples, respectively (P > 0.01). The performance of this PCR-based quantitative assay was similar for both serum and blood samples. We recommend serum samples as the most convenient hematological sample to use for Aspergillus DNA quantification when serial determinations are done.

  12. A NEW MULTI-SPECTRAL THRESHOLD NORMALIZED DIFFERENCE WATER INDEX (MST-NDWI WATER EXTRACTION METHOD – A CASE STUDY IN YANHE WATERSHED

    Directory of Open Access Journals (Sweden)

    Y. Zhou

    2018-05-01

    Full Text Available Accurate remote sensing water extraction is one of the primary tasks of watershed ecological environment study. Since the Yanhe water system has typical characteristics of a small water volume and narrow river channel, which leads to the difficulty for conventional water extraction methods such as Normalized Difference Water Index (NDWI. A new Multi-Spectral Threshold segmentation of the NDWI (MST-NDWI water extraction method is proposed to achieve the accurate water extraction in Yanhe watershed. In the MST-NDWI method, the spectral characteristics of water bodies and typical backgrounds on the Landsat/TM images have been evaluated in Yanhe watershed. The multi-spectral thresholds (TM1, TM4, TM5 based on maximum-likelihood have been utilized before NDWI water extraction to realize segmentation for a division of built-up lands and small linear rivers. With the proposed method, a water map is extracted from the Landsat/TM images in 2010 in China. An accuracy assessment is conducted to compare the proposed method with the conventional water indexes such as NDWI, Modified NDWI (MNDWI, Enhanced Water Index (EWI, and Automated Water Extraction Index (AWEI. The result shows that the MST-NDWI method generates better water extraction accuracy in Yanhe watershed and can effectively diminish the confusing background objects compared to the conventional water indexes. The MST-NDWI method integrates NDWI and Multi-Spectral Threshold segmentation algorithms, with richer valuable information and remarkable results in accurate water extraction in Yanhe watershed.

  13. MST e Escola Nacional Florestan Fernandes: formação, comunicação e socialização política

    Directory of Open Access Journals (Sweden)

    Pablo Nabarrete Bastos

    Full Text Available Resumo Este artigo apresenta resultados de pesquisa sobre a formação política do Movimento dos Trabalhadores Rurais Sem Terra (MST a partir da comunicação e socialização com o trabalhador urbano. Utiliza-se o método dialético e são aplicadas técnicas qualitativas, entrevistas semiestruturadas com lideranças do MST, e pesquisa antropológica na Escola Nacional Florestan Fernandes (ENFF. A ENFF, fundada pelo MST no município de Guararema, Estado de São Paulo, em 2005, é um dos principais espaços de formação política dos movimentos sociais da América Latina. Constitui também espaço estratégico para a formação, comunicação e socialização política entre a classe trabalhadora do campo e da cidade. A ENFF possui potencial para ser espaço de construção da hegemonia popular por meio da sociabilidade entre movimentos sociais do campo e da cidade, por meio da produção simbólica comum e da educação universalizante, contudo, ainda é um espaço em que prevalecem a hegemonia política e a cultura do MST.

  14. Quando o Movimento dos Trabalhadores Rurais Sem Terra - MST - ocupa a escola: A educação da infância em uma escola em movimento

    Directory of Open Access Journals (Sweden)

    Arenhart, Deise

    2007-12-01

    Full Text Available This text has as an objective to reflect on an educational experience that has grown within the Pedagogy of Brazil’s Landless Rural Workers Movement- MST. The goal is to build an understanding of the social movement as an educational agent and, at the same time, to highlight the experience of a school that is based on the Pedagogy of the MST. Research was conducted in a settlement of the MST, through observations and interviews with adults and children of the settlement and associated sections in the organization of the Movement. The analysis is grounded on critical studies in the fields of Education and Sociology, in particular the Sociology of Childhood. The study indicates that to be in motion is a human formative experience born out of the Pedagogy of a social movement which attempts to become a historical project. Solidarity, class conscience, child participation, cultivating of social memory, collectivism, valuing of rural culture and a recognition of human beings as historical agents are some of the practices observed in the context under study that reflect the presence of MST as educational agent. This article is written in Portugese

  15. Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

    Science.gov (United States)

    Saingam, Prakit; Li, Bo; Yan, Tao

    2018-06-01

    DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Refletindo sobre os vínculos com a carreira dos militantes do MST: Entrincheiramento em análise.

    Directory of Open Access Journals (Sweden)

    Denilson Aparecido Leite Freire

    2013-06-01

    Full Text Available Este estudo analisou o entrincheiramento na carreira dos trabalhadores queatuam no Movimento Sem Terra (MST, através de um levantamento quantitativo com99 participantes do movimento. O entrincheiramento é um construto que engloba apercepção de falta de alternativas na carreira, custos emocionais e investimento nacarreira. Foram utilizadas escalas validadas, com um KMO de 0.741. Os resultadosmostraram níveis de entrincheiramento maiores entre: assalariados, com relação aosvoluntários; mulheres, com relação aos homens; e público das regiões Sul e Sudestedevido à questões históricas ligadas à Terra.

  17. A qPCR-Based Tool to Diagnose the Presence of Harmful Cyanobacteria and Cyanotoxins in Drinking Water Sources

    Directory of Open Access Journals (Sweden)

    Yi-Ting Chiu

    2017-05-01

    Full Text Available Harmful cyanobacteria have been an important concern for drinking water quality for quite some time, as they may produce cyanotoxins and odorants. Microcystis and Cylindrospermopsis are two common harmful cyanobacterial genera detected in freshwater lakes and reservoirs, with microcystins (MCs and cylindrospermopsin (CYN as their important metabolites, respectively. In this study, two sets of duplex qPCR systems were developed, one for quantifying potentially-toxigenic Microcystis and Microcystis, and the other one for cylindrospermopsin-producing cyanobacteria and Cylindrospermopsis. The duplex qPCR systems were developed and validated in the laboratory by using 338 samples collected from 29 reservoirs in Taiwan and her offshore islands. Results show that cell numbers of Microcystis and Cylindorspermopsis enumerated with microscopy, and MCs and CYN concentrations measured with the enzyme-linked immuno-sorbent assay method, correlated well with their corresponding gene copies determined with the qPCR systems (range of coefficients of determination R2 = 0.392−0.740. The developed qPCR approach may serve as a useful tool for the water industry to diagnose the presence of harmful cyanobacteria and the potential presence of cyanotoxins in source waters.

  18. A qPCR-Based Tool to Diagnose the Presence of Harmful Cyanobacteria and Cyanotoxins in Drinking Water Sources.

    Science.gov (United States)

    Chiu, Yi-Ting; Chen, Yi-Hsuan; Wang, Ting-Shaun; Yen, Hung-Kai; Lin, Tsair-Fuh

    2017-05-20

    Harmful cyanobacteria have been an important concern for drinking water quality for quite some time, as they may produce cyanotoxins and odorants. Microcystis and Cylindrospermopsis are two common harmful cyanobacterial genera detected in freshwater lakes and reservoirs, with microcystins (MCs) and cylindrospermopsin (CYN) as their important metabolites, respectively. In this study, two sets of duplex qPCR systems were developed, one for quantifying potentially-toxigenic Microcystis and Microcystis , and the other one for cylindrospermopsin-producing cyanobacteria and Cylindrospermopsis . The duplex qPCR systems were developed and validated in the laboratory by using 338 samples collected from 29 reservoirs in Taiwan and her offshore islands. Results show that cell numbers of Microcystis and Cylindorspermopsis enumerated with microscopy, and MCs and CYN concentrations measured with the enzyme-linked immuno-sorbent assay method, correlated well with their corresponding gene copies determined with the qPCR systems (range of coefficients of determination R² = 0.392-0.740). The developed qPCR approach may serve as a useful tool for the water industry to diagnose the presence of harmful cyanobacteria and the potential presence of cyanotoxins in source waters.

  19. A new PCR-based method shows that blue crabs (Callinectes sapidus (Rathbun)) consume winter flounder (Pseudopleuronectes americanus (Walbaum)).

    Science.gov (United States)

    Collier, Jackie L; Fitzgerald, Sean P; Hice, Lyndie A; Frisk, Michael G; McElroy, Anne E

    2014-01-01

    Winter flounder (Pseudopleuronectes americanus) once supported robust commercial and recreational fisheries in the New York (USA) region, but since the 1990s populations have been in decline. Available data show that settlement of young-of-the-year winter flounder has not declined as sharply as adult abundance, suggesting that juveniles are experiencing higher mortality following settlement. The recent increase of blue crab (Callinectes sapidus) abundance in the New York region raises the possibility that new sources of predation may be contributing to juvenile winter flounder mortality. To investigate this possibility we developed and validated a method to specifically detect winter flounder mitochondrial control region DNA sequences in the gut contents of blue crabs. A survey of 55 crabs collected from Shinnecock Bay (along the south shore of Long Island, New York) in July, August, and September of 2011 showed that 12 of 42 blue crabs (28.6%) from which PCR-amplifiable DNA was recovered had consumed winter flounder in the wild, empirically supporting the trophic link between these species that has been widely speculated to exist. This technique overcomes difficulties with visual identification of the often unrecognizable gut contents of decapod crustaceans, and modifications of this approach offer valuable tools to more broadly address their feeding habits on a wide variety of species.

  20. Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene.

    Science.gov (United States)

    Abdeldaim, Guma; Svensson, Erik; Blomberg, Jonas; Herrmann, Björn

    2016-11-01

    A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay. © 2016 APMIS. Published by John Wiley & Sons Ltd.

  1. PCR based diagnostic assay targeting the beta tubulin gene for the detection of Trichomonas vaginalis infection in vaginal swab samples of symptomatic and asymptomatic women in India

    Directory of Open Access Journals (Sweden)

    Surya Prakash Dwivedi

    2012-10-01

    Full Text Available Objective: To develop an in-house PCR based diagnostic assay for identification of strains isolated from symptomatic and asymptomatic subjects of India, targeting the 毬 -tubulin gene using specific primers. Methods: In the present study a primer set is designed to target a well-conserved region in the beta-tubulin gene of Trichomonas vaginalis (T. vaginalis. All strains of T. vaginalis were tested and successfully detected by PCR yielding a single predicted product of 198 bp in gel electrophoresis, while there was negative response with DNA from Giardia lamblia, Toxoplasma gondii, Leishmania donovani and Entamoeba histolytica. The sensitivity and specificity for a single T. vaginalis cell per PCR was achieved. Axenic Culture, performed with long term axenized T. vaginalis culture system, was routinely examined to identify T. vaginalis. Results: The PCR based investigations with 498 vaginal swab samples from women attending OPD clinics of Halberg Hospital Moradabad and Queen Mary ’s Hospital, Lucknow, India and 17 long term axenic cultures maintained at PGIMER, Chandigarh, India using primer set BTUB 1 & BTUB 2 showed sensitivity and specificity response of 98% and 100%, respectively, while wet preparation in clinically isolated samples responded up to 62.5%. The PCR product sequencing result of symptomatic strains (SS1 of T. vaginalis (744 bp long was submitted to NCBI (Accession No: JF513200. It shows maximum identity 98 % with XM_001284521 Trichomonas vaginalis G-3 beta-tubulin (btub putative partial mRNA. Conclusions: The data gathered in the present study entail that the diagnosis of T. vaginalis infection by PCR may be established as a sensitive and specific protocol, to be incorporated into a joint strategy for the screening of multiple STDs by employing molecular amplification technique. The merits and precautions of the protocol have been discussed.

  2. Performance of Droplet Digital PCR in Non-Invasive Fetal RHD Genotyping - Comparison with a Routine Real-Time PCR Based Approach.

    Directory of Open Access Journals (Sweden)

    Iveta Svobodová

    Full Text Available Detection and characterization of circulating cell-free fetal DNA (cffDNA from maternal circulation requires an extremely sensitive and precise method due to very low cffDNA concentration. In our study, droplet digital PCR (ddPCR was implemented for fetal RHD genotyping from maternal plasma to compare this new quantification alternative with real-time PCR (qPCR as a golden standard for quantitative analysis of cffDNA. In the first stage of study, a DNA quantification standard was used. Clinical samples, including 10 non-pregnant and 35 pregnant women, were analyzed as a next step. Both methods' performance parameters-standard curve linearity, detection limit and measurement precision-were evaluated. ddPCR in comparison with qPCR has demonstrated sufficient sensitivity for analysing of cffDNA and determination of fetal RhD status from maternal circulation, results of both methods strongly correlated. Despite the more demanding workflow, ddPCR was found to be slightly more precise technology, as evaluated using quantitative standard. Regarding the clinical samples, the precision of both methods equalized with decreasing concentrations of tested DNA samples. In case of cffDNA with very low concentrations, variance parameters of both techniques were comparable. Detected levels of fetal cfDNA in maternal plasma were slightly higher than expected and correlated significantly with gestational age as measured by both methods (ddPCR r = 0.459; qPCR r = 0.438.

  3. Organisational interventions to combat stress risks in the Netherlands: design oriented approach

    NARCIS (Netherlands)

    Oeij, P.R.A.; Houtman, I.L.D.; Vaas, S.; Wiezer, N.M.

    2004-01-01

    One of several organisational interventions is described, namely Combat Workstress Approach (CWA), and its background in modern sociotechnology (MST) as a design oriented approach. CWA’s central goal is to assess and eliminate the sources of distur-bances in the work environment. Interventions aim

  4. tavgU_3d_mst_Cp: MERRA 3D IAU Diagnostic, Moist Physics, Diurnal 1.25 x 1.25 degree V5.2.0 (MATUCPMST) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — The MATUCPMST or tavgU_3d_mst_Cp data product is the MERRA Data Assimilation System 3-Dimensional moist process diagnostic that is time averaged on pressure levels...

  5. tavgM_3d_mst_Cp: MERRA 3D IAU Diagnostic, Moist Physics, Monthly Mean 1.25 x 1.25 degree V5.2.0 (MATMCPMST) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — The MATMCPMST or tavgM_3d_mst_Cp data product is the MERRA Data Assimilation System 3-Dimensional moist process diagnostic that is time averaged on pressure levels...

  6. Task completion report for investigating why output signal-variable values differ from their output component-parameter values in test problem MST2

    International Nuclear Information System (INIS)

    Steinke, R.G.

    1997-01-01

    Signal-variable values and their component-parameter values differ in an end-of-timestep edit to the TRCOUT and TRCGRF files because signal variables have beginning-of-timestep values, and component parameters have end-of-timestep values. Oscillatory divergence in the MST2 standard test problem after 9000 s occurs because of TRAC-P's numerical evaluation at a 1000 material Courant number. The magnitude of that divergence has diminished by a factor of 3.5 from Version 5.3.01 to 5.4.15 and by a factor of 25 from Version 5.4.15 to 5.4.28. That divergence can be eliminated by evaluating MST2 with a maximum material Courant number of 500

  7. Development of a high-throughput real time PCR based on a hot-start alternative for Pfu mediated by quantum dots

    Science.gov (United States)

    Sang, Fuming; Yang, Yang; Yuan, Lin; Ren, Jicun; Zhang, Zhizhou

    2015-09-01

    Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy.Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour

  8. A estrutura organizacional do MST: lógica política e lógica prática

    Directory of Open Access Journals (Sweden)

    Roberto de Sousa Miranda

    Full Text Available Nosso objetivo é compreender as relações entre a base do Movimento dos Trabalhadores Rurais Sem Terra (MST e suas lideranças, tomando como elemento de mediação a estrutura organizacional formalmente adotada em 2003. Para tanto, três chaves analíticas são utilizadas: Clastres, que explora a ideia de estrutura separada do corpo social; Leach, que opõe um modelo abstrato de organização às situações práticas observadas e interpretadas a partir da materialidade do comportamento dos assentados e acampados; o Neo-institucionalismo, que trata as instituições enquanto regras e normas que regulamentam a vida social. As análises foram baseadas em observações realizadas no XII Encontro Estadual do MST na Paraíba e nos assentamentos rurais José Antonio Eufrosino e Osiel Pereira, localizados no município de Campina Grande. Recusando as abordagens que tentam medir o grau de adoção dos modelos organizacionais formais pelos grupos sociais, tentamos revelar as incongruências produtoras das dinâmicas de reestruturação da organização do MST.

  9. An energy confinement study of the MST [Madison Symmetric Torus] reversed field pinch using a Thomson scattering diagnostic

    International Nuclear Information System (INIS)

    Den Hartog, D.J.

    1989-11-01

    Thomson scattering measurements of the central electron temperature and density during the plasma current peak have been performed on the MST Reversed Field Pinch (RFP). This Thomson scattering diagnostic was calibrated for absolute electron density measurements. These measurements of T e and n e , when combined with profile assumptions, were used to calculate estimates of energy confinement time (τ E ) and poloidal beta (β θ ). A standard discharge with I p ∼ 400 kA, F ∼ -0.1, and θ ∼ 1.6 typically exhibited T e ∼ 275 eV, n e ∼ 2.0 x 10 13 cm -3 , τ E ≤ 1 ms, and β θ ≤ 8%. The results of a limited plasma current scaling study did not indicate a strong scaling of T e or τ E with I p . The Thomson scattering diagnostic was used in conjunction with a bolometer, VUV radiation monitor, and edge magnetic coils to study the loss of energy from the plasma. Results indicate that thermal transport from stochastic magnetic fields, particle loss, and radiation are important energy loss processes. The experiments done for this study included an F-scan, a paddle limiter insertion series, and an argon doping series. The plasma maintained a constant βτ during these perturbation experiments, suggesting that increases in one energy loss channel are compensated by drops in other channels and increases in input power to the plasma

  10. O MST e a “radicalização democrática”: quando o conservadorismo parece progressista

    Directory of Open Access Journals (Sweden)

    Frederico Daia Firmiano

    2011-04-01

    Full Text Available Este texto faz uma discussão sobre a perspectiva da radicalização democrática e a abordagem baseada no “ambiente institucional possibilitador aliado às organizações populares autônomas” de Miguel Carter, apontando alguns de seus limites e a necessidade de sua superação por teorias que consideram os movimentos de luta pela reforma agrária, como o MST, experiências que portam a sociedade futura, a sociedade socialista.

  11. Generation of a reliable full-length cDNA of infectiousTembusu virus using a PCR-based protocol.

    Science.gov (United States)

    Liang, Te; Liu, Xiaoxiao; Cui, Shulin; Qu, Shenghua; Wang, Dan; Liu, Ning; Wang, Fumin; Ning, Kang; Zhang, Bing; Zhang, Dabing

    2016-02-02

    Full-length cDNA of Tembusu virus (TMUV) cloned in a plasmid has been found instable in bacterial hosts. Using a PCR-based protocol, we generated a stable full-length cDNA of TMUV. Different cDNA fragments of TMUV were amplified by reverse transcription (RT)-PCR, and cloned into plasmids. Fragmented cDNAs were amplified and assembled by fusion PCR to produce a full-length cDNA using the recombinant plasmids as templates. Subsequently, a full-length RNA was transcribed from the full-length cDNA in vitro and transfected into BHK-21 cells; infectious viral particles were rescued successfully. Following several passages in BKH-21 cells, the rescued virus was compared with the parental virus by genetic marker checks, growth curve determinations and animal experiments. These assays clearly demonstrated the genetic and biological stabilities of the rescued virus. The present work will be useful for future investigations on the molecular mechanisms involved in replication and pathogenesis of TMUV. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Bacterial Diversity in the Digestive Tracts of Four Indian Air-Breathing Fish Species Investigated by PCR Based Denaturing Gradient Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Suxu He

    Full Text Available ABSTRACT An investigation was conducted to identify the allochthonous microbiota (entire intestine and the autochthonous microbiota in proximal intestine (PI and distal intestine (DI of four species of Indian air-breathing fish (climbing perch; Anabas testudineus, murrel; Channa punctatus, walking catfish; Clarias batrachus and stinging catfish; Heteropneustes fossilis by PCR based denaturing gradient gel electrophoresis (DGGE. High similarities of the allochthonous microbiota were observed between climbing perch and murrel, walking catfish and stinging catfish, indicating similar food behavior. The autochthonous microbiota of PI and DI from climbing perch and murrel revealed more similarity, than the result obtained from walking catfish and stinging catfish. The autochthonous microbiota of climbing perch and murrel were similar with regard to the allochthonous microbiota, but no such similarity was observed in case of walking catfish and stinging catfish. The fish genotype and intestinal bacteria are well matched and show co-evolutionary relationship. Three fish species has its unique bacteria; autochthonous Enterobacter cloacae, Edwardsiella tarda and Sphingobium sp. in DI of climbing perch, Pseudomonas sp.; allochthonous and autochthonous in PI of walking catfish and uncultured bacterium (EU697160.1, uncultured bacterium (JF018065.1 and uncultured bacterium (EU697160.1 for stinging catfish. In murrel, no unique bacteria were detected.

  13. Molecular typing of methicillin-resistant Staphylococcus aureus: Comparison of PCR-based open reading frame typing, multilocus sequence typing, and Staphylococcus protein A gene typing.

    Science.gov (United States)

    Ogihara, Shinji; Saito, Ryoichi; Sawabe, Etsuko; Kozakai, Takahiro; Shima, Mari; Aiso, Yoshibumi; Fujie, Toshihide; Nukui, Yoko; Koike, Ryuji; Hagihara, Michio; Tohda, Shuji

    2018-04-01

    The recently developed PCR-based open reading frame typing (POT) method is a useful molecular typing tool. Here, we evaluated the performance of POT for molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) isolates and compared its performance to those of multilocus sequence typing (MLST) and Staphylococcus protein A gene typing (spa typing). Thirty-seven MRSA isolates were collected between July 2012 and May 2015. MLST, spa typing, and POT were performed, and their discriminatory powers were evaluated using Simpson's index analysis. The MRSA isolates were classified into 11, 18, and 33 types by MLST, spa typing, and POT, respectively. The predominant strains identified by MLST, spa typing, and POT were ST8 and ST764, t002, and 93-191-127, respectively. The discriminatory power of MLST, spa typing, and POT was 0.853, 0.875, and 0.992, respectively, indicating that POT had the highest discriminatory power. Moreover, the results of MLST and spa were available after 2 days, whereas that of POT was available in 5 h. Furthermore, POT is rapid and easy to perform and interpret. Therefore, POT is a superior molecular typing tool for monitoring nosocomial transmission of MRSA. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  14. Comparative performance of PCR-based assay versus microscopy and culture for the direct detection of Mycobacterium tuberculosis in clinical respiratory specimens in Lebanon.

    Science.gov (United States)

    Araj, G F; Talhouk, R S; Itani, L Y; Jaber, W; Jamaleddine, G W

    2000-09-01

    American University of Beirut Medical Center, Lebanon. To assess the performance of a polymerase chain reaction (PCR) using primers that flank 542 bp within IS6110 in Mycobacterium tuberculosis (TB) vs. microscopy and BACTEC culture, in the diagnosis of tuberculosis. A total of 82 clinical respiratory pulmonary specimens and 73 samples from BACTEC vials were tested by the three methods. Of 24 smear-positive culture-positive (SP-CP) and 11 smear-negative culture-positive (SN-CP) TB specimens, PCR detected 83% and 64%, respectively. Among 17 specimens yielding mycobacteria other than tuberculosis (MOTT), the PCR was positive in 33% SP-CP and 14% SN-CP specimens. Among the 73 BACTEC vials, PCR was positive in 36 of 38 (95%) yielding culture-positive TB, and in one of 20 (5%) yielding culture positive MOTT. None of the 30 smear-negative culture-negative (SN-CN) clinical specimens and 15 of the CN vials were positive by PCR. The overall sensitivity of PCR was 77% and 95% for TB detection in respiratory specimens and BACTEC vials, respectively, and the specificity was 94% in both. Because a substantial number of TB cases are missed, especially in SN-CP specimens, a PCR-based assay utilizing these primers cannot be used reliably, alone, in clinical laboratory diagnosis of mycobacterial respiratory infections.

  15. LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis

    Science.gov (United States)

    Lehle, Simon; Hildebrand, Dominic G.; Merz, Britta; Malak, Peter N.; Becker, Michael S.; Schmezer, Peter; Essmann, Frank; Schulze-Osthoff, Klaus; Rothfuss, Oliver

    2014-01-01

    DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify DNA lesions, and these techniques are tedious or only detect global DNA damage. In this study, we present a high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) in both the mitochondrial and nuclear genome. While most conventional methods are of low-sensitivity or restricted to abundant mitochondrial DNA samples, we established a protocol that enables the accurate sequence-specific quantification of DNA damage in >3-kb probes for any mitochondrial or nuclear DNA sequence. In order to validate the sensitivity of this method, we compared LORD-Q with a previously published qPCR-based method and the standard single-cell gel electrophoresis assay, demonstrating a superior performance of LORD-Q. Exemplarily, we monitored induction of DNA damage and repair processes in human induced pluripotent stem cells and isogenic fibroblasts. Our results suggest that LORD-Q provides a sequence-specific and precise method to quantify DNA damage, thereby allowing the high-throughput assessment of DNA repair, genotoxicity screening and various other processes for a wide range of life science applications. PMID:24371283

  16. Application of FTA sample collection and DNA purification system on the determination of CTG trinucleotide repeat size by PCR-based Southern blotting.

    Science.gov (United States)

    Hsiao, K M; Lin, H M; Pan, H; Li, T C; Chen, S S; Jou, S B; Chiu, Y L; Wu, M F; Lin, C C; Li, S Y

    1999-01-01

    Myotonic dystrophy (DM) is caused by a CTG trinucleotide expansion mutation at exon 15 of the myotonic dystrophy protein kinase gene. The clinical severity of this disease correlates with the length of the CTG trinucleotide repeats. Determination of the CTG repeat length has been primarily relied on by Southern blot analysis of restriction enzyme-digested genomic DNA. The development of PCR-based Southern blotting methodology provides a much more sensitive and simpler protocol for DM diagnosis. However, the quality of the template and the high (G+C) ratio of the amplified region hamper the use of PCR on the diagnosis of DM. A modified PCR protocol to amplify different lengths of CTG repeat region using various concentrations of 7deaza-dGTP has been reported (1). Here we describe a procedure including sample collection, DNA purification, and PCR analysis of CTG repeat length without using 7-deaza-dGTP. This protocol is very sensitive and convenient because only a small number of nucleate cells are needed for detection of CTG expansion. Therefore, it could be very useful in clinical and prenatal diagnosis as well as in prevalence study of DM.

  17. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  18. Novel treatments of mood disorders based on brain circuitry (ECT, MST, TMS, VNS, DBS).

    Science.gov (United States)

    George, Mark S; Nahas, Ziad; Li, Xiangbao; Kozel, F Andrew; Anderson, Berry; Yamanaka, Kaori; Chae, Jeong-Ho; Foust, Milton J

    2002-10-01

    Advances in understanding the functional and structural anatomy of depression outlined in this issue set the stage for attempting to manipulate implicated brain regions as potential antidepressant therapies. On the one hand, these circuit- and device-based approaches to treating depression are not new. Electroconvulsive therapy (ECT) dates back to the beginning of modern biologic psychiatry with the discovery and rapid increase of first chemical (around 1910), and then later ECT. On the other hand, this area represents an important paradigm shift with treatments that are radical and different. A dizzying array of diverse technologies now allows researchers to stimulate the brain in undreamed of ways. However, the approaches described in this article are still considered experimental and are not approved for use in the United States by the Food and Drug Administration (FDA), except ECT, which predates the FDA. These device-based approaches to brain stimulation offer promise as potential acute and even longterm treatments. Additionally, the research determining whether and how these devices work to influence mood promises to help unravel the neurophysiology of mood regulation. These novel treatments are thus the translational tools to bridge from advances in brain imaging, into new treatments for depressed patients. Copyright 2002, Elsevier Science (USA). All rights reserved.

  19. Protein phosphatase 2a (PP2A binds within the oligomerization domain of striatin and regulates the phosphorylation and activation of the mammalian Ste20-Like kinase Mst3

    Directory of Open Access Journals (Sweden)

    Jones Candace A

    2011-10-01

    Full Text Available Abstract Background Striatin, a putative protein phosphatase 2A (PP2A B-type regulatory subunit, is a multi-domain scaffolding protein that has recently been linked to several diseases including cerebral cavernous malformation (CCM, which causes symptoms ranging from headaches to stroke. Striatin association with the PP2A A/C (structural subunit/catalytic subunit heterodimer alters PP2A substrate specificity, but targets and roles of striatin-associated PP2A are not known. In addition to binding the PP2A A/C heterodimer to form a PP2A holoenzyme, striatin associates with cerebral cavernous malformation 3 (CCM3 protein, the mammalian Mps one binder (MOB homolog, Mob3/phocein, the mammalian sterile 20-like (Mst kinases, Mst3, Mst4 and STK25, and several other proteins to form a large signaling complex. Little is known about the molecular architecture of the striatin complex and the regulation of these sterile 20-like kinases. Results To help define the molecular organization of striatin complexes and to determine whether Mst3 might be negatively regulated by striatin-associated PP2A, a structure-function analysis of striatin was performed. Two distinct regions of striatin are capable of stably binding directly or indirectly to Mob3--one N-terminal, including the coiled-coil domain, and another more C-terminal, including the WD-repeat domain. In addition, striatin residues 191-344 contain determinants necessary for efficient association of Mst3, Mst4, and CCM3. PP2A associates with the coiled-coil domain of striatin, but unlike Mob3 and Mst3, its binding appears to require striatin oligomerization. Deletion of the caveolin-binding domain on striatin abolishes striatin family oligomerization and PP2A binding. Point mutations in striatin that disrupt PP2A association cause hyperphosphorylation and activation of striatin-associated Mst3. Conclusions Striatin orchestrates the regulation of Mst3 by PP2A. It binds Mst3 likely as a dimer with CCM3 via

  20. PCR-based detection of bacterial DNA after antimicrobial treatment is indicative of persistent, viable bacteria in the chinchilla model of otitis media.

    Science.gov (United States)

    Post, J C; Aul, J J; White, G J; Wadowsky, R M; Zavoral, T; Tabari, R; Kerber, B; Doyle, W J; Ehrlich, G D

    1996-01-01

    Bacterial deoxyribonucleic acid (DNA) has been previously detected by polymerase chain reactions (PCR) in a significant percentage of culturally-sterile pediatric middle-ear effusions. The current study was designed to determine whether this represents the existence of viable bacteria or the persistence of residual DNA in the middle-ear cleft. The middle-ear cavities of two sets of chinchillas were inoculated with either: 1) 100 colony-forming units (CFU) of live Haemophilus influenzae, 2.2 x 10(6) CFU of pasteurized Moraxella catarrhalis, and 1000 ng of DNA (>10(8) genomic equivalents) from Streptococcus pneumoniae; or 2) 100 CFU of live S pneumoniae, 2.2 x 10(6) CFU of pasteurized M catarrhalis and 1000 ng of purified DNA from H influenzae. Animals were treated with ampicillin for 5 days beginning on day 3. A single-point longitudinal study design was used for sampling to eliminate the possibility of contamination. No DNA was detectable from the heat-killed bacteria or the purified DNA after day 3. However, DNA from the live bacteria persisted through day 21, even though all specimens were culture-negative following the initiation of antimicrobial therapy. These findings indicate that purified DNA and DNA from intact but nonviable bacteria do not persist in the middle-ear cleft in the presence of an effusion, even following high copy inoculation. In contrast, antibiotic-treated bacteria persist in some viable state for weeks as evidenced by the differential ability of the PCR-based assay systems to detect the live bacteria, but not detect the heat-killed organisms.

  1. Eukaryote-Made Thermostable DNA Polymerase Enables Rapid PCR-Based Detection of Mycoplasma, Ureaplasma and Other Bacteria in the Amniotic Fluid of Preterm Labor Cases.

    Science.gov (United States)

    Ueno, Tomohiro; Niimi, Hideki; Yoneda, Noriko; Yoneda, Satoshi; Mori, Masashi; Tabata, Homare; Minami, Hiroshi; Saito, Shigeru; Kitajima, Isao

    2015-01-01

    Intra-amniotic infection has long been recognized as the leading cause of preterm delivery. Microbial culture is the gold standard for the detection of intra-amniotic infection, but several days are required, and many bacterial species in the amniotic fluid are difficult to cultivate. We developed a novel nested-PCR-based assay for detecting Mycoplasma, Ureaplasma, other bacteria and fungi in amniotic fluid samples within three hours of sample collection. To detect prokaryotes, eukaryote-made thermostable DNA polymerase, which is free from bacterial DNA contamination, is used in combination with bacterial universal primers. In contrast, to detect eukaryotes, conventional bacterially-made thermostable DNA polymerase is used in combination with fungal universal primers. To assess the validity of the PCR assay, we compared the PCR and conventional culture results using 300 amniotic fluid samples. Based on the detection level (positive and negative), 93.3% (280/300) of Mycoplasma, 94.3% (283/300) of Ureaplasma, 89.3% (268/300) of other bacteria and 99.7% (299/300) of fungi matched the culture results. Meanwhile, concerning the detection of bacteria other than Mycoplasma and Ureaplasma, 228 samples were negative according to the PCR method, 98.2% (224/228) of which were also negative based on the culture method. Employing the devised primer sets, mixed amniotic fluid infections of Mycoplasma, Ureaplasma and/or other bacteria could be clearly distinguished. In addition, we also attempted to compare the relative abundance in 28 amniotic fluid samples with mixed infection, and judged dominance by comparing the Ct values of quantitative real-time PCR. We developed a novel PCR assay for the rapid detection of Mycoplasma, Ureaplasma, other bacteria and fungi in amniotic fluid samples. This assay can also be applied to accurately diagnose the absence of bacteria in samples. We believe that this assay will positively contribute to the treatment of intra-amniotic infection and

  2. Observation of Polar Mesosphere Summer Echoes using the northernmost MST radar at Eureka (80°N)

    Science.gov (United States)

    Swarnalingam, N.; Hocking, W.; Janches, D.; Drummond, J.

    2017-09-01

    We investigate long-term Polar Mesosphere Summer Echoes (PMSEs) observations conducted by the northernmost geographically located MST radar at Eureka (80°N, 86°W). While PMSEs are a well recognized summer phenomenon in the polar regions, previous calibrated studies at Resolute Bay and Eureka using 51.5 MHz and 33 MHz radars respectively, showed that PMSE backscatter signal strengths are relatively weak in the polar cap sites, compared to the auroral zone sites (Swarnalingam et al., 2009b; Singer et al., 2010). Complications arise with PMSEs in which the echo strength is controlled by the electrons, which are, in turn, influenced by heavily charged ice particles as well as the variability in the D-region plasma. In recent years, PMSE experiments were conducted inside the polar cap utilizing a 51 MHz radar located at Eureka. In this paper, we investigate calibrated observations, conducted during 2009-2015. Seasonal and diurnal variations of the backscatter signal strengths are discussed and compared to previously published results from the ALOMAR radar, which is a radar of similar design located in the auroral zone at Andenes, Norway (69°N, 16°E). At Eureka, while PMSEs are present with a daily occurrence rate which is comparable to the rate observed at the auroral zone site for at least two seasons, they show a great level of inter-annual variability. The occurrence rate for the strong echoes tends to be low. Furthermore, comparison of the absolute backscatter signal strengths at these two sites clearly indicates that the PMSE backscatter signal strength at Eureka is weak. Although this difference could be caused by several factors, we investigate the intensity of the neutral air turbulence at Eureka from the measurements of the Doppler spectrum of the PMSE backscatter signals. We found that the level of the turbulence intensity at Eureka is weak relative to previously reported results from three high latitude sites.

  3. ENTREVISTA: A Rica Experiência de Formação do e com o MST

    Directory of Open Access Journals (Sweden)

    Maristela Dal Moro*; Geraldo Gasparin**

    2012-02-01

    Full Text Available

    Na perspectiva de uma maior concretude do projeto ético-político do Serviço Social no Brasil, tem havido nos últimos anos uma forte aproximação entre as unidades de formação profissional e os movimentos sociais, dentre os quais se destaca o Movimento Nacional dos Trabalhadores Sem Terra – MST. Esse importante movimento tem desencadeado uma estratégia de formação de seus militantes e de outros movimentos sociais e, a partir disso, fundou a Escola Nacional Florestan Fernandes. Ali, os militantes tomam contato com um variado cardápio crítico de conteúdos que vão desde a teoria social, o entendimento do modo de produção capitalista, a formação social brasileira e suas particularidades, até discussões sobre o movimento e os processos de formação da consciência. Contudo, essa estratégia vem passando também pelo estreitamento de laços com as universidades públicas, por meio muitas vezes do Serviço Social, criando cursos de graduação para turmas especiais, como na UFRJ, formadas por militantes dos movimentos. Nossa entrevista com Maristela Dal Moro e Geraldo Gasparin interpela dois protagonistas desse processo, na perspectiva de socializar a experiência e, sobretudo, de mostrar como a formação profissional em Serviço Social pode fortalecer os movimentos sociais.

    Por  Alba Tereza Barroso de Castro

  4. Melding Infant Mental Health and Multisystemic Therapy Approaches to Community-Based Treatment

    Science.gov (United States)

    Willoughby, Jay C.; Carubia, Beau A.; Murgolo, Marisa A.; Carter, Debbie R.; Frankel, Karen A.

    2013-01-01

    A recent partnership between the Irving Harris Program in Child Development and Infant Mental Health and the Community Based Psychiatry Program at University of Colorado Hospital joined two different approaches to child mental health treatment: infant mental health and multisystemic therapy (MST). This article illustrates the compatibility of…

  5. Genotyping for DQA1 and PM loci in urine using PCR-based amplification: effects of sample volume, storage temperature, preservatives, and aging on DNA extraction and typing.

    Science.gov (United States)

    Vu, N T; Chaturvedi, A K; Canfield, D V

    1999-05-31

    Urine is often the sample of choice for drug screening in aviation/general forensic toxicology and in workplace drug testing. In some instances, the origin of the submitted samples may be challenged because of the medicolegal and socioeconomic consequences of a positive drug test. Methods for individualization of biological samples have reached a new boundary with the application of the polymerase chain reaction (PCR) in DNA profiling, but a successful characterization of the urine specimens depends on the quantity and quality of DNA present in the samples. Therefore, the present study investigated the influence of storage conditions, sample volume, concentration modes, extraction procedures, and chemical preservations on the quantity of DNA recovered, as well as the success rate of PCR-based genotyping for DQA1 and PM loci in urine. Urine specimens from male and female volunteers were divided and stored at various temperatures for up to 30 days. The results suggested that sample purification by dialfiltration, using 3000-100,000 molecular weight cut-off filters, did not enhance DNA recovery and typing rate as compared with simple centrifugation procedures. Extraction of urinary DNA by the organic method and by the resin method gave comparable typing results. Larger sample volume yielded a higher amount of DNA, but the typing rates were not affected for sample volumes between 1 and 5 ml. The quantifiable amounts of DNA present were found to be greater in female (14-200 ng/ml) than in male (4-60 ng/ml) samples and decreased with the elapsed time under both room temperature (RT) and frozen storage. Typing of the male samples also demonstrated that RT storage samples produced significantly higher success rates than that of frozen samples, while there was only marginal difference in the DNA typing rates among the conditions tested using female samples. Successful assignment of DQA1 + PM genotype was achieved for all samples of fresh urine, independent of gender

  6. A multiplex PCR-based method to identify strongylid parasite larvae recovered from ovine faecal cultures and/or pasture samples.

    Science.gov (United States)

    Bisset, S A; Knight, J S; Bouchet, C L G

    2014-02-24

    A multiplex PCR-based method was developed to overcome the limitations of microscopic examination as a means of identifying individual infective larvae from the wide range of strongylid parasite species commonly encountered in sheep in mixed sheep-cattle grazing situations in New Zealand. The strategy employed targets unique species-specific sequence markers in the second internal transcribed spacer (ITS-2) region of ribosomal DNA of the nematodes and utilises individual larval lysates as reaction templates. The basic assay involves two sets of reactions designed to target the ten strongylid species most often encountered in ovine faecal cultures under New Zealand conditions (viz. Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus axei, Trichostrongylus colubriformis, Trichostrongylus vitrinus, Cooperia curticei, Cooperia oncophora, Nematodirus spathiger, Chabertia ovina, and Oesophagostomum venulosum). Five species-specific primers, together with a pair of "generic" (conserved) primers, are used in each of the reactions. Two products are generally amplified, one by the generic primer pair regardless of species (providing a positive PCR control) and the other (whose size is indicative of the species present) by the appropriate species-specific primer in combination with one or other of the generic primers. If necessary, any larvae not identified by these reactions can subsequently be tested using primers designed specifically to detect those species less frequently encountered in ovine faecal cultures (viz. Ostertagia ostertagi, Ostertagia leptospicularis, Cooperia punctata, Nematodirus filicollis, and Bunostomum trigonocephalum). Results of assays undertaken on >5500 nematode larvae cultured from lambs on 16 different farms distributed throughout New Zealand indicated that positive identifications were initially obtained for 92.8% of them, while a further 4.4% of reactions gave a generic but no visible specific product and 2.8% gave no discernible

  7. O fato e a notícia. A mídia impressa e o movimento dos trabalhadores rurais sem-terra (MST.

    Directory of Open Access Journals (Sweden)

    Sônia Maria Ribeiro de Souza

    2011-11-01

    Full Text Available Este texto expressa os primeiros passos rumo às investigações sobre as manifestações ideológicas e os juízos de valor veiculados pelos meios de comunicação em Presidente Prudente especificamente os jornais O Imparcial e o Oeste Notícias, tendo como referência a luta pela terra no Pontal do Paranapanema e o contexto de organização social do Movimento dos Trabalhadores Rurais Sem-Terra (MST.

  8. ANOTAÇÕES SOBRE A AUTO-ORGANIZAÇÃO DAS MULHERES: O EXEMPLO DA VIA CAMPESINA NO BRASIL E DO MST

    Directory of Open Access Journals (Sweden)

    Claúdia Mazzei Nogueira

    2011-12-01

    Full Text Available Esse texto trata, em especial, da luta por uma divisão sócio-sexual do trabalho mais justa, travada pelas mulheres inseridas nos movimentos sociais presentes no espaço rural, que tem como objetivo a igualdade substantiva. Para tanto, indicamos e analisamos, introdutoriamente, alguns elementos que perfazem a auto-organização das mulheres do MST e Via Campesina no Brasil, que tem como apoio a centralidade do trabalho enquanto fundamento ontológico necessário para a luta da classe trabalhadora contra a “exploração” agroindustrial.

  9. Validation of a PCR-based method for the detection of various rendered materials in feedstuffs using a forensic DNA extraction kit.

    Science.gov (United States)

    Myers, Michael J; Yancy, Haile F; Araneta, Michael; Armour, Jennifer; Derr, Janice; Hoostelaere, Lawrence A D; Farmer, Doris; Jackson, Falana; Kiessling, William M; Koch, Henry; Lin, Huahua; Liu, Yan; Mowlds, Gabrielle; Pinero, David; Riter, Ken L; Sedwick, John; Shen, Yuelian; Wetherington, June; Younkins, Ronsha

    2006-01-01

    A method trial was initiated to validate the use of a commercial DNA forensic kit to extract DNA from animal feed as part of a PCR-based method. Four different PCR primer pairs (one bovine pair, one porcine pair, one ovine primer pair, and one multispecies pair) were also evaluated. Each laboratory was required to analyze a total of 120 dairy feed samples either not fortified (control, true negative) or fortified with bovine meat and bone meal, porcine meat and bone meal (PMBM), or lamb meal. Feeds were fortified with the animal meals at a concentration of 0.1% (wt/wt). Ten laboratories participated in this trial, and each laboratory was required to evaluate two different primer pairs, i.e., each PCR primer pair was evaluated by five different laboratories. The method was considered to be validated for a given animal source when three or more laboratories achieved at least 97% accuracy (29 correct of 30 samples for 96.7% accuracy, rounded up to 97%) in detecting the fortified samples for that source. Using this criterion, the method was validated for the bovine primer because three laboratories met the criterion, with an average accuracy of 98.9%. The average false-positive rate was 3.0% in these laboratories. A fourth laboratory was 80% accurate in identifying the samples fortified with bovine meat and bone meal. A fifth laboratory was not able to consistently extract the DNA from the feed samples and did not achieve the criterion for accuracy for either the bovine or multispecies PCR primers. For the porcine primers, the method was validated, with four laboratories meeting the criterion for accuracy with an average accuracy of 99.2%. The fifth laboratory had a 93.3% accuracy outcome for the porcine primer. Collectively, these five laboratories had a 1.3% false-positive rate for the porcine primer. No laboratory was able to meet the criterion for accuracy with the ovine primers, most likely because of problems with the synthesis of the primer pair; none of the

  10. High-frequency fluctuation measurements by far-infrared laser Faraday-effect polarimetry-interferometry and forward scattering system on MST.

    Science.gov (United States)

    Ding, W X; Lin, L; Duff, J R; Brower, D L

    2014-11-01

    Magnetic fluctuation-induced transport driven by global tearing modes has been measured by Faraday-effect polarimetry and interferometry (phase measurements) in the MST reversed field pinch. However, the role of small-scale broadband magnetic and density turbulence in transport remains unknown. In order to investigate broadband magnetic turbulence, we plan to upgrade the existing detector system by using planar-diode fundamental waveguide mixers optimized for high sensitivity. Initial tests indicate these mixers have ×10 sensitivity improvement compared to currently employed corner-cube Schottky-diode mixers and ×5 lower noise. Compact mixer design will allow us to resolve the wavenumbers up to k ∼ 1-2 cm(-1) for beam width w = 1.5 cm and 15 cm(-1) for beam width w = 2 mm. The system can also be used to measure the scattered signal (amplitude measurement) induced by both plasma density and magnetic fluctuations.

  11. AS PRÁTICAS EDUCATIVAS EM AGROECOLOGIA DO MOVIMENTO DOS TRABALHADORES RURAIS SEM TERRA (MST E OS DESAFIOS FRENTE AS ORDENS IMPOSTAS PELO CAPITALISMO NO CAMPO BRASILEIRO

    Directory of Open Access Journals (Sweden)

    Claudia Maria Bernava Aguillar

    2017-01-01

    Full Text Available O cenário atual do campo brasileiro faz parte do processo de inserção e intervenção das práticas impostas pelo modo de produção capitalista, capitaneadas pela classe dominante burguesa, que têm como projeto articulador, a implantação e implementação da chamnada "revolução verde", a qual revela as políticas ofensivas para dinamizar e aumentar a concentração de riquezas por meio da produção e reprodução do capital, em detrimento da luta dos trabalhadores rurais pelo acesso à terra e o cumprimento de sua função social. Para enfrentar o desafio de minimizar as ofensivas do capital, o Movimento dos Trabalhadores Rurais Sem Terra (MST criou a educação agroecologica, com o objetivo de conceber as manipulações embutidas nas contradições impostas pelo sistema, como a falta de interação das disciplinas e a fragmentação do conhecimento em virtude da falta de organicidade dos professores, a dificuldade de apropriação teórica dos alunos, a falta de investimentos para a manutenção das escolas e incentivos à pesquisa em agroecologia. As práticas educativas em Agroecologia do MST, frente às políticas neoliberais impostas pela classe dominante, se constituem no foco das reflexões iluminadas pela fundamentação teórica e a pesquisa exploratória, as quais contribuem para a análise das questões postas.

  12. Whole Genome Amplification of Day 3 or Day 5 Human Embryos Biopsies Provides a Suitable DNA Template for PCR-Based Techniques for Genotyping, a Complement of Preimplantation Genetic Testing

    Directory of Open Access Journals (Sweden)

    Elizabeth Schaeffer

    2017-01-01

    Full Text Available Our objective was to determine if whole genome amplification (WGA provides suitable DNA for qPCR-based genotyping for human embryos. Single blastomeres (Day 3 or trophoblastic cells (Day 5 were isolated from 342 embryos for WGA. Comparative Genomic Hybridization determined embryo sex as well as Trisomy 18 or Trisomy 21. To determine the embryo’s sex, qPCR melting curve analysis for SRY and DYS14 was used. Logistic regression indicated a 4.4%, 57.1%, or 98.8% probability of a male embryo when neither gene, SRY only, or both genes were detected, respectively (accuracy = 94.1%, kappa = 0.882, and p<0.001. Fluorescent Capillary Electrophoresis for the amelogenin genes (AMEL was also used to determine sex. AMELY peak’s height was higher and this peak’s presence was highly predictive of male embryos (AUC = 0.93, accuracy = 81.7%, kappa = 0.974, and p<0.001. Trisomy 18 and Trisomy 21 were determined using the threshold cycle difference for RPL17 and TTC3, respectively, which were significantly lower in the corresponding embryos. The Ct difference for TTC3 specifically determined Trisomy 21 (AUC = 0.89 and RPL17 for Trisomy 18 (AUC = 0.94. Here, WGA provides adequate DNA for PCR-based techniques for preimplantation genotyping.

  13. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms

    OpenAIRE

    Manuel Ares-Arroyo; Cristina Bernabe-Balas; Alfonso Santos-Lopez; Maria R. Baquero; Kashi N. Prasad; Dolores Cid; Carmen Martin-Espada; Alvaro San Millan; Bruno Gonzalez-Zorn

    2018-01-01

    ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic an...

  14. PCR-based assays versus direct sequencing for evaluating the effect of KRAS status on anti-EGFR treatment response in colorectal cancer patients: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Lianfeng Shan

    Full Text Available The survival rate of colorectal cancer (CRC patients carrying wild-type KRAS is significantly increased by combining anti-EGFR monoclonal antibody (mAb with standard chemotherapy. However, conflicting data exist in both the wild-type KRAS and mutant KRAS groups, which strongly challenge CRC anti-EGFR treatment. Here we conducted a meta-analysis in an effort to provide more reliable information regarding anti-EGFR treatment in CRC patients.We searched full reports of randomized clinical trials using Medline, the American Society of Clinical Oncology (ASCO, and the European Society for Medical Oncology (ESMO. Two investigators independently screened the published literature according to our inclusive and exclusive criteria and the relative data were extracted. We used Review Manager 5.2 software to analyze the data.The addition of anti-EGFR mAb to standard chemotherapy significantly improved both progression-free survival (PFS and median overall survival (mOS in the wild-type KRAS group; hazard ratios (HRs for PFS and mOS were 0.70 [95% confidence interval (CI, 0.58-0.84] and 0.83 [95% CI, 0.75-0.91], respectively. In sub-analyses of the wild-type KRAS group, when PCR-based assays are employed, PFS and mOS notably increase: the HRs were 0.74 [95% CI, 0.62-0.88] and 0.87 [95% CI, 0.78-0.96], respectively. In sub-analyses of the mutant KRAS group, neither PCR-based assays nor direct sequencing enhance PFS or mOS.Our data suggest that PCR-based assays with high sensitivity and specificity allow accurate identification of patients with wild-type KRAS and thus increase PFS and mOS. Furthermore, such assays liberate patients with mutant KRAS from unnecessary drug side effects, and provide them an opportunity to receive appropriate treatment. Thus, establishing a precise standard reference test will substantially optimize CRC-targeted therapies.

  15. Measuring urban forms from inter-building distances: Combining MST graphs with a Local Index of Spatial Association

    OpenAIRE

    Caruso , Geoffrey; Hilal , Mohamed; Thomas , Isabelle

    2017-01-01

    A new method is proposed for characterising local urban patterns at the scale of a large urban region. The approach overcomes the difficulties of surface-based representations of built-up morphologies and provides an efficient way to account for the proximity of built and non-built land. The strength of the approach resides in the direct use of the coordinates of each building, a very parsimonious input of external parameters, and a local spatial statistical perspective. The method consists i...

  16. A página virtual do movimento dos trabalhadores rurais sem terra (MST) como instrumento de contrainformação na luta político-ideológica pela reforma agrária

    OpenAIRE

    Engelmann, Solange Inês

    2013-01-01

    O presente trabalho teve como objetivo a análise da página nacional de internet do Movimento dos Trabalhadores Rurais Sem Terra (MST), criada em 1997. Nosso propósito foi compreender o processo de construção do portal e qual a importância desse novo aparato de comunicação na divulgação das demandas do MST e no debate da Reforma Agrária no Brasil, para o diálogo com a classe trabalhadora urbana e sua base social. Para tanto, inicialmente apresentamos uma discussão sobre o novo processo de t...

  17. Riems influenza a typing array (RITA): An RT-qPCR-based low density array for subtyping avian and mammalian influenza a viruses.

    Science.gov (United States)

    Hoffmann, Bernd; Hoffmann, Donata; Henritzi, Dinah; Beer, Martin; Harder, Timm C

    2016-06-03

    Rapid and sensitive diagnostic approaches are of the utmost importance for the detection of humans and animals infected by specific influenza virus subtype(s). Cascade-like diagnostics starting with the use of pan-influenza assays and subsequent subtyping devices are normally used. Here, we demonstrated a novel low density array combining 32 TaqMan(®) real-time RT-PCR systems in parallel for the specific detection of the haemagglutinin (HA) and neuraminidase (NA) subtypes of avian and porcine hosts. The sensitivity of the newly developed system was compared with that of the pan-influenza assay, and the specificity of all RT-qPCRs was examined using a broad panel of 404 different influenza A virus isolates representing 45 different subtypes. Furthermore, we analysed the performance of the RT-qPCR assays with diagnostic samples obtained from wild birds and swine. Due to the open format of the array, adaptations to detect newly emerging influenza A virus strains can easily be integrated. The RITA array represents a competitive, fast and sensitive subtyping tool that requires neither new machinery nor additional training of staff in a lab where RT-qPCR is already established.

  18. Development of a PCR-based marker utilizing a deletion mutation in the dihydroflavonol 4-reductase (DFR) gene responsible for the lack of anthocyanin production in yellow onions (Allium cepa).

    Science.gov (United States)

    Kim, Sunggil; Yoo, Kil Sun; Pike, Leonard M

    2005-02-01

    Bulb color in onions (Allium cepa) is an important trait, but the mechanism of color inheritance is poorly understood at the molecular level. A previous study showed that inactivation of the dihydroflavonol 4-reductase (DFR) gene at the transcriptional level resulted in a lack of anthocyanin production in yellow onions. The objectives of the present study were the identification of the critical mutations in the DFR gene (DFR-A) and the development of a PCR-based marker for allelic selection. We report the isolation of two additional DFR homologs (DFR-B and DFR-C). No unique sequences were identified in either DFR homolog, even in the untranslated region (UTR). Both genes shared more than 95% nucleotide sequence identity with the DFR-A gene. To obtain a unique sequence from each gene, we isolated the promoter regions. Sequences of the DFR-A and DFR-B promoters differed completely from one another, except for an approximately 100-bp sequence adjacent to the 5'UTR. It was possible to specifically amplify only the DFR-A gene using primers designed to anneal to the unique promoter region. The sequences of yellow and red DFR-A alleles were the same except for a single base-pair change in the promoter and an approximately 800-bp deletion within the 3' region of the yellow DFR-A allele. This deletion was used to develop a co-dominant PCR-based marker that segregated perfectly with color phenotypes in the F2 population. These results indicate that a deletion mutation in the yellow DFR-A gene results in the lack of anthocyanin production in yellow onions.

  19. Turbulence characteristics in the tropical mesosphere as obtained by MST radar at Gadanki (13.5° N, 79.2° E

    Directory of Open Access Journals (Sweden)

    M. N. Sasi

    2001-08-01

    Full Text Available Turbulent kinetic energy dissipation rates (ε and eddy diffusion coefficients (Kz in the tropical mesosphere over Gadanki (13.5° N, 79.2° E, estimated from Doppler widths of MST radar echoes (vertical beam, observed over a 3-year period, show a seasonal variation with a dominant summer maximum. The observed seasonal variation of ε and Kz in the mesosphere is only partially consistent with that of gravity wave activity inferred from mesospheric winds and temperatures measured by rockets for a period of 9 years at Trivandrum (8.5° N, 77° E (which shows two equinox and one summer maxima lying close to Gadanki. The summer maximum of mesospheric ε and Kz values appears to be related to the enhanced gravity wave activity over the low-latitude Indian subcontinent during the southwest monsoon period (June – September. Both ε and Kz in the mesosphere over Gadanki show an increase with an increase in height during all seasons. The absolute values of observed ε and Kz in the mesosphere (above ~80 km does not show significant differences from those reported for high latitudes. Comparison of observed Kz values during the winter above Gadanki with those over Arecibo (18.5° N, 66° W shows that they are not significantly different from each other above the ~80 km altitude.Key words. Meteorology and atmospheric dynamics (middle atmosphere dynamics; tropical meteorology; wave and tides

  20. O discurso político da agroecologia no MST: O caso do Assentamento 17 de Abril em Eldorado dos Carajás, Pará

    Directory of Open Access Journals (Sweden)

    Caetano De’ Carli

    2013-10-01

    Full Text Available O presente artigo visa debater a agroecologia enquanto discurso político. Parte‑se das pesquisas de Altieri, Nichols, Gliessman, Gúzman, Cristoffoli, entre outros autores, para evidenciar as trajetórias da agroecologia enquanto ciência e as tentativas da sua materialização em áreas da reforma agrária. Após essas perspectivas, aborda‑se a agroecologia na prática política do Movimento dos Trabalhadores Rurais Sem‑Terra, tanto no que se refere às suas experiências‑modelos como ao discurso político que assume, em contraposição com o modelo hegemônico da Revolução Verde. Por fim, debruça‑se sobre o caso do Assentamento 17 de Abril em Eldorado dos Carajás, ressaltando como esse discurso político representa uma importante estratégia do MST em relação a uma mudança de paradigma na mentalidade dos assentados e das lideranças locais do movimento, destacando ser esse um importante passo para a materialização de produções agropecuárias alternativas nas áreas de reforma agrária no Brasil.

  1. Observations on Stratospheric-Mesospheric-Thermospheric temperatures using Indian MST radar and co-located LIDAR during Leonid Meteor Shower (LMS

    Directory of Open Access Journals (Sweden)

    R. Selvamurugan

    2002-11-01

    Full Text Available The temporal and height statistics of the occurrence of meteor trails during the Leonid meteor shower revealed the capability of the Indian MST radar to record large numbers of meteor trails. The distribution of radio meteor trails due to a Leonid meteor shower in space and time provided a unique opportunity to construct the height profiles of lower thermospheric temperatures and winds, with good time and height resolution. There was a four-fold increase in the meteor trails observed during the LMS compared to a typical non-shower day. The temperatures were found to be in excellent continuity with the temperature profiles below the radio meteor region derived from the co-located Nd-Yag LIDAR and the maximum height of the temperature profile was extended from the LIDAR to ~110 km. There are, how-ever, some significant differences between the observed profiles and the CIRA-86 model profiles. The first results on the meteor statistics and neutral temperature are presented and discussed below.  Key words. Atmospheric composition and structure (pres-sure, density, and temperature History of geophysics (at-mospheric sciences Meteorology and atmospheric dynamics (middle atmosphere dynamics

  2. Radial transport effects on ECCD in the TCV and DIII-D tokamaks and on Ohmic discharges in the MST RFP

    International Nuclear Information System (INIS)

    Harvey, R.W.; Sauter, O.; Nikkola, P.; Prater, R.; O'Connell, R.; Forest, C.B.

    2003-01-01

    The comprehensive CQL3D Fokker-Planck/Quasilinear simulation code has been benchmarked against experiment over a wide range of electron cyclotron conditions in the DIII-D tokamak (C.C. Petty et al., 14. Topical Conf. on RF Power in Plasmas, 2002). The same code, in disagreement with experiment, gives 560 kA of ECCD for a well documented, completely ECCD-driven, 100 kA TCV shot [O. Sauter et al, PRL, 2000]. Recent work (R.W. Harvey et al, Phys. Rev. Lett., 2002) has resolved the differences as due to radial transport at a level closely consistent with ITER scaling. Transport does not substantially affect DIII-D ECCD, but at similar ECH power has an overwhelming effect on the much smaller TCV. The transport is consistent with electrostatic-type diffusion (D ρρ constant in velocity space) and not with a magnetic-type diffusion (D ρρ ∝ |v || |). Fokker-Planck simulation of Ohmic reversed field pinch (RFP) discharges in the MST device reveals transport velocity dependence stronger than |v || |) will give agreement with current and soft X-ray spectra in standard discharges, but in the higher confinement, current profile controlled PPCD discharges, transport is again electrostatic-like. This is consistent with the object of PPCD, which is to replace magnetic turbulence driven current with auxiliary CD to improve transport. The tokamak and high-confinement RFP results mutually reinforce the constant-in-velocity-space 'electrostatic-type turbulence' conclusion. The steady-state energy and toroidal current are governed by the same radial transport equation. (authors)

  3. RADIAL TRANSPORT EFFECTS ON ECCD IN THE TCV AND DIII-D TOKAMAKS AND ON OHMIC DISCHARGES IN THE MST RFP

    International Nuclear Information System (INIS)

    HARVEY, R.W.; SAUTER, O.; PRATER, R.; NIKKOLA, P.; O'CONNELL, R.; FOREST, C.B.

    2002-01-01

    The comprehensive CQL3D Fokker-Planck/Quasilinear simulation code has been benchmarked against experiment over a wide range of electron cyclotron conditions in the DIII-D tokamak (C.C. Petty et al., 14th Topical Conf. on RF Power in Plasmas, 2002). The same code, in disagreement with experiment, gives 560 kA of ECCD for a well documented, completely ECCD-driven, 100 kA TCV shot [O. Sauter et al, PRL, 2000]. Recent work (R.W. Harvey et al, Phys. Rev. Lett., 2002) has resolved the differences as due to radial transport at a level closely consistent with ITER scaling. Transport does not substantially affect DIII-D ECCD, but at similar ECH power has an overwhelming effect on the much smaller TCV. The transport is consistent with electrostatic-type diffusion (D ρρ constant in velocity-space) and not with a magnetic-type diffusion (D ρρ ∝ |v(parallel)|). Fokker-Planck simulation of Ohmic reversed field pinch (RFP) discharges in the MST device reveals transport velocity dependence stronger than |v(parallel)| will give agreement with current and soft X-ray spectra in standard discharges, but in the higher confinement, current profile controlled PPCD discharges, transport is again electrostatic-like. This is consistent with the object of PPCD, which is to replace magnetic turbulence driven current with auxiliary CD to improve transport. The tokamak and high-confinement RFP results mutually reinforce the constant-in-velocity-space ''electrostatic-type turbulence'' conclusion. The steady-state energy and toroidal current are governed by the same radial transport equation

  4. Turbulence characteristics in the tropical mesosphere as obtained by MST radar at Gadanki (13.5° N, 79.2° E

    Directory of Open Access Journals (Sweden)

    M. N. Sasi

    Full Text Available Turbulent kinetic energy dissipation rates (ε and eddy diffusion coefficients (Kz in the tropical mesosphere over Gadanki (13.5° N, 79.2° E, estimated from Doppler widths of MST radar echoes (vertical beam, observed over a 3-year period, show a seasonal variation with a dominant summer maximum. The observed seasonal variation of ε and Kz in the mesosphere is only partially consistent with that of gravity wave activity inferred from mesospheric winds and temperatures measured by rockets for a period of 9 years at Trivandrum (8.5° N, 77° E (which shows two equinox and one summer maxima lying close to Gadanki. The summer maximum of mesospheric ε and Kz values appears to be related to the enhanced gravity wave activity over the low-latitude Indian subcontinent during the southwest monsoon period (June – September. Both ε and Kz in the mesosphere over Gadanki show an increase with an increase in height during all seasons. The absolute values of observed ε and Kz in the mesosphere (above ~80 km does not show significant differences from those reported for high latitudes. Comparison of observed Kz values during the winter above Gadanki with those over Arecibo (18.5° N, 66° W shows that they are not significantly different from each other above the ~80 km altitude.

    Key words. Meteorology and atmospheric dynamics (middle atmosphere dynamics; tropical meteorology; wave and tides

  5. Relações de saúde e trabalho em assentamento rural do MST na região de fronteira Brasil-Paraguai Health and work relations in a rural settlement of the MST in the Brazil-Paraguay border region

    Directory of Open Access Journals (Sweden)

    Eduardo Espíndola Fontoura Júnior

    2011-11-01

    Full Text Available Com o presente artigo, busca-se relatar e analisar as relações entre saúde e trabalho de pequenos produtores rurais do Movimento dos Trabalhadores Rurais Sem Terra (MST. Quanto à metodologia, adotou-se o aporte da investigação participativa e as bases da educação popular. O estudo realizado tornou possível uma compreensão de saúde e de trabalho mediante as narrativas dos trabalhadores e histórias relativas às lutas coletivas contra a exclusão e a violência no campo. Constataram-se importantes aspectos próprios a esse grupo populacional, como o sentido de conquista da propriedade da terra, os conflitos advindos da 'militância' e as diferenças de gênero e geração. Com base nos relatos, analisaram-se também os acidentes e os riscos relacionados à atividade de trabalho no assentamento rural, principalmente a exposição ao agrotóxico. Confirmaram-se, ainda, a solidariedade e a cooperação como valores importantes e como base de novas relações, um modo distinto de organização social coletiva do trabalho.In this article, we aim to report on and analyze the relationship between health and work of small farmers of the Landless Workers Movement (MST. So far as the methodology is concerned, we used participatory research and the basics of popular education. The study allowed for an understanding of health and work based on the workers' narratives, stories relating to collective struggles against exclusion and violence in the countryside. Important aspects related to this population group as were discovered, such as, for example, the sense of conquest of land ownership, the conflicts arising from 'activism,' and the differences of gender and generations. From the reports that were provided, we also examined the accidents and risks related to work in the rural settlement, particularly exposure to pesticides. It was also found that solidarity and cooperation are important values, basic elements for new relations and a distinctive

  6. Bauer, Carlos. Educação, terra e liberdade: princípios educacionais do MST em perspectiva histórica. São Paulo: Ediciones Pulsar - Xamã, 2009. 151 p.

    Directory of Open Access Journals (Sweden)

    Diana Crucelly González Rey

    2011-05-01

    Full Text Available El trabajo del Carlos Bauer, es producto de su tesis pos-doctoral desarrollada conjunto al núcleo de estudios sobre movimientos sociales, educación y ciudadanía (GEMDEC de la Uni-versidad Estatal de Campinas en São Paulo, Brasil. Esta edición es publicada en portugués en el año 2009, siendo la educación en el Movimiento Sin Tierra (MST su objeto principal del estudio.

  7. "Jag tror ju på allas lika värde oavsett kön" En studie om hur förskollärares resonemang kring sitt jämställdhetsuppdrag kommer till uttryck i mötet med barn.

    OpenAIRE

    Gisslén, Mia

    2013-01-01

    Denna studie har som syfte att belysa relationen mellan förskollärares resonemang om sitt jämställdhetsuppdrag och hur det kommer till uttryck i det direkta mötet med barn. Studiens empiri har samlats ihop genom två halvstrukturerade intervjuer med två förskollärare och tre löpande observationer i samlingssituation vid en förskola. Resultatet visar att förskollärarna resonerar kring sitt jämställdhetsuppdrag på ett professionellt sätt. De visar hög medvetenhet när de resonerar om sitt jämstäl...

  8. Enseñanza de lengua extranjera española en la educación de jóvenes y adultos del campo – Un proyecto del PRONERA/ UFSC y el MST/SC

    Directory of Open Access Journals (Sweden)

    Luana Lopes de Oliveira

    2013-07-01

    Full Text Available Resumen: Brasil en  torno a la problemática de la enseñanza de la lengua española para jóvenes y adultos de escuelas de asentamientos del Movimiento de Trabajadores Rurales sin Tierra (MST. La enseñanza del idioma español como problema cultural y político. Se plantea la enseñanza como “semilla para el internacionalismo”. En el texto relata el trabajo conjunto entre la Universidad Estadual de Santa Catarina con programas educativos en asentamientos de la reforma Agraria y puntualmente desarrolla el trabajo concreto de planificación de la enseñanza de la lengua española remitiéndonos a referentes teóricos y empíricos que han sustentado este trabajo tales como el mismo educador Pistrak en la revolución rusa, referente que sirve de sustento en la praxis de las escuelas del MST. Palabras claves: enseñanza de la lengua española, idioma español como problema cultural y político, internacionalismo

  9. A field trial of a PCR-based Mansonella ozzardi diagnosis assay detects high-levels of submicroscopic M. ozzardi infections in both venous blood samples and FTA card dried blood spots.

    Science.gov (United States)

    Medeiros, Jansen Fernandes; Almeida, Tatiana Amaral Pires; Silva, Lucyane Bastos Tavares; Rubio, Jose Miguel; Crainey, James Lee; Pessoa, Felipe Arley Costa; Luz, Sergio Luiz Bessa

    2015-05-20

    Mansonella ozzardi is a poorly understood human filarial parasite with a broad distribution throughout Latin America. Most of what is known about its parasitism has come from epidemiological studies that have estimated parasite incidence using light microscopy. Light microscopy can, however, miss lighter, submicroscopic, infections. In this study we have compared M. ozzardi incidence estimates made using light microscopy, with estimates made using PCR. 214 DNA extracts made from Large Volume Venous Blood Samples (LVVBS) were taken from volunteers from two study sites in the Rio Solimões region: Codajás [n = 109] and Tefé [n = 105] and were subsequently assayed for M. ozzardi parasitism using a diagnostic PCR (Mo-dPCR). Peripheral finger-prick blood samples were taken from the same individuals and used for microscopic examination. Finger-prick blood, taken from individuals from Tefé, was also used for the creation of FTAcard dried blood spots (DBS) that were subsequently subjected to Mo-dPCR. Overall M. ozzardi incidence estimates made with LVVBS PCRs were 1.8 times higher than those made using microscopy (44.9% [96/214] compared with 24.3% [52/214]) and 1.5 times higher than the PCR estimates made from FTAcard DBS (48/105 versus 31/105). PCR-based detection of FTAcard DBS proved 1.3 times more sensitive at diagnosing infections from peripheral blood samples than light microscopy did: detecting 24/105 compared with 31/105. PCR of LVVBS reported the fewest number of false negatives, detecting: 44 of 52 (84.6%) individuals diagnosed by microscopy; 27 of 31 (87.1%) of those diagnosed positive from DBSs and 17 out of 18 (94.4%) of those diagnosed as positive by both alternative methodologies. In this study, Mo-dPCR of LVVBS was by far the most sensitive method of detecting M. ozzardi infections and detected submicroscopic infections. Mo-dPCR FTAcard DBS also provided a more sensitive test for M. ozzardi diagnosis than light microscopy based diagnosis did and

  10. DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract

    NARCIS (Netherlands)

    Zoetendal, E.G.; Ben-Amor, K.; Akkermans, A.D.L.; Abee, T.; Vos, de W.M.

    2001-01-01

    A major concern in molecular ecological studies is the lysis efficiency of different bacteria in a complex ecosystem. We used a PCR-based 16S rDNA approach to determine the effect of two DNA isolation protocols (i.e. the bead beating and Triton-X100 method) on the detection limit of seven

  11. Approaches for cytogenetic and molecular analyses of small flow-sorted cell populations from childhood leukemia bone marrow samples

    DEFF Research Database (Denmark)

    Obro, Nina Friesgaard; Madsen, Hans O.; Ryder, Lars Peter

    2011-01-01

    defined cell populations with subsequent analyses of leukemia-associated cytogenetic and molecular marker. The approaches described here optimize the use of the same tube of unfixed, antibody-stained BM cells for flow-sorting of small cell populations and subsequent exploratory FISH and PCR-based analyses....

  12. PCR-based plasmid typing in Enterococcus faecium strains reveals widely distributed pRE25-, pRUM-, pIP501-and pHT beta-related replicons associated with glycopeptide resistance and stabilizing toxin-antitoxin systems

    DEFF Research Database (Denmark)

    Rosvoll, T.C.S.; Pedersen, T.; Sletvold, H.

    2010-01-01

    A PCR-based typing scheme was applied to identify plasmids in an epidemiologically and geographically diverse strain collection of Enterococcus faecium (n=93). Replicon types of pRE25 (n=56), pRUM (n=41), pIP501 (n=17) and pHT beta (n=14) were observed in 83% of the strains, while pS86, pCF10, pA...

  13. Entre as FARC o MST, entre a violência no campo o Estado policial na América Latina: Aspectos distintos de conflitos agrários históricos no Brasil e Colômbia

    Directory of Open Access Journals (Sweden)

    Fernando Antonio Alves

    2012-01-01

    Full Text Available Este estudio tiene como objetivo dar una visión general de las principales luchas sociales en América Latina desarrolladas en los últimos años, particularmente en relación con disputas por la tierra, dando como resultado la aparición de dos movimientos históricos en las zonas rurales: el Movimiento de Trabajadores Rurales Sin Tierra - MST en Brasil y las FARC - Fuerzas Armadas Revolucionarias de Colombia. El objetivo del trabajo es establecer en qué medida estos movimientos surgieron en el contexto de los grupos sociales excluidos, que buscaban en el campo, a través de la lucha campesina, diversas formas de reivindicación de los derechos en diversas situaciones sociales, dando lugar a diferentes formas y diferentes grados de uso de la fuerza y la violencia en el campo. Por lo tanto, se discute hasta qué punto el conflicto social agrario dio lugar a una reacción de los poderes dentro de una realidad de clase durante un período de democratización de las naciones latinoamericanas, desde la perspectiva de los regímenes constitucionales, sentado en un Estado democrático, un policía del Estado anómalo, más que el ejercicio de los derechos fundamentales como la libertad de reunión y de asociación. Por otra parte, un proceso de creciente criminalización del MST en Brasil, como ocurre en los enfrentamientos entre el gobierno y las FARC en Colombia, contribuyendo a un proceso de militarización del aparato represivo del Estado, que no contribuye en nada al mantenimiento de la paz y la promover la inclusión social en América Latina.

  14. What can we learn from the network approach in finance?

    Science.gov (United States)

    Janos, Kertesz

    2005-03-01

    Correlations between variations of stock prices reveal information about relationships between companies. Different methods of analysis have been applied to such data in order to uncover the taxonomy of the market. We use Mantegna's miminum spanning tree (MST) method for daily data in a dynamic way: By introducing a moving window we study the temporal changes in the structure of the network defined by this ``asset tree.'' The MST is scale free with a significantly changing exponent of the degree distribution for crash periods, which demonstrates the restructuring of the network due to the enhancement of correlations. This approach is compared to that based on what we call ``asset graphs:'' We start from an empty graph with no edges where the vertices correspond to stocks and then, one by one, we insert edges between the vertices according to the rank of their correlation strength. We study the properties of the creatred (weighted) networks, such as topologically different growth types, number and size of clusters and clustering coefficient. Furthermore, we define new tools like subgraph intensity and coherence to describe the role of the weights. We also investigate the time shifted cross correlation functions for high frequency data and find a characteristic time delay in many cases representing that some stocks lead the price changes while others follow them. These data can be used to construct a directed network of influence.

  15. A novel library-independent approach based on high-throughput cultivation in Bioscreen and fingerprinting by FTIR spectroscopy for microbial source tracking in food industry.

    Science.gov (United States)

    Shapaval, V; Møretrø, T; Wold Åsli, A; Suso, H P; Schmitt, J; Lillehaug, D; Kohler, A

    2017-05-01

    Microbiological source tracking (MST) for food industry is a rapid growing area of research and technology development. In this paper, a new library-independent approach for MST is presented. It is based on a high-throughput liquid microcultivation and FTIR spectroscopy. In this approach, FTIR spectra obtained from micro-organisms isolated along the production line and a product are compared to each other. We tested and evaluated the new source tracking approach by simulating a source tracking situation. In this simulation study, a selection of 20 spoilage mould strains from a total of six genera (Alternaria, Aspergillus, Mucor, Paecilomyces, Peyronellaea and Phoma) was used. The simulation of the source tracking situation showed that 80-100% of the sources could be correctly identified with respect to genus/species level. When performing source tracking simulations, the FTIR identification diverged for Phoma glomerata strain in the reference collection. When reidentifying the strain by sequencing, it turned out that the strain was a Peyronellaea arachidicola. The obtained results demonstrated that the proposed approach is a versatile tool for identifying sources of microbial contamination. Thus, it has a high potential for routine control in the food industry due to low costs and analysis time. The source tracking of fungal contamination in the food industry is an important aspect of food safety. Currently, all available methods are time consuming and require the use of a reference library that may limit the accuracy of the identification. In this study, we report for the first time, a library-independent FTIR spectroscopic approach for MST of fungal contamination along the food production line. It combines high-throughput microcultivation and FTIR spectroscopy and is specific on the genus and species level. Therefore, such an approach possesses great importance for food safety control in food industry. © 2016 The Society for Applied Microbiology.

  16. Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

    DEFF Research Database (Denmark)

    Solassol, Jérôme; Vendrell, Julie; Märkl, Bruno

    2016-01-01

    , was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE...

  17. Redes de dominação e conflitos no campo: uma problematização da análise sobre o Movimento dos Trabalhadores Rurais Sem-Terra (MST

    Directory of Open Access Journals (Sweden)

    Wagner Venceslau Dias

    1997-06-01

    Full Text Available O objetivo deste texto é adequar a noção de redes de dominação às formas de sujeição dos camponeses ao modo de organização política e social da estrutura fundiária no Brasil. Para isso, serão repassados aspectos de trabalhos de alguns pensadores destas realidades históricas, em suas mais diferentes formas, seguindo um percurso dentro da história brasileira, chegando à atual posição de luta pela tera e da chamada Reforma Agrária, proposta pelo Movimento dos Trabalhadores Rurais Sem-Terra (MST. Portanto, pretende-se entender a rede que amarra ou disciplina as lutas sociais no campo, mesmo quando ela aparece de maneira mais moderna e eficaz; procurar-se-á evidenciar questões políticas postas em jogo, como as da mediação, partidarização e sindicalização no campo.

  18. Vinte anos do MST: a psicologia nesta história Veinte años de lo movimiento de los trabajadores rurales sin tierra: la psicología en esta historia Landless peasants’ movement after twenty years: psychology and the movement’s history

    Directory of Open Access Journals (Sweden)

    Eliane Domingues

    2007-12-01

    Full Text Available O Movimento dos Trabalhadores Rurais Sem Terra (MST completou vinte anos em 2004. Ao longo de sua existência vem despertando o interesse de pesquisadores de diversas áreas, principalmente da Educação e da Sociologia. No entanto, ainda existem poucos trabalhos na Psicologia sobre o MST. Mapear a produção científica geral sobre o MST e analisar a produção específica da Psicologia sobre esta temática é o que se propôs esta pesquisa. Com esse objetivo, foi realizada uma busca online no banco de teses da Capes, abrangendo o período de 1987 a 2004. Todos os resumos encontrados foram impressos e categorizados. Através dos resumos foram identificadas as teses e dissertações desenvolvidas em programas de pós-graduação em Psicologia, as quais, por sua vez, foram lidas em sua totalidade, buscando-se identificar as questões orientadoras, principais resultados e conclusões das pesquisas. Destaca-se a necessidade de estudos sobre a infância, desterritorialização e sofrimento psíquico e saúde mental no campo.El movimiento de los Trabajadores Rurales Sin Tierra (MST ha cumplido veinte años en 2004. A lo largo de su existencia viene despertando el interés de los investigadores de diversas áreas, principalmente, de la Educación y Sociología. Sin embargo, aun existen pocos trabajadores en la Psicología sobre el MST. Mapear la producción científica general sobre el MST y analizar la producción específica de la Psicología, sobre esta temática es lo que se ha propuesto con esta encuesta. Con ese objetivo ha sido realizada una búsqueda online en el banco de tesis de la CAPES, abarcando el período de 1987 a 2004. Todos los resúmenes encontrados fueron impresos y puesto en categorías. A través de los resúmenes fueron identificadas las tesis y disertaciones desarrolladas en Programas de Postgrado en Psicología que, por su vez, fueron leídas en su totalidad, buscando identificar las cuestiones orientadoras, principales

  19. In-planta detection and monitorization of endophytic colonization by a Beauveria bassiana strain using a new-developed nested and quantitative PCR-based assay and confocal laser scanning microscopy.

    Science.gov (United States)

    Landa, B B; López-Díaz, C; Jiménez-Fernández, D; Montes-Borrego, M; Muñoz-Ledesma, F J; Ortiz-Urquiza, A; Quesada-Moraga, E

    2013-10-01

    Beauveria bassiana strain 04/01-Tip obtained from larvae of the opium poppy stem gall Iraella luteipes endophytically colonizes opium poppy plants and protect it against this pest. Development of a specific, rapid and sensitive technique that allows accurately determining the process and factors leading to the establishment of this strain in opium poppy plants would be essential to achieve its efficient control in a large field scale. For that purpose in the present study, species-specific primers that can be used in conventional or quantitative PCR protocols were developed for specifically identification and detection of B. bassiana in plant tissues. The combination of the designed BB.fw/BB.rv primer set with the universal ITS1-F/ITS4 primer set in a two-step nested-PCR approach, has allowed the amplification of up to 10fg of B. bassiana. This represented an increase in sensitivity of 10000- and 1000-fold of detection than when using the BB.fw/BB.rv primers in a single or single-tube semi-nested PCR approaches, respectively. The BB.fw and BB.rv primer set were subsequently optimized to be used in real time quantitative PCR assays and allowed to accurately quantify B. bassiana DNA in different plant DNA backgrounds (leaves and seeds) without losing accuracy and efficiency. The qPCR protocol was used to monitor the endophytic colonization of opium poppy leaves byB. bassiana after inoculation with the strain EABb 04/01-Tip, detecting as low as 26fg of target DNA in leaves and a decrease in fungal biomass over time. PCR quantification data were supported in parallel with CLMS by the monitoring of spatial and temporal patterns of leaf and stem colonization using a GFP-tagged transformant of the B. bassiana EABb 04/01-Tip strain, which enabled to demonstrate that B. bassiana effectively colonizes aerial tissues of opium poppy plants mainly through intercellular spaces and even leaf trichomes. A decline in endophytic colonization was also observed by the last sampling

  20. Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

    Directory of Open Access Journals (Sweden)

    Puisieux Alain

    2003-10-01

    Full Text Available Abstract Background Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. Results We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC in peripheral blood mononuclear cells; the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. Conclusion Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting.

  1. Complexity of major UK companies between 2006 and 2010: Hierarchical structure method approach

    Science.gov (United States)

    Ulusoy, Tolga; Keskin, Mustafa; Shirvani, Ayoub; Deviren, Bayram; Kantar, Ersin; Çaǧrı Dönmez, Cem

    2012-11-01

    This study reports on topology of the top 40 UK companies that have been analysed for predictive verification of markets for the period 2006-2010, applying the concept of minimal spanning tree and hierarchical tree (HT) analysis. Construction of the minimal spanning tree (MST) and the hierarchical tree (HT) is confined to a brief description of the methodology and a definition of the correlation function between a pair of companies based on the London Stock Exchange (LSE) index in order to quantify synchronization between the companies. A derivation of hierarchical organization and the construction of minimal-spanning and hierarchical trees for the 2006-2008 and 2008-2010 periods have been used and the results validate the predictive verification of applied semantics. The trees are known as useful tools to perceive and detect the global structure, taxonomy and hierarchy in financial data. From these trees, two different clusters of companies in 2006 were detected. They also show three clusters in 2008 and two between 2008 and 2010, according to their proximity. The clusters match each other as regards their common production activities or their strong interrelationship. The key companies are generally given by major economic activities as expected. This work gives a comparative approach between MST and HT methods from statistical physics and information theory with analysis of financial markets that may give new valuable and useful information of the financial market dynamics.

  2. Assessment of statistical methods used in library-based approaches to microbial source tracking.

    Science.gov (United States)

    Ritter, Kerry J; Carruthers, Ethan; Carson, C Andrew; Ellender, R D; Harwood, Valerie J; Kingsley, Kyle; Nakatsu, Cindy; Sadowsky, Michael; Shear, Brian; West, Brian; Whitlock, John E; Wiggins, Bruce A; Wilbur, Jayson D

    2003-12-01

    Several commonly used statistical methods for fingerprint identification in microbial source tracking (MST) were examined to assess the effectiveness of pattern-matching algorithms to correctly identify sources. Although numerous statistical methods have been employed for source identification, no widespread consensus exists as to which is most appropriate. A large-scale comparison of several MST methods, using identical fecal sources, presented a unique opportunity to assess the utility of several popular statistical methods. These included discriminant analysis, nearest neighbour analysis, maximum similarity and average similarity, along with several measures of distance or similarity. Threshold criteria for excluding uncertain or poorly matched isolates from final analysis were also examined for their ability to reduce false positives and increase prediction success. Six independent libraries used in the study were constructed from indicator bacteria isolated from fecal materials of humans, seagulls, cows and dogs. Three of these libraries were constructed using the rep-PCR technique and three relied on antibiotic resistance analysis (ARA). Five of the libraries were constructed using Escherichia coli and one using Enterococcus spp. (ARA). Overall, the outcome of this study suggests a high degree of variability across statistical methods. Despite large differences in correct classification rates among the statistical methods, no single statistical approach emerged as superior. Thresholds failed to consistently increase rates of correct classification and improvement was often associated with substantial effective sample size reduction. Recommendations are provided to aid in selecting appropriate analyses for these types of data.

  3. PCR-based clonality assessment in patients with lymphocytic ...

    Indian Academy of Sciences (India)

    study was to assess the clinical benefits of clonality testing with previously evaluated .... with the samples, negative controls containing no DNA were ..... 2003 Standardization and quality con- ... In Molecular cloning, a laboratory manual (ed.

  4. Microscopic identification and PCR based assay in feed analysis

    Directory of Open Access Journals (Sweden)

    G. Savoini

    2011-03-01

    Full Text Available which 20% is manufactured compound feed (Brookes, 2001. This production level imposes an adequate high quality standards especially with regard to the EU Commission’s ban on the use of processed animal proteins. From this point of view a complete separation of plants dedicated to feed production from plants processing raw material, stretcher rules for traceability of animal by-products, as well as feed analysis and feed inspection of raw material or compound feed, are all critical points in food safety. In a previous study (Pinotti et al., 2002 it was suggested that higher protein level in compound feed could be a risk factor for low level cross contamination with meat and bone meal. This could be associated with the same route followed by protein sources, in the feed processing/manufacturing (collection, transport, milling, etc...........

  5. Internal quality control of PCR-based genotyping methods

    DEFF Research Database (Denmark)

    Bladbjerg, Else-Marie; Gram, Jørgen; Jespersen, Jørgen

    2002-01-01

    Internal quality control programmes for genetic analyses are needed. We have focused on quality control aspects of selected polymorphism analyses used in thrombosis research. DNA was isolated from EDTA-blood (n = 500) and analysed for 18 polymorphisms by polymerase chain reaction (PCR), i...... because of positive reagent blanks (controls (Control of data handling revealed 0.1% reading mistakes and 0.5% entry mistakes. Based on our experiences, we propose an internal quality control programme......, electrophoresis (analytical factors), result reading and entry into a database (post-analytical factors). Furthermore, we evaluated a procedure for result confirmation. Isolated DNA was of good quality (42 micrograms/ml blood, A260/A280 ratio > 1.75, negative DNAsis tests). Occasionally, results were reanalysed...

  6. Quality control for quantitative PCR based on amplification compatibility test

    Czech Academy of Sciences Publication Activity Database

    Tichopád, Aleš; Bar, T.; Pecen, Ladislav; Kitchen, R.R.; Kubista, Mikael; Pfaffl, M.W.

    2010-01-01

    Roč. 50, č. 4 (2010), s. 308-312 ISSN 1046-2023 R&D Projects: GA AV ČR IAA500520809; GA AV ČR IAA500970904 Institutional research plan: CEZ:AV0Z50520701 Keywords : Quantitative PCR * Quality control * Amplification efficiency Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.527, year: 2010

  7. Long-term MST radar observations of vertical wave number spectra of gravity waves in the tropical troposphere over Gadanki (13.5° N, 79.2° E: comparison with model spectra

    Directory of Open Access Journals (Sweden)

    S. Vijaya Bhaskara Rao

    2008-06-01

    Full Text Available The potential utility of Mesosphere-Stratosphere-Troposphere (MST radar measurements of zonal, meridional and vertical winds for divulging the gravity wave vertical wave number spectra is discussed. The data collected during the years 1995–2004 are used to obtain the mean vertical wave number spectra of gravity wave kinetic energy in the tropical troposphere over Gadanki (13.5° N, 79.2° E. First, the climatology of 3-dimensional wind components is developed using ten years of radar observations, for the first time, over this latitude. This climatology brought out the salient features of background tropospheric winds over Gadanki. Further, using the second order polynomial fit as background, the day-to-day wind anomalies are estimated. These wind anomalies in the 4–14 km height regions are used to estimate the profiles of zonal, meridional and vertical kinetic energy per unit mass, which are then used to estimate the height profile of total kinetic energy. Finally, the height profiles of total kinetic energy are subjected to Fourier analysis to obtain the monthly mean vertical wave number spectra of gravity wave kinetic energy. The monthly mean vertical wave number spectra are then compared with a saturation spectrum predicted by gravity wave saturation theory. A slope of 5/3 is used for the model gravity wave spectrum estimation. In general, the agreement is good during all the months. However, it is noticed that the model spectrum overestimates the PSD at lower vertical wave numbers and underestimates it at higher vertical wave numbers, which is consistently observed during all the months. The observed discrepancies are attributed to the differences in the slopes of theoretical and observed gravity wave spectra. The slopes of the observed vertical wave number spectra are estimated and compared with the model spectrum slope, which are in good agreement. The estimated slopes of the observed monthly vertical wave number spectra are in the

  8. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    Science.gov (United States)

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.

  9. Diagnosis of Lower Hybrid on MST

    International Nuclear Information System (INIS)

    Burke, D. R.; Goetz, J. A.; Kaufman, M. C.; Almagri, A. F.; Anderson, J. K.; Forest, C. B.; Prager, S. C.

    2007-01-01

    RF driven current has never been demonstrated in a Reversed Field Pinch. Recently the lower hybrid system on the Madison Symmetric Torus reached a new operating regime. This upgrade allows RF powers of up to 5% of the Ohmic input power to be injected. It is therefore anticipated that the lower hybrid system is on the threshold of producing meaningful changes to the RFP equilibrium. A diagnostic set is under development to facilitate the study of such changes and lay the foundation for near megawatt operations. Many measurements are being studied for viability. These include electron cyclotron emission, examinations of bulk ion and electron heating, surface perturbation pickup coils, magnetic probe measurements, and Langmuir probe measurements. In addition, several x-ray diagnostics are in operation: pulse height analysis is performed on detector arrays to determine the 5-200 keV spectrum. An insertable target probe is available to create x-rays from fast electrons. Tomographic inversion of 2-D Soft x-ray detectors yields equilibrium information through island structure. Results from experiments with source power up to 225 kW will be presented. Preliminary results from CQL3D Fokker-Planck simulations will also be presented

  10. Vad är den främst avgörande faktorn vid privatkundens val av marginalbank? : en studie om hur demografiska skillnader påverkar privatkunders val av marginalbank samt se hur deras val kan användas vid segmentering

    OpenAIRE

    Lindh, Jenni; Persson, Frida

    2012-01-01

    Syfte: Syftet med detta examensarbete är att förklara vad som är den främst avgörande faktorn vid privatkundens val av marginalbank, genom att jämföra med demografiska variabler samt hur deras val kan användas vid segmentering. Dessutom vill vi titta på vilka typer av banker privatkunder har. Metod: För att nå fram till resultat för analysen har ett positivistiskt angreppssätt och en deduktiv ansats använts. Det empiriska materialet är baserat på en enkätundersökning gjord på personer i Hässl...

  11. Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

    Directory of Open Access Journals (Sweden)

    Warish Ahmed

    2016-05-01

    Full Text Available Microbial source tracking (MST endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or “markers” of sewage pollution, including known advantages and deficiencies of the many polymerase chain reaction (PCR-based methods that have been published since 2000. Host specificity is a paramount criterion for confidence that detection of a marker is a true indicator of the target host. Host sensitivity, or the prevalence of the marker in feces/waste from the target host, is necessary for confidence that absence of the marker is indicative of the absence of the pollution source. Each of these parameters can vary widely depending on the type of waste assessed and the geographic location. Differential decay characteristics of bacterial targets and their associated DNA contribute to challenges in interpreting MST results in the context of human health risks. The HF183 marker, derived from the 16S rRNA gene of Bacteroides dorei and closely related taxa, has been used for almost two decades in MST studies, and is well characterized regarding host sensitivity and specificity, and in prevalence and concentration in sewage in many countries. Other markers such as HumM2 and HumM3 show promise, but require further performance testing to demonstrate their widespread utility. An important limitation of the one-marker-one-assay approach commonly used for MST is that given the complexities of microbial persistence in environmental waters, and

  12. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

    Science.gov (United States)

    Côté, Nathalie M L; Daligault, Julien; Pruvost, Mélanie; Bennett, E Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.

  13. Reação em Cadeia da Polimerase (PCR baseada no gene cpx para detecção de Actinobacillus pleuropneumoniae em suínos natural e experimentalmente infectados Polymerase Chain Reaction (PCR based on the cpx gene for detection of Actinobacillus pleuropneumoniae in natural and experimentally infected pigs

    Directory of Open Access Journals (Sweden)

    Karina Koerich de Souza

    2008-10-01

    Full Text Available A pleuropneumonia suína é uma das mais importantes doenças respiratórias dos suínos, estando presente em todos os países produtores. Para o controle e o monitoramento da pleuropneumonia, é necessário o desenvolvimento de métodos rápidos e acurados de diagnóstico. Com o objetivo de validar a técnica da PCR, baseada no gene cpx de Actinobacillus pleuropneumoniae, em suínos sabidamente positivos, primeiramente foi realizada inoculação experimental com amostras de A. pleuropneumoniae sorotipo 5B e coletadas amostras por meio de suabe de tonsila, biópsia de tonsila e sangue para realização da técnica de PCR, isolamento bacteriológico e teste de ELISA, respectivamente. Posteriormente, estas técnicas foram aplicadas em suínos naturalmente infectados, em três rebanhos com diferentes situações sanitárias quanto à apresentação clínica da doença. De cada rebanho, foram analisados cinco grupos de suínos com idades diferentes, sendo coletado de cada animal biópsia de tonsila para isolamento bacteriológico e PCR e sangue para determinação do perfil sorológico. Os resultados obtidos na inoculação experimental confirmaram que, mesmo com o estabelecimento da infecção comprovada pelo isolamento bacteriológico, após o período de 45 dias, não foi possível detectar o agente pela técnica de PCR. Em animais naturalmente infectados, a técnica de PCR apresentou maior sensibilidade quando comparado com o isolamento. A associação entre PCR e ELISA demonstrou ser uma boa alternativa para definir a situação sanitária do rebanho quanto à infecção por A. pleuropneumoniae.Swine pleuropneumonia is one of the most important pig respiratory diseases and has been found in all producer countries. For control and monitoring of pleuropneumonia, it is necessary the development of fast and specific methods of diagnosis. To validate PCR based on the cpx gene of Actinobacillus pleuropneumoniae in positive pigs, an experimental

  14. Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage

    Directory of Open Access Journals (Sweden)

    Tomáš ePánek

    2015-11-01

    Full Text Available We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida, an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids - 60 % or 80 %, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists – Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.

  15. Multiplex PCR from Menstrual Blood: A Non-Invasive Cost-Effective Approach to Reduce Diagnostic Dilemma for Genital Tuberculosis.

    Science.gov (United States)

    Paine, Suman K; Basu, Analabha; Choudhury, Rajib Gon; Bhattacharya, Basudev; Chatterjee, Sidhartha; Bhattacharya, Chandra

    2018-03-16

    Genital tuberculosis (GTB) is a potent contributor to irreversible damage to the reproductive system and infertility in females. As no gold standard diagnostic tool is yet available, clinical suspicion and relatively insensitive approaches such as histopathology, laparoscopy and hysterosalpingogram are currently critical determinants in the diagnosis of GTB. Although a polymerase chain reaction (PCR)-based assay using endometrial tissue seems promising, sampling does require an invasive procedure. We hypothesized that menstrual blood may provide an alternate non-invasive source of samples for PCR-based GTB diagnosis. We enrolled 195 women with primary infertility in whom GTB was suspected. We obtained ethics committee approval from our institution and written informed consent from subjects. Endometrial tissue and menstrual blood was collected from the subjects and culture, histopathology, and multiplex PCR with both sample type was performed for each subject. The sensitivity and specificity of multiplex PCR was, respectively, 90.2 and 86.1% for menstrual blood, 95.8 and 84.3% for endometrial tissue, and 64.8 and 93.2% for histopathology staining. A strong clinical suspicion aided with multiplex PCR using menstrual blood may significantly reduce the diagnostic dilemma for GTB diagnosis in a non-invasive, sensitive, rapid, and cost-effective manner.

  16. Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?

    Science.gov (United States)

    Dib, Julián R.; Wagenknecht, Martin; Farías, María E.; Meinhardt, Friedhelm

    2015-01-01

    The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions. PMID:26074886

  17. Investigation of Alternative Approaches for Cleaning Mott Porous Metal Filters

    International Nuclear Information System (INIS)

    Poirier, M.R.

    2003-01-01

    The Department of Energy selected Caustic Side Solvent Extraction (CSSX) as the preferred cesium removal technology for Savannah River Site (SRS) waste. As a pretreatment step for the CSSX flowsheet, the incoming salt solution that contains entrained sludge is contacted with monosodium titanate (MST) to adsorb strontium and select actinides. The resulting slurry is filtered to remove the sludge and MST. Filter fouling occurs during this process. At times, personnel can increase the filtrate rate by backpulsing or scouring. At other times, the filtrate rate drops significantly and only chemical cleaning will restore filter performance. The current baseline technology for filter cleaning uses 0.5 M oxalic acid. The Salt Processing Project (SPP) at SRS, through the Tanks Focus Area, requested an evaluation of other cleaning agents to determine their effectiveness at removing trapped sludge and MST solids compared with the baseline oxalic acid method. A review of the technical literature identified compounds that appear effective at dissolving solid compounds. Consultation with the SPP management team, engineering personnel, and researchers led to a selection of oxalic acid, nitric acid, citric acid, and ascorbic acid for testing. Tests used simulated waste and actual waste as follows. Personnel placed simulated or actual SRS High Level Waste sludge and MST in a beaker. They added the selected cleaning agents, stirred the beakers, and collected supernate samples periodically analyzing for dissolved metals

  18. Detecting false positive sequence homology: a machine learning approach.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Bybee, Seth M

    2016-02-24

    Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

  19. A collimated neutron detector for RFP plasmas in MST

    Energy Technology Data Exchange (ETDEWEB)

    Capecchi, W. J., E-mail: capecchi@wisc.edu; Anderson, J. K.; Bonofiglo, P. J.; Kim, J.; Sears, S. [University of Wisconsin- Madison, Madison, Wisconsin 53706 (United States)

    2016-11-15

    The neutron emissivity profile in the Madison Symmetric Torus is being reconstructed through the use of a collimated neutron detector. A scintillator-photomultiplier tube (PMT) system is employed to detect the fusion neutrons with the plasma viewing volume defined by a 55 cm deep, 5 cm diameter aperture. Effective detection of neutrons from the viewing volume is achieved through neutron moderation using 1300 lbs of high density polyethylene shielding, which modeling predicts attenuates the penetrating flux by a factor of 10{sup 4} or more. A broad spectrum of gamma radiation is also present due to the unconfined fusion proton bombardment of the thick aluminum vacuum vessel. A 15 cm cylindrical liquid scintillator of 3.8 cm diameter is used to further increase directional sensitivity. A fast (5 ns rise time) preamplifier and digitization at 500 MHz prevent pulse pile-up even at high count rates (∼10{sup 4}/s). The entire neutron camera system is situated on an adjustable inclining base which provides the differing plasma viewing volumes necessary for reconstruction of the neutron emissivity profile. This profile, directly related to the fast-ion population, allows for an investigation of the critical fast-ion pressure gradient required to destabilize a neutral beam driven Alfvénic mode which has been shown to transport fast ions.

  20. Radio frequency wave experiments on the MST reversed field pinch

    International Nuclear Information System (INIS)

    Forest, C.B.; Chattopadhyay, P.K.; Nornberg, M.D.; Prager, S.C.; Thomas, M.A.; Harvey, R.W.; Ram, A.K.

    1999-04-01

    Experiments, simulations, and theory all indicate that the magnetic fluctuations responsible for the poor confinement in the reversed field pinch (RFP) can be controlled by altering the radial profile of the current density. The magnetic fluctuations in the RFP are due to resistive MHD instabilities caused by current profile peaking; thus confinement in the RFP is ultimately the result of a misalignment between inductively driven current profiles and the stable current profiles characteristic of the Taylor state. If a technique such as rf current drive can be developed to non-inductively sustain a Taylor state (a current profile linearly stable to all tearing modes), the confinement of the RFP and its potential as a reactor concept are likely to increase. Whether there is a self-consistent path from poor confinement to greatly improved confinement through current profile modification is an issue for future experiments to address if and only if near term experiments can demonstrate: (1) coupling to and the propagation of rf waves in RFP plasmas, (2) efficient current drive, and (3) control of the power deposition which will make it possible to control the current profile. In this paper, modeling results and experimental plans are presented for two rf experiments which have the potential of satisfying these three goals: high-n parallel lower hybrid (LH) waves and electron Bernstein waves (EBWs)

  1. Phased-array design for MST and ST radars

    Science.gov (United States)

    Ecklund, W. L.

    1986-01-01

    All of the existing radar systems fully dedicated to clear-air radar studies use some type of phased-array antennas. The effects of beam-steering techniques including feed networks and phase shifters; sidelobe control; ground-clutter suppression; low altitude coverage; arrays with integrated radiating elements and feed networks; analysis of coaxial-collinear antennas; use of arrays with multiple beams; and array testing and measure on structural design of the antenna are discussed.

  2. Pedagogical approaches

    DEFF Research Database (Denmark)

    Lund Larsen, Lea

    questions are: How (much) and what do teachers learn from experience? And how do teachers of adults develop their pedagogical approach? I examine the field of adult learners from the teachers’ perspective. Firstly, I identify some of the commonly described characteristics of adults as learners...... in formal settings, but in most teaching settings, the teachers act alone and develop their pedagogical approaches/- teaching strategies with no synchronous sparring from a colleague. Adult learners have particular needs and characteristics that their teachers must be able to address (cf. Knowles...

  3. Capability approach

    DEFF Research Database (Denmark)

    Jensen, Niels Rosendal; Kjeldsen, Christian Christrup

    Lærebogen er den første samlede danske præsentation af den af Amartya Sen og Martha Nussbaum udviklede Capability Approach. Bogen indeholder en præsentation og diskussion af Sen og Nussbaums teoretiske platform. I bogen indgår eksempler fra såvel uddannelse/uddannelsespolitik, pædagogik og omsorg....

  4. Materials Science and Technology (MST) Division, Nuclear Materials Process Technology Group (MST-12), chemical process research and development report

    International Nuclear Information System (INIS)

    Clifton, D.G.

    1984-04-01

    A process for the recovery of plutonium and americium from molten salt extraction (MSE) salt residues has been demonstrated. It is based upon a new chloride anion-exchange process at low acidity that eliminates corrosive HCl fumes. The Los Alamos americium oxide production line has been improved to give more product with a concurrent lowering of personnel radiation exposure. A cost study has been made for the disposal of americium-contaminated calcium metal buttons that were obtained by pyrochemical recovery of plutonium from MSE salts. The waste form used in the study conforms to WIPP-Facility standards and current state-of-the-art radioactive waste disposal. The cost estimate is approx. $300/g 241 Am. Plutonium decontamination factors of approx. 300 have been obtained from lead-platinum alloy dissolution experiments carried out in alumina crucibles using lead oxide slag to getter the plutonium

  5. mställdhet : definitioner, attityder och jämställdhetsåtgärder i praktiken

    OpenAIRE

    Wistus, Sofia

    2002-01-01

    The object of this essay is to discuss the relationship between the definition of the concept of gender equality and attitudes towards gender equality and their consequences for gender equality measures. The point of departure is feminist political theory and interviews about attitudes towards gender equality at a department at the University of Linköping. The conclusions of this study is that there are a wide range of definitions and attitudes, and these conceptions are not necessarily the s...

  6. The Technical Course in Cooperatives by PRONERA: an analysis based on the People’s Capabilities Approach

    Directory of Open Access Journals (Sweden)

    Conceição Coutinho Melo

    2018-02-01

    Full Text Available This paper presents results from a research about the Cooperatives Thechnical Course (TAC, originated in the 90’s after a need of the MST for forming technical staff for working in cooperatives located in rural settlements as part of the Land Reform. Nowadays, the course is taught through the National Program of Education within the Land Reform (PRONERA, under the paradigm of Rural Education. Rural Education is understood as one of the motivations for the rural development, from a multidimensional viewpoint. Therefore, a challenging dialogue between Economy and Rural Education emerged, and contributed to a field little explored under the aegis of the People’s Capabilities Approach. In such approach, developed by the Indian Amartya Sen, development is seen as people’s capabilities expansion for living the lives they yearn, where monetary income is not essential for the well-being, but other variables (education, health, political liberty, etc.. The goal in this research was to investigate if the TAC contributes to the expansion of capabilities of its graduates and to the development of rural settlements. All the people interviewed graduated, and after that, worked in entities related to rural settlements. The TAC has contributed to the graduates’ liberty expansion.

  7. A PCR-based survey of selected Babesia and Theileria parasites in cattle in Sri Lanka.

    Science.gov (United States)

    Sivakumar, Thillaiampalam; Kothalawala, Hemal; Abeyratne, Sembukutti Arachchige Eranga; Vimalakumar, Singarayar Caniciyas; Meewewa, Asela Sanjeewa; Hadirampela, Dilhani Thilanka; Puvirajan, Thamotharampillai; Sukumar, Subramaniyam; Kuleswarakumar, Kulanayagam; Chandrasiri, Alawattage Don Nimal; Igarashi, Ikuo; Yokoyama, Naoaki

    2012-11-23

    Hemoprotozoan parasites are responsible for significant economic losses in cattle. We screened Sri Lankan cattle populations for the presence of Babesia bovis, Babesia bigemina, Theileria annulata, and Theileria orientalis, using species-specific PCR assays. Out of 316 samples collected from animals in four different districts of Sri Lanka (Nuwara Eliya, Polonnaruwa, Ampara, and Jaffna), 231 (73.1%) were positive for at least one parasite species. All four parasite species were detected among the study groups from all of the districts surveyed. The first and second commonest hemoprotozoan parasites identified were T. orientalis (53.5%) and B. bigemina (30.1%), respectively. We found that the dry zones (Polonnaruwa, Ampara, and Jaffna) had more Babesia-positive animals than the hill country wet zone (Nuwara Eliya). In contrast, T. orientalis was the predominant species detected in Nuwara Eliya, while infection with T. annulata was more common in the dry zones. In addition, 81 (35.1%) of the 231 positive samples were infected with more than one parasite species. The presence of multiple parasite species among the different cattle populations is of clinical and economic significance. Therefore, island-wide control and prevention programs against bovine babesiosis and theileriosis are needed to minimize the financial burden caused by these parasites. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses

    Science.gov (United States)

    Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R.

    2012-01-01

    Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. PMID:23029501

  9. Review: Diagnostic accuracy of PCR-based detection tests for Helicobacter Pylori in stool samples.

    Science.gov (United States)

    Khadangi, Fatemeh; Yassi, Maryam; Kerachian, Mohammad Amin

    2017-12-01

    Although different methods have been established to detect Helicobacter pylori (H. pylori) infection, identifying infected patients is an ongoing challenge. The aim of this meta-analysis was to provide pooled diagnostic accuracy measures for stool PCR test in the diagnosis of H. pylori infection. In this study, a systematic review and meta-analysis were carried out on various sources, including MEDLINE, Web of Sciences, and the Cochrane Library from April 1, 1999, to May 1, 2016. This meta-analysis adheres to the guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses report (PRISMA Statement). The clinical value of DNA stool PCR test was based on the pooled false positive, false negative, true positive, and true negative of different genes. Twenty-six of 328 studies identified met the eligibility criteria. Stool PCR test had a performance of 71% (95% CI: 68-73) sensitivity, 96% (95% CI: 94-97) specificity, and 65.6 (95% CI: 30.2-142.5) diagnostic odds ratio (DOR) in diagnosis of H. pylori. The DOR of genes which showed the highest performance of stool PCR tests was as follows: 23S rRNA 152.5 (95% CI: 55.5-418.9), 16S rRNA 67.9 (95%CI: 6.4-714.3), and glmM 68.1 (95%CI: 20.1-231.7). The sensitivity and specificity of stool PCR test are relatively in the same spectrum of other diagnostic methods for the detection of H. pylori infection. In descending order of significance, the most diagnostic candidate genes using PCR detection were 23S rRNA, 16S rRNA, and glmM. PCR for 23S rRNA gene which has the highest performance could be applicable to detect H. pylori infection. © 2017 John Wiley & Sons Ltd.

  10. A PCR-based epidemiological survey of Hepatozoon canis in dogs in Nigeria.

    Science.gov (United States)

    Sasaki, Mizuki; Omobowale, Olutayo; Ohta, Kaisaku; Tozuka, Morito; Matsuu, Aya; Hirata, Haruyuki; Nottidge, Helen Oyebukola; Ikadai, Hiromi; Oyamada, Takashi

    2008-07-01

    The prevalence of Hepatozoon canis infections in dogs in Nigeria was surveyed using molecular methods. DNA was extracted from blood samples obtained from 400 dogs. A primer set that amplified the Babesia canis 18S rRNA gene, which has high similarity to the H. canis 18S rRNA gene, was used for the PCR. As a result, samples from 81 dogs (20.3%) produced 757 bp bands, which differed from the 698 bp band that corresponded to B. canis infection. The sequence of the PCR products of 10 samples were determined, all of which corresponded with the H. canis sequence.

  11. Comparison of three PCR-based assays for SNP genotyping in sugar beet

    Science.gov (United States)

    Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved t...

  12. PCR-based method for the rapid identification of astaxanthin-accumulating yeasts (Phaffia spp.).

    Science.gov (United States)

    Colabella, Fernando; Libkind, Diego

    2016-01-01

    It has been recently found that the natural distribution, habitat, and genetic diversity of astaxanthin-producing yeasts (i.e. Phaffia rhodozyma, synonym Xanthophyllomyces dendrorhous) is much greater than previously thought. P. rhodozyma is biotechnologically exploited due to its ability to produce the carotenoid pigment astaxanthin and thus, it is used as a natural source of this pigment for aquaculture. P. rhodozyma was also capable of synthesizing the potent UVB sunscreen mycosporine-glutaminol-glucoside (MGG). Therefore, further environmental studies are needed to elucidate its ecological aspects and detect new potential strains for the production of astaxanthin and MGG. However, obtaining new isolates of P. rhodozyma and related species is not always easy due to its low abundance and the presence of other sympatric and pigmented yeasts. In this work we report a successful development of a species-specific primer which has the ability to quickly and accurately detecting isolates representing all known lineages of the genus Phaffia (including novel species of the genus) and excluding closely related taxa. For this purpose, a primer of 20 nucleotides (called PhR) was designed to be used in combination with universal primers ITS3 and NL4 in a multiplex amplification. The proposed method has the sensitivity and specificity required for the precise detection of new isolates, and therefore represents an important tool for the environmental search for novel astaxanthin-producing yeasts. Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  13. The PCR based technique RAPD is popular not only because it ...

    African Journals Online (AJOL)

    renu.bhatnagar

    2015-04-01

    Apr 1, 2015 ... preliminary screening for their ability to produce clear and reproducible patterns of multiple bands. ... Exeter Biological Software, Setauket, NY, Rohlf, 1993). The. SIMQUAL program was used to calculate ... was obtained from this test which provided one measure of relatedness between the two matrices.

  14. Use of PCR based technologies for risk assessment of a winter ...

    African Journals Online (AJOL)

    Toxic freshwater cyanobacterial blooms are potential health hazards in water supply reservoirs and therefore predicting bloom events is an important goal of monitoring fresh water programmes. The recent identification of the mcy genes in the production of microcystin synthetase for the first time provides an avenue to study ...

  15. The PCR-Based Diagnosis of Central Nervous System Tuberculosis: Up to Date

    Directory of Open Access Journals (Sweden)

    Teruyuki Takahashi

    2012-01-01

    Full Text Available Central nervous system (CNS tuberculosis, particularly tuberculous meningitis (TBM, is the severest form of Mycobacterium tuberculosis (M.Tb infection, causing death or severe neurological defects in more than half of those affected, in spite of recent advancements in available anti-tuberculosis treatment. The definitive diagnosis of CNS tuberculosis depends upon the detection of M.Tb bacilli in the cerebrospinal fluid (CSF. At present, the diagnosis of CNS tuberculosis remains a complex issue because the most widely used conventional “gold standard” based on bacteriological detection methods, such as direct smear and culture identification, cannot rapidly detect M.Tb in CSF specimens with sufficient sensitivity in the acute phase of TBM. Recently, instead of the conventional “gold standard”, the various molecular-based methods including nucleic acid amplification (NAA assay technique, particularly polymerase chain reaction (PCR assay, has emerged as a promising new method for the diagnosis of CNS tuberculosis because of its rapidity, sensitivity and specificity. In addition, the innovation of nested PCR assay technique is worthy of note given its contribution to improve the diagnosis of CNS tuberculosis. In this review, an overview of recent progress of the NAA methods, mainly highlighting the PCR assay technique, was presented.

  16. PCR-based isolation of multigene families: lessons from the avian MHC class IIB

    Czech Academy of Sciences Publication Activity Database

    Burri, R.; Promerová, Marta; Goebel, J.; Fumagalli, L.

    2014-01-01

    Roč. 14, č. 4 (2014), s. 778-788 ISSN 1755-098X R&D Projects: GA ČR GAP505/10/1871 Institutional support: RVO:68081766 Keywords : Birds * Major histocompatibility complex * Multigene families * PCR bias Subject RIV: EG - Zoology Impact factor: 3.712, year: 2014

  17. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

    OpenAIRE

    Aljanabi, S M; Martinez, I

    1997-01-01

    A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

  18. Novel extraction strategy of ribosomal RNA and genomic DNA from cheese for PCR-based investigations.

    Science.gov (United States)

    Bonaïti, Catherine; Parayre, Sandrine; Irlinger, Françoise

    2006-03-15

    Cheese microorganisms, such as bacteria and fungi, constitute a complex ecosystem that plays a central role in cheeses ripening. The molecular study of cheese microbial diversity and activity is essential but the extraction of high quality nucleic acid may be problematic: the cheese samples are characterised by a strong buffering capacity which negatively influenced the yield of the extracted rRNA. The objective of this study is to develop an effective method for the direct and simultaneous isolation of yeast and bacterial ribosomal RNA and genomic DNA from the same cheese samples. DNA isolation was based on a protocol used for nucleic acids isolation from anaerobic digestor, without preliminary washing step with the combined use of the action of chaotropic agent (acid guanidinium thiocyanate), detergents (SDS, N-lauroylsarcosine), chelating agent (EDTA) and a mechanical method (bead beating system). The DNA purification was carried out by two washing steps of phenol-chloroform. RNA was isolated successfully after the second acid extraction step by recovering it from the phenolic phase of the first acid extraction. The novel method yielded pure preparation of undegraded RNA accessible for reverse transcription-PCR. The extraction protocol of genomic DNA and rRNA was applicable to complex ecosystem of different cheese matrices.

  19. PCR-based detection of resistance genes in anaerobic bacteria isolated from intra-abdominal infections.

    Science.gov (United States)

    Tran, Chau Minh; Tanaka, Kaori; Watanabe, Kunitomo

    2013-04-01

    Little information is available on the distribution of antimicrobial resistance genes in anaerobes in Japan. To understand the background of antimicrobial resistance in anaerobes involved in intra-abdominal infections, we investigated the distribution of eight antimicrobial resistance genes (cepA, cfiA, cfxA, ermF, ermB, mefA, tetQ, and nim) and a mutation in the gyrA gene in a total of 152 organisms (Bacteroides spp., Prevotella spp., Fusobacterium spp., Porphyromonas spp., Bilophila wadsworthia, Desulfovibrio desulfuricans, Veillonella spp., gram-positive cocci, and non-spore-forming gram-positive bacilli) isolated between 2003 and 2004 in Japan. The cepA gene was distributed primarily in Bacteroides fragilis. Gene cfxA was detected in about 9 % of the Bacteroides isolates and 75 % of the Prevotella spp. isolates and did not appear to contribute to cephamycin resistance. Two strains of B. fragilis contained the metallo-β-lactamase gene cfiA, but they did not produce the protein product. Gene tetQ was detected in about 81, 44, and 63 % of B. fragilis isolates, other Bacteroides spp., and Prevotella spp. isolates, respectively. The ermF gene was detected in 25, 13, 56, 64, and 16 % of Bacteroides spp., Prevotella spp., Fusobacterium spp., B. wadsworthia, and anaerobic cocci, respectively. Gene mefA was found in only 10 % of the B. fragilis strains and 3 % of the non-B. fragilis strains. Genes nim and ermB were not detected in any isolate. Substitution at position 82 (Ser to Phe) in gyrA was detected in B. fragilis isolates that were less susceptible or resistant to moxifloxacin. This study is the first report on the distribution of resistance genes in anaerobes isolated from intra-abdominal infections in Japan. We expect that the results might help in understanding the resistance mechanisms of specific anaerobes.

  20. 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.

  1. BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

    Directory of Open Access Journals (Sweden)

    Abi S.A. Marques

    2008-01-01

    Full Text Available The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662 and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

  2. A Rapid and Inexpensive PCR-Based STR Genotyping Method for Identifying Forensic Specimens

    Science.gov (United States)

    2006-06-01

    this report) 20. Security Classif. (of this page) 21 . No. of Pages 22. Price Unclassified Unclassified 18 Form DOT F 1700.7 (8-72) Reproduction of...Promega PowerPlex 2.1 system (7) except that the buffer was 1x Amplitaq gold reaction buffer, 0.1% TritonX-100, and 0.2mM each dNTP in a 25µl final...electrophoresis were done using the PowerPlex 16 System (Promega Corp.; Madison, WI). rEsulTs ANd dIsCussION The goal of this study was to develop a simple DNA

  3. A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Baggesen, Dorte Lau; Porting, P.H.

    1999-01-01

    The purpose of the present study was to investigate the application of ready-to-go Salmonella PCR tests, based on dry chemistry, for final identification of rough presumptive Salmonella isolates. The results were compared with two different biotyping methods performed at two different laboratories......, which did not result in any DNA band. A total of 32 out of the 36 rough presumptive isolates were positive in the PCR. All but one isolate were also identified as Salmonella by the two biochemical methods. All 80 Salmonella strains were also tested in the two multiplex serogroup tests based on PCR beads....... The sensitivity of the BAX Salmonella PCR test was assessed by testing a total of 80 Salmonella isolates, covering most serogroups, which correctly identified all the Salmonella strains by resulting in one 800-bp band in the sample tubes. The specificity of the PCR was assessed using 20 non-Salmonella strains...

  4. Genomic characterization of Flavobacterium psychrophilum serotypes and development of a multiplex PCR-based serotyping scheme

    DEFF Research Database (Denmark)

    Rochat, Tatiana; Fujiwara-Nagata, Erina; Calvez, Ségolène

    2017-01-01

    Flavobacterium psychrophilum is a devastating bacterial pathogen of salmonids reared in freshwater worldwide. So far, serological diversity between isolates has been described but the underlying molecular factors remain unknown. By combining complete genome sequence analysis and the serotyping me...... for bacterial coldwater disease resistance and future vaccine formulation....

  5. Evaluation of DNA extraction methods for PCR-based detection of Listeria monocytogenes from vegetables.

    Science.gov (United States)

    Vojkovska, H; Kubikova, I; Kralik, P

    2015-03-01

    Epidemiological data indicate that raw vegetables are associated with outbreaks of Listeria monocytogenes. Therefore, there is a demand for the availability of rapid and sensitive methods, such as PCR assays, for the detection and accurate discrimination of L. monocytogenes. However, the efficiency of PCR methods can be negatively affected by inhibitory compounds commonly found in vegetable matrices that may cause false-negative results. Therefore, the sample processing and DNA isolation steps must be carefully evaluated prior to the introduction of such methods into routine practice. In this study, we compared the ability of three column-based and four magnetic bead-based commercial DNA isolation kits to extract DNA of the model micro-organism L. monocytogenes from raw vegetables. The DNA isolation efficiency of all isolation kits was determined using a triplex real-time qPCR assay designed to specifically detect L. monocytogenes. The kit with best performance, the PowerSoil(™) Microbial DNA Isolation Kit, is suitable for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. Coupled with the triplex real-time qPCR assay, this DNA isolation kit is applicable to the samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. Several recent outbreaks of Listeria monocytogenes have been associated with the consumption of fruits and vegetables. Real-time PCR assays allow fast detection and accurate quantification of microbes. However, the success of real-time PCR is dependent on the success with which template DNA can be extracted. The results of this study suggest that the PowerSoil(™) Microbial DNA Isolation Kit can be used for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. This method is applicable to samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. © 2014 The Society for Applied Microbiology.

  6. Detection of MPL mutations by a novel allele-specific PCR-based strategy.

    Science.gov (United States)

    Furtado, Larissa V; Weigelin, Helmut C; Elenitoba-Johnson, Kojo S J; Betz, Bryan L

    2013-11-01

    MPL mutation testing is recommended in patients with suspected primary myelofibrosis or essential thrombocythemia who lack the JAK2 V617F mutation. MPL mutations can occur at allelic levels below 15%, which may escape detection by commonly used mutation screening methods such as Sanger sequencing. We developed a novel multiplexed allele-specific PCR assay capable of detecting most recurrent MPL exon 10 mutations associated with primary myelofibrosis and essential thrombocythemia (W515L, W515K, W515A, and S505N) down to a sensitivity of 2.5% mutant allele. Test results were reviewed from 15 reference cases and 1380 consecutive specimens referred to our laboratory for testing. Assay performance was compared to Sanger sequencing across a series of 58 specimens with MPL mutations. Positive cases consisted of 45 with W515L, 6 with S505N, 5 with W515K, 1 with W515A, and 1 with both W515L and S505N. Seven cases had mutations below 5% that were undetected by Sanger sequencing. Ten additional cases had mutation levels between 5% and 15% that were not consistently detected by sequencing. All results were easily interpreted in the allele-specific test. This assay offers a sensitive and reliable solution for MPL mutation testing. Sanger sequencing appears insufficiently sensitive for robust MPL mutation detection. Our data also suggest the relative frequency of S505N mutations may be underestimated, highlighting the necessity for inclusion of this mutation in MPL test platforms. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. Inverse PCR-based method for isolating novel SINEs from genome.

    Science.gov (United States)

    Han, Yawei; Chen, Liping; Guan, Lihong; He, Shunping

    2014-04-01

    Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.

  8. Analysis of the progression of fibroepithelial tumours of the breast by PCR-based clonality assay

    NARCIS (Netherlands)

    Kuijper, Arno; Buerger, H.; Simon, R.; Schaefer, K-L.; Croonen, A.; Boecker, W.; Wall, E. van der; Diest, P.J. van

    2002-01-01

    Fibroadenoma and phyllodes tumour of the breast are both fibroepithelial tumours. Although progression to epithelial malignancy has been described, the behaviour of most fibroadenomas is benign. Phyllodes tumours, on the other hand, can display locally destructive growth and can even metastasize. A

  9. A novel PCR-based method to enumerate Salmonella in animal feed

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Andersson, Gunnar; Häggblom, Per

    2010-01-01

    and pellets) only three gave results that differed between the PCR and MSRV methods. Ct values for naturally contaminated samples were higher compared to samples artificially contaminated with low numbers (approx. 2 CFU/25 g feed) of stressed Salmonella. To allow quantification of low numbers of Salmonella...

  10. HLA-DQA1 typing in Danes by two polymerase chain reaction (PCR) based methods

    DEFF Research Database (Denmark)

    Cowland, J B; Madsen, H O; Morling, N

    1995-01-01

    (ASA) method, which together recognise eight alleles. In 146 unrelated Danish individuals, the HLA-DQA1 alleles were in Hardy-Weinberg equilibrium. For identity testing, the power of discrimination (PD) of HLA-DQA1 was 0.932 with the RDB method and 0.942 with the PCR-RFLP/ASA method. For paternity...

  11. Engineered XcmI cassette-containing vector for PCR-based ...

    Indian Academy of Sciences (India)

    Unknown

    A simple and general method is described to construct a new vector bearing a synthetic XcmI cassette for direct cloning of PCR-amplified genes of interest. Cleavage of the vector with XcmI generates a linearized molecule with a single thymidine (T) overhang at the 3′ ends (T-vector) that facilitates TA cloning of PCR ...

  12. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review.

    Science.gov (United States)

    Gryson, Nicolas

    2010-03-01

    The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials.

  13. PCR Based Detection of Genetically Modified Soy in Processed Foods Commercially Available in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Ibrahim Abdullah Alaraidh

    2009-06-01

    Full Text Available In this research, PCR (polymerase chain reaction technique was applied to detect the presence of GMO sold in the Saudi Arabian market. This method was applied to detect genetically modified soy (GM-soy in particular the roundup ready soy (RRS. To confirm the presence of soy, samples were first tested for the existence of the soy specific lectin gene.  A total of eighty samples were tested out of which two samples tested positive as GM-soy. Not surprisingly, the findings showed the existence of GM-soy in food products in Saudi. This supports the necessity of developing precise quantitative and qualitative ways for routine analyses and detection of GMO products in the Saudi Arabian market. With the discovery of GM products in the Saudi Arabian market it would be of no surprise that other Middle Eastern nations also knowingly or unknowingly import GM crops.

  14. Excised radicle tips as a source of genomic DNA for PCR-based ...

    Indian Academy of Sciences (India)

    2012-12-13

    Dec 13, 2012 ... Cotton; cry1Ac; genomic DNA isolation; high-resolution melting curve analysis; radicle tip; seed purity testing .... cooled to 40°C. Fluorescence data for melting curves were ... greatly increased by introducing automation.

  15. PCR-based identification of selected pathogens associated with endodontic infections in deciduous and permanent teeth.

    Science.gov (United States)

    Cogulu, Dilsah; Uzel, Atac; Oncag, Ozant; Eronat, Cemal

    2008-09-01

    The aim of the present study was to evaluate the presence of the selected pathogens in samples from deciduous and permanent tooth root canals by using PCR method and to determine the association of these organisms with clinical symptoms. A total of 145 children, 5 to 13 years old, were involved in this study. The presence of selected pathogens (Actinomyces israelii, Candida albicans, Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus intermedius, Treponema denticola, Parvimonas micra, Tannerella forsythensis, Enterococcus faecium, Prevotella melaninogenica) in infected root canals was studied using PCR. T. denticola (P = .012, .02) and E. faecalis (P = .012, .04) were highly associated with periapical radiolucency and previous pain, while P. gingivalis was associated with tenderness to percussion in both deciduous and permanent teeth (P = .01, .015). The results of the present study confirm that certain species of microorganisms are associated with clinical signs and symptoms of endodontic disease in both deciduous and permanent teeth.

  16. PCR Based Detection of Shiga Toxin Producing E. coli in Commercial Poultry and Related Environments

    Directory of Open Access Journals (Sweden)

    Homaira Anzum Himi

    2015-02-01

    Full Text Available Shiga toxin (Stx-producing E. coli (STEC is the most important foodborne pathogen which is the causal agent of mild diarrhea, bloody diarrhea, hemolytic-uremic syndrome (HUS in human. The present study was designed to determine the prevalence and identification of Shiga toxin (Stx-producing E. coli in poultry, detection of its source of infection in poultry and transmission pattern to human. For this purpose a total of 150 samples (cloacal swab-60, feed -15, water-15 and egg -60 were collected and analyzed in bacteriology laboratory by cultured in different bacteriological media followed by gram’s staining, biochemical tests and Polymerase Chain reaction (PCR. The PCR was performed by targeting 16s rRNA gene and shiga toxin producing gene in E. coli. Out of 150 collected samples, E. coli was found in 81 (54% samples. Presence of E. coli was 100% in both feed (n=15 and egg (n=60, whereas 10% in cloacal swab (n=6. Water samples were totally free of E. coli. The stx2 gene was detected in all samples whether all samples were negative for stx1 gene. The study revealed that, poultry feed acts as a source of E. coli infection in poultry, which may be transmitted to environment and human via meat or eggs. Antibiotic sensitivity test revealed that isolated bacteria were highly sensitive to Ciprofloxacin.

  17. Identification of PCR-base markers linked to wood splitting in Eucalyptus Grandis

    CSIR Research Space (South Africa)

    Barros, E

    2002-07-01

    Full Text Available Institute Inc., SAS Users Guide: Basics (1985) 5th Edition. Cary, NC, USA. [5] Verryn S.D., Roux C.Z., A memory-friendly algorithmic strategy for Best Linear Prediction (BLP), in: Tree Improvement for Sustainable Tropical Forestry-Conference Proceeding...

  18. A rapid and direct real time PCR-based method for identification of Salmonella spp

    DEFF Research Database (Denmark)

    Rodriguez-Lazaro, D.; Hernández, Marta; Esteve, T.

    2003-01-01

    The aim of this work was the validation of a rapid, real-time PCR assay based on TaqMan((R)) technology for the unequivocal identification of Salmonella spp. to be used directly on an agar-grown colony. A real-time PCR system targeting at the Salmonella spp. invA gene was optimized and validated ...

  19. Narrative approaches

    DEFF Research Database (Denmark)

    Stelter, Reinhard

    2012-01-01

    Narrative coaching is representative of the new wave – or third generation – of coaching practice . The theory and practice of narrative coaching takes into account the social and cultural conditions of late modern society, and must be seen as intertwined with them. Some initial conceptualizations...... of narrative coaching were developed by David Drake (2006, 2007, 2008, 2009) in the USA and Australia, by Ho Law in the UK (Law, 2007a + b; Law & Stelter, 2009) and by Reinhard Stelter (2007, 2009, 2012, in preparation; Stelter & Law, 2010) in Denmark. In the following chapter the aim is to present coaching...... as a narrative-collaborative practice, an approach that is based on phenomenology, social constructionism and narrative theory. Seeing narrative coaching as a collaborative practice also leads to reflecting on the relationship between coach and coachee(s) in a new way, where both parts contribute to the dialogue...

  20. Oriented Approach

    Directory of Open Access Journals (Sweden)

    Seyed Mohammad Moghimi

    2013-12-01

    Full Text Available Promoting productivity is one of the goals of usinginformation technology in organizations. The purpose of this research isexamining the impact of IT on organizational productivity andrecognizing its mechanisms based on process-oriented approach. For thisend, by reviewing the literature of the subject a number of impacts of ITon organizational processes were identified. Then, through interviewswith IT experts, seven main factors were selected and presented in aconceptual model. This model was tested through a questionnaire in 148industrial companies. Data analysis shows that impact of IT onproductivity can be included in the eight major categories: Increasing ofthe Automation, Tracking, Communication, Improvement, Flexibility,Analytic, Coordination and Monitoring in organizational processes.Finally, to improve the impact of information technology onorganizational productivity, some suggestions are presented.

  1. Approaches for enhancing in situ detection of enterocin genes in thermized milk, and selective isolation of enterocin-producing Enterococcus faecium from Baird-Parker agar.

    Science.gov (United States)

    Vandera, Elpiniki; Tsirka, Georgia; Kakouri, Athanasia; Koukkou, Anna-Irini; Samelis, John

    2018-05-21

    Enterococci are naturally selected for growth in thermized ewes'/goats' milk mixtures used for traditional cooked hard cheese processing in Greece. A culture-independent PCR-based approach was applied to detect the presence of enterocin-encoding genes in naturally culture-enriched thermized milk (TM). Portions of TM (63 °C, 30 s) collected from a commercial cheese plant before addition of starters were fermented at 37 °C for 48 h to facilitate growth of indigenous enterococci. The multiple enterocin-producing (m-Ent+) Enterococcus faecium KE82 and the nisin A-producing Lactococcus lactis subsp. cremoris M104 served as bacteriocin-positive inocula in separate TM treatments. The PCR results revealed a constant presence of the enterocin A, B and P genes in TM fermented naturally at 37 °C. Eleven out of 42 (26.2%) lactic isolates from the enriched TM cultures without inoculation were Ent+ E. faecium assigned to three biotypes. Biotype I (4 isolates) included single entA possessors, whereas biotype II (5 isolates) and biotype III (2 isolates) were m-Ent+ variants profiling entA-entB-entP and entA-entB genes, respectively. Biotype II displayed the strongest antilisterial activity in vitro. Surprisingly, 85.7% (6/7) of the m-Ent+ E. faecium were selectively isolated from Baird-Parker agar, reflecting their natural resistance to 0.01% tellurite contained in the egg yolk supplement. No cytolysin-positive E. faecalis or other Ent+ Enterococcus spp. were isolated. In conclusion, commercially thermized Greek milk is a natural pool or 'reservoir' of antagonistic Ent+ or m-Ent+ E. faecium strains that can be easily detected and recovered by applying this PCR-based approach to naturally fermented milks or cheese products. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

    Directory of Open Access Journals (Sweden)

    Rogier Christophe

    2009-04-01

    Full Text Available Abstract Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the

  3. Numerical comparison between Maxwell stress method and equivalent multipole approach for calculation of the dielectrophoretic force in single-cell traps.

    Science.gov (United States)

    Rosales, Carlos; Lim, Kian Meng

    2005-06-01

    This paper presents detailed numerical calculations of the dielectrophoretic force in traps designed for single-cell trapping. A trap with eight planar electrodes is studied for spherical and ellipsoidal particles using the boundary element method (BEM). Multipolar approximations of orders one to three are compared with the full Maxwell stress tensor (MST) calculation of the electrical force on spherical particles. Ellipsoidal particles are also studied, but in their case only the dipolar approximation is available for comparison with the MST solution. The results show that a small number of multipolar terms need to be considered in order to obtain accurate results for spheres, even in the proximity of the electrodes, and that the full MST calculation is only required in the study of non-spherical particles.

  4. Modulation of Stem Cells Differentiation and Myostatin as an approach to Counteract fibrosis in Muscle Dystrophy and Regeneration after Injury

    Science.gov (United States)

    2010-03-01

    Duchenne muscular dystrophy (DMD), hampers cell therapy in the muscle , and is a feasible therapeutic target. Myostatin (Mst), a...17 Figure 18 Figure 19 Figure 20 Figure 21 • Muscle lipofibrotic degeneration characterizes Duchenne muscular dystrophy (DMD), hampers cell therapy...SUBJECT TERMS Myostatin, muscle dystrophy , stem cells, myogenesis, Oct-4; Duchenne 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION OF ABSTRACT

  5. Bioinformatic approach in the identification of arabidopsis gene homologous in amaranthus

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2015-05-01

    Full Text Available Bioinfomatics offers an efficient tool for molecular genetics applications and sequence homology search algorithms became an inevitable part for many different research strategies. Appropriate managing of known data that are stored in public available databases can be used in many ways in the research. Here, we report the identification of RmlC-like cupins superfamily protein DNA sequence than is known in Arabidopsis genome for the Amaranthus - plant specie where this sequence was still not sequenced. A BLAST based approach was used to identify the homologous sequences in the nucleotide database and to find suitable parts of the Arabidopsis sequence were primers can be designed. In total, 64 hits were found in nucleotide database for Arabidopsis RmlC-like cupins sequence. A query cover ranged from 10% up to the 100% among RmlC-like cupins nucleotides and its homologues that are actually stored in public nucleotide databases. The most conserved region was identified for matches that posses nucleotides in the range of 1506 up to the 1925 bp of RmlC-like cupins DNA sequence stored in the database. The in silico approach was subsequently used in PCR analysis where the specifity of designed primers was approved. A unique, 250 bp long fragment was obtained for Amaranthus cruentus and a hybride Amaranthus hypochondriacus x hybridus in our analysis. Bioinformatic based analysis of unknown parts of the plant genomes as showed in this study is a very good additional tool in PCR based analysis of plant variability. This approach is suitable in the case for plants, where concrete genomic data are still missing for the appropriate genes, as was demonstrated for Amaranthus. 

  6. Life Span Developmental Approach

    OpenAIRE

    Ali Eryilmaz

    2011-01-01

    The Life Span Developmental Approach examines development of individuals which occurs from birth to death. Life span developmental approach is a multi-disciplinary approach related with disciplines like psychology, psychiatry, sociology, anthropology and geriatrics that indicates the fact that development is not completed in adulthood, it continues during the life course. Development is a complex process that consists of dying and death. This approach carefully investigates the development of...

  7. The sustainable livelihoods approach

    DEFF Research Database (Denmark)

    Oelofse, Myles; Jensen, Henning Høgh

    2008-01-01

    food chain has on producers and their families, an analysis was conducted of the use of the Sustainable Livelihoods Approach (SLA). The SLA provides a holistic and integrative approach which researchers can use as the overriding frame for their research. The application of the approach is recommended...

  8. Molecular approaches to Taenia asiatica.

    Science.gov (United States)

    Jeon, Hyeong-Kyu; Eom, Keeseon S

    2013-02-01

    Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

  9. Molecular Approaches to Taenia asiatica

    Science.gov (United States)

    Jeon, Hyeong-Kyu

    2013-01-01

    Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms. PMID:23467738

  10. Alternative Auditing Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Kandt, Alicen J [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-09-15

    This presentation for the 2017 Energy Exchange in Tampa, Florida, offers information about advanced auditing technologies and techniques including alternative auditing approaches and considerations and caveats.

  11. Evaluating six soft approaches

    DEFF Research Database (Denmark)

    Sørensen, Lene; Vidal, Rene Victor Valqui

    2006-01-01

    ’s interactive planning principles to be supported by soft approaches in carrying out the principles in action. These six soft approaches are suitable for supporting various steps of the strategy development and planning process. These are the SWOT analysis, the Future Workshop, the Scenario methodology......, Strategic Option Development and Analysis, Strategic Choice Approach and Soft Systems Methodology. Evaluations of each methodology are carried out using a conceptual framework in which the organisation, the result, the process and the technology of the specific approach are taken into consideration. Using...

  12. Evaluating Six Soft Approaches

    DEFF Research Database (Denmark)

    Sørensen, Lene Tolstrup; Valqui Vidal, René Victor

    2008-01-01

    's interactive planning principles to be supported by soft approaches in carrying out the principles in action. These six soft approaches are suitable forsupporting various steps of the strategy development and planning process. These are the SWOT analysis, the Future Workshop, the Scenario methodology......, Strategic Option Development and Analysis, Strategic Choice Approach and Soft Systems Methodology. Evaluations of each methodology are carried out using a conceptual framework in which the organisation, the result, the process and the technology of the specific approach are taken into consideration. Using...

  13. Evaluating six soft approaches

    DEFF Research Database (Denmark)

    Sørensen, Lene Tolstrup; Vidal, Rene Victor Valqui

    2008-01-01

    's interactive planning principles to be supported by soft approaches in carrying out the principles in action. These six soft approaches are suitable forsupporting various steps of the strategy development and planning process. These are the SWOT analysis, the Future Workshop, the Scenario methodology......, Strategic Option Development and Analysis, Strategic Choice Approach and Soft Systems Methodology. Evaluations of each methodology are carried out using a conceptual framework in which the organisation, the result, the process and the technology of the specific approach are taken into consideration. Using...

  14. Identification of Actinobacillus pleuropneumoniae serotypes 1, 7, and 12 by multiplex PCR based on genes involved in encapsulation

    DEFF Research Database (Denmark)

    Angen, Øystein; Jessing, Stine Graakjær; Ahrens, Peter

    2005-01-01

    . However, a number of isolates show cross-reaction between serotypes and this has urged the development of quick, serotype specific DNA-based methods necessary. Serotype specific tests have until now been described for the serotypes 2, 5, and 6 (Jessing et al, 2003) and serotypes 1, 2 and 8 (Schuchert et...

  15. Efficient One-Step Fusion PCR Based on Dual-Asymmetric Primers and Two-Step Annealing

    DEFF Research Database (Denmark)

    Liu, Yilan; Chen, Jinjin; Thygesen, Anders

    2018-01-01

    Gene splicing by fusion PCR is a versatile and widely used methodology, especially in synthetic biology. We here describe a rapid method for splicing two fragments by one-round fusion PCR with a dual-asymmetric primers and two-step annealing (ODT) method. During the process, the asymmetric...... intermediate fragments were generated in the early stage. Thereafter, they were hybridized in the subsequent cycles to serve as template for the target full-length product. The process parameters such as primer ratio, elongation temperature and cycle numbers were optimized. In addition, the fusion products...

  16. PCR-based cDNA library construction: general cDNA libraries at the level of a few cells.

    OpenAIRE

    Belyavsky, A; Vinogradova, T; Rajewsky, K

    1989-01-01

    A procedure for the construction of general cDNA libraries is described which is based on the amplification of total cDNA in vitro. The first cDNA strand is synthesized from total RNA using an oligo(dT)-containing primer. After oligo(dG) tailing the total cDNA is amplified by PCR using two primers complementary to oligo(dA) and oligo(dG) ends of the cDNA. For insertion of the cDNA into a vector a controlled trimming of the 3' ends of the cDNA by Klenow enzyme was used. Starting from 10 J558L ...

  17. PCR-based diagnosis, molecular characterization and detection of atypical strains of avian Chlamydia psittaci in companion and wild birds.

    Science.gov (United States)

    Madani, S A; Peighambari, S M

    2013-02-01

    Chlamydiosis is one of the most important infectious diseases of birds. In this study, 253 clinical samples were taken from 27 bird species belonging to seven orders. Thirty-two (12.6%) samples were positive for Chlamydia psittaci major outer membrane gene (ompA) DNA by a nested polymerase chain reaction (PCR). Twelve nested PCR-positive specimens were typed by ompA gene-based PCR-restricted fragment length polymorphism, using CTU/CTL primers and AluI restriction enzyme. Four restriction patterns were identified, including genotype A (two specimens from an African grey parrot [Psittacus erithacus] and a lorikeet [Trichoglossus haematodus]), genotype B (two specimens from a rock dove [Columbia livia] and a canary [Serinus canaria]), a third new restriction pattern (six specimens from African grey parrots), and a fourth new restriction pattern (two specimens from a ring-necked parakeet [Psittacula krameri] and an Alexandrine parakeet [Psittacula eupatria]). The third and the fourth restriction patterns are suggested to be provisional genotypes I and J, respectively. Partial sequencing of the ompA gene of seven specimens completely correlated with the results of PCR-restricted fragment length polymorphism and confirmed the presence of genotypes A and B and the two new provisional genotypes I and J. The two new genotypes have the closest identity with C. psittaci genotype F and Chlamydia abortus, respectively. From an evolutionary perspective, both new genotypes, particularly genotype J, are intermediate between the two species, C. psittaci and C. abortus.

  18. PCR-based identification of the pathogenic bacterium, Acaricomes phytoseiuli, in the biological control agent Phytoseiulus persimilis (Acari: Phytoseiidae)

    NARCIS (Netherlands)

    Gols, R.; Schütte, C.; Stouthamer, R.; Dicke, M.

    2007-01-01

    The predatory mite, Phytoseiulus persimilis is an important biological control agent of herbivorous spider mites. This species is also intensively used in the study of tritrophic effects of plant volatiles in interactions involving plants, herbivores, and their natural enemies. Recently, a novel

  19. Optimization of a Real Time PCR based method for the detection of Listeria monocytogenes in pork meat.

    Science.gov (United States)

    Gattuso, Antonietta; Gianfranceschi, Monica Virginia; Sonnessa, Michele; Delibato, Elisabetta; Marchesan, Massimo; Hernandez, Marta; De Medici, Dario; Rodriguez-Lazaro, David

    2014-08-01

    The aim of this study was to optimize a Real-Time PCR protocol for a rapid detection of Listeria monocytogenes in pork meat, using reduced volumes of primary selective enrichment broth and times of incubation to decrease the cost and time for analysis. Forty-five samples of pork meat were artificially contaminated with two different levels of L. monocytogenes (1-10 CFU per sample and 10-100 CFU per sample), homogenized in three different volumes of Half Fraser Broth (1:3; 1:5 and 1:10) and incubated at 30°C ± 1°C for 5h, 8h and 24h. The detection was conducted in parallel by Real-Time PCR and the ISO standard 11290-1 methods. L. monocytogenes was detected in all the samples after 24h by Real-Time PCR method, also using reduced volumes of Half Fraser Broth. This represents a clear advantage as the time to final detection and the inherent costs were significantly reduced compared to the ISO reference method. All samples artificially contaminated were correctly detected also after 8 of incubation at 30°C ± 1°C in Half Fraser Broth and 24h in Fraser Broth at 37°C ± 1°C using cultural method. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing

    Science.gov (United States)

    Gille, Johan J. P.; Floor, Karijn; Kerkhoven, Lianne; Ameziane, Najim; Joenje, Hans; de Winter, Johan P.

    2012-01-01

    Fanconi anemia (FA) is a rare inherited disease characterized by developmental defects, short stature, bone marrow failure, and a high risk of malignancies. FA is heterogeneous: 15 genetic subtypes have been distinguished so far. A clinical diagnosis of FA needs to be confirmed by testing cells for sensitivity to cross-linking agents in a chromosomal breakage test. As a second step, DNA testing can be employed to elucidate the genetic subtype of the patient and to identify the familial mutations. This knowledge allows preimplantation genetic diagnosis (PGD) and enables prenatal DNA testing in future pregnancies. Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative. We describe a strategy and optimized conditions for the screening of FANCA, FANCB, FANCC, FANCE, FANCF, and FANCG and present the results obtained in a cohort of 54 patients referred to our diagnostic service since 2008. In addition, the follow up with respect to genetic counseling and carrier screening in the families is discussed. PMID:22778927

  1. Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing

    Directory of Open Access Journals (Sweden)

    Johan J. P. Gille

    2012-01-01

    Full Text Available Fanconi anemia (FA is a rare inherited disease characterized by developmental defects, short stature, bone marrow failure, and a high risk of malignancies. FA is heterogeneous: 15 genetic subtypes have been distinguished so far. A clinical diagnosis of FA needs to be confirmed by testing cells for sensitivity to cross-linking agents in a chromosomal breakage test. As a second step, DNA testing can be employed to elucidate the genetic subtype of the patient and to identify the familial mutations. This knowledge allows preimplantation genetic diagnosis (PGD and enables prenatal DNA testing in future pregnancies. Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative. We describe a strategy and optimized conditions for the screening of FANCA, FANCB, FANCC, FANCE, FANCF, and FANCG and present the results obtained in a cohort of 54 patients referred to our diagnostic service since 2008. In addition, the follow up with respect to genetic counseling and carrier screening in the families is discussed.

  2. Cloning of the koi herpesvirus (KHV gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

    Directory of Open Access Journals (Sweden)

    Gilad Oren

    2005-03-01

    Full Text Available Abstract Background Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV. Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary. Results A robust and sensitive PCR assay based on a defined gene sequence of KHV was developed to improve the diagnosis of KHV infection. From a KHV genomic library, a hypothetical thymidine kinase gene (TK was identified, subcloned and expressed as a recombinant protein. Preliminary characterization of the recombinant TK showed that it has a kinase activity using dTTP but not dCTP as a substrate. A PCR assay based on primers selected from the defined DNA sequence of the TK gene was developed and resulted in a 409 bp amplified fragment. The TK based PCR assay did not amplify the DNAs of other fish herpesviruses such as Herpesvirus cyprini (CHV and the channel catfish virus (CCV. The TK based PCR assay was specific for the detection of KHV and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions. The TK based PCR was compared to previously described PCR assays and to viral culture in diseased fish and was shown to be the most sensitive method of diagnosis of KHV infection. Conclusion The TK based PCR assay developed in this work was shown to be specific for the detection of KHV. The TK based PCR assay was more sensitive for the detection of KHV than previously described PCR assays; it was as sensitive as virus isolation which is the golden standard method for KHV diagnosis and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions.

  3. Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)

    Science.gov (United States)

    Chiang, Tzen-Yuh; Tzeng, Tzong-Der; Lin, Hung-Du; Cho, Ching-Ju; Lin, Feng-Jiau

    2012-01-01

    The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. PMID:22489123

  4. PCR-Based Detection of Trypanosoma evansi Infection in Semi-Captive Asiatic Black Bears (Ursus thibetanus

    Directory of Open Access Journals (Sweden)

    Maliha Shahid, Safia Janjua*, Fakhar-i-Abbas and Jan Schmidt Burbach1

    2013-11-01

    Full Text Available Clinical signs, viz lethargy, increased heart rate and reduced appetite, making trypanosomiasis a possible differential diagnosis, were found in five out of twenty semi-captive Asiatic black bears (Ursus thibetanus in a sanctuary, located in Kund, District Sawabi, KPK, Pakistan. Microscopic examination of blood samples of bears expressing clinical signs and symptoms revealed the presence of haemoflagellates, which was found to be trypanosomes. Subsequently, the PCR technique was exploited to screen for the presence of trypanosomal species in all bears’ blood samples. Blood samples from 20 individual bears were screened using three sets of primers specific to Trypanosoma evansi species. Three primer pairs used are equally effective in successful detection of the parasite. Two out of five, diseased bears died prior to any trypanosoma specific medication while the rest were given an administered dose of Melarsomine (Immiticide. The treated bears survived and were assured to be aparasitemic on post-treatment examination after six weeks.

  5. A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia

    Directory of Open Access Journals (Sweden)

    Jakub Sawicki

    2011-07-01

    Full Text Available RAPDs, ISJs, ISSRs, ITS and katGs were applied to determine genetic relationships between common Sphagnum species of the section Acutifolia. Twenty populations were genotyped using ten ISJ primers, 12 pairs of katG primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and katG markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.

  6. Novel One-Step Multiplex PCR-Based Method for HLA Typing and Preimplantational Genetic Diagnosis of -Thalassemia

    Directory of Open Access Journals (Sweden)

    Raquel M. Fernández

    2013-01-01

    Full Text Available Preimplantation genetic diagnosis (PGD of single gene disorders, combined with HLA matching (PGD-HLA, has emerged as a tool for couples at risk of transmitting a genetic disease to select unaffected embryos of an HLA tissue type compatible with that of an existing affected child. Here, we present a novel one-step multiplex PCR to genotype a spectrum of STRs to simultaneously perform HLA typing and PGD for -thalassemia. This method is being routinely used for PGD-HLA cycles in our department, with a genotyping success rate of 100%. As an example, we present the first successful PGD-HLA typing in Spain, which resulted in the birth of a boy and subsequent successful HSC transplantation to his affected brother, who is doing well 4 years following transplantation. The advantage of our method is that it involves only a round of single PCR for multiple markers amplification (up to 10 markers within the HLA and 6 markers at the -globin loci. This strategy has allowed us to considerably reduce the optimization of the PCR method for each specific PGD-HLA family as well as the time to obtain molecular results in each cycle.

  7. Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida

    DEFF Research Database (Denmark)

    Høie, S.; Dalsgaard, Inger; Aase, I.L.

    1999-01-01

    . salmonicida subsp. salmonicida isolates tested, belonged to group 1. The PCR primer-sets separated A. salmonicida from other reference strains of Aeromonas species and related bacteria with the exception of Aeromonas hydrophila. The results indicated that PCR typing is a useful framework for characterization...

  8. Cost-effective optimization of real-time PCR based detection of Campylobacter and Salmonella with inhibitor tolerant DNA polymerases

    DEFF Research Database (Denmark)

    Fachmann, Mette Sofie Rousing; Josefsen, Mathilde Hasseldam; Hoorfar, Jeffrey

    2015-01-01

    bacterial cells in two validated real-time PCR assays for Campylobacter and Salmonella. The five best performing (based on: limit of detection (LOD), maximum fluorescence, shape of amplification curves, and amplification efficiency) were subsequently applied to meat and fecal samples. The VeriQuest q......PCR master mix performed best for both meat and fecal samples (LODs of 102 and 104 CFU ml-1 in the purest and crudest DNA extractions, respectively) compared with Tth (LOD=102 -103 and 105 -106 CFU ml-1 ). AmpliTaqGold and HotMasterTaq both performed well (LOD=102 -104 CFU ml-1 ) with meat samples and poorly...... (LOD=103 -106 CFU ml-1 /not detected) with fecal samples. CONCLUSIONS: Applying the VeriQuest qPCR master mix in the two tested real-time PCR assays could allow for simpler sample preparation and thus a reduction in cost. SIGNIFICANCE AND IMPACT OF STUDY: This work exemplifies a cost-effective strategy...

  9. High-Density Real-Time PCR-Based in Vivo Toxicogenomic Screen to Predict Organ-Specific Toxicity

    Directory of Open Access Journals (Sweden)

    Laszlo G. Puskas

    2011-09-01

    Full Text Available Toxicogenomics, based on the temporal effects of drugs on gene expression, is able to predict toxic effects earlier than traditional technologies by analyzing changes in genomic biomarkers that could precede subsequent protein translation and initiation of histological organ damage. In the present study our objective was to extend in vivo toxicogenomic screening from analyzing one or a few tissues to multiple organs, including heart, kidney, brain, liver and spleen. Nanocapillary quantitative real-time PCR (QRT-PCR was used in the study, due to its higher throughput, sensitivity and reproducibility, and larger dynamic range compared to DNA microarray technologies. Based on previous data, 56 gene markers were selected coding for proteins with different functions, such as proteins for acute phase response, inflammation, oxidative stress, metabolic processes, heat-shock response, cell cycle/apoptosis regulation and enzymes which are involved in detoxification. Some of the marker genes are specific to certain organs, and some of them are general indicators of toxicity in multiple organs. Utility of the nanocapillary QRT-PCR platform was demonstrated by screening different references, as well as discovery of drug-like compounds for their gene expression profiles in different organs of treated mice in an acute experiment. For each compound, 896 QRT-PCR were done: four organs were used from each of the treated four animals to monitor the relative expression of 56 genes. Based on expression data of the discovery gene set of toxicology biomarkers the cardio- and nephrotoxicity of doxorubicin and sulfasalazin, the hepato- and nephrotoxicity of rotenone, dihydrocoumarin and aniline, and the liver toxicity of 2,4-diaminotoluene could be confirmed. The acute heart and kidney toxicity of the active metabolite SN-38 from its less toxic prodrug, irinotecan could be differentiated, and two novel gene markers for hormone replacement therapy were identified, namely fabp4 and pparg, which were down-regulated by estradiol treatment.

  10. 18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells

    Directory of Open Access Journals (Sweden)

    Kuchipudi Suresh V

    2012-10-01

    Full Text Available Abstract Background One requisite of quantitative reverse transcription PCR (qRT-PCR is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, under different experimental settings. However, ACTB and GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. To date no detailed study has been described that compares the suitability of commonly used housekeeping genes in influenza virus infections. The present study evaluated several commonly used housekeeping genes [ACTB, GAPDH, 18S ribosomal RNA (18S rRNA, ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9 (ATP5G1] to identify the most stably expressed gene in human, pig, chicken and duck cells infected with a range of influenza A virus subtypes. Results The relative expression stability of commonly used housekeeping genes were determined in primary human bronchial epithelial cells (HBECs, pig tracheal epithelial cells (PTECs, and chicken and duck primary lung-derived cells infected with five influenza A virus subtypes. Analysis of qRT-PCR data from virus and mock infected cells using NormFinder and BestKeeper software programmes found that 18S rRNA was the most stable gene in HBECs, PTECs and avian lung cells. Conclusions Based on the presented data from cell culture models (HBECs, PTECs, chicken and duck lung cells infected with a range of influenza viruses, we found that 18S rRNA is the most stable reference gene for normalising qRT-PCR data. Expression levels of the other housekeeping genes evaluated in this study (including ACTB and GPADH were highly affected by influenza virus infection and hence are not reliable as reference genes for RNA normalisation.

  11. PCR-based verification of positive rapid diagnostic tests for intestinal protozoa infections with variable test band intensity.

    Science.gov (United States)

    Becker, Sören L; Müller, Ivan; Mertens, Pascal; Herrmann, Mathias; Zondie, Leyli; Beyleveld, Lindsey; Gerber, Markus; du Randt, Rosa; Pühse, Uwe; Walter, Cheryl; Utzinger, Jürg

    2017-10-01

    Stool-based rapid diagnostic tests (RDTs) for pathogenic intestinal protozoa (e.g. Cryptosporidium spp. and Giardia intestinalis) allow for prompt diagnosis and treatment in resource-constrained settings. Such RDTs can improve individual patient management and facilitate population-based screening programmes in areas without microbiological laboratories for confirmatory testing. However, RDTs are difficult to interpret in case of 'trace' results with faint test band intensities and little is known about whether such ambiguous results might indicate 'true' infections. In a longitudinal study conducted in poor neighbourhoods of Port Elizabeth, South Africa, a total of 1428 stool samples from two cohorts of schoolchildren were examined on the spot for Cryptosporidium spp. and G. intestinalis using an RDT (Crypto/Giardia DuoStrip; Coris BioConcept). Overall, 121 samples were positive for G. intestinalis and the RDT suggested presence of cryptosporidiosis in 22 samples. After a storage period of 9-10 months in cohort 1 and 2-3 months in cohort 2, samples were subjected to multiplex PCR (BD Max™ Enteric Parasite Panel, Becton Dickinson). Ninety-three percent (112/121) of RDT-positive samples for G. intestinalis were confirmed by PCR, with a correlation between RDT test band intensity and quantitative pathogen load present in the sample. For Cryptosporidium spp., all positive RDTs had faintly visible lines and these were negative on PCR. The performance of the BD Max™ PCR was nearly identical in both cohorts, despite the prolonged storage at disrupted cold chain conditions in cohort 1. The Crypto/Giardia DuoStrip warrants further validation in communities with a high incidence of diarrhoea. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Real-time PCR-based detection of Bordetella pertussis and Bordetella parapertussis in an Irish paediatric population.

    LENUS (Irish Health Repository)

    Grogan, Juanita A

    2011-06-01

    Novel real-time PCR assays targeting the Bordetella pertussis insertion sequence IS481, the toxin promoter region and Bordetella parapertussis insertion sequence IS1001 were designed. PCR assays were capable of detecting ≤10 copies of target DNA per reaction, with an amplification efficiency of ≥90 %. From September 2003 to December 2009, per-nasal swabs and nasopharyngeal aspirates submitted for B. pertussis culture from patients ≤1 month to >15 years of age were examined by real-time PCR. Among 1324 patients, 76 (5.7 %) were B. pertussis culture positive and 145 (10.95 %) were B. pertussis PCR positive. Of the B. pertussis PCR-positive patients, 117 (81 %) were aged 6 months or less. A total of 1548 samples were examined, of which 87 (5.6 %) were culture positive for B. pertussis and 169 (10.92 %) were B. pertussis PCR positive. All culture-positive samples were PCR positive. Seven specimens (0.5 %) were B. parapertussis culture positive and 10 (0.8 %) were B. parapertussis PCR positive, with all culture-positive samples yielding PCR-positive results. A review of patient laboratory records showed that of the 1324 patients tested for pertussis 555 (42 %) had samples referred for respiratory syncytial virus (RSV) testing and 165 (30 %) were positive, as compared to 19.4 % of the total 5719 patients tested for RSV in this period. Analysis of the age distribution of RSV-positive patients identified that 129 (78 %) were aged 6 months or less, similar to the incidence observed for pertussis in that patient age group. In conclusion, the introduction of the real-time PCR assays for the routine detection of B. pertussis resulted in a 91 % increase in the detection of the organism as compared to microbiological culture. The incidence of infection with B. parapertussis is low while the incidence of RSV infection in infants suspected of having pertussis is high, with a similar age distribution to B. pertussis infection.

  13. Pulmonary toxoplasmosis in immunocompromised patients with interstitial pneumonia: a single-centre prospective study assessing PCR-based diagnosis.

    Science.gov (United States)

    Desoubeaux, Guillaume; Cabanne, Églantine; Franck-Martel, Claire; Gombert, Martin; Gyan, Emmanuel; Lissandre, Séverine; Renaud, Marc; Monjanel, Hélène; Dartigeas, Caroline; Bailly, Éric; Van Langendonck, Nathalie; Chandenier, Jacques

    2016-08-01

    Pulmonary toxoplasmosis has become a very rare parasitic infection since the advent of highly active antiretroviral therapies. It is generally diagnosed by the direct microscopic observation of Toxoplasma gondii tachyzoites in bronchoalveolar lavage fluid (BALF). The aim of this study was to assess possible improvements in diagnostic performance associated with the use of real-time PCR. This prospective study was carried out on BALFs obtained from immunocompromised patients over a 2-year period. We systematically compared the results of conventional staining with those of molecular detection. Two cases of pulmonary toxoplasmosis were diagnosed for a total of 336 samples. PCR did not detect any additional cases and was more time-consuming than conventional staining. Conventional staining is a reliable technique and is probably the most appropriate method for experienced microbiology laboratories, whereas T. gondii-specific PCR may be useful for laboratories with less experience in parasitology. 2015_030, May 27th 2015. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  14. PCR-based methods for identification of potentially zoonotic ascaridoid parasites of the dog, fox and cat.

    Science.gov (United States)

    Jacobs, D E; Zhu, X; Gasser, R B; Chilton, N B

    1997-11-01

    Genomic DNA was extracted from ascaridoid nematodes collected from dogs, foxes and cats. A region spanning the second internal transcribed spacer (ITS-2) of the ribosomal DNA of each sample was amplified by PCR. Representative ITS-2 products for each nematode species (Toxocara canis, Toxocara cati and Toxascaris leonina) were sequenced. Restriction sites were identified for use as genetic markers in a PCR-linked RFLP assay. The three species could be differentiated from each other and from other ascaridoids that may be found in human tissues by use of two endonucleases, HinfI and RsaI. Primers were designed to unique regions of the ITS-2 sequences of the three species for use in diagnostic PCR procedures and primer sets evaluated against panels of homologous and heterologous DNA samples. Results suggest that both methods are good candidates for further development for the detection and/or identification of ascaridoid larvae in human tissues.

  15. PCR-based molecular characterization of Toxocara spp. using feces of stray cats: a study from Southwest Iran.

    Science.gov (United States)

    Khademvatan, Shahram; Rahim, Fakher; Tavalla, Mahdi; Abdizadeh, Rahman; Hashemitabar, Mahmoud

    2013-01-01

    Feces of stray cat are potential sources of gastrointestinal parasites and play a crucial role in spreading and transmitting parasite eggs, larvae, and oocysts through contamination of soil, food, or water. In this study, we investigated the prevalence of Toxocara spp. infection in stray cats in Ahvaz city, southwest Iran. Eggs of Toxocara spp. in feces of stray cats were detected by the sucrose flotation method, and identification was conducted by polymerase chain reaction (PCR) and DNA sequencing. Of the 140 fecal samples that were randomly collected from public environments during the months of January to May 2012, 45% were found to harbour Toxocara spp. eggs. The highest prevalence of Toxocara spp. eggs was found in the central area of Ahvaz city (28.6%). T. canis eggs were found in 4 (6.34%) of the 63 positive samples. Stray cats are found in parks, playgrounds, and other public places and may be a potential contamination risk. Identification of Toxocara spp. using molecular methods is sufficiently sensitive to detect low levels of parasites and identify the different Toxocara spp. in feces. The relatively high prevalence of Toxocara spp. infection may continue to increase due to lack of effective environmental hygiene control in Iran. Consequently, there is a need to plan adequate programs to detect, identify, and control this infection as well as stray cats in the region.

  16. PCR-Based Molecular Characterization of Toxocara spp. Using Feces of Stray Cats: A Study from Southwest Iran

    OpenAIRE

    Khademvatan, Shahram; Rahim, Fakher; Tavalla, Mahdi; Abdizadeh, Rahman; Hashemitabar, Mahmoud

    2013-01-01

    Feces of stray cat are potential sources of gastrointestinal parasites and play a crucial role in spreading and transmitting parasite eggs, larvae, and oocysts through contamination of soil, food, or water. In this study, we investigated the prevalence of Toxocara spp. infection in stray cats in Ahvaz city, southwest Iran. Eggs of Toxocara spp. in feces of stray cats were detected by the sucrose flotation method, and identification was conducted by polymerase chain reaction (PCR) and DNA sequ...

  17. DNA carryover in milk samples from routine milk recording used for PCR-based diagnosis of bovine Staphylococcus aureus mastitis

    DEFF Research Database (Denmark)

    Mahmmod, Yasser Saadeldien Ibrahim; Klaas, Ilka Christine; Enevoldsen, Carsten

    2017-01-01

    milking order must be considered in mastitis control efforts. We suggest a practical interpretation of PCR results: cows with a Ct-value 37 and 32-37 can be labeled "very likely to be negative for Staph. aureus...

  18. Application of PCR-Based Tools to Explore Strongyloides Infection in People in Parts of Northern Australia

    Directory of Open Access Journals (Sweden)

    Gemma J. Robertson

    2017-12-01

    Full Text Available Strongyloidiasis, which is caused by infection with the nematode Strongyloides stercoralis, is endemic to areas of northern Australia. Diagnosis in this region remains difficult due to the distances between endemic communities and diagnostic laboratories, leading to lengthy delays in stool processing for microscopy and culture. PCR represents a viable solution to this difficulty, having potential for high sensitivity detection of S. stercoralis, even in older, unpreserved faecal samples. We prospectively collected 695 faecal specimens that were submitted to The Townsville Hospital Microbiology Laboratory from the North Queensland region for routine parasitological examination, and subjected them to a Strongyloides sp. real-time (qPCR. Results were confirmed with a novel nested conventional PCR assay targeting the 18S rRNA gene, followed by single-strand conformation polymorphism analysis (SSCP. Of the 695 specimens tested, S. stercoralis was detected in three specimens (0.4% by classical parasitological methods (direct microscopy and formyl-ether acetate concentration, whereas 42 positives were detected by qPCR (6.0%. Conventional PCR confirmed the real-time PCR results in 24 of the samples (3.5%. Several apparent false-positive results occurred at higher cycle times (Ct in the qPCR. Use of real-time PCR in these populations is promising for the enhanced detection of disease and to support eradication efforts.

  19. Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

    NARCIS (Netherlands)

    Morton, C.O.; White, P.L.; Barnes, R.A.; Klingspor, L.; Cuenca-Estrella, M.; Lagrou, K.; Bretagne, S.; Melchers, W.J.; Mengoli, C.; Caliendo, A.M.; Cogliati, M.; Debets-Ossenkopp, Y.; Gorton, R.; Hagen, F.; Halliday, C.; Hamal, P.; Harvey-Wood, K.; Jaton, K.; Johnson, G.; Kidd, S.; Lengerova, M.; Lass-Florl, C.; Linton, C.; Millon, L.; Morrissey, C.O.; Paholcsek, M.; Talento, A.F.; Ruhnke, M.; Willinger, B.; Donnelly, J.P.; Loeffler, J.

    2017-01-01

    A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help

  20. Development and validation of PCR-based assays for diagnosis of American cutaneous leishmaniasis and identificatio nof the parasite species

    Directory of Open Access Journals (Sweden)

    Grazielle Cardoso da Graça

    2012-08-01

    Full Text Available In this study, PCR assays targeting different Leishmania heat-shock protein 70 gene (hsp70 regions, producing fragments ranging in size from 230-390 bp were developed and evaluated to determine their potential as a tool for the specific molecular diagnosis of cutaneous leishmaniasis (CL. A total of 70 Leishmania strains were analysed, including seven reference strains (RS and 63 previously typed strains. Analysis of the RS indicated a specific region of 234 bp in the hsp70 gene as a valid target that was highly sensitive for detection of Leishmania species DNA with capacity of distinguishing all analyzed species, after polymerase chain reaction-restriction fragment length polymorfism (PCR-RFLP. This PCR assay was compared with other PCR targets used for the molecular diagnosis of leishmaniasis: hsp70 (1400-bp region, internal transcribed spacer (ITS1 and glucose-6-phosphate dehydrogenase (G6pd. A good agreement among the methods was observed concerning the Leishmania species identification. Moreover, to evaluate the potential for molecular diagnosis, we compared the PCR targets hsp70-234 bp, ITS1, G6pd and mkDNA using a panel of 99 DNA samples from tissue fragments collected from patients with confirmed CL. Both PCR-hsp70-234 bp and PCR-ITS1 detected Leishmania DNA in more than 70% of the samples. However, using hsp70-234 bp PCR-RFLP, identification of all of the Leishmania species associated with CL in Brazil can be achieved employing a simpler and cheaper electrophoresis protocol.

  1. Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

    Science.gov (United States)

    Morton, C Oliver; White, P Lewis; Barnes, Rosemary A; Klingspor, Lena; Cuenca-Estrella, Manuel; Lagrou, Katrien; Bretagne, Stéphane; Melchers, Willem; Mengoli, Carlo; Caliendo, Angela M; Cogliati, Massimo; Debets-Ossenkopp, Yvette; Gorton, Rebecca; Hagen, Ferry; Halliday, Catriona; Hamal, Petr; Harvey-Wood, Kathleen; Jaton, Katia; Johnson, Gemma; Kidd, Sarah; Lengerova, Martina; Lass-Florl, Cornelia; Linton, Chris; Millon, Laurence; Morrissey, C Orla; Paholcsek, Melinda; Talento, Alida Fe; Ruhnke, Markus; Willinger, Birgit; Donnelly, J Peter; Loeffler, Juergen

    2017-06-01

    A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Optimization of a 12-hour TaqMan PCR-based method for detection of Salmonella bacteria in meat

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Krause, Michael; Hansen, F.

    2007-01-01

    no positive effects and resulted in decreased reproducibility. Increasing the amount of PCR template DNA from 5 to 20 mu l improved the threshold cycle value by approximately 2. The improved 12-h PCR method was successfully compared to a reference culture method with 100 minced meat and poultry samples...... the highest number of salmonellae. When analyzing minced meat samples, positive effects of increasing the initial sampling volume from 1 to 5 ml and increasing the amount of paramagnetic particles to 90 mu l were observed. However, washing the pellet and eluting the DNA in reduced volumes (25 and 50 mu l) had...

  3. PCR-based molecular characterization of Toxocara spp. using feces of stray cats: a study from Southwest Iran.

    Directory of Open Access Journals (Sweden)

    Shahram Khademvatan

    Full Text Available Feces of stray cat are potential sources of gastrointestinal parasites and play a crucial role in spreading and transmitting parasite eggs, larvae, and oocysts through contamination of soil, food, or water. In this study, we investigated the prevalence of Toxocara spp. infection in stray cats in Ahvaz city, southwest Iran. Eggs of Toxocara spp. in feces of stray cats were detected by the sucrose flotation method, and identification was conducted by polymerase chain reaction (PCR and DNA sequencing. Of the 140 fecal samples that were randomly collected from public environments during the months of January to May 2012, 45% were found to harbour Toxocara spp. eggs. The highest prevalence of Toxocara spp. eggs was found in the central area of Ahvaz city (28.6%. T. canis eggs were found in 4 (6.34% of the 63 positive samples. Stray cats are found in parks, playgrounds, and other public places and may be a potential contamination risk. Identification of Toxocara spp. using molecular methods is sufficiently sensitive to detect low levels of parasites and identify the different Toxocara spp. in feces. The relatively high prevalence of Toxocara spp. infection may continue to increase due to lack of effective environmental hygiene control in Iran. Consequently, there is a need to plan adequate programs to detect, identify, and control this infection as well as stray cats in the region.

  4. Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear.

    Science.gov (United States)

    Hassanpour, Gholamreza; Mirhendi, Hossein; Mohebali, Mehdi; Raeisi, Ahmad; Zeraati, Hojjat; Keshavarz, Hossein

    2016-01-01

    We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan- Plasmodium real-time PCR for accurate screening of individuals suspected of malaria. A single primer/probe set for pan-species Plasmodium -specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction. The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum . All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR. By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.

  5. Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear

    Directory of Open Access Journals (Sweden)

    Gholamreza HASSANPOUR

    2016-12-01

    Full Text Available Background: We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan-Plasmodium real-time PCR for accurate screening of individuals suspected of malaria.Methods: A single primer/probe set for pan-species Plasmodium-specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction.Results: The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum. All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR.Conclusion: By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.

  6. Evaluation and In-House Validation of Five DNA Extraction Methods for PCR-based STR Analysis of Bloodstained Denims

    Directory of Open Access Journals (Sweden)

    Henry Perdigon

    2004-06-01

    Full Text Available One type of crime scene evidence commonly submitted for analysis is bloodstain on denim. However, chemicals (e.g., indigo used to produce denim materials may co-purify with DNA and hence, affect subsequent DNA analysis. The present study compared five methods (e.g., standard organic, organic with hydrogen peroxide (H2O2, modified FTA™, organic/Chelex®-Centricon®, and QIAamp® DNA Mini Kit-based procedures for the isolation of blood DNA from denim. A Short Tandem Repeat (STR-based analysis across two to nine STR markers, namely, HUMvWA, HUMTH01, D8S306, HUMFES/FPS, HUMDHFRP2, HUMF13A01, HUMFGA, HUMTPOX, and HUMCSF1PO, was used to evaluate successful amplification of blood DNA extracted from light indigo, dark indigo, indigo-sulfur, pure indigo, sulfur-top, and sulfur-bottom denim materials. The results of the present study support the utility of organic/Chelex®-Centricon® and QIAamp® Kit procedures in extracting PCR-amplifiable DNA from five different types of denim materials for STR analysis. Furthermore, a solid-based method using FTA™ classic cards was modified to provide a simple, rapid, safe, and cost-effective procedure for extracting blood DNA from light, dark indigo and pure indigo denim materials. However, DNA eluted from bloodstained sulfur-dyed denims (e.g., sulfur-top and sulfur-bottom using FTA™ procedure was not readily amplifiable.

  7. Simulating an Investigative Study of Clinical Cancer Samples: Use of Tissue Slides and PCR-based Promoter-Hypermethylation Analysis

    Science.gov (United States)

    Chew, Yuan Yuan; Chin, Cheen Fei; Yeong, Foong May

    2015-01-01

    Topics on the molecular basis underlying cancer are quite popular among students. Also, excellent textbooks abound that provide interesting materials for discussion during lectures and tutorials about major events leading to cancer formation and progression. However, much less is available for students to conduct experiments for the analysis of…

  8. Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

    Science.gov (United States)

    Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

    2016-03-01

    The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea.

  9. Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

    Science.gov (United States)

    Kim, Jaai; Lim, Juntaek; Lee, Changsoo

    2013-12-01

    Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Stuttering-Psycholinguistic Approach

    Science.gov (United States)

    Hategan, Carolina Bodea; Anca, Maria; Prihoi, Lacramioara

    2012-01-01

    This research promotes psycholinguistic paradigm, it focusing in delimitating several specific particularities in stuttering pathology. Structural approach, on language sides proves both the recurrent aspects found within specialized national and international literature and the psycholinguistic approaches dependence on the features of the…

  11. Approaches to understand culture

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard; Rauner, Felix

    1996-01-01

    Different approaches to understand the concept ofculture are presented and evaluated. The author'sconcept of culture is defined. Different aspectsof the concept are discussed.......Different approaches to understand the concept ofculture are presented and evaluated. The author'sconcept of culture is defined. Different aspectsof the concept are discussed....

  12. Flipped Classroom Approach

    Science.gov (United States)

    Ozdamli, Fezile; Asiksoy, Gulsum

    2016-01-01

    Flipped classroom is an active, student-centered approach that was formed to increase the quality of period within class. Generally this approach whose applications are done mostly in Physical Sciences, also attracts the attention of educators and researchers in different disciplines recently. Flipped classroom learning which wide-spreads rapidly…

  13. The Geodynamic Approach

    DEFF Research Database (Denmark)

    Steenfelt, Jørgen S.; Ibsen, Lars Bo

    1996-01-01

    The Danish National lecture: The Geodynamic approach - problem or possibility? - mirrors the authors involvement in projects and research focusing on the impact of the geodynamic approach. The lecture discusses the why and how of some of the geotechnical anomalies and the differences in traditional...

  14. Life Span Developmental Approach

    Directory of Open Access Journals (Sweden)

    Ali Eryilmaz

    2011-03-01

    Full Text Available The Life Span Developmental Approach examines development of individuals which occurs from birth to death. Life span developmental approach is a multi-disciplinary approach related with disciplines like psychology, psychiatry, sociology, anthropology and geriatrics that indicates the fact that development is not completed in adulthood, it continues during the life course. Development is a complex process that consists of dying and death. This approach carefully investigates the development of individuals with respect to developmental stages. This developmental approach suggests that scientific disciplines should not explain developmental facts only with age changes. Along with aging, cognitive, biological, and socioemotional development throughout life should also be considered to provide a reasonable and acceptable context, guideposts, and reasonable expectations for the person. There are three important subjects whom life span developmental approach deals with. These are nature vs nurture, continuity vs discontinuity, and change vs stability. Researchers using life span developmental approach gather and produce knowledge on these three most important domains of individual development with their unique scientific methodology.

  15. Otoplasty: A graduated approach.

    Science.gov (United States)

    Foda, H M

    1999-01-01

    Numerous otoplastic techniques have been described for the correction of protruding ears. Technique selection in otoplasty should be done only after careful analysis of the abnormal anatomy responsible for the protruding ear deformity. A graduated surgical approach is presented which is designed to address all contributing factors to the presenting auricular deformity. The approach starts with the more conservative cartilage-sparing suturing techniques, then proceeds to incorporate other more aggressive cartilage weakening maneuvers. Applying this approach resulted in better long-term results with less postoperative lateralization than that encountered on using the cartilage-sparing techniques alone.

  16. Introducing Systems Approaches

    Science.gov (United States)

    Reynolds, Martin; Holwell, Sue

    Systems Approaches to Managing Change brings together five systems approaches to managing complex issues, each having a proven track record of over 25 years. The five approaches are: System Dynamics (SD) developed originally in the late 1950s by Jay Forrester Viable Systems Model (VSM) developed originally in the late 1960s by Stafford Beer Strategic Options Development and Analysis (SODA: with cognitive mapping) developed originally in the 1970s by Colin Eden Soft Systems Methodology (SSM) developed originally in the 1970s by Peter Checkland Critical Systems Heuristics (CSH) developed originally in the late 1970s by Werner Ulrich

  17. Flipped Classroom Approach

    Directory of Open Access Journals (Sweden)

    Fezile Ozdamli

    2016-07-01

    Full Text Available Flipped classroom is an active, student-centered approach that was formed to increase the quality of period within class. Generally this approach whose applications are done mostly in Physical Sciences, also attracts the attention of educators and researchers in different disciplines recently. Flipped classroom learning which wide-spreads rapidly in the world, is not well recognized in our country. That is why the aim of study is to attract attention to its potential in education field and provide to make it recognize more by educators and researchers. With this aim, in the study what flipped classroom approach is, flipped classroom technology models, its advantages and limitations were explained.

  18. Multidisciplinary Approaches to Allergies

    NARCIS (Netherlands)

    Gao Zhongshan,; Shen, Hua-Hao; Zheng, M.; Frewer, L.J.; Gilissen, L.J.W.J.

    2012-01-01

    Allergy is an immunological disease caused by multiple factors and characterized by variability, specificity and complexity. "Multidisciplinary Approaches to Allergies" covers diverse aspects ranging from basic molecular mechanisms to societal issues within the framework of multidisciplinary

  19. Behavioral based safety approaches

    International Nuclear Information System (INIS)

    Maria Michael Raj, I.

    2009-01-01

    Approach towards the establishment of positive safety culture at Heavy Water Plant, Tuticorin includes the adoption of several important methodologies focused on human behavior and culminates with achievement of Total Safety Culture where Quality and Productivity are integrated with Safety

  20. The transformativity approach

    DEFF Research Database (Denmark)

    Holm, Isak Winkel; Lauta, Kristian Cedervall

    2017-01-01

    During the last five to ten years, a considerable body of research has begun to explore how disasters, real and imagined, trigger social transformations. Even if the contributions to this this research stems from a multitude of academic disciplines, we argue in the article, they constitute...... an identifiable and promising approach for future disaster research. We suggest naming it the transformativity approach. Whereas the vulnerability approach explores the social causation of disasters, the transformativity approach reverses the direction of the gaze and investigates the social transformation...... brought about by disasters. Put simply, the concept of vulnerability is about the upstream causes of disaster and the concept of transformativity about the downstream effects. By discussing three recent contributions (by the historian Greg Bankoff, the legal sociologist Michelle Dauber...

  1. RNA/PNA Approach

    Indian Academy of Sciences (India)

    In this approach we want to develop structural analogue of the leader that might have higher affinity towards the Phosphoprotein, but would impair the dimerization process and viral leader RNA binding.

  2. a Capability approach

    African Journals Online (AJOL)

    efforts towards gender equality in education as a means of achieving social justice. ... should mean that a lot of capability approach-oriented commentators are ... processes, their forms of exercising power, and their rules, unwritten cultures, ...

  3. A Theoretical Approach

    African Journals Online (AJOL)

    NICO

    L-rhamnose and L-fucose: A Theoretical Approach ... L-ramnose and L-fucose, by means of the Monte Carlo conformational search method. The energy of the conformers ..... which indicates an increased probability for the occurrence of.

  4. Approach To Absolute Zero

    Indian Academy of Sciences (India)

    more and more difficult to remove heat as one approaches absolute zero. This is the ... A new and active branch of engineering ... This temperature is called the critical temperature, Te' For sulfur dioxide the critical ..... adsorbent charcoal.

  5. Revitalizing the setting approach

    DEFF Research Database (Denmark)

    Bloch, Paul; Toft, Ulla; Reinbach, Helene Christine

    2014-01-01

    BackgroundThe concept of health promotion rests on aspirations aiming at enabling people to increase control over and improve their health. Health promotion action is facilitated in settings such as schools, homes and work places. As a contribution to the promotion of healthy lifestyles, we have ...... approach is based on ecological and whole-systems thinking, and stipulates important principles and values of integration, participation, empowerment, context and knowledge-based development....... further developed the setting approach in an effort to harmonise it with contemporary realities (and complexities) of health promotion and public health action. The paper introduces a modified concept, the supersetting approach, which builds on the optimised use of diverse and valuable resources embedded...... in local community settings and on the strengths of social interaction and local ownership as drivers of change processes. Interventions based on a supersetting approach are first and foremost characterised by being integrated, but also participatory, empowering, context-sensitive and knowledge...

  6. Flipped Classroom Approach

    OpenAIRE

    Fezile Ozdamli; Gulsum Asiksoy

    2016-01-01

    Flipped classroom is an active, student-centered approach that was formed to increase the quality of period within class. Generally this approach whose applications are done mostly in Physical Sciences, also attracts the attention of educators and researchers in different disciplines recently. Flipped classroom learning which wide-spreads rapidly in the world, is not well recognized in our country. That is why the aim of study is to attract attention to its potential in education field and pr...

  7. STUTTERING-PSYCHOLINGUISTIC APPROACH

    OpenAIRE

    Maria Anca; Carolina Bodea Haţegan; Lăcrămioara Prihoi

    2012-01-01

    This research promotes psycholinguistic paradigm, it focusing in delimitating several specific particularities in stuttering pathology. Structural approach, on language sides proves both the recurrent aspects found within specialized national and international literature and the psycholinguistic approaches dependence on the features of the linguistic material. Thus, the conclusions of this research study offer the possibility of promoting cross-cultural and cross-linguistic researches, with t...

  8. An approach to measurement

    International Nuclear Information System (INIS)

    Gudder, S.P.

    1984-01-01

    A new approach to measurement theory is presented. The definition of measurement is motivated by direct laboratory procedures as they are carried out in practice. The theory is developed within the quantum logic framework. The work clarifies an important problem in the quantum logic approach; namely, where the Hilbert space comes from. The relationship between measurements and observables is considered, and a Hilbert space embedding theorem is presented. Charge systems are also discussed. (author)

  9. The Knowledge Governance Approach

    DEFF Research Database (Denmark)

    Foss, Nicolai J.

    with diverse capabilities of handling these transactions. Various open research issues that a knowledge governance approach may illuminate are sketched. Although knowledge governance draws clear inspiration from organizational economics and `rational' organization theory, it recognizes that knowledge......An attempt is made to characterize a `knowledge governance approach' as a distinctive, emerging field that cuts across the fields of knowledge management, organisation studies, strategy and human resource management. Knowledge governance is taken up with how the deployment of administrative...

  10. Theoretical Approaches to Coping

    Directory of Open Access Journals (Sweden)

    Sofia Zyga

    2013-01-01

    Full Text Available Introduction: Dealing with stress requires conscious effort, it cannot be perceived as equal to individual's spontaneous reactions. The intentional management of stress must not be confused withdefense mechanisms. Coping differs from adjustment in that the latter is more general, has a broader meaning and includes diverse ways of facing a difficulty.Aim: An exploration of the definition of the term "coping", the function of the coping process as well as its differentiation from other similar meanings through a literature review.Methodology: Three theoretical approaches of coping are introduced; the psychoanalytic approach; approaching by characteristics; and the Lazarus and Folkman interactive model.Results: The strategic methods of the coping approaches are described and the article ends with a review of the approaches including the functioning of the stress-coping process , the classificationtypes of coping strategies in stress-inducing situations and with a criticism of coping approaches.Conclusions: The comparison of coping in different situations is difficult, if not impossible. The coping process is a slow process, so an individual may select one method of coping under one set ofcircumstances and a different strategy at some other time. Such selection of strategies takes place as the situation changes.

  11. Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach.

    Science.gov (United States)

    Borner, Janus; Pick, Christian; Thiede, Jenny; Kolawole, Olatunji Matthew; Kingsley, Manchang Tanyi; Schulze, Jana; Cottontail, Veronika M; Wellinghausen, Nele; Schmidt-Chanasit, Jonas; Bruchhaus, Iris; Burmester, Thorsten

    2016-01-01

    The apicomplexan order Haemosporida is a clade of unicellular blood parasites that infect a variety of reptilian, avian and mammalian hosts. Among them are the agents of human malaria, parasites of the genus Plasmodium, which pose a major threat to human health. Illuminating the evolutionary history of Haemosporida may help us in understanding their enormous biological diversity, as well as tracing the multiple host switches and associated acquisitions of novel life-history traits. However, the deep-level phylogenetic relationships among major haemosporidian clades have remained enigmatic because the datasets employed in phylogenetic analyses were severely limited in either gene coverage or taxon sampling. Using a PCR-based approach that employs a novel set of primers, we sequenced fragments of 21 nuclear genes from seven haemosporidian parasites of the genera Leucocytozoon, Haemoproteus, Parahaemoproteus, Polychromophilus and Plasmodium. After addition of genomic data from 25 apicomplexan species, the unreduced alignment comprised 20,580 bp from 32 species. Phylogenetic analyses were performed based on nucleotide, codon and amino acid data employing Bayesian inference, maximum likelihood and maximum parsimony. All analyses resulted in highly congruent topologies. We found consistent support for a basal position of Leucocytozoon within Haemosporida. In contrast to all previous studies, we recovered a sister group relationship between the genera Polychromophilus and Plasmodium. Within Plasmodium, the sauropsid and mammal-infecting lineages were recovered as sister clades. Support for these relationships was high in nearly all trees, revealing a novel phylogeny of Haemosporida, which is robust to the choice of the outgroup and the method of tree inference. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. A retrospective cross-sectional quantitative molecular approach in biological samples from patients with syphilis.

    Science.gov (United States)

    Pinto, Miguel; Antelo, Minia; Ferreira, Rita; Azevedo, Jacinta; Santo, Irene; Borrego, Maria José; Gomes, João Paulo

    2017-03-01

    Syphilis is the sexually transmitted disease caused by Treponema pallidum, a pathogen highly adapted to the human host. As a multistage disease, syphilis presents distinct clinical manifestations that pose different implications for diagnosis. Nevertheless, the inherent factors leading to diverse disease progressions are still unknown. We aimed to assess the association between treponemal loads and dissimilar disease outcomes, to better understand syphilis. We retrospectively analyzed 309 DNA samples distinct anatomic sites associated with particular syphilis manifestations. All samples had previously tested positive by a PCR-based diagnostic kit. An absolute quantitative real-time PCR procedure was used to precisely quantify the number of treponemal and human cells to determine T. pallidum loads in each sample. In general, lesion exudates presented the highest T. pallidum loads in contrast with blood-derived samples. Within the latter, a higher dispersion of T. pallidum quantities was observed for secondary syphilis. T. pallidum was detected in substantial amounts in 37 samples of seronegative individuals and in 13 cases considered as syphilis-treated. No association was found between treponemal loads and serological results or HIV status. This study suggests a scenario where syphilis may be characterized by: i) heterogeneous and high treponemal loads in primary syphilis, regardless of the anatomic site, reflecting dissimilar duration of chancres development and resolution; ii) high dispersion of bacterial concentrations in secondary syphilis, potentially suggesting replication capability of T. pallidum while in the bloodstream; and iii) bacterial evasiveness, either to the host immune system or antibiotic treatment, while remaining hidden in privileged niches. This work highlights the importance of using molecular approaches to study uncultivable human pathogens, such as T. pallidum, in the infection process. Copyright © 2017 Elsevier Ltd. All rights

  13. Approaching a Postcolonial Arctic

    DEFF Research Database (Denmark)

    Jensen, Lars

    2016-01-01

    This article explores different postcolonially configured approaches to the Arctic. It begins by considering the Arctic as a region, an entity, and how the customary political science informed approaches are delimited by their focus on understanding the Arctic as a region at the service...... of the contemporary neoliberal order. It moves on to explore how different parts of the Arctic are inscribed in a number of sub-Arctic nation-state binds, focusing mainly on Canada and Denmark. The article argues that the postcolonial can be understood as a prism or a methodology that asks pivotal questions to all...... approaches to the Arctic. Yet the postcolonial itself is characterised by limitations, not least in this context its lack of interest in the Arctic, and its bias towards conventional forms of representation in art. The article points to the need to develop a more integrated critique of colonial and neo...

  14. Life History Approach

    DEFF Research Database (Denmark)

    Olesen, Henning Salling

    2015-01-01

    as in everyday life. Life histories represent lived lives past, present and anticipated future. As such they are interpretations of individuals’ experiences of the way in which societal dynamics take place in the individual body and mind, either by the individual him/herself or by another biographer. The Life...... History approach was developing from interpreting autobiographical and later certain other forms of language interactive material as moments of life history, i.e. it is basically a hermeneutic approach. Talking about a psycho-societal approach indicates the ambition of attacking the dichotomy...... of the social and the psychic, both in the interpretation procedure and in some main theoretical understandings of language, body and mind. My article will present the reflections on the use of life history based methodology in learning and education research as a kind of learning story of research work....

  15. Technical approach document

    International Nuclear Information System (INIS)

    1989-12-01

    The Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978, Public Law 95-604 (PL95-604), grants the Secretary of Energy the authority and responsibility to perform such actions as are necessary to minimize radiation health hazards and other environmental hazards caused by inactive uranium mill sites. This Technical Approach Document (TAD) describes the general technical approaches and design criteria adopted by the US Department of Energy (DOE) in order to implement remedial action plans (RAPS) and final designs that comply with EPA standards. It does not address the technical approaches necessary for aquifer restoration at processing sites; a guidance document, currently in preparation, will describe aquifer restoration concerns and technical protocols. This document is a second revision to the original document issued in May 1986; the revision has been made in response to changes to the groundwater standards of 40 CFR 192, Subparts A--C, proposed by EPA as draft standards. New sections were added to define the design approaches and designs necessary to comply with the groundwater standards. These new sections are in addition to changes made throughout the document to reflect current procedures, especially in cover design, water resources protection, and alternate site selection; only minor revisions were made to some of the sections. Sections 3.0 is a new section defining the approach taken in the design of disposal cells; Section 4.0 has been revised to include design of vegetated covers; Section 8.0 discusses design approaches necessary for compliance with the groundwater standards; and Section 9.0 is a new section dealing with nonradiological hazardous constituents. 203 refs., 18 figs., 26 tabs

  16. Homogenization approach in engineering

    International Nuclear Information System (INIS)

    Babuska, I.

    1975-10-01

    Homogenization is an approach which studies the macrobehavior of a medium by its microproperties. Problems with a microstructure play an essential role in such fields as mechanics, chemistry, physics, and reactor engineering. Attention is concentrated on a simple specific model problem to illustrate results and problems typical of the homogenization approach. Only the diffusion problem is treated here, but some statements are made about the elasticity of composite materials. The differential equation is solved for linear cases with and without boundaries and for the nonlinear case. 3 figures, 1 table

  17. Thematic curriculum approach

    Directory of Open Access Journals (Sweden)

    Šefer Jasmina P.

    2003-01-01

    Full Text Available Thematic curriculum combines disciplines and media. The process is problem-oriented and the scenario most often follows the logic of exploring or storytelling. Those two approaches to teaching are appropriate because they fit into interdisciplinary and creative open-ended problem solving through play, as insisted upon by thematic curriculum. The matrix, where seven types of abilities intersect with five types of problems according to their degree of openness, defines well the outcomes of teaching. However, it did not prove to be suitable for planning the majority of activities in thematic curriculum, for it follows with difficulty the process of exploring or storytelling i.e. it disrupts the subject matter coherence of thematic curriculum. Therefore, it is suggested that matrix should be used for disciplinary curriculum planning but for that of thematic curriculum only in exclusive cases. The matrix should be used primarily as a framework for evaluating the distribution of various types of abilities and problem situations in teaching. The logic of diverse approaches to teaching reflects itself in the manner of planning and organizing the teaching process. Conceptual, visual-graphic, structural and other aids employed during educational process planning should suit the nature of the approach chosen. On the basis of qualitative investigations of educational process, in the present paper considerations are given to various approaches to teaching development of various drafts for the planning of teaching, and recognition of the logic of storytelling and exploring in thematic curriculum.

  18. Islamic approach in counseling.

    Science.gov (United States)

    Hanin Hamjah, Salasiah; Mat Akhir, Noor Shakirah

    2014-02-01

    A religious approach is one of the matters emphasized in counseling today. Many researchers find that there is a need to apply the religious element in counseling because religion is important in a client's life. The purpose of this research is to identify aspects of the Islamic approach applied in counseling clients by counselors at Pusat Kaunseling Majlis Agama Islam Negeri Sembilan (PKMAINS). In addition, this research also analyses the Islamic approach applied in counseling at PKMAINS with reference to al-Quran and al-Sunnah. This is a qualitative research in the form of case study at PKMAINS. The main method used in this research is interview. The research instrument used is interview protocol. The respondents in this study include 9 counselors who serve in one of the counseling centers in Malaysia. This study also uses questionnaire as an additional instrument, distributed to 36 clients who receive counseling service at the center. The findings of the study show that the Islamic approach applied in counseling at PKMAINS may be categorized into three main aspects: aqidah (faith), ibadah (worship/ultimate devotion and love for God) and akhlaq (moral conduct). Findings also show that the counseling in these aspects is in line with Islamic teachings as contained in al-Quran and al-Sunnah.

  19. A green chemistry approach

    Indian Academy of Sciences (India)

    Administrator

    One-pot synthesis of quinaldine derivatives by using microwave irradiation without any solvent – A green chemistry approach. JAVAD SAFARI*, SAYED HOSSEIN BANITABA and SEPEHR SADEGH SAMIEI. Department of Chemistry, The Faculty of sciences, University of Kashan, Kashan,. P.O. Box 87317-51167, I.R. Iran.

  20. Realistic Approach to Innovation.

    Science.gov (United States)

    Dawson, Garth C.

    Part of the Omaha police in-service training program was devoted to innovative approaches to solving police department problems and improving community relations. The sessions were an attempt to use the brainstorming technique to elicit new solutions to everyday problems faced by the rank-and-file members of the police department. The report…

  1. Salt repository design approach

    International Nuclear Information System (INIS)

    Matthews, S.C.

    1983-01-01

    This paper presents a summary discussion of the approaches that have been and will be taken in design of repository facilities for use with disposal of radioactive wastes in salt formations. Since specific sites have yet to be identified, the discussion is at a general level, supplemented with illustrative examples where appropriate. 5 references, 1 figure

  2. The Capability Approach

    NARCIS (Netherlands)

    I.A.M. Robeyns (Ingrid)

    2011-01-01

    textabstract In its most general description, the capability approach is a flexible and multi-purpose normative framework, rather than a precise theory of well-being, freedom or justice. At its core are two normative claims: first, the claim that the freedom to achieve well-being is of primary

  3. Orion Emergency Mask Approach

    Science.gov (United States)

    Tuan, George C.; Graf, John C.

    2009-01-01

    Emergency mask approach on Orion poses a challenge to the traditional Shuttle or Station approaches. Currently, in the case of a fire or toxic spill event, the crew utilizes open loop oxygen masks that provide the crew with oxygen to breath, but also dumps the exhaled oxygen into the cabin. For Orion, with a small cabin volume, the extra oxygen will exceed the flammability limit within a short period of time, unless a nitrogen purge is also provided. Another approach to a fire or toxic spill event is the use of a filtering emergency masks. These masks utilize some form of chemical beds to scrub the air clean of toxic providing the crew safe breathing air for a period without elevating the oxygen level in the cabin. Using the masks and a form of smoke-eater filter, it may be possible to clean the cabin completely or to a level for safe transition to a space suit to perform a cabin purge. Issues with filters in the past have been the reaction time, breakthroughs, and high breathing resistance. Development in a new form of chemical filters has shown promise to make the filtering approach feasible.

  4. Approach to neonatal sepsis

    Directory of Open Access Journals (Sweden)

    Shankar Narayan

    2015-01-01

    The treatment includes supportive care along with administration of appropriate antibiotics. Adjuvant treatment includes IVIG, GCSF, exchange transfusion and pentoxifylline administration. This paper aims to present an algorithmic approach to neonatal sepsis to expedite the diagnosis along with providing appropriate and adequate treatment.

  5. Approaches to acceptable risk

    International Nuclear Information System (INIS)

    Whipple, C.

    1997-01-01

    Several alternative approaches to address the question open-quotes How safe is safe enough?close quotes are reviewed and an attempt is made to apply the reasoning behind these approaches to the issue of acceptability of radiation exposures received in space. The approaches to the issue of the acceptability of technological risk described here are primarily analytical, and are drawn from examples in the management of environmental health risks. These include risk-based approaches, in which specific quantitative risk targets determine the acceptability of an activity, and cost-benefit and decision analysis, which generally focus on the estimation and evaluation of risks, benefits and costs, in a framework that balances these factors against each other. These analytical methods tend by their quantitative nature to emphasize the magnitude of risks, costs and alternatives, and to downplay other factors, especially those that are not easily expressed in quantitative terms, that affect acceptance or rejection of risk. Such other factors include the issues of risk perceptions and how and by whom risk decisions are made

  6. Health: An Ecosystem Approach

    International Development Research Centre (IDRC) Digital Library (Canada)

    In the early days, the research supported was largely biomedical: vaccines, ... editor of Découvrir magazine in Montréal, who produced the first draft of the book, ...... Their transdisciplinary approach included gender-specific parameters. ..... Over time, some progress was made against malaria, but the war was far from won.

  7. NEW APPROACHES: Toppling trains

    Science.gov (United States)

    Parry, Malcolm

    1998-03-01

    This article explains a novel way of approaching centripetal force: theory is used to predict an orbital period at which a toy train will topple from a circular track. The demonstration has proved useful in A-level, GNVQ and undergraduate Physics and Engineering schemes.

  8. Approach to Absolute Zero

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 10. Approach to Absolute Zero Below 10 milli-Kelvin. R Srinivasan. Series Article Volume 2 Issue 10 October 1997 pp 8-16. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/002/10/0008-0016 ...

  9. Fuel cycle oriented approach

    International Nuclear Information System (INIS)

    Petit, A.

    1987-01-01

    The term fuel cycle oriented approach is currently used to designate two quite different things: the attempt to consider all or part of a national fuel cycle as one material balance area (MBA) or to consider individual MBAs existing in a state while designing a unique safeguards approach for each and applying the principle of nondiscrimination to fuel cycles as a whole, rather than to individual facilities. The merits of such an approach are acceptability by the industry and comparison with the contemplated establishment of long-term criteria. The following points concern the acceptability by the industry: (1) The main interest of the industry is to keep an open international market and therefore, to have effective and efficient safeguards. (2) The main concerns of the industry regarding international safeguards are economic burden, intrusiveness, and discrimination. Answers to these legitimate concerns, which retain the benefits of a fuel cycle oriented approach, are needed. More specifically, the problem of reimbursing the operator the costs that he has incurred for the safeguards must be considered

  10. Financial Management: An Organic Approach

    Science.gov (United States)

    Laux, Judy

    2013-01-01

    Although textbooks present corporate finance using a topical approach, good financial management requires an organic approach that integrates the various assignments financial managers confront every day. Breaking the tasks into meaningful subcategories, the current article offers one approach.

  11. Ecosystem approach in education

    Science.gov (United States)

    Nabiullin, Iskander

    2017-04-01

    Environmental education is a base for sustainable development. Therefore, in our school we pay great attention to environmental education. Environmental education in our school is based on ecosystem approach. What is an ecosystem approach? Ecosystem is a fundamental concept of ecology. Living organisms and their non-living environments interact with each other as a system, and the biosphere planet functions as a global ecosystem. Therefore, it is necessary for children to understand relationships in ecosystems, and we have to develop systems thinking in our students. Ecosystem approach and systems thinking should help us to solve global environmental problems. How do we implement the ecosystem approach? Students must understand that our biosphere functions as a single ecosystem and even small changes can lead to environmental disasters. Even the disappearance of one plant or animal species can lead to irreversible consequences. So in the classroom we learn the importance of each living organism for the nature. We pay special attention to endangered species, which are listed in the Red Data List. Kids are doing projects about these organisms, make videos, print brochures and newspapers. Fieldwork also plays an important role for ecosystem approach. Every summer, we go out for expeditions to study species of plants and animals listed in the Red Data List of Tatarstan. In class, students often write essays on behalf of any endangered species of plants or animals, this also helps them to understand the importance of each living organism in nature. Each spring we organise a festival of environmental projects among students. Groups of 4-5 students work on a solution of environmental problems, such as water, air or soil pollution, waste recycling, the loss of biodiversity, etc. Participants shoot a clip about their project, print brochures. Furthermore, some of the students participate in national and international scientific Olympiads with their projects. In addition to

  12. Domain Approach: An Alternative Approach in Moral Education

    Science.gov (United States)

    Vengadasalam, Chander; Mamat, Wan Hasmah Wan; Mail, Fauziah; Sudramanian, Munimah

    2014-01-01

    This paper discusses the use of the domain approach in moral education in an upper secondary school in Malaysia. Moral Education needs a creative and an innovative approach. Therefore, a few forms of approaches are used in the teaching-learning of Moral Education. This research describes the use of domain approach which comprises the moral domain…

  13. Rail transport systems approach

    CERN Document Server

    2017-01-01

    This book shows how the systems approach is employed by scientists in various countries to solve specific problems concerning railway transport. In particular, the book describes the experiences of scientists from Romania, Germany, the Czech Republic, the UK, Russia, Ukraine, Lithuania and Poland. For many of these countries there is a problem with the historical differences between the railways. In particular, there are railways with different rail gauges, with different signaling and communication systems, with different energy supplies and, finally, with different political systems, which are reflected in the different approaches to the management of railway economies. The book’s content is divided into two main parts, the first of which provides a systematic analysis of individual means of providing and maintaining rail transport. In turn, the second part addresses infrastructure and management development, with particular attention to security issues. Though primarily written for professionals involved...

  14. Approach to reliability assessment

    International Nuclear Information System (INIS)

    Green, A.E.; Bourne, A.J.

    1975-01-01

    Experience has shown that reliability assessments can play an important role in the early design and subsequent operation of technological systems where reliability is at a premium. The approaches to and techniques for such assessments, which have been outlined in the paper, have been successfully applied in variety of applications ranging from individual equipments to large and complex systems. The general approach involves the logical and systematic establishment of the purpose, performance requirements and reliability criteria of systems. This is followed by an appraisal of likely system achievment based on the understanding of different types of variational behavior. A fundamental reliability model emerges from the correlation between the appropriate Q and H functions for performance requirement and achievement. This model may cover the complete spectrum of performance behavior in all the system dimensions

  15. Thermodynamics an engineering approach

    CERN Document Server

    Cengel, Yunus A

    2014-01-01

    Thermodynamics, An Engineering Approach, eighth edition, covers the basic principles of thermodynamics while presenting a wealth of real-world engineering examples so students get a feel for how thermodynamics is applied in engineering practice. This text helps students develop an intuitive understanding by emphasizing the physics and physical arguments. Cengel and Boles explore the various facets of thermodynamics through careful explanations of concepts and use of numerous practical examples and figures, having students develop necessary skills to bridge the gap between knowledge and the confidence to properly apply their knowledge. McGraw-Hill is proud to offer Connect with the eighth edition of Cengel/Boles, Thermodynamics, An Engineering Approach. This innovative and powerful new system helps your students learn more efficiently and gives you the ability to assign homework problems simply and easily. Problems are graded automatically, and the results are recorded immediately. Track individual stude...

  16. Electronics a systems approach

    CERN Document Server

    Storey, Neil

    2017-01-01

    Electronics plays a central role in our everyday lives. It is at the heart of almost all of today's essential technology, from mobile phones to computers and from cars to power stations. As such, all engineers, scientists and technologists need to have a fundamental understanding of this exciting subject, and for many this will just be the beginning. Now in its sixth edition, Electronics: A Systems Approach provides an outstanding introduction to this fast-moving and important field. Comprehensively revised and updated to cover the latest developments in the world of electronics, the text continues to use Neil Storey's established and well-respected systems approach. It introduces the basic concepts first before progressing to a more advanced analysis, enabling you to contextualise what a system is designed to achieve before tackling the intricacies of designing or analysing its various components with confidence. This book is accompanied by a website which contains over 100 video tutorials to help explain ke...

  17. Transaction based approach

    Science.gov (United States)

    Hunka, Frantisek; Matula, Jiri

    2017-07-01

    Transaction based approach is utilized in some methodologies in business process modeling. Essential parts of these transactions are human beings. The notion of agent or actor role is usually used for them. The paper on a particular example describes possibilities of Design Engineering Methodology for Organizations (DEMO) and Resource-Event-Agent (REA) methodology. Whereas the DEMO methodology can be regarded as a generic methodology having its foundation in the theory of Enterprise Ontology the REA methodology is regarded as the domain specific methodology and has its origin in accountancy systems. The results of these approaches is that the DEMO methodology captures everything that happens in the reality with a good empirical evidence whereas the REA methodology captures only changes connected with economic events. Economic events represent either change of the property rights to economic resource or consumption or production of economic resources. This results from the essence of economic events and their connection to economic resources.

  18. Approaching comparative company law

    OpenAIRE

    Donald, David C.

    2008-01-01

    This paper identifies some common errors that occur in comparative law, offers some guidelines to help avoid such errors, and provides a framework for entering into studies of the company laws of three major jurisdictions. The first section illustrates why a conscious approach to comparative company law is useful. Part I discusses some of the problems that can arise in comparative law and offers a few points of caution that can be useful for practical, theoretical and legislative comparative ...

  19. Approaching Service Innovation Patterns

    OpenAIRE

    Andrea NAGY

    2013-01-01

    The present paper aims at analyzing the types of innovation in the field of services. First, the concept of innovation is defined and second, field literature is reviewed from the perspective of service innovation. The main types of innovation are identified based on several attempts at defining innovation, the most notable being Schumpeter’s. Thus, it is possible to approach concepts such as product and process innovation, incremental and radical innovation. Another aim has been to regard se...

  20. Robust Approaches to Forecasting

    OpenAIRE

    Jennifer Castle; David Hendry; Michael P. Clements

    2014-01-01

    We investigate alternative robust approaches to forecasting, using a new class of robust devices, contrasted with equilibrium correction models. Their forecasting properties are derived facing a range of likely empirical problems at the forecast origin, including measurement errors, implulses, omitted variables, unanticipated location shifts and incorrectly included variables that experience a shift. We derive the resulting forecast biases and error variances, and indicate when the methods ar...

  1. The Branding Management Approaches

    Institute of Scientific and Technical Information of China (English)

    YAKOUBI; Mohamed Lamine

    2014-01-01

    [Abstract]We wil try to present,through the display of the various branding concepts and theories, the different branding management approaches.This wil present the different visions of the discipline depending on the author to try and demonstrate their differences,at first, and their complementarities at last to help the different branding management practitioners (brand managers,marketing managers,advertisers,media-planners……) apprehend the right brand positioning strategy to engage.

  2. Towards a Dual Approach

    DEFF Research Database (Denmark)

    Holli, Anne Maria; Harder, Mette Marie Stæhr

    2016-01-01

    Drawing on insights from state feminism and legislative studies on parliamentary committees, this article develops a dual approach for the comparative analysis of committees on gender equality. Empirically, it compares the standing committees on gender equality in Denmark and Finland, two Nordic...... as measured by legislative outputs and oversight differs, however, in line with differing committee system characteristics: the Finnish committee has more impact on legislative outputs while the Danish committee has more impact on overseeing government....

  3. CoMStOC vs. International Solar Month - Experience gained and lessons learned from SMM campaigns

    Science.gov (United States)

    Schmelz, J. T.

    1991-01-01

    The factors that should be addressed by the organizers of a solar observing campaign are outlined and described. Two recent solar observing campaigns are compared and discussed. Lessons learned from these and other campaigns involving the SMM satellite are analyzed and advice for future campaigns is offered.

  4. A neural model of motion processing and visual navigation by cortical area MST.

    Science.gov (United States)

    Grossberg, S; Mingolla, E; Pack, C

    1999-12-01

    Cells in the dorsal medial superior temporal cortex (MSTd) process optic flow generated by self-motion during visually guided navigation. A neural model shows how interactions between well-known neural mechanisms (log polar cortical magnification, Gaussian motion-sensitive receptive fields, spatial pooling of motion-sensitive signals and subtractive extraretinal eye movement signals) lead to emergent properties that quantitatively simulate neurophysiological data about MSTd cell properties and psychophysical data about human navigation. Model cells match MSTd neuron responses to optic flow stimuli placed in different parts of the visual field, including position invariance, tuning curves, preferred spiral directions, direction reversals, average response curves and preferred locations for stimulus motion centers. The model shows how the preferred motion direction of the most active MSTd cells can explain human judgments of self-motion direction (heading), without using complex heading templates. The model explains when extraretinal eye movement signals are needed for accurate heading perception, and when retinal input is sufficient, and how heading judgments depend on scene layouts and rotation rates.

  5. Enhanced confinement with plasma biasing in the MST reversed field pinch

    International Nuclear Information System (INIS)

    Craig, D.; Almagri, A.F.; Anderson, J.K.

    1997-06-01

    We report an increase in particle confinement with plasma biasing in a reversed field pinch. Miniature plasma sources are used as electrodes to negatively bias the plasma at the edge (r/a ∼ 0.9). Particle content increases and H α radiation decreases upon application of bias and global particle confinement roughly doubles as a result. Measurements of plasma potential, impurity flow, and floating potential fluctuations indicate that strong flows are produced and that electrostatic fluctuations are reduced

  6. X-ray analysis of electron Bernstein wave heating in MST

    Energy Technology Data Exchange (ETDEWEB)

    Seltzman, A. H., E-mail: seltzman@wisc.edu; Anderson, J. K.; DuBois, A. M.; Almagri, A.; Forest, C. B. [Department of Physics, University of Wisconsin, Madison, Wisconsin 53706 (United States)

    2016-11-15

    A pulse height analyzing x-ray tomography system has been developed to detect x-rays from electron Bernstein wave heated electrons in the Madison symmetric torus reversed field pinch (RFP). Cadmium zinc telluride detectors are arranged in a parallel beam array with two orthogonal multi-chord detectors that may be used for tomography. In addition a repositionable 16 channel fan beam camera with a 55° field of view is used to augment data collected with the Hard X-ray array. The chord integrated signals identify target emission from RF heated electrons striking a limiter located 12° toroidally away from the RF injection port. This provides information on heated electron spectrum, transport, and diffusion. RF induced x-ray emission from absorption on harmonic electron cyclotron resonances in low current (<250 kA) RFP discharges has been observed.

  7. MAARSY - The new MST radar on Andøya: System description and first results

    Science.gov (United States)

    Latteck, Ralph; Zecha, Marius; Rapp, Markus; Stober, Gunter; Singer, Werner; Renkwitz, Toralf

    2012-07-01

    In 2011 the Leibniz-Institute of Atmospheric Physics in Kühlungsborn completed the installation of the Middle Atmosphere Alomar Radar System ({MAARSY}) on the North-Norwegian island Andøya. MAARSY is a 53.5 MHz monostatic radar with an active phased array antenna consisting of 433 Yagi antennas. The 3-element Yagi antennas are arranged in an equilateral triangular grid forming a circular aperture of approximately 6300 m^2. Each individual antenna is connected to its own transceiver with independent phase control and a scalable power output of up to 2 kW. This arrangement provides very high flexibility of beam forming and beam steering with a symmetric radar beam of a minimum beam width of 3.6°. The system allows classical beam swinging operation as well as experiments with simultaneous multiple beams and the use of interferometric applications for improved studies of the Arctic atmosphere from the troposphere up to the lower thermosphere with high spatio-temporal resolution. Standard observations of tropospheric winds and polar mesosphere summer echoes started immediately with an initial stage of expansion in spring 2010. Meteor head echo experiments and 3D observations of polar mesospheric winter echoes were conducted after an upgrade of the system in December 2010. Multi-beam experiments using up to 97 beams quasi-simultaneously in the mesosphere have been carried out during campaigns in summer 2011 with the completed system. We present a system description of MAARSY including beam pattern validation and show initial results from various campaigns obtained during the first 2 years of operation.

  8. MAARSY: The new MST radar on Andøya—System description and first results

    Science.gov (United States)

    Latteck, R.; Singer, W.; Rapp, M.; Vandepeer, B.; Renkwitz, T.; Zecha, M.; Stober, G.

    2012-02-01

    The Middle Atmosphere Alomar Radar System (MAARSY) on the North-Norwegian island Andøya is a 53.5 MHz monostatic radar with an active phased array antenna consisting of 433 Yagi antennas. The 3-element Yagi antennas are arranged in an equilateral triangle grid forming a circular aperture of approximately 6300 m2. Each individual antenna is connected to its own transceiver with independent phase control and a scalable power output up to 2 kW. This arrangement provides a very high flexibility of beam forming and beam steering with a symmetric radar beam of a minimum beam width of 3.6° allowing classical beam swinging operation as well as experiments with simultaneous multiple beams and the use of interferometric applications for improved studies of the Arctic atmosphere from the troposphere up to the lower thermosphere with high spatio-temporal resolution. The installation of the antenna array was completed in August 2009. The radar control and data acquisition hardware as well as an initial expansion stage of 196 transceiver modules was installed in spring 2010 and upgraded to 343 transceiver modules in November 2010. The final extension to 433 transceiver modules has recently been completed in May 2011. Beside standard observations of tropospheric winds and Polar Mesosphere Summer Echoes, the first multi-beam experiments using up to 97 quasi-simultaneous beams in the mesosphere have been carried out in 2010 and 2011. These results provide a first insight into the horizontal variability of polar mesosphere summer and winter echoes with time resolutions between 3 and 9 minutes. In addition, first meteor head echo observations were conducted during the Geminid meteor shower in December 2010.

  9. Core fluctuations and current profile dynamics in the MST reversed-field pinch

    International Nuclear Information System (INIS)

    Brower, D.L.; Ding, W.X.; Lei, J.

    2003-01-01

    First measurements of the current density profile, magnetic field fluctuations and electrostatic (e.s.) particle flux in the core of a high-temperature reversed-field pinch (RFP) are presented. We report three new results: (1) The current density peaks during the slow ramp phase of the sawtooth cycle and flattens promptly at the crash. Profile flattening can be linked to magnetic relaxation and the dynamo which is predicted to drive anti-parallel current in the core. Measured core magnetic fluctuations are observed to increases four-fold at the crash. Between sawtooth crashes, measurements indicate the particle flux driven by e.s. fluctuations is too small to account for the total radial particle flux. (2) Core magnetic fluctuations are observed to decrease at least twofold in plasmas where energy confinement time improves ten-fold. In this case, the radial particle flux is also reduced, suggesting core e.s. fluctuation-induced transport may play role in confinement. (3) The parallel current density increases in the outer region of the plasma during high confinement, as expected, due to the applied edge parallel electric field. However, the core current density also increases due to dynamo reduction and the emergence of runaway electrons. (author)

  10. mställdhet nästa! Samhällsplanering ur ett genusperspektiv

    OpenAIRE

    Larsson, Anita; Jalakas, Anne

    2008-01-01

    The book develops ideas and tools to meet the Swedish government’s aim to mainstream the policy of equal opportunities into all policy areas. To apply the gender perspective at the level of strategic planning, instead of at a detailed level, is stressed. To start, concepts such as equal opportunities and gender perspective are elaborated in relation to the field of planning. Through applying gender theory it is shown how conventional planning may contribute to gender inequality by neglecting ...

  11. A high-resolution study of mesospheric fine structure with the Jicamarca MST radar

    Directory of Open Access Journals (Sweden)

    R. Sheth

    2006-07-01

    Full Text Available Correlation studies performed on data from recent mesospheric experiments conducted with the 50-MHz Jicamarca radar in May 2003 and July 2004 are reported. The study is based on signals detected from a combination of vertical and off-vertical beams. The nominal height resolution was 150 m and spectral estimates were obtained after ~1 min integration. Spectral widths and backscattered power generally show positive correlations at upper mesospheric heights in agreement with earlier findings (e.g., Fukao et al., 1980 that upper mesospheric echoes are dominated by isotropic Bragg scatter. In many instances in the upper mesosphere, a weakening of positive correlation away from layer centers (towards top and bottom boundaries was observed with the aid of improved height resolution. This finding supports the idea that layer edges are dominated by anisotropic turbulence. The data also suggests that negative correlations observed at lower mesospheric heights are caused by scattering from anisotropic structures rather than reflections from sharp vertical gradients in electron density.

  12. BRAVEMIND: Advancing the Virtual Iraq/Afghanistan PTSD Exposure Therapy for MST

    Science.gov (United States)

    2016-06-01

    It has three questions that ask the frequency and amount of alcohol consumed . Psychophysiological Patient Report: This is a brief self-report...to sleep without nightmares waking him, and began challenging some of his fears around going to restaurants , movies, etc. At follow-up, John’s...Jones-Alexander, J., Buckley, T. C., & Forneris, C. A. (1996). Psychometric properties of the PTSD checklist (PCL). Behaviour Research and Therapy, 34

  13. A high-resolution study of mesospheric fine structure with the Jicamarca MST radar

    Science.gov (United States)

    Sheth, R.; Kudeki, E.; Lehmacher, G.; Sarango, M.; Woodman, R.; Chau, J.; Guo, L.; Reyes, P.

    2006-07-01

    Correlation studies performed on data from recent mesospheric experiments conducted with the 50-MHz Jicamarca radar in May 2003 and July 2004 are reported. The study is based on signals detected from a combination of vertical and off-vertical beams. The nominal height resolution was 150 m and spectral estimates were obtained after ~1 min integration. Spectral widths and backscattered power generally show positive correlations at upper mesospheric heights in agreement with earlier findings (e.g., Fukao et al., 1980) that upper mesospheric echoes are dominated by isotropic Bragg scatter. In many instances in the upper mesosphere, a weakening of positive correlation away from layer centers (towards top and bottom boundaries) was observed with the aid of improved height resolution. This finding supports the idea that layer edges are dominated by anisotropic turbulence. The data also suggests that negative correlations observed at lower mesospheric heights are caused by scattering from anisotropic structures rather than reflections from sharp vertical gradients in electron density.

  14. Study of equatorial Kelvin waves using the MST radar and radiosonde observations

    Directory of Open Access Journals (Sweden)

    P. Kishore

    2005-06-01

    Full Text Available In this paper an attempt has been made to study equatorial Kelvin waves using a high power coherent VHF radar located at Gadanki (13.5° N, 79.2° E, a tropical station in the Indian sub-continent. Simultaneous radiosonde observations taken from a nearby meteorological station located in Chennai (13.04° N, 80.17° E were also used to see the coherence in the observed structures. These data sets were analyzed to study the mean winds and equatorial waves in the troposphere and lower stratosphere. Equatorial waves with different periodicities were identified. In the present study, particular attention has been given to the fast Kelvin wave (6.5-day and slow Kelvin wave (16-day. Mean zonal wind structures were similar at both locations. The fast Kelvin wave amplitudes were somewhat similar in both observations and the maximum amplitude is about 8m/s. The phase profiles indicated a slow downward progression. The slow Kelvin wave (16-day amplitudes shown by the radiosonde measurements are a little larger than the radar derived amplitudes. The phase profiles showed downward phase progression and it translates into a vertical wavelength of ~10-12km. The radar and radiosonde derived amplitudes of fast and slow Kelvin waves are larger at altitudes near the tropopause (15-17km, where the mean wind attains westward maximum.

  15. BRAVEMIND: Advancing the Virtual Iraq/Afghanistan PTSD Exposure Therapy for MST

    Science.gov (United States)

    2017-08-01

    including psychological history, suicidality , and alcohol/substance abuse/dependence, and ability to wear VR headset were briefly reviewed according to a...There were no significant differences between study completers and study non- completers on pre-treatment measures of PTSD and depression . See Table 1...participants in the VRET group would show statistically and clinically meaningful reductions in PTSD and depression (PCL-5, CAPS, PHQ-9 scores and

  16. Classical confinement and outward convection of impurity ions in the MST RFP

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S. T. A.; Den Hartog, D. J.; Mirnov, V. V.; Eilerman, S.; Nornberg, M.; Reusch, J. A.; Sarff, J. S. [Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Center for Magnetic Self-Organization in Laboratory and Astrophysical Plasmas, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Caspary, K. J.; Chapman, B. E.; Parke, E. [Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Magee, R. M. [Department of Physics, West Virginia University, Morgantown, WV 26506 (United States); Brower, D. L.; Ding, W. X.; Lin, L. [Department of Physics and Astronomy, University of California, Los Angeles, California 90095 (United States); Craig, D. [Physics Department, Wheaton College, Wheaton, Illinois 60187 (United States); Fiksel, G. [Center for Magnetic Self-Organization in Laboratory and Astrophysical Plasmas, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Laboratory for Laser Energetics, University of Rochester, Rochester, New York (United States)

    2012-05-15

    Impurity ion dynamics measured with simultaneously high spatial and temporal resolution reveal classical ion transport in the reversed-field pinch. The boron, carbon, oxygen, and aluminum impurity ion density profiles are obtained in the Madison Symmetric Torus [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)] using a fast, active charge-exchange-recombination-spectroscopy diagnostic. Measurements are made during improved-confinement plasmas obtained using inductive control of tearing instability to mitigate stochastic transport. At the onset of the transition to improved confinement, the impurity ion density profile becomes hollow, with a slow decay in the core region concurrent with an increase in the outer region, implying an outward convection of impurities. Impurity transport from Coulomb collisions in the reversed-field pinch is classical for all collisionality regimes, and analysis shows that the observed hollow profile and outward convection can be explained by the classical temperature screening mechanism. The profile agrees well with classical expectations. Experiments performed with impurity pellet injection provide further evidence for classical impurity ion confinement.

  17. Measurement of current density fluctuations and ambipolar particle flux due to magnetic fluctuations in MST

    International Nuclear Information System (INIS)

    Shen, Weimin.

    1992-08-01

    Studies of magnetic fluctuation induced particle transport on Reversed Field Pinch plasmas were done on the Madison Symmetric Torus. Plasma current density and current density fluctuations were measured using a multi-coil magnetic probes. The low frequency (f parallel B r >. The result of zero net charged particle loss was obtained, meaning the flux is ambipolar. The ambipolarity of low frequency global tearing modes is satisfied through the phase relations determined by tearing instabilities. The ambipolarity of high frequency localized modes could be partially explained by the simple model of Waltz based on the radial average of small scale turbulence

  18. APPROACHES FOR SUSTAINABLE MANUFACTURING

    Institute of Scientific and Technical Information of China (English)

    G(U)NTHER Seliger; SEBASTIAN Kernbaum; MARCO Zettl

    2007-01-01

    Sustainable development is a holistic approach harmonizing ecological, economical and socio-political needs with respect to the superior objective of enhancing human living standards. Thereby the availability of natural resources and the conservation of the ecosystems have to be considered that future generations have the possibility to meet their own needs. A long-term economical development demands the transition from a source-sink economy to a cycle economy as a result of limited resources, limited environmental capacities to absorb waste and emissions as well as increasing needs of a growing population. A reference model for sustainability in manufacturing is presented and used to illustrate sustainable approaches with respect to management, technology, process and product. Adaptation of products and components is a vital element for supporting efficient reuse of products and components. Consequently adaptation contributes to the ambitious goals of sustainability. Technological enablers for adaptation as modularity, information and communication technology are exemplarily introduced. Moreover, approaches for disseminating knowledge in sustainability are given.

  19. Dynamic Portfolio Strategy Using Clustering Approach.

    Science.gov (United States)

    Ren, Fei; Lu, Ya-Nan; Li, Sai-Ping; Jiang, Xiong-Fei; Zhong, Li-Xin; Qiu, Tian

    2017-01-01

    The problem of portfolio optimization is one of the most important issues in asset management. We here propose a new dynamic portfolio strategy based on the time-varying structures of MST networks in Chinese stock markets, where the market condition is further considered when using the optimal portfolios for investment. A portfolio strategy comprises two stages: First, select the portfolios by choosing central and peripheral stocks in the selection horizon using five topological parameters, namely degree, betweenness centrality, distance on degree criterion, distance on correlation criterion and distance on distance criterion. Second, use the portfolios for investment in the investment horizon. The optimal portfolio is chosen by comparing central and peripheral portfolios under different combinations of market conditions in the selection and investment horizons. Market conditions in our paper are identified by the ratios of the number of trading days with rising index to the total number of trading days, or the sum of the amplitudes of the trading days with rising index to the sum of the amplitudes of the total trading days. We find that central portfolios outperform peripheral portfolios when the market is under a drawup condition, or when the market is stable or drawup in the selection horizon and is under a stable condition in the investment horizon. We also find that peripheral portfolios gain more than central portfolios when the market is stable in the selection horizon and is drawdown in the investment horizon. Empirical tests are carried out based on the optimal portfolio strategy. Among all possible optimal portfolio strategies based on different parameters to select portfolios and different criteria to identify market conditions, 65% of our optimal portfolio strategies outperform the random strategy for the Shanghai A-Share market while the proportion is 70% for the Shenzhen A-Share market.

  20. Dynamic Portfolio Strategy Using Clustering Approach.

    Directory of Open Access Journals (Sweden)

    Fei Ren

    Full Text Available The problem of portfolio optimization is one of the most important issues in asset management. We here propose a new dynamic portfolio strategy based on the time-varying structures of MST networks in Chinese stock markets, where the market condition is further considered when using the optimal portfolios for investment. A portfolio strategy comprises two stages: First, select the portfolios by choosing central and peripheral stocks in the selection horizon using five topological parameters, namely degree, betweenness centrality, distance on degree criterion, distance on correlation criterion and distance on distance criterion. Second, use the portfolios for investment in the investment horizon. The optimal portfolio is chosen by comparing central and peripheral portfolios under different combinations of market conditions in the selection and investment horizons. Market conditions in our paper are identified by the ratios of the number of trading days with rising index to the total number of trading days, or the sum of the amplitudes of the trading days with rising index to the sum of the amplitudes of the total trading days. We find that central portfolios outperform peripheral portfolios when the market is under a drawup condition, or when the market is stable or drawup in the selection horizon and is under a stable condition in the investment horizon. We also find that peripheral portfolios gain more than central portfolios when the market is stable in the selection horizon and is drawdown in the investment horizon. Empirical tests are carried out based on the optimal portfolio strategy. Among all possible optimal portfolio strategies based on different parameters to select portfolios and different criteria to identify market conditions, 65% of our optimal portfolio strategies outperform the random strategy for the Shanghai A-Share market while the proportion is 70% for the Shenzhen A-Share market.

  1. Peritonitis: laparoscopic approach

    Directory of Open Access Journals (Sweden)

    Agresta Ferdinando

    2006-03-01

    Full Text Available Abstract Background Laparoscopy has became as the preferred surgical approach to a number of different diseases because it allows a correct diagnosis and treatment at the same time. In abdominal emergencies, both components of treatment – exploration to identify the causative pathology and performance of an appropriate operation – can often be accomplished via laparoscopy. There is still a debate of peritonitis as a contraindication to this kind of approach. Aim of the present work is to illustrate retrospectively the results of a case-control experience of laparoscopic vs. open surgery for abdominal peritonitis emergencies carried out at our institution. Methods From January 1992 and January 2002 a total of 935 patients (mean age 42.3 ± 17.2 years underwent emergent and/or urgent surgery. Among them, 602 (64.3% were operated on laparoscopically (of whom 112 -18.7% – with peritonitis, according to the presence of a surgical team trained in laparoscopy. Patients with a history of malignancy, more than two previous major abdominal surgeries or massive bowel distension were not treated Laparoscopically. Peritonitis was not considered contraindication to Laparoscopy. Results The conversion rate was 23.2% in patients with peritonitis and was mainly due to the presence of dense intra-abdominal adhesions. Major complications ranged as high as 5.3% with a postoperative mortality of 1.7%. A definitive diagnosis was accomplished in 85.7% (96 pat. of cases, and 90.6% (87 of these patients were treated successfully by Laparoscopy. Conclusion Even if limited by its retrospective feature, the present experience let us to consider the Laparoscopic approach to abdominal peritonitis emergencies a safe and effective as conventional surgery, with a higher diagnostic yield and allows for lesser trauma and a more rapid postoperative recovery. Such features make Laparoscopy a challenging alternative to open surgery in the management algorithm for abdominal

  2. Standardised approach to optimisation

    International Nuclear Information System (INIS)

    Warren-Forward, Helen M.; Beckhaus, Ronald

    2004-01-01

    Optimisation of radiographic images is said to have been obtained if the patient has achieved an acceptable level of dose and the image is of diagnostic value. In the near future, it will probably be recommended that radiographers measure patient doses and compare them to reference levels. The aim of this paper is to describe a standardised approach to optimisation of radiographic examinations in a diagnostic imaging department. A three-step approach is outlined with specific examples for some common examinations (chest, abdomen, pelvis and lumbar spine series). Step One: Patient doses are calculated. Step Two: Doses are compared to existing reference levels and the technique used compared to image quality criteria. Step Three: Appropriate action is taken if doses are above the reference level. Results: Average entrance surface doses for two rooms were as follows AP Abdomen (6.3mGy and 3.4mGy); AP Lumbar Spine (6.4mGy and 4.1mGy) for AP Pelvis (4.8mGy and 2.6mGy) and PA chest (0.19mGy and 0.20mGy). Comparison with the Commission of the European Communities (CEC) recommended techniques identified large differences in the applied potential. The kVp values in this study were significantly lower (by up to lOkVp) than the CEC recommendations. The results of this study have indicated that there is a need to monitor radiation doses received by patients undergoing diagnostic radiography examinations. Not only has the assessment allowed valuable comparison with International Diagnostic Reference Levels and Radiography Good Practice but has demonstrated large variations in mean doses being delivered from different rooms of the same radiology department. Following the simple 3-step approach advocated in this paper should either provide evidence that department are practising the ALARA principle or assist in making suitable changes to current practice. Copyright (2004) Australian Institute of Radiography

  3. Experimental approaches and applications

    CERN Document Server

    Crasemann, Bernd

    1975-01-01

    Atomic Inner-Shell Processes, Volume II: Experimental Approaches and Applications focuses on the physics of atomic inner shells, with emphasis on experimental aspects including the use of radioactive atoms for studies of atomic transition probabilities. Surveys of modern techniques of electron and photon spectrometry are also presented, and selected practical applications of inner-shell processes are outlined. Comprised of six chapters, this volume begins with an overview of the general principles underlying the experimental techniques that make use of radioactive isotopes for inner-sh

  4. Craniopharyngioma - Transnasal Endoscopic Approach

    Directory of Open Access Journals (Sweden)

    Sanjeev Bhagat,

    2011-01-01

    Full Text Available Craniopharyngiomas are slow growing tumours arising from remnants of the craniopharyngeal duct and occupy the sellar region. The patients may remain asymptomatic for long duration or present with headache or visual disturbances. Surgery is the mainstay of the treatment. Traditionally these tumours have been removed by neurosurgeons through the cranial approach but the advent of nasal endoscopes has opened new avenues for ENT surgeons to treat such patients. We hereby present a case of craniopharyngioma who was successfully treated by Trans-nasal Hypophysectomy.

  5. URBAN POLITICS: KEY APPROACHES

    Directory of Open Access Journals (Sweden)

    Ledyaeva Ol'ga Mikhaylovna

    2012-10-01

    Full Text Available Several approaches that underlie urban politics are discussed in the paper. They include neo-liberalism, political economy discourse, elitist/pluralist debates, and postmodernism. The neoliberal approach focuses on the limited role of the state and individual responsibility. The legal framework protects both the rights and responsibilities of individuals and regulates the operation of the market. It is the market that fosters individual choices and provides goods and services by virtue of the processes which are flexible, efficient and transparent. The political economy approaches (regulation theory, public choice theory, neo-Marxism explain urban politics via the analysis of national and international economic processes and changes in contemporary capitalism. Changes in national and international economies determine what solutions are possible. The discourse has been influenced by the debate on globalization of capital and labour markets. Modern elitism and neopluralism are represented by theories of "growth machines" and "urban regimes". The former focuses on bargaining alliances between political and business leaders in order to manage the urban system and to promote its growth. The latter develops neopluralist explanations of power within local communities with an emphasis on the fragmented nature of the government where local authorities lack comprehensive governing powers. Postmodernism views the city as the site of the crisis of late capitalism which leads to segregation of neighbourhoods onto prosperous areas and ghettoes. In contrast to the modern city, the postmodern city is not defined by its industrial base; rather, it is determined by its consumerist environment of malls and museums, characterized by revivalist architecture. At the same time, the suburban shopping mall and a motorway network make nonsense of the idea of the city as a unique and well-defined space. These and other approaches encompass a wide spectrum of possibilities

  6. New Encrypted Steganography Approach

    Directory of Open Access Journals (Sweden)

    Saba Mohammed Husain‎

    2017-12-01

    Full Text Available The proposed research Provides an approach for hiding an encrypted text in side a digital image. Where the text is encrypted in a complex manner used method of PlayFair to encrypt clear text and to increase security put lettering ciphertext on the geometric shape clockwise and then we write the ciphertext output in the form of lines, taken new ciphertext and converted to Ascii code and then to binary and hidden text in bits least importance in the picture. The results were good by PNSR scale

  7. The Capability Approach

    OpenAIRE

    Robeyns, Ingrid

    2011-01-01

    textabstract In its most general description, the capability approach is a flexible and multi-purpose normative framework, rather than a precise theory of well-being, freedom or justice. At its core are two normative claims: first, the claim that the freedom to achieve well-being is of primary moral importance, and second, that freedom to achieve well-being is to be understood in terms of people’s capabilities, that is, their real opportunities to do and be what they have reason to value. Thi...

  8. The collaboratory approach

    International Nuclear Information System (INIS)

    Peskin, A.M.

    1997-01-01

    A open-quotes collaboratoryclose quotes has been defined as a center without walls, in which researchers can perform their work without regard to geographical location. To an increasing degree, engineering design and development is also taking the form of far-flung collaborations among divisions of a plant, subcontractors, university consultants and customers. It has long been recognized that quality engineering education presents the student with an environment that duplicates as much as possible that which the graduate will encounter in industry. To that end, it is important that engineering schools begin to introduce the collaboratory approach in its preparation, and even use it in delivery of subject matter to students

  9. Diagnostic Approach to Myelopathies

    International Nuclear Information System (INIS)

    Granados Sanchez, Ana Maria; Garcia Posada, Lina Maria; Ortega Toscano, Cesar Andres; Lopez Lopez, Alejandra

    2011-01-01

    Myelopathy is a broad term that refers to spinal cord involvement of multiple etiologies. Spinal cord diseases often have devastating consequences, ranging from quadriplegia and paraplegia to severe sensory deficits due to its confinement in a very small area. Many of these diseases are potentially reversible if they are recognized on time, hence the importance of recognizing the significance of magnetic resonance imaging when approaching a multifactorial disease considered as one of the most critical neurological emergencies, where prognosis depends on an early and accurate diagnosis.

  10. HEDR modeling approach

    International Nuclear Information System (INIS)

    Shipler, D.B.; Napier, B.A.

    1992-07-01

    This report details the conceptual approaches to be used in calculating radiation doses to individuals throughout the various periods of operations at the Hanford Site. The report considers the major environmental transport pathways--atmospheric, surface water, and ground water--and projects and appropriate modeling technique for each. The modeling sequence chosen for each pathway depends on the available data on doses, the degree of confidence justified by such existing data, and the level of sophistication deemed appropriate for the particular pathway and time period being considered

  11. The collaboratory approach

    Energy Technology Data Exchange (ETDEWEB)

    Peskin, A.M.

    1997-04-01

    A {open_quotes}collaboratory{close_quotes} has been defined as a center without walls, in which researchers can perform their work without regard to geographical location. To an increasing degree, engineering design and development is also taking the form of far-flung collaborations among divisions of a plant, subcontractors, university consultants and customers. It has long been recognized that quality engineering education presents the student with an environment that duplicates as much as possible that which the graduate will encounter in industry. To that end, it is important that engineering schools begin to introduce the collaboratory approach in its preparation, and even use it in delivery of subject matter to students.

  12. Pharmacogenetics approach to therapeutics.

    Science.gov (United States)

    Koo, Seok Hwee; Lee, Edmund Jon Deoon

    2006-01-01

    1. Pharmacogenetics refers to the study of genetically controlled variations in drug response. Functional variants caused by single nucleotide polymorphisms (SNPs) in genes encoding drug-metabolising enzymes, transporters, ion channels and drug receptors have been known to be associated with interindividual and interethnic variation in drug response. Genetic variations in these genes play a role in influencing the efficacy and toxicity of medications. 2. Rapid, precise and cost-effective high-throughput technological platforms are essential for performing large-scale mutational analysis of genetic markers involved in the aetiology of variable responses to drug therapy. 3. The application of a pharmacogenetics approach to therapeutics in general clinical practice is still far from being achieved today owing to various constraints, such as limited accessibility of technology, inadequate knowledge, ambiguity of the role of variants and ethical concerns. 4. Drug actions are determined by the interplay of several genes encoding different proteins involved in various biochemical pathways. With rapidly emerging SNP discovery technological platforms and widespread knowledge on the role of SNPs in disease susceptibility and variability in drug response, the pharmacogenetics approach to therapeutics is anticipated to take off in the not-too-distant future. This will present profound clinical, economic and social implications for health care.

  13. Proteomic approach to nanotoxicity.

    Science.gov (United States)

    Matysiak, Magdalena; Kapka-Skrzypczak, Lucyna; Brzóska, Kamil; Gutleb, Arno C; Kruszewski, Marcin

    2016-03-30

    In recent years a large number of engineered nanomaterials (NMs) have been developed with promising technical benefits for consumers and medical appliances. In addition to already known potentially advantageous biological properties (antibiotic, antifungal and antiviral activity) of NMs, many new medical applications of NMs are foreseen, such as drug carriers, contrast agents, radiopharmaceuticals and many others. However, there is increasing concern about potential environmental and health effects due to NMs exposure. An increasing body of evidence suggests that NMs may trigger undesirable hazardous interactions with biological systems with potential to generate harmful effects. In this review we summarized a current state of knowledge on the proteomics approaches to nanotoxicity, including protein corona formation, in vitro and in vivo effects of exposure to NMs on proteome of different classes of organisms, from bacteria and plants to mammals. The effects of NMs on the proteome of environmentally relevant organisms are also described. Despite the benefit that development of nanotechnology may bring to the society, there are still major gaps of knowledge on the influence of nanomaterials on human health and the environment. Thus, it seems necessary to conduct further interdisciplinary research to fill the knowledge gaps in NM toxicity, using more holistic approaches than offered by conventional biological techniques. “OMICS” techniques will certainly help researchers in this field. In this paper we summarized the current stage of knowledge of the effects of nanoparticles on the proteome of different organisms, including those commonly used as an environmentally relevant indicator organisms.

  14. Endoscopic approach to achalasia

    Science.gov (United States)

    Müller, Michaela; Eckardt, Alexander J; Wehrmann, Till

    2013-01-01

    Achalasia is a primary esophageal motor disorder. The etiology is still unknown and therefore all treatment options are strictly palliative with the intention to weaken the lower esophageal sphincter (LES). Current established endoscopic therapeutic options include pneumatic dilation (PD) or botulinum toxin injection. Both treatment approaches have an excellent symptomatic short term effect, and lead to a reduction of LES pressure. However, the long term success of botulinum toxin (BT) injection is poor with symptom recurrence in more than 50% of the patients after 12 mo and in nearly 100% of the patients after 24 mo, which commonly requires repeat injections. In contrast, after a single PD 40%-60% of the patients remain asymptomatic for ≥ 10 years. Repeated on demand PD might become necessary and long term remission can be achieved with this approach in up to 90% of these patients. The main positive predictors for a symptomatic response to PD are an age > 40 years, a LES-pressure reduction to 40 years, was nearly equivalent to surgery. A new promising technique might be peroral endoscopic myotomy, although long term results are needed and practicability as well as safety issues must be considered. Treatment with a temporary self expanding stent has been reported with favorable outcomes, but the data are all from one study group and must be confirmed by others before definite recommendations can be made. In addition to its use as a therapeutic tool, endoscopy also plays an important role in the diagnosis and surveillance of patients with achalasia. PMID:23951393

  15. Interstage Flammability Analysis Approach

    Science.gov (United States)

    Little, Jeffrey K.; Eppard, William M.

    2011-01-01

    The Interstage of the Ares I launch platform houses several key components which are on standby during First Stage operation: the Reaction Control System (ReCS), the Upper Stage (US) Thrust Vector Control (TVC) and the J-2X with the Main Propulsion System (MPS) propellant feed system. Therefore potentially dangerous leaks of propellants could develop. The Interstage leaks analysis addresses the concerns of localized mixing of hydrogen and oxygen gases to produce deflagration zones in the Interstage of the Ares I launch vehicle during First Stage operation. This report details the approach taken to accomplish the analysis. Specified leakage profiles and actual flammability results are not presented due to proprietary and security restrictions. The interior volume formed by the Interstage walls, bounding interfaces with the Upper and First Stages, and surrounding the J2-X engine was modeled using Loci-CHEM to assess the potential for flammable gas mixtures to develop during First Stage operations. The transient analysis included a derived flammability indicator based on mixture ratios to maintain achievable simulation times. Validation of results was based on a comparison to Interstage pressure profiles outlined in prior NASA studies. The approach proved useful in the bounding of flammability risk in supporting program hazard reviews.

  16. Ethnographic Approaches in Primatology.

    Science.gov (United States)

    Dore, Kerry M; Radford, Lucy; Alexander, Sherrie; Waters, Siân

    2018-01-01

    The shared evolutionary histories and anatomical similarities between humans and non-human primates create dynamic interconnections between these alloprimates. In this foreword to Folia Primatologica's special issue on "Ethnographic Approaches in Primatology," we review the ethnographic method and existing literature at the intersection of primatology and ethnography. We summarize, compare and contrast the 5 contributions to this special issue to highlight why the human-non-human primate interface is a compelling area to investigate via ethnographic approaches and to encourage increased incorporation of ethnography into the discipline of primatology. Ethnography is a valuable and increasingly popular tool with its use no longer limited to anthropological practitioners investigating traditional, non-Western peoples. Scholars from many disciplines now use ethnographic methods to investigate all members of our globalised world, including non-humans. As our closest living relatives, non-human primates (hereafter "primates") are compelling subjects and thus appear in a range of contexts within ethnographic investigations. The goal of this special issue is to highlight the trajectory of research at the intersection of primatology and ethnography and to illustrate the importance of ethnographic methods for the advancement of primatology as a discipline. © 2018 S. Karger AG, Basel.

  17. Approaches for Stereo Matching

    Directory of Open Access Journals (Sweden)

    Takouhi Ozanian

    1995-04-01

    Full Text Available This review focuses on the last decade's development of the computational stereopsis for recovering three-dimensional information. The main components of the stereo analysis are exposed: image acquisition and camera modeling, feature selection, feature matching and disparity interpretation. A brief survey is given of the well known feature selection approaches and the estimation parameters for this selection are mentioned. The difficulties in identifying correspondent locations in the two images are explained. Methods as to how effectively to constrain the search for correct solution of the correspondence problem are discussed, as are strategies for the whole matching process. Reasons for the occurrence of matching errors are considered. Some recently proposed approaches, employing new ideas in the modeling of stereo matching in terms of energy minimization, are described. Acknowledging the importance of computation time for real-time applications, special attention is paid to parallelism as a way to achieve the required level of performance. The development of trinocular stereo analysis as an alternative to the conventional binocular one, is described. Finally a classification based on the test images for verification of the stereo matching algorithms, is supplied.

  18. Technical approach document

    International Nuclear Information System (INIS)

    1988-04-01

    This document describes the general technical approaches and design criteria adopted by the US Department of Energy (DOE) in order to implement Remedial Action Plans (RAPs) and final designs that comply with EPS standards. This document is a revision to the original document. Major revisions were made to the sections in riprap selection and sizing, and ground-water; only minor revisions were made to the remainder of the document. The US Nuclear Regulatory Commission (NRC) has prepared a Standard Review Plan (NRC-SRP) which describes factors to be considered by the NRC in approving the RAP. Sections 3.0, 4.0, 5.0, and 7.0 of this document are arranged under the same headings as those used in the NRC-SRP. This approach is adopted in order to facilitate joint use of the documents. Section 2.0 (not included in the NRC-SRP) discusses design considerations; Section 3.0 describes surface-water hydrology and erosion control; Section 4.0 describes geotechnical aspects of pile design; Section 5.0 discusses the Alternate Site Selection Process; Section 6.0 deals with radiological issues (in particular, the design of the radon barrier); Section 7.0 discusses protection of groundwater resources; and Section 8.0 discusses site design criteria for the RAC

  19. Fournier's gangrene current approaches.

    Science.gov (United States)

    Ozkan, Omer F; Koksal, Neset; Altinli, Ediz; Celik, Atilla; Uzun, Mehmet A; Cıkman, Oztekin; Akbas, Alpaslan; Ergun, Ersin; Kiraz, Hasan A; Karaayvaz, Muammer

    2016-10-01

    Fournier's gangrene is a rare but highly mortal infectious disease characterised by fulminant necrotising fasciitis involving the genital and perineal regions. The objective of this study is to analyse the demographics, clinical feature and treatment approaches as well as outcomes of Fournier's gangrene. Data were collected retrospectively from medical records and operative notes. Patient data were analysed by demographics, aetiological factors, clinical features, treatment approaches and outcomes. Twelve patients (five female and seven male) were enrolled in this study. The most common aetiology was perianal abscess (41·6%). Wound cultures showed a mixture of microorganisms in six (50%) patients. For faecal diversion, while colostomy was performed in six cases (50%), Flexi-Seal was used in two cases (16·6%). In four patients (33·4%), no faecal diversion was performed. Negative pressure wound therapy (NPWT) system was effective in the last four patients (33·4%). The mean hospitalisation period in patients who used NPWT was 18 days, while it was 20 days in the others. NPWT in Fournier's gangrene is a safe dressing method. It promotes granulation formation. Flexi-Seal faecal management is an alternative method to colostomy and provides protection from its associated complications. The combination of two devices (Flexi-Seal and NPWT) is an effective and comfortable method in the management of Fournier's gangrene in appropriate patients. © 2014 The Authors. International Wound Journal © 2014 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

  20. Breakfast: a multidisciplinary approach.

    Science.gov (United States)

    Affinita, Antonio; Catalani, Loredana; Cecchetto, Giovanna; De Lorenzo, Gianfranco; Dilillo, Dario; Donegani, Giorgio; Fransos, Lucia; Lucidi, Fabio; Mameli, Chiara; Manna, Elisa; Marconi, Paolo; Mele, Giuseppe; Minestroni, Laura; Montanari, Massimo; Morcellini, Mario; Rovera, Giuseppe; Rotilio, Giuseppe; Sachet, Marco; Zuccotti, Gian Vincenzo

    2013-07-10

    The role of breakfast as an essential part of an healthy diet has been only recently promoted even if breakfast practices were known since the Middle Age. The growing scientific evidences on this topic are extremely sector-based nevertheless breakfast could be regarded from different point of views and from different expertises. This approach, that take into account history, sociology, anthropology, medicine, psychology and pedagogy, is useful to better understand the value of this meal in our culture. The aim of this paper was to analyse breakfast-related issues based on a multidisciplinary approach with input by specialists from different fields of learning. Breakfast is now recommended as part of a diet because it is associated with healthier macro- and micronutrient intakes, body mass index and lifestyle. Moreover recent studies showed that breakfast improves cognitive function, intuitive perception and academic performance. Research demonstrates the importance of providing breakfast not only to children but in adults and elderly too. Although the important role breakfast plays in maintaining the health, epidemiological data from industrialised countries reveal that many individuals either eat a nutritionally unhealthy breakfast or skip it completely. The historical, bio-psychological and educational value of breakfast in our culture is extremely important and should be recognized and stressed by the scientific community. Efforts should be done to promote this practice for the individual health and well-being.

  1. Systemic approaches to biodegradation.

    Science.gov (United States)

    Trigo, Almudena; Valencia, Alfonso; Cases, Ildefonso

    2009-01-01

    Biodegradation, the ability of microorganisms to remove complex chemicals from the environment, is a multifaceted process in which many biotic and abiotic factors are implicated. The recent accumulation of knowledge about the biochemistry and genetics of the biodegradation process, and its categorization and formalization in structured databases, has recently opened the door to systems biology approaches, where the interactions of the involved parts are the main subject of study, and the system is analysed as a whole. The global analysis of the biodegradation metabolic network is beginning to produce knowledge about its structure, behaviour and evolution, such as its free-scale structure or its intrinsic robustness. Moreover, these approaches are also developing into useful tools such as predictors for compounds' degradability or the assisted design of artificial pathways. However, it is the environmental application of high-throughput technologies from the genomics, metagenomics, proteomics and metabolomics that harbours the most promising opportunities to understand the biodegradation process, and at the same time poses tremendous challenges from the data management and data mining point of view.

  2. Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches.

    Science.gov (United States)

    Drewes, Stephan; Straková, Petra; Drexler, Jan F; Jacob, Jens; Ulrich, Rainer G

    2017-01-01

    Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further

  3. Advanced intelligence and mechanism approach

    Institute of Scientific and Technical Information of China (English)

    ZHONG Yixin

    2007-01-01

    Advanced intelligence will feature the intelligence research in next 50 years.An understanding of the concept of advanced intelligence as well as its importance will be provided first,and detailed analysis on an approach,the mechanism approach.suitable to the advanced intelligence research will then be flolowed.And the mutual relationship among mechanism approach,traditional approaches existed in artificial intelligence research,and the cognitive informatics will be discussed.It is interesting to discover that mechanism approach is a good one to the Advanced Intelligence research and a tmified form of the existed approaches to artificial intelligence.

  4. Quantitative approach to track lipase producing Pseudomonas sp. S1 in nonsterilized solid state fermentation.

    Science.gov (United States)

    Sahoo, R K; Subudhi, E; Kumar, M

    2014-06-01

    Proliferation of the inoculated Pseudomonas sp. S1 is quantitatively evaluated using ERIC-PCR during the production of lipase in nonsterile solid state fermentation an approach to reduce the cost of enzyme production. Under nonsterile solid state fermentation with olive oil cake, Pseudomonas sp. S1 produced 57·9 IU g(-1) of lipase. DNA fingerprints of unknown bacterial isolates obtained on Bushnell Haas agar (BHA) + tributyrin exactly matched with that of Pseudomonas sp. S1. Using PCR-based enumeration, population of Pseudomonas sp. S1 was proliferated from 7·6 × 10(4) CFU g(-1) after 24 h to 4·6 × 10(8) CFU g(-1) after 96 h, which tallied with the maximum lipase activity as compared to control. Under submerged fermentation (SmF), Pseudomonas sp. S1 produced maximum lipase (49 IU ml(-1) ) using olive oil as substrate, while lipase production was 9·754 IU ml(-1) when Pseudomonas sp. S1 was grown on tributyrin. Optimum pH and temperature of the crude lipase was 7·0 and 50°C. Crude enzyme activity was 71·2% stable at 50°C for 360 min. Pseudomonas sp. S1 lipase was also stable in methanol showing 91·6% activity in the presence of 15% methanol, whereas 75·5 and 51·1% of activity were retained in the presence of 20 and 30% methanol, respectively. Thus, lipase produced by Pseudomonas sp. S1 is suitable for the production of biodiesel as well as treatment of oily waste water. This study presents the first report on the production of thermophilic organic solvent tolerant lipase using agro-industry waste in nonsterile solid state fermentation. Positive correlation between survival of Pseudomonas sp. S1 and lipase production under nonsterile solid state fermentation was established, which may emphasize the need to combine molecular tools and solid state fermentation in future studies. Our study brings new insights into the lipase production in cost-effective manner, which is an industrially relevant approach. © 2014 The Society for Applied Microbiology.

  5. Proteomics - new analytical approaches

    International Nuclear Information System (INIS)

    Hancock, W.S.

    2001-01-01

    Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

  6. A Model for the Detailed Analysis of Radio Links Involving Tree Canopies

    Directory of Open Access Journals (Sweden)

    F. Perez-Fontan

    2016-12-01

    Full Text Available Detailed analysis of tree canopy interaction with incident radiowaves has mainly been limited to remote sensing for the purpose of forest classification among many other applications. This represents a monostatic configuration, unlike the case of communication links, which are bistatic. In general, link analyses have been limited to the application of simple, empirical formulas based on the use of specific attenuation values in dB/m and the traversed vegetated mass as, e.g., the model in Recommendation ITU-R P.833-8 [1]. In remote sensing, two main techniques are used: Multiple Scattering Theory (MST [2][5] and Radiative Transfer Theory (RT, [5] and [6]. We have paid attention in the past to MST [7][10]. It was shown that a full application of MST leads to very long computation times which are unacceptable in the case where we have to analyze a scenario with several trees. Extensive work using MST has been also presented by others in [11][16] showing the interest in this technique. We have proposed a simplified model for scattering from tree canopies based on a hybridization of MST and a modified physical optics (PO approach [16]. We assume that propagation through a canopy is accounted for by using the complex valued propagation constant obtained by MST. Unlike the case when the full MST is applied, the proposed approach offers significant benefits including a direct software implementation and acceptable computation times even for high frequencies and electrically large canopies. The proposed model thus replaces the coherent component in MST, significant in the forward direction, but keeps the incoherent or diffuse scattering component present in all directions. The incoherent component can be calculated within reasonable times. Here, we present tests of the proposed model against MST using an artificial single-tree scenario at 2 GHz and 10 GHz.

  7. Stochastic approach to microphysics

    Energy Technology Data Exchange (ETDEWEB)

    Aron, J.C.

    1987-01-01

    The presently widespread idea of ''vacuum population'', together with the quantum concept of vacuum fluctuations leads to assume a random level below that of matter. This stochastic approach starts by a reminder of the author's previous work, first on the relation of diffusion laws with the foundations of microphysics, and then on hadron spectrum. Following the latter, a random quark model is advanced; it gives to quark pairs properties similar to those of a harmonic oscillator or an elastic string, imagined as an explanation to their asymptotic freedom and their confinement. The stochastic study of such interactions as electron-nucleon, jets in e/sup +/e/sup -/ collisions, or pp -> ..pi../sup 0/ + X, gives form factors closely consistent with experiment. The conclusion is an epistemological comment (complementarity between stochastic and quantum domains, E.P.R. paradox, etc...).

  8. Mouthsticks - A Participatory Approach.

    Science.gov (United States)

    Ernst, Waltraud; Nussbaum, Gerhard; Berger, Veronika M; Major, Zoltan

    2017-01-01

    Mouthsticks are quite an old kind of assistive technology (AT) but nevertheless they are up to now the Swiss army knives among AT. Unfortunately the popularity of mouthsticks massively decreased during the 1990s with the result that knowledge about how to produce good mouthsticks got lost and that there are hardly any adaptable mouthsticks available on the market. This paper discusses the development of a personalized mouthstick with the involvement of end users - people with severe physical disabilities - and occupational therapists as experts of everyday use. A participatory approach was chosen. The results of the analysis of a standardized questionnaire, group discussions and a collaborative workshop with IT-designers, polymer engineers, end users, occupational therapists and gender and diversity researchers are presented and discussed. This proved the necessity of the development of a personalized mouthstick.

  9. Globalization - Different approaches

    Directory of Open Access Journals (Sweden)

    Viorica Puscaciu

    2014-11-01

    Full Text Available In this paper we investigate the different approaches of the globalization phenomenon. Despite the geographical distancesm, the link between people are ever more strong on different ways and plans: from technology between political, economical, cultural world events, and many other aspects. So, the link between globalization and democracy, and its impact on the most important social and economic matters. We also surprise the impact of the internet revolution and its corolar e-commerce, and its consequences, sometimes unpredictible ones. Another annalysed problem is that of the governments trying, and sometimes succeeding to controll the money, products, peole and their ideas that freely move inside the national frontiers, thus going to slower or to stop the progress. Nevertheless, this global interraction between people also create phenomena of insecurity on different ways: terrorism, traffic of arms, drugs, economical aggresions causing the environment, and other inconvenient facts and situations.

  10. Engineering students' sustainability approaches

    Science.gov (United States)

    Haase, S.

    2014-05-01

    Sustainability issues are increasingly important in engineering work all over the world. This article explores systematic differences in self-assessed competencies, interests, importance, engagement and practices of newly enrolled engineering students in Denmark in relation to environmental and non-environmental sustainability issues. The empirical base of the article is a nation-wide, web-based survey sent to all newly enrolled engineering students in Denmark commencing their education in the fall term 2010. The response rate was 46%. The survey focused on a variety of different aspects of what can be conceived as sustainability. By means of cluster analysis, three engineering student approaches to sustainability are identified and described. The article provides knowledge on the different prerequisites of engineering students in relation to the role of sustainability in engineering. This information is important input to educators trying to target new engineering students and contribute to the provision of engineers equipped to meet sustainability challenges.

  11. Cognitive approaches to emotions.

    Science.gov (United States)

    Oatley, Keith; Johnson-Laird, P N

    2014-03-01

    Cognitive approaches offer clear links between how emotions are thought about in everyday life and how they are investigated psychologically. Cognitive researchers have focused on how emotions are caused when events or other people affect concerns and on how emotions influence processes such as reasoning, memory, and attention. Three representative cognitive theories of emotion continue to develop productively: the action-readiness theory, the core-affect theory, and the communicative theory. Some principles are common to them and divergences can be resolved by future research. Recent explanations have included how emotions structure social relationships, how they function in psychological illnesses, and how they are central to music and fiction. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Radiolab - three different approaches

    DEFF Research Database (Denmark)

    Lønstrup, Ansa

    2012-01-01

    , who methodologically operates within tree levels of investigation: 1) the syntax, 2) the semantic and 3) the ontology level. Accordingly, this analysis is conducted, as if the sound object was performed by a vocal ensemble oscillating ‘between a musical and a speech act’. Torben Sangild’s paper......Radiolab – three different approaches The three papers in this ‘suite’ have a special background and context. At the 2010 conference SoundActs in Aarhus the three panellists were each given the task to provide a paper with an analysis of the same sound object, thus exhibiting and contrasting...... via his own repeated listening process – as a scholarly-analytical analysis of the subjectiv act of creating meaning. He draws on presumptions and prejudices, demonstrating the impossibility of a purely structural listening. The analysis relates these hermeneutical reflections to formal musicological...

  13. Slurry pipeline design approach

    Energy Technology Data Exchange (ETDEWEB)

    Betinol, Roy; Navarro R, Luis [Brass Chile S.A., Santiago (Chile)

    2009-12-19

    Compared to other engineering technologies, the design of a commercial long distance Slurry Pipeline design is a relatively new engineering concept which gained more recognition in the mid 1960 's. Slurry pipeline was first introduced to reduce cost in transporting coal to power generating units. Since then this technology has caught-up worldwide to transport other minerals such as limestone, copper, zinc and iron. In South America, the use of pipeline is commonly practiced in the transport of Copper (Chile, Peru and Argentina), Iron (Chile and Brazil), Zinc (Peru) and Bauxite (Brazil). As more mining operations expand and new mine facilities are opened, the design of the long distance slurry pipeline will continuously present a commercially viable option. The intent of this paper is to present the design process and discuss any new techniques and approach used today to ensure a better, safer and economical slurry pipeline. (author)

  14. Bioengineering a conceptual approach

    CERN Document Server

    Pavlovic, Mirjana

    2015-01-01

    This book explores critical principles and new concepts in bioengineering, integrating the biological, physical and chemical laws and principles that provide a foundation for the field. Both biological and engineering perspectives are included, with key topics such as the physical-chemical properties of cells, tissues and organs; principles of molecules; composition and interplay in physiological scenarios; and the complex physiological functions of heart, neuronal cells, muscle cells and tissues. Chapters evaluate the emerging fields of nanotechnology, drug delivery concepts, biomaterials, and regenerative therapy. The leading individuals and events are introduced along with their critical research. Bioengineering: A Conceptual Approach is a valuable resource for professionals or researchers interested in understanding the central elements of bioengineering. Advanced-level students in biomedical engineering and computer science will also find this book valuable as a secondary textbook or reference.

  15. Integration a functional approach

    CERN Document Server

    Bichteler, Klaus

    1998-01-01

    This book covers Lebesgue integration and its generalizations from Daniell's point of view, modified by the use of seminorms. Integrating functions rather than measuring sets is posited as the main purpose of measure theory. From this point of view Lebesgue's integral can be had as a rather straightforward, even simplistic, extension of Riemann's integral; and its aims, definitions, and procedures can be motivated at an elementary level. The notion of measurability, for example, is suggested by Littlewood's observations rather than being conveyed authoritatively through definitions of (sigma)-algebras and good-cut-conditions, the latter of which are hard to justify and thus appear mysterious, even nettlesome, to the beginner. The approach taken provides the additional benefit of cutting the labor in half. The use of seminorms, ubiquitous in modern analysis, speeds things up even further. The book is intended for the reader who has some experience with proofs, a beginning graduate student for example. It might...

  16. [Psychosomatic approach to encopresis].

    Science.gov (United States)

    Boige, N; Missonnier, S; Bellaïche, M; Foucaud, P

    1999-12-01

    Encopresis most often results from functional constipation and a behaviour disorder characterised by retention of faeces. Rarely it is a passive or active expulsion of normal faeces. It indicates a failure in the education of sphincter control, often with a preferential development of autoerotic versus relational investments. A depressive component is frequent. We propose a bidisciplinary approach with a somatic and psychological evaluation of the encopretic child from the first visit. The physical examination assesses constipation and stercoral stasis. Associated psychopathological symptoms or a pathogenic psychosocial situation must be sought. The therapeutic means must be directed towards the different etiologic features. Explanations of the physiopathology of the symptom and discussion with the child and the parents on the origin of the dysfunction must be accomplished first. A medical treatment of the constipation is generally indicated. Psychotherapy is initiated according to the background and associated psychopathological symptoms.

  17. Microscopic approach to polaritons

    DEFF Research Database (Denmark)

    Skettrup, Torben

    1981-01-01

    contrary to experimental experience. In order to remove this absurdity the semiclassical approach must be abandoned and the electromagnetic field quantized. A simple microscopic polariton model is then derived. From this the wave function for the interacting exciton-photon complex is obtained...... of light of the crystal. The introduction of damping smears out the excitonic spectra. The wave function of the polariton, however, turns out to be very independent of damping up to large damping values. Finally, this simplified microscopic polariton model is compared with the exact solutions obtained...... for the macroscopic polariton model by Hopfield. It is seen that standing photon and exciton waves must be included in an exact microscopic polariton model. However, it is concluded that for practical purposes, only the propagating waves are of importance and the simple microscopic polariton wave function derived...

  18. Investigational Approaches for Mesothelioma

    International Nuclear Information System (INIS)

    Surmont, Veerle F.; Thiel, Eric R. E. van; Vermaelen, Karim; Meerbeeck, Jan P. van

    2011-01-01

    Malignant pleural mesothelioma (MPM) is a rare, aggressive tumor with a poor prognosis. In view of the poor survival benefit from first-line chemotherapy and the lack of subsequent effective treatment options, there is a strong need for the development of more effective treatment approaches for patients with MPM. This review will provide a comprehensive state of the art of new investigational approaches for mesothelioma. In an introductory section, the etiology, epidemiology, natural history, and standard of care treatment for MPM will be discussed. This review provide an update of the major clinical trials that impact mesothelioma treatment, discuss the impact of novel therapeutics, and provide perspective on where the clinical research in mesothelioma is moving. The evidence was collected by a systematic analysis of the literature (2000–2011) using the databases Medline (National Library of Medicine, USA), Embase (Elsevier, Netherlands), Cochrane Library (Great Britain), National Guideline Clearinghouse (USA), HTA Database (International Network of Agencies for Health Technology Assessment – INAHTA), NIH database (USA), International Pleural Mesothelioma Program – WHOLIS (WHO Database), with the following keywords and filters: mesothelioma, guidelines, treatment, surgery, chemotherapy, radiotherapy, review, investigational, drugs. Currently different targeted therapies and biologicals are under investigation for MPM. It is important that the molecular biologic research should first focus on mesothelioma-specific pathways and biomarkers in order to have more effective treatment options for this disease. The use of array technology will be certainly an implicit gain in the identification of new potential prognostic or biomarkers or important pathways in the MPM pathogenesis. Probably a central mesothelioma virtual tissue bank may contribute to the ultimate goal to identify druggable targets and to develop personalized treatment for the MPM patients.

  19. Investigational approaches for mesothelioma

    Directory of Open Access Journals (Sweden)

    Veerle F Surmont

    2011-08-01

    Full Text Available MPM is a rare, aggressive tumour with a poor prognosis. In view of the poor survival benefit from first-line chemotherapy and the lack of subsequent effective treatment options, there is a strong need for the development of more effective treatment approaches for patients with MPM. This review will provide a comprehensive state of the art of new investigational approaches for mesothelioma. In an introductory section, the aetiology, epidemiology, natural history and standard of care treatment for MPM will be discussed. This review provide an update of the major clinical trials that impact mesothelioma treatment, discuss the impact of novel therapeutics and provide perspective on where the clinical research in mesothelioma is moving.The evidence was collected by a systematic analysis of the literature (2000–2011 using the databases Medline (National Library of Medicine, USA, Embase (Elsevier, Netherlands, Cochrane Library (Great Britain, National Guideline Clearinghouse (USA, HTA Database (International Network of Agencies for Health Technology Assessment – INAHTA, NIH database (USA, International Pleural Mesothelioma Program – WHOLIS (WHO Database , with the following keywords and filters: mesothelioma, guidelines, treatment, surgery, chemotherapy, radiotherapy, review, investigational, drugsCurrently different targeted therapies and biologicals are under investigation for MPM. It is important that the molecular biologic research should first focus on mesothelioma-specific pathways and biomarkers in order to have more effective treatment options for this disease. The use of array technology will be certainly an implicit gain in the identification of new potential prognostic or biomarkers or important pathways in the MPM pathogenesis. Probably a central mesothelioma virtual tissue bank may contribute to the ultimate goal to identify druggable targets and to develop personalized treatment for the MPM patients.

  20. Structural Sustainability - Heuristic Approach

    Science.gov (United States)

    Rostański, Krzysztof

    2017-10-01

    Nowadays, we are faced with a challenge of having to join building structures with elements of nature, which seems to be the paradigm of modern planning and design. The questions arise, however, with reference to the following categories: the leading idea, the relation between elements of nature and buildings, the features of a structure combining such elements and, finally, our perception of this structure. If we consider both the overwhelming globalization and our attempts to preserve local values, the only reasonable solution is to develop naturalistic greenery. It can add its uniqueness to any building and to any developed area. Our holistic model, presented in this paper, contains the above mentioned categories within the scope of naturalism. The model is divided into principles, actions related, and possible effects to be obtained. It provides a useful tool for determining the ways and priorities of our design. Although it is not possible to consider all possible actions and solutions in order to support sustainability in any particular design, we can choose, however, a proper mode for our design according to the local conditions by turning to the heuristic method, which helps to choose priorities and targets. Our approach is an attempt to follow the ways of nature as in the natural environment it is optimal solutions that appear and survive, idealism being the domain of mankind only. We try to describe various natural processes in a manner comprehensible to us, which is always a generalization. Such definitions, however, called artificial by naturalists, are presented as art or the current state of knowledge by artists and engineers. Reality, in fact, is always more complicated than its definitions. The heuristic method demonstrates the way how to optimize our design. It requires that all possible information about the local environment should be gathered, as the more is known, the fewer mistakes are made. Following the unquestionable principles, we can

  1. Approach to team skills training

    International Nuclear Information System (INIS)

    Koontz, J.L.; Roe, M.L.; Gaddy, C.D.

    1987-01-01

    The US commercial nuclear power industry has recognized the importance of team skills in control room operation. The desire to combine training of team interaction skills, like communications, with technical knowledge of reactor operations requires a unique approach to training. An NRC-sponsored study identified a five-phase approach to team skills training designed to be consistent with the systems approach to training currently endorsed by the NRC Policy Statement on Training and Qualification. This paper describes an approach to team skills training with emphasis on the nuclear power plant control room crew. An approach to team skills training

  2. Developing regulatory approaches

    International Nuclear Information System (INIS)

    Axelsson, Lars

    2012-01-01

    Lars Axelsson presented SSM progress on oversight of LMfS/SC since the Chester 1 Workshop in 2007. Current SSM approaches for safety culture oversight include targeted safety management and safety culture inspections, compliance inspections which cover aspects of safety management/safety culture and multi-disciplinary team inspections. Examples of themes for targeted inspections include management of ambiguous operational situations or other weak signals, understanding of and attitudes to Human Performance tools, the Safety Department's role and authority and Leadership for safety. All regulatory activities provide inputs for the SSM yearly safety evaluation of each licensee. A form has been developed to capture safety culture observations from inspections and other interactions with licensees. Analysis will be performed to identify patterns and provide information to support planning of specific Safety Culture activities. Training has been developed for regulatory staff to enhance the quality of regulatory interventions on safety culture. This includes a half-day seminar to provide an overview of safety culture, and a workshop which provides more in-depth discussion on cultural issues and how to capture those during regulatory activities. Future plans include guidance for inspectors, and informal seminars on safety culture with licensees

  3. Light cone approach

    International Nuclear Information System (INIS)

    Brodsky, Stan

    1993-01-01

    One of the most challenging problems in theoretical high energy physics is to compute the bound state structure of the proton and other hadrons from quantum chromodynamics (QCD), the field theory of quarks and gluons. The goal is not only to calculate the spectrum of hadrons masses from first principles, but also to derive the momentum and spin distributions of the quarks and gluons which control high energy hadron interactions. One approach to these difficult calculations is to simulate QCD on an artificial lattice. Recently, several new methods based on ''light-cone'' quantization have been proposed as alternatives to lattice theory for solving non-perturbative problems in QCD and other field theories. The basic idea is a generalization of Heisenberg's pioneer matrix formulation of quantum mechanics: if one could numerically diagonalize the matrix of the Hamiltonian representing the underlying QCD interaction, then the resulting eigenvalues would give the hadron spectrum, while the corresponding eigenstates would describe each hadron in terms of its quark and gluon degrees of freedom

  4. Combined approach for gynecomastia

    Directory of Open Access Journals (Sweden)

    El-Sabbagh, Ahmed Hassan

    2016-02-01

    Full Text Available Background: Gynecomastia is a deformity of male chest. Treatment of gynecomastia varied from direct surgical excision to other techniques (mainly liposuction to a combination of both. Skin excision is done according to the grade. In this study, experience of using liposuction adjuvant to surgical excision was described. Patients and methods: Between September 2012 and April 2015, a total of 14 patients were treated with liposuction and surgical excision through a periareolar incision. Preoperative evaluation was done in all cases to exclude any underlying cause of gynecomastia. Results: All fourteen patients were treated bilaterally (28 breast tissues. Their ages ranged between 13 and 33 years. Two patients were classified as grade I, and four as grade IIa, IIb or III, respectively. The first showed seroma. Partial superficial epidermolysis of areola occurred in 2 cases. Superficial infection of incision occurred in one case and was treated conservatively. Conclusion: All grades of gynecomastia were managed by the same approach. Skin excision was added to a patient that had severe skin excess with limited activity and bad skin complexion. No cases required another setting or asked for 2 opinion.

  5. Combined approach for gynecomastia.

    Science.gov (United States)

    El-Sabbagh, Ahmed Hassan

    2016-01-01

    Gynecomastia is a deformity of male chest. Treatment of gynecomastia varied from direct surgical excision to other techniques (mainly liposuction) to a combination of both. Skin excision is done according to the grade. In this study, experience of using liposuction adjuvant to surgical excision was described. Between September 2012 and April 2015, a total of 14 patients were treated with liposuction and surgical excision through a periareolar incision. Preoperative evaluation was done in all cases to exclude any underlying cause of gynecomastia. All fourteen patients were treated bilaterally (28 breast tissues). Their ages ranged between 13 and 33 years. Two patients were classified as grade I, and four as grade IIa, IIb or III, respectively. The first 3 patients showed seroma. Partial superficial epidermolysis of areola occurred in 2 cases. Superficial infection of incision occurred in one case and was treated conservatively. All grades of gynecomastia were managed by the same approach. Skin excision was added to a patient that had severe skin excess with limited activity and bad skin complexion. No cases required another setting or asked for 2(nd) opinion.

  6. Approaches to refractory epilepsy

    Directory of Open Access Journals (Sweden)

    Jerome Engel

    2014-01-01

    Full Text Available Epilepsy is one of the most common serious neurological conditions, and 30 to 40% of people with epilepsy have seizures that are not controlled by medication. Patients are considered to have refractory epilepsy if disabling seizures continue despite appropriate trials of two antiseizure drugs, either alone or in combination. At this point, patients should be referred to multidisciplinary epilepsy centers that perform specialized diagnostic testing to first determine whether they are, in fact, pharmacoresistant, and then, if so, offer alternative treatments. Apparent pharmacoresistance can result from a variety of situations, including noncompliance, seizures that are not epileptic, misdiagnosis of the seizure type or epilepsy syndrome, inappropriate use of medication, and lifestyle issues. For patients who are pharmacoresistant, surgical treatment offers the best opportunity for complete freedom from seizures. Surgically remediable epilepsy syndromes have been identified, but patients with more complicated epilepsy can also benefit from surgical treatment and require more specialized evaluation, including intracranial EEG monitoring. For patients who are not surgical candidates, or who are unwilling to consider surgery, a variety of other alternative treatments can be considered, including peripheral or central neurostimulation, ketogenic diet, and complementary and alternative approaches. When such alternative treatments are not appropriate or effective, quality of life can still be greatly improved by the psychological and social support services offered by multidisciplinary epilepsy centers. A major obstacle remains the fact that only a small proportion of patients with refractory epilepsy are referred for expert evaluation and treatment.

  7. Approaches to adenomyomectomy

    Directory of Open Access Journals (Sweden)

    Serene Thain

    2015-08-01

    Full Text Available Adenomyosis is a common gynecological condition that affects women, causing menstrual disturbances, pain, and subfertility. Adenomyomectomy as an alternative to hysterectomy has been widely performed in those who have not completed childbearing or those refusing a hysterectomy for a variety of reasons. Whichever the surgical route, the challenges of adenomyomectomy include possible misdiagnosis, defining the extent of resection, technical difficulties, dealing with the associated complications, and managing the risks of uterine rupture during a subsequent pregnancy. The principles of surgery mimic those of myomectomy, but the evolution of adenomyomectomy has been relatively unexciting with a general paucity of published data to date. Laparoscopic techniques have proven feasible generally, avoiding the risks of open surgery while conferring the benefits of microsurgery. Limitations in tactile feedback and access constraints have been the main drawbacks via this route. Meticulous stitching and repair is still of paramount importance in these operations. Preoperative gonadotropin-releasing hormone agonists have proven effective in shrinking the disease and reducing blood loss during surgery, whereas the postoperative use has resulted in a dramatic reduction in symptoms. Uterine artery ligation techniques have also been shown to be useful adjuncts, although we still need to be mindful of the potential effects in those desiring fertility. Furthermore, there is still no foolproof way in predicting those at risk of uterine rupture after adenomyomectomy. Hence, a nonprescriptive approach in managing adenomyomas is advised, where proper patient selection and counseling are important.

  8. A comprehensive approach to identify reliable reference gene candidates to investigate the link between alcoholism and endocrinology in Sprague-Dawley rats.

    Directory of Open Access Journals (Sweden)

    Faten A Taki

    Full Text Available Gender and hormonal differences are often correlated with alcohol dependence and related complications like addiction and breast cancer. Estrogen (E2 is an important sex hormone because it serves as a key protein involved in organism level signaling pathways. Alcoholism has been reported to affect estrogen receptor signaling; however, identifying the players involved in such multi-faceted syndrome is complex and requires an interdisciplinary approach. In many situations, preliminary investigations included a straight forward, yet informative biotechniques such as gene expression analyses using quantitative real time PCR (qRT-PCR. The validity of qRT-PCR-based conclusions is affected by the choice of reliable internal controls. With this in mind, we compiled a list of 15 commonly used housekeeping genes (HKGs as potential reference gene candidates in rat biological models. A comprehensive comparison among 5 statistical approaches (geNorm, dCt method, NormFinder, BestKeeper, and RefFinder was performed to identify the minimal number as well the most stable reference genes required for reliable normalization in experimental rat groups that comprised sham operated (SO, ovariectomized rats in the absence (OVX or presence of E2 (OVXE2. These rat groups were subdivided into subgroups that received alcohol in liquid diet or isocalroic control liquid diet for 12 weeks. Our results showed that U87, 5S rRNA, GAPDH, and U5a were the most reliable gene candidates for reference genes in heart and brain tissue. However, different gene stability ranking was specific for each tissue input combination. The present preliminary findings highlight the variability in reference gene rankings across different experimental conditions and analytic methods and constitute a fundamental step for gene expression assays.

  9. The narrative approach to personalisation

    Science.gov (United States)

    Conlan, Owen; Staikopoulos, Athanasios; Hampson, Cormac; Lawless, Séamus; O'keeffe, Ian

    2013-06-01

    This article describes the narrative approach to personalisation. This novel approach to the generation of personalised adaptive hypermedia experiences employs runtime reconciliation between a personalisation strategy and a number of contextual models (e.g. user and domain). The approach also advocates the late binding of suitable content and services to the generated personalised pathway resulting in an interactive composition that comprises services as well as content. This article provides a detailed definition of the narrative approach to personalisation and showcases the approach through the examination of two use-cases: the personalised digital educational games developed by the ELEKTRA and 80Days projects; and the personalised learning activities realised as part of the AMAS project. These use-cases highlight the general applicability of the narrative approach and how it has been applied to create a diverse range of real-world systems.

  10. Field theory approach to gravitation

    International Nuclear Information System (INIS)

    Yilmaz, H.

    1978-01-01

    A number of authors considered the possibility of formulating a field-theory approach to gravitation with the claim that such an approach would uniquely lead to Einstein's theory of general relativity. In this article it is shown that the field theory approach is more generally applicable and uniqueness cannot be claimed. Theoretical and experimental reasons are given showing that the Einsteinian limit appears to be unviable

  11. The paramedian supracerebellar infratentorial approach.

    Science.gov (United States)

    La Pira, Biagia; Sorenson, Thomas; Quillis-Quesada, Vicent; Lanzino, Giuseppe

    2017-08-01

    Lesions of the superior cerebellar surface, pineal region, lateral and dorsal midbrain and mesial temporal lobe are challenging to treat and often require neurosurgical intervention. The paramedian variation of the supracerebellar infratentorial approach utilizes the downward slope of the cerebellum to facilitate exposure and the lower density of cerebellar bridging veins away from the midline decreases the need to sacrifice larger venous channels. We also discuss our experiences with the approach, and some of the drawbacks and nuances that we have encountered as it has evolved over the years. This approach is versatile and effective and the authors' surgical approach of choice for resecting these challenging lesions.

  12. An Approach to Interface Synthesis

    DEFF Research Database (Denmark)

    Madsen, Jan; Hald, Bjarne

    1995-01-01

    Presents a novel interface synthesis approach based on a one-sided interface description. Whereas most other approaches consider interface synthesis as optimizing a channel to existing client/server modules, we consider the interface synthesis as part of the client/server module synthesis (which...... may contain the re-use of existing modules). The interface synthesis approach describes the basic transformations needed to transform the server interface description into an interface description on the client side of the communication medium. The synthesis approach is illustrated through a point...

  13. Molecular approach of uranyl/mineral surfaces: experimental approach

    International Nuclear Information System (INIS)

    Drot, R.

    2009-01-01

    The author reports an experimental approach in which different spectroscopic approaches are coupled (laser spectroscopy, X-ray absorption spectroscopy, vibrational spectroscopy) to investigate the mechanisms controlling actinide sorption processes by different substrates, in order to assess radioactive waste storage site safety. Different substrates have been considered: monocrystalline or powdered TiO 2 , montmorillonite, and gibbsite

  14. MBO: A Rational Approach and a Comparative Frameworks Approach

    Science.gov (United States)

    Harries, T. W.

    1974-01-01

    Considering an organizational phenomenon from more than one theoretical perspective may be more fruitful than using a single rational approach. There is a danger that the restriction of information generation caused by the single approach may produce a false certainty engendered in part through the methodology itself. (Author/WM)

  15. Operations management approach to hospitals.

    Science.gov (United States)

    Harvey, J; Duguay, C R

    1988-06-01

    An operations management systems approach can be a useful tool for coordinating and planning in a complex organization. The authors argue for adapting such an approach to health care from the manufacturing industries in order to facilitate strategy formulation, communication and implementation.

  16. The CAPM approach to materiality

    OpenAIRE

    Hadjieftychiou, Aristarchos

    1993-01-01

    Materiality is a pervasive accounting concept that has defied a precise quantitative definition. The Capital Asset Pricing Model (CAPM) approach to materiality provides a means for determining the limits that bound materiality. Also, the approach makes it possible to locate the point estimate within these limits based on certain assumptions.

  17. Cognitive Approaches to Automated Instruction.

    Science.gov (United States)

    Regian, J. Wesley, Ed.; Shute, Valerie J., Ed.

    This book contains a snapshot of state-of-the-art research on the design of automated instructional systems. Selected cognitive psychologists were asked to describe their approach to instruction and cognitive diagnosis, the theoretical basis of the approach, its utility and applicability, and the knowledge engineering or task analysis methods…

  18. Extending cosmology: the metric approach

    OpenAIRE

    Mendoza, S.

    2012-01-01

    Comment: 2012, Extending Cosmology: The Metric Approach, Open Questions in Cosmology; Review article for an Intech "Open questions in cosmology" book chapter (19 pages, 3 figures). Available from: http://www.intechopen.com/books/open-questions-in-cosmology/extending-cosmology-the-metric-approach

  19. [Alternative approaches in thyroid surgery].

    Science.gov (United States)

    Maurer, E; Wächter, S; Bartsch, D K

    2017-08-01

    In thyroid surgery multiple different cervical minimally invasive (partly endoscopically assisted) and extracervical endoscopic (partly robot-assisted) approaches have been developed in the last 20 years. The aim of all these alternative approaches to the thyroid gland is optimization of the cosmetic result. The indications for the use of alternative and conventional approaches are principally the same. Important requirements for the use of alternative methods are nevertheless a broad experience in conventional thyroid operations of the thyroid and adequate patient selection under consideration of the size of the thyroid and the underlying pathology. Contraindications for the use of alternative approaches are a large size of the thyroid gland including local symptoms, advanced carcinomas, reoperations and previous radiations of the anterior neck. The current article gives an overview of the clinically implemented alternative approaches for thyroid surgery. Of those the majority must still be considered as experimental. The alternative approaches to the thyroid gland can be divided in cervical minimally invasive, extracervical endosopic (robot-assisted) and transoral operations (natural orifice transluminal endoscopic surgery, NOTES). Since conventional thyroid operations are standardized procedures with low complication rates, alternative approaches to the thyroid gland are considered critically in Germany. The request for a perfect cosmetic result should not overweigh patients' safety. Only a few alternative approaches (e. g. MIVAT, RAT) can yet be considered as a safe addition in experienced hands in highly selected patients.

  20. Artificial intelligence approaches in statistics

    International Nuclear Information System (INIS)

    Phelps, R.I.; Musgrove, P.B.

    1986-01-01

    The role of pattern recognition and knowledge representation methods from Artificial Intelligence within statistics is considered. Two areas of potential use are identified and one, data exploration, is used to illustrate the possibilities. A method is presented to identify and separate overlapping groups within cluster analysis, using an AI approach. The potential of such ''intelligent'' approaches is stressed