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Sample records for accurate rapid diagnostic

  1. Rapid diagnostic tests for malaria

    PubMed Central

    Daily, Jennifer; Hotte, Nora; Dolkart, Caitlin; Cunningham, Jane; Yadav, Prashant

    2015-01-01

    Abstract Maintaining quality, competitiveness and innovation in global health technology is a constant challenge for manufacturers, while affordability, access and equity are challenges for governments and international agencies. In this paper we discuss these issues with reference to rapid diagnostic tests for malaria. Strategies to control and eliminate malaria depend on early and accurate diagnosis. Rapid diagnostic tests for malaria require little training and equipment and can be performed by non-specialists in remote settings. Use of these tests has expanded significantly over the last few years, following recommendations to test all suspected malaria cases before treatment and the implementation of an evaluation programme to assess the performance of the malaria rapid diagnostic tests. Despite these gains, challenges exist that, if not addressed, could jeopardize the progress made to date. We discuss recent developments in rapid diagnostic tests for malaria, highlight some of the challenges and provide suggestions to address them. PMID:26668438

  2. Rapid infectious diseases diagnostics using Smartphones

    PubMed Central

    Bates, Matthew

    2015-01-01

    The “Smartphone” is an almost universal possession in high-income populations, and is rapidly becoming so in lower-income regions, particularly among urban populations, and serves social networking and a quest for information and knowledge. The field of infectious disease diagnostics is at a potential watershed moment, with the essential building blocks for the development of diagnostic assays being ever more available and affordable, which is leading to creative innovative approaches to developing much-needed accurate and simple point-of-care (POC) diagnostic tools for high disease burden, low-income settings. We review the importance and implications of a paper published in Science Translational Medicine on the development of a smartphone-powered and -controlled multiplex immunological assay that tests for HIV and syphilis simultaneously. This is reviewed in the context of other prototype smartphone-enabled/assisted diagnostic devices, and how such developments might shape the future of the POC diagnostics field. PMID:26488011

  3. SOPROLIFE System: An Accurate Diagnostic Enhancer

    PubMed Central

    Zeitouny, Mona; Feghali, Mireille; Nasr, Assaad; Abou-Samra, Philippe; Saleh, Nadine; Bourgeois, Denis; Farge, Pierre

    2014-01-01

    Objectives. The aim of this study was to evaluate a light-emitting diode fluorescence tool, the SOPROLIFE light-induced fluorescence evaluator, and compare it to the international caries detection and assessment system-II (ICDAS-II) in the detection of occlusal caries. Methods. A total of 219 permanent posterior teeth in 21 subjects, with age ranging from 15 to 65 years, were examined. An intraclass correlation coefficient (ICC) was computed to assess the reliability between the two diagnostic methods. Results. The results showed a high reliability between the two methods (ICC = 0.92; IC = 0.901–0.940; P < 0.001). The SOPROLIFE blue fluorescence mode had a high sensitivity (87%) and a high specificity (99%) when compared to ICDAS-II. Conclusion. Compared to the most used visual method in the diagnosis of occlusal caries lesions, the finding from this study suggests that SOPROLIFE can be used as a reproducible and reliable assessment tool. At a cut-off point, categorizing noncarious lesions and visual change in enamel, SOPROLIFE shows a high sensitivity and specificity. We can conclude that financially ICDAS is better than SOPROLIFE. However SOPROLIFE is easier for clinicians since it is a simple evaluation of images. Finally in terms of efficiency SOPROLIFE is not superior to ICDAS but tends to be equivalent with the same advantages. PMID:25401161

  4. Rapid Diagnostics of Onboard Sequences

    NASA Technical Reports Server (NTRS)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  5. A rapid diagnostic test for schistosomiasis mansoni

    PubMed Central

    Mello-Silva, Clélia Christina; João, Roberto Carlos; Augusto, Ronaldo de Carvalho; Santos, Claudia Portes

    2013-01-01

    This article presents an improvement to the Kato-Katz (KK) method, making it faster and more efficient for the visualisation of fertile eggs in stool samples. This modified KK method uses sodium acetate formalin as a fixative and reveals the intensity of infection in less than 1 h, reducing the diagnostic time without increasing the cost. This modified method may contribute to future epidemiological studies in both hospitals and the field due to its rapid and precise diagnostic, which allow for immediate treatment. PMID:24402146

  6. Rapid molecular diagnostic tools for avian influenza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An accurate and early diagnosis of a foreign animal disease is crucial for rapid control and eradication of an outbreak in a country previously free of the disease. Historically many animal diseases have been controlled based solely on clinical signs of disease. However with avian influenza virus ...

  7. Rapid Accurate Identification of Bacterial and Viral Pathogens

    SciTech Connect

    Dunn, John

    2007-03-09

    The goals of this program were to develop two assays for rapid, accurate identification of pathogenic organisms at the strain level. The first assay "Quantitative Genome Profiling or QGP" is a real time PCR assay with a restriction enzyme-based component. Its underlying concept is that certain enzymes should cleave genomic DNA at many sites and that in some cases these cuts will interrupt the connection on the genomic DNA between flanking PCR primer pairs thereby eliminating selected PCR amplifications. When this occurs the appearance of the real-time PCR threshold (Ct) signal during DNA amplification is totally eliminated or, if cutting is incomplete, greatly delayed compared to an uncut control. This temporal difference in appearance of the Ct signal relative to undigested control DNA provides a rapid, high-throughput approach for DNA-based identification of different but closely related pathogens depending upon the nucleotide sequence of the target region. The second assay we developed uses the nucleotide sequence of pairs of shmi identifier tags (-21 bp) to identify DNA molecules. Subtle differences in linked tag pair combinations can also be used to distinguish between closely related isolates..

  8. Uncomplicated malaria in children: The place of rapid diagnostic test

    PubMed Central

    Elechi, Hassan Abdullahi; Rabasa, Adamu Ibrahim; Bashir, Muhammad Faruk; Gofama, Mustapha Modu; Ibrahim, Halima Abubakar; Askira, Umoru Muhammed

    2015-01-01

    Background: Malaria has remained a major cause of morbidity and mortality among the under-five children in Nigeria. Prompt and accurate diagnosis of malaria is necessary in controlling this high burden and preventing unnecessary use of anti-malarial drugs. Malaria rapid diagnostic test (MRDT) offers the hope of achieving this goal. However, the performance of these kits among the most vulnerable age group to malaria is inadequate. Materials and Methods: In this cross-sectional study, 433 out-patients, aged <5 years with fever or history of fever were enrolled. Each candidate was tested for malaria parasitaemia using ACON; malaria pf. Thick and thin films were also prepared from the same finger prick blood for each candidate. Result: Malaria rapid diagnostic test had sensitivity of 8.3%, specificity of 100%, positive predictive value (PPV) of 100% and negative predictive value (NPV) of 74%. The sensitivity of MRDT increased with increasing age. This effect of age on sensitivity was statistically significant (P = 0.007). Similarly parasite density had significant effect on the sensitivity of MRDT (P = <0.001). Conclusion: Histidine-rich protein-2 based MRDT is not a reliable mean of diagnosing malaria in the under-five age children with acute uncomplicated malaria. PMID:25838621

  9. Rapid Diagnostic Algorithms as a Screening Tool for Tuberculosis: An Assessor Blinded Cross-Sectional Study

    PubMed Central

    Ratzinger, Franz; Bruckschwaiger, Harald; Wischenbart, Martin; Parschalk, Bernhard; Fernandez-Reyes, Delmiro; Lagler, Heimo; Indra, Alexandra; Graninger, Wolfgang; Winkler, Stefan; Krishna, Sanjeev; Ramharter, Michael

    2012-01-01

    Background A major obstacle to effectively treat and control tuberculosis is the absence of an accurate, rapid, and low-cost diagnostic tool. A new approach for the screening of patients for tuberculosis is the use of rapid diagnostic classification algorithms. Methods We tested a previously published diagnostic algorithm based on four biomarkers as a screening tool for tuberculosis in a Central European patient population using an assessor-blinded cross-sectional study design. In addition, we developed an improved diagnostic classification algorithm based on a study population at a tertiary hospital in Vienna, Austria, by supervised computational statistics. Results The diagnostic accuracy of the previously published diagnostic algorithm for our patient population consisting of 206 patients was 54% (CI: 47%–61%). An improved model was constructed using inflammation parameters and clinical information. A diagnostic accuracy of 86% (CI: 80%–90%) was demonstrated by 10-fold cross validation. An alternative model relying solely on clinical parameters exhibited a diagnostic accuracy of 85% (CI: 79%–89%). Conclusion Here we show that a rapid diagnostic algorithm based on clinical parameters is only slightly improved by inclusion of inflammation markers in our cohort. Our results also emphasize the need for validation of new diagnostic algorithms in different settings and patient populations. PMID:23185397

  10. Review of rapid molecular diagnostic tools for avian influenza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular diagnostics tests are commonly used to diagnose avian influenza virus (AIV) because they are sensitive, can be performed rapidly, with high throughput, and at a moderate cost. Molecular diagnostic tests have recently proven themselves to be invaluable in controlling disease outbreaks arou...

  11. A novel technique for detecting antibiotic-resistant typhoid from rapid diagnostic tests.

    PubMed

    Nic Fhogartaigh, Caoimhe; Dance, David A B; Davong, Viengmon; Tann, Pisey; Phetsouvanh, Rattanaphone; Turner, Paul; Dittrich, Sabine; Newton, Paul N

    2015-05-01

    Fluoroquinolone-resistant typhoid is increasing. An antigen-detecting rapid diagnostic test (RDT) can rapidly diagnose typhoid from blood cultures. A simple, inexpensive molecular technique performed with DNA from positive RDTs accurately identified gyrA mutations consistent with phenotypic susceptibility testing results. Field diagnosis combined with centralized molecular resistance testing could improve typhoid management and surveillance in low-resource settings. PMID:25762768

  12. The role of rapid diagnostics in managing Ebola epidemics

    PubMed Central

    Nouvellet, Pierre; Garske, Tini; Mills, Harriet L.; Nedjati-Gilani, Gemma; Hinsley, Wes; Blake, Isobel M.; Van Kerkhove, Maria D.; Cori, Anne; Dorigatti, Ilaria; Jombart, Thibaut; Riley, Steven; Fraser, Christophe; Donnelly, Christl A.; Ferguson, Neil M.

    2016-01-01

    Ebola emerged in West Africa around December 2013 and swept through Guinea, Sierra Leone and Liberia, giving rise to 27,748 confirmed, probable and suspected cases reported by 29 July 2015. Case diagnoses during the epidemic have relied on polymerase chain reaction-based tests. Owing to limited laboratory capacity and local transport infrastructure, the delays from sample collection to test results being available have often been 2 days or more. Point-of-care rapid diagnostic tests offer the potential to substantially reduce these delays. We review Ebola rapid diagnostic tests approved by the World Health Organization and those currently in development. Such rapid diagnostic tests could allow early triaging of patients, thereby reducing the potential for nosocomial transmission. In addition, despite the lower test accuracy, rapid diagnostic test-based diagnosis may be beneficial in some contexts because of the reduced time spent by uninfected individuals in health-care settings where they may be at increased risk of infection; this also frees up hospital beds. We use mathematical modelling to explore the potential benefits of diagnostic testing strategies involving rapid diagnostic tests alone and in combination with polymerase chain reaction testing. Our analysis indicates that the use of rapid diagnostic tests with sensitivity and specificity comparable with those currently under development always enhances control, whether evaluated at a health-care-unit or population level. If such tests had been available throughout the recent epidemic, we estimate, for Sierra Leone, that their use in combination with confirmatory polymerase chain-reaction testing might have reduced the scale of the epidemic by over a third. PMID:26633764

  13. The role of rapid diagnostics in managing Ebola epidemics.

    PubMed

    Nouvellet, Pierre; Garske, Tini; Mills, Harriet L; Nedjati-Gilani, Gemma; Hinsley, Wes; Blake, Isobel M; Van Kerkhove, Maria D; Cori, Anne; Dorigatti, Ilaria; Jombart, Thibaut; Riley, Steven; Fraser, Christophe; Donnelly, Christl A; Ferguson, Neil M

    2015-12-01

    Ebola emerged in West Africa around December 2013 and swept through Guinea, Sierra Leone and Liberia, giving rise to 27,748 confirmed, probable and suspected cases reported by 29 July 2015. Case diagnoses during the epidemic have relied on polymerase chain reaction-based tests. Owing to limited laboratory capacity and local transport infrastructure, the delays from sample collection to test results being available have often been 2 days or more. Point-of-care rapid diagnostic tests offer the potential to substantially reduce these delays. We review Ebola rapid diagnostic tests approved by the World Health Organization and those currently in development. Such rapid diagnostic tests could allow early triaging of patients, thereby reducing the potential for nosocomial transmission. In addition, despite the lower test accuracy, rapid diagnostic test-based diagnosis may be beneficial in some contexts because of the reduced time spent by uninfected individuals in health-care settings where they may be at increased risk of infection; this also frees up hospital beds. We use mathematical modelling to explore the potential benefits of diagnostic testing strategies involving rapid diagnostic tests alone and in combination with polymerase chain reaction testing. Our analysis indicates that the use of rapid diagnostic tests with sensitivity and specificity comparable with those currently under development always enhances control, whether evaluated at a health-care-unit or population level. If such tests had been available throughout the recent epidemic, we estimate, for Sierra Leone, that their use in combination with confirmatory polymerase chain-reaction testing might have reduced the scale of the epidemic by over a third. PMID:26633764

  14. Rapid and Accurate Evaluation of the Quality of Commercial Organic Fertilizers Using Near Infrared Spectroscopy

    PubMed Central

    Wang, Chang; Huang, Chichao; Qian, Jian; Xiao, Jian; Li, Huan; Wen, Yongli; He, Xinhua; Ran, Wei; Shen, Qirong; Yu, Guanghui

    2014-01-01

    The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers. PMID:24586313

  15. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology

    PubMed Central

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10−3 for bcr1 and bcr3 and 10−2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362

  16. Rapid and Accurate Identification of Candida albicans Isolates by Use of PNA FISHFlow▿

    PubMed Central

    Trnovsky, Jan; Merz, William; Della-Latta, Phyllis; Wu, Fann; Arendrup, Maiken Cavling; Stender, Henrik

    2008-01-01

    We developed the simple, rapid (1 h), and accurate PNA FISHFlow method for the identification of Candida albicans. The method exploits unique in solution in situ hybridization conditions under which the cells are simultaneously fixed and hybridized. This method facilitates the accurate identification of clinical yeast isolates using two scoring techniques: flow cytometry and fluorescence microscopy. PMID:18287325

  17. Commercial dengue rapid diagnostic tests for point-of-care application: recent evaluations and future needs?

    PubMed

    Blacksell, Stuart D

    2012-01-01

    Dengue fever, dengue haemorrhagic fever, and dengue shock syndrome (DF/DHF/DSS) are tropical diseases that cause significant humanitarian and economic hardship. It is estimated that more than 2.5 billion people are at risk of infection and more than 100 countries have endemic dengue virus transmission. Laboratory tests are essential to provide an accurate diagnosis of dengue virus infection so that appropriate treatment and patient management may be administered. In many dengue endemic settings, laboratory diagnostic resources are limited and simple rapid diagnostic tests (RDTs) provide opportunities for point-of-care diagnosis. This paper addresses current issues relating to the application of commercial dengue RDTs for the diagnosis of acute dengue virus infection, recent diagnostic evaluations, and identifies future needs. PMID:22654479

  18. [Rapidly progressive glomerulonephritis: a diagnostic and therapeutic emergency].

    PubMed

    Halfon, Matthieu; Teta, Daniel; Rotman, Samuel; Pruijm, Menno; Humbert, Antoine

    2014-02-26

    Rapidly progressive glomerulonephritis (RPG) is a rare clinical syndrome characterized by kidney damage that can lead to irreversible kidney failure. RPG can be caused by primary glomerular disease or can be part of a systemic autoimmune disorder. All RPG have a similar pathophysiology (proliferation of cells in Bowman's capsule and formation of crescents) and clinical evolution (rapidly progressive kidney failure with proteinuria and an active urine sediment). Immunosuppressive therapy and sometimes plasma exchanges are required. Overall- and kidney survival are closely linked to the blood creatinine level at presentation, the percentage of damaged glomeruli, and to the underlying cause. RPG is therefore a diagnostic and therapeutic emergency that needs quick referral to a nephrologist. PMID:24665657

  19. Temperature and the Field Stability of a Dengue Rapid Diagnostic Test in the Tropics

    PubMed Central

    Phommasone, Koukeo; Sengvilaipaseuth, Onanong; de Lamballerie, Xavier; Vongsouvath, Manivanh; Phonemixay, Ooyanong; Blacksell, Stuart D.; Newton, Paul N.; Dubot-Pérès, Audrey

    2015-01-01

    The global incidence of dengue has increased significantly in recent decades, resulting in a large public health burden in tropical and subtropical countries. Dengue rapid diagnostic tests (RDTs) can provide accurate, rapid accessible diagnosis for patient management and may be easily used by health workers in rural areas. However, in dengue-endemic areas, ambient temperatures are often higher than manufacturer's recommendation. We therefore evaluated the effect of high temperature over time on the performance of one commonly used dengue RDT, the Standard Diagnostics Bioline Dengue Duo. RDTs were kept in five different conditions (at 4°C, 35°C, 45°C, 60°C, and at fluctuant ambient temperatures in a free-standing hut) for between 2 days and 2 years in the Lao People's Democratic Republic (PDR). RDTs were tested with four control sera (negative, dengue nonstructural protein 1 [NS1], anti-dengue immunoglobulin [Ig] M, and anti-dengue IgG positive). The RDTs had 100% consistency over the 2-year study, despite high temperatures, including in the hut in which temperatures exceeded the manufacturer's recommendations for 29% of time points. These data suggest that the diagnostic accuracy of the SD Bioline Dengue Duo RDT remains stable even after long-term storage at high temperatures. Therefore, use at such ambient temperatures in tropical areas should not jeopardize the dengue diagnostic outcome. PMID:25962773

  20. Diagnostic methodology is critical for accurately determining the prevalence of ichthyophonus infections in wild fish populations

    USGS Publications Warehouse

    Kocan, R.; Dolan, H.; Hershberger, P.

    2011-01-01

    Several different techniques have been employed to detect and identify Ichthyophonus spp. in infected fish hosts; these include macroscopic observation, microscopic examination of tissue squashes, histological evaluation, in vitro culture, and molecular techniques. Examination of the peer-reviewed literature revealed that when more than 1 diagnostic method is used, they often result in significantly different results; for example, when in vitro culture was used to identify infected trout in an experimentally exposed population, 98.7% of infected trout were detected, but when standard histology was used to confirm known infected tissues from wild salmon, it detected ~50% of low-intensity infections and ~85% of high-intensity infections. Other studies on different species reported similar differences. When we examined a possible mechanism to explain the disparity between different diagnostic techniques, we observed non-random distribution of the parasite in 3-dimensionally visualized tissue sections from infected hosts, thus providing a possible explanation for the different sensitivities of commonly used diagnostic techniques. Based on experimental evidence and a review of the peer-reviewed literature, we have concluded that in vitro culture is currently the most accurate diagnostic technique for determining infection prevalence of Ichthyophonus, particularly when the exposure history of the population is not known.

  1. Diagnostic methodology is critical for accurately determining the prevalence of Ichthyophonus infections in wild fish populations.

    PubMed

    Kocan, Richard; Dolan, Heather; Hershberger, Paul

    2011-04-01

    Several different techniques have been employed to detect and identify Ichthyophonus spp. in infected fish hosts; these include macroscopic observation, microscopic examination of tissue squashes, histological evaluation, in vitro culture, and molecular techniques. Examination of the peer-reviewed literature revealed that when more than 1 diagnostic method is used, they often result in significantly different results; for example, when in vitro culture was used to identify infected trout in an experimentally exposed population, 98.7% of infected trout were detected, but when standard histology was used to confirm known infected tissues from wild salmon, it detected ~50% of low-intensity infections and ~85% of high-intensity infections. Other studies on different species reported similar differences. When we examined a possible mechanism to explain the disparity between different diagnostic techniques, we observed non-random distribution of the parasite in 3-dimensionally visualized tissue sections from infected hosts, thus providing a possible explanation for the different sensitivities of commonly used diagnostic techniques. Based on experimental evidence and a review of the peer-reviewed literature, we have concluded that in vitro culture is currently the most accurate diagnostic technique for determining infection prevalence of Ichthyophonus , particularly when the exposure history of the population is not known. PMID:21506773

  2. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics.

    PubMed

    James, Ameh; Macdonald, Joanne

    2015-01-01

    Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA. PMID:26517245

  3. Integrated Rapid-Diagnostic-Test Reader Platform on a Cellphone

    PubMed Central

    Mudanyali, Onur; Dimitrov, Stoyan; Sikora, Uzair; Padmanabhan, Swati; Navruz, Isa; Ozcan, Aydogan

    2012-01-01

    We demonstrate a cellphone based Rapid-Diagnostic-Test (RDT) reader platform that can work with various lateral flow immuno-chromatographic assays and similar tests to sense the presence of a target analyte in a sample. This compact and cost-effective digital RDT reader, weighing only ~65 grams, mechanically attaches to the existing camera unit of a cellphone, where various types of RDTs can be inserted to be imaged in reflection or transmission modes under light-emitting-diode (LED) based illumination. Captured raw images of these tests are then digitally processed (within less than 0.2 sec/image) through a smart application running on the cellphone for validation of the RDT as well as for automated reading of its diagnostic result. The same smart application running on the cellphone then transmits the resulting data, together with the RDT images and other related information (e.g., demographic data) to a central server, which presents the diagnostic results on a world-map through geo-tagging. This dynamic spatio-temporal map of various RDT results can then be viewed and shared using internet browsers or through the same cellphone application. We tested this platform using malaria, tuberculosis (TB) as well as HIV RDTs by installing it on both Android based smart-phones as well as an iPhone. Providing real-time spatio-temporal statistics for the prevalence of various infectious diseases, this smart RDT reader platform running on cellphones might assist health-care professionals and policy makers to track emerging epidemics worldwide and help epidemic preparedness. PMID:22596243

  4. Integrated rapid-diagnostic-test reader platform on a cellphone.

    PubMed

    Mudanyali, Onur; Dimitrov, Stoyan; Sikora, Uzair; Padmanabhan, Swati; Navruz, Isa; Ozcan, Aydogan

    2012-08-01

    We demonstrate a cellphone-based rapid-diagnostic-test (RDT) reader platform that can work with various lateral flow immuno-chromatographic assays and similar tests to sense the presence of a target analyte in a sample. This compact and cost-effective digital RDT reader, weighing only ~65 g, mechanically attaches to the existing camera unit of a cellphone, where various types of RDTs can be inserted to be imaged in reflection or transmission modes under light-emitting diode (LED)-based illumination. Captured raw images of these tests are then digitally processed (within less than 0.2 s per image) through a smart application running on the cellphone for validation of the RDT, as well as for automated reading of its diagnostic result. The same smart application then transmits the resulting data, together with the RDT images and other related information (e.g., demographic data), to a central server, which presents the diagnostic results on a world map through geo-tagging. This dynamic spatio-temporal map of various RDT results can then be viewed and shared using internet browsers or through the same cellphone application. We tested this platform using malaria, tuberculosis (TB) and HIV RDTs by installing it on both Android-based smartphones and an iPhone. Providing real-time spatio-temporal statistics for the prevalence of various infectious diseases, this smart RDT reader platform running on cellphones might assist healthcare professionals and policymakers to track emerging epidemics worldwide and help epidemic preparedness. PMID:22596243

  5. Performance of rapid influenza diagnostic testing in outbreak settings.

    PubMed

    Peci, Adriana; Winter, Anne-Luise; King, Eddie-Chong; Blair, Joanne; Gubbay, Jonathan B

    2014-12-01

    Rapid influenza diagnostic tests (RIDTs) may be useful during institutional respiratory disease outbreaks to identify influenza and enable antivirals to be rapidly administered to patients and for the prophylactic treatment of those exposed to the virus but not yet symptomatic. The performance of RIDTs at the outbreak level is not well documented in the literature. This study aimed to evaluate the performance of RIDTs in comparison with that of real-time reverse transcription (rRT)-PCR in the context of institutional respiratory disease outbreaks. This study included outbreak-related respiratory specimens tested for influenza virus at Public Health Ontario Laboratories by both RIDT and rRT-PCR, from 1 September 2010 to 30 April 2013. At the outbreak level, performance testing of RIDTs compared to rRT-PCR for the detection of any influenza virus type demonstrated an overall sensitivity of 76.5%, a specificity of 99.7%, a positive predictive value (PPV) of 99.5%, and a negative predictive value of 85.3%. Because of their high specificity and PPV, even outside of the influenza season, RIDTs can play a role in screening for influenza virus in outbreaks and instituting antiviral therapy in a timely manner when positive. RIDTs can also be useful in remote settings where molecular virology testing is not easily accessible. Suboptimal sensitivity of RIDTs can be addressed by the use of molecular testing. PMID:25320225

  6. Performance of Rapid Influenza Diagnostic Testing in Outbreak Settings

    PubMed Central

    Winter, Anne-Luise; King, Eddie-Chong; Blair, Joanne; Gubbay, Jonathan B.

    2014-01-01

    Rapid influenza diagnostic tests (RIDTs) may be useful during institutional respiratory disease outbreaks to identify influenza and enable antivirals to be rapidly administered to patients and for the prophylactic treatment of those exposed to the virus but not yet symptomatic. The performance of RIDTs at the outbreak level is not well documented in the literature. This study aimed to evaluate the performance of RIDTs in comparison with that of real-time reverse transcription (rRT)-PCR in the context of institutional respiratory disease outbreaks. This study included outbreak-related respiratory specimens tested for influenza virus at Public Health Ontario Laboratories by both RIDT and rRT-PCR, from 1 September 2010 to 30 April 2013. At the outbreak level, performance testing of RIDTs compared to rRT-PCR for the detection of any influenza virus type demonstrated an overall sensitivity of 76.5%, a specificity of 99.7%, a positive predictive value (PPV) of 99.5%, and a negative predictive value of 85.3%. Because of their high specificity and PPV, even outside of the influenza season, RIDTs can play a role in screening for influenza virus in outbreaks and instituting antiviral therapy in a timely manner when positive. RIDTs can also be useful in remote settings where molecular virology testing is not easily accessible. Suboptimal sensitivity of RIDTs can be addressed by the use of molecular testing. PMID:25320225

  7. Using Copula Distributions to Support More Accurate Imaging-Based Diagnostic Classifiers for Neuropsychiatric Disorders

    PubMed Central

    Bansal, Ravi; Hao, Xuejun; Liu, Jun; Peterson, Bradley S.

    2014-01-01

    Many investigators have tried to apply machine learning techniques to magnetic resonance images (MRIs) of the brain in order to diagnose neuropsychiatric disorders. Usually the number of brain imaging measures (such as measures of cortical thickness and measures of local surface morphology) derived from the MRIs (i.e., their dimensionality) has been large (e.g. >10) relative to the number of participants who provide the MRI data (<100). Sparse data in a high dimensional space increases the variability of the classification rules that machine learning algorithms generate, thereby limiting the validity, reproducibility, and generalizability of those classifiers. The accuracy and stability of the classifiers can improve significantly if the multivariate distributions of the imaging measures can be estimated accurately. To accurately estimate the multivariate distributions using sparse data, we propose to estimate first the univariate distributions of imaging data and then combine them using a Copula to generate more accurate estimates of their multivariate distributions. We then sample the estimated Copula distributions to generate dense sets of imaging measures and use those measures to train classifiers. We hypothesize that the dense sets of brain imaging measures will generate classifiers that are stable to variations in brain imaging measures, thereby improving the reproducibility, validity, and generalizability of diagnostic classification algorithms in imaging datasets from clinical populations. In our experiments, we used both computer-generated and real-world brain imaging datasets to assess the accuracy of multivariate Copula distributions in estimating the corresponding multivariate distributions of real-world imaging data. Our experiments showed that diagnostic classifiers generated using imaging measures sampled from the Copula were significantly more accurate and more reproducible than were the classifiers generated using either the real-world imaging

  8. Fiber-optic immuno-biosensor for rapid and accurate detection of nerve growth factor in human blood.

    PubMed

    Tang, Liang; Cha, Yong-Mei; Li, Hongmei; Chen, Peng-Sheng; Lin, Shien-Fong

    2006-01-01

    An accurate and rapid assay of cardiac nerve growth factor (NGF) levels in blood can provide physicians with critical information regarding myocardial injury and neural remodeling in cardiac tissues to identify patients at risk of impending heart attack, thereby enabling them to receive appropriate lifesaving treatment more quickly. Currently used assay methods, such as enzyme-linked immunosorbent assay (ELISA), are usually time-consuming (hours to days), expensive and technically complicated. In this paper, we described the development and clinical study of a rapid and sensitive method for detection and quantification of NGF in human blood plasma. This method utilizes a fiber-optic, immuno-biosensing system which performs a fluorophore-mediated sandwich immunoassay on the surface of an optical fiber. Physiological concentrations of NGF could be quantified in both buffer and human blood plasma samples within 5 minutes. The NGF concentrations determined by the fiberoptic sensor were comparable to those by the gold standard, ELISA. Preliminary study of NGF assay in cardiac patient plasma samples showed a great potential of the fiber-optic sensor as a rapid diagnostic and prognostic tool in clinical applications. PMID:17946002

  9. Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR

    PubMed Central

    Cunha, Pricila da Silva; Pena, Heloisa B.; D'Angelo, Carla Sustek; Koiffmann, Celia P.; Rosenfeld, Jill A.; Shaffer, Lisa G.; Stofanko, Martin; Gonçalves-Dornelas, Higgor; Pena, Sérgio Danilo Junho

    2014-01-01

    Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH), which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR) assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH), and/or multiplex ligation-dependent probe amplification (MLPA) all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs. PMID:24839341

  10. Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison

    PubMed Central

    2013-01-01

    Background Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. Results We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. Conclusion CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets. PMID:23617892

  11. Ascitic Fluid Calprotectin and Serum Procalcitonin as Accurate Diagnostic Markers for Spontaneous Bacterial Peritonitis

    PubMed Central

    Abdel-Razik, Ahmed; Mousa, Nasser; Elhammady, Dina; Elhelaly, Rania; Elzehery, Rasha; Elbaz, Sherif; Eissa, Mohamed; El-Wakeel, Niveen; Eldars, Waleed

    2016-01-01

    Background/Aims The diagnosis of spontaneous bacterial peritonitis (SBP) is based on a polymorphonuclear leukocytes (PMNs) exceeding 250/μL in ascitic fluid. The aim of the study was to evaluate serum procalcitonin and ascitic fluid calprotectin as accurate diagnostic markers for detecting SBP. Methods Seventy-nine patients with cirrhotic ascites were included. They were divided into a SBP group, including 52 patients, and a non-SBP group of 27 patients. Serum procalcitonin, ascitic calprotectin, and serum and ascitic levels of tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6) were measured using an enzyme-linked immunosorbent assay. Results Serum procalcitonin and ascitic calprotectin were significantly higher in SBP patients than in non-SBP patients. Significant increases in both serum and ascitic levels of TNF-α and IL-6 were observed in SBP patients versus non-SBP patients. At a cutoff value of 0.94 ng/mL, serum procalcitonin had 94.3% sensitivity and 91.8% specificity for detecting SBP. In addition, at a cutoff value of 445 ng/mL, ascitic calprotectin had 95.4% sensitivity and 85.2% specificity for detecting SBP. Both were positively correlated with ascitic fluid proteins, PMN count, TNF-α, and IL-6. Conclusions According to our findings, determination of serum procalcitonin levels and ascitic calprotectin appears to provide satisfactory diagnostic markers for the diagnosis of SBP. PMID:26601826

  12. Research on the Rapid and Accurate Positioning and Orientation Approach for Land Missile-Launching Vehicle

    PubMed Central

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  13. Research on the rapid and accurate positioning and orientation approach for land missile-launching vehicle.

    PubMed

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  14. Rapid non-invasive tests for diagnostics of infectious diseases

    NASA Astrophysics Data System (ADS)

    Malamud, Daniel

    2014-06-01

    A rapid test for an infectious disease that can be used at point-of-care at a physician's office, a pharmacy, or in the field is critical for the prompt and appropriate therapeutic intervention. Ultimately by treating infections early on will decrease transmission of the pathogen. In contrast to metabolic diseases or cancer where multiple biomarkers are required, infectious disease targets (e.g. antigen, antibody, nucleic acid) are simple and specific for the pathogen causing the disease. Our laboratory has focused on three major infectious disease; HIV, Tuberculosis, and Malaria. These diseases are pandemic in much of the world thus putting natives, tourists and military personnel at risk for becoming infected, and upon returning to the U.S., transmitting these diseases to their contacts. Our devices are designed to detect antigens, antibodies or nucleic acids in blood or saliva samples in less than 30 minutes. An overview describing the current status of each of the three diagnostic platforms is presented. These microfluidic point-of-care devices will be relatively inexpensive, disposable, and user friendly.

  15. Polymeric rapid prototyping for inexpensive and portable medical diagnostics

    NASA Astrophysics Data System (ADS)

    Ma, Tianchi; Northrup, Victoria; Fung, Andrew O.; Glerum, D. Moira; Backhouse, Christopher J.

    2012-10-01

    The advent of inexpensive CO2 laser systems has led to a wide range of demonstrations of microfabricated lab on chip systems built of acrylic. However, there has been little application of these systems to building microfluidics for DNA analysis. In this work we explore the use of CO2 laser systems for building microfluidics for DNA analysis and relate the artifacts of the fabrication technology to the performance of the system. We show that surface roughness that leads to significant constrictions in the separation channel provides an upper limit of the size of DNA that can be analysed. Below that upper limit, the resolution of the chip is strongly affected by the degree to which the separation channel is exposed to redeposited by-products of the ablation process. We show that by controlling these effects we are reliably able to discern two types of PCR product as a test representative of a real application. By being able to do this is in microfluidic devices the size of a postage stamp we have shown that we can now use CO2 laser systems for the development of extremely inexpensive diagnostic systems using a rapid prototyping approach.

  16. A Novel Automatic Rapid Diagnostic Test Reader Platform

    PubMed Central

    Ozkan, Haydar; Kayhan, Osman Semih

    2016-01-01

    A novel automatic Rapid Diagnostic Test (RDT) reader platform is designed to analyze and diagnose target disease by using existing consumer cameras of a laptop-computer or a tablet. The RDT reader is useable with numerous lateral immunochromatographic assays and similar biomedical tests. The system has two different components, which are 3D-printed, low-cost, tiny, and compact stand and a decision program named RDT-AutoReader 2.0. The program takes the image of RDT, crops the region of interest (ROI), and extracts the features from the control end test lines to classify the results as invalid, positive, or negative. All related patient's personal information, image of ROI, and the e-report are digitally saved and transferred to the related clinician. Condition of the patient and the progress of the disease can be monitored by using the saved data. The reader platform has been tested by taking image from used cassette RDTs of rotavirus (RtV)/adenovirus (AdV) and lateral flow strip RDTs of Helicobacter pylori (H. pylori) before discarding them. The created RDT reader can also supply real-time statistics of various illnesses by using databases and Internet. This can help to inhibit propagation of contagious diseases and to increase readiness against epidemic diseases worldwide. PMID:27190549

  17. Safety of falciparum malaria diagnostic strategy based on rapid diagnostic tests in returning travellers and migrants: a retrospective study

    PubMed Central

    2012-01-01

    Background Rapid diagnostic tests for malaria (RDTs) allow accurate diagnosis and prompt treatment. Validation of their usefulness in travellers with fever was needed. The safety of a strategy to diagnose falciparum malaria based on RDT followed by immediate or delayed microscopy reading at first attendance was evaluated in one referral hospital in Switzerland. Methods A retrospective study was conducted in the outpatient clinic and emergency ward of University Hospital, covering a period of eight years (1999–2007). The study was conducted in the outpatient clinic and emergency ward of University Hospital. All adults suspected of malaria with a diagnostic test performed were included. RDT and microscopy as immediate tests were performed during working hours, and RDT as immediate test and delayed microscopy reading out of laboratory working hours. The main outcome measure was occurrence of specific complications in RDT negative and RDT positive adults. Results 2,139 patients were recruited. 1987 had both initial RDT and blood smear (BS) result negative. Among those, 2/1987 (0.1%) developed uncomplicated malaria with both RDT and BS positive on day 1 and day 6 respectively. Among the 152 patients initially malaria positive, 137 had both RDT and BS positive, four only BS positive and five only RDT positive (PCR confirmed) (six had only one test performed). None of the four initially RDT negative/BS positive and none of the five initially BS negative/RDT positive developed severe malaria while 6/137 of both RDT and BS positive did so. The use of RDT allowed a reduction of a median of 2.1 hours to get a first malaria test result. Conclusions A malaria diagnostic strategy based on RDTs and a delayed BS is safe in non-immune populations, and shortens the time to first malaria test result. PMID:23158019

  18. Clinical Evaluation of Rapid Diagnostic Test Kit for Scrub Typhus with Improved Performance

    PubMed Central

    2016-01-01

    Diagnosis of scrub typhus is challenging due to its more than twenty serotypes and the similar clinical symptoms with other acute febrile illnesses including leptospirosis, murine typhus and hemorrhagic fever with renal syndrome. Accuracy and rapidity of a diagnostic test to Orientia tsutsugamushi is an important step to diagnose this disease. To discriminate scrub typhus from other diseases, the improved ImmuneMed Scrub Typhus Rapid Diagnostic Test (RDT) was evaluated in Korea and Sri Lanka. The sensitivity at the base of each IgM and IgG indirect immunofluorescent assay (IFA) in Korean patients was 98.6% and 97.1%, and the specificity was 98.2% and 97.7% respectively. The sensitivity and specificity for retrospective diagnosis at the base of IFA in Sri Lanka was 92.1% and 96.1%. ImmuneMed RDT was not reactive to any serum from seventeen diseases including hemorrhagic fever with renal syndrome (n = 48), leptospirosis (n = 23), and murine typhus (n = 48). ImmuneMed RDT shows superior sensitivity (98.6% and 97.1%) compared with SD Bioline RDT (84.4% at IgM and 83.3% at IgG) in Korea. The retrospective diagnosis of ImmuneMed RDT exhibits 94.0% identity with enzyme-linked Immunosorbent assay (ELISA) using South India patient serum samples. These results suggest that this RDT can replace other diagnostic tests and is applicable for global diagnosis of scrub typhus. This rapid and accurate diagnosis will be beneficial for diagnosing and managing scrub typhus. PMID:27478327

  19. The SUCCESS model for laboratory performance and execution of rapid molecular diagnostics in patients with sepsis.

    PubMed

    Dekmezian, Mhair; Beal, Stacy G; Damashek, Mary Jane; Benavides, Raul; Dhiman, Neelam

    2015-04-01

    Successful performance and execution of rapid diagnostics in a clinical laboratory hinges heavily on careful validation, accurate and timely communication of results, and real-time quality monitoring. Laboratories must develop strategies to integrate diagnostics with stewardship and evidence-based clinical practice guidelines. We present a collaborative SUCCESS model for execution and monitoring of rapid sepsis diagnostics to facilitate timely treatment. Six months after execution of the Verigene Gram-Positive Blood Culture (BC-GP) and the AdvanDx PNA-FISH assays, data were collected on 579 and 28 episodes of bacteremia and fungemia, respectively. Clinical testing was executed using a SUCCESS model comprising the following components: stewardship, utilization of resources, core strategies, concierge services, education, support, and surveillance. Stewardship needs were identified by evaluating the specialty services benefiting from new testing. Utilization of resources was optimized by reviewing current treatment strategies and antibiogram and formulary options. Core strategies consisted of input from infectious disease leadership, pharmacy, and laboratory staff. Concierge services included automated Micro-eUpdate and physician-friendly actionable reports. Education modules were user-specific, and support was provided through a dedicated 24/7 microbiology hotline. Surveillance was performed by daily audit by the director. Using the SUCCESS model, the turnaround time for the detailed report with actionable guidelines to the physician was ∼3 hours from the time of culture positivity. The overall correlation between rapid methods and culture was 94% (546/579). Discrepant results were predominantly contaminants such as a coagulase-negative staphylococci or viridans streptococci in mixed cultures. SUCCESS is a cost-effective and easily adaptable model for clinical laboratories with limited stewardship resources. PMID:25829640

  20. Clinical Evaluation of Rapid Diagnostic Test Kit for Scrub Typhus with Improved Performance.

    PubMed

    Kim, Young-Jin; Park, Sungman; Premaratna, Ranjan; Selvaraj, Stephen; Park, Sang-Jin; Kim, Sora; Kim, Donghwan; Kim, Min Soo; Shin, Dong Hoon; Choi, Kyung-Chan; Kwon, Soon-Hwan; Seo, Wonjun; Lee, Nam Taek; Kim, Seung-Han; Kang, Heui Keun; Kim, Yoon-Won

    2016-08-01

    Diagnosis of scrub typhus is challenging due to its more than twenty serotypes and the similar clinical symptoms with other acute febrile illnesses including leptospirosis, murine typhus and hemorrhagic fever with renal syndrome. Accuracy and rapidity of a diagnostic test to Orientia tsutsugamushi is an important step to diagnose this disease. To discriminate scrub typhus from other diseases, the improved ImmuneMed Scrub Typhus Rapid Diagnostic Test (RDT) was evaluated in Korea and Sri Lanka. The sensitivity at the base of each IgM and IgG indirect immunofluorescent assay (IFA) in Korean patients was 98.6% and 97.1%, and the specificity was 98.2% and 97.7% respectively. The sensitivity and specificity for retrospective diagnosis at the base of IFA in Sri Lanka was 92.1% and 96.1%. ImmuneMed RDT was not reactive to any serum from seventeen diseases including hemorrhagic fever with renal syndrome (n = 48), leptospirosis (n = 23), and murine typhus (n = 48). ImmuneMed RDT shows superior sensitivity (98.6% and 97.1%) compared with SD Bioline RDT (84.4% at IgM and 83.3% at IgG) in Korea. The retrospective diagnosis of ImmuneMed RDT exhibits 94.0% identity with enzyme-linked Immunosorbent assay (ELISA) using South India patient serum samples. These results suggest that this RDT can replace other diagnostic tests and is applicable for global diagnosis of scrub typhus. This rapid and accurate diagnosis will be beneficial for diagnosing and managing scrub typhus. PMID:27478327

  1. Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homology.

    PubMed

    Fujita, Y; Shibayama, H; Suzuki, Y; Karita, S; Takamatsu, S

    2005-12-01

    The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3-7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics. PMID:18492168

  2. New Rapid Diagnostic Tests for Neisseria meningitidis Serogroups A, W135, C, and Y

    PubMed Central

    Chanteau, Suzanne; Dartevelle, Sylvie; Mahamane, Ali Elhadj; Djibo, Saacou; Boisier, Pascal; Nato, Farida

    2006-01-01

    Background Outbreaks of meningococcal meningitis (meningitis caused by Neisseria meningitidis) are a major public health concern in the African “meningitis belt,” which includes 21 countries from Senegal to Ethiopia. Of the several species that can cause meningitis, N. meningitidis is the most important cause of epidemics in this region. In choosing the appropriate vaccine, accurate N. meningitidis serogroup determination is key. To this end, we developed and evaluated two duplex rapid diagnostic tests (RDTs) for detecting N. meningitidis polysaccharide (PS) antigens of several important serogroups. Methods and Findings Mouse monoclonal IgG antibodies against N. meningitidis PS A, W135/Y, Y, and C were used to develop two immunochromatography duplex RDTs, RDT1 (to detect serogroups A and W135/Y) and RDT2 (to detect serogroups C and Y). Standards for Reporting of Diagnostic Accuracy criteria were used to determine diagnostic accuracy of RDTs on reference strains and cerebrospinal fluid (CSF) samples using culture and PCR, respectively, as reference tests. The cutoffs were 105 cfu/ml for reference strains and 1 ng/ml for PS. Sensitivities and specificities were 100% for reference strains, and 93.8%–100% for CSF serogroups A, W135, and Y in CSF. For CSF serogroup A, the positive and negative likelihood ratios (± 95% confidence intervals [CIs]) were 31.867 (16.1–63.1) and 0.065 (0.04–0.104), respectively, and the diagnostic odds ratio (± 95% CI) was 492.9 (207.2–1,172.5). For CSF serogroups W135 and Y, the positive likelihood ratio was 159.6 (51.7–493.3) Both RDTs were equally reliable at 25 °C and 45 °C. Conclusions These RDTs are important new bedside diagnostic tools for surveillance of meningococcus serogroups A and W135, the two serogroups that are responsible for major epidemics in Africa. PMID:16953658

  3. Rapid detection of Serpulina hyodysenteriae in diagnostic specimens by PCR.

    PubMed Central

    Elder, R O; Duhamel, G E; Schafer, R W; Mathiesen, M R; Ramanathan, M

    1994-01-01

    total DNA obtained from normal swine feces inoculated with decreasing concentrations of S. hyodysenteriae cells, the sensitivity of the PCR assay was calculated to be between 1 and 10 organisms per 0.1 g of feces. The PCR assay was 1,000 times more sensitive than conventional culture of dysenteric feces on selective medium. There was complete agreement between the results of PCR assays and anaerobic culture on selective agar medium with diagnostic specimen (n = 9) obtained from six farms on which there were cases with clinical signs suggestive of swine dysentery. Detection of S. hyodysenteriae by PCR amplification of DNA has great potential for rapid identification of S. hyodysenteriae in diagnostic specimens. Images PMID:8077394

  4. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection

    PubMed Central

    Abd El Wahed, Ahmed; Patel, Pranav; Faye, Oumar; Thaloengsok, Sasikanya; Heidenreich, Doris; Matangkasombut, Ponpan; Manopwisedjaroen, Khajohnpong; Sakuntabhai, Anavaj; Sall, Amadou A.; Hufert, Frank T.; Weidmann, Manfred

    2015-01-01

    Background Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF). Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR) are the standard method for molecular detection of the dengue virus (DENV). Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA) assays were developed to detect DENV1-4. Methodology/Principal Findings Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4) to 241 (DENV1-3) RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal) and in Bangkok (Thailand). In Kedougou, the RT-RPA was operated at an ambient temperature of 38°C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31) and 100% (n=23), respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90) and 100%(n=41), respectively. Conclusions/Significance During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations. PMID:26075598

  5. Rapid and accurate broadband absorption cross-section measurement of human bodies in a reverberation chamber

    NASA Astrophysics Data System (ADS)

    Flintoft, Ian D.; Melia, Gregory C. R.; Robinson, Martin P.; Dawson, John F.; Marvin, Andy C.

    2015-06-01

    A measurement methodology for polarization and angle of incidence averaged electromagnetic absorption cross-section using a reverberation chamber is presented. The method is optimized for simultaneous rapid and accurate determination of average absorption cross-section over the frequency range 1-15 GHz, making it suitable for use in human absorption and exposure studies. The typical measurement time of the subject is about 8 min with a corresponding statistical uncertainty of about 3% in the measured absorption cross-section. The method is validated by comparing measurements on a spherical phantom with Mie series calculations. The efficacy of the method is demonstrated with measurements of the posture dependence of the absorption cross-section of a human subject and an investigation of the effects of clothing on the measured absorption which are important considerations for the practical design of experiments for studies on human subjects.

  6. Rapid and Accurate Identification of Coagulase-Negative Staphylococci by Real-Time PCR

    PubMed Central

    Edwards, K. J.; Kaufmann, M. E.; Saunders, N. A.

    2001-01-01

    Biprobe identification assays based on real-time PCR were designed for 15 species of coagulase-negative staphylococci (CNS). Three sets of primers and four biprobes were designed from two variable regions of the 16S rRNA gene. An identification scheme was developed based on the pattern of melting peaks observed with the four biprobes that had been tested on 24 type strains. This scheme was then tested on 100 previously identified clinical isolates and 42 blindly tested isolates. For 125 of the 142 clinical isolates there was a perfect correlation between the biprobe identification and the result of the ID 32 Staph phenotypic tests and PCR. For 12 of the other isolates a 300-bp portion of the 16S rRNA gene was sequenced to determine identity. The remaining five isolates could not be fully identified. LightCycler real-time PCR allowed rapid and accurate identification of the important CNS implicated in infection. PMID:11526126

  7. Diagnostic values of Helicobacter pylori diagnostic tests: stool antigen test, urea breath test, rapid urease test, serology and histology*

    PubMed Central

    Kazemi, Shadi; Tavakkoli, Hamid; Habizadeh, Mohamad Reza; Emami, Mohammad Hasan

    2011-01-01

    BACKGROUND: The purpose of this study is to compare validity of 5 diagnostic tests of helicobacter pylori with each other: stool antigen test, urea breath test (UBT), rapid urease test (RUT), serology and histology. METHODS: A total of 94 patients who had indication of endoscopy entered the study. All of the 5 tests were performed for each patient. When the results of at least 2 tests were positive (except serology), Helicobacter pylori infection was considered to be positive. The sensitivity, specificity, positive predictive value, negative predictive value, accuracy and area under receiver operating characteristic (ROC) curve of these 5 tests were determined. RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, accuracy and area under ROC curve of these 5 tests are as below, respectively. Histology: 89%, 78%, 93%, 91%, 85% and 0.881; RUT: 93%, 75%, 95%, 94%, 86% and 0.831; serology: 50%, 54%, 46%, 61%, 52% and 0.563; stool antigen test: 96%, 83%, 98%, 96%, 91% and 0.897; UBT: 89%, 73%, 92%, 90%, 82% and 0.892. CONCLUSIONS: Stool antigen test is the most accurate test for Helicobacter pylori diagnosis before eradication of these bacteria. PMID:22973378

  8. Rapid Diagnostic Tests for Dengue Virus Infection in Febrile Cambodian Children: Diagnostic Accuracy and Incorporation into Diagnostic Algorithms

    PubMed Central

    Carter, Michael J.; Emary, Kate R.; Moore, Catherine E.; Parry, Christopher M.; Sona, Soeng; Putchhat, Hor; Reaksmey, Sin; Chanpheaktra, Ngoun; Stoesser, Nicole; Dobson, Andrew D. M.; Day, Nicholas P. J.; Kumar, Varun; Blacksell, Stuart D.

    2015-01-01

    Background Dengue virus (DENV) infection is prevalent across tropical regions and may cause severe disease. Early diagnosis may improve supportive care. We prospectively assessed the Standard Diagnostics (Korea) BIOLINE Dengue Duo DENV rapid diagnostic test (RDT) to NS1 antigen and anti-DENV IgM (NS1 and IgM) in children in Cambodia, with the aim of improving the diagnosis of DENV infection. Methodology and principal findings We enrolled children admitted to hospital with non-localised febrile illnesses during the 5-month DENV transmission season. Clinical and laboratory variables, and DENV RDT results were recorded at admission. Children had blood culture and serological and molecular tests for common local pathogens, including reference laboratory DENV NS1 antigen and IgM assays. 337 children were admitted with non-localised febrile illness over 5 months. 71 (21%) had DENV infection (reference assay positive). Sensitivity was 58%, and specificity 85% for RDT NS1 and IgM combined. Conditional inference framework analysis showed the additional value of platelet and white cell counts for diagnosis of DENV infection. Variables associated with diagnosis of DENV infection were not associated with critical care admission (70 children, 21%) or mortality (19 children, 6%). Known causes of mortality were melioidosis (4), other sepsis (5), and malignancy (1). 22 (27%) children with a positive DENV RDT had a treatable other infection. Conclusions The DENV RDT had low sensitivity for the diagnosis of DENV infection. The high co-prevalence of infections in our cohort indicates the need for a broad microbiological assessment of non-localised febrile illness in these children. PMID:25710684

  9. Clinical Evaluation of Rapid Diagnostic Test Kit Using the Polysaccharide as a Genus-Specific Diagnostic Antigen for Leptospirosis in Korea, Bulgaria, and Argentina

    PubMed Central

    2016-01-01

    Leptospirosis, a zoonotic disease that is caused by many serovars which are more than 200 in the world, is an emerging worldwide disease. Accurate and rapid diagnostic tests for leptospirosis are a critical step to diagnose the disease. There are some commercial kits available for diagnosis of leptospirosis, but the obscurity of a species- or genus-specific antigen of pathogenic Leptospira interrogans causes the reduced sensitivity and specificity. In this study, the polysaccharide derived from lipopolysaccharide (LPS) of nonpathogenic Leptospira biflexa serovar patoc was prepared, and the antigenicity was confirmed by immunoblot and enzyme linked immunosorbent assay (ELISA). The performance of the rapid diagnostic test (RDT) kit using the polysaccharide as a diagnostic antigen was evaluated in Korea, Bulgaria and Argentina. The sensitivity was 93.9%, 100%, and 81.0% and the specificity was 97.9%, 100%, and 95.4% in Korea (which is a rare region occurring with 2 serovars mostly), Bulgaria (epidemic region with 3 serovars chiefly) and Argentina (endemic region with 19 serovars mainly) respectively. These results indicate that this RDT is applicable for global diagnosis of leptospirosis. This rapid and effective diagnosis will be helpful for diagnosis and manage of leptospirosis to use and the polysaccharide of Leptospira may be called as genus specific antigen for diagnosis. PMID:26839470

  10. Clinical Evaluation of Rapid Diagnostic Test Kit Using the Polysaccharide as a Genus-Specific Diagnostic Antigen for Leptospirosis in Korea, Bulgaria, and Argentina.

    PubMed

    Lee, Jin-Woo; Park, Sungman; Kim, Seung Han; Christova, Iva; Jacob, Paulina; Vanasco, Norma B; Kang, Yeon-Mi; Woo, Ye-Ju; Kim, Min Soo; Kim, Young-Jin; Cho, Min-Kee; Kim, Yoon-Won

    2016-02-01

    Leptospirosis, a zoonotic disease that is caused by many serovars which are more than 200 in the world, is an emerging worldwide disease. Accurate and rapid diagnostic tests for leptospirosis are a critical step to diagnose the disease. There are some commercial kits available for diagnosis of leptospirosis, but the obscurity of a species- or genus-specific antigen of pathogenic Leptospira interrogans causes the reduced sensitivity and specificity. In this study, the polysaccharide derived from lipopolysaccharide (LPS) of nonpathogenic Leptospira biflexa serovar patoc was prepared, and the antigenicity was confirmed by immunoblot and enzyme linked immunosorbent assay (ELISA). The performance of the rapid diagnostic test (RDT) kit using the polysaccharide as a diagnostic antigen was evaluated in Korea, Bulgaria and Argentina. The sensitivity was 93.9%, 100%, and 81.0% and the specificity was 97.9%, 100%, and 95.4% in Korea (which is a rare region occurring with 2 serovars mostly), Bulgaria (epidemic region with 3 serovars chiefly) and Argentina (endemic region with 19 serovars mainly) respectively. These results indicate that this RDT is applicable for global diagnosis of leptospirosis. This rapid and effective diagnosis will be helpful for diagnosis and manage of leptospirosis to use and the polysaccharide of Leptospira may be called as genus specific antigen for diagnosis. PMID:26839470

  11. Highly Accurate Antibody Assays for Early and Rapid Detection of Tuberculosis in African and Asian Elephants ▿

    PubMed Central

    Greenwald, Rena; Lyashchenko, Olena; Esfandiari, Javan; Miller, Michele; Mikota, Susan; Olsen, John H.; Ball, Ray; Dumonceaux, Genevieve; Schmitt, Dennis; Moller, Torsten; Payeur, Janet B.; Harris, Beth; Sofranko, Denise; Waters, W. Ray; Lyashchenko, Konstantin P.

    2009-01-01

    Tuberculosis (TB) in elephants is a reemerging zoonotic disease caused primarily by Mycobacterium tuberculosis. Current methods for screening and diagnosis rely on trunk wash culture, which has serious limitations due to low test sensitivity, slow turnaround time, and variable sample quality. Innovative and more efficient diagnostic tools are urgently needed. We describe three novel serologic techniques, the ElephantTB Stat-Pak kit, multiantigen print immunoassay, and dual-path platform VetTB test, for rapid antibody detection in elephants. The study was performed with serum samples from 236 captive African and Asian elephants from 53 different locations in the United States and Europe. The elephants were divided into three groups based on disease status and history of exposure: (i) 26 animals with culture-confirmed TB due to M. tuberculosis or Mycobacterium bovis, (ii) 63 exposed elephants from known-infected herds that had never produced a culture-positive result from trunk wash samples, and (iii) 147 elephants without clinical symptoms suggestive of TB, with consistently negative trunk wash culture results, and with no history of potential exposure to TB in the past 5 years. Elephants with culture-confirmed TB and a proportion of exposed but trunk wash culture-negative elephants produced robust antibody responses to multiple antigens of M. tuberculosis, with seroconversions detectable years before TB-positive cultures were obtained from trunk wash specimens. ESAT-6 and CFP10 proteins were immunodominant antigens recognized by elephant antibodies during disease. The serologic assays demonstrated 100% sensitivity and 95 to 100% specificity. Rapid and accurate antibody tests to identify infected elephants will likely allow earlier and more efficient treatment, thus limiting transmission of infection to other susceptible animals and to humans. PMID:19261770

  12. Comparative evaluation of two rapid field tests for malaria diagnosis: Partec Rapid Malaria Test® and Binax Now® Malaria Rapid Diagnostic Test

    PubMed Central

    2011-01-01

    Background About 90% of all malaria deaths in sub-Saharan Africa occur in children under five years. Fast and reliable diagnosis of malaria requires confirmation of the presence of malaria parasites in the blood of patients with fever or history suggestive of malaria; hence a prompt and accurate diagnosis of malaria is the key to effective disease management. Confirmation of malaria infection requires the availability of a rapid, sensitive, and specific testing at an affordable cost. We compared two recent methods (the novel Partec Rapid Malaria Test® (PT) and the Binax Now® Malaria Rapid Diagnostic Test (BN RDT) with the conventional Giemsa stain microscopy (GM) for the diagnosis of malaria among children in a clinical laboratory of a hospital in a rural endemic area of Ghana. Methods Blood samples were collected from 263 children admitted with fever or a history of fever to the pediatric clinic of the Agogo Presbyterian Hospital. The three different test methods PT, BN RDT and GM were performed independently by well trained and competent laboratory staff to assess the presence of malaria parasites. Results were analyzed and compared using GM as the reference standard. Results In 107 (40.7%) of 263 study participants, Plasmodium sp. was detected by GM. PT and BN RDT showed positive results in 111 (42.2%) and 114 (43.4%), respectively. Compared to GM reference standard, the sensitivities of the PT and BN RDT were 100% (95% CI: 96.6-100) and 97.2% (95% CI: 92.0-99.4), respectively, specificities were 97.4% (95% CI: 93.6-99.3) and 93.6% (95% CI: 88.5-96.9), respectively. There was a strong agreement (kappa) between the applied test methods (GM vs PT: 0.97; p < 0.001 and GM vs BN RDT: 0.90; p < 0.001). The average turnaround time per tests was 17 minutes. Conclusion In this study two rapid malaria tests, PT and BN RDT, demonstrated a good quality of their performance compared to conventional GM. Both methods require little training, have short turnaround times, are

  13. Development and clinical evaluation of a rapid diagnostic kit for feline leukemia virus infection

    PubMed Central

    Kim, Won-Shik; Chong, Chom-Kyu; Kim, Hak-Yong; Lee, Gyu-Cheol; Jeong, Wooseog; An, Dong-Jun; Jeoung, Hye-Young; Lee, Jae-In

    2014-01-01

    Feline leukemia virus (FeLV) causes a range of neoplastic and degenerative diseases in cats. To obtain a more sensitive and convenient diagnosis of the disease, we prepared monoclonal antibodies specific for the FeLV p27 to develop a rapid diagnostic test with enhanced sensitivity and specificity. Among these antibodies, we identified two clones (hybridomas 8F8B5 and 8G7D1) that specifically bound to FeLV and were very suitable for a diagnostic kit. The affinity constants for 8F8B5 and 8G7D1 were 0.35 × 109 and 0.86 × 109, respectively. To investigate the diagnostic abilities of the rapid kit using these antibodies, we performed several clinical studies. Assessment of analytical sensitivity revealed that the detection threshold of the rapid diagnostic test was 2 ng/mL for recombinant p27 and 12.5 × 104 IU/mL for FeLV. When evaluating 252 cat sera samples, the kit was found to have a kappa value of 0.88 compared to polymerase chain reaction (PCR), indicating a significant correlation between data from the rapid diagnostic test and PCR. Sensitivity and specificity of the kit were 95.2% (20/21) and 98.5% (257/261), respectively. Our results demonstrated that the rapid diagnostic test would be a suitable diagnostic tool for the rapid detection of FeLV infection in cats. PMID:24136209

  14. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

    PubMed

    Neal, Stephen; Nip, Alex M; Zhang, Haiyan; Wishart, David S

    2003-07-01

    A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http

  15. Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

    PubMed Central

    Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

    2012-01-01

    Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

  16. Rapid diagnostics for avian influenza -- Advances in testing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A variety of tools are available for the diagnosis of avian influenza virus. They can be generally divided into the serologic diagnostic tests and direct virus detection tests. The serologic tests are important primarily for active surveillance to assure our poultry flocks are free of avian influe...

  17. Hospital discharge diagnostic and procedure codes for upper gastro-intestinal cancer: how accurate are they?

    PubMed Central

    2012-01-01

    Background Population-level health administrative datasets such as hospital discharge data are used increasingly to evaluate health services and outcomes of care. However information about the accuracy of Australian discharge data in identifying cancer, associated procedures and comorbidity is limited. The Admitted Patients Data Collection (APDC) is a census of inpatient hospital discharges in the state of New South Wales (NSW). Our aim was to assess the accuracy of the APDC in identifying upper gastro-intestinal (upper GI) cancer cases, procedures for associated curative resection and comorbidities at the time of admission compared to data abstracted from medical records (the ‘gold standard’). Methods We reviewed the medical records of 240 patients with an incident upper GI cancer diagnosis derived from a clinical database in one NSW area health service from July 2006 to June 2007. Extracted case record data was matched to APDC discharge data to determine sensitivity, positive predictive value (PPV) and agreement between the two data sources (κ-coefficient). Results The accuracy of the APDC diagnostic codes in identifying site-specific incident cancer ranged from 80-95% sensitivity. This was comparable to the accuracy of APDC procedure codes in identifying curative resection for upper GI cancer. PPV ranged from 42-80% for cancer diagnosis and 56-93% for curative surgery. Agreement between the data sources was >0.72 for most cancer diagnoses and curative resections. However, APDC discharge data was less accurate in reporting common comorbidities - for each condition, sensitivity ranged from 9-70%, whilst agreement ranged from κ = 0.64 for diabetes down to κ < 0.01 for gastro-oesophageal reflux disorder. Conclusions Identifying incident cases of upper GI cancer and curative resection from hospital administrative data is satisfactory but under-ascertained. Linkage of multiple population-health datasets is advisable to maximise case ascertainment and

  18. Rapid and Accurate Machine Learning Recognition of High Performing Metal Organic Frameworks for CO2 Capture.

    PubMed

    Fernandez, Michael; Boyd, Peter G; Daff, Thomas D; Aghaji, Mohammad Zein; Woo, Tom K

    2014-09-01

    In this work, we have developed quantitative structure-property relationship (QSPR) models using advanced machine learning algorithms that can rapidly and accurately recognize high-performing metal organic framework (MOF) materials for CO2 capture. More specifically, QSPR classifiers have been developed that can, in a fraction of a section, identify candidate MOFs with enhanced CO2 adsorption capacity (>1 mmol/g at 0.15 bar and >4 mmol/g at 1 bar). The models were tested on a large set of 292 050 MOFs that were not part of the training set. The QSPR classifier could recover 945 of the top 1000 MOFs in the test set while flagging only 10% of the whole library for compute intensive screening. Thus, using the machine learning classifiers as part of a high-throughput screening protocol would result in an order of magnitude reduction in compute time and allow intractably large structure libraries and search spaces to be screened. PMID:26278259

  19. An improved method for accurate and rapid measurement of flight performance in Drosophila.

    PubMed

    Babcock, Daniel T; Ganetzky, Barry

    2014-01-01

    Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a "drop tube" to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens. PMID:24561810

  20. Final Progress Report: Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes Feasibility Study

    SciTech Connect

    Rawool-Sullivan, Mohini; Bounds, John Alan; Brumby, Steven P.; Prasad, Lakshman; Sullivan, John P.

    2012-04-30

    This is the final report of the project titled, 'Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes,' PMIS project number LA10-HUMANID-PD03. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). It summarizes work performed over the FY10 time period. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). Human analysts begin analyzing a spectrum based on features in the spectrum - lines and shapes that are present in a given spectrum. The proposed work was to carry out a feasibility study that will pick out all gamma ray peaks and other features such as Compton edges, bremsstrahlung, presence/absence of shielding and presence of neutrons and escape peaks. Ultimately success of this feasibility study will allow us to collectively explain identified features and form a realistic scenario that produced a given spectrum in the future. We wanted to develop and demonstrate machine learning algorithms that will qualitatively enhance the automated identification capabilities of portable radiological sensors that are currently being used in the field.

  1. Rapid, accurate, and direct determination of total lycopene content in tomato paste

    NASA Astrophysics Data System (ADS)

    Bicanic, D.; Anese, M.; Luterotti, S.; Dadarlat, D.; Gibkes, J.; Lubbers, M.

    2003-01-01

    Lycopene that imparts red color to the tomato fruit is the most potent antioxidant among carotenes, an important nutrient and also used as a color ingredient in many food formulations. Since cooked and processed foods derived from tomatoes were shown to provide optimal lycopene boost, products such as paste, puree, juice, etc. are nowadays gaining popularity as dietary sources. The analysis of lycopene in tomato paste (partially dehydrated product prepared by vacuum concentrating tomato juice) is carried out using either high pressure liquid chromatography (HPLC), spectrophotometry, or by evaluating the color. The instability of lycopene during processes of extraction, etc., handling, and disposal of organic solvents makes the preparation of a sample for the analysis a delicate task. Despite a recognized need for accurate and rapid assessment of lycopene in tomato products no such method is available at present. The study described here focuses on a direct determination of a total lycopene content in different tomato pastes by means of the laser optothermal window (LOW) method at 502 nm. The concentration of lycopene in tomato paste ranged between 25 and 150 mg per 100 g product; the results are in excellent agreement with those obtained by spectrophotometry. The time needed to complete LOW analysis is very short, so that decomposition of pigment and the formation of artifacts are minimized. Preliminary results indicate a good degree of reproducibility making the LOW method suitable for routine assays of lycopene content in tomato paste.

  2. Evaluation of Three Rapid Diagnostic Methods for Direct Identification of Microorganisms in Positive Blood Cultures

    PubMed Central

    Martinez, Raquel M.; Bauerle, Elizabeth R.; Fang, Ferric C.

    2014-01-01

    The identification of organisms from positive blood cultures generally takes several days. However, recently developed rapid diagnostic methods offer the potential for organism identification within only a few hours of blood culture positivity. In this study, we evaluated the performance of three commercial methods to rapidly identify organisms directly from positive blood cultures: QuickFISH (AdvanDx, Wolburn, MA), Verigene Gram-Positive Blood Culture (BC-GP; Nanosphere, Northbrook, IL), and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) with Sepsityper processing (Bruker Daltonics, Billerica, MA). A total of 159 blood cultures (VersaTREK Trek Diagnostic Systems, Cleveland, OH) positive for Gram-positive and Gram-negative bacteria as well as yeast were analyzed with QuickFISH and MALDI-TOF MS. In all, 102 blood cultures were analyzed using the BC-GP assay. For monomicrobial cultures, we observed 98.0% concordance with routine methods for both QuickFISH (143/146) and the BC-GP assay (93/95). MALDI-TOF MS demonstrated 80.1% (117/146) and 87.7% (128/146) concordance with routine methods to the genus and species levels, respectively. None of the methods tested were capable of consistently identifying polymicrobial cultures in their entirety or reliably differentiating Streptococcus pneumoniae from viridans streptococci. Nevertheless, the methods evaluated in this study are convenient and accurate for the most commonly encountered pathogens and have the potential to dramatically reduce turnaround time for the provision of results to the treating physician. PMID:24808235

  3. [Usefulness of clinical data and rapid diagnostic tests to identify bacterial etiology in adult respiratory infections].

    PubMed

    Toledano-Sierra, Pilar; Arriola-Hernández, Maite; Orueta-Sánchez, Ramón

    2015-01-01

    Respiratory tract infections are a common complaint and most of them, such as common cold and laryngitis, are viral in origin, so antibiotic use should be exceptional. However, there are other respiratory tract infections (sinusitis, pharyngitis, lower respiratory tract infections, and exacerbations of chronic obstructive pulmonary disease) where a bacterial etiology is responsible for a non-negligible percentage, and antibiotics are often empirically indicated. The aim of the study is to identify the strength of the data obtained from the symptoms, physical examination and rapid diagnostic methods in respiratory infections in which antibiotic use is frequently proposed in order to improve diagnosis and influence the decision to prescribe these drugs. The review concludes that history, physical examination and rapid tests are useful to guide the need for antibiotic treatment in diseases such as acute sinusitis, acute pharyngitis, exacerbation of lower respiratory tract infection and chronic obstructive pulmonary disease. However, no isolated data is accurate enough by itself to confirm or rule out the need for antibiotics. Therefore, clinical prediction rules bring together history and physical examination, thereby improving the accuracy of the decision to indicate or not antibiotics. PMID:25646631

  4. A hybrid approach for rapid, accurate, and direct kilovoltage radiation dose calculations in CT voxel space

    SciTech Connect

    Kouznetsov, Alexei; Tambasco, Mauro

    2011-03-15

    Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.

  5. Rapid variability of OB-stars: nature and diagnostic value.

    NASA Astrophysics Data System (ADS)

    Baade, D.

    In the past decade, rapid photospheric variability has been recognized as the non-standard property that perhaps is the most common one among early-type stars. These proceedings offer an unusually complete overview of the existing observations. They are equally complete in their reflectance of the presently considered models. Because the simple definition 'on a rotational time scale' of the qualifier 'rapid' used in the title is very adequate for many stars, modulation is a strong contender also as a general model. The model that can be made to formally reproduce the widest range of observations is nonradial pulsation which, therefore, has earned itself the somewhat ambiguous reputation as a model for everything. An attraction of this model is that it would give the possibility to infer also structural and evolutionary quantities. It was the second purpose of the workshop to offer at least a glimpse of this potential.

  6. The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis

    PubMed Central

    Carranza-Rodríguez, Cristina; Pérez-Arellano, José Luis; Vicente, Belén; López-Abán, Julio; Muro, Antonio

    2015-01-01

    Background Urogenital schistosomiasis due to Schistosoma haematobium is a serious underestimated public health problem affecting 112 million people - particularly in sub-Saharan Africa. Microscopic examination of urine samples to detect parasite eggs still remains as definitive diagnosis. This work was focussed on developing a novel loop-mediated isothermal amplification (LAMP) assay for detection of S. haematobium DNA in human urine samples as a high-throughput, simple, accurate and affordable diagnostic tool to use in diagnosis of urogenital schistosomiasis. Methodology/Principal Findings A LAMP assay targeting a species specific sequence of S. haematobium ribosomal intergenic spacer was designed. The effectiveness of our LAMP was assessed in a number of patients´ urine samples with microscopy confirmed S. haematobium infection. For potentially large-scale application in field conditions, different DNA extraction methods, including a commercial kit, a modified NaOH extraction method and a rapid heating method were tested using small volumes of urine fractions (whole urine, supernatants and pellets). The heating of pellets from clinical samples was the most efficient method to obtain good-quality DNA detectable by LAMP. The detection limit of our LAMP was 1 fg/µL of S. haematobium DNA in urine samples. When testing all patients´ urine samples included in our study, diagnostic parameters for sensitivity and specificity were calculated for LAMP assay, 100% sensitivity (95% CI: 81.32%-100%) and 86.67% specificity (95% CI: 75.40%-94.05%), and also for microscopy detection of eggs in urine samples, 69.23% sensitivity (95% CI: 48.21% -85.63%) and 100% specificity (95% CI: 93.08%-100%). Conclusions/Significance We have developed and evaluated, for the first time, a LAMP assay for detection of S. haematobium DNA in heated pellets from patients´ urine samples using no complicated requirement procedure for DNA extraction. The procedure has been named the Rapid

  7. Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting.

    PubMed

    Muhamadali, Howbeer; Subaihi, Abdu; Mohammadtaheri, Mahsa; Xu, Yun; Ellis, David I; Ramanathan, Rajesh; Bansal, Vipul; Goodacre, Royston

    2016-08-15

    Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the

  8. Using ground-based geophysics to rapidly and accurately map sub-surface acidity

    NASA Astrophysics Data System (ADS)

    Wong, Vanessa; Triantafilis, John; Johnston, Scott; Nhan, Terence; Page, Donald; Wege, Richard; Hirst, Phillip; Slavich, Peter

    2013-04-01

    Globally, large areas of coastal and estuarine floodplains are underlain by sulfidic sediments and acid sulfate soils (ASS). These soils can be environmentally hazardous due to their high acidity and large pool of potentially mobile metals. The floodplains are characterised by high spatial and temporal heterogeneity. On coastal floodplains, ASS are of moderate to high salinity, with salts derived mainly from either connate marine sources or oxidation of biogenic sulfides and the subsequent increases in soluble ions (e.g. SO42-) and acidity that follow oxidation. Enhanced acidity also increases the mobilisation of pH-sensitive trace metals such as Fe, Al, Mn, Zn and Ni and contributes to increasing apparent salinity. Ground-based geophysics using electromagnetic (EM) induction techniques have been used successfully and extensively to rapidly map soils for salinity management and precision agriculture. EM induction techniques measure apparent soil electrical conductivity (ECa), which is a function of salinity, clay content, water content, soil mineralogy and temperature to determine the spatial distribution of sub-surface conductivity. In this study, we used ECa as a proxy to map the surface and sub-surface spatial distribution of ASS and associated acidic groundwater. Three EM instruments were used, EM38, DUALEM-421 and EM34, which focus on different depth layers, in a survey of a coastal floodplain in eastern Australia. The EM surveys were calibrated with limited soil sampling and analysis (pH, EC, soluble and exchangeable salts and metals, particle size and titratable actual acidity (TAA)). Using fuzzy k-means clustering analysis, the EM38 and elevation data, from a digital elevation model, clearly identified three classes in the near-surface (0-2m) layers: i) levee soils, ii) fluvial sediment capping and iii) ASS (Fig. 4). Increasing the number of classes did not alter the classes identified. Joint inversion of the DUALEM-421 and EM34 data also identified

  9. A potentiometric biosensor for rapid on-site disease diagnostics.

    PubMed

    Tarasov, Alexey; Gray, Darren W; Tsai, Meng-Yen; Shields, Niall; Montrose, Armelle; Creedon, Niamh; Lovera, Pierre; O'Riordan, Alan; Mooney, Mark H; Vogel, Eric M

    2016-05-15

    Quantitative point-of-care (POC) devices are the next generation for serological disease diagnosis. Whilst pathogen serology is typically performed by centralized laboratories using Enzyme-Linked ImmunoSorbent Assay (ELISA), faster on-site diagnosis would infer improved disease management and treatment decisions. Using the model pathogen Bovine Herpes Virus-1 (BHV-1) this study employs an extended-gate field-effect transistor (FET) for direct potentiometric serological diagnosis. BHV-1 is a major viral pathogen of Bovine Respiratory Disease (BRD), the leading cause of economic loss ($2 billion annually in the US only) to the cattle and dairy industry. To demonstrate the sensor capabilities as a diagnostic tool, BHV-1 viral protein gE was expressed and immobilized on the sensor surface to serve as a capture antigen for a BHV-1-specific antibody (anti-gE), produced in cattle in response to viral infection. The gE-coated immunosensor was shown to be highly sensitive and selective to anti-gE present in commercially available anti-BHV-1 antiserum and in real serum samples from cattle with results being in excellent agreement with Surface Plasmon Resonance (SPR) and ELISA. The FET sensor is significantly faster than ELISA (<10 min), a crucial factor for successful disease intervention. This sensor technology is versatile, amenable to multiplexing, easily integrated to POC devices, and has the potential to impact a wide range of human and animal diseases. PMID:26765531

  10. Microbial inactivation for safe and rapid diagnostics of infectious samples.

    PubMed

    Sagripanti, Jose-Luis; Hülseweh, Birgit; Grote, Gudrun; Voss, Luzie; Böhling, Katrin; Marschall, Hans-Jürgen

    2011-10-01

    The high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log(10)) of bacterial spores (Bacillus atrophaeus), vegetative bacteria (Pseudomonas aeruginosa), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost. PMID:21856830

  11. Development of a High Throughput Assay for Rapid and Accurate 10-Plex Detection of Citrus Pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The need to reliably detect and identify multiple plant pathogens simultaneously, especially in woody perennial hosts, has led to development of new molecular diagnostic approaches. In this study, a Luminex-based system was developed that provided a robust and sensitive test for simultaneous detect...

  12. Accurate Point-of-Care Detection of Ruptured Fetal Membranes: Improved Diagnostic Performance Characteristics with a Monoclonal/Polyclonal Immunoassay

    PubMed Central

    Rogers, Linda C.; Scott, Laurie; Block, Jon E.

    2016-01-01

    OBJECTIVE Accurate and timely diagnosis of rupture of membranes (ROM) is imperative to allow for gestational age-specific interventions. This study compared the diagnostic performance characteristics between two methods used for the detection of ROM as measured in the same patient. METHODS Vaginal secretions were evaluated using the conventional fern test as well as a point-of-care monoclonal/polyclonal immunoassay test (ROM Plus®) in 75 pregnant patients who presented to labor and delivery with complaints of leaking amniotic fluid. Both tests were compared to analytical confirmation of ROM using three external laboratory tests. Diagnostic performance characteristics were calculated including sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy. RESULTS Diagnostic performance characteristics uniformly favored ROM detection using the immunoassay test compared to the fern test: sensitivity (100% vs. 77.8%), specificity (94.8% vs. 79.3%), PPV (75% vs. 36.8%), NPV (100% vs. 95.8%), and accuracy (95.5% vs. 79.1%). CONCLUSIONS The point-of-care immunoassay test provides improved diagnostic accuracy for the detection of ROM compared to fern testing. It has the potential of improving patient management decisions, thereby minimizing serious complications and perinatal morbidity. PMID:27199579

  13. Assessment of Clinical Diagnosis, Microscopy, Rapid Diagnostic Tests, and Polymerase Chain Reaction in the Diagnosis of Plasmodium falciparum in Nigeria

    PubMed Central

    Ojurongbe, Olusola; Adegbosin, Olunike Olayeni; Taiwo, Sunday Samuel; Alli, Oyebode Armstrong Terry; Olowe, Olugbenga Adekunle; Ojurongbe, Taiwo Adetola; Bolaji, Oloyede Samuel; Adeyeba, Oluwaseyi Adegboyega

    2013-01-01

    This study compares the performance of clinical diagnosis and three laboratory diagnostic methods (thick film microscopy (TFM), rapid diagnostic test (RDT), and polymerase chain reaction (PCR)) for the diagnosis of Plasmodium falciparum in Nigeria. Using clinical criteria, 217 children were recruited into the study out of which 106 (48.8%) were positive by TFM, 84 (38.7%) by RDT, and 125 (57.6%) by PCR. Using a composite reference method generated from the three diagnostic methods, 71 (32.7%) patients were found to be truly infected and 90 (41.5%) truly uninfected, while 56 (25.8%) were misidentified as infected or noninfected. When each of the 3 diagnostic methods was compared with the composite reference, PCR had sensitivity of 97.3%, specificity of 62.5%, positive predictive value (PPV) of 56.8%, and negative predictive value (NPV) of 97.8%; microscopy had sensitivity of 77.2%, specificity of 72%, PPV of 66.9%, and NPV of 81.1%, while RDT had sensitivity of 62.3%, specificity of 87.4%, PPV of 67.7%, and NPV of 84.5%. PCR test performed best among the three methods followed by TFM and RDT in that order. The result of this study shows that clinical diagnosis cannot be relied upon for accurate diagnosis of P. falciparum in endemic areas. PMID:24371538

  14. Fluorescence polarization immunoassays for rapid, accurate, and sensitive determination of mycotoxins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analytical methods for the determination of mycotoxins in foods are commonly based on chromatographic techniques (GC, HPLC or LC-MS). Although these methods permit a sensitive and accurate determination of the analyte, they require skilled personnel and are time-consuming, expensive, and unsuitable ...

  15. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  16. A rapid method of accurate detection and differentiation of Newcastle disease virus pathotypes by demonstrating multiple bands in degenerate primer based nested RT-PCR.

    PubMed

    Desingu, P A; Singh, S D; Dhama, K; Kumar, O R Vinodh; Singh, R; Singh, R K

    2015-02-01

    A rapid and accurate method of detection and differentiation of virulent and avirulent Newcastle disease virus (NDV) pathotypes was developed. The NDV detection was carried out for different domestic avian field isolates and pigeon paramyxo virus-1 (25 field isolates and 9 vaccine strains) by using APMV-I "fusion" (F) gene Class II specific external primer A and B (535bp), internal primer C and D (238bp) based reverses transcriptase PCR (RT-PCR). The internal degenerative reverse primer D is specific for F gene cleavage position of virulent strain of NDV. The nested RT-PCR products of avirulent strains showed two bands (535bp and 424bp) while virulent strains showed four bands (535bp, 424bp, 349bp and 238bp) on agar gel electrophoresis. This is the first report regarding development and use of degenerate primer based nested RT-PCR for accurate detection and differentiation of NDV pathotypes by demonstrating multiple PCR band patterns. Being a rapid, simple, and economical test, the developed method could serve as a valuable alternate diagnostic tool for characterizing NDV isolates and carrying out molecular epidemiological surveillance studies for this important pathogen of poultry. PMID:25449112

  17. Laboratory Evaluation of Three Rapid Diagnostic Tests for Dual Detection of HIV and Treponema pallidum Antibodies

    PubMed Central

    Woo, Jennifer S.; Chung, Jun Ho; Sokovic, Anita; Bristow, Claire C.; Klausner, Jeffrey D.

    2014-01-01

    The performance of three research-use-only, dual HIV and syphilis rapid diagnostic tests (RDTs) was evaluated for 150 patient serum samples and compared to reference HIV and Treponema pallidum antibody detection methods. The RDTs performed comparably, with sensitivities of 93 to 99% and specificities of 97 to 100%. The kappa statistic between the RDTs was 0.95. PMID:25297332

  18. Laboratory evaluation of three rapid diagnostic tests for dual detection of HIV and Treponema pallidum antibodies.

    PubMed

    Humphries, Romney M; Woo, Jennifer S; Chung, Jun Ho; Sokovic, Anita; Bristow, Claire C; Klausner, Jeffrey D

    2014-12-01

    The performance of three research-use-only, dual HIV and syphilis rapid diagnostic tests (RDTs) was evaluated for 150 patient serum samples and compared to reference HIV and Treponema pallidum antibody detection methods. The RDTs performed comparably, with sensitivities of 93 to 99% and specificities of 97 to 100%. The kappa statistic between the RDTs was 0.95. PMID:25297332

  19. RT-PCR is a more accurate diagnostic tool for detection of BCR-ABL rearrangement

    SciTech Connect

    Zehnbauer, B.A.; Allen, A.P.; McGrath, S.D.

    1994-09-01

    Detection of the Philadelphia chromosome (Ph1) or genomic Southern hybridization for clonal gene rearrangement (GSH-R) has provided very specific identification of BCR-ABL gene rearrangement. Reverse transcriptase-polymerase chain reaction (RT-PCR) is diagnostic for patterns of BCR-ABL expression which are undetected by GSH-R and/or Ph1 and provides increased sensitivity both at diagnosis and in detection of minimal residual leukemia. Fifty-three specimens (of 150 tested from 119 consecutive leukemia patients) were RT-PCR positive for BCR-ABL gene expression confirmed by hybridization of PCR products with b{sub 3}a{sub 2}, b{sub 2}a{sub 2}, or e{sub 1}a{sub 2} junction-specific oligonucleotides. In 6 cases of CML with GSH-R{sup {minus}}at diagnosis, RT-PCR provided specific BCR-ABL identification. Deletion of BCR regions, low mitotic index, or e{sub 1}a{sub 2} expression caused failure to detect GSH-R or Ph1 translocation.

  20. There is need for antigen-based rapid diagnostic tests to identify common acute tropical illnesses.

    PubMed

    Wilde, Henry; Suankratay, Chusana

    2007-01-01

    Enteric fever, typhus, leptospirosis, dengue, melioidosis, and tuberculous meningitis present urgent diagnostic problems that require experience and clinical judgment to make early evidence-based management decisions. Basic and applied research dealing with reliable antigen-based diagnostics has been published and confirmed for several of these infections. This should have initiated commercial production but has not. Established international firms see little profit in such diagnostic kits since they would be used in poor countries with little prospects for return of investment capital. We attempt to illustrate this issue, using common causes of acute febrile illnesses in the Southeast Asian region. We believe that rapid diagnostic technology could prevent significant delay in starting appropriate therapy, reduce hospital expenses, and even save lives. PMID:17617848

  1. Raman Spectroscopy Provides a Powerful Diagnostic Tool for Accurate Determination of Albumin Glycation

    PubMed Central

    Dingari, Narahara Chari; Horowitz, Gary L.; Kang, Jeon Woong; Dasari, Ramachandra R.; Barman, Ishan

    2012-01-01

    We present the first demonstration of glycated albumin detection and quantification using Raman spectroscopy without the addition of reagents. Glycated albumin is an important marker for monitoring the long-term glycemic history of diabetics, especially as its concentrations, in contrast to glycated hemoglobin levels, are unaffected by changes in erythrocyte life times. Clinically, glycated albumin concentrations show a strong correlation with the development of serious diabetes complications including nephropathy and retinopathy. In this article, we propose and evaluate the efficacy of Raman spectroscopy for determination of this important analyte. By utilizing the pre-concentration obtained through drop-coating deposition, we show that glycation of albumin leads to subtle, but consistent, changes in vibrational features, which with the help of multivariate classification techniques can be used to discriminate glycated albumin from the unglycated variant with 100% accuracy. Moreover, we demonstrate that the calibration model developed on the glycated albumin spectral dataset shows high predictive power, even at substantially lower concentrations than those typically encountered in clinical practice. In fact, the limit of detection for glycated albumin measurements is calculated to be approximately four times lower than its minimum physiological concentration. Importantly, in relation to the existing detection methods for glycated albumin, the proposed method is also completely reagent-free, requires barely any sample preparation and has the potential for simultaneous determination of glycated hemoglobin levels as well. Given these key advantages, we believe that the proposed approach can provide a uniquely powerful tool for quantification of glycation status of proteins in biopharmaceutical development as well as for glycemic marker determination in routine clinical diagnostics in the future. PMID:22393405

  2. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

    PubMed Central

    Huang, Helen J.; Falchook, Gerald S.; Devogelaere, Benoit; Kockx, Mark; Bempt, Isabelle Vanden; Reijans, Martin; Naing, Aung; Fu, Siqing; Piha-Paul, Sarina A.; Hong, David S.; Holley, Veronica R.; Tsimberidou, Apostolia M.; Stepanek, Vanda M.; Patel, Sapna P.; Kopetz, E. Scott; Subbiah, Vivek; Wheler, Jennifer J.; Zinner, Ralph G.; Karp, Daniel D.; Luthra, Rajyalakshmi; Roy-Chowdhuri, Sinchita; Sablon, Erwin; Meric-Bernstam, Funda; Maertens, Geert; Kurzrock, Razelle

    2015-01-01

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTM BRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction–based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTM BRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation–detecting tests. PMID:26330075

  3. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system.

    PubMed

    Janku, Filip; Claes, Bart; Huang, Helen J; Falchook, Gerald S; Devogelaere, Benoit; Kockx, Mark; Bempt, Isabelle Vanden; Reijans, Martin; Naing, Aung; Fu, Siqing; Piha-Paul, Sarina A; Hong, David S; Holley, Veronica R; Tsimberidou, Apostolia M; Stepanek, Vanda M; Patel, Sapna P; Kopetz, E Scott; Subbiah, Vivek; Wheler, Jennifer J; Zinner, Ralph G; Karp, Daniel D; Luthra, Rajyalakshmi; Roy-Chowdhuri, Sinchita; Sablon, Erwin; Meric-Bernstam, Funda; Maertens, Geert; Kurzrock, Razelle

    2015-09-29

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction-based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTMBRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation-detecting tests. PMID:26330075

  4. Bacterial Cytological Profiling (BCP) as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus

    PubMed Central

    Quach, D.T.; Sakoulas, G.; Nizet, V.; Pogliano, J.; Pogliano, K.

    2016-01-01

    Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP), which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA) and -resistant (MRSA) clinical isolates of S. aureus (n = 71) within 1–2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS) from daptomycin non-susceptible (DNS) S. aureus strains (n = 20) within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice. PMID:26981574

  5. Bacterial Cytological Profiling (BCP) as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus.

    PubMed

    Quach, D T; Sakoulas, G; Nizet, V; Pogliano, J; Pogliano, K

    2016-02-01

    Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP), which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA) and -resistant (MRSA) clinical isolates of S. aureus (n = 71) within 1-2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS) from daptomycin non-susceptible (DNS) S. aureus strains (n = 20) within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice. PMID:26981574

  6. Rapid and accurate determination of the lignin content of lignocellulosic biomass by solid-state NMR

    PubMed Central

    Fu, Li; McCallum, Scott A.; Miao, Jianjun; Hart, Courtney; Tudryn, Gregory J.; Zhang, Fuming; Linhardt, Robert J.

    2014-01-01

    Biofuels and biomaterials, produced from lignocellulosic feedstock, require facile access to cellulose and hemicellulose to be competitive with petroleum processing and sugar-based fermentation. Physical-chemical barriers resulting from lignin complicates the hydrolysis biomass into fermentable sugars. Thus, the amount of lignin within a substrate is critical in determining biomass processing. The application of 13C cross-polarization, magic-angle spinning, and solid-state nuclear magnetic resonance for the direct quantification of lignin content in biomass is examined. Using a standard curve constructed from pristine lignin and cellulose, the lignin content of a biomass sample is accurately determined through direct measurement without chemical or enzymatic pre-treatment. PMID:25404762

  7. Accurate and rapid optical characterization of an anisotropic guided structure based on a neural method.

    PubMed

    Robert, Stéphane; Battie, Yann; Jamon, Damien; Royer, Francois

    2007-04-10

    Optimal performances of integrated optical devices are obtained by the use of an accurate and reliable characterization method. The parameters of interest, i.e., optical indices and thickness of the waveguide structure, are calculated from effective indices by means of an inversion procedure. We demonstrate how an artificial neural network can achieve such a process. The artificial neural network used is a multilayer perceptron. The first result concerns a simulated anisotropic waveguide. The accuracy in the determination of optical indices and waveguide thickness is 5 x 10(-5) and 4 nm, respectively. Then an experimental application on a silica-titania thin film is performed. In addition, effective indices are measured by m-lines spectroscopy. Finally, a comparison with a classical optimization algorithm demonstrates the robustness of the neural method. PMID:17384718

  8. Rapid and accurate determination of the lignin content of lignocellulosic biomass by solid-state NMR.

    PubMed

    Fu, Li; McCallum, Scott A; Miao, Jianjun; Hart, Courtney; Tudryn, Gregory J; Zhang, Fuming; Linhardt, Robert J

    2015-02-01

    Biofuels and biomaterials, produced from lignocellulosic feedstock, require facile access to cellulose and hemicellulose to be competitive with petroleum processing and sugar-based fermentation. Physical-chemical barriers resulting from lignin complicates the hydrolysis biomass into fermentable sugars. Thus, the amount of lignin within a substrate is critical in determining biomass processing. The application of (13)C cross-polarization, magic-angle spinning, and solid-state nuclear magnetic resonance for the direct quantification of lignin content in biomass is examined. Using a standard curve constructed from pristine lignin and cellulose, the lignin content of a biomass sample is accurately determined through direct measurement without chemical or enzymatic pre-treatment. PMID:25404762

  9. Biosensors and rapid diagnostic tests on the frontier between analytical and clinical chemistry for biomolecular diagnosis of dengue disease: a review.

    PubMed

    Teles, Fernando Sérgio Rodrigues Ribeiro

    2011-02-14

    The past decades have witnessed enormous technological improvements towards the development of simple, cost-effective and accurate rapid diagnostic tests for detection and identification of infectious pathogens. Among them is dengue virus, the etiologic agent of the mosquito-borne dengue disease, one of the most important emerging infectious pathologies of nowadays. Dengue fever may cause potentially deadly hemorrhagic symptoms and is endemic in the tropical and sub-tropical world, being also a serious threat to temperate countries in the developed world. Effective diagnostics for dengue should be able to discriminate among the four antigenically related dengue serotypes and fulfill the requirements for successful decentralized (point-of-care) testing in the harsh environmental conditions found in most tropical regions. The accurate identification of circulating serotypes is crucial for the successful implementation of vector control programs based on reliable epidemiological predictions. This paper briefly summarizes the limitations of the main conventional techniques for biomolecular diagnosis of dengue disease and critically reviews some of the most relevant biosensors and rapid diagnostic tests developed, implemented and reported so far for point-of-care testing of dengue infections. The invaluable contributions of microfluidics and nanotechnology encompass the whole paper, while evaluation concerns of rapid diagnostic tests and foreseen technological improvements in this field are also overviewed for the diagnosis of dengue and other infectious and tropical diseases as well. PMID:21241843

  10. Rapid and accurate processing of multiple objects in briefly presented scenes.

    PubMed

    Railo, Henry; Karhu, Veli-Matti; Mast, Jeremy; Pesonen, Henri; Koivisto, Mika

    2016-01-01

    Humans can detect multiple objects in briefly presented natural visual scenes, but the mechanisms through which the objects are segmented from the background and consciously accessed remain open. By asking participants to report how many humans natural photos presented for 50 ms contain, we show that up to three items can be rapidly enumerated from natural scenes without compromising speed or accuracy. In contrast to standard parallel and serial models of object selection, our results revealed that the participants were fastest in enumerating two objects; even enumerating one single item required additional processing time. Also enumeration accuracy slightly increased in the subitizing range as number increased. Our results suggest that the visual system is tuned to process multiple items, which may underlie spatial and numerical cognition, and be beneficial in real-world situations that often require dealing with more than one object at a time. PMID:26849070

  11. Preoperative Ultrasound Guided Fine Needle Aspiration Cytology of Ovarian Lesions- Is It a Rapid and Effective Diagnostic Modality?

    PubMed Central

    Datta, Saikat; Chaudhuri, Snehamay; Paul, Prabir Chandra; Khandakar, Binny; Mandal, Sonali

    2016-01-01

    Introduction The deep seated ovarian lesions unapproachable by unguided aspiration cytology were easily done under ultrasound guidance. It gave a before hand cytological diagnosis of the lesion to the surgeon determining the modality of treatment for the patient. Aim To find the diagnostic accuracy of the method of ultrasound guided cytological assessment of ovarian lesion. Materials and Methods The study was conducted as a prospective observational study over a period of one year, in hospital setting, where ultrasound guided fine needle aspiration had been used to aspirate ovarian lesions, giving a rapid cytological diagnosis. In 43 sample cases, aspiration of fluid done from ovarian lesions were followed by cyto-centrifugation and staining by May-Grunwald-Giemsa (MGG) and Papanicolaou (Pap) stain providing a cytological opinion regarding benign/malignant nature of the lesion and further categorization. Later the cytological diagnosis was compared with final histopathological diagnosis, taking it as a gold standard. Results The overall sensitivity, specificity, and diagnostic accuracy of ultrasound guided aspiration and cytological analysis were high, 96%, 76.92% and 89.47% respectively as calculated by comparing the cytological diagnosis with histological diagnosis, taking it as gold standard. Conclusion This method has evolved as a highly sensitive, rapid, simple and effective modality for screening and as well as accurate preoperative diagnosis of ovarian lesions. PMID:27134878

  12. Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis

    PubMed Central

    Payne, Samuel H.; Yau, Margaret; Smolka, Marcus B.; Tanner, Stephen; Zhou, Huilin; Bafna, Vineet

    2008-01-01

    The promise of mass spectrometry as a tool for probing signal-transduction is predicated on reliable identification of post-translational modifications. Phosphorylations are key mediators of cellular signaling, yet are hard to detect, partly because of unusual fragmentation patterns of phosphopeptides. In addition to being accurate, MS/MS identification software must be robust and efficient to deal with increasingly large spectral data sets. Here, we present a new scoring function for the Inspect software for phosphorylated peptide tandem mass spectra for ion-trap instruments, without the need for manual validation. The scoring function was modeled by learning fragmentation patterns from 7677 validated phosphopeptide spectra. We compare our algorithm against SEQUEST and X!Tandem on testing and training data sets. At a 1% false positive rate, Inspect identified the greatest total number of phosphorylated spectra, 13% more than SEQUEST and 39% more than X!Tandem. Spectra identified by Inspect tended to score better in several spectral quality measures. Furthermore, Inspect runs much faster than either SEQUEST or X!Tandem, making desktop phosphoproteomics feasible. Finally, we used our new models to reanalyze a corpus of 423 000 LTQ spectra acquired for a phosphoproteome analysis of Saccharomyces cerevisiae DNA damage and repair pathways and discovered 43% more phosphopeptides than the previous study. PMID:18563926

  13. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.

    PubMed

    Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K

    2016-07-01

    Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods. PMID:25830555

  14. Rapid and accurate tumor-target bio-imaging through specific in vivo biosynthesis of a fluorescent europium complex.

    PubMed

    Ye, Jing; Wang, Jianling; Li, Qiwei; Dong, Xiawei; Ge, Wei; Chen, Yun; Jiang, Xuerui; Liu, Hongde; Jiang, Hui; Wang, Xuemei

    2016-04-22

    A new and facile method for rapidly and accurately achieving tumor targeting fluorescent images has been explored using a specifically biosynthesized europium (Eu) complex in vivo and in vitro. It demonstrated that a fluorescent Eu complex could be bio-synthesized through a spontaneous molecular process in cancerous cells and tumors, but not prepared in normal cells and tissues. In addition, the proteomics analyses show that some biological pathways of metabolism, especially for NADPH production and glutamine metabolism, are remarkably affected during the relevant biosynthesis process, where molecular precursors of europium ions are reduced to fluorescent europium complexes inside cancerous cells or tumor tissues. These results proved that the specific self-biosynthesis of a fluorescent Eu complex by cancer cells or tumor tissues can provide a new strategy for accurate diagnosis and treatment strategies in the early stages of cancers and thus is beneficial for realizing precise surgical intervention based on the relevant cheap and readily available agents. PMID:26810592

  15. A Rapid, Fully Automated, Molecular-Based Assay Accurately Analyzes Sentinel Lymph Nodes for the Presence of Metastatic Breast Cancer

    PubMed Central

    Hughes, Steven J.; Xi, Liqiang; Raja, Siva; Gooding, William; Cole, David J.; Gillanders, William E.; Mikhitarian, Keidi; McCarty, Kenneth; Silver, Susan; Ching, Jesus; McMillan, William; Luketich, James D.; Godfrey, Tony E.

    2006-01-01

    Objective: To develop a fully automated, rapid, molecular-based assay that accurately and objectively evaluates sentinel lymph nodes (SLN) from breast cancer patients. Summary Background Data: Intraoperative analysis for the presence of metastatic cancer in SLNs from breast cancer patients lacks sensitivity. Even with immunohistochemical staining (IHC) and time-consuming review, alarming discordance in the interpretation of SLN has been observed. Methods: A total of 43 potential markers were evaluated for the ability to accurately characterize lymph node specimens from breast cancer patients as compared with complete histologic analysis including IHC. Selected markers then underwent external validation on 90 independent SLN specimens using rapid, multiplex quantitative reverse transcription-polymerase chain reaction (QRT-PCR) assays. Finally, 18 SLNs were analyzed using a completely automated RNA isolation, reverse transcription, and quantitative PCR instrument (GeneXpert). Results: Following analysis of potential markers, promising markers were evaluated to establish relative level of expression cutoff values that maximized classification accuracy. A validation set of 90 SLNs from breast cancer patients was prospectively characterized using 4 markers individually or in combinations, and the results compared with histologic analysis. A 2-marker assay was found to be 97.8% accurate (94% sensitive, 100% specific) compared with histologic analysis. The fully automated GeneXpert instrument produced comparable and reproducible results in less than 35 minutes. Conclusions: A rapid, fully automated QRT-PCR assay definitively characterizes breast cancer SLN with accuracy equal to conventional pathology. This approach is superior to intraoperative SLN analysis and can provide standardized, objective results to assist in pathologic diagnosis. PMID:16495705

  16. Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping.

    PubMed

    Lee, Han B; Schwab, Tanya L; Koleilat, Alaa; Ata, Hirotaka; Daby, Camden L; Cervera, Roberto Lopez; McNulty, Melissa S; Bostwick, Hannah S; Clark, Karl J

    2016-06-01

    Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98-100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score

  17. Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping

    PubMed Central

    Lee, Han B.; Schwab, Tanya L.; Koleilat, Alaa; Ata, Hirotaka; Daby, Camden L.; Cervera, Roberto Lopez; McNulty, Melissa S.; Bostwick, Hannah S.; Clark, Karl J.

    2016-01-01

    Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98–100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score

  18. Rapid diagnostic tests for diagnosing uncomplicated non-falciparum or Plasmodium vivax malaria in endemic countries

    PubMed Central

    Abba, Katharine; Kirkham, Amanda J; Olliaro, Piero L; Deeks, Jonathan J; Donegan, Sarah; Garner, Paul; Takwoingi, Yemisi

    2014-01-01

    specificities are presented alongside 95% confidence intervals (95% CI). Main results We included 47 studies enrolling 22,862 participants. Patient characteristics, sampling methods and reference standard methods were poorly reported in most studies. RDTs detecting 'non-falciparum' parasitaemia Eleven studies evaluated Type 2 tests compared with microscopy, 25 evaluated Type 3 tests, and 11 evaluated Type 4 tests. In meta-analyses, average sensitivities and specificities were 78% (95% CI 73% to 82%) and 99% (95% CI 97% to 99%) for Type 2 tests, 78% (95% CI 69% to 84%) and 99% (95% CI 98% to 99%) for Type 3 tests, and 89% (95% CI 79% to 95%) and 98% (95% CI 97% to 99%) for Type 4 tests, respectively. Type 4 tests were more sensitive than both Type 2 (P = 0.01) and Type 3 tests (P = 0.03). Five studies compared Type 3 tests with PCR; in meta-analysis, the average sensitivity and specificity were 81% (95% CI 72% to 88%) and 99% (95% CI 97% to 99%) respectively. RDTs detecting P.vivax parasitaemia Eight studies compared pLDH tests to microscopy; the average sensitivity and specificity were 95% (95% CI 86% to 99%) and 99% (95% CI 99% to 100%), respectively. Authors' conclusions RDTs designed to detect P. vivax specifically, whether alone or as part of a mixed infection, appear to be more accurate than older tests designed to distinguish P. falciparum malaria from non-falciparum malaria. Compared to microscopy, these tests fail to detect around 5% ofP. vivax cases. This Cochrane Review, in combination with other published information about in vitro test performance and stability in the field, can assist policy-makers to choose between the available RDTs. PLAIN LANGUAGE SUMMARY Rapid tests for diagnosing malaria caused by Plasmodium vivax or other less common parasites This review summarises trials evaluating the accuracy of rapid diagnostic tests (RDTs) for diagnosing malaria due to Plasmodium vivax or other non-falciparum species. After searching for relevant studies up to December

  19. Use of quality rapid diagnostic testing for safe blood transfusion in resource-limited settings.

    PubMed

    Mbanya, D

    2013-05-01

    Blood safety in sub-Saharan Africa is jeopardized by multiple and diverse factors, including the predominance of high-risk family/replacement donors and the high prevalence of transfusion-transmissible infections (TTIs). Thus, stringent diagnostic strategies are vital. Western blotting is costly and technically demanding, and nucleic acid testing technologies, which have been reported to reliably reduce the rate of TTI, are not available in resource-limited settings. Therefore, there is a need for reliable and affordable testing alternatives in these settings. Rapid diagnostic testing has been widely adopted in developing countries, but, for effectiveness in blood safety, highly sensitive tests and the strict selection of low-risk blood donors are indispensable. Although the pre-serological window period remains a source of residual risk for transmission of TTIs during blood transfusion, the combination antigen-antibody rapid tests could contribute significantly to shortening the window period. Thus, despite its limitations, rapid diagnostic testing continues to contribute significantly to blood safety, as a cost-effective means of enhancing screening for TTIs and reducing their transmission in resource-limited rural settings. PMID:23464853

  20. A Novel Malaria Pf/Pv Ab Rapid Diagnostic Test Using a Differential Diagnostic Marker Identified by Network Biology.

    PubMed

    Cho, Sung Jin; Lee, Jihoo; Lee, Hyun Jae; Jo, Hyun-Young; Sinniah, Mangalam; Kim, Hak-Yong; Chong, Chom-Kyu; Song, Hyun-Ok

    2016-01-01

    Rapid diagnostic tests (RDTs) can detect anti-malaria antibodies in human blood. As they can detect parasite infection at the low parasite density, they are useful in endemic areas where light infection and/or re-infection of parasites are common. Thus, malaria antibody tests can be used for screening bloods in blood banks to prevent transfusion-transmitted malaria (TTM), an emerging problem in malaria endemic areas. However, only a few malaria antibody tests are available in the microwell-based assay format and these are not suitable for field application. A novel malaria antibody (Ab)-based RDT using a differential diagnostic marker for falciparum and vivax malaria was developed as a suitable high-throughput assay that is sensitive and practical for blood screening. The marker, merozoite surface protein 1 (MSP1) was discovered by generation of a Plasmodium-specific network and the hierarchical organization of modularity in the network. Clinical evaluation revealed that the novel Malaria Pf/Pv Ab RDT shows improved sensitivity (98%) and specificity (99.7%) compared with the performance of a commercial kit, SD BioLine Malaria P.f/P.v (95.1% sensitivity and 99.1% specificity). The novel Malaria Pf/Pv Ab RDT has potential for use as a cost-effective blood-screening tool for malaria and in turn, reduces TTM risk in endemic areas. PMID:27313496

  1. A Novel Malaria Pf/Pv Ab Rapid Diagnostic Test Using a Differential Diagnostic Marker Identified by Network Biology

    PubMed Central

    Cho, Sung Jin; Lee, Jihoo; Lee, Hyun Jae; Jo, Hyun-Young; Sinniah, Mangalam; Kim, Hak-Yong; Chong, Chom-Kyu; Song, Hyun-Ok

    2016-01-01

    Rapid diagnostic tests (RDTs) can detect anti-malaria antibodies in human blood. As they can detect parasite infection at the low parasite density, they are useful in endemic areas where light infection and/or re-infection of parasites are common. Thus, malaria antibody tests can be used for screening bloods in blood banks to prevent transfusion-transmitted malaria (TTM), an emerging problem in malaria endemic areas. However, only a few malaria antibody tests are available in the microwell-based assay format and these are not suitable for field application. A novel malaria antibody (Ab)-based RDT using a differential diagnostic marker for falciparum and vivax malaria was developed as a suitable high-throughput assay that is sensitive and practical for blood screening. The marker, merozoite surface protein 1 (MSP1) was discovered by generation of a Plasmodium-specific network and the hierarchical organization of modularity in the network. Clinical evaluation revealed that the novel Malaria Pf/Pv Ab RDT shows improved sensitivity (98%) and specificity (99.7%) compared with the performance of a commercial kit, SD BioLine Malaria P.f/P.v (95.1% sensitivity and 99.1% specificity). The novel Malaria Pf/Pv Ab RDT has potential for use as a cost-effective blood-screening tool for malaria and in turn, reduces TTM risk in endemic areas. PMID:27313496

  2. Assessing the impact of next-generation rapid diagnostic tests on Plasmodium falciparum malaria elimination strategies.

    PubMed

    Slater, Hannah C; Ross, Amanda; Ouédraogo, André Lin; White, Lisa J; Nguon, Chea; Walker, Patrick G T; Ngor, Pengby; Aguas, Ricardo; Silal, Sheetal P; Dondorp, Arjen M; La Barre, Paul; Burton, Robert; Sauerwein, Robert W; Drakeley, Chris; Smith, Thomas A; Bousema, Teun; Ghani, Azra C

    2015-12-01

    Mass-screen-and-treat and targeted mass-drug-administration strategies are being considered as a means to interrupt transmission of Plasmodium falciparum malaria. However, the effectiveness of such strategies will depend on the extent to which current and future diagnostics are able to detect those individuals who are infectious to mosquitoes. We estimate the relationship between parasite density and onward infectivity using sensitive quantitative parasite diagnostics and mosquito feeding assays from Burkina Faso. We find that a diagnostic with a lower detection limit of 200 parasites per microlitre would detect 55% of the infectious reservoir (the combined infectivity to mosquitoes of the whole population weighted by how often each individual is bitten) whereas a test with a limit of 20 parasites per microlitre would detect 83% and 2 parasites per microlitre would detect 95% of the infectious reservoir. Using mathematical models, we show that increasing the diagnostic sensitivity from 200 parasites per microlitre (equivalent to microscopy or current rapid diagnostic tests) to 2 parasites per microlitre would increase the number of regions where transmission could be interrupted with a mass-screen-and-treat programme from an entomological inoculation rate below 1 to one of up to 4. The higher sensitivity diagnostic could reduce the number of treatment rounds required to interrupt transmission in areas of lower prevalence. We predict that mass-screen-and-treat with a highly sensitive diagnostic is less effective than mass drug administration owing to the prophylactic protection provided to uninfected individuals by the latter approach. In low-transmission settings such as those in Southeast Asia, we find that a diagnostic tool with a sensitivity of 20 parasites per microlitre may be sufficient for targeted mass drug administration because this diagnostic is predicted to identify a similar village population prevalence compared with that currently detected using

  3. Evaluation of three rapid diagnostic tests for the detection of human infections with Plasmodium knowlesi

    PubMed Central

    2014-01-01

    Background Plasmodium knowlesi, a malaria parasite of Southeast Asian macaques, infects humans and can cause fatal malaria. It is difficult to diagnose by microscopy because of morphological similarity to Plasmodium malariae. Nested PCR assay is the most accurate method to distinguish P. knowlesi from other Plasmodium species but is not cost effective in resource-poor settings. Rapid diagnostic tests (RDTs) are recommended for settings where malaria is prevalent. In this study, the effectiveness of three RDTs in detecting P. knowlesi from fresh and frozen patient blood samples was evaluated. Methods Forty malaria patients (28 P. knowlesi, ten P. vivax and two P. falciparum) diagnosed by microscopy were recruited in Sarawak, Malaysian Borneo during a 16-month period. Patient blood samples were used to determine parasitaemia by microscopy, confirm the Plasmodium species present by PCR and evaluate three RDTs: OptiMAL-IT, BinaxNOW® Malaria and Paramax-3. The RDTs were also evaluated using frozen blood samples from 41 knowlesi malaria patients. Results OptiMAL-IT was the most sensitive RDT, with a sensitivity of 71% (20/28; 95% CI = 54-88%) for fresh and 73% (30/41; 95% CI = 59-87%) for frozen knowlesi samples. However, it yielded predominantly falciparum-positive results due to cross-reactivity of the P. falciparum test reagent with P. knowlesi. BinaxNOW® Malaria correctly detected non-P. falciparum malaria in P. knowlesi samples but was the least sensitive, detecting only 29% (8/28; 95% CI = 12-46%) of fresh and 24% (10/41; 95% CI = 11-37%) of frozen samples. The Paramax-3 RDT tested positive for P. vivax with PCR-confirmed P. knowlesi samples with sensitivities of 40% (10/25; 95% CI = 21-59%) with fresh and 32% (13/41; 95% CI = 17-46%) with frozen samples. All RDTs correctly identified P. falciparum- and P. vivax-positive controls with parasitaemias above 2,000 parasites/μl blood. Conclusions The RDTs detected Plasmodium in P. knowlesi-infected blood samples with

  4. Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review.

    PubMed

    Ahmad, Farhan; Hashsham, Syed A

    2012-07-01

    Point-of-care (POC) genetic diagnostics critically depends on miniaturization and integration of sample processing, nucleic acid amplification, and detection systems. Polymerase chain reaction (PCR) assays have extensively applied for the diagnosis of genetic markers of disease. Microfluidic chips for microPCR with different materials and designs have been reported. Temperature cycling systems with varying thermal masses and conductivities, thermal cycling times, flow-rates, and cross-sectional areas, have also been developed to reduce the nucleic acid amplification time. Similarly, isothermal amplification techniques (e.g., loop-mediated isothermal amplification or LAMP), which are still are emerging, have a better potential as an alternative to PCR for POC diagnostics. Isothermal amplification techniques have: (i) moderate incubation temperature leading to simplified heating and low power consumption, (ii) yield high amount of amplification products, which can be detected either visually or by simple detectors, (iii) allow direct genetic amplification from bacterial cells due to the superior tolerance to substances that typically inhibit PCR, (iv) have high specificity, and sensitivity, and (v) result in rapid detection often within 10-20 min. The aim of this review is to provide a better understanding of the advantages and limitations of microPCR and microLAMP systems for rapid and POC diagnostics. PMID:22704369

  5. Introducing malaria rapid diagnostic tests at registered drug shops in Uganda: limitations of diagnostic testing in the reality of diagnosis.

    PubMed

    Chandler, Clare I R; Hall-Clifford, Rachel; Asaph, Turinde; Pascal, Magnussen; Clarke, Siân; Mbonye, Anthony K

    2011-03-01

    In Uganda, around two thirds of medicines are procured from the private sector, mostly from drug shops. The introduction of malaria rapid diagnostic tests (RDTs) at drug shops therefore has the potential to make a significant contribution to targeting antimalarial drugs to those with malaria parasites. We undertook formative research in a district in Uganda in preparation for a randomised trial of RDTs in drug shops. In May to July 2009, we interviewed 9 drug shop workers, 5 health workers and 4 district health officials and carried out 10 focus group discussions with a total of 75 community members to investigate the role of drug shops and the potential for implementation of RDTs at these health care outlets. Drug shops were seen to provide an important service to community members, the nature of which is determined by responsiveness to client demands. However, drug shops hold a liminal status: in the eyes of different actors, these outlets are at once a shop and clinic; legitimate and illegitimate; and trusted and distrusted. Malaria treatment was found to be synonymous with diagnosis. Diagnostic testing was deemed useful in theory, and community members were curious about the results, with the expectation that a test would decrease uncertainty and help secure an end to illness. However, whether testing would be sought as a routine step in treatment decisions in practice is uncertain, since the appeal of the tests waned in light of their costs and potential for results to conflict with presumed diagnosis. Interventions that increase awareness of multiple causes and management of malaria-like illness will be needed to support the new rationalisation for malaria treatment represented by parasitological diagnosis. PMID:21349623

  6. Introducing malaria rapid diagnostic tests at registered drug shops in Uganda: Limitations of diagnostic testing in the reality of diagnosis.

    PubMed Central

    Hall-Clifford, Rachel; Asaph, Turinde; Magnussen, Pascal; Clarke, Siân; Mbonye, Anthony K

    2014-01-01

    In Uganda, around two thirds of medicines are procured from the private sector, mostly from drug shops. The introduction of malaria rapid diagnostic tests (RDTs) at drug shops therefore has the potential to make a significant contribution to targeting antimalarial drugs to those with malaria parasites. We undertook formative research in a district in Uganda in preparation for a randomised trial of RDTs in drug shops. In May to July 2009, we interviewed 9 drug shop workers, 5 health workers and 4 district health officials and carried out 10 focus group discussions with a total of 75 community members to investigate the role of drug shops and the potential for implementation of RDTs at these health care outlets. Drug shops were seen to provide an important service to community members, the nature of which is determined by responsiveness to client demands. However, drug shops hold a liminal status: in the eyes of different actors, these outlets are at once a shop and clinic; legitimate and illegitimate; and trusted and distrusted. Malaria treatment was found to be synonymous with diagnosis. Diagnostic testing was deemed useful in theory, and community members were curious about the results, with the expectation that a test would decrease uncertainty and help secure an end to illness. However, whether testing would be sought as a routine step in treatment decisions in practice is uncertain, since the appeal of the tests waned in light of their costs and potential for results to conflict with presumed diagnosis. Interventions that increase awareness of multiple causes and management of malaria-like illness will be needed to support the new rationalisation for malaria treatment represented by parasitological diagnosis. PMID:21349623

  7. A rapid, economical, and accurate method to determining the physical risk of storm marine inundations using sedimentary evidence

    NASA Astrophysics Data System (ADS)

    Nott, Jonathan F.

    2015-04-01

    The majority of physical risk assessments from storm surge inundations are derived from synthetic time series generated from short climate records, which can often result in inaccuracies and are time-consuming and expensive to develop. A new method is presented here for the wet tropics region of northeast Australia. It uses lidar-generated topographic cross sections of beach ridge plains, which have been demonstrated to be deposited by marine inundations generated by tropical cyclones. Extreme value theory statistics are applied to data derived from the cross sections to generate return period plots for a given location. The results suggest that previous methods to estimate return periods using synthetic data sets have underestimated the magnitude/frequency relationship by at least an order of magnitude. The new method promises to be a more rapid, economical, and accurate assessment of the physical risk of these events.

  8. Application of a cell microarray chip system for accurate, highly sensitive, and rapid diagnosis for malaria in Uganda

    PubMed Central

    Yatsushiro, Shouki; Yamamoto, Takeki; Yamamura, Shohei; Abe, Kaori; Obana, Eriko; Nogami, Takahiro; Hayashi, Takuya; Sesei, Takashi; Oka, Hiroaki; Okello-Onen, Joseph; Odongo-Aginya, Emmanuel I.; Alai, Mary Auma; Olia, Alex; Anywar, Dennis; Sakurai, Miki; Palacpac, Nirianne MQ; Mita, Toshihiro; Horii, Toshihiro; Baba, Yoshinobu; Kataoka, Masatoshi

    2016-01-01

    Accurate, sensitive, rapid, and easy operative diagnosis is necessary to prevent the spread of malaria. A cell microarray chip system including a push column for the recovery of erythrocytes and a fluorescence detector was employed for malaria diagnosis in Uganda. The chip with 20,944 microchambers (105 μm width and 50 μm depth) was made of polystyrene. For the analysis, 6 μl of whole blood was employed, and leukocytes were practically removed by filtration through SiO2-nano-fibers in a column. Regular formation of an erythrocyte monolayer in each microchamber was observed following dispersion of an erythrocyte suspension in a nuclear staining dye, SYTO 21, onto the chip surface and washing. About 500,000 erythrocytes were analyzed in a total of 4675 microchambers, and malaria parasite-infected erythrocytes could be detected in 5 min by using the fluorescence detector. The percentage of infected erythrocytes in each of 41 patients was determined. Accurate and quantitative detection of the parasites could be performed. A good correlation between examinations via optical microscopy and by our chip system was demonstrated over the parasitemia range of 0.0039–2.3438% by linear regression analysis (R2 = 0.9945). Thus, we showed the potential of this chip system for the diagnosis of malaria. PMID:27445125

  9. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    PubMed

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  10. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    PubMed Central

    Ross, Charles W.; Simonsick, William J.; Bogusky, Michael J.; Celikay, Recep W.; Guare, James P.; Newton, Randall C.

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  11. Application of a cell microarray chip system for accurate, highly sensitive, and rapid diagnosis for malaria in Uganda.

    PubMed

    Yatsushiro, Shouki; Yamamoto, Takeki; Yamamura, Shohei; Abe, Kaori; Obana, Eriko; Nogami, Takahiro; Hayashi, Takuya; Sesei, Takashi; Oka, Hiroaki; Okello-Onen, Joseph; Odongo-Aginya, Emmanuel I; Alai, Mary Auma; Olia, Alex; Anywar, Dennis; Sakurai, Miki; Palacpac, Nirianne Mq; Mita, Toshihiro; Horii, Toshihiro; Baba, Yoshinobu; Kataoka, Masatoshi

    2016-01-01

    Accurate, sensitive, rapid, and easy operative diagnosis is necessary to prevent the spread of malaria. A cell microarray chip system including a push column for the recovery of erythrocytes and a fluorescence detector was employed for malaria diagnosis in Uganda. The chip with 20,944 microchambers (105 μm width and 50 μm depth) was made of polystyrene. For the analysis, 6 μl of whole blood was employed, and leukocytes were practically removed by filtration through SiO2-nano-fibers in a column. Regular formation of an erythrocyte monolayer in each microchamber was observed following dispersion of an erythrocyte suspension in a nuclear staining dye, SYTO 21, onto the chip surface and washing. About 500,000 erythrocytes were analyzed in a total of 4675 microchambers, and malaria parasite-infected erythrocytes could be detected in 5 min by using the fluorescence detector. The percentage of infected erythrocytes in each of 41 patients was determined. Accurate and quantitative detection of the parasites could be performed. A good correlation between examinations via optical microscopy and by our chip system was demonstrated over the parasitemia range of 0.0039-2.3438% by linear regression analysis (R(2) = 0.9945). Thus, we showed the potential of this chip system for the diagnosis of malaria. PMID:27445125

  12. Rapid, Precise, and Accurate Counts of Symbiodinium Cells Using the Guava Flow Cytometer, and a Comparison to Other Methods

    PubMed Central

    Caruso, Carlo; Burriesci, Matthew S.; Cella, Kristen; Pringle, John R.

    2015-01-01

    In studies of both the establishment and breakdown of cnidarian-dinoflagellate symbiosis, it is often necessary to determine the number of Symbiodinium cells relative to the quantity of host tissue. Ideally, the methods used should be rapid, precise, and accurate. In this study, we systematically evaluated methods for sample preparation and storage and the counting of algal cells using the hemocytometer, a custom image-analysis program for automated counting of the fluorescent algal cells, the Coulter Counter, or the Millipore Guava flow-cytometer. We found that although other methods may have value in particular applications, for most purposes, the Guava flow cytometer provided by far the best combination of precision, accuracy, and efficient use of investigator time (due to the instrument's automated sample handling), while also allowing counts of algal numbers over a wide range and in small volumes of tissue homogenate. We also found that either of two assays of total homogenate protein provided a precise and seemingly accurate basis for normalization of algal counts to the total amount of holobiont tissue. PMID:26291447

  13. QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

    PubMed Central

    Karabiber, Fethullah; McGinnis, Jennifer L.; Favorov, Oleg V.; Weeks, Kevin M.

    2013-01-01

    Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experiments. PMID:23188808

  14. Rapid and accurate measurement of transverse relaxation times using a single shot multi-echo echo-planar imaging sequence.

    PubMed

    Tyler, Damian J; Moore, Rachel J; Marciani, Luca; Gowland, Penny A

    2004-09-01

    Methods for making rapid and accurate measurements and maps of the transverse relaxation time from a single free induction decay (FID) are proposed. The methods use a multi-echo sequence in combination with B1 insensitive (hyperbolic secant or BIREF2b) refocusing pulses and rapid echo-planar imaging techniques. The results were calibrated against a single spin echo echo-planar imaging sequence using a phantom containing a range of CuSO4 concentrations. The mean percentage absolute difference between the multi-echo and single-echo results was 3% for the multi-echo sequence using the hyperbolic secant refocusing pulse, and 7% for the multi-echo sequence using the BIREF2b refocusing pulse, compared to 13% for a multi-echo sequence using a nonselective sinc refocusing pulse. The use of the sequences in vivo has been demonstrated in studies of gastric function, i.e., the measurement of gastric dilution and monitoring of formation of a raft of alginate polysaccharide within the stomach. PMID:15288145

  15. Ion chromatography as highly suitable method for rapid and accurate determination of antibiotic fosfomycin in pharmaceutical wastewater.

    PubMed

    Zeng, Ping; Xie, Xiaolin; Song, Yonghui; Liu, Ruixia; Zhu, Chaowei; Galarneau, Anne; Pic, Jean-Stéphane

    2014-01-01

    A rapid and accurate ion chromatography (IC) method (limit of detection as low as 0.06 mg L(-1)) for fosfomycin concentration determination in pharmaceutical industrial wastewater was developed. This method was compared with the performance of high performance liquid chromatography determination (with a high detection limit of 96.0 mg L(-1)) and ultraviolet spectrometry after reacting with alizarin (difficult to perform in colored solutions). The accuracy of the IC method was established in the linear range of 1.0-15.0 mg L(-1) and a linear correlation was found with a correlation coefficient of 0.9998. The recoveries of fosfomycin from industrial pharmaceutical wastewater at spiking concentrations of 2.0, 5.0 and 8.0 mg L(-1) ranged from 81.91 to 94.74%, with a relative standard deviation (RSD) from 1 to 4%. The recoveries of effluent from a sequencing batch reactor treated fosfomycin with activated sludge at spiking concentrations of 5.0, 8.0, 10.0 mg L(-1) ranging from 98.25 to 99.91%, with a RSD from 1 to 2%. The developed IC procedure provided a rapid, reliable and sensitive method for the determination of fosfomycin concentration in industrial pharmaceutical wastewater and samples containing complex components. PMID:24845315

  16. Rapid mass spectrometric DNA diagnostics for assessing microbial community activity during bioremediation. 1997 annual progress report

    SciTech Connect

    Benner, W.H.; Hunter-Cevera, J.

    1997-01-01

    'The effort of the past year''s activities, which covers the first year of the project, was directed at developing DNA-based diagnostic procedures for implementation in high through-put analytical instrumentation. The diagnostic procedures under evaluation are designed to identify specific genes in soil microorganisms that code for pollutant-degrading enzymes. Current DNA-based diagnostic procedures, such as the ligase chain reaction (LCR) and the polymerase chain reaction (PCR), rely on gel electrophoresis as a way to score a diagnostic test. The authors are attempting to implement time-of-flight (TOF) mass spectrometry as a replacement for gel separations because of its speed advantage and potential for sample automation. The authors anticipate that if TOF techniques can be implemented in the procedures, then a very large number of microorganisms and soil samples can be screened for the presence of specific pollutant-degrading genes. The use of DNA-based procedures for the detection of biodegrading organisms or genes that code for pollutant-degrading enzymes constitutes a critical technology for following biochemical transformation and substantiating the impact of bioremediation. DNA-based technology has been demonstrated to be a sensitive technique for tracking micro-organism activity at the molecular level. These procedures can be tuned to identify groups of organisms, specific organisms, and activity at the molecular level. They are developing a P-monitoring strategy that relies on the combined use of DNA diagnostics with mass spectrometry as the detection scheme. The intent of this work is a two-fold evaluation of (1) the feasibility of replacing the use of gel separations for identifying polymerase chain reaction (PCR) products with a rapid and automatable form of electrospray mass spectrometry and (2) the use of matrix-assisted-laser-desorption-ionization mass spectrometry (MALDI-MS) as a tool to score oligonucleotide ligation assays (OLA).'

  17. Malaria surveillance in the Democratic Republic of the Congo: comparison of microscopy, PCR, and rapid diagnostic test.

    PubMed

    Doctor, Stephanie M; Liu, Yunhao; Whitesell, Amy; Thwai, Kyaw L; Taylor, Steve M; Janko, Mark; Emch, Michael; Kashamuka, Melchior; Muwonga, Jérémie; Tshefu, Antoinette; Meshnick, Steven R

    2016-05-01

    Malaria surveillance is critical for control efforts, but diagnostic methods frequently disagree. Here, we compare microscopy, PCR, and a rapid diagnostic test in 7137 samples from children in the Democratic Republic of the Congo using latent class analysis. PCR had the highest sensitivity (94.6%) and microscopy had the lowest (76.7%). PMID:26915637

  18. Rapid Technology Assessment via Unified Deployment of Global Optical and Virtual Diagnostics

    NASA Technical Reports Server (NTRS)

    Jordan, Jeffrey D.; Watkins, A. Neal; Fleming, Gary A.; Leighty, Bradley D.; Schwartz, Richard J.; Ingram, JoAnne L.; Grinstead, Keith D., Jr.; Oglesby, Donald M.; Tyler, Charles

    2003-01-01

    This paper discusses recent developments in rapid technology assessment resulting from an active collaboration between researchers at the Air Force Research Laboratory (AFRL) at Wright Patterson Air Force Base (WPAFB) and the NASA Langley Research Center (LaRC). This program targets the unified development and deployment of global measurement technologies coupled with a virtual diagnostic interface to enable the comparative evaluation of experimental and computational results. Continuing efforts focus on the development of seamless data translation methods to enable integration of data sets of disparate file format in a common platform. Results from a successful low-speed wind tunnel test at WPAFB in which global surface pressure distributions were acquired simultaneously with model deformation and geometry measurements are discussed and comparatively evaluated with numerical simulations. Intensity- and lifetime-based pressure-sensitive paint (PSP) and projection moire interferometry (PMI) results are presented within the context of rapid technology assessment to enable simulation-based R&D.

  19. Diagnostic performance characteristics of a rapid field test for anthrax in cattle.

    PubMed

    Muller, Janine; Gwozdz, Jacek; Hodgeman, Rachel; Ainsworth, Catherine; Kluver, Patrick; Czarnecki, Jill; Warner, Simone; Fegan, Mark

    2015-07-01

    Although diagnosis of anthrax can be made in the field with a peripheral blood smear, and in the laboratory with bacterial culture or molecular based tests, these tests require either considerable experience or specialised equipment. Here we report on the evaluation of the diagnostic sensitivity and specificity of a simple and rapid in-field diagnostic test for anthrax, the anthrax immunochromatographic test (AICT). The AICT detects the protective antigen (PA) component of the anthrax toxin present within the blood of an animal that has died from anthrax. The test provides a result in 15min and offers the advantage of avoiding the necessity for on-site necropsy and subsequent occupational risks and environmental contamination. The specificity of the test was determined by testing samples taken from 622 animals, not infected with Bacillus anthracis. Diagnostic sensitivity was estimated on samples taken from 58 animals, naturally infected with B. anthracis collected over a 10-year period. All samples used to estimate the diagnostic sensitivity and specificity of the AICT were also tested using the gold standard of bacterial culture. The diagnostic specificity of the test was estimated to be 100% (99.4-100%; 95% CI) and the diagnostic sensitivity was estimated to be 93.1% (83.3-98.1%; 95% CI) (Clopper-Pearson method). Four samples produced false negative AICT results. These were among 9 samples, all of which tested positive for B. anthracis by culture, where there was a time delay between collection and testing of >48h and/or the samples were collected from animals that were >48h post-mortem. A statistically significant difference (P<0.001; Fishers exact test) was found between the ability of the AICT to detect PA in samples from culture positive animals <48h post-mortem, 49 of 49, Se=100% (92.8-100%; 95% CI) compared with samples tested >48h post-mortem 5 of 9 Se=56% (21-86.3%; 95% CI) (Clopper-Pearson method). Based upon these results a post hoc cut-off for use of

  20. Rapid and Accurate Detection of Urinary Pathogens by Mobile IMS-Based Electronic Nose: A Proof-of-Principle Study

    PubMed Central

    Roine, Antti; Saviauk, Taavi; Kumpulainen, Pekka; Karjalainen, Markus; Tuokko, Antti; Aittoniemi, Janne; Vuento, Risto; Lekkala, Jukka; Lehtimäki, Terho; Tammela, Teuvo L.; Oksala, Niku K. J.

    2014-01-01

    Urinary tract infection (UTI) is a common disease with significant morbidity and economic burden, accounting for a significant part of the workload in clinical microbiology laboratories. Current clinical chemisty point-of-care diagnostics rely on imperfect dipstick analysis which only provides indirect and insensitive evidence of urinary bacterial pathogens. An electronic nose (eNose) is a handheld device mimicking mammalian olfaction that potentially offers affordable and rapid analysis of samples without preparation at athmospheric pressure. In this study we demonstrate the applicability of ion mobility spectrometry (IMS) –based eNose to discriminate the most common UTI pathogens from gaseous headspace of culture plates rapidly and without sample preparation. We gathered a total of 101 culture samples containing four most common UTI bacteries: E. coli, S. saprophyticus, E. faecalis, Klebsiella spp and sterile culture plates. The samples were analyzed using ChemPro 100i device, consisting of IMS cell and six semiconductor sensors. Data analysis was conducted by linear discriminant analysis (LDA) and logistic regression (LR). The results were validated by leave-one-out and 5-fold cross validation analysis. In discrimination of sterile and bacterial samples sensitivity of 95% and specificity of 97% were achieved. The bacterial species were identified with sensitivity of 95% and specificity of 96% using eNose as compared to urine bacterial cultures. In conclusion: These findings strongly demonstrate the ability of our eNose to discriminate bacterial cultures and provides a proof of principle to use this method in urinanalysis of UTI. PMID:25526592

  1. Rapid diagnostic methods for influenza virus in clinical specimens - A comparative study

    NASA Technical Reports Server (NTRS)

    Evans, A. S.; Olson, B.

    1982-01-01

    A comparison of five rapid viral diagnostic techniques for identifying influenza virus in nasopharyngeal aspirates has been made on patients with influenza-like illnesses. Initial results with immune electron microscopy were positive in only one of 11 specimens from which virus was isolated and further work abandoned. Four other rapid tests were carried out on 39 specimens from which influenza virus had been isolated in tissue culture in 28. Of these 28 specimens yielding virus, 24 (85.7 percent) were positive by an indirect fluorescent antibody test (IFAT) on nasopharyngeal cells, 18 (64.3 percent) by enzyme-linked immunosorbent assay (ELISA), 19 (67.8 percent) by enzyme-linked fluorescent assay (ELFA), and 26 (92.8 percent) by a rapid tissue culture amplification method (TCA) in a continuous Rhesus monkey kidney line (LLC-MK2) with identification of virus by fluorescent antibody. In terms of sensitivity, simplicity, and rapidity, a combination of the IFAT and TCA methods seems to be very useful.

  2. Addressing Barriers to the Development and Adoption of Rapid Diagnostic Tests in Global Health

    PubMed Central

    Miller, Eric; Sikes, Hadley D.

    2015-01-01

    Immunochromatographic rapid diagnostic tests (RDTs) have demonstrated significant potential for use as point-of-care diagnostic tests in resource-limited settings. Most notably, RDTs for malaria have reached an unparalleled level of technological maturity and market penetration, and are now considered an important complement to standard microscopic methods of malaria diagnosis. However, the technical development of RDTs for other infectious diseases, and their uptake within the global health community as a core diagnostic modality, has been hindered by a number of extant challenges. These range from technical and biological issues, such as the need for better affinity agents and biomarkers of disease, to social, infrastructural, regulatory and economic barriers, which have all served to slow their adoption and diminish their impact. In order for the immunochromatographic RDT format to be successfully adapted to other disease targets, to see widespread distribution, and to improve clinical outcomes for patients on a global scale, these challenges must be identified and addressed, and the global health community must be engaged in championing the broader use of RDTs. PMID:26594252

  3. Controversies in Antimicrobial Stewardship: Focus on New Rapid Diagnostic Technologies and Antimicrobials

    PubMed Central

    Wenzler, Eric; Wong, Jordan R.; Goff, Debra A.; Jankowski, Christopher A.; Bauer, Karri A.

    2016-01-01

    Antimicrobial stewardship programs (ASPs) are challenged with ensuring appropriate antimicrobial use while minimizing expenditures. ASPs have consistently demonstrated improved patient outcomes and significant cost reductions but are continually required to justify the costs of their existence and interventions due to the silo mentality often adopted by hospital administrators. As new technologies and antimicrobials emerge, ASPs are in a constant tug-of-war between providing optimal clinical outcomes and ensuring cost containment. Additionally, robust data on cost-effectiveness of new rapid diagnostic technologies and antimicrobials with subsequent ASP interventions to provide justification are lacking. As the implementation of an ASP will soon be mandatory for acute care hospitals in the United States, ASPs must find ways to justify novel interventions to align themselves with healthcare administrators. This review provides a framework for the justification of implementing a rapid diagnostic test or adding a new antimicrobial to formulary with ASP intervention, reviews approaches to demonstrating cost-effectiveness, and proposes methods for which ASPs may reduce healthcare expenditures via alternative tactics. PMID:27025521

  4. HistoStitcher© : An Interactive Program for Accurate and Rapid Reconstruction of Digitized Whole Histological Sections from Tissue Fragments

    PubMed Central

    Chappelow, Jonathan; Tomaszewski, John E.; Feldman, Michael; Shih, Natalie; Madabhushi, Anant

    2011-01-01

    We present an interactive program called HistoStitcher© for accurate and rapid reassembly of histology fragments into a pseudo-whole digitized histological section. HistoStitcher© provides both an intuitive graphical interface to assist the operator in performing the stitch of adjacent histology fragments by selecting pairs of anatomical landmarks, and a set of computational routines for determining and applying an optimal linear transformation to generate the stitched image. Reconstruction of whole histological sections from images of slides containing smaller fragments is required in applications where preparation of whole sections of large tissue specimens is not feasible or efficient, and such whole mounts are required to facilitate (a) disease annotation and (b) image registration with radiological images. Unlike manual reassembly of image fragments in a general purpose image editing program (such as Photoshop), HistoStitcher© provides memory efficient operation on high resolution digitized histology images and a highly flexible stitching process capable of producing more accurate results in less time. Further, by parameterizing the series of transformations determined by the stitching process, the stitching parameters can be saved, loaded at a later time, refined, or reapplied to multi-resolution scans, or quickly transmitted to another site. In this paper, we describe in detail the design of HistoStitcher© and the mathematical routines used for calculating the optimal image transformation, and demonstrate its operation for stitching high resolution histology quadrants of a prostate specimen to form a digitally reassembled whole histology section, for 8 different patient studies. To evaluate stitching quality, a 6 point scoring scheme, which assesses the alignment and continuity of anatomical structures important for disease annotation, is employed by three independent expert pathologists. For 6 studies compared with this scheme, reconstructed sections

  5. Prospective Evaluation of Three Rapid Diagnostic Tests for Diagnosis of Human Leptospirosis

    PubMed Central

    Goris, Marga G. A.; Leeflang, Mariska M. G.; Loden, Martin; Wagenaar, Jiri F. P.; Klatser, Paul R.; Hartskeerl, Rudy A.; Boer, Kimberly R.

    2013-01-01

    Background Diagnosis of leptospirosis by the microscopic agglutination test (MAT) or by culture is confined to specialized laboratories. Although ELISA techniques are more common, they still require laboratory facilities. Rapid Diagnostic Tests (RDTs) can be used for easy point-of-care diagnosis. This study aims to evaluate the diagnostic performance of the RDTs LeptoTek Dri Dot, LeptoTek Lateral Flow, and Leptocheck-WB, prospectively. Methodology During 2001 to 2012, one or two of the RDTs at the same time have been applied prior to routine diagnostics (MAT, ELISA and culture) on serum specimens from participants sent in for leptospirosis diagnosis. The case definition was based on MAT, ELISA and culture results. Participants not fulfilling the case definition were considered not to have leptospirosis. The diagnostic accuracy was determined based on the 1st submitted sample and paired samples, either in an overall analysis or stratified according to days post onset of illness. Results The overall sensitivity and specificity for the LeptoTek Dri Dot was 75% respectively 96%, for the LeptoTek Lateral Flow 78% respectively 95%, and for the Leptocheck-WB 78% respectively 98%. Based on the 1st submitted sample the sensitivity was low (51% for LeptoTek Dri Dot, 69% for LeptoTek Lateral Flow, and 55% for Leptocheck-WB), but substantially increased when the results of paired samples were combined, although accompanied by a lower specificity (82% respectively 91% for LeptoTek Dri Dot, 86% respectively 84% for LeptoTek Lateral Flow, and 80% respectively 93% for Leptocheck-WB). Conclusions All three tests present antibody tests contributing to the diagnosis of leptospirosis, thus supporting clinical suspicion and contributing to awareness. Since the overall sensitivity of the tested RDTs did not exceed 80%, one should be cautious to rely only on an RDT result, and confirmation by reference tests is strongly recommended. PMID:23875034

  6. Touch imprint cytology: a rapid diagnostic tool for oral squamous cell carcinoma.

    PubMed

    Geetha, L; Astekar, M; Ashok, K N; Sowmya, G V

    2015-07-01

    Techniques for intraoperative pathologic examination of oral squamous cell carcinoma are rare in the literature. We evaluated the advantages and limitations of touch imprint cytology for intraoperative diagnosis of oral squamous cell carcinoma. We used 30 incisional biopsies of clinically diagnosed oral squamous cell carcinoma and compared touch imprint cytology to histopathological sections. Touch imprint cytology showed 24 specimens positive for malignancy, two suspicious for malignancy and four inadequate specimens. The accuracy of the test was 93.2%. Touch imprint cytology is an accurate, simple, rapid and cost-effective method that aids diagnosis of oral squamous cell carcinoma during operation, but it does not replace incisional biopsy. PMID:25801179

  7. Rapid and Accurate U-Th Dating of Ancient Carbonates using Inductively Coupled Plasma-Quadrupole Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Douville, Eric; Sallé, Eline; Frank, Norbert; Eisele, Markus; Pons-Branchu, Edwige; Ayrault, Sophie

    2010-05-01

    Here, the potential for rapid and accurate U-Th dating technique of marine aragonite skeletons (deep-sea corals, Lophelia pertusa) and secondary calcite deposits (speleothems and stalagmites) has been explored using inductively-coupled plasma-quadrupole mass spectrometry (ICP-QMS). The analytical procedure includes a largely simplified chemical separation technique for uranium (U) and thorium (Th) using UTEVA resin. The developed technique permits simultaneous quantification of uranium [238U] and thorium [232Th] concentrations and their respective isotopic composition, required for U-series disequilibrium dating. Up to 50 U-Th dates per day can be achieved through ICP-QMS with 234U and 230Th reproducibility (2sigma) of 3-4 permil and 1 percent, respectively. The high sensitivity (> 300 000 cps/ppb) together with low background (<0.5 cps) on each mass between 228-236 amu allowed U-Th dating of ancient deep water corals (15-260 kyrs) and stalagmites (30-85 kyrs) at precision levels of less than 2%. Consequently, the combination of simplified chemistry using UTEVA with state-of-the-art ICP-QMS isotopic measurements that do not require a U-Th separation step now provides an extremely rapid and low-cost U-series dating technology. The level of precision is most convenient for numerous geochronological applications, such as the determination of climatic influences on ecosystem development and carbonate precipitation. As a first-example application we present ICP-QMS U-Th dates of North Atlantic deep-water coral fragments retrieved in the southeastern Porcupine Seabight (MD01-2463G, Mound Thérèse), indicating a purely interglacial growth of deep-water corals on so-called carbonate mounds over several climate cycles.

  8. SMS messages increase adherence to rapid diagnostic test results among malaria patients: results from a pilot study in Nigeria

    PubMed Central

    2014-01-01

    Background The World Health Organization now recommends parasitological confirmation for malaria case management. Rapid diagnostic tests (RDTs) for malaria are an accurate and simple diagnostic to confirm parasite presence in blood. However, where they have been deployed, adherence to RDT results has been poor, especially when the test result is negative. Few studies have examined adherence to RDTs distributed or purchased through the private sector. Methods The Rapid Examination of Malaria and Evaluation of Diagnostic Information (REMEDI) study assessed the acceptability of and adherence to RDT results for patients seeking care from private sector drug retailers in two cities in Oyo State in south-west Nigeria. In total, 465 adult participants were enrolled upon exit from a participating drug shop having purchased anti-malaria drugs for themselves. Participants were given a free RDT and the appropriate treatment advice based on their RDT result. Short Message Service (SMS) text messages reiterating the treatment advice were sent to a randomly selected half of the participants one day after being tested. Participants were contacted via phone four days after the RDT was conducted to assess adherence to the RDT information and treatment advice. Results Adherence to RDT results was 14.3 percentage points (P-val <0.001) higher in the treatment group who were sent the SMS. The higher adherence in the treatment group was robust to several specification tests and the estimated difference in adherence ranged from 9.7 to 16.1 percentage points. Further, the higher adherence to the treatment advice was specific to the treatment advice for anti-malarial drugs and not other drugs purchased to treat malaria symptoms in the RDT-negative participants who bought both anti-malarial and symptom drugs. There was no difference in adherence for the RDT-positive participants who were sent the SMS. Conclusions SMS text messages substantially increased adherence to RDT results for

  9. Development and evaluation of a liquid chromatography-mass spectrometry method for rapid, accurate quantitation of malondialdehyde in human plasma.

    PubMed

    Sobsey, Constance A; Han, Jun; Lin, Karen; Swardfager, Walter; Levitt, Anthony; Borchers, Christoph H

    2016-09-01

    Malondialdhyde (MDA) is a commonly used marker of lipid peroxidation in oxidative stress. To provide a sensitive analytical method that is compatible with high throughput, we developed a multiple reaction monitoring-mass spectrometry (MRM-MS) approach using 3-nitrophenylhydrazine chemical derivatization, isotope-labeling, and liquid chromatography (LC) with electrospray ionization (ESI)-tandem mass spectrometry assay to accurately quantify MDA in human plasma. A stable isotope-labeled internal standard was used to compensate for ESI matrix effects. The assay is linear (R(2)=0.9999) over a 20,000-fold concentration range with a lower limit of quantitation of 30fmol (on-column). Intra- and inter-run coefficients of variation (CVs) were <2% and ∼10% respectively. The derivative was stable for >36h at 5°C. Standards spiked into plasma had recoveries of 92-98%. When compared to a common LC-UV method, the LC-MS method found near-identical MDA concentrations. A pilot project to quantify MDA in patient plasma samples (n=26) in a study of major depressive disorder with winter-type seasonal pattern (MDD-s) confirmed known associations between MDA concentrations and obesity (p<0.02). The LC-MS method provides high sensitivity and high reproducibility for quantifying MDA in human plasma. The simple sample preparation and rapid analysis time (5x faster than LC-UV) offers high throughput for large-scale clinical applications. PMID:27437618

  10. Successful application of enzyme-labeled oligonucleotide probe for rapid and accurate cholera diagnosis in a clinical laboratory.

    PubMed

    Miyagi, K; Matsumoto, Y; Hayashi, K; Yoh, M; Yamamoto, K; Honda, T

    1994-01-01

    Two cholera cases were diagnosed using an enzyme-labeled oligonucleotide probe (ELONP) hybridization test for detection of cholera toxin gene (ctx) in a clinical laboratory at Osaka Airport Quarantine Station. The ELONP test with suspicious colonies of Vibrio cholerae O1 grown on TCBS or Vibrio agar plates gave positive result for ctx within 3 hr. We also tried to apply the ELONP test for direct detection of ctx in their stool and their non-selective culture. Specimens from Case #1, which contained 5.9 x 10(5) CFU/g of V. cholerae O1 in the stool, cultured for 7-8 hr or longer in alkaline peptone water or Marine broth at 37C, became positive for ctx. On the other hand, specimens from Case #2, which contained 8.7 x 10(8) CFU/ml (of V. cholerae O1 in the stool), gave positive result in this stool itself without any further culture. These data suggest that the ELONP test provides successfully a more rapid and accurate means of identifying "toxigenic" V. cholerae O1 in a clinical laboratory. PMID:7935049

  11. Evaluation of a rapid diagnostic test for assessing the burden of malaria at delivery in India.

    PubMed

    Singh, Neeru; Saxena, Ajay; Awadhia, S B; Shrivastava, Rita; Singh, M P

    2005-11-01

    All pregnant women who came for delivery at a district hospital in Mandla and a civil hospital in Maihar were screened for Plasmodium falciparum (placental parasitemia using a rapid test and microscopy and peripheral and umbilical cord parasitemia using microscopy alone). Two rapid diagnostic tests (RDTs), Paracheck Pf and ParaHITf, were used. At Mandla, the sensitivity and specificity of the Paracheck Pf for P. falciparum were 93% and 84%, respectively. The positive predictive values (PPVs) and negative predictive values (NPVs) were 50% and 99%, respectively. At Maihar, the sensitivity and specificity of the ParaHITf for P. falciparum were 87.5% and 97%, respectively. The PPVs and NPVs were 75.4% and 98.7%, respectively. Placental infection was significantly associated with low birth weight. The RDTs for the identification of P. falciparum were more sensitive in placental blood than the placental blood smear by microscopy. Thus, the RDTs should be useful for rapid assessment of malaria at delivery. PMID:16282293

  12. Brain tumour differentiation: rapid stratified serum diagnostics via attenuated total reflection Fourier-transform infrared spectroscopy.

    PubMed

    Hands, James R; Clemens, Graeme; Stables, Ryan; Ashton, Katherine; Brodbelt, Andrew; Davis, Charles; Dawson, Timothy P; Jenkinson, Michael D; Lea, Robert W; Walker, Carol; Baker, Matthew J

    2016-05-01

    The ability to diagnose cancer rapidly with high sensitivity and specificity is essential to exploit advances in new treatments to lead significant reductions in mortality and morbidity. Current cancer diagnostic tests observing tissue architecture and specific protein expression for specific cancers suffer from inter-observer variability, poor detection rates and occur when the patient is symptomatic. A new method for the detection of cancer using 1 μl of human serum, attenuated total reflection-Fourier transform infrared spectroscopy and pattern recognition algorithms is reported using a 433 patient dataset (3897 spectra). To the best of our knowledge, we present the largest study on serum mid-infrared spectroscopy for cancer research. We achieve optimum sensitivities and specificities using a Radial Basis Function Support Vector Machine of between 80.0 and 100 % for all strata and identify the major spectral features, hence biochemical components, responsible for the discrimination within each stratum. We assess feature fed-SVM analysis for our cancer versus non-cancer model and achieve 91.5 and 83.0 % sensitivity and specificity respectively. We demonstrate the use of infrared light to provide a spectral signature from human serum to detect, for the first time, cancer versus non-cancer, metastatic cancer versus organ confined, brain cancer severity and the organ of origin of metastatic disease from the same sample enabling stratified diagnostics depending upon the clinical question asked. PMID:26874961

  13. Rapid diagnostic imaging and pathologic evaluation of surgical tissue using video rate structured illumination microscopy (VR-SIM) (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wang, Mei; Tulman, David; Elfer, Kate; Sholl, Andrew; Brown, J. Quincy

    2016-03-01

    Currently available pathology techniques for obtaining a rapid tissue diagnosis, or for determining the adequacy of specimens intended for downstream analysis, are too slow, labor-intensive, and destructive for point-of-care (POC) applications. We previously demonstrated video-rate structured illumination microscopy (VR-SIM) for accurate, high-throughput, non-destructive diagnostic imaging of fluorescently-stained prostate biopsies in seconds per biopsy, with an area under the ROC curve of 0.82-0.88 after pathologist review. In addition, we have demonstrated that it is feasible to use VR-SIM to routinely image very large gross pathology specimens, such as entire prostate resection surfaces, in relatively short timeframes at subcellular resolution. However, our prior work has focused on applications in prostate cancer; the utility in other organ sites has not been explored. Here we extended our technology to varying size kidney, liver, and lung biopsies. We conducted a validation study of VR-SIM against histopathology on a variety of human tissues, including both small biopsies and large slices of tissue. We conducted a blinded study in which the study pathologist accurately identified the organs based on VR-SIM images alone. The results were then used to create a clinical atlas between VR-SIM and H and E images for the different tissues of interest. This clinical atlas will be used to aid in pathologist interpretation in future POC clinical applications of VR-SIM in kidney, liver, and lung. Such applications could include on-site identification of the presence of kidney glomeruli for to ensure successful downstream IHC analysis, or determination of the adequacy of lung cancer biopsies for genomic analysis.

  14. Validation of Three Early Ejaculation Diagnostic Tools: A Composite Measure Is Accurate and More Adequate for Diagnosis by Updated Diagnostic Criteria

    PubMed Central

    Jern, Patrick; Piha, Juhana; Santtila, Pekka

    2013-01-01

    Purpose To validate three early ejaculation diagnostic tools, and propose a new tool for diagnosis in line with proposed changes to diagnostic criteria. Significant changes to diagnostic criteria are expected in the near future. Available screening tools do not necessarily reflect proposed changes. Materials and Methods Data from 148 diagnosed early ejaculation patients (Mage = 42.8) and 892 controls (Mage = 33.1 years) from a population-based sample were used. Participants responded to three different questionnaires (Premature Ejaculation Profile; Premature Ejaculation Diagnostic Tool; Multiple Indicators of Premature Ejaculation). Stopwatch measured ejaculation latency times were collected from a subsample of early ejaculation patients. We used two types of responses to the questionnaires depending on the treatment status of the patients 1) responses regarding the situation before starting pharmacological treatment and 2) responses regarding current situation. Logistic regressions and Receiver Operating Characteristics were used to assess ability of both the instruments and individual items to differentiate between patients and controls. Results All instruments had very good precision (Areas under the Curve ranging from .93-.98). A new five-item instrument (named CHecklist for Early Ejaculation Symptoms – CHEES) consisting of high-performance variables selected from the three instruments had validity (Nagelkerke R2 range .51-.79 for backwards/forwards logistic regression) equal to or slightly better than any individual instrument (i.e., had slightly higher validity statistics, but these differences did not achieve statistical significance). Importantly, however, this instrument was more in line with proposed changes to diagnostic criteria. Conclusions All three screening tools had good validity. A new 5-item diagnostic tool (CHEES) based on the three instruments had equal or somewhat more favorable validity statistics compared to the other three tools, but is

  15. RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

    PubMed Central

    Srivastava, Avi; Sarkar, Hirak; Gupta, Nitish; Patro, Rob

    2016-01-01

    Motivation: The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in the de novo setting or when a trusted reference annotation is available), care must be taken to report the potentially large number of multi-mapping locations per read. This can pose a substantial computational burden for existing aligners, and can considerably slow downstream analysis. Results: We introduce a novel concept, quasi-mapping, and an efficient algorithm implementing this approach for mapping sequencing reads to a transcriptome. By attempting only to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by which it derives from the reference, RapMap—our tool implementing quasi-mapping—is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools. The algorithm we use to implement quasi-mapping uses several efficient data structures and takes advantage of the special structure of shared sequence prevalent in transcriptomes to rapidly provide highly-accurate mapping information. We demonstrate how quasi-mapping can be successfully applied to the problems of transcript-level quantification from RNA-seq reads and the clustering of contigs from de novo assembled transcriptomes into biologically meaningful groups. Availability and implementation: RapMap is implemented in C ++11 and is available as open-source software, under GPL v3, at https://github.com/COMBINE-lab/RapMap. Contact: rob.patro@cs.stonybrook.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307617

  16. A False Positive Dengue Fever Rapid Diagnostic Test Result in a Case of Acute Parvovirus B19 Infection.

    PubMed

    Izumida, Toshihide; Sakata, Hidenao; Nakamura, Masahiko; Hayashibara, Yumiko; Inasaki, Noriko; Inahata, Ryo; Hasegawa, Sumiyo; Takizawa, Takenori; Kaya, Hiroyasu

    2016-01-01

    An outbreak of dengue fever occurred in Japan in August 2014. We herein report the case of a 63-year-old man who presented with a persistent fever in September 2014. Acute parvovirus B19 infection led to a false positive finding of dengue fever on a rapid diagnostic test (Panbio Dengue Duo Cassette(TM)). To the best of our knowledge, there are no previous reports of a false positive result for dengue IgM with the dengue rapid diagnostic test. We believe that epidemiological information on the prevalence of parvovirus B19 is useful for guiding the interpretation of a positive result with the dengue rapid diagnostic test. PMID:27181552

  17. Rapid Sampling of Molecules via Skin for Diagnostic and Forensic Applications

    PubMed Central

    Paliwal, Sumit; Ogura, Makoto

    2010-01-01

    ABSTRACT Purpose Skin provides an excellent portal for diagnostic monitoring of a variety of entities; however, there is a dearth of reliable methods for patient-friendly sampling of skin constituents. This study describes the use of low-frequency ultrasound as a one-step methodology for rapid sampling of molecules from the skin. Methods Sampling was performed using a brief exposure of 20 kHz ultrasound to skin in the presence of a sampling fluid. In vitro sampling from porcine skin was performed to assess the effectiveness of the method and its ability to sample drugs and endogenous epidermal biomolecules from the skin. Dermal presence of an antifungal drug—fluconazole and an abused substance, cocaine—was assessed in rats. Results Ultrasonic sampling captured the native profile of various naturally occurring moisturizing factors in skin. A high sampling efficiency (79 ± 13%) of topically delivered drug was achieved. Ultrasound consistently sampled greater amounts of drug from the skin compared to tape stripping. Ultrasonic sampling also detected sustained presence of cocaine in rat skin for up to 7 days as compared to its rapid disappearance from the urine. Conclusions Ultrasonic sampling provides significant advantages including enhanced sampling from deeper layers of skin and high temporal sampling sensitivity. PMID:20238151

  18. Multiplex PCR Allows Rapid and Accurate Diagnosis of Bloodstream Infections in Newborns and Children with Suspected Sepsis▿†§

    PubMed Central

    Lucignano, Barbara; Ranno, Stefania; Liesenfeld, Oliver; Pizzorno, Beatrice; Putignani, Lorenza; Bernaschi, Paola; Menichella, Donato

    2011-01-01

    Sepsis is a major health problem in newborns and children. Early detection of pathogens allows initiation of appropriate antimicrobial therapy that strongly correlates with positive outcomes. Multiplex PCR has the potential to rapidly identify bloodstream infections, compensating for the loss of blood culture sensitivity. In an Italian pediatric hospital, multiplex PCR (the LightCycler SeptiFast test) was compared to routine blood culture with 1,673 samples obtained from 803 children with suspected sepsis; clinical and laboratory information was used to determine the patient infection status. Excluding results attributable to contaminants, SeptiFast showed a sensitivity of 85.0% (95% confidence interval [CI] = 78.7 to 89.7%) and a specificity of 93.5% (95% CI = 92.1 to 94.7%) compared to blood culture. The rate of positive results was significantly higher with SeptiFast (14.6%) than blood culture (10.3%) (P < 0.0001), and the overall positivity rate was 16.1% when the results of both tests were combined. Staphylococcus aureus (11.6%), coagulase-negative staphylococci (CoNS) (29.6%), Pseudomonas aeruginosa (16.5%), and Klebsiella spp. (10.1%) were the most frequently detected. SeptiFast identified 97 additional isolates that blood culture failed to detect (24.7% P. aeruginosa, 23.7% CoNS, 14.4% Klebsiella spp., 14.4% Candida spp.). Among specimens taken from patients receiving antibiotic therapy, we also observed a significantly higher rate of positivity of SeptiFast than blood culture (14.1% versus 6.5%, respectively; P < 0.0001). On the contrary, contaminants were significantly more frequent among blood cultures than SeptiFast (n = 97 [5.8%] versus n = 26 [1.6%]), respectively; P < 0.0001). SeptiFast served as a highly valuable adjunct to conventional blood culture in children, adding diagnostic value and shortening the time to result (TTR) to 6 h. PMID:21471340

  19. Pfhrp2 and pfhrp3 polymorphisms in Plasmodium falciparum isolates from Dakar, Senegal: impact on rapid malaria diagnostic tests

    PubMed Central

    2013-01-01

    Background An accurate diagnosis is essential for the rapid and appropriate treatment of malaria. The accuracy of the histidine-rich protein 2 (PfHRP2)-based rapid diagnostic test (RDT) Palutop+4® was assessed here. One possible factor contributing to the failure to detect malaria by this test is the diversity of the parasite PfHRP2 antigens. Methods PfHRP2 detection with the Palutop+4® RDT was carried out. The pfhrp2 and pfhrp3 genes were amplified and sequenced from 136 isolates of Plasmodium falciparum that were collected in Dakar, Senegal from 2009 to 2011. The DNA sequences were determined and statistical analyses of the variation observed between these two genes were conducted. The potential impact of PfHRP2 and PfHRP3 sequence variation on malaria diagnosis was examined. Results Seven P. falciparum isolates (5.9% of the total isolates, regardless of the parasitaemia; 10.7% of the isolates with parasitaemia ≤0.005% or ≤250 parasites/μl) were undetected by the PfHRP2 Palutop+4® RDT. Low parasite density is not sufficient to explain the PfHRP2 detection failure. Three of these seven samples showed pfhrp2 deletion (2.4%). The pfhrp3 gene was deleted in 12.8%. Of the 122 PfHRP2 sequences, 120 unique sequences were identified. Of the 109 PfHRP3 sequences, 64 unique sequences were identified. Using the Baker’s regression model, at least 7.4% of the P. falciparum isolates in Dakar were likely to be undetected by PfHRP2 at a parasite density of ≤250 parasites/μl (slightly lower than the evaluated prevalence of 10.7%). This predictive prevalence increased significantly between 2009 and 2011 (P = 0.0046). Conclusion In the present work, 10.7% of the isolates with a parasitaemia ≤0.005% (≤250 parasites/μl) were undetected by the PfHRP2 Palutop+4® RDT (7.4% by the predictive Baker’model). In addition, all of the parasites with pfhrp2 deletion (2.4% of the total samples) and 2.1% of the parasites with parasitaemia >0.005% and presence of pfhrp2 were

  20. Rapid Bayesian point source inversion using pattern recognition --- bridging the gap between regional scaling relations and accurate physical modelling

    NASA Astrophysics Data System (ADS)

    Valentine, A. P.; Kaeufl, P.; De Wit, R. W. L.; Trampert, J.

    2014-12-01

    Obtaining knowledge about source parameters in (near) real-time during or shortly after an earthquake is essential for mitigating damage and directing resources in the aftermath of the event. Therefore, a variety of real-time source-inversion algorithms have been developed over recent decades. This has been driven by the ever-growing availability of dense seismograph networks in many seismogenic areas of the world and the significant advances in real-time telemetry. By definition, these algorithms rely on short time-windows of sparse, local and regional observations, resulting in source estimates that are highly sensitive to observational errors, noise and missing data. In order to obtain estimates more rapidly, many algorithms are either entirely based on empirical scaling relations or make simplifying assumptions about the Earth's structure, which can in turn lead to biased results. It is therefore essential that realistic uncertainty bounds are estimated along with the parameters. A natural means of propagating probabilistic information on source parameters through the entire processing chain from first observations to potential end users and decision makers is provided by the Bayesian formalism.We present a novel method based on pattern recognition allowing us to incorporate highly accurate physical modelling into an uncertainty-aware real-time inversion algorithm. The algorithm is based on a pre-computed Green's functions database, containing a large set of source-receiver paths in a highly heterogeneous crustal model. Unlike similar methods, which often employ a grid search, we use a supervised learning algorithm to relate synthetic waveforms to point source parameters. This training procedure has to be performed only once and leads to a representation of the posterior probability density function p(m|d) --- the distribution of source parameters m given observations d --- which can be evaluated quickly for new data.Owing to the flexibility of the pattern

  1. A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics

    PubMed Central

    Chan, Kamfai; Wong, Pui-Yan; Yu, Peter; Hardick, Justin; Wong, Kah-Yat; Wilson, Scott A.; Wu, Tiffany; Hui, Zoe; Gaydos, Charlotte; Wong, Season S.

    2016-01-01

    The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC’s ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC’s performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings. PMID:26872358

  2. Malaria rapid diagnostic test evaluation at private retail pharmacies in Kumasi, Ghana

    PubMed Central

    Audu, Rauf; Anto, Berko Panyin; Koffuor, George Asumeng; Abruquah, Akua Afriyie; Buabeng, Kwame Ohene

    2016-01-01

    Objective: Malaria rapid diagnostic test (MRDT) provides a good alternative to malaria microscopy diagnosis, particularly in resource-constrained settings. This study therefore evaluated MRDT in private retail pharmacies (PRPs) as a critical step in community case malaria management. Methods: In a prospective, cross-over, validation survey at six PRPs in the Ashanti Region of Ghana, 1200 patients presenting with fever in the preceding 48 h were sampled. Fingerstick blood samples were collected for preparation of thick and thin blood films for malaria microscopy. Categorized patients (600 each) went through the processes of MRDT or presumptive diagnosis (PD) of malaria. The malaria disease prevalence of the study area was established. Selectivity (Se), specificity (Sp), positive predictive value (PPV) along with false discovery rate (FDR), and negative predictive value (NPV) along with the false omission rate (FOR), and diagnostic odds ratio (DOR) of MRDT were then calculated. Findings: While 43.0% tested positive using the MRDT, 57.0% tested negative. However, 62.0% MRDT-negative patients in addition to all the MRDT positives were given artemether-lumefantrine. Of those diagnosed by PD, 98.2% were prescribed with an antimalarial (microscopy however confirmed only 70.3% as positive). Se and Sp of the MRDT were 90.68 ± 11.18% and 98.68 ± 1.19%, respectively. Malaria prevalence was estimated to be 43.3%. PPV was 98.0%, FDR was 2.0%, NPV was 98.0%, FOR was 2.0%, and DOR was 2366.43. Conclusion: Results highlighted good performance of MRDTs at PRPs which could inform decision toward its implementation. PMID:27512708

  3. A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics.

    PubMed

    Chan, Kamfai; Wong, Pui-Yan; Yu, Peter; Hardick, Justin; Wong, Kah-Yat; Wilson, Scott A; Wu, Tiffany; Hui, Zoe; Gaydos, Charlotte; Wong, Season S

    2016-01-01

    The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC's ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC's performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings. PMID:26872358

  4. Development of a quantitative rapid diagnostic test for multibacillary leprosy using smart phone technology

    PubMed Central

    2013-01-01

    Background Despite efforts to eliminate leprosy as public health problem, delayed diagnosis and disabilities still occur in many countries. Leprosy diagnosis remains based on clinical manifestations and the number of clinicians with expertise in leprosy diagnosis is in decline. We have developed a new immunochromatographic test with the goal of producing a simple and rapid system that can be used, with a minimal amount of training, to provide an objective and consistent diagnosis of multibacillary leprosy. Methods The test immobilizes two antigens that have been recognized as excellent candidates for serologic diagnosis (the PGL-I mimetic, ND-O, and LID-1), on a nitrocellulose membrane. This allows the detection of specific IgM and IgG antibodies within 20 minutes of the addition of patient sera. Furthermore, we coupled the NDO-LID® rapid tests with a new cell phone-based test reader platform (Smart Reader®) to provide objective interpretation that was both quantifiable and consistent. Results Direct comparison of serologic responses indicated that the rapid test detected a greater proportion of leprosy patients than a lab-based PGL-I ELISA. While positive responses were detected by PGL-I ELISA in 83.3% of multibacillary patients and 15.4% of paucibacillary patients, these numbers were increased to 87% and 21.2%, respectively, when a combination of the NDO-LID® test and Smart Reader® was used. Among multibacillary leprosy the sensitivity of NDO-LID® test assessed by Smart Reader® was 87% (95% CI, 79.2-92.7%) and the specificity was 96.1% (95% CI, 91.7- 98.6%). The positive predictive value and the negative predictive value of NDO-LID® tests were 94% (95% CI, 87.4-97.8%) and 91.4% (95% CI, 85.9-95.2%), respectively. Conclusion The widespread provision of rapid diagnostic tests to facilitate the diagnosis or prognosis of multibacillary leprosy could impact on leprosy control programs by aiding early detection, directing appropriate treatment and potentially

  5. Surface enhanced Raman spectroscopy based nanoparticle assays for rapid, point-of-care diagnostics

    NASA Astrophysics Data System (ADS)

    Driscoll, Ashley J.

    Nucleotide and immunoassays are important tools for disease diagnostics. Many of the current laboratory-based analytical diagnostic techniques require multiple assay steps and long incubation times before results are acquired. In the development of bioassays designed for detecting the emergence and spread of diseases in point-of-care (POC) and remote settings, more rapid and portable analytical methods are necessary. Nanoparticles provide simple and reproducible synthetic methods for the preparation of substrates that can be applied in colloidal assays, providing gains in kinetics due to miniaturization and plasmonic substrates for surface enhanced spectroscopies. Specifically, surface enhanced Raman spectroscopy (SERS) is finding broad application as a signal transduction method in immunological and nucleotide assays due to the production of narrow spectral peaks from the scattering molecules and the potential for simultaneous multiple analyte detection. The application of SERS to a no-wash, magnetic capture assay for the detection of West Nile Virus Envelope and Rift Valley Fever Virus N antigens is described. The platform utilizes colloid based capture of the target antigen in solution, magnetic collection of the immunocomplexes and acquisition of SERS spectra by a handheld Raman spectrometer. The reagents for a core-shell nanoparticle, SERS based assay designed for the capture of target microRNA implicated in acute myocardial infarction are also characterized. Several new, small molecule Raman scatterers are introduced and used to analyze the enhancing properties of the synthesized gold coated-magnetic nanoparticles. Nucleotide and immunoassay platforms have shown improvements in speed and analyte capture through the miniaturization of the capture surface and particle-based capture systems can provide a route to further surface miniaturization. A reaction-diffusion model of the colloidal assay platform is presented to understand the interplay of system

  6. Rapid diagnostic method for the identification of Mycoplasma pneumoniae respiratory tract infection.

    PubMed

    Miyashita, Naoyuki; Kawai, Yasuhiro; Kato, Tadashi; Tanaka, Takaaki; Akaike, Hiroto; Teranishi, Hideto; Nakano, Takashi; Ouchi, Kazunobu; Okimoto, Niro

    2016-05-01

    Rapid diagnostic tests are useful tools in the early diagnosis of respiratory tract infections (RTIs) caused by a specific pathogens. We investigated the sensitivity and specificity of a rapid and simple antigen test for the detection of Mycoplasma pneumoniae, Ribotest Mycoplasma(®) in adolescent and adult patients with RTIs. In addition, we evaluated the accuracy of clinical and laboratory findings for the early presumptive diagnosis of M. pneumoniae RTI. We compared 55 cases with laboratory-confirmed M. pneumoniae infection using serology, culture, and polymerase chain reaction (PCR) and 346 cases without laboratory-confirmed M. pneumoniae infection. Pneumonia cases were excluded in this study. Among patients with M. pneumoniae infection, the incidences of cough, sore throat, and sputum production were high, with rates of 98%, 61%, and 67%, respectively, but the specificity was low. The prevalence of nasal symptoms was significantly lower in patients with M. pneumoniae infection (9%) than in non-M. pneumoniae infection (70%; p < 0.0001). When PCR was used as the control test, the sensitivity, specificity, and overall agreement rates with Ribotest(®) were 71%, 89%, and 87%, respectively. Clinical symptoms and laboratory data were of limited value in making the diagnosis of M. pneumoniae RTI in adolescent and adult patients. Our results suggested that Ribotest(®) may be helpful in distinguishing M. pneumoniae RTI patients from those without the disease. Physicians should consider the use of Ribotest(®) when patients have a persistent cough without nasal symptoms. PMID:26993174

  7. Pocket pathologist: A mobile application for rapid diagnostic surgical pathology consultation

    PubMed Central

    Hartman, Douglas J.; Parwani, Anil V.; Cable, Bill; Cucoranu, Ioan C.; McHugh, Jeff S.; Kolowitz, Brian J.; Yousem, Samuel A.; Palat, Vijaykumar; Reden, Anna Von; Sloka, Stephen; Lauro, Gonzalo Romero; Ahmed, Ishtiaque; Pantanowitz, Liron

    2014-01-01

    Introduction: Telepathology allows the digital transmission of images for rapid access to pathology experts. Recent technologic advances in smartphones have allowed them to be used to acquire and transmit digital images of the glass slide, representing cost savings and efficiency gains over traditional forms of telepathology. We report our experience with developing an iPhone application (App - Pocket Pathologist) to facilitate rapid diagnostic pathology teleconsultation utilizing a smartphone. Materials and Methods: A secure, web-based portal (http://pathconsult.upmc.com/) was created to facilitate remote transmission of digital images for teleconsultation. The App augments functionality of the web-based portal and allows the user to quickly and easily upload digital images for teleconsultation. Image quality of smartphone cameras was evaluated by capturing images using different adapters that directly attach phones to a microscope ocular lens. Results: The App was launched in August 2013. The App facilitated easy submission of cases for teleconsultation by limiting the number of data entry fields for users and enabling uploading of images from their smartphone's gallery wirelessly. Smartphone cameras properly attached to a microscope create static digital images of similar quality to a commercial digital microscope camera. Conclusion: Smartphones have great potential to support telepathology because they are portable, provide ubiquitous internet connectivity, contain excellent digital cameras, and can be easily attached to a microscope. The Pocket Pathologist App represents a significant reduction in the cost of creating digital images and submitting them for teleconsultation. The iPhone App provides an easy solution for global users to submit digital pathology images to pathology experts for consultation. PMID:24843822

  8. Development of a rapid diagnostic test for pertussis: direct detection of pertussis toxin in respiratory secretions.

    PubMed Central

    Friedman, R L; Paulaitis, S; McMillan, J W

    1989-01-01

    Monoclonal antibodies (MAb) were produced against the specific Bordetella pertussis antigen pertussis toxin (PT). In preliminary studies, one MAb (IB12) was selected and used in an enzyme-linked dot blot immunoassay to evaluate the ability of the method to detect known amounts of PT in control experiments and to test its potential for direct detection of PT in nasopharyngeal secretion (NP) specimens from patients with confirmed cases of whooping cough. The dot blot assay was able to detect PT at levels as low as 10 ng per dot in either buffer or control NP specimens. The assay demonstrated specificity, reacting only with dot blots of whole B. pertussis and not Bordetella bronchiseptica, Bordetella parapertussis, or other bacterial strains. In preliminary studies, NP aspirate, swab, and wash specimens were compared. The specimen of choice was found to be the NP aspirate, for which 100% positive results were found in the assay. These initial studies suggest that the dot blot immunoassay in which a MAb is used for direct detection of PT in NP specimens may be useful as a rapid diagnostic test for pertussis. Images PMID:2808670

  9. Evaluation of a rapid diagnostic test for yaws infection in a community surveillance setting.

    PubMed

    Marks, Michael; Goncalves, Adriana; Vahi, Ventis; Sokana, Oliver; Puiahi, Elliot; Zhang, Zaixing; Dalipanda, Tenneth; Bottomley, Christian; Mabey, David; Solomon, Anthony W

    2014-09-01

    Yaws is a non-venereal treponemal infection caused by Treponema pallidum ssp. pertenue. The WHO has launched a worldwide control programme, which aims to eradicate yaws by 2020. The development of a rapid diagnostic test (RDT) for serological diagnosis in the isolated communities affected by yaws is a key requirement for the successful implementation of the WHO strategy. We conducted a study to evaluate the utility of the DPP test in screening for yaws, utilizing samples collected as part of a community prevalence survey conducted in the Solomon Islands. 415 serum samples were tested using both traditional syphilis serology (TPPA and quantitative RPR) and the Chembio DPP Syphilis Screen and Confirm RDT. We calculated the sensitivity and specificity of the RDT as compared to gold standard serology. The sensitivity of the RDT against TPPA was 58.5% and the specificity was 97.6%. The sensitivity of the RDT against RPR was 41.7% and the specificity was 95.2%. The sensitivity of the DPP was strongly related to the RPR titre with a sensitivity of 92.0% for an RPR titre of >1/16. Wider access to DPP testing would improve our understanding of worldwide yaws case reporting and the test may play a key role in assessing patients presenting with yaws like lesions in a post-mass drug administration (MDA) setting. PMID:25211018

  10. Variability in the diagnostic performance of a bedside rapid diagnostic influenza test over four epidemic seasons in a pediatric emergency department.

    PubMed

    Avril, E; Lacroix, S; Vrignaud, B; Moreau-Klein, A; Coste-Burel, M; Launay, E; Gras-Le Guen, C

    2016-07-01

    We wanted to determine the diagnostic performance of a rapid influenza diagnostic test (RIDT) used bedside in a pediatric emergency department (PED). This was a prospective study over four consecutive winters (2009-2013), comparing the results of a RIDT (QuickVue®) with RT-PCR in children admitted to a PED. Among the 764 children included, we did not observe any significant differences in the diagnostic performance of RIDT except during the H1N1 pandemic. The overall sensitivity of the test was 0.82; the specificity 0.98; the positive and negative likelihood ratios 37.8 and 0.19. The positive and negative post-test probabilities of infection were 98% and 17%. The diagnostic performance was increased for influenza B cases (P = 0.03). RIDTs are suitable for use every winter with few differences in its diagnostic value, except during specific pandemic periods. This test could limit unnecessary complementary exams and guide the prescription of antivirals during influenza epidemic periods in PEDs. PMID:27139081

  11. Rapid fecal calprotectin testing to assess for endoscopic disease activity in inflammatory bowel disease: A diagnostic cohort study

    PubMed Central

    Kwapisz, Lukasz; Mosli, Mahmoud; Chande, Nilesh; Yan, Brian; Beaton, Melanie; Micsko, Jessica; Mennill, Pauline W.; Barnett, William; Bax, Kevin; Ponich, Terry; Howard, John; Tirolese, Anthony; Lannigan, Robert; Gregor, James

    2015-01-01

    Background and Aim: With increasing numbers of patients diagnosed with inflammatory bowel disease (IBD), it is important to identify noninvasive methods of detecting disease activity. The aim of this study is to examine the diagnostic accuracy of fecal rapid calprotectin (FC) testing in the detection of endoscopically active IBD. Patients and Methods: All consecutive patients presenting to outpatient clinics with lower gastrointestinal symptoms were prospectively recruited. Patients provided FC samples. Sensitivity (Sn), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV) for FC were calculated. Receiver–operator characteristics (ROC) curve was used to identify the ideal FC cutoff that predicts endoscopic disease activity. Correlation between FC and endoscopic disease activity, disease location, and C-reactive protein (CRP) levels were measured. Results: One hundred and twenty-six patients, of whom 52% were females, were included in the final analysis with a mean age of 44.4 ± 16.7 years. Comparing FC to endoscopic findings, the following results were calculated: A cutoff point of 100 μg/g showed Sn = 83%, Sp = 67%, PPV = 65%, and NPV = 85%; and 200 μg/g showed Sn = 66%, Sp = 82%, PPV = 73%, and NPV = 77%. Based on ROC curve, the best FC cutoff point to predict endoscopic disease activity was 140 μg/g. Using this reference, FC levels strongly correlated with colorectal, ileocolonic, and ileal disease and predicted endoscopic activity. Conclusions: FC is an accurate test when used as an initial screening tool for patients suspected of having active IBD. Given its noninvasive nature, it may prove to reduce the need for colonoscopy and be an added tool in the management of IBD. PMID:26655130

  12. Comparison of the Diagnostic Accuracy of Three Rapid Tests for the Serodiagnosis of Hepatic Cystic Echinococcosis in Humans

    PubMed Central

    Tamarozzi, Francesca; Covini, Ilaria; Mariconti, Mara; Narra, Roberta; Tinelli, Carmine; De Silvestri, Annalisa; Manzoni, Federica; Casulli, Adriano; Ito, Akira; Neumayr, Andreas; Brunetti, Enrico

    2016-01-01

    Background The diagnosis of cystic echinococcosis (CE) is based primarily on imaging, in particular with ultrasound for abdominal CE, complemented by serology when imaging results are unclear. In rural endemic areas, where expertise in ultrasound may be scant and conventional serology techniques are unavailable due to lack of laboratory equipment, Rapid Diagnostic Tests (RDTs) are appealing. Methodology/Principal Findings We evaluated the diagnostic accuracy of 3 commercial RDTs for the diagnosis of hepatic CE. Sera from 59 patients with single hepatic CE cysts in well-defined ultrasound stages (gold standard) and 25 patients with non-parasitic cysts were analyzed by RDTs VIRapid HYDATIDOSIS (Vircell, Spain), Echinococcus DIGFA (Unibiotest, China), ADAMU-CE (ICST, Japan), and by RIDASCREEN Echinococcus IgG ELISA (R-Biopharm, Germany). Sensitivity, specificity and ROC curves were compared with McNemar and t-test. For VIRapid and DIGFA, correlation between semiquantitative results and ELISA OD values were evaluated by Spearman’s coefficient. Reproducibility was assessed on 16 randomly selected sera with Cohen’s Kappa coefficient. Sensitivity and Specificity of VIRapid (74%, 96%) and ADAMU-CE (57%, 100%) did not differ from ELISA (69%, 96%) while DIGFA (72%, 72%) did (p = 0.045). ADAMU-CE was significantly less sensitive in the diagnosis of active cysts (p = 0.019) while DIGFA was significantly less specific (p = 0.014) compared to ELISA. All tests were poorly sensitive in diagnosing inactive cysts (33.3% ELISA and ADAMU-CE, 42.8% DIGFA, 47.6% VIRapid). The reproducibility of all RDTs was good-very good. Band intensity of VIRapid and DIGFA correlated with ELISA OD values (r = 0.76 and r = 0.79 respectively, p<0.001). Conclusions/Significance RDTs may be useful in resource-poor settings to complement ultrasound diagnosis of CE in uncertain cases. VIRapid test appears to perform best among the examined kits, but all tests are poorly sensitive in the presence of

  13. Does ultrasonography accurately diagnose acute cholecystitis? Improving diagnostic accuracy based on a review at a regional hospital

    PubMed Central

    Hwang, Hamish; Marsh, Ian; Doyle, Jason

    2014-01-01

    Background Acute cholecystitis is one of the most common diseases requiring emergency surgery. Ultrasonography is an accurate test for cholelithiasis but has a high false-negative rate for acute cholecystitis. The Murphy sign and laboratory tests performed independently are also not particularly accurate. This study was designed to review the accuracy of ultrasonography for diagnosing acute cholecystitis in a regional hospital. Methods We studied all emergency cholecystectomies performed over a 1-year period. All imaging studies were reviewed by a single radiologist, and all pathology was reviewed by a single pathologist. The reviewers were blinded to each other’s results. Results A total of 107 patients required an emergency cholecystectomy in the study period; 83 of them underwent ultrasonography. Interradiologist agreement was 92% for ultrasonography. For cholelithiasis, ultrasonography had 100% sensitivity, 18% specificity, 81% positive predictive value (PPV) and 100% negative predictive value (NPV). For acute cholecystitis, it had 54% sensitivity, 81% specificity, 85% PPV and 47% NPV. All patients had chronic cholecystitis and 67% had acute cholecystitis on histology. When combined with positive Murphy sign and elevated neutrophil count, an ultrasound showing cholelithiasis or acute cholecystitis yielded a sensitivity of 74%, specificity of 62%, PPV of 80% and NPV of 53% for the diagnosis of acute cholecystitis. Conclusion Ultrasonography alone has a high rate of false-negative studies for acute cholecystitis. However, a higher rate of accurate diagnosis can be achieved using a triad of positive Murphy sign, elevated neutrophil count and an ultrasound showing cholelithiasis or cholecystitis. PMID:24869607

  14. Clinical performance of an automated reader in interpreting malaria rapid diagnostic tests in Tanzania

    PubMed Central

    2013-01-01

    Background Parasitological confirmation of malaria is now recommended in all febrile patients by the World Health Organization (WHO) to reduce inappropriate use of anti-malarial drugs. Widespread implementation of rapid diagnostic tests (RDTs) is regarded as an effective strategy to achieve this goal. However, the quality of diagnosis provided by RDTs in remote rural dispensaries and health centres is not ideal. Feasible RDT quality control programmes in these settings are challenging. Collection of information regarding diagnostic events is also very deficient in low-resource countries. Methods A prospective cohort of consecutive patients aged more than one year from both genders, seeking routine care for febrile episodes at dispensaries located in the Bagamoyo district of Tanzania, were enrolled into the study after signing an informed consent form. Blood samples were taken for thick blood smear (TBS) microscopic examination and malaria RDT (SD Bioline Malaria Antigen Pf/Pan™ (SD RDT)). RDT results were interpreted by both visual interpretation and Deki Reader™ device. Results of visual interpretation were used for case management purposes. Microscopy was considered the “gold standard test” to assess the sensitivity and specificity of the Deki Reader interpretation and to compare it to visual interpretation. Results In total, 1,346 febrile subjects were included in the final analysis. The SD RDT, when used in conjunction with the Deki Reader and upon visual interpretation, had sensitivities of 95.3% (95% CI, 90.6-97.7) and 94.7% (95% CI, 89.8–97.3) respectively, and specificities of 94.6% (95% CI, 93.5–96.1) and 95.6% (95% CI, 94.2–96.6), respectively to gold standard. There was a high percentage of overall agreement between the two methods of interpretation. Conclusion The sensitivity and specificity of the Deki Reader in interpretation of SD RDTs were comparable to previous reports and showed high agreement to visual interpretation (>98%). The

  15. Rapid targeted somatic mutation analysis of solid tumors in routine clinical diagnostics

    PubMed Central

    Francaviglia, Ilaria; Dal Cin, Elena; Barbieri, Gianluca; Arrigoni, Gianluigi; Pecciarini, Lorenza; Doglioni, Claudio; Cangi, Maria Giulia

    2015-01-01

    Tumor genotyping is an essential step in routine clinical practice and pathology laboratories face a major challenge in being able to provide rapid, sensitive and updated molecular tests. We developed a novel mass spectrometry multiplexed genotyping platform named PentaPanel to concurrently assess single nucleotide polymorphisms in 56 hotspots of the 5 most clinically relevant cancer genes, KRAS, NRAS, BRAF, EGFR and PIK3CA for a total of 221 detectable mutations. To both evaluate and validate the PentaPanel performance,we investigated 1025 tumor specimens of 6 different cancer types (carcinomas of colon, lung, breast, pancreas, and biliary tract, and melanomas), systematically addressing sensitivity, specificity, and reproducibility of our platform. Sanger sequencing was also performed for all the study samples. Our data showed that PentaPanel is a high throughput and robust tool, allowing genotyping for targeted therapy selection of 10 patients in the same run, with a practical turnaround time of 2 working days. Importantly, it was successfully used to interrogate different DNAs isolated from routinely processed specimens (formalin-fixed paraffin embedded, frozen, and cytological samples), covering all the requirements of clinical tests. In conclusion, the PentaPanel platform can provide an immediate, accurate and cost effective multiplex approach for clinically relevant gene mutation analysis in many solid tumors and its utility across many diseases can be particularly relevant in multiple clinical trials, including the new basket trial approach, aiming to identify appropriate targeted drug combination strategies. PMID:26435479

  16. Evaluation of the Accuracy of the EasyTest™ Malaria Pf/Pan Ag, a Rapid Diagnostic Test, in Uganda

    PubMed Central

    Chong, Chom-Kyu; Cho, Pyo Yun; Na, Byoung-Kuk; Ahn, Seong Kyu; Kim, Jin Su; Lee, Jin-Soo; Lee, Sung-Keun; Han, Eun-Taek; Kim, Hak-Yong; Park, Yun-Kyu; Cha, Seok Ho

    2014-01-01

    In recent years, rapid diagnostic tests (RDTs) have been widely used for malaria detection, primarily because of their simple operation, fast results, and straightforward interpretation. The Asan EasyTest™ Malaria Pf/Pan Ag is one of the most commonly used malaria RDTs in several countries, including Korea and India. In this study, we tested the diagnostic performance of this RDT in Uganda to evaluate its usefulness for field diagnosis of malaria in this country. Microscopic and PCR analyses, and the Asan EasyTest™ Malaria Pf/Pan Ag rapid diagnostic test, were performed on blood samples from 185 individuals with suspected malaria in several villages in Uganda. Compared to the microscopic analysis, the sensitivity of the RDT to detect malaria infection was 95.8% and 83.3% for Plasmodium falciparum and non-P. falciparum, respectively. Although the diagnostic sensitivity of the RDT decreased when parasitemia was ≤500 parasites/µl, it showed 96.8% sensitivity (98.4% for P. falciparum and 93.8% for non-P. falciparum) in blood samples with parasitemia ≥100 parasites/µl. The specificity of the RDT was 97.3% for P. falciparum and 97.3% for non-P. falciparum. These results collectively suggest that the accuracy of the Asan EasyTest™ Malaria Pf/Pan Ag makes it an effective point-of-care diagnostic tool for malaria in Uganda. PMID:25352698

  17. Use of Rapid, Point-of-Care Assays by Private Practitioners in Chennai, India: Priorities for Tuberculosis Diagnostic Testing

    PubMed Central

    Ananthakrishnan, Ramya; Sukumar, Sumanya; Augustine, Sheela; Krishnan, Nalini; Pai, Madhukar; Dowdy, David W.

    2016-01-01

    Setting Private practitioners are frequently the first point of healthcare contact for patients with tuberculosis (TB) in India. As new molecular tests are developed for point-of-care (POC) diagnosis of TB, it is imperative to understand these individuals’ practices and preferences for POC testing. Objective To evaluate rapid testing practices and identify priorities for novel POC TB tests among private practitioners in Chennai. Design We conducted a cross-sectional survey of 228 practitioners practicing in the private sector from January 2014 to February 2015 who saw at least one TB patient in the previous year. Practitioners were randomly selected from both the general community and a list of practitioners who referred patients to a public-private mix program for TB treatment. We used standardized questionnaires to collect data on current practices related to point-of-care diagnosis and interest in hypothetical POC tests. We used multivariable Poisson regression with robust estimates of standard error to calculate measures of association. Results Among 228 private practitioners, about half (48%) utilized any rapid testing in their current practice, most commonly for glucose (43%), pregnancy (21%), and malaria (5%). Providers using POC tests were more likely to work in hospitals (56% vs. 43%, P = 0.05) and less likely to be chest specialists (21% vs. 54%, P<0.001). Only half (51%) of providers would use a hypothetical POC test for TB that was accurate, equipment-free, and took 20 minutes to complete. Chest specialists were half as likely to express interest in performing the hypothetical POC TB test in-house as other practitioners (aPR 0.5, 95%CI: 0.2–0.9). Key challenges to performing POC testing for TB in this study included time constraints, easy access to local private labs and lack of an attached lab facility. Conclusion As novel POC tests for TB are developed and scaled up, attention must be paid to integrating these diagnostics into healthcare

  18. Field evaluation of a rapid diagnostic test to detect antibodies in human toxocariasis.

    PubMed

    Lim, P K C; Yamasaki, H; Mak, J W; Wong, S F; Chong, C W; Yap, I K S; Ambu, S; Kumarasamy, V

    2015-08-01

    Human toxocariasis which is caused mainly by the larvae of Toxocara canis and Toxocara cati, is a worldwide zoonotic disease that can be a potentially serious human infection. The enzyme-linked immunosorbent assay (ELISA) using T. canis excretory-secretory (TES) antigens harvested from T. canis larvae is currently the serological test for confirming toxocariasis. An alternative to producing large amounts of Toxocara TES and improved diagnosis for toxocariasis is through the development of highly specific recombinant antigens such as the T. canis second stage larva excretory-secretory 30 kDa protein (recTES-30). The aim of this study was to evaluate the sensitivity and specificity of a rapid diagnostic kit (RDT, named as iToxocara kit) in comparison to recTES-30 ELISA in Serendah Orang Asli village in Selangor, Malaysia. A total of 133 subjects were included in the study. The overall prevalence rates by ELISA and RDT were 29.3% and 33.1%, respectively, with more positive cases detected in males than females. However, no association was found between toxocariasis and gender or age. The percentage sensitivity, specificity, positive predictive value and negative predictive value of RDT were 85.7%, 90.1%, 80% and 93.2%, respectively. The prevalence for toxocariasis in this population using both ELISA and RDT was 27.1% (36/133) and the K-concordance test suggested good agreement of the two tests with a Cohen's kappa of 0.722, P<0.01. In addition, the followed-up Spearman rank correlation showed a moderately high correlation at R=0.704 and P<0.01. In conclusion, the RDT kit was faster and easier to use than an ELISA and is useful for the laboratory diagnosis of hospitalized cases of toxocariasis. PMID:25910623

  19. Rapid, culture-independent, optical diagnostics of centrifugally captured bacteria from urine samples

    PubMed Central

    Schröder, Ulrich-Christian; Bokeloh, Frank; O'Sullivan, Mary; Glaser, Uwe; Wolf, Katharina; Pfister, Wolfgang; Popp, Jürgen; Ducrée, Jens; Neugebauer, Ute

    2015-01-01

    This work presents a polymeric centrifugal microfluidic platform for the rapid and sensitive identification of bacteria directly from urine, thus eliminating time-consuming cultivation steps. This “Lab-on-a-Disc” platform utilizes the rotationally induced centrifugal field to efficiently capture bacteria directly from suspension within a glass-polymer hybrid chip. Once trapped in an array of small V-shaped structures, the bacteria are readily available for spectroscopic characterization, such as Raman spectroscopic fingerprinting, providing valuable information on the characteristics of the captured bacteria. Utilising fluorescence microscopy, quantification of the bacterial load has been achieved for concentrations above 2 × 10−7 cells ml−1 within a 4 μl sample. As a pilot application, we characterize urine samples from patients with urinary tract infections. Following minimal sample preparation, Raman spectra of the bacteria are recorded following centrifugal capture in stopped-flow sedimentation mode. Utilizing advanced analysis algorithms, including extended multiplicative scattering correction, high-quality Raman spectra of different pathogens, such as Escherichia coli or Enterococcus faecalis, are obtained from the analyzed patient samples. The whole procedure, including sample preparation, requires about 1 h to obtain a valuable result, marking a significant reduction in diagnosis time when compared to the 24 h and more typically required for standard microbiological methods. As this cost-efficient centrifugal cartridge can be operated using low-complexity, widely automated instrumentation, while providing valuable bacterial identification in urine samples in a greatly reduced time-period, our opto-microfluidic Lab-on-a-Disc device demonstrates great potential for next-generation patient diagnostics at the of point-of-care. PMID:26339318

  20. Development of an antigen-based rapid diagnostic test for the identification of blowfly (Calliphoridae) species of forensic significance.

    PubMed

    McDonagh, Laura; Thornton, Chris; Wallman, James F; Stevens, Jamie R

    2009-06-01

    In this study we examine the limitations of currently used sequence-based approaches to blowfly (Calliphoridae) identification and evaluate the utility of an immunological approach to discriminate between blowfly species of forensic importance. By investigating antigenic similarity and dissimilarity between the first instar larval stages of four forensically important blowfly species, we have been able to identify immunoreactive proteins of potential use in the development of species-specific immuno-diagnostic tests. Here we outline our protein-based approach to species determination, and describe how it may be adapted to develop rapid diagnostic assays for the 'on-site' identification of blowfly species. PMID:19414163

  1. A new automatic blood pressure kit auscultates for accurate reading with a smartphone: A diagnostic accuracy study.

    PubMed

    Wu, Hongjun; Wang, Bingjian; Zhu, Xinpu; Chu, Guang; Zhang, Zhi

    2016-08-01

    The widely used oscillometric automated blood pressure (BP) monitor was continuously questioned on its accuracy. A novel BP kit named Accutension which adopted Korotkoff auscultation method was then devised. Accutension worked with a miniature microphone, a pressure sensor, and a smartphone. The BP values were automatically displayed on the smartphone screen through the installed App. Data recorded in the phone could be played back and reconfirmed after measurement. They could also be uploaded and saved to the iCloud. The accuracy and consistency of this novel electronic auscultatory sphygmomanometer was preliminarily verified here. Thirty-two subjects were included and 82 qualified readings were obtained. The mean differences ± SD for systolic and diastolic BP readings between Accutension and mercury sphygmomanometer were 0.87 ± 2.86 and -0.94 ± 2.93 mm Hg. Agreements between Accutension and mercury sphygmomanometer were highly significant for systolic (ICC = 0.993, 95% confidence interval (CI): 0.989-0.995) and diastolic (ICC = 0.987, 95% CI: 0.979-0.991). In conclusion, Accutension worked accurately based on our pilot study data. The difference was acceptable. ICC and Bland-Altman plot charts showed good agreements with manual measurements. Systolic readings of Accutension were slightly higher than those of manual measurement, while diastolic readings were slightly lower. One possible reason was that Accutension captured the first and the last korotkoff sound more sensitively than human ear during manual measurement and avoided sound missing, so that it might be more accurate than traditional mercury sphygmomanometer. By documenting and analyzing of variant tendency of BP values, Accutension helps management of hypertension and therefore contributes to the mobile heath service. PMID:27512876

  2. A rapid and precise diagnostic method for detecting the Pinewood nematode Bursaphelenchus xylophilus by loop-mediated isothermal amplification.

    PubMed

    Kikuchi, Taisei; Aikawa, Takuya; Oeda, Yuka; Karim, Nurul; Kanzaki, Natsumi

    2009-12-01

    ABSTRACT Bursaphelenchus xylophilus is the causal agent of pine wilt disease, which is a major forest disease in Japan, Korea, China, Taiwan, and Portugal. A diagnostic method which is rapid, precise, and simple could greatly help the proper management of this disease. Here, we present a novel detection method using loop-mediated isothermal amplification (LAMP) targeting the internal transcribed spacer region of ribosomal DNA of the nematode. Specificity of the primers and LAMP was confirmed using DNA from various nematode species related to B. xylophilus. Our experimental results suggest that LAMP can detect B. xylophilus faster and with higher sensitivity than the traditional diagnostic method. Moreover, because it does not require expensive equipment or specialized techniques, this LAMP-based diagnostic method has the potential to be used under field conditions. PMID:19900002

  3. Immediate-early gene transcriptional activation in hippocampus CA1 and CA3 does not accurately reflect rapid, pattern completion-based retrieval of context memory

    PubMed Central

    Pevzner, Aleksandr

    2015-01-01

    No studies to date have examined whether immediate-early gene (IEG) activation is driven by context memory recall. To address this question, we utilized the context preexposure facilitation effect (CPFE) paradigm. In CPFE, animals acquire contextual fear conditioning through hippocampus-dependent rapid retrieval of a previously formed contextual representation. Despite differences in behavior, we did not find any difference in CA1 or CA3 IEG activity associated with this rapid recall phase when comparing context preexposed and non-pre-exposed groups. These findings indicate that IEG activation in CA1 and CA3 is not an accurate readout of the neural activity associated with hippocampus-dependent rapid memory retrieval. PMID:25512571

  4. Field evaluation of a rapid diagnostic test (Parascreen™) for malaria diagnosis in the Peruvian Amazon

    PubMed Central

    2010-01-01

    Background The rapid diagnostic tests for malaria (RDT) constitute a fast and opportune alternative for non-complicated malaria diagnosis in areas where microscopy is not available. The objective of this study was to validate a RDT named Parascreen™ under field conditions in Iquitos, department of Loreto, Peru. Parascreen™ is a RDT that detects the histidine-rich protein 2 (HRP2) antigen from Plasmodium falciparum and lactate deshydrogenase from all Plasmodium species. Methods Parascreen™ was compared with microscopy performed by experts (EM) and polymerase chain reaction (PCR) using the following indicators: sensitivity (Se), specificity (Sp), positive (PV+) and negative predictive values (PV-), positive (LR+) and negative likehood ratio (LR-). Results 332 patients with suspected non-complicated malaria who attended to the MOH health centres were enrolled between October and December 2006. For P. falciparum malaria, Parascreen™ in comparison with EM, had Se: 53.5%, Sp: 98.7%, PV+: 66.7%, PV-: 97.8%, LR+: 42.27 and LR-: 0.47; and for non-P. falciparum malaria, Se: 77.1%, Sp: 97.6%, PV+: 91.4%, PV-: 92.7%, LR+: 32.0 and LR-: 0.22. The comparison of Parascreen™ with PCR showed, for P. falciparum malaria, Se: 81.8%, Sp: 99.1%, PV+: 75%, PV-: 99.4, LR+: 87.27 and LR-: 0.18; and for non-P. falciparum malaria Se: 76.1%, Sp: 99.2%, PV+: 97.1%, PV-: 92.0%, LR+: 92.51 and LR-: 0.24. Conclusions The study results indicate that Parascreen™ is not a valid and acceptable test for malaria diagnosis under the field conditions found in the Peruvian Amazon. The relative proportion of Plasmodium species, in addition to the genetic characteristics of the parasites in the area, must be considered before applying any RDT, especially after the finding of P. falciparum malaria parasites lacking pfhrp2 gene in this region. PMID:20529273

  5. Comparative feasibility of implementing rapid diagnostic test and microscopy for parasitological diagnosis of malaria in Uganda

    PubMed Central

    2011-01-01

    Background In Uganda, parasite-based diagnosis is recommended for every patient suspected to have malaria before prescribing anti-malarials. However, the majority of patients are still treated presumptively especially in low-level health units. The feasibility of implementing parasite-based diagnosis for uncomplicated malaria in rural health centres (HCs) was investigated with a view to recommending measures for scaling up the policy. Methods Thirty HCs were randomized to implement parasite-based diagnosis based on rapid diagnostic tests [RDTs] (n = 10), blood microscopy (n = 10) and presumptive diagnosis (control arm) (n = 10). Feasibility was assessed by comparing the proportion of patients who received parasite-based diagnosis; with a positive malaria parasite-based diagnosis who received artemether-lumefantrine (AL); with a negative malaria parasite-based diagnosis who received AL; and patient waiting time. Clinicaltrials.gov: NCT00565071. Results 102, 087 outpatients were enrolled. Patients were more likely to be tested in the RDT 44, 565 (96.6%) than in microscopy arm 19, 545 (60.9%) [RR: 1.59]. RDTs reduced patient waiting time compared to microscopy and were more convenient to health workers and patients. Majority 23, 804 (99.7%) in presumptive arm were prescribed AL. All (100%) of patients who tested positive for malaria in RDT and microscopy arms were prescribed anti-malarials. Parasitological-based diagnosis significantly reduced AL prescription in RDT arm [RR: 0.62] and microscopy arm [RR: 0.72] compared to presumptive treatment. Among patients not tested in the two intervention arms, 12, 044 (96.1%) in microscopy and 965 (61.6%) in RDT arm were treated with AL [RR: 1.56]. Overall 10, 558 (29.4%) with negative results [5, 110 (23.4%) in RDT and 5, 448 (39.0%) in microscopy arms] were prescribed AL. Conclusion It was more feasible to implement parasite-based diagnosis for malaria using RDT than with microscopy. A high proportion of patients with negative

  6. Assessment of desiccants and their instructions for use in rapid diagnostic tests

    PubMed Central

    2012-01-01

    Background Malaria rapid diagnostic tests (RDTs) are protected from humidity-caused degradation by a desiccant added to the device packaging. The present study assessed malaria RDT products for the availability, type and design of desiccants and their information supplied in the instructions for use (IFU). Methods Criteria were based on recommendations of the World Health Organization (WHO), the European Community (CE) and own observations. Silica gel sachets were defined as self-indicating (all beads coated with a humidity indicator that changes colour upon saturation), partial-indicating (part of beads coated) and non-indicating (none of the beads coated). Indicating silica gel sachets were individually assessed for humidity saturation and (in case of partial-indicating silica gels) for the presence of indicating beads. Results Fifty malaria RDT products from 25 manufacturers were assessed, 14 (28%) products were listed by the “Global Fund Quality Assurance Policy” and 31 (62%) were CE-marked. All but one product contained a desiccant, mostly (47/50, 94%) silica gel. Twenty (40%) RDT products (one with no desiccant and 19 with non-indicating desiccant) did not meet the WHO guidelines recommending indicating desiccant. All RDT products with self- or partial-indicating silica gel (n = 22 and 8 respectively) contained the toxic cobalt dichloride as humidity indicator. Colour change indicating humidity saturation was observed for 8/16 RDT products, at a median incidence of 0.8% (range 0.05%-4.6%) of sachets inspected. In all RDTs with partial-indicating silica gel, sachets with no colour indicating beads were found (median proportion 13.5% (0.6% - 17.8%) per product) and additional light was needed to assess the humidity colour. Less than half (14/30, 47%) IFUs of RDT products with indicating desiccants mentioned to check the humidity saturation before using the test. Information on properties, safety hazards and disposal of the desiccant was not included in

  7. Community acceptability of use of rapid diagnostic tests for malaria by community health workers in Uganda

    PubMed Central

    2010-01-01

    Background Many malarious countries plan to introduce artemisinin combination therapy (ACT) at community level using community health workers (CHWs) for treatment of uncomplicated malaria. Use of ACT with reliance on presumptive diagnosis may lead to excessive use, increased costs and rise of drug resistance. Use of rapid diagnostic tests (RDTs) could address these challenges but only if the communities will accept their use by CHWs. This study assessed community acceptability of the use of RDTs by Ugandan CHWs, locally referred to as community medicine distributors (CMDs). Methods The study was conducted in Iganga district using 10 focus group discussions (FGDs) with CMDs and caregivers of children under five years, and 10 key informant interviews (KIIs) with health workers and community leaders. Pre-designed FGD and KII guides were used to collect data. Manifest content analysis was used to explore issues of trust and confidence in CMDs, stigma associated with drawing blood from children, community willingness for CMDs to use RDTs, and challenges anticipated to be faced by the CMDs. Results CMDs are trusted by their communities because of their commitment to voluntary service, access, and the perceived effectiveness of anti-malarial drugs they provide. Some community members expressed fear that the blood collected could be used for HIV testing, the procedure could infect children with HIV, and the blood samples could be used for witchcraft. Education level of CMDs is important in their acceptability by the community, who welcome the use of RDTs given that the CMDs are trained and supported. Anticipated challenges for CMDs included transport for patient follow-up and picking supplies, adults demanding to be tested, and caregivers insisting their children be treated instead of being referred. Conclusion Use of RDTs by CMDs is likely to be acceptable by community members given that CMDs are properly trained, and receive regular technical supervision and logistical

  8. REEVALUATION OF MALARIA PARASITES IN EL-FAYOUM GOVERNORATE, EGYPT USING RAPID DIAGNOSTIC TESTS (RDTS).

    PubMed

    Dahesh, Salwa M A; Mostafa, Heba I

    2015-12-01

    Malaria as a disease has been identified in Egypt since ancient times. Malaria was endemic in almost all parts of the country but prevalence showed a steady decrease by 1990, and regressed in most of the Governorates. Then by the end of 1998 till now Egypt become free from local transmission of malaria. All reported cases were imported mainly from Sudan. However, the outbreak of falciparum (1 case) and vivax (23 cases) that occurred (May 2014) in Aswan Governorate strongly indicated that malaria is reemerging in the country. El-Fayoum should be take special attention, rather than being the last residual focus. The efficient malaria vector A. sergenti, the proven vector A. pharoensis and the suspected vector A. multicolor were encountered. This work reevaluated malaria status by using RDTs in survey and Giemsa stained thick films to confirm positive cases and estimation of parasite rate, formula, densities and species, also to study the ecological and entomological efficacy factors. The result showed that out of 2044 examined persons, 14 (0.68%) were passive cases, i.e., attending themselves to El-Fayoum Malaria Units after their return from Sudan. Microscopic examination of their stained thick films obtained from MOH&P shows that 9 (64.2%) out of passive cases were positive 3 of them are P. falciparum (33.3%) and the rest P. vivax 6 (66.7%) The species formulas of P. falciparum and P. vivax were 33.3% and 66.7% respectively. Concerning the density class, only one vivax case was of low density class while the other cases were of high density class. All positive cases were males, imported from Sudan and most of them were merchants having trade activities in Sudan. All examined persons during active case detection ACD (1551) and neighborhood of detected cases NOD (479) were malaria negative by rapid diagnostic tests. The areas recording the highest number of imported cases were Abu Shanap, Aboxa (Ballona) and Kafr Aboud (Abshaway Center) but no Anopheline spp larvae

  9. Swift Gamma-Ray Burst Explorer: Mission Design for Rapid, Accurate Location of Gamma-ray Bursts

    NASA Technical Reports Server (NTRS)

    Bundas, David J.

    2004-01-01

    The Swift Gamma-ray Burst Explorer is a NASA Mid-sized Explorer (MIDEX) with the primary mission of determining the origins of Gamma-Ray Bursts (GRBs). It will be the first mission to autonomously respond to newly-discovered GRBs and provide immediate follow-up narrow field instruments capable of multi-wavelength (UV, Optical, X-ray) observations. The characteristics of GRBs that are the key mission design drivers, are their non-repeating and brief duration bursts of multi-wavelength photons. In addition, rapid notification of the location and characteristics of the GRBs to ground-and-space- based observatories drive the end-to-end data analysis and distribution requirements. The Swift mission is managed by the GSFC, and includes an international team of contributors that each bring their unique perspective that have proven invaluable to the mission. The spacecraft bus, provided by Spectrum Astro, Inc. was procured through a Rapid Spacecraft Development Office (RSDO) contract by the GSFC. There are three instruments: the Burst Alert Telescope (BAT) provided by the GSFC; the X-Ray Telescope (XRT) provided by a team led by the Pennsylvania State University (PSU); and the Ultra-Violet Optical Telescope (UVOT), again managed by PSU. The Mission Operations Center (MOC) was developed by and is located at PSU. Science archiving and data analysis centers are located at the GSFC, in the UK and in Italy.

  10. Rapid and accurate determination of total lung capacity (TLC) from routine chest radiograms using a programmable hand-held calculator.

    PubMed

    Rodgers, R P; Tannen, R

    1983-01-01

    Since its appearance in 1960, the method of Barnhard and associates for the determination of total lung capacity (TLC) from routine chest radiograms has been widely studied in normal and diseased subjects. The method appears to be as accurate as the current definitive procedure, total body plethysmography. The method is in routine use in major medical institutions where the procedure has been automated, but the method does not seem to have gained the wide use it deserves. This is likely due to the tedium of the technique when performed manually--a single determination can require 30 min. We present here an implementation of the Barnhard method for the HP41-C hand-held programmable calculator. In conjunction with the use of a transparent reticle used for obtaining the required measurements, the program allows a single measurement to be made in under 12 minutes. We hope this technique will make radiographic TLC measurements more broadly accessible to the medical profession. PMID:6872526

  11. Applications of a Rapid and Sensitive Dengue DUO Rapid Immunochromatographic Test Kit as a Diagnostic Strategy during a Dengue Type 2 Epidemic in an Urban City

    PubMed Central

    Shih, Hsin-I; Hsu, Hsiang-Chin; Wu, Chi-Jung; Lin, Chih-Hao; Chang, Chia-Ming; Tu, Yi-Fang; Hsieh, Chih-Chia; Chi, Chih-Hsien; Sung, Tzu-Ching

    2016-01-01

    Dengue infection is a major health problem in tropical and subtropical countries. A prospective observational study in a university-affiliated hospital was conducted between August 2015 and September 2015. Patients who visited the emergency department (ED) with a presentation of any symptoms of dengue were eligible for the dengue non-structural protein 1 (NS1), IgM/IgG rapid immunochromatographic tests and real-time polymerase chain reaction (RT-PCR) to evaluate the performance of the rapid tests. Considering the RT-PCR as the gold standard for the dengue diagnosis, the ideal primary results of sensitivity (80–100%), specificity (60–84%), positive predicted value(75%-95%), and negative predicted value (70–100%) suggested that the NS1-based test with or without a combination of IgM and IgG tests have good diagnostic performances in detecting dengue infections, even in the afebrile or elderly populations. PMID:27415767

  12. Applications of a Rapid and Sensitive Dengue DUO Rapid Immunochromatographic Test Kit as a Diagnostic Strategy during a Dengue Type 2 Epidemic in an Urban City.

    PubMed

    Shih, Hsin-I; Hsu, Hsiang-Chin; Wu, Chi-Jung; Lin, Chih-Hao; Chang, Chia-Ming; Tu, Yi-Fang; Hsieh, Chih-Chia; Chi, Chih-Hsien; Sung, Tzu-Ching

    2016-01-01

    Dengue infection is a major health problem in tropical and subtropical countries. A prospective observational study in a university-affiliated hospital was conducted between August 2015 and September 2015. Patients who visited the emergency department (ED) with a presentation of any symptoms of dengue were eligible for the dengue non-structural protein 1 (NS1), IgM/IgG rapid immunochromatographic tests and real-time polymerase chain reaction (RT-PCR) to evaluate the performance of the rapid tests. Considering the RT-PCR as the gold standard for the dengue diagnosis, the ideal primary results of sensitivity (80-100%), specificity (60-84%), positive predicted value(75%-95%), and negative predicted value (70-100%) suggested that the NS1-based test with or without a combination of IgM and IgG tests have good diagnostic performances in detecting dengue infections, even in the afebrile or elderly populations. PMID:27415767

  13. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects.

    PubMed

    Zumla, Alimuddin; Al-Tawfiq, Jaffar A; Enne, Virve I; Kidd, Mike; Drosten, Christian; Breuer, Judy; Muller, Marcel A; Hui, David; Maeurer, Markus; Bates, Matthew; Mwaba, Peter; Al-Hakeem, Rafaat; Gray, Gregory; Gautret, Philippe; Al-Rabeeah, Abdullah A; Memish, Ziad A; Gant, Vanya

    2014-11-01

    Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics. PMID:25189349

  14. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

    PubMed Central

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  15. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry.

    PubMed

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  16. Swift Gamma-ray Burst Explorer: Mission Design for Rapid, Accurate Location of Gamma-ray Bursts

    NASA Technical Reports Server (NTRS)

    Bundas, David J.

    2005-01-01

    The Swift Gamma-ray Burst Explorer is a NASA Mid-sized Explorer (MIDEX) with the primary mission of determining the origins of Gamma-Ray Bursts (GRBs). It will be the first mission to autonomously respond to newly-discovered GRBs and provide immediate follow-up with narrow field instruments capable of multi-wavelength (UT, Optical, X-ray) observations. The characteristics of GRBs that are the key mission design drivers, are their non-repeating and brief duration bursts of multi-wavelength photons. In addition, rapid notification of the location and characteristics of the GRBs to ground-and-space-based observatories drive the end-to-end data analysis and distribution requirements.

  17. Swift Gamma-Ray Burst Explorer: Mission Design for Rapid, Accurate Location of Gamma-ray Bursts

    NASA Technical Reports Server (NTRS)

    Bundas, David J.

    2004-01-01

    The Swift Gamma-ray Burst Explorer is a NASA Mid-sized Explorer (MIDEX) with the primary mission of determining the origins of Gamma-Ray Bursts (GRBs). It will be the first mission to autonomously respond to newly-discovered GRBs and provide immediate follow-up with narrow field instruments capable of multi-wavelength (UV, Optical, X-ray) observations. The characteristics of GRBs that are the key mission design drivers, are their non-repeating and brief duration bursts of multi-wavelength photons. In addition, rapid notification of the location and characteristics of the GRBs to ground-and-space-based observatories drive the end-to-end data analysis and distribution requirements.

  18. Comparison of the diagnostic accuracy of a rapid immunochromatographic test and the rapid plasma reagin test for antenatal syphilis screening in Mozambique.

    PubMed Central

    Montoya, Pablo J.; Lukehart, Sheila A.; Brentlinger, Paula E.; Blanco, Ana J.; Floriano, Florencia; Sairosse, Josefa; Gloyd, Stephen

    2006-01-01

    OBJECTIVE: Programmes to control syphilis in developing countries are hampered by a lack of laboratory services, delayed diagnosis, and doubts about current screening methods. We aimed to compare the diagnostic accuracy of an immunochromatographic strip (ICS) test and the rapid plasma reagin (RPR) test with the combined gold standard (RPR, Treponema pallidum haemagglutination assay and direct immunofluorescence stain done at a reference laboratory) for the detection of syphilis in pregnancy. METHODS: We included test results from 4789 women attending their first antenatal visit at one of six health facilities in Sofala Province, central Mozambique. We compared diagnostic accuracy (sensitivity, specificity, and positive and negative predictive values) of ICS and RPR done at the health facilities and ICS performed at the reference laboratory. We also made subgroup comparisons by human immunodeficiency virus (HIV) and malaria status. FINDINGS: For active syphilis, the sensitivity of the ICS was 95.3% at the reference laboratory, and 84.1% at the health facility. The sensitivity of the RPR at the health facility was 70.7%. Specificity and positive and negative predictive values showed a similar pattern. The ICS outperformed RPR in all comparisons (P<0.001). CONCLUSION: The diagnostic accuracy of the ICS compared favourably with that of the gold standard. The use of the ICS in Mozambique and similar settings may improve the diagnosis of syphilis in health facilities, both with and without laboratories. PMID:16501726

  19. ID Learning Unit—Diagnostics Update: Current Laboratory Methods for Rapid Pathogen Identification in Patients With Bloodstream Infections

    PubMed Central

    Rubach, Matthew P.; Hanson, Kimberly E.

    2015-01-01

    Diagnostic assays that rapidly identify bloodstream pathogens have the potential to improve patient outcomes and antibiotic stewardship efforts. Current tests are based on the detection of nucleic acids that are specific to a targeted pathogen or based on organism identification using mass spectrometry. Most rapid assays require a positive blood culture as their sample input and expedite pathogen identification by 24–72 hours. For those assays that also report detection of drug resistance markers, information on antimicrobial resistance is expedited by 48–96 hours. This learning unit reviews the basic principles of rapid microorganism identification assays for bloodstream infections with the aim of assisting clinicians in the interpretation and optimal utilization of test results. PMID:26719845

  20. ID Learning Unit-Diagnostics Update: Current Laboratory Methods for Rapid Pathogen Identification in Patients With Bloodstream Infections.

    PubMed

    Rubach, Matthew P; Hanson, Kimberly E

    2015-12-01

    Diagnostic assays that rapidly identify bloodstream pathogens have the potential to improve patient outcomes and antibiotic stewardship efforts. Current tests are based on the detection of nucleic acids that are specific to a targeted pathogen or based on organism identification using mass spectrometry. Most rapid assays require a positive blood culture as their sample input and expedite pathogen identification by 24-72 hours. For those assays that also report detection of drug resistance markers, information on antimicrobial resistance is expedited by 48-96 hours. This learning unit reviews the basic principles of rapid microorganism identification assays for bloodstream infections with the aim of assisting clinicians in the interpretation and optimal utilization of test results. PMID:26719845

  1. FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes.

    PubMed

    Kirchmair, Johannes; Williamson, Mark J; Afzal, Avid M; Tyzack, Jonathan D; Choy, Alison P K; Howlett, Andrew; Rydberg, Patrik; Glen, Robert C

    2013-11-25

    FAst MEtabolizer (FAME) is a fast and accurate predictor of sites of metabolism (SoMs). It is based on a collection of random forest models trained on diverse chemical data sets of more than 20 000 molecules annotated with their experimentally determined SoMs. Using a comprehensive set of available data, FAME aims to assess metabolic processes from a holistic point of view. It is not limited to a specific enzyme family or species. Besides a global model, dedicated models are available for human, rat, and dog metabolism; specific prediction of phase I and II metabolism is also supported. FAME is able to identify at least one known SoM among the top-1, top-2, and top-3 highest ranked atom positions in up to 71%, 81%, and 87% of all cases tested, respectively. These prediction rates are comparable to or better than SoM predictors focused on specific enzyme families (such as cytochrome P450s), despite the fact that FAME uses only seven chemical descriptors. FAME covers a very broad chemical space, which together with its inter- and extrapolation power makes it applicable to a wide range of chemicals. Predictions take less than 2.5 s per molecule in batch mode on an Ultrabook. Results are visualized using Jmol, with the most likely SoMs highlighted. PMID:24219364

  2. Rapid Leptospira identification by direct sequencing of the diagnostic PCR products in New Caledonia

    PubMed Central

    2010-01-01

    Background Most of the current knowledge of leptospirosis epidemiology originates from serological results obtained with the reference Microscopic Agglutination Test (MAT). However, inconsistencies and weaknesses of this diagnostic technique are evident. A growing use of PCR has improved the early diagnosis of leptospirosis but a drawback is that it cannot provide information on the infecting Leptospira strain which provides important epidemiologic data. Our work is aimed at evaluating if the sequence polymorphism of diagnostic PCR products could be used to identify the infecting Leptospira strains in the New Caledonian environment. Results Both the lfb1 and secY diagnostic PCR products displayed a sequence polymorphism that could prove useful in presumptively identifying the infecting leptospire. Using both this polymorphism and MLST results with New Caledonian isolates and clinical samples, we confirmed the epidemiological relevance of the sequence-based identification of Leptospira strains. Additionally, we identified one cluster of L. interrogans that contained no reference strain and one cluster of L. borgpetersenii found only in the introduced Rusa deer Cervus timorensis russa that is its probable reservoir. Conclusions The sequence polymorphism of diagnostic PCR products proved useful in presumptively identifying the infecting Leptospira strains. This could contribute to a better understanding of leptospirosis epidemiology by providing epidemiological information that cannot be directly attained from the use of PCR as an early diagnostic test for leptospirosis. PMID:21176235

  3. Should countries implementing an artemisinin-based combination malaria treatment policy also introduce rapid diagnostic tests?

    PubMed Central

    Zikusooka, Charlotte M; McIntyre, Diane; Barnes, Karen I

    2008-01-01

    Background Within the context of increasing antimalarial costs and or decreasing malaria transmission, the importance of limiting antimalarial treatment to only those confirmed as having malaria parasites becomes paramount. This motivates for this assessment of the cost-effectiveness of routine use of rapid diagnostic tests (RDTs) as an integral part of deploying artemisinin-based combination therapies (ACTs). Methods The costs and cost-effectiveness of using RDTs to limit the use of ACTs to those who actually have Plasmodium falciparum parasitaemia in two districts in southern Mozambique were assessed. To evaluate the potential impact of introducing definitive diagnosis using RDTs (costing $0.95), five scenarios were considered, assuming that the use of definitive diagnosis would find that between 25% and 75% of the clinically diagnosed malaria patients are confirmed to be parasitaemic. The base analysis compared two ACTs, artesunate plus sulfadoxine/pyrimethamine (AS+SP) costing $1.77 per adult treatment and artemether-lumefantrine (AL) costing $2.40 per adult treatment, as well as the option of restricting RDT use to only those older than six years. Sensitivity analyses considered lower cost ACTs and RDTs and different population age distributions. Results Compared to treating patients on the basis of clinical diagnosis, the use of RDTs in all clinically diagnosed malaria cases results in cost savings only when 29% and 52% or less of all suspected malaria cases test positive for malaria and are treated with AS+SP and AL, respectively. These cut-off points increase to 41.5% (for AS+SP) and to 74% (for AL) when the use of RDTs is restricted to only those older than six years of age. When 25% of clinically diagnosed patients are RDT positive and treated using AL, there are cost savings per malaria positive patient treated of up to $2.12. When more than 29% of clinically diagnosed cases are malaria test positive, the incremental cost per malaria positive patient

  4. Rapid and Accurate Identification by Real-Time PCR of Biotoxin-Producing Dinoflagellates from the Family Gymnodiniaceae

    PubMed Central

    Smith, Kirsty F.; de Salas, Miguel; Adamson, Janet; Rhodes, Lesley L.

    2014-01-01

    The identification of toxin-producing dinoflagellates for monitoring programmes and bio-compound discovery requires considerable taxonomic expertise. It can also be difficult to morphologically differentiate toxic and non-toxic species or strains. Various molecular methods have been used for dinoflagellate identification and detection, and this study describes the development of eight real-time polymerase chain reaction (PCR) assays targeting the large subunit ribosomal RNA (LSU rRNA) gene of species from the genera Gymnodinium, Karenia, Karlodinium, and Takayama. Assays proved to be highly specific and sensitive, and the assay for G. catenatum was further developed for quantification in response to a bloom in Manukau Harbour, New Zealand. The assay estimated cell densities from environmental samples as low as 0.07 cells per PCR reaction, which equated to three cells per litre. This assay not only enabled conclusive species identification but also detected the presence of cells below the limit of detection for light microscopy. This study demonstrates the usefulness of real-time PCR as a sensitive and rapid molecular technique for the detection and quantification of micro-algae from environmental samples. PMID:24608972

  5. Genotyping of Trypanosoma cruzi: Systematic Selection of Assays Allowing Rapid and Accurate Discrimination of All Known Lineages

    PubMed Central

    Lewis, Michael D.; Ma, Jonathan; Yeo, Matthew; Carrasco, Hernán J.; Llewellyn, Martin S.; Miles, Michael A.

    2010-01-01

    Trypanosoma cruzi, the agent of Chagas disease, can be subdivided into six discrete typing units (DTUs), TcI, TcIIa, TcIIb, TcIIc, TcIId or TcIIe, each having distinct epidemiologically important features. Dozens of genetic markers are available to determine the DTU to which a T. cruzi isolate belongs, but there is no consensus on which should be used. We selected five assays: three polymerase chain reaction (PCR)-restriction fragment length polymorphisms based on single nucleotide polymorphisms (SNPs) in the HSP60, Histone H1, and GPI loci, and PCR product size polymorphism of the LSU rDNA and mini-exon loci. Each assay was tested for its capacity to differentiate between DTUs using a panel of 48 genetically diverse T. cruzi clones. Some markers allowed unequivocal identification of individual DTUs, however, only by using a combination of multiple markers could all six DTUs be resolved. Based upon the results we recommend a triple-assay comprising the LSU rDNA, HSP60 and GPI markers for reliable, rapid, low-cost DTU assignment. PMID:19996435

  6. Three-dimensional digital holographic aperture synthesis for rapid and highly-accurate large-volume metrology

    NASA Astrophysics Data System (ADS)

    Crouch, Stephen; Kaylor, Brant M.; Barber, Zeb W.; Reibel, Randy R.

    2015-09-01

    Currently large volume, high accuracy three-dimensional (3D) metrology is dominated by laser trackers, which typically utilize a laser scanner and cooperative reflector to estimate points on a given surface. The dependency upon the placement of cooperative targets dramatically inhibits the speed at which metrology can be conducted. To increase speed, laser scanners or structured illumination systems can be used directly on the surface of interest. Both approaches are restricted in their axial and lateral resolution at longer stand-off distances due to the diffraction limit of the optics used. Holographic aperture ladar (HAL) and synthetic aperture ladar (SAL) can enhance the lateral resolution of an imaging system by synthesizing much larger apertures by digitally combining measurements from multiple smaller apertures. Both of these approaches only produce two-dimensional imagery and are therefore not suitable for large volume 3D metrology. We combined the SAL and HAL approaches to create a swept frequency digital holographic 3D imaging system that provides rapid measurement speed for surface coverage with unprecedented axial and lateral resolution at longer standoff ranges. The technique yields a "data cube" of Fourier domain data, which can be processed with a 3D Fourier transform to reveal a 3D estimate of the surface. In this paper, we provide the theoretical background for the technique and show experimental results based on an ultra-wideband frequency modulated continuous wave (FMCW) chirped heterodyne ranging system showing ~100 micron lateral and axial precisions at >2 m standoff distances.

  7. Sensitivity and Specificity of a New Vertical Flow Rapid Diagnostic Test for the Serodiagnosis of Human Leptospirosis

    PubMed Central

    Goarant, Cyrille; Bourhy, Pascale; D'Ortenzio, Eric; Dartevelle, Sylvie; Mauron, Carine; Soupé-Gilbert, Marie-Estelle; Bruyère-Ostells, Lilian; Gourinat, Ann-Claire; Picardeau, Mathieu; Nato, Faridabano; Chanteau, Suzanne

    2013-01-01

    Background: Leptospirosis is a growing public health concern in many tropical and subtropical countries. However, its diagnosis is difficult because of non-specific symptoms and concurrent other endemic febrile diseases. In many regions, the laboratory diagnosis is not available due to a lack of preparedness and simple diagnostic assay or difficult access to reference laboratories. Yet, an early antibiotic treatment is decisive to the outcome. The need for Rapid Diagnostic Tests (RDTs) for bedside diagnosis of leptospirosis has been recognized. We developed a vertical flow immunochromatography strip RDT detecting anti-Leptospira human IgM and evaluated it in patients from New Caledonia, France, and French West Indies. Methodology/Principal Findings: Whole killed Leptospira fainei cells were used as antigen for the test line and purified human IgM as the control line. The mobile phase was made of gold particles conjugated with goat anti-human IgM. Standards for Reporting of Diagnostic Accuracy criteria were used to assess the performance of this RDT. The Microscopic Agglutination Test (MAT) was used as the gold standard with a cut-off titer of ≥400. The sensitivity was 89.8% and the specificity 93.7%. Positive and negative Likelihood Ratios of 14.18 and 0.108 respectively, and a Diagnostic Odds Ratio of 130.737 confirmed its usefulness. This RDT had satisfactory reproducibility, repeatability, thermal tolerance and shelf-life. The comparison with MAT evidenced the earliness of the RDT to detect seroconversion. When compared with other RDT, the Vertical Flow RDT developed displayed good diagnostic performances. Conclusions/Significance This RDT might be used as a point of care diagnostic tool in limited resources countries. An evaluation in field conditions and in other epidemiological contexts should be considered to assess its validity over a wider range of serogroups or when facing different endemic pathogens. It might prove useful in endemic contexts or

  8. Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

    PubMed Central

    Kates-Harbeck, Julian; Tilloy, Antoine; Prentiss, Mara

    2016-01-01

    Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites. PMID:23944487

  9. The use of rapid dengue diagnostic tests in a routine clinical setting in a dengue-endemic area of Colombia

    PubMed Central

    Osorio, Lyda; Uribe, Marcela; Ardila, Gloria Ines; Orejuela, Yaneth; Velasco, Margarita; Bonelo, Anilza; Parra, Beatriz

    2015-01-01

    There is insufficient evidence of the usefulness of dengue diagnostic tests under routine conditions. We sought to analyse how physicians are using dengue diagnostics to inform research and development. Subjects attending 14 health institutions in an endemic area of Colombia with either a clinical diagnosis of dengue or for whom a dengue test was ordered were included in the study. Patterns of test-use are described herein. Factors associated with the ordering of dengue diagnostic tests were identified using contingency tables, nonparametric tests and logistic regression. A total of 778 subjects were diagnosed with dengue by the treating physician, of whom 386 (49.5%) were tested for dengue. Another 491 dengue tests were ordered in subjects whose primary diagnosis was not dengue. Severe dengue classification [odds ratio (OR) 2.2; 95% confidence interval (CI) 1.1-4.5], emergency consultation (OR 1.9; 95% CI 1.4-2.5) and month of the year (OR 3.1; 95% CI 1.7-5.5) were independently associated with ordering of dengue tests. Dengue tests were used both to rule in and rule out diagnosis. The latter use is not justified by the sensitivity of current rapid dengue diagnostic tests. Ordering of dengue tests appear to depend on a combination of factors, including physician and institutional preferences, as well as other patient and epidemiological factors. PMID:25993399

  10. Introducing rapid diagnostic tests for malaria to drug shops in Uganda: a cluster-randomized controlled trial

    PubMed Central

    Fink, Günther; Maloney, Kathleen; Berg, Katrina; Jordan, Matthew; Svoronos, Theodore; Aber, Flavia; Dickens, William

    2015-01-01

    Abstract Objective To evaluate the impact – on diagnosis and treatment of malaria – of introducing rapid diagnostic tests to drug shops in eastern Uganda. Methods Overall, 2193 households in 79 study villages with at least one licensed drug shop were enrolled and monitored for 12 months. After 3 months of monitoring, drug shop vendors in 67 villages randomly selected for the intervention were offered training in the use of malaria rapid diagnostic tests and – if trained – offered access to such tests at a subsidized price. The remaining 12 study villages served as controls. A difference-in-differences regression model was used to estimate the impact of the intervention. Findings Vendors from 92 drug shops successfully completed training and 50 actively stocked and performed the rapid tests. Over 9 months, trained vendors did an average of 146 tests per shop. Households reported 22 697 episodes of febrile illness. The availability of rapid tests at local drug shops significantly increased the probability of any febrile illness being tested for malaria by 23.15% (P = 0.015) and being treated with an antimalarial drug by 8.84% (P = 0.056). The probability that artemisinin combination therapy was bought increased by a statistically insignificant 5.48% (P = 0.574). Conclusion In our study area, testing for malaria was increased by training drug shop vendors in the use of rapid tests and providing them access to such tests at a subsidized price. Additional interventions may be needed to achieve a higher coverage of testing and a higher rate of appropriate responses to test results.

  11. Cost-Effectiveness and Validity Assessment of Cyscope Microscope, Quantitative Buffy Coat Microscope, and Rapid Diagnostic Kit for Malaria Diagnosis among Clinic Attendees in Ibadan, Nigeria

    PubMed Central

    Dada-Adegbola, Hannah; Ajayi, Ikeoluwapo O.; Olayinka, Adebola; Oyibo, Wellington A.; Fawole, Olufunmilayo I.

    2016-01-01

    Background. Unavailability of accurate, rapid, reliable, and cost-effective malaria diagnostic instruments constitutes major a challenge to malaria elimination. We validated alternative malaria diagnostic instruments and assessed their comparative cost-effectiveness. Method. Using a cross-sectional study design, 502 patients with malaria symptoms at selected health facilities in Ibadan between January and April 2014 were recruited consecutively. We examined malaria parasites using Cyscope®, QBC, and CareStart™ and results were compared to light microscopy (LM). Validity was determined by assessing sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Costs per hour of use for instruments and turnaround time were determined. Result. Sensitivity of the instruments was 76.0% (CareStart), 95.0% (Cyscope), and 98.1% (QBC). Specificity was 96.0% (CareStart), 87.3% (Cyscope), and 85.5% (QBC). PPV were 65.2%, 67.5%, and 84.7%, while NPV were 93.6%, 98.6%, and 99.4% for CareStart, Cyscope, and QBC with Kappa values of 0.75 (CI = 0.68–0.82) for CareStart, 0.72 (CI = 0.65–0.78) for Cyscope, and 0.71 (CI = 0.64–0.77) for QBC. Average cost per hour of use was the lowest ($2.04) with the Cyscope. Turnaround time was the fastest with Cyscope (5 minutes). Conclusion. Cyscope fluorescent microscope had the shortest turnaround time and is the most cost-effective of all the malaria diagnostic instruments evaluated. PMID:27493827

  12. Cost-Effectiveness and Validity Assessment of Cyscope Microscope, Quantitative Buffy Coat Microscope, and Rapid Diagnostic Kit for Malaria Diagnosis among Clinic Attendees in Ibadan, Nigeria.

    PubMed

    Ogunniyi, Abiodun; Dairo, Magbagbeola David; Dada-Adegbola, Hannah; Ajayi, Ikeoluwapo O; Olayinka, Adebola; Oyibo, Wellington A; Fawole, Olufunmilayo I; Ajumobi, Olufemi

    2016-01-01

    Background. Unavailability of accurate, rapid, reliable, and cost-effective malaria diagnostic instruments constitutes major a challenge to malaria elimination. We validated alternative malaria diagnostic instruments and assessed their comparative cost-effectiveness. Method. Using a cross-sectional study design, 502 patients with malaria symptoms at selected health facilities in Ibadan between January and April 2014 were recruited consecutively. We examined malaria parasites using Cyscope®, QBC, and CareStart™ and results were compared to light microscopy (LM). Validity was determined by assessing sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Costs per hour of use for instruments and turnaround time were determined. Result. Sensitivity of the instruments was 76.0% (CareStart), 95.0% (Cyscope), and 98.1% (QBC). Specificity was 96.0% (CareStart), 87.3% (Cyscope), and 85.5% (QBC). PPV were 65.2%, 67.5%, and 84.7%, while NPV were 93.6%, 98.6%, and 99.4% for CareStart, Cyscope, and QBC with Kappa values of 0.75 (CI = 0.68-0.82) for CareStart, 0.72 (CI = 0.65-0.78) for Cyscope, and 0.71 (CI = 0.64-0.77) for QBC. Average cost per hour of use was the lowest ($2.04) with the Cyscope. Turnaround time was the fastest with Cyscope (5 minutes). Conclusion. Cyscope fluorescent microscope had the shortest turnaround time and is the most cost-effective of all the malaria diagnostic instruments evaluated. PMID:27493827

  13. Recent advances in the use of laser-induced breakdown spectroscopy (LIBS) as a rapid point-of-care pathogen diagnostic

    NASA Astrophysics Data System (ADS)

    Rehse, Steven J.; Miziolek, Andrzej W.

    2012-06-01

    Laser-induced breakdown spectroscopy (LIBS) has made tremendous progress in becoming a viable technology for rapid bacterial pathogen detection and identification. The significant advantages of LIBS include speed (< 1 sec analysis), portability, robustness, lack of consumables, little to no need for sample preparation, lack of genetic amplification, and the ability to identify all bacterial pathogens without bias (including spore-forms and viable but nonculturable specimens). In this manuscript, we present the latest advances achieved in LIBS-based bacterial sensing including the ability to uniquely identify species from more than five bacterial genera with high-sensitivity and specificity. Bacterial identifications are completely unaffected by environment, nutrition media, or state of growth and accurate diagnoses can be made on autoclaved or UV-irradiated specimens. Efficient discrimination of bacteria at the strain level has been demonstrated. A rapid urinary tract infection diagnosis has been simulated with no sample preparation and a one second diagnosis of a pathogen surrogate has been demonstrated using advanced chemometric analysis with a simple "stop-light" user interface. Stand-off bacterial identification at a 20-m distance has been demonstrated on a field-portable instrument. This technology could be implemented in doctors' offices, clinics, or hospital laboratories for point-of-care medical specimen analysis; mounted on military medical robotic platforms for in-the- field diagnostics; or used in stand-off configuration for remote sensing and detection.

  14. Global profiling and rapid matching of natural products using diagnostic product ion network and in silico analogue database: Gastrodia elata as a case study.

    PubMed

    Lai, Chang-Jiang-Sheng; Zha, Liangping; Liu, Da-Hui; Kang, Liping; Ma, Xiaojing; Zhan, Zhi-Lai; Nan, Tie-Gui; Yang, Jian; Li, Fajie; Yuan, Yuan; Huang, Lu-Qi

    2016-07-22

    Rapid discovery of novel compounds of a traditional herbal medicine is of vital significance for pharmaceutical industry and plant metabolic pathway analysis. However, discovery of unknown or trace natural products is an ongoing challenge. This study presents a universal targeted data-independent acquisition and mining strategy to globally profile and effectively match novel natural product analogues from an herbal extract. The famous medical plant Gastrodia elata was selected as an example. This strategy consists of three steps: (i) acquisition of accurate parent and adduct ions (PAIs) and the product ions data of all eluting compounds by untargeted full-scan MS(E) mode; (ii) rapid compound screening using diagnostic product ions (DPIs) network and in silico analogue database with SUMPRODUCT function to find novel candidates; and (iii) identification and isomerism discrimination of multiple types of compounds using ClogP and ions fragment behavior analyses. Using above data mining methods, a total of 152 compounds were characterized, and 70 were discovered for the first time, including series of phospholipids and novel gastroxyl derivatives. Furthermore, a number of gastronucleosides and phase II metabolites of gastrodin and parishins were discovered, including glutathionylated, cysteinylglycinated and cysteinated compounds, and phosphatidylserine analogues. This study extended the application of classical DPIs filter strategy and developed a structure-based screening approach with the potential for significant increase of efficiency for discovery and identification of trace novel natural products. PMID:27318507

  15. Characterization of adhesive properties of red blood cells using surface acoustic wave induced flows for rapid diagnostics

    NASA Astrophysics Data System (ADS)

    Sivanantha, Ninnuja; Ma, Charles; Collins, David J.; Sesen, Muhsincan; Brenker, Jason; Coppel, Ross L.; Neild, Adrian; Alan, Tuncay

    2014-09-01

    This letter presents a method which employs surface acoustic wave induced acoustic streaming to differentially peel treated red blood cells (RBCs) off a substrate based on their adhesive properties and separate populations of pathological cells from normal ones. We demonstrate the principle of operation by comparing the applied power and time required to overcome the adhesion displayed by healthy, glutaraldehyde-treated or malaria-infected human RBCs. Our experiments indicate that the method can be used to differentiate between various cell populations contained in a 9 μl droplet within 30 s, suggesting potential for rapid diagnostics.

  16. Can Rapid Diagnostic Testing for Malaria Increase Adherence to Artemether-Lumefantrine?: A Randomized Controlled Trial in Uganda.

    PubMed

    Saran, Indrani; Yavuz, Elif; Kasozi, Howard; Cohen, Jessica

    2016-04-01

    Most patients with suspected malaria do not receive diagnostic confirmation before beginning antimalarial treatment. We investigated the extent to which uncertainty about malaria diagnosis contributes to patient nonadherence to artemether-lumefantrine (AL) treatment through a randomized controlled trial in central Uganda. Among 1,525 patients purchasing a course of AL at private drug shops, we randomly offered 37.6% a free malaria rapid diagnostic test (RDT) and then assessed adherence through home visits 3 days later. Of these subjects, 68.4% tested positive for malaria and 65.8% adhered overall. Patients who tested positive did not have significantly higher odds of adherence than those who were not offered the test (adjusted odds ratio [OR]: 1.07, 95% confidence interval [CI]: 0.734-1.57,P= 0.719). Patients who received a positive malaria test had 0.488 fewer pills remaining than those not offered the test (95% CI: -1.02 to 0.043,P= 0.072). We found that patients who felt relatively healthy by the second day of treatment had lower odds of completing treatment (adjusted OR: 0.532, 95% CI: 0.394-0.719,P< 0.001). Our results suggest that diagnostic testing may not improve artemisinin-based combination therapy adherence unless efforts are made to persuade patients to continue taking the full course of drugs even if symptoms have resolved. PMID:26928828

  17. Human Plasmodium knowlesi Infection Detected by Rapid Diagnostic Tests for Malaria

    PubMed Central

    van Hellemond, Jaap J.; Rutten, Marijke; Koelewijn, Rob; Zeeman, Anne-Marie; Verweij, Jaco J.; Wismans, Pieter J.; Kocken, Clemens H.

    2009-01-01

    We describe a PCR-confirmed case of Plasmodium knowlesi infection with a high parasitemia level and clinical signs of severe malaria in a migrant worker from Malaysian Borneo in the Netherlands. Investigations showed that commercially available rapid antigen tests for detection of human Plasmodium infections can detect P. knowlesi infections in humans. PMID:19788819

  18. The generation of monoclonal antibodies and their use in rapid diagnostic tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Antibodies are the most important component of an immunoassay. In these proceedings we outline novel methods used to generate and select monoclonal antibodies that meet performance criteria for use in rapid lateral flow and microfluidic immunoassay tests for the detection of agricultural pathogens ...

  19. Placental Plasmodium falciparum malaria infection: Operational accuracy of HRP2 rapid diagnostic tests in a malaria endemic setting

    PubMed Central

    2011-01-01

    Background Malaria has a negative effect on the outcome of pregnancy. Pregnant women are at high risk of severe malaria and severe haemolytic anaemia, which contribute 60-70% of foetal and perinatal losses. Peripheral blood smear microscopy under-estimates sequestered placental infections, therefore malaria rapid diagnostic tests (RDTs) detecting histidine rich protein-2 antigen (HRP-2) in peripheral blood are a potential alternative. Methods HRP-2 RDTs accuracy in detecting malaria in pregnancy (MIP >28 weeks gestation) and placental Plasmodium falciparum malaria (after childbirth) were conducted using Giemsa microscopy and placental histopathology respectively as the reference standard. The study was conducted in Mbale Hospital, using the midwives to perform and interpret the RDT results. Discordant results samples were spot checked using PCR techniques. Results Among 433 febrile women tested, RDTs had a sensitivity of 96.8% (95% CI 92-98.8), specificity of 73.5% (95% CI 67.8-78.6), a positive predictive value (PPV) of 68.0% (95% CI 61.4-73.9), and negative predictive value (NPV) of 97.5% (95% CI 94.0-99.0) in detecting peripheral P. falciparum malaria during pregnancy. At delivery, in non-symptomatic women, RDTs had a 80.9% sensitivity (95% CI 57.4-93.7) and a 87.5% specificity (95%CI 80.9-92.1), PPV of 47.2% (95% CI 30.7-64.2) and NPV of 97.1% (95% CI 92.2-99.1) in detecting placental P. falciparum infections among 173 samples. At delivery, 41% of peripheral infections were detected by microscopy without concurrent placental infection. The combination of RDTs and microscopy improved the sensitivity to 90.5% and the specificity to 98.4% for detecting placental malaria infection (McNemar's X 2> 3.84). RDTs were not superior to microscopy in detecting placental infection (McNemar's X 2< 3.84). Presence of malaria in pregnancy and active placental malaria infection were 38% and 12% respectively. Placental infections were associated with poor pregnancy outcome [pre

  20. Rapid and Accurate Determination of Lipopolysaccharide O-Antigen Types in Klebsiella pneumoniae with a Novel PCR-Based O-Genotyping Method

    PubMed Central

    Shih, Yun-Jui; Cheong, Cheng-Man; Yi, Wen-Ching

    2015-01-01

    Klebsiella pneumoniae, a Gram-negative bacillus that causes life-threatening infections in both hospitalized patients and ambulatory persons, can be classified into nine lipopolysaccharide (LPS) O-antigen serotypes. The O-antigen type has important clinical and epidemiological significance. However, K. pneumoniae O serotyping is cumbersome, and the reagents are not commercially available. To overcome the limitations of conventional serotyping methods, we aimed to create a rapid and accurate PCR method for K. pneumoniae O genotyping. We sequenced the genetic determinants of LPS O antigen from serotypes O1, O2a, O2ac, O3, O4, O5, O8, O9, and O12. We established a two-step genotyping scheme, based on the two genomic regions associated with O-antigen biosynthesis. The first set of PCR primers, which detects alleles at the wzm-wzt loci of the wb gene cluster, distinguishes between O1/O2, O3, O4, O5, O8, O9, and O12. The second set of PCR primers, which detects alleles at the wbbY region, further differentiates between O1, O2a, and O2ac. We verified the specificity of O genotyping against the O-serotype reference strains. We then tested the sensitivity and specificity of O genotyping in K. pneumoniae, using the 56 K-serotype reference strains with known O serotypes determined by an inhibition enzyme-linked immunosorbent assay (iELISA). There is a very good correlation between the O genotypes and classical O serotypes. Three discrepancies were observed and resolved by nucleotide sequencing—all in favor of O genotyping. The PCR-based O genotyping, which can be easily performed in clinical and research microbiology laboratories, is a rapid and accurate method for determining the LPS O-antigen types of K. pneumoniae isolates. PMID:26719438

  1. Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR.

    PubMed

    Shams, M; Vial, L; Chapulliot, D; Nesme, X; Lavire, C

    2013-07-01

    Agrobacteria are common soil bacteria that interact with plants as commensals, plant growth promoting rhizobacteria or alternatively as pathogens. Indigenous agrobacterial populations are composites, generally with several species and/or genomic species and several strains per species. We thus developed a recA-based PCR approach to accurately identify and specifically detect agrobacteria at various taxonomic levels. Specific primers were designed for all species and/or genomic species of Agrobacterium presently known, including 11 genomic species of the Agrobacterium tumefaciens complex (G1-G9, G13 and G14, among which only G2, G4, G8 and G14 still received a Latin epithet: pusense, radiobacter, fabrum and nepotum, respectively), A. larrymoorei, A. rubi, R. skierniewicense, A. sp. 1650, and A. vitis, and for the close relative Allorhizobium undicola. Specific primers were also designed for superior taxa, Agrobacterium spp. and Rhizobiaceace. Primer specificities were assessed with target and non-target pure culture DNAs as well as with DNAs extracted from composite agrobacterial communities. In addition, we showed that the amplicon cloning-sequencing approach used with Agrobacterium-specific or Rhizobiaceae-specific primers is a way to assess the agrobacterial diversity of an indigenous agrobacterial population. Hence, the agrobacterium-specific primers designed in the present study enabled the first accurate and rapid identification of all species and/or genomic species of Agrobacterium, as well as their direct detection in environmental samples. PMID:23578959

  2. Meningitis Dipstick Rapid Test: Evaluating Diagnostic Performance during an Urban Neisseria meningitidis Serogroup A Outbreak, Burkina Faso, 2007

    PubMed Central

    Rose, Angela M. C.; Mueller, Judith E.; Gerstl, Sibylle; Njanpop-Lafourcade, Berthe-Marie; Page, Anne-Laure; Nicolas, Pierre; Traoré, Ramata Ouédraogo; Caugant, Dominique A.; Guerin, Philippe J.

    2010-01-01

    Meningococcal meningitis outbreaks occur every year during the dry season in the “meningitis belt” of sub-Saharan Africa. Identification of the causative strain is crucial before launching mass vaccination campaigns, to assure use of the correct vaccine. Rapid agglutination (latex) tests are most commonly available in district-level laboratories at the beginning of the epidemic season; limitations include a short shelf-life and the need for refrigeration and good technical skills. Recently, a new dipstick rapid diagnostic test (RDT) was developed to identify and differentiate disease caused by meningococcal serogroups A, W135, C and Y. We evaluated the diagnostic performance of this dipstick RDT during an urban outbreak of meningitis caused by N. meningitidis serogroup A in Ouagadougou, Burkina Faso; first against an in-country reference standard of culture and/or multiplex PCR; and second against culture and/or a highly sensitive nested PCR technique performed in Oslo, Norway. We included 267 patients with suspected acute bacterial meningitis. Using the in-country reference standard, 50 samples (19%) were positive. Dipstick RDT sensitivity (N = 265) was 70% (95%CI 55–82) and specificity 97% (95%CI 93–99). Using culture and/or nested PCR, 126/259 (49%) samples were positive; dipstick RDT sensitivity (N = 257) was 32% (95%CI 24–41), and specificity was 99% (95%CI 95–100). We found dipstick RDT sensitivity lower than values reported from (i) assessments under ideal laboratory conditions (>90%), and (ii) a prior field evaluation in Niger [89% (95%CI 80–95)]. Specificity, however, was similar to (i), and higher than (ii) [62% (95%CI 48–75)]. At this stage in development, therefore, other tests (e.g., latex) might be preferred for use in peripheral health centres. We highlight the value of field evaluations for new diagnostic tests, and note relatively low sensitivity of a reference standard using multiplex vs. nested PCR. Although the former is

  3. Evaluation of triple stage mass spectrometry as a robust and accurate diagnostic tool for determination of free cordycepin in designer egg.

    PubMed

    Chen, Yi Hsin; Lim, Chee Wei; Chan, Sheot Harn

    2014-05-01

    Direct determination of free cordycepin in designer egg using a highly selective mass spectrometric (MS) technique aided by a rapid and efficient dilute-and-shoot workflow would enhance their application as diagnostic tools in food fraud control. Here, triple stage mass spectrometry (MS(3)) demonstrated excellent analyte selectivity capability even when incomplete chromatographic separation was performed. Method validation was performed at six concentration levels of 100, 200, 400, 800, 1200 and 1600ngg(-1). Spiking experiments were examined at three concentration levels of 200, 400, and 1200ngg(-1) in individual egg white and egg yolk, measured over 2days. MS(3) enabled ion chromatograms with zero-background interference to be made in egg extracts. MS(3) eliminated severe over recovery (p<0.05) observed in all fortified samples, a challenge that MRM-transition could not address in a single step. Matrix-matched calibrants were needed to compensate for over recovery observed under MRM-transition mode. PMID:24360442

  4. Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

    PubMed

    Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

    2016-08-17

    A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

  5. Accurate mass fragment library for rapid analysis of pesticides on produce using ambient pressure desorption ionization with high-resolution mass spectrometry.

    PubMed

    Kern, Sara E; Lin, Lora A; Fricke, Frederick L

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]⁺) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]⁺ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]⁺ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli

  6. Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The

  7. Systematic review and meta-analysis: rapid diagnostic tests versus placental histology, microscopy and PCR for malaria in pregnant women

    PubMed Central

    2011-01-01

    Background During pregnancy, malaria infection with Plasmodium falciparum or Plasmodium vivax is related to adverse maternal health and poor birth outcomes. Diagnosis of malaria, during pregnancy, is complicated by the absence or low parasite densities in peripheral blood. Diagnostic methods, other than microscopy, are needed for detection of placental malaria. Therefore, the diagnostic accuracy of rapid diagnostic tests (RDTs), detecting antigen, and molecular techniques (PCR), detecting DNA, for the diagnosis of Plasmodium infections in pregnancy was systematically reviewed. Methods MEDLINE, EMBASE and Web of Science were searched for studies assessing the diagnostic accuracy of RDTs, PCR, microscopy of peripheral and placental blood and placental histology for the detection of malaria infection (all species) in pregnant women. Results The results of 49 studies were analysed in metandi (Stata), of which the majority described P. falciparum infections. Although both placental and peripheral blood microscopy cannot reliably replace histology as a reference standard for placental P. falciparum infection, many studies compared RDTs and PCR to these tests. The proportion of microscopy positives in placental blood (sensitivity) detected by peripheral blood microscopy, RDTs and PCR are respectively 72% [95% CI 62-80], 81% [95% CI 55-93] and 94% [95% CI 86-98]. The proportion of placental blood microscopy negative women that were negative in peripheral blood microscopy, RDTs and PCR (specificity) are 98% [95% CI 95-99], 94% [95% CI 76-99] and 77% [95% CI 71-82]. Based on the current data, it was not possible to determine if the false positives in RDTs and PCR are caused by sequestered parasites in the placenta that are not detected by placental microscopy. Conclusion The findings suggest that RDTs and PCR may have good performance characteristics to serve as alternatives for the diagnosis of malaria in pregnancy, besides any other limitations and practical considerations

  8. Are Treponema pallidum Specific Rapid and Point-of-Care Tests for Syphilis Accurate Enough for Screening in Resource Limited Settings? Evidence from a Meta-Analysis

    PubMed Central

    Jafari, Yalda; Peeling, Rosanna W.; Shivkumar, Sushmita; Claessens, Christiane; Joseph, Lawrence; Pai, Nitika Pant

    2013-01-01

    Background Rapid and point-of-care (POC) tests for syphilis are an invaluable screening tool, yet inadequate evaluation of their diagnostic accuracy against best reference standards limits their widespread global uptake. To fill this gap, a systematic review and meta-analysis was conducted to evaluate the sensitivity and specificity of rapid and POC tests in blood and serum samples against Treponema pallidum (TP) specific reference standards. Methods Five electronic databases (1980–2012) were searched, data was extracted from 33 articles, and Bayesian hierarchical models were fit. Results In serum samples, against a TP specific reference standard point estimates with 95% credible intervals (CrI) for the sensitivities of popular tests were: i) Determine, 90.04% (80.45, 95.21), ii) SD Bioline, 87.06% (75.67, 94.50), iii) VisiTect, 85.13% (72.83, 92.57), and iv) Syphicheck, 74.48% (56.85, 88.44), while specificities were: i) Syphicheck, 99.14% (96.37, 100), ii) Visitect, 96.45% (91.92, 99.29), iii) SD Bioline, 95.85% (89.89, 99.53), and iv) Determine, 94.15% (89.26, 97.66). In whole blood samples, sensitivities were: i) Determine, 86.32% (77.26, 91.70), ii) SD Bioline, 84.50% (78.81, 92.61), iii) Syphicheck, 74.47% (63.94, 82.13), and iv) VisiTect, 74.26% (53.62, 83.68), while specificities were: i) Syphicheck, 99.58% (98.91, 99.96), ii) VisiTect, 99.43% (98.22, 99.98), iii) SD Bioline, 97.95%(92.54, 99.33), and iv) Determine, 95.85% (92.42, 97.74). Conclusions Rapid and POC treponemal tests reported sensitivity and specificity estimates comparable to laboratory-based treponemal tests. In resource limited settings, where access to screening is limited and where risk of patients lost to follow up is high, the introduction of these tests has already been shown to improve access to screening and treatment to prevent stillbirths and neonatal mortality due to congenital syphilis. Based on the evidence, it is concluded that rapid and POC tests are useful in resource

  9. Rapid, absolute calibration of x-ray filters employed by laser-produced plasma diagnostics.

    PubMed

    Brown, G V; Beiersdorfer, P; Emig, J; Frankel, M; Gu, M F; Heeter, R F; Magee, E; Thorn, D B; Widmann, K; Kelley, R L; Kilbourne, C A; Porter, F S

    2008-10-01

    The Electron Beam Ion Trap (EBIT) facility at the Lawrence Livermore National Laboratory is being used to absolutely calibrate the transmission efficiency of x-ray filters employed by diodes and spectrometers used to diagnose laser-produced plasmas. EBIT emits strong, discrete monoenergetic lines at appropriately chosen x-ray energies. X rays are detected using the high resolution EBIT Calorimeter Spectrometer (ECS), developed for LLNL at the NASA/Goddard Space Flight Center. X-ray filter transmission efficiency is determined by dividing the x-ray counts detected when the filter is in the line of sight by those detected when out of the line of sight. Verification of filter thickness can be completed in only a few hours, and absolute efficiencies can be calibrated in a single day over a broad range from about 0.1 to 15 keV. The EBIT calibration lab has been used to field diagnostics (e.g., the OZSPEC instrument) with fully calibrated x-ray filters at the OMEGA laser. Extensions to use the capability for calibrating filter transmission for the DANTE instrument on the National Ignition Facility are discussed. PMID:19044471

  10. Rapid, absolute calibration of x-ray filters employed by laser-produced plasma diagnostics

    SciTech Connect

    Brown, G. V.; Beiersdorfer, P.; Emig, J.; Frankel, M.; Gu, M. F.; Heeter, R. F.; Magee, E.; Thorn, D. B.; Widmann, K.; Kelley, R. L.; Kilbourne, C. A.; Porter, F. S.

    2008-10-15

    The Electron Beam Ion Trap (EBIT) facility at the Lawrence Livermore National Laboratory is being used to absolutely calibrate the transmission efficiency of x-ray filters employed by diodes and spectrometers used to diagnose laser-produced plasmas. EBIT emits strong, discrete monoenergetic lines at appropriately chosen x-ray energies. X rays are detected using the high resolution EBIT Calorimeter Spectrometer (ECS), developed for LLNL at the NASA/Goddard Space Flight Center. X-ray filter transmission efficiency is determined by dividing the x-ray counts detected when the filter is in the line of sight by those detected when out of the line of sight. Verification of filter thickness can be completed in only a few hours, and absolute efficiencies can be calibrated in a single day over a broad range from about 0.1 to 15 keV. The EBIT calibration lab has been used to field diagnostics (e.g., the OZSPEC instrument) with fully calibrated x-ray filters at the OMEGA laser. Extensions to use the capability for calibrating filter transmission for the DANTE instrument on the National Ignition Facility are discussed.

  11. Rapid, Absolute Calibration of X-ray Filters Employed By Laser-Produced Plasma Diagnostics

    SciTech Connect

    Brown, G V; Beiersdorfer, P; Emig, J; Frankel, M; Gu, M F; Heeter, R F; Magee, E; Thorn, D B; Widmann, K; . Kelley, R L; Kilbourne, C A; Porter, F S

    2008-05-11

    The electron beam ion trap (EBIT) facility at the Lawrence Livermore National Laboratory is being used to absolutely calibrate the transmission efficiency of X-ray filters employed by diodes and spectrometers used to diagnose laser-produced plasmas. EBIT emits strong, discrete monoenergetic lines at appropriately chosen X-ray energies. X-rays are detected using the high-resolution EBIT calorimeter spectrometer (ECS), developed for LLNL at the NASA/Goddard Space Flight Center. X-ray filter transmission efficiency is determined by dividing the X-ray counts detected when the filter is in the line of sight by those detected when out of the line of sight. Verification of filter thickness can be completed in only a few hours, and absolute efficiencies can be calibrated in a single day over a broad range from about 0.1 to 15 keV. The EBIT calibration lab has been used to field diagnostics (e.g., the OZSPEC instrument) with fully calibrated X-ray filters at the OMEGA laser. Extensions to use the capability for calibrating filter transmission for the DANTE instrument on the National Ignition Facility are discussed.

  12. The diagnostic accuracy of rapid urease biopsy test compared to histopathology in implementing “test and treat” policy for Helicobacter pylori

    PubMed Central

    Roy, Asitava Deb; Deuri, Swapna; Dutta, Umesh Chandra

    2016-01-01

    Background: Helicobacter pylori is one of the most important causes of the varied spectrum of gastroduodenal diseases. It is important to have a rapid diagnostic method to detect the organism so as to initiate the treatment early and check its progression to malignancy. Aims: To evaluate the diagnostic accuracy of rapid urease biopsy test in detecting H. pylori infection and implementation of “test and treat” policy. Materials and Methods: All patients of chronic dyspepsia not responding to conventional treatment were subjected to endoscopy, and mucosal biopsy samples were collected. A rapid urease test (RUT) and histopathology was performed on these samples and taking histopathology as gold standard for H. pylori demonstration, the diagnostic accuracy of RUT was evaluated. Results: The specificity, sensitivity, positive predictive value, negative predictive value, and diagnostic accuracy of RUT were 97.22%, 94.04%, 98.75%, 87.5%, and 95%, respectively. Conclusion: Use of a rapid diagnostic test viz., rapid urease biopsy test to confirm H. pylori infection is recommended for early diagnosis and treatment of H. pylori associated gastroduodenal diseases. PMID:26958517

  13. Further Evaluation of a Rapid Diagnostic Test for Melioidosis in an Area of Endemicity

    PubMed Central

    O'Brien, Mathew; Freeman, Kevin; Lum, Gary; Cheng, Allen C.; Jacups, Susan P.; Currie, Bart J.

    2004-01-01

    Immunochromatographic test (ICT) kits for the rapid detection of immunoglobulin G (IgG) and IgM antibodies to Burkholderia pseudomallei were compared to the indirect hemagglutination (IHA) assay. In 138 culture-confirmed melioidosis cases, sensitivities were 80, 77, and 88% for IHA, ICT IgG, and ICT IgM, respectively. In a prospective study of 160 consecutive sera samples sent for melioidosis serology, respective specificities were 91, 90, and 69, positive predictive values were 41, 32, and 18, and negative predictive values were 99, 98, and 100%. ICT IgM kits are unreliable for diagnosis of melioidosis, but ICT IgG kits may be useful for diagnosing travelers presenting with possible melioidosis who return from regions where melioidosis is endemic. PMID:15131200

  14. Rapid and Multiplexed MicroRNA Diagnostic Assay Using Quantum Dot-Based Förster Resonance Energy Transfer.

    PubMed

    Qiu, Xue; Hildebrandt, Niko

    2015-08-25

    The detection of next generation microRNA (miRNA) biomarkers has become a highly important aspect for clinical diagnostics. We use multiplexed Förster resonance energy transfer (FRET) between a luminescent Tb complex and three different semiconductor quantum dots (QDs) to sensitively detect three different miRNAs from a single 150 μL sample with ca. 1 nM (subpicomol) detection limits. The rapid and amplification-free mix-and-measure assay format is based on careful design of miRNA base pairing and stacking to selectively detect different miRNAs with very strong sequence homologies. Clinical applicability is demonstrated by sensitive multiplexed quantification of three miRNAs at low (2 to 10 nM) and varying concentrations in samples that contained up to 10% serum. PMID:26192765

  15. Rapid Capture Next-Generation Sequencing in Clinical Diagnostics of Kinase Pathway Aberrations in B-Cell Precursor ALL.

    PubMed

    Stadt, Udo Zur; Escherich, Gabriele; Indenbirken, Daniela; Alawi, Malik; Adao, Manuela; Horstmann, Martin A

    2016-07-01

    Comprehensive next-generation sequencing (NGS) applications have recently identified various recurrent kinase and cytokine receptor rearrangements in Ph-like B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) amenable to tyrosin kinase inhibitor treatment. For rapid diagnostics of kinase pathway aberrations in minimal residual disease (MRD) high-risk BCP-ALL, we developed a PCR-independent NGS custom enrichment capture panel targeting recurrent genomic alterations, which allows for the identification of unknown 5' fusion partner genes and precise mapping of variable genomic breakpoints. Using a standardized bioinformatics algorithm, we identified kinase and cytokine receptor rearrangements in the majority of ALL patients with high burden of postinduction MRD and enrichment of IKZF1 mutation or deletion (IKZF1(del) ). PMID:27007619

  16. Screening for transfusion transmissible infections using rapid diagnostic tests in Africa: a potential hazard to blood safety?

    PubMed

    Prugger, C; Laperche, S; Murphy, E L; Bloch, E M; Kaidarova, Z; Tafflet, M; Lefrère, J-J; Jouven, X

    2016-02-01

    Rapid diagnostic tests (RDTs) are routinely used in African blood centres. We analysed data from two cross-sectional studies representing 95 blood centres in 29 African countries. Standardized panels of sera containing varying concentrations of anti-human immunodeficiency virus (HIV) antibodies (Ab), hepatitis B virus antigen (HBsAg) and antihepatitis C virus (HCV) Ab were screened using routine operational testing procedures at the centres. Sensitivity of detection using RDTs was high for HIV Ab-positive samples, but low for intermediately HBsAg (51·5%) and HCV Ab (40·6%)-positive samples. These findings suggest that current RDT use in Africa could pose a hazard to blood safety. PMID:26646317

  17. Noninvasive optoacoustic system for rapid diagnostics and management of circulatory shock

    NASA Astrophysics Data System (ADS)

    Esenaliev, Rinat O.; Petrov, Irene Y.; Petrov, Yuriy; Kinsky, Michael; Prough, Donald S.

    2012-02-01

    Circulatory shock is lethal, if not promptly diagnosed and effectively treated. Typically, circulatory shock resuscitation is guided by blood pressure, heart rate, and mental status, which have poor predictive value. In patients, in whom early goaldirected therapy was applied using central venous oxygenation measurement, a substantial reduction of mortality was reported (from 46.5% to 30%). However, central venous catheterization is invasive, time-consuming and often results in complications. We proposed to use the optoacoustic technique for noninvasive, rapid assessment of central venous oxygenation. In our previous works we demonstrated that the optoacoustic technique can provide measurement of blood oxygenation in veins and arteries due to high contrast and high resolution. In this work we developed a novel optoacoustic system for noninvasive, automatic, real-time, and continuous measurement of central venous oxygenation. We performed pilot clinical tests of the system in human subjects with different oxygenation in the internal jugular vein and subclavian vein. A novel optoacoustic interface incorporating highly-sensitive optoacoustic probes and standard ultrasound imaging probes were developed and built for the study. Ultrasound imaging systems Vivid i and hand-held Vscan (GE Healthcare) as well as Site-Rite 5 (C.R. Bard) were used in the study. We developed a special algorithm for oxygenation monitoring with minimal influence of overlying tissue. The data demonstrate that the system provides precise measurement of venous oxygenation continuously and in real time. Both current value of the venous oxygenation and trend (in absolute values and for specified time intervals) are displayed in the system. The data indicate that: 1) the optoacoustic system developed by our group is capable of noninvasive measurement of blood oxygenation in specific veins; 2) clinical ultrasound imaging systems can facilitate optoacoustic probing of specific blood vessels; 3) the

  18. A new rapid method for Clostridium difficile DNA extraction and detection in stool: toward point-of-care diagnostic testing.

    PubMed

    Freifeld, Alison G; Simonsen, Kari A; Booth, Christine S; Zhao, Xing; Whitney, Scott E; Karre, Teresa; Iwen, Peter C; Viljoen, Hendrik J

    2012-01-01

    We describe a new method for the rapid diagnosis of Clostridium difficile infection, with stool sample preparation and DNA extraction by heat and physical disruption in a single-use lysis microreactor (LMR), followed by a rapid PCR amplification step. All steps can be accomplished in <20 minutes overall. Gel electrophoresis is currently used to detect the amplification product, pending real-time availability with an ultra-rapid thermocycler. Compared with the dual enzyme immunoassay (EIA) screening test (C. diff Quik Chek Complete; Techlab, Blacksburg, VA), the novel LMR/PCR assay showed complete concordance with all glutamate dehydrogenase (GDH) results (GDH(+)/toxin(+), n = 48; GDH(-)/toxin(-), n = 81). All 69 stool samples with discordant EIA results (GDH(+)/toxin(-)) were tested by both the LMR/PCR assay and the loop-mediated isothermal amplification test (LAMP) (Illumigene C. difficile; Meridian Bioscience, Cincinnati, OH). In 64/69 EIA-discordant samples, LAMP and LMR/PCR results matched (both positive in 29 sample and both negative in 35 samples); in the remaining 5 samples, results were discrepant between the LAMP assay (all five negative) and the LMR/PCR assay (all 5 positive). Overall, LMR/PCR testing matched the current algorithm of EIA and/or LAMP reflex testing in 193/198 (97.5%) samples. The present proof-of-concept study suggests that the novel LMR/PCR technique described here may be developed as an inexpensive, rapid, and reliable point-of-care diagnostic test for C. difficile infection and other infectious diseases. PMID:22402170

  19. Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance

    PubMed Central

    Lawn, Stephen D; Nicol, Mark P

    2011-01-01

    Global TB control efforts have been severely hampered by the lack of diagnostic tests that are accurate, simple to use and can be applied at the point of clinical care. This has been further compounded by the widespread inability to test for drug resistance. The Xpert® MTB/RIF assay is a rapid molecular assay that can be used close to the point of care by operators with minimal technical expertise, enabling diagnosis of TB and simultaneous assessment of rifampicin resistance to be completed within 2 h. Moreover, this can be accomplished using unprocessed sputum samples as well as clinical specimens from extrapulmonary sites. We review in detail the development of this assay, its evaluation within the laboratory, its utility among adult and pediatric TB suspects, its use as a screening tool for HIV-associated TB and studies of its implementation at the district and sub-district levels in resource-limited settings. Following endorsement by the WHO in 2010, we consider the next steps in the implementation of the assay and its potential impact in high burden settings. PMID:21958145

  20. Diagnostic accuracy of rapid immunoassays for heparin-induced thrombocytopenia. A systematic review and meta-analysis.

    PubMed

    Sun, Lova; Gimotty, Phyllis A; Lakshmanan, Suvasini; Cuker, Adam

    2016-05-01

    The platelet factor 4/heparin ELISA has limited specificity for heparin-induced thrombocytopenia (HIT) and frequently does not provide same-day results. Rapid immunoassays (RIs) have been developed which provide results in 30 minutes or less. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of RIs for HIT. We searched the literature for studies in which samples from patients with suspected HIT were tested using a RI and a functional assay against which the performance of the RI could be measured. We performed sensitivity analyses of studies that directly compared different RIs with each other and with ELISAs. Estimates of sensitivity and specificity for each RI were calculated. Twenty-three articles, collectively involving six different RIs, met eligibility criteria. All RIs exhibited high sensitivity (0.96 to 1.00); there was wider variability in specificity (0.68 to 0.94). Specificity of the IgG-specific chemiluminescent assay (IgG-CA) was greater than the polyspecific chemiluminescent assay [0.94 (95 %CI 0.89-0.99) vs 0.82 (0.77-0.87)]. The particle gel immunoassay demonstrated greater specificity than the polyspecific ELISA [0.96 (0.95-0.97) vs 0.91 (0.89-0.92)]. The IgG-CA and lateral flow immunoassay [0.94 (0.91-0.97)] exhibited greater specificity than the IgG-specific ELISA [0.86 (0.82-0.90)]. Given their high sensitivity and rapid turnaround time, RIs are a reliable means of excluding HIT at the point-of-care in patients with low or intermediate clinical probability. Additionally, some RIs have greater specificity than HIT ELISAs. In summary, IgG-specific RIs appear to have improved diagnostic accuracy compared with ELISAs in patients with suspected HIT and may reduce misdiagnosis and overtreatment. PMID:26763074

  1. Navigating the Rapids: The Development of Regulated Next-Generation Sequencing-Based Clinical Trial Assays and Companion Diagnostics

    PubMed Central

    Pant, Saumya; Weiner, Russell; Marton, Matthew J.

    2014-01-01

    Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts. PMID:24860780

  2. Cost effectiveness of OptiMal® rapid diagnostic test for malaria in remote areas of the Amazon Region, Brazil

    PubMed Central

    2010-01-01

    Background In areas with limited structure in place for microscopy diagnosis, rapid diagnostic tests (RDT) have been demonstrated to be effective. Method The cost-effectiveness of the Optimal® and thick smear microscopy was estimated and compared. Data were collected on remote areas of 12 municipalities in the Brazilian Amazon. Data sources included the National Malaria Control Programme of the Ministry of Health, the National Healthcare System reimbursement table, hospitalization records, primary data collected from the municipalities, and scientific literature. The perspective was that of the Brazilian public health system, the analytical horizon was from the start of fever until the diagnostic results provided to patient and the temporal reference was that of year 2006. The results were expressed in costs per adequately diagnosed cases in 2006 U.S. dollars. Sensitivity analysis was performed considering key model parameters. Results In the case base scenario, considering 92% and 95% sensitivity for thick smear microscopy to Plasmodium falciparum and Plasmodium vivax, respectively, and 100% specificity for both species, thick smear microscopy is more costly and more effective, with an incremental cost estimated at US$549.9 per adequately diagnosed case. In sensitivity analysis, when sensitivity and specificity of microscopy for P. vivax were 0.90 and 0.98, respectively, and when its sensitivity for P. falciparum was 0.83, the RDT was more cost-effective than microscopy. Conclusion Microscopy is more cost-effective than OptiMal® in these remote areas if high accuracy of microscopy is maintained in the field. Decision regarding use of rapid tests for diagnosis of malaria in these areas depends on current microscopy accuracy in the field. PMID:20937094

  3. Optical and analytical investigations on dengue virus rapid diagnostic test for IgM antibody detection.

    PubMed

    Jahanshahi, Peyman; Sekaran, Shamala Devi; Adikan, Faisal Rafiq Mahamd

    2015-08-01

    Evaluation of binding between analytes and its relevant ligands on surface plasmon resonance (SPR) biosensor is of considerable importance for accurate determination and screening of an interference in immunosensors. Dengue virus serotype 2 was used as a case study in this investigation. This research work compares and interprets the results obtained from analytical analysis with the experimental ones. Both the theoretical calculations and experimental results are verified with one sample from each category of dengue serotypes 2 (low, mid, and high positive), which have been examined in the database of established laboratorial diagnosis. In order to perform this investigation, the SPR angle variations are calculated, analyzed, and then validated via experimental SPR angle variations. Accordingly, the error ratios of 5.35, 6.54, and 3.72% were obtained for the low-, mid-, and high-positive-specific immune globulins of patient serums, respectively. In addition, the magnetic fields of the biosensor are numerically simulated to show the effect of different binding mediums. PMID:25791696

  4. Rapid optical heating of blood for clinical point-of-care diagnostics

    NASA Astrophysics Data System (ADS)

    Catanzaro, Brian E.; Hill, Ted; Hankins, Steve; Gandola, Kent

    2010-02-01

    Clinical testing of human blood requires adherence to a number of regulatory standards, including maintaining a temperature that is representative of the human body (e.g. 37 C). The economics of private and public healthcare drives blood assays to be conducted using low cost, disposable assay devices that also eliminate the possibility of cross contamination. Unfortunately, the materials that meet the economic and disposable constraints of the marketplace are thermal insulators, not ideal for rapid heating. We present a novel means of optically heating blood samples in plastic assay devices within a time period suitable for point-of-care use. The novel approach uses LED's in the red portion of the visible spectrum. The lower absorption of optical radiation in the visible spectrum enables the absorption of energy deep into the assay device. This produces even heating, avoiding the gradients that can occur by surface heating (conduction) or surface absorption (highly absorbing wavelengths). Analytical and computational models will be discussed. A specific application to a point-of-care blood assay instrument will be reviewed. In this application, optical heating was achieved using a small array of high brightness LED's. Experimental results will be discussed. The experimental results with this instrument validated the predictions.

  5. Microbial Inactivation for Safe and Rapid Diagnostics of Infectious Samples ▿ †

    PubMed Central

    Sagripanti, Jose-Luis; Hülseweh, Birgit; Grote, Gudrun; Voß, Luzie; Böhling, Katrin; Marschall, Hans-Jürgen

    2011-01-01

    The high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log10) of bacterial spores (Bacillus atrophaeus), vegetative bacteria (Pseudomonas aeruginosa), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost. PMID:21856830

  6. Direct Blood Dry LAMP: A Rapid, Stable, and Easy Diagnostic Tool for Human African Trypanosomiasis

    PubMed Central

    Hayashida, Kyoko; Kajino, Kiichi; Hachaambwa, Lottie; Namangala, Boniface; Sugimoto, Chihiro

    2015-01-01

    Loop-mediated isothermal amplification (LAMP) is a rapid and sensitive tool used for the diagnosis of a variety of infectious diseases. One of the advantages of this method over the polymerase chain reaction is that DNA amplification occurs at a constant temperature, usually between 60–65°C; therefore, expensive devices are unnecessary for this step. However, LAMP still requires complicated sample preparation steps and a well-equipped laboratory to produce reliable and reproducible results, which limits its use in resource-poor laboratories in most developing countries. In this study, we made several substantial modifications to the technique to carry out on-site diagnosis of Human African Trypanosomiasis (HAT) in remote areas using LAMP. The first essential improvement was that LAMP reagents were dried and stabilized in a single tube by incorporating trehalose as a cryoprotectant to prolong shelf life at ambient temperature. The second technical improvement was achieved by simplifying the sample preparation step so that DNA or RNA could be amplified directly from detergent-lysed blood samples. With these modifications, diagnosis of HAT in local clinics or villages in endemic areas becomes a reality, which could greatly impact on the application of diagnosis not only for HAT but also for other tropical diseases. PMID:25769046

  7. Optical nanotechnology enables rapid label-free diagnostics for cancer biomarker screening

    NASA Astrophysics Data System (ADS)

    Wawro, Debra; Zimmerman, Shelby; Magnusson, Robert; Koulen, Peter

    2011-07-01

    A high-accuracy biosensor system has been developed to provide rapid detection of biomarker proteins as indicators of ovarian cancer. This photonic detection system is based upon guided-mode resonance sensor technology. The buildup of the attaching biolayer can be monitored directly, without use of chemical tags, by following the corresponding resonance shift with a spectrometer or detector array. Additionally, these high-resolution sensors employ multiple resonance peaks at identical physical location on the sensor surface. Each of these resonance peaks responds uniquely to the detection event, thereby enriching the data set available for quantification. The peaks result from individual, polarization-dependent resonant leaky modes that are the foundation of this technology. Examples are presented for detection of ovarian cancer biomarkers (fibronectin and apoliprotein A-1) in serum and cell culture supernatant, with detection sensitivities to ~20 ng/ml. Minimal nonspecific binding was measured in cell media and serum backgrounds. We also present an example dual-polarization resonance response with corresponding backfitting results that illustrate the capability to distinguish between changes at the sensor surface due to biolayer adhesion and those due to sample background changes.

  8. Evaluation of the MRL Diagnostics Dengue Fever Virus IgM Capture ELISA and the PanBio Rapid Immunochromatographic Test for Diagnosis of Dengue Fever in Jamaica

    PubMed Central

    Palmer, Carol J.; King, S. Dorothy; Cuadrado, Raul R.; Perez, Eddy; Baum, Mariana; Ager, Arba L.

    1999-01-01

    We evaluated two new commercial dengue diagnostic tests, the MRL Diagnostics Dengue Fever Virus IgM Capture ELISA and the PanBio Rapid Immunochromatographic Test, on serum samples collected during a dengue epidemic in Jamaica. The MRL ELISA method correctly identified 98% (78 of 80) of the samples as dengue positive, while the PanBio test identified 100% (80 of 80). Both tests were 100% (20 samples of 20) specific. PMID:10203534

  9. Evaluation of the MRL diagnostics dengue fever virus IgM capture ELISA and the PanBio Rapid Immunochromatographic Test for diagnosis of dengue fever in Jamaica.

    PubMed

    Palmer, C J; King, S D; Cuadrado, R R; Perez, E; Baum, M; Ager, A L

    1999-05-01

    We evaluated two new commercial dengue diagnostic tests, the MRL Diagnostics Dengue Fever Virus IgM Capture ELISA and the PanBio Rapid Immunochromatographic Test, on serum samples collected during a dengue epidemic in Jamaica. The MRL ELISA method correctly identified 98% (78 of 80) of the samples as dengue positive, while the PanBio test identified 100% (80 of 80). Both tests were 100% (20 samples of 20) specific. PMID:10203534

  10. Rapid, Accurate, and Non-Invasive Measurement of Zebrafish Axial Length and Other Eye Dimensions Using SD-OCT Allows Longitudinal Analysis of Myopia and Emmetropization

    PubMed Central

    Collery, Ross F.; Veth, Kerry N.; Dubis, Adam M.; Carroll, Joseph; Link, Brian A.

    2014-01-01

    Refractive errors in vision can be caused by aberrant axial length of the eye, irregular corneal shape, or lens abnormalities. Causes of eye length overgrowth include multiple genetic loci, and visual parameters. We evaluate zebrafish as a potential animal model for studies of the genetic, cellular, and signaling basis of emmetropization and myopia. Axial length and other eye dimensions of zebrafish were measured using spectral domain-optical coherence tomography (SD-OCT). We used ocular lens and body metrics to normalize and compare eye size and relative refractive error (difference between observed retinal radial length and controls) in wild-type and lrp2 zebrafish. Zebrafish were dark-reared to assess effects of visual deprivation on eye size. Two relative measurements, ocular axial length to body length and axial length to lens diameter, were found to accurately normalize comparisons of eye sizes between different sized fish (R2 = 0.9548, R2 = 0.9921). Ray-traced focal lengths of wild-type zebrafish lenses were equal to their retinal radii, while lrp2 eyes had longer retinal radii than focal lengths. Both genetic mutation (lrp2) and environmental manipulation (dark-rearing) caused elongated eye axes. lrp2 mutants had relative refractive errors of −0.327 compared to wild-types, and dark-reared wild-type fish had relative refractive errors of −0.132 compared to light-reared siblings. Therefore, zebrafish eye anatomy (axial length, lens radius, retinal radius) can be rapidly and accurately measured by SD-OCT, facilitating longitudinal studies of regulated eye growth and emmetropization. Specifically, genes homologous to human myopia candidates may be modified, inactivated or overexpressed in zebrafish, and myopia-sensitizing conditions used to probe gene-environment interactions. Our studies provide foundation for such investigations into genetic contributions that control eye size and impact refractive errors. PMID:25334040

  11. A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

    PubMed Central

    Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

    2015-01-01

    Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID

  12. Metaanalysis of the Performance of a Combined Treponemal and Nontreponemal Rapid Diagnostic Test for Syphilis and Yaws

    PubMed Central

    Marks, Michael; Yin, Yue-Ping; Chen, Xiang-Sheng; Castro, Arnold; Causer, Louise; Guy, Rebecca; Wangnapi, Regina; Mitjà, Oriol; Aziz, Abdul; Castro, Rita; da Luz Martins Pereira, Filomena; Taleo, Fasihah; Guinard, Jérôme; Bélec, Laurent; Tun, Ye; Bottomley, Christian; Ballard, Ronald C.; Mabey, David C.W.

    2016-01-01

    Background. The human treponematoses are important causes of disease. Mother-to-child transmission of syphilis remains a major cause of stillbirth and neonatal death. There are also almost 100 000 cases of endemic treponemal disease reported annually, predominantly yaws. Rapid diagnostic tests (RDTs) would improve access to screening for these diseases. Most RDTs cannot distinguish current and previous infection. The Dual Path Platform (DPP) Syphilis Screen & Confirm test includes both a treponemal (T1) and nontreponemal (T2) component and may improve the accuracy of diagnosis. Methods. We conducted a metaanalysis of published and unpublished evaluations of the DPP-RDT for the diagnosis of syphilis and yaws. We calculated the sensitivity, specificity, and overall agreement of the test compared with reference laboratory tests. Results. Nine evaluations, including 7267 tests, were included. Sensitivity was higher in patients with higher titer rapid plasma reagin (≥1:16) for both the T1 (98.2% vs 90.1%, P < .0001) and the T2 component (98.2% vs 80.6%, P < .0001). Overall agreement between the DPP test and reference serology was 85.2% (84.4%–86.1%). Agreement was highest for high-titer active infection and lowest for past infection. Conclusions. The RDT has good sensitivity and specificity of the treponemal and nontreponemal components both in cases of suspected syphilis and yaws, although the sensitivity is decreased at lower antibody titers. PMID:27217216

  13. Rapid, Sensitive, and Accurate Evaluation of Drug Resistant Mutant (NS5A-Y93H) Strain Frequency in Genotype 1b HCV by Invader Assay.

    PubMed

    Yoshimi, Satoshi; Ochi, Hidenori; Murakami, Eisuke; Uchida, Takuro; Kan, Hiromi; Akamatsu, Sakura; Hayes, C Nelson; Abe, Hiromi; Miki, Daiki; Hiraga, Nobuhiko; Imamura, Michio; Aikata, Hiroshi; Chayama, Kazuaki

    2015-01-01

    Daclatasvir and asunaprevir dual oral therapy is expected to achieve high sustained virological response (SVR) rates in patients with HCV genotype 1b infection. However, presence of the NS5A-Y93H substitution at baseline has been shown to be an independent predictor of treatment failure for this regimen. By using the Invader assay, we developed a system to rapidly and accurately detect the presence of mutant strains and evaluate the proportion of patients harboring a pre-treatment Y93H mutation. This assay system, consisting of nested PCR followed by Invader reaction with well-designed primers and probes, attained a high overall assay success rate of 98.9% among a total of 702 Japanese HCV genotype 1b patients. Even in serum samples with low HCV titers, more than half of the samples could be successfully assayed. Our assay system showed a better lower detection limit of Y93H proportion than using direct sequencing, and Y93H frequencies obtained by this method correlated well with those of deep-sequencing analysis (r = 0.85, P <0.001). The proportion of the patients with the mutant strain estimated by this assay was 23.6% (164/694). Interestingly, patients with the Y93H mutant strain showed significantly lower ALT levels (p=8.8 x 10-4), higher serum HCV RNA levels (p=4.3 x 10-7), and lower HCC risk (p=6.9 x 10-3) than those with the wild type strain. Because the method is both sensitive and rapid, the NS5A-Y93H mutant strain detection system established in this study may provide important pre-treatment information valuable not only for treatment decisions but also for prediction of disease progression in HCV genotype 1b patients. PMID:26083687

  14. A rapid and accurate quantification method for real-time dynamic analysis of cellular lipids during microalgal fermentation processes in Chlorella protothecoides with low field nuclear magnetic resonance.

    PubMed

    Wang, Tao; Liu, Tingting; Wang, Zejian; Tian, Xiwei; Yang, Yi; Guo, Meijin; Chu, Ju; Zhuang, Yingping

    2016-05-01

    The rapid and real-time lipid determination can provide valuable information on process regulation and optimization in the algal lipid mass production. In this study, a rapid, accurate and precise quantification method of in vivo cellular lipids of Chlorella protothecoides using low field nuclear magnetic resonance (LF-NMR) was newly developed. LF-NMR was extremely sensitive to the algal lipids with the limits of the detection (LOD) of 0.0026g and 0.32g/L in dry lipid samples and algal broth, respectively, as well as limits of quantification (LOQ) of 0.0093g and 1.18g/L. Moreover, the LF-NMR signal was specifically proportional to the cellular lipids of C. protothecoides, thus the superior regression curves existing in a wide detection range from 0.02 to 0.42g for dry lipids and from 1.12 to 8.97gL(-1) of lipid concentration for in vivo lipid quantification were obtained with all R(2) higher than 0.99, irrespective of the lipid content and fatty acids profile variations. The accuracy of this novel method was further verified to be reliable by comparing lipid quantification results to those obtained by GC-MS. And the relative standard deviation (RSD) of LF-NMR results were smaller than 2%, suggesting the precision of this method. Finally, this method was successfully used in the on-line lipid monitoring during the algal lipid fermentation processes, making it possible for better understanding of the lipid accumulation mechanism and dynamic bioprocess control. PMID:26948045

  15. New Pathogens and Rapid Diagnostic Methods -Clinical Microbiology in the 21st Century-

    PubMed

    Koontz

    1998-11-25

    This presentation is actually a predictive opinion piece from the author's experience. No one really knows what new pathogens are awaiting us around the year of 2000 corner but, in 1985, the author was asked by the NCCLS (USA) to predict the emerging pathogens for the 1990's in the U.S. and hit on 80% of them. Thus, using the experience of this decade, we can predict what will happen in the U.S. in the first decade of the new century with 80-90% accuracy of those we predict. In the next millennium we will see a marked increase in the infection rate of the atypical (non-TB) mycobacteria, the environmental fungi, and even greater problems with the "water organisms". All of this will be described in detail with the preliminary data that indicates these trends for the years "2000 and beyond". In the area of what will be new in rapid testing, whether manual or automated, the future is even more cloudy. Manufacturers will not discuss with consumers what their long-range plans are for new products. Even long-time associations with Becton-Dickinson, Gen-Probe, Vitek, etc., has yielded little if any indication of their company's plans for the years "2000 and beyond". One can, however, conceive and get into their minds to some degree based on their previous track records. We think these companies are working very hard on current tests or instruments to upgrade and improve their products yielding tests with greater sensitivity and specificity, while decreasing the technicians "hands-on time". We anticipate the increased utilization of chromogenic detectors rather than nucleotides due to the inherent problem of disposal of radioactive compounds regardless of how few actual "micro-curies" involved. The use of ligand assay technology to supplement or replace currently employed PCR technology is totally predictable and will occur. One must remember that industry faces the same problems as we do with the "new pathogens" of the future. They will need to develop detection and

  16. Rapid and Accurate Species-Level Identification of Coagulase-Negative Staphylococci by Using the sodA Gene as a Target

    PubMed Central

    Poyart, Claire; Quesne, Gilles; Boumaila, Claire; Trieu-Cuot, Patrick

    2001-01-01

    Simple PCR and sequencing assays that utilize a single pair of degenerate primers were used to characterize a 429-bp-long DNA fragment internal (sodAint) to the sodA gene encoding the manganese-dependent superoxide dismutase in 40 coagulase-negative staphylococcal (CNS) type strains. The topology of the phylogenetic tree obtained was in general agreement with that which was inferred from an analysis of their 16S rRNA or hsp60 gene sequences. Sequence analysis revealed that the staphylococcal sodA genes exhibit a higher divergence than does the corresponding 16S ribosomal DNA. These results confirm that the sodA gene constitutes a highly discriminative target sequence for differentiating closely related bacterial species. Clinical isolates that could not be identified at the species level by phenotypical tests were identified by use of this database. These results demonstrate the usefulness of this method for rapid and accurate species identification of CNS isolates, although it does not allow discrimination of subspecies. The sodA sequence polymorphisms observed with staphylococcal species offer good opportunities for the development of assays based on DNA chip technologies. PMID:11724835

  17. Improving patient flow and timeliness in the diagnosis and management of breast abnormalities: the impact of a rapid diagnostic unit

    PubMed Central

    Racz, J.M.; Holloway, C.M.B.; Huang, W.; Hong, N.J. Look

    2016-01-01

    Background Efforts to streamline the diagnosis and treatment of breast abnormalities are necessary to limit patient anxiety and expedite care. In the present study, we examined the effect of a rapid diagnostic unit (rdu) on wait times to clinical investigations and definitive treatment. Methods A retrospective before–after series, each considering a 1-year period, examined consecutive patients with suspicious breast lesions before and after initiation of the rdu. Patient consultations, clinical investigations, and lesion characteristics were captured from time of patient referral to initiation of definitive treatment. Outcomes included time (days) to clinical investigations, to delivery of diagnosis, and to management. Groups were compared using the Fisher exact test or Student t-test. Results The non-rdu group included 287 patients with 164 invasive breast carcinomas. The rdu group included 260 patients with 154 invasive carcinomas. The rdu patients had more single visits for biopsy (92% rdu vs. 78% non-rdu, p < 0.0001). The rdu group also had a significantly shorter wait time from initial consultation to delivery of diagnosis (mean: 2.1 days vs. 16.7 days, p = 0.0001) and a greater chance of receiving neoadjuvant chemotherapy (37% vs. 24%, p = 0.0106). Overall time from referral to management remained statistically unchanged (mean: 53 days with the rdu vs. 50 days without the rdu, p = 0.3806). Conclusions Introduction of a rdu appears to reduce wait times to definitive diagnosis, but not to treatment initiation, suggesting that obstacles to care delivery can occur at several points along the diagnostic trajectory. Multipronged efforts to reduce system-related delays to definitive treatment are needed. PMID:27330363

  18. Field Application of SD Bioline Malaria Ag Pf/Pan Rapid Diagnostic Test for Malaria in Greece

    PubMed Central

    Tseroni, Maria; Pervanidou, Danai; Tserkezou, Persefoni; Rachiotis, George; Pinaka, Ourania; Baka, Agoritsa; Georgakopoulou, Theano; Vakali, Annita; Dionysopoulou, Martha; Terzaki, Irene; Marka, Andriani; Detsis, Marios; Evlampidou, Zafiroula; Mpimpa, Anastasia; Vassalou, Evdokia; Tsiodras, Sotirios; Tsakris, Athanasios; Kremastinou, Jenny; Hadjichristodoulou, Christos

    2015-01-01

    Greece, a malaria-free country since 1974, has experienced re-emergence of Plasmodium vivax autochthonous malaria cases in some agriculture areas over the last three years. In early 2012, an integrated control programme (MALWEST Project) was launched in order to prevent re-establishment of the disease. In the context of this project, the rapid diagnostic tests (RDT) of SD Bioline Malaria Ag Pf/Pan that detects hrp-2 and pan-LDH antigens were used. The aim of this study was to assess the field application of the RDT for the P. vivax diagnosis in comparison to light microscopy and polymerase chain reaction (PCR). A total of 955 samples were tested with all three diagnostic tools. Agreement of RDT against microscopy and PCR for the diagnosis of P. vivax was satisfactory (K value: 0.849 and 0.976, respectively). The sensitivity, specificity and positive predictive value of RDT against PCR was 95.6% (95% C.I.: 84.8-99.3), 100% (95% C.I.: 99.6-100.0) and 100% (95% CI: 91.7-100.0) respectively, while the sensitivity, specificity and positive predictive value of RDT against microscopic examination was 97.4% (95% C.I.: 86.1-99.6), 99.4% (95% C.I.: 98.6-99.8) and 86.1% (95% CI: 72.1-94.7), respectively. Our results indicate that RDT performed satisfactory in a non-endemic country and therefore is recommended for malaria diagnosis, especially in areas where health professionals lack experience on light microscopy. PMID:25803815

  19. Cost-effectiveness of malaria microscopy and rapid diagnostic tests versus presumptive diagnosis: implications for malaria control in Uganda

    PubMed Central

    2011-01-01

    Background Current Uganda National Malaria treatment guidelines recommend parasitological confirmation either by microscopy or rapid diagnostic test (RDT) before treatment with artemether-lumefantrine (AL). However, the cost-effectiveness of these strategies has not been assessed at rural operational primary care centres. Methods Three health centres (HCs) were randomized to three diagnostic arms (microscopy, RDT and presumptive diagnosis) in a district of low and another of high malaria transmission intensities in Uganda. Some 22,052 patients presenting with fever at outpatients departments were enrolled from March 2010 to February 2011. Of these, a random sample of 1,627 was selected to measure additional socio-economic characteristics. Costing was performed following the standard step-down cost allocation and the ingredients approach. Effectiveness was measured as the number and proportion of patients correctly diagnosed and treated. Incremental Cost-Effectiveness Ratios (ICERs) were estimated from the societal perspective (http://Clinicaltrials.gov, NCT00565071). Results Overall RDT was most cost-effective with lowest ICER US$5.0 compared to microscopy US$9.61 per case correctly diagnosed and treated. In the high transmission setting, ICER was US$4.38 for RDT and US$12.98 for microscopy. The corresponding ICERs in the low transmission setting were US$5.85 and US$7.63 respectively. The difference in ICERs between RDT and microscopy was greater in the high transmission area (US$8.9) than in low transmission setting (US$1.78). At a willingness to pay of US$2.8, RDT remained cost effective up to a threshold value of the cost of treatment of US$4.7. Conclusion RDT was cost effective in both low and high transmission settings. With a global campaign to reduce the costs of AL and RDT, the Malaria Control Programme and stakeholders need a strategy for malaria diagnosis because as the cost of AL decreases, presumptive treatment is likely to become more attractive. PMID

  20. A Cluster Randomised Trial Introducing Rapid Diagnostic Tests into Registered Drug Shops in Uganda: Impact on Appropriate Treatment of Malaria

    PubMed Central

    Mbonye, Anthony K.; Magnussen, Pascal; Lal, Sham; Hansen, Kristian S.; Cundill, Bonnie; Chandler, Clare; Clarke, Siân E.

    2015-01-01

    Background Inappropriate treatment of malaria is widely reported particularly in areas where there is poor access to health facilities and self-treatment of fevers with anti-malarial drugs bought in shops is the most common form of care-seeking. The main objective of the study was to examine the impact of introducing rapid diagnostic tests for malaria (mRDTs) in registered drug shops in Uganda, with the aim to increase appropriate treatment of malaria with artemisinin-based combination therapy (ACT) in patients seeking treatment for fever in drug shops. Methods A cluster-randomized trial of introducing mRDTs in registered drug shops was implemented in 20 geographical clusters of drug shops in Mukono district, central Uganda. Ten clusters were randomly allocated to the intervention (diagnostic confirmation of malaria by mRDT followed by ACT) and ten clusters to the control arm (presumptive treatment of fevers with ACT). Treatment decisions by providers were validated by microscopy on a reference blood slide collected at the time of consultation. The primary outcome was the proportion of febrile patients receiving appropriate treatment with ACT defined as: malaria patients with microscopically-confirmed presence of parasites in a peripheral blood smear receiving ACT or rectal artesunate, and patients with no malaria parasites not given ACT. Findings A total of 15,517 eligible patients (8672 intervention and 6845 control) received treatment for fever between January-December 2011. The proportion of febrile patients who received appropriate ACT treatment was 72·9% versus 33·7% in the control arm; a difference of 36·1% (95% CI: 21·3 – 50·9), p<0·001. The majority of patients with fever in the intervention arm accepted to purchase an mRDT (97·8%), of whom 58·5% tested mRDT-positive. Drug shop vendors adhered to the mRDT results, reducing over-treatment of malaria by 72·6% (95% CI: 46·7– 98·4), p<0·001) compared to drug shop vendors using presumptive

  1. Evaluation of the Becton Dickinson Rapid Influenza Diagnostic Tests in Outpatients in Germany during Seven Influenza Seasons

    PubMed Central

    Eggers, Maren; Enders, Martin; Terletskaia-Ladwig, Elena

    2015-01-01

    Background An extensive retrospective study spanning several seasons was undertaken to evaluate the diagnostic performance of the BD rapid influenza diagnostic test (RIDT) in comparison with the RT-PCR assay. Methods A total of 2,179 respiratory samples were tested in parallel by in-house RT-PCR and the RIDT. During the 2003-2004, 2006-2007, 2007-2008, and 2008-2009 (n=1671) seasons, the BD Directigen Flu A+B test was used, and during the 2010-2011, 2011-2012 and 2012-2013 (n=508) seasons, the BD Directigen EZ Flu A+B test b was used. Results The sensitivity, specificity, PPV and NPV for the BD Directigen Flu A+B test calculated for types A and B together were 39%, 99%, 98%, and 56%, respectively. For the BD Directigen EZ Flu A+B test, these values were 47%, 100%, 100%, 55%, respectively. The sensitivity of the BD Directigen Flu A+B test did not differ significantly from season to season or between types A (44%) and B (37%). The sensitivity of the BD Directigen EZ Flu A+B test calculated for type A only was 59%, which was considerably higher than the sensitivity of this test for type B (23%). The sensitivity of the RIDT was approximately 40-50% in children and teenagers, but it was only 18.% in adults aged 20 years and older. The specificity of both RIDTs was very high (>99%) during all seasons. Conclusions Due to their rapid turnaround time, RIDTs can help guide decisions about the clinical management of influenza. Because of the high specificity, a positive result can be interpreted as a true positive, and antiviral therapy as well as appropriate measures to prevent the transmission of influenza can be initiated. The best sensitivity of the RIDT is achieved in children. However, even in this group, the RIDT will only recognize influenza infection in approximately half of the cases, and influenza should still be considered in patients with negative results; negative RIDT results must be confirmed by PCR. PMID:26011531

  2. High-Resolution Rapid Diagnostic Imaging of Whole Prostate Biopsies Using Video-Rate Fluorescence Structured Illumination Microscopy.

    PubMed

    Wang, Mei; Kimbrell, Hillary Z; Sholl, Andrew B; Tulman, David B; Elfer, Katherine N; Schlichenmeyer, Tyler C; Lee, Benjamin R; Lacey, Michelle; Brown, J Quincy

    2015-10-01

    Rapid assessment of prostate core biopsy pathology at the point-of-procedure could provide benefit in a variety of clinical situations. Even with advanced transrectal ultrasound guidance and saturation biopsy protocols, prostate cancer can be missed in up to half of all initial biopsy procedures. In addition, collection of tumor specimens for downstream histologic, molecular, and genetic analysis is hindered by low tumor yield due to inability to identify prostate cancer grossly. However, current point-of-procedure pathology protocols, such as frozen section analysis (FSA), are destructive and too time- and labor-intensive to be practical or economical. Ex vivo microscopy of the excised specimens, stained with fast-acting fluorescent histology dyes, could be an attractive nondestructive alternative to FSA. In this work, we report the first demonstration of video-rate structured illumination microscopy (VR-SIM) for rapid high-resolution diagnostic imaging of prostate biopsies in realistic point-of-procedure timeframes. Large mosaic images of prostate biopsies stained with acridine orange are rendered in seconds and contain excellent contrast and detail, exhibiting close correlation with corresponding hematoxylin and eosin histology. A clinically relevant review of VR-SIM images of 34 unfixed and uncut prostate core biopsies by two independent pathologists resulted in an area under the receiver operative curve (AUC) of 0.82-0.88, with a sensitivity ranging from 63% to 88% and a specificity ranging from 78% to 89%. When biopsies contained more than 5% tumor content, the sensitivity improved to 75% to 92%. The image quality, speed, minimal complexity, and ease of use of VR-SIM could prove to be features in favor of adoption as an alternative to destructive pathology at the point-of-procedure. PMID:26282168

  3. Field performance of malaria rapid diagnostic test for the detection of Plasmodium falciparum infection in Odisha State, India

    PubMed Central

    Sahu, S.S.; Gunasekaran, K.; Jambulingam, P.

    2015-01-01

    Background & objectives: Rapid diagnostic tests (RDTs) have become an essential surveillance tool in the malaria control programme in India. The current study aimed to assess the performance of ParaHIT-f, a rapid test in diagnosis of Plasmodium falciparum infection through detecting its specific antigen, histidine rich protein 2 (PfHRP-2), in Odisha State, India. Methods: The study was undertaken in eight falciparum malaria endemic southern districts of Odisha State. Febrile patients included through active case detection, were diagnosed by Accredited Social Health Activists (ASHAs) for P. falciparum infection using the RDT, ParaHIT-f. The performance of ParaHIT-f was evaluated using microscopy as the gold standard. Results: A total of 1030 febrile patients were screened by both microscopy and the RDT for P. falciparum infection. The sensitivity of ParaHIT-f was 63.6% (95% CI: 56.0-70.6) and specificity was 98.9% (95% CI: 97.9-99.5), with positive and negative predictive values (PPV and NPV) of 92.6% (95% CI: 86.0-96.3) and 93.0% (95% CI: 91.0-94.5), respectively. When related to parasitaemia, the RDT sensitivity was 47.8% at the low parasitaemia of 4 to 40 parasites/μl of blood. Interpretation & conclusions: The results showed that the performance of the RDT, ParaHIT-f, was not as sensitive as microscopy in detecting true falciparum infections; a high specificity presented a low frequency of false-positive RDT results. The sensitivity of ParaHIT-f was around 60 per cent. It is, therefore, essential to improve the efficiency (sensitivity) of the kit so that the true falciparum infections will not be missed especially in areas where P. falciparum has been the predominant species causing cerebral malaria. PMID:26905242

  4. Performance of the Directigen EZ Flu A+B rapid influenza diagnostic test to detect pandemic influenza A/H1N1 2009.

    PubMed

    Boyanton, Bobby L; Almradi, Amro; Mehta, Tejal; Robinson-Dunn, Barbara

    2014-04-01

    The Directigen EZ Flu A+B rapid influenza diagnostic test, as compared to real-time reverse transcriptase polymerase chain reaction, demonstrated suboptimal performance to detect pandemic influenza A/H1N1 2009. Age- and viral load-stratified test sensitivity ranged from 33.3 to 84.6% and 0 to 100%, respectively. PMID:24582319

  5. Development of a rapid diagnostic assay for the detection of tomato chlorotic dwarf viroid based on isothermal reverse-transcription-recombinase polymerase amplification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A molecular diagnostic assay utilizing reverse transcription-recombinase polymerase amplification (RT-RPA) at an isothermal constant temperature of 39 °C and target-specific primers and probe were developed for the rapid, sensitive, and specific detection of tomato chlorotic dwarf viroid (TCDVd) in ...

  6. Phytochip: development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species.

    PubMed

    Noyer, Charlotte; Abot, Anne; Trouilh, Lidwine; Leberre, Véronique Anton; Dreanno, Catherine

    2015-05-01

    Detection of harmful algal blooms has become a challenging concern because of the direct impacts on public health and economy. The identification of toxic dinoflagellates and diatoms in monitoring programs requires an extensive taxonomic expertise and is time consuming. Advances in molecular biology have allowed the development of new approaches, more rapid, accurate and cost-effective for detecting these microorganisms. In this context, we developed a new DNA microarray (called, Phytochip) for the simultaneous detection of multiple HAB species with a particular emphasis on Pseudo-nitzschia species. Oligonucleotide probes were designed along the rRNA operon. After DNA extraction, the target rDNA genes were amplified and labeled using an asymmetric PCR; then, the amplicons were hybridized to the oligonucleotide probes present on the chips. The total assay from seawater sampling to data acquisition can be performed within a working day. Specificity and sensitivity were assessed by using monoclonal cultures, mixtures of species and field samples spiked with a known amount of cultured cells. The Phytochip with its 81 validated oligonucleotide probes was able to detect 12 species of Pseudo-nitzschia and 11 species of dinoflagellates among which were 3 species of Karenia and 3 species of Alexandrium. The Phytochip was applied to environmental samples already characterized by light microscopy and cloned into DNA libraries. The hybridizations on the Phytochip were in good agreement with the sequences retrieved from the clone libraries and the microscopic observations. The Phytochip enables a reliable multiplex detection of phytoplankton and can assist a water quality monitoring program as well as more general ecological research. PMID:25765159

  7. Analyzing Deoxyribose Nucleic Acid from Malaria Rapid Diagnostic Tests to Study Plasmodium falciparum Genetic Diversity in Mali.

    PubMed

    Nabet, Cécile; Doumbo, Safiatou; Jeddi, Fakhri; Sagara, Issaka; Manciulli, Tommaso; Tapily, Amadou; L'Ollivier, Coralie; Djimde, Abdoulaye; Doumbo, Ogobara K; Piarroux, Renaud

    2016-06-01

    We evaluated the use of positive malaria rapid diagnostic tests (mRDTs) to determine genetic diversity of Plasmodium falciparum in Mali. Genetic diversity was assessed via multiple loci variable number of tandem repeats analysis (MLVA). We performed DNA extraction from 104 positive and 30 negative used mRDTs that had been stored at ambient temperature for up to 14 months. Extracted DNA was analyzed via quantitative polymerase chain reaction (qPCR), and MLVA genotyping was then assessed on positive qPCR samples. Eighty-three of the positive mRDTs (83/104, 79.8%) and none of the negative mRDTs were confirmed P. falciparum positive via qPCR. We achieved complete genotyping of 90.4% (75/83) of the qPCR-positive samples. Genotyping revealed high genetic diversity among P. falciparum populations in Mali and an absence of population clustering. We show that mRDTs are useful to monitor P. falciparum genetic diversity and thereby can provide essential data to guide malaria control programs. PMID:27001760

  8. Estimation of Plasmodium falciparum Transmission Intensity in Lilongwe, Malawi, by Microscopy, Rapid Diagnostic Testing, and Nucleic Acid Detection.

    PubMed

    Parr, Jonathan B; Belson, Connor; Patel, Jaymin C; Hoffman, Irving F; Kamthunzi, Portia; Martinson, Francis; Tegha, Gerald; Thengolose, Isaac; Drakeley, Chris; Meshnick, Steven R; Escamillia, Veronica; Emch, Michael; Juliano, Jonathan J

    2016-08-01

    Estimates of malaria transmission intensity (MTI) typically rely upon microscopy or rapid diagnostic testing (RDT). However, these methods are less sensitive than nucleic acid amplification techniques and may underestimate parasite prevalence. We compared microscopy, RDT, and polymerase chain reaction (PCR) for the diagnosis of Plasmodium falciparum parasitemia as part of an MTI study of 800 children and adults conducted in Lilongwe, Malawi. PCR detected more cases of parasitemia than microscopy or RDT. Age less than 5 years predicted parasitemia detected by PCR alone (adjusted odds ratio = 1.61, 95% confidence interval = 1.09-2.38, Wald P = 0.02). In addition, we identified one P. falciparum parasite with a false-negative RDT result due to a suspected deletion of the histidine-rich protein 2 (hrp2) gene and used a novel, ultrasensitive PCR assay to detect low-level parasitemia missed by traditional PCR. Molecular methods should be considered for use in future transmission studies as a supplement to RDT or microscopy. PMID:27325802

  9. Cost Savings with Rapid Diagnostic Tests for Malaria in Low-Transmission Areas: Evidence from Dar es Salaam, Tanzania

    PubMed Central

    Yukich, Joshua; D'Acremont, Valerie; Kahama, Judith; Swai, Ndeniria; Lengeler, Christian

    2010-01-01

    Rapid diagnostic tests (RDTs) for malaria may help rationalize antimalarial drug use. However, the economic effects of these tests may vary. Data on costs were collected from 259 patients in 6 health facilities by using exit and in-charge interviews and record reviews during a trial of RDT rollout in Dar es Salaam, Tanzania. The RDTs decreased patient expenditure on drugs (savings = U.S. $0.36; P = 0.002) and provider drug costs (savings = U.S. $0.43; P = 0.034) compared with control facilities. However, RDT introduction did not significantly reduce patients' overall expenditures (U.S. $1.02, 95% confidence interval [CI] = $0.76–$1.36 versus U.S. $1.33 95% CI = $0.99–$1.77) and may increase total provider costs (U.S. $3.63, 95% CI = $3.40–$3.89 versus U.S. $2.32, 95% CI = $1.99–$2.69) compared with control facilities. Clinician's compliance with test results was higher with RDTs than with routine microscopy (95% versus 82%; P = 0.002). The RDTs reduced drug costs in this setting but did not offset the cost of the tests, although they also resulted in non-monetary benefits, including improved management of patients and increased compliance with test results. PMID:20595479

  10. Distribution of Plasmodium species on the island of Grande Comore on the basis of DNA extracted from rapid diagnostic tests.

    PubMed

    Papa Mze, Nasserdine; Ahouidi, Ambroise D; Diedhiou, Cyrille K; Silai, Rahamatou; Diallo, Mouhamadou; Ndiaye, Daouda; Sembene, Mbacké; Mboup, Souleymane

    2016-01-01

    In the Union of Comoros, interventions for combating malaria have contributed to a spectacular decrease in the prevalence of the disease. We studied the current distribution of Plasmodium species on the island of Grande Comore using nested PCR. The rapid diagnostic tests (RDTs) currently used in the Comoros are able to identify Plasmodium falciparum but no other Plasmodium species. In this study, we tested 211 RDTs (158 positive and 53 negative). Among the 158 positive RDTs, 22 were positive for HRP2, 3 were positive only for pLDH, and 133 were positive for HRP2 and pLDH. DNA was extracted from a proximal part of the nitrocellulose membrane of RDTs. A total of 159 samples were positive by nested PCR. Of those, 156 (98.11%) were positive for P. falciparum, 2 (1.25%) were positive for P. vivaxI, and 1 (0.62%) was positive for P. malariae. None of the samples were positive for P. ovale. Our results show that P. falciparum is still the most dominant species on the island of Grande Comore, but P. vivax and P. malariae are present at a low prevalence. PMID:27561250

  11. Distribution of Plasmodium species on the island of Grande Comore on the basis of DNA extracted from rapid diagnostic tests

    PubMed Central

    Papa Mze, Nasserdine; Ahouidi, Ambroise D.; Diedhiou, Cyrille K.; Silai, Rahamatou; Diallo, Mouhamadou; Ndiaye, Daouda; Sembene, Mbacké; Mboup, Souleymane

    2016-01-01

    In the Union of Comoros, interventions for combating malaria have contributed to a spectacular decrease in the prevalence of the disease. We studied the current distribution of Plasmodium species on the island of Grande Comore using nested PCR. The rapid diagnostic tests (RDTs) currently used in the Comoros are able to identify Plasmodium falciparum but no other Plasmodium species. In this study, we tested 211 RDTs (158 positive and 53 negative). Among the 158 positive RDTs, 22 were positive for HRP2, 3 were positive only for pLDH, and 133 were positive for HRP2 and pLDH. DNA was extracted from a proximal part of the nitrocellulose membrane of RDTs. A total of 159 samples were positive by nested PCR. Of those, 156 (98.11%) were positive for P. falciparum, 2 (1.25%) were positive for P. vivaxI, and 1 (0.62%) was positive for P. malariae. None of the samples were positive for P. ovale. Our results show that P. falciparum is still the most dominant species on the island of Grande Comore, but P. vivax and P. malariae are present at a low prevalence. PMID:27561250

  12. Malaria Rapid Diagnostic Devices: Performance Characteristics of the ParaSight F Device Determined in a Multisite Field Study

    PubMed Central

    Forney, J. Russ; Magill, Alan J.; Wongsrichanalai, Chansuda; Sirichaisinthop, Jeeraphat; Bautista, Christian T.; Heppner, D. Gray; Miller, R. Scott; Ockenhouse, Christian F.; Gubanov, Alex; Shafer, Robyn; DeWitt, Caroline Cady; Quino-Ascurra, Higinio A.; Kester, Kent E.; Kain, Kevin C.; Walsh, Douglas S.; Ballou, W. Ripley; Gasser, Robert A.

    2001-01-01

    Microscopic detection of parasites has been the reference standard for malaria diagnosis for decades. However, difficulty in maintaining required technical skills and infrastructure has spurred the development of several nonmicroscopic malaria rapid diagnostic devices based on the detection of malaria parasite antigen in whole blood. The ParaSight F test is one such device. It detects the presence of Plasmodium falciparum-specific histidine-rich protein 2 by using an antigen-capture immunochromatographic strip format. The present study was conducted at outpatient malaria clinics in Iquitos, Peru, and Maesod, Thailand. Duplicate, blinded, expert microscopy was employed as the reference standard for evaluating device performance. Of 2,988 eligible patients, microscopy showed that 547 (18%) had P. falciparum, 658 (22%) had P. vivax, 2 (0.07%) had P. malariae, and 1,750 (59%) were negative for Plasmodium. Mixed infections (P. falciparum and P. vivax) were identified in 31 patients (1%). The overall sensitivity of ParaSight F for P. falciparum was 95%. When stratified by magnitude of parasitemia (no. of asexual parasites per microliter of whole blood), sensitivities were 83% (>0 to 500 parasites/μl), 87% (501 to 1,000/μl), 98% (1,001 to 5,000/μl), and 98% (>5,000/μl). Device specificity was 86%. PMID:11474008

  13. Improving Access to Malaria Rapid Diagnostic Test in Niger State, Nigeria: An Assessment of Implementation up to 2013

    PubMed Central

    Awoleye, Olatunji Joshua; Thron, Chris

    2016-01-01

    Nigeria's 2009–2013 malaria strategic plan adopted WHO diagnosis and treatment guidelines, which include the use of rapid diagnostic tests (RDTs) prior to prescribing treatment with artemisinin combination therapies (ACTs). The current study explores accessibility barriers to the use of RDTs in Niger State and makes recommendations for improving the uptake of RDTs. The study employs literature review, review of data from the Niger State Health Management Information System for January–October 2013, and application of Peters' conceptual framework for assessing access to health services. Data showed that 27 percent of public health facilities (HFs) implemented RDTs, with the aid of donor funds. In these facilities, 77 percent of fever cases presented during the study period were tested with RDTs; 53 percent of fever cases were confirmed cases of malaria, while 60 percent of fever cases were treated. Stockouts of RDTs were a major constraint, and severe fever tended to trigger presumptive treatment. We conclude that although implementation of RDTs led to a reduction in the use of ACTs at HFs, more substantial reduction could be achieved if the state government directed more resources towards the acquisition of RDTs as well as raising the level of awareness of potential users. PMID:27042376

  14. Improving Access to Malaria Rapid Diagnostic Test in Niger State, Nigeria: An Assessment of Implementation up to 2013.

    PubMed

    Awoleye, Olatunji Joshua; Thron, Chris

    2016-01-01

    Nigeria's 2009-2013 malaria strategic plan adopted WHO diagnosis and treatment guidelines, which include the use of rapid diagnostic tests (RDTs) prior to prescribing treatment with artemisinin combination therapies (ACTs). The current study explores accessibility barriers to the use of RDTs in Niger State and makes recommendations for improving the uptake of RDTs. The study employs literature review, review of data from the Niger State Health Management Information System for January-October 2013, and application of Peters' conceptual framework for assessing access to health services. Data showed that 27 percent of public health facilities (HFs) implemented RDTs, with the aid of donor funds. In these facilities, 77 percent of fever cases presented during the study period were tested with RDTs; 53 percent of fever cases were confirmed cases of malaria, while 60 percent of fever cases were treated. Stockouts of RDTs were a major constraint, and severe fever tended to trigger presumptive treatment. We conclude that although implementation of RDTs led to a reduction in the use of ACTs at HFs, more substantial reduction could be achieved if the state government directed more resources towards the acquisition of RDTs as well as raising the level of awareness of potential users. PMID:27042376

  15. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study.

    PubMed Central

    Pankhurst, Louise; Macfarlane-Smith, Louissa; Buchanan, James; Anson, Luke; Davies, Kerrie; O'Connor, Lily; Ashwin, Helen; Pike, Graham; Dingle, Kate E; Peto, Timothy Ea; Wordsworth, Sarah; Walker, A Sarah; Wilcox, Mark H; Crook, Derrick W

    2014-01-01

    BACKGROUND Every year approximately 5000-9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are 'blocked' by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients. OBJECTIVE To evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens: Clostridium difficile, Campylobacter spp., Salmonella spp. and norovirus. DESIGN A retrospective study of fixed numbers of samples positive for C. difficile (n = 200), Campylobacter spp. (n = 200), Salmonella spp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out. SETTING MassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts. MAIN OUTCOME MEASURES Sensitivity and specificity to detect C. difficile, Campylobacter spp., Salmonella spp., and norovirus. RESULTS Nucleic acids were extracted from 948 clinical samples using an optimised protocol (200 Campylobacter spp., 199 C. difficile, 60 S. enterica, 199 norovirus and 295 negative

  16. A Rapid and Accurate Method to Evaluate Helicobacter pylori Infection, Clarithromycin Resistance, and CYP2C19 Genotypes Simultaneously From Gastric Juice.

    PubMed

    Kuo, Chao-Hung; Liu, Chung-Jung; Yang, Ching-Chia; Kuo, Fu-Chen; Hu, Huang-Ming; Shih, Hsiang-Yao; Wu, Meng-Chieh; Chen, Yen-Hsu; Wang, Hui-Min David; Ren, Jian-Lin; Wu, Deng-Chyang; Chang, Lin-Li

    2016-05-01

    Because Helicobacter pylori (H pylori) would cause carcinogenesis of the stomach, we need sufficient information for deciding on an appropriate strategy of eradication. Many factors affect the efficacy of eradication including antimicrobial resistance (especially clarithromycin resistance) and CYP2C19 polymorphism. This study was to survey the efficiency of gastric juice for detecting H pylori infection, clarithromycin resistance, and CYP2C19 polymorphism.The specimens of gastric juice were collected from all patients while receiving gastroscopy. DNA was extracted from gastric juice and then urease A and cag A were amplified by polymerase chain reaction (PCR) for detecting the existence of H pylori. By PCR-restriction fragment length polymorphism (PCR-RFLP), the 23S rRNA of H pylori and CYP2C19 genotypes of host were examined respectively. During endoscopy examination, biopsy-based specimens were also collected for rapid urease test, culture, and histology. The blood samples were also collected for analysis of CYP2C19 genotypes. We compared the results of gastric juice tests with the results of traditional clinical tests.When compared with the results from traditional clinical tests, our results from gastric juice showed that the sensitivity (SEN), specificity (SPE), positive predictive value (PPV), negative predictive value (NPV), and accuracy to detect H pylori infection were 92.1% (105/114), 92.9% (143/154), 90.5% (105/116), 94.1% (143/152), and 92.5% (248/268), respectively. The SEN, SPE, PPV, and NPV to detect clarithromycin resistance were 97.3% (36/37), 91.5% (43/47), 90.0% (36/40), and 97.7% (43/44), respectively. By using PCR-RFLP, the consistency of human CYP2C19 gene polymorphism from blood samples and gastric juice was as high as 94.9% (149/157).The manipulated gastric juice is actually an effective diagnostic sample for evaluation of H pylori existence, clarithromycin resistance, and host CYP2C19 polymorphism. PMID:27227911

  17. A Rapid and Accurate Method to Evaluate Helicobacter pylori Infection, Clarithromycin Resistance, and CYP2C19 Genotypes Simultaneously From Gastric Juice

    PubMed Central

    Kuo, Chao-Hung; Liu, Chung-Jung; Yang, Ching-Chia; Kuo, Fu-Chen; Hu, Huang-Ming; Shih, Hsiang-Yao; Wu, Meng-Chieh; Chen, Yen-Hsu; Wang, Hui-Min David; Ren, Jian-Lin; Wu, Deng-Chyang; Chang, Lin-Li

    2016-01-01

    Abstract Because Helicobacter pylori (H pylori) would cause carcinogenesis of the stomach, we need sufficient information for deciding on an appropriate strategy of eradication. Many factors affect the efficacy of eradication including antimicrobial resistance (especially clarithromycin resistance) and CYP2C19 polymorphism. This study was to survey the efficiency of gastric juice for detecting H pylori infection, clarithromycin resistance, and CYP2C19 polymorphism. The specimens of gastric juice were collected from all patients while receiving gastroscopy. DNA was extracted from gastric juice and then urease A and cag A were amplified by polymerase chain reaction (PCR) for detecting the existence of H pylori. By PCR-restriction fragment length polymorphism (PCR-RFLP), the 23S rRNA of H pylori and CYP2C19 genotypes of host were examined respectively. During endoscopy examination, biopsy-based specimens were also collected for rapid urease test, culture, and histology. The blood samples were also collected for analysis of CYP2C19 genotypes. We compared the results of gastric juice tests with the results of traditional clinical tests. When compared with the results from traditional clinical tests, our results from gastric juice showed that the sensitivity (SEN), specificity (SPE), positive predictive value (PPV), negative predictive value (NPV), and accuracy to detect H pylori infection were 92.1% (105/114), 92.9% (143/154), 90.5% (105/116), 94.1% (143/152), and 92.5% (248/268), respectively. The SEN, SPE, PPV, and NPV to detect clarithromycin resistance were 97.3% (36/37), 91.5% (43/47), 90.0% (36/40), and 97.7% (43/44), respectively. By using PCR-RFLP, the consistency of human CYP2C19 gene polymorphism from blood samples and gastric juice was as high as 94.9% (149/157). The manipulated gastric juice is actually an effective diagnostic sample for evaluation of H pylori existence, clarithromycin resistance, and host CYP2C19 polymorphism. PMID:27227911

  18. Willingness-to-pay for a rapid malaria diagnostic test and artemisinin-based combination therapy from private drug shops in Mukono district, Uganda

    PubMed Central

    Hansen, Kristian Schultz; Pedrazzoli, Debora; Mbonye, Anthony; Clarke, Sian; Cundill, Bonnie; Magnussen, Pascal; Yeung, Shunmay

    2013-01-01

    In Uganda, as in many parts of Africa, the majority of the population seek treatment for malaria in drug shops as their first point of care; however, parasitological diagnosis is not usually offered in these outlets. Rapid diagnostic tests (RDTs) for malaria have attracted interest in recent years as a tool to improve malaria diagnosis, since they have proved accurate and easy to perform with minimal training. Although RDTs could feasibly be performed by drug shop vendors, it is not known how much customers would be willing to pay for an RDT if offered in these settings. We conducted a contingent valuation survey among drug shop customers in Mukono District, Uganda. Exit interviews were undertaken with customers aged 15 years and above after leaving a drug shop having purchased an antimalarial and/or paracetamol. The bidding game technique was used to elicit the willingness-to-pay (WTP) for an RDT and a course of artemisinin-based combination therapy (ACT) with and without RDT confirmation. Factors associated with WTP were investigated using linear regression. The geometric mean WTP for an RDT was US$0.53, US$1.82 for a course of ACT and US$2.05 for a course of ACT after a positive RDT. Factors strongly associated with a higher WTP for these commodities included having a higher socio-economic status, no fever/malaria in the household in the past 2 weeks and if a malaria diagnosis had been obtained from a qualified health worker prior to visiting the drug shop. The findings further suggest that the WTP for an RDT and a course of ACT among drug shop customers is considerably lower than prevailing and estimated end-user prices for these commodities. Increasing the uptake of ACTs in drug shops and restricting the sale of ACTs to parasitologically confirmed malaria will therefore require additional measures. PMID:22589226

  19. Willingness-to-pay for a rapid malaria diagnostic test and artemisinin-based combination therapy from private drug shops in Mukono District, Uganda.

    PubMed

    Hansen, Kristian Schultz; Pedrazzoli, Debora; Mbonye, Anthony; Clarke, Sian; Cundill, Bonnie; Magnussen, Pascal; Yeung, Shunmay

    2013-03-01

    In Uganda, as in many parts of Africa, the majority of the population seek treatment for malaria in drug shops as their first point of care; however, parasitological diagnosis is not usually offered in these outlets. Rapid diagnostic tests (RDTs) for malaria have attracted interest in recent years as a tool to improve malaria diagnosis, since they have proved accurate and easy to perform with minimal training. Although RDTs could feasibly be performed by drug shop vendors, it is not known how much customers would be willing to pay for an RDT if offered in these settings. We conducted a contingent valuation survey among drug shop customers in Mukono District, Uganda. Exit interviews were undertaken with customers aged 15 years and above after leaving a drug shop having purchased an antimalarial and/or paracetamol. The bidding game technique was used to elicit the willingness-to-pay (WTP) for an RDT and a course of artemisinin-based combination therapy (ACT) with and without RDT confirmation. Factors associated with WTP were investigated using linear regression. The geometric mean WTP for an RDT was US$0.53, US$1.82 for a course of ACT and US$2.05 for a course of ACT after a positive RDT. Factors strongly associated with a higher WTP for these commodities included having a higher socio-economic status, no fever/malaria in the household in the past 2 weeks and if a malaria diagnosis had been obtained from a qualified health worker prior to visiting the drug shop. The findings further suggest that the WTP for an RDT and a course of ACT among drug shop customers is considerably lower than prevailing and estimated end-user prices for these commodities. Increasing the uptake of ACTs in drug shops and restricting the sale of ACTs to parasitologically confirmed malaria will therefore require additional measures. PMID:22589226

  20. Global sequence variation in the histidine-rich proteins 2 and 3 of Plasmodium falciparum: implications for the performance of malaria rapid diagnostic tests

    PubMed Central

    2010-01-01

    Background Accurate diagnosis is essential for prompt and appropriate treatment of malaria. While rapid diagnostic tests (RDTs) offer great potential to improve malaria diagnosis, the sensitivity of RDTs has been reported to be highly variable. One possible factor contributing to variable test performance is the diversity of parasite antigens. This is of particular concern for Plasmodium falciparum histidine-rich protein 2 (PfHRP2)-detecting RDTs since PfHRP2 has been reported to be highly variable in isolates of the Asia-Pacific region. Methods The pfhrp2 exon 2 fragment from 458 isolates of P. falciparum collected from 38 countries was amplified and sequenced. For a subset of 80 isolates, the exon 2 fragment of histidine-rich protein 3 (pfhrp3) was also amplified and sequenced. DNA sequence and statistical analysis of the variation observed in these genes was conducted. The potential impact of the pfhrp2 variation on RDT detection rates was examined by analysing the relationship between sequence characteristics of this gene and the results of the WHO product testing of malaria RDTs: Round 1 (2008), for 34 PfHRP2-detecting RDTs. Results Sequence analysis revealed extensive variations in the number and arrangement of various repeats encoded by the genes in parasite populations world-wide. However, no statistically robust correlation between gene structure and RDT detection rate for P. falciparum parasites at 200 parasites per microlitre was identified. Conclusions The results suggest that despite extreme sequence variation, diversity of PfHRP2 does not appear to be a major cause of RDT sensitivity variation. PMID:20470441

  1. Multiplex real-time quantitative PCR, microscopy and rapid diagnostic immuno-chromatographic tests for the detection of Plasmodium spp: performance, limit of detection analysis and quality assurance

    PubMed Central

    2009-01-01

    Background Accurate laboratory diagnosis of malaria species in returning travelers is paramount in the treatment of this potentially fatal infectious disease. Materials and methods A total of 466 blood specimens from returning travelers to Africa, Asia, and South/Central America with suspected malaria infection were collected between 2007 and 2009 at the reference public health laboratory. These specimens were assessed by reference microscopy, multipex real-time quantitative polymerase chain reaction (QPCR), and two rapid diagnostic immuno-chromatographic tests (ICT) in a blinded manner. Key clinical laboratory parameters such as limit of detection (LOD) analysis on clinical specimens by parasite stage, inter-reader variability of ICTs, staffing implications, quality assurance and cost analysis were evaluated. Results QPCR is the most analytically sensitive method (sensitivity 99.41%), followed by CARESTART (sensitivity 88.24%), and BINAXNOW (sensitivity 86.47%) for the diagnosis of malaria in returning travelers when compared to reference microscopy. However, microscopy was unable to specifically identify Plasmodia spp. in 18 out of 170 positive samples by QPCR. Moreover, the 17 samples that were negative by microscopy and positive by QPCR were also positive by ICTs. Quality assurance was achieved for QPCR by exchanging a blinded proficiency panel with another reference laboratory. The Kappa value of inter-reader variability among three readers for BINAXNOW and CARESTART was calculated to be 0.872 and 0.898 respectively. Serial dilution studies demonstrated that the QPCR cycle threshold correlates linearly with parasitemia (R2 = 0.9746) in a clinically relevant dynamic range and retains a LOD of 11 rDNA copies/μl for P. falciparum, which was several log lower than reference microscopy and ICTs. LOD for QPCR is affected not only by parasitemia but the parasite stage distribution of each clinical specimen. QPCR was approximately 6-fold more costly than reference

  2. Multicountry prospective clinical evaluation of two enzyme-linked immunosorbent assays and two rapid diagnostic tests for diagnosing dengue fever.

    PubMed

    Pal, Subhamoy; Dauner, Allison L; Valks, Andrea; Forshey, Brett M; Long, Kanya C; Thaisomboonsuk, Butsaya; Sierra, Gloria; Picos, Victor; Talmage, Sara; Morrison, Amy C; Halsey, Eric S; Comach, Guillermo; Yasuda, Chadwick; Loeffelholz, Michael; Jarman, Richard G; Fernandez, Stefan; An, Ung Sam; Kochel, Tadeusz J; Jasper, Louis E; Wu, Shuenn-Jue L

    2015-04-01

    We evaluated four dengue diagnostic devices from Alere, including the SD Bioline Dengue Duo (nonstructural [NS] 1 Ag and IgG/IgM), the Panbio Dengue Duo Cassette (IgM/IgG) rapid diagnostic tests (RDTs), and the Panbio dengue IgM and IgG capture enzyme-linked immunosorbent assays (ELISAs) in a prospective, controlled, multicenter study in Peru, Venezuela, Cambodia, and the United States, using samples from 1,021 febrile individuals. Archived, well-characterized samples from an additional 135 febrile individuals from Thailand were also used. Reference testing was performed on all samples using an algorithm involving virus isolation, in-house IgM and IgG capture ELISAs, and plaque reduction neutralization tests (PRNT) to determine the infection status of the individual. The primary endpoints were the clinical sensitivities and specificities of these devices. The SD Bioline Dengue Duo had an overall sensitivity of 87.3% (95% confidence interval [CI], 84.1 to 90.2%) and specificity of 86.8% (95% CI, 83.9 to 89.3%) during the first 14 days post-symptom onset (p.s.o.). The Panbio Dengue Duo Cassette demonstrated a sensitivity of 92.1% (87.8 to 95.2%) and specificity of 62.2% (54.5 to 69.5%) during days 4 to 14 p.s.o. The Panbio IgM capture ELISA had a sensitivity of 87.6% (82.7 to 91.4%) and specificity of 88.1% (82.2 to 92.6%) during days 4 to 14 p.s.o. Finally, the Panbio IgG capture ELISA had a sensitivity of 69.6% (62.1 to 76.4%) and a specificity of 88.4% (82.6 to 92.8%) during days 4 to 14 p.s.o. for identification of secondary dengue infections. This multicountry prospective study resulted in reliable real-world performance data that will facilitate data-driven laboratory test choices for managing patient care during dengue outbreaks. PMID:25588659

  3. Feasibility of Distributing Rapid Diagnostic Tests for Malaria in the Retail Sector: Evidence from an Implementation Study in Uganda

    PubMed Central

    Cohen, Jessica; Fink, Günther; Berg, Katrina; Aber, Flavia; Jordan, Matthew; Maloney, Kathleen; Dickens, William

    2012-01-01

    Background Despite the benefits of malaria diagnosis, most presumed malaria episodes are never tested. A primary reason is the absence of diagnostic tests in retail establishments, where many patients seek care. Malaria rapid diagnostic tests (RDTs) in drug shops hold promise for guiding appropriate treatment. However, retail providers generally lack awareness of RDTs and training to administer them. Further, unsubsidized RDTs may be unaffordable to patients and unattractive to retailers. This paper reports results from an intervention study testing the feasibility of RDT distribution in Ugandan drug shops. Methods and Findings 92 drug shops in 58 villages were offered subsidized RDTs for sale after completing training. Data on RDT purchases, storage, administration and disposal were collected, and samples were sent for quality testing. Household surveys were conducted to capture treatment outcomes. Estimated daily RDT sales varied substantially across shops, from zero to 8.46 RDTs per days. Overall compliance with storage, treatment and disposal guidelines was excellent. All RDTs (100%) collected from shops passed quality testing. The median price charged for RDTs was 1000USH ($0.40), corresponding to a 100% markup, and the same price as blood slides in local health clinics. RDTs affected treatment decisions. RDT-positive patients were 23 percentage points more likely to buy Artemisinin Combination Therapies (ACTs) (p = .005) and 33.1 percentage points more likely to buy other antimalarials (p<.001) than RDT-negative patients, and were 5.6 percentage points more likely to buy ACTs (p = .05) and 31.4 percentage points more likely to buy other antimalarials (p<.001) than those not tested at all. Conclusions Despite some heterogeneity, shops demonstrated a desire to stock RDTs and use them to guide treatment recommendations. Most shops stored, administered and disposed of RDTs properly and charged mark-ups similar to those charged on common medicines. Results

  4. Field and laboratory comparative evaluation of rapid malaria diagnostic tests versus traditional and molecular techniques in India

    PubMed Central

    2010-01-01

    Background Malaria presents a diagnostic challenge in most tropical countries. Microscopy remains the gold standard for diagnosing malaria infections in clinical practice and research. However, microscopy is labour intensive, requires significant skills and time, which causes therapeutic delays. The objective of obtaining result quickly from the examination of blood samples from patients with suspected malaria is now made possible with the introduction of rapid malaria diagnostic tests (RDTs). Several RDTs are available, which are fast, reliable and simple to use and can detect Plasmodium falciparum and non-falciparum infections or both. A study was conducted in tribal areas of central India to measure the overall performance of several RDTs for diagnosis of P. falciparum and non-falciparum infections in comparison with traditional and molecular techniques. Such data will be used to guide procurement decisions of policy makers and programme managers. Methods Five commercially available RDTs were tested simultaneously in field in parallel with peripheral blood smears in outbreak-affected areas. The evaluation is designed to provide comparative data on the performance of each RDT. In addition, molecular method i.e. polymerase chain reaction (PCR) was also carried out to compare all three methods. Results A total of 372 patients with a clinical suspicion of malaria from Bajag Primary Health Centre (PHC) of district Dindori and Satanwada PHC of district Shivpuri attending the field clinics of Regional Medical Research Centre were included in the study. The analysis revealed that the First Response Malaria Antigen pLDH/HRP2 combo test was 94.7% sensitive (95% CI 89.5-97.7) and 69.9% specific (95% CI 63.6-75.6) for P. falciparum. However, for non-falciparum infections (Plasmodium vivax) the test was 84.2% sensitive (95% CI 72.1-92.5) and 96.5% specific (95% CI 93.8-98.2). The Parascreen represented a good alternative. All other RDTs were relatively less sensitive for

  5. Multicountry Prospective Clinical Evaluation of Two Enzyme-Linked Immunosorbent Assays and Two Rapid Diagnostic Tests for Diagnosing Dengue Fever

    PubMed Central

    Dauner, Allison L.; Valks, Andrea; Forshey, Brett M.; Long, Kanya C.; Thaisomboonsuk, Butsaya; Sierra, Gloria; Picos, Victor; Talmage, Sara; Morrison, Amy C.; Halsey, Eric S.; Comach, Guillermo; Yasuda, Chadwick; Loeffelholz, Michael; Jarman, Richard G.; Fernandez, Stefan; An, Ung Sam; Kochel, Tadeusz J.; Jasper, Louis E.; Wu, Shuenn-Jue L.

    2015-01-01

    We evaluated four dengue diagnostic devices from Alere, including the SD Bioline Dengue Duo (nonstructural [NS] 1 Ag and IgG/IgM), the Panbio Dengue Duo Cassette (IgM/IgG) rapid diagnostic tests (RDTs), and the Panbio dengue IgM and IgG capture enzyme-linked immunosorbent assays (ELISAs) in a prospective, controlled, multicenter study in Peru, Venezuela, Cambodia, and the United States, using samples from 1,021 febrile individuals. Archived, well-characterized samples from an additional 135 febrile individuals from Thailand were also used. Reference testing was performed on all samples using an algorithm involving virus isolation, in-house IgM and IgG capture ELISAs, and plaque reduction neutralization tests (PRNT) to determine the infection status of the individual. The primary endpoints were the clinical sensitivities and specificities of these devices. The SD Bioline Dengue Duo had an overall sensitivity of 87.3% (95% confidence interval [CI], 84.1 to 90.2%) and specificity of 86.8% (95% CI, 83.9 to 89.3%) during the first 14 days post-symptom onset (p.s.o.). The Panbio Dengue Duo Cassette demonstrated a sensitivity of 92.1% (87.8 to 95.2%) and specificity of 62.2% (54.5 to 69.5%) during days 4 to 14 p.s.o. The Panbio IgM capture ELISA had a sensitivity of 87.6% (82.7 to 91.4%) and specificity of 88.1% (82.2 to 92.6%) during days 4 to 14 p.s.o. Finally, the Panbio IgG capture ELISA had a sensitivity of 69.6% (62.1 to 76.4%) and a specificity of 88.4% (82.6 to 92.8%) during days 4 to 14 p.s.o. for identification of secondary dengue infections. This multicountry prospective study resulted in reliable real-world performance data that will facilitate data-driven laboratory test choices for managing patient care during dengue outbreaks. PMID:25588659

  6. The development of effective behaviour change interventions to support the use of malaria rapid diagnostic tests by Tanzanian clinicians

    PubMed Central

    2014-01-01

    Background Parasitological confirmation is now recommended for all cases of suspected malaria. The roll-out of rapid diagnostic tests (RDTs) is hoped to enable this goal in low resource settings through point of care testing. However, simply making RDTs available has not led to high uptake of the tests or adherence to results by clinicians, with malaria continuing to be overdiagnosed in many settings. We undertook to design an evidence-based intervention package that would be sufficient to support the introduction of RDTs at dispensaries in Tanzania, to be evaluated through the Targeting Artemisinin Combination Therapy (TACT) cluster randomised controlled trial. Methods We describe five steps in our intervention design: formative research, review of existing evidence and theory, a workshop to define the intervention approach and content and results of formative research, engagement with behaviour change theory and literature, detailed design of intervention materials and piloting and pretesting of intervention materials. This involved fieldwork with a total of 19 health workers and 212 community members in northeast Tanzania. Results The formative research suggested that RDTs were a potential source of conflict in the health worker-patient interaction, but that health workers used various techniques to resolve this, including provision of antimalarial drugs for RDT-negative patients. Our reviews showed that evidence was mixed regarding the effectiveness of different methods and theories to support change in prescribing practice. Our design process is presented, drawing from this collective evidence. We describe the final TACT intervention package (including interactive small group workshops, feedback text messages, motivational text messages and patient information leaflets and posters) in terms of its programme theory and implementation theory. Conclusions Our study suggests that evidence-based design of complex interventions is possible. The use of formative

  7. Evaluation of a smartphone-based rapid fluorescent diagnostic system for H9N2 virus in specific-pathogen-free chickens.

    PubMed

    Yeo, Seon-Ju; Cuc, Bui Thi; Sung, Haan Woo; Park, Hyun

    2016-08-01

    Repeated interspecies transmission of H9N2 virus from poultry to humans and human infections transmitted via aerosols highlight the need for a highly sensitive, rapid diagnostic system for the detection of this virus. However, no such test exhibiting high performance has been developed. In this study, the performance of a smartphone-based rapid fluorescent diagnostic system (SRFDS) was optimized for the diagnosis of an H9N2-virus-infected animal. To suppress the nonspecific reactivity of the bioconjugate in oropharyngeal (OP) and cloacal (CL) samples derived from chickens, different blocking reagents were tested, and a mixture of casein and sucrose was found to be optimal. To assess the performance of SRFDS, OP and CL samples were obtained from specific-pathogen-free chickens and used for comparison of this method with real-time reverse transcription PCR (rRT-PCR) at time points of three, five, and seven days postinfection (dpi). The limit of detection of SRFDS was found to be 7.5 PFU/mL, which was 138-fold higher than that of a conventional colloidal-gold-based avian influenza rapid diagnostic test. In the animal study, the presence of viral antigen was monitored with SRFDS, and the relative sensitivity (relative to rRT-PCR results) was 94.44 % (17/18) and 95.23 % (20/21) in OP and CL specimens, respectively. The specificity of SRFDS was 100 %. These results imply that the diagnostic performance of SRFDS might be comparable to that of rRT-PCR for diagnosis of H9N2 in chickens and that this test can be used as a highly sensitive rapid diagnostic method in field studies on broiler poultry and wild birds. PMID:27287435

  8. Diagnostic performance of a rapid in-clinic test for the detection of Canine Parvovirus under different storage conditions and vaccination status.

    PubMed

    Kantere, Maria C; Athanasiou, Labrini V; Spyrou, Vassiliki; Kyriakis, Constantinos S; Kontos, Vassilios; Chatzopoulos, Dimitrios C; Tsokana, Constantina N; Billinis, Charalambos

    2015-04-01

    Canine parvovirus (CPV) is one of the most common causes of acute haemorrhagic enteritis in young dogs, while clinical diagnosis is often indecisive. The aim of our study was to evaluate the diagnostic accuracy of an in-clinic rapid test in the detection of CPV infection in dogs. To this end, we compared the Rapid Diagnostic Kit of Canine Parvovirus, Coronavirus and Rotavirus antigen (Quicking(®)) to PCR, which is considered as the most reliable diagnostic method. A total of 78 duplicated faecal samples were collected from diarrhoeic dogs. Vaccination history within a month prior to the onset of diarrhoea was reported for 12 of the sampled dogs. The rapid diagnostic test was performed in 23 of the faecal samples directly, while the rest were placed into a sterile cotton tipped swab suitable for collection and transportation of viruses (Sigma Σ-VCM(®)) and stored at -20 °C. The sensitivity of the Quicking rapid diagnostic test compared to PCR in the total number of samples, in samples from non-vaccinated dogs and in samples tested directly after collection were 22.22% (95% CI: 13.27-33.57%), 26.67% (95% CI: 16.08-39.66%) and 76.47% (95% CI: 50.10-93.04%) respectively, while the specificity of the test was 100% in any case. In conclusion, negative results do not exclude parvoenteritis from the differential diagnosis, especially in dogs with early vaccination history, but a positive result almost certainly indicates CPV infection. An improved sensitivity may be expected when the test is performed immediately. PMID:25707551

  9. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    PubMed Central

    2011-01-01

    Background This study describes the use of malaria rapid diagnostic tests (RDTs) as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test) were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60), Plasmodium vivax (n = 10), Plasmodium ovale (n = 10) and Plasmodium malariae (n = 10). Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20) gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the best method of RDT

  10. Socially-marketed rapid diagnostic tests and ACT in the private sector: ten years of experience in Cambodia.

    PubMed

    Yeung, Shunmay; Patouillard, Edith; Allen, Henrietta; Socheat, Duong

    2011-01-01

    Whilst some populations have recently experienced dramatic declines in malaria, the majority of those most at risk of Plasmodium falciparum malaria still lack access to effective treatment with artemisinin combination therapy (ACT) and others are already facing parasites resistant to artemisinins.In this context, there is a crucial need to improve both access to and targeting of ACT through greater availability of good quality ACT and parasitological diagnosis. This is an issue of increasing urgency notably in the private commercial sector, which, in many countries, plays an important role in the provision of malaria treatment. The Affordable Medicines Facility for malaria (AMFm) is a recent initiative that aims to increase the provision of affordable ACT in public, private and NGO sectors through a manufacturer-level subsidy. However, to date, there is little documented experience in the programmatic implementation of subsidized ACT in the private sector. Cambodia is in the unique position of having more than 10 years of experience not only in implementing subsidized ACT, but also rapid diagnostic tests (RDT) as part of a nationwide social marketing programme. The programme includes behaviour change communication and the training of private providers as well as the sale and distribution of Malarine, the recommended ACT, and Malacheck, the RDT. This paper describes and evaluates this experience by drawing on the results of household and provider surveys conducted since the start of the programme. The available evidence suggests that providers' and consumers' awareness of Malarine increased rapidly, but that of Malacheck much less so. In addition, improvements in ACT and RDT availability and uptake were relatively slow, particularly in more remote areas.The lack of standardization in the survey methods and the gaps in the data highlight the importance of establishing a clear system for monitoring and evaluation for similar initiatives. Despite these limitations, a

  11. Use of a Cholera Rapid Diagnostic Test during a Mass Vaccination Campaign in Response to an Epidemic in Guinea, 2012

    PubMed Central

    Martinez-Pino, Isabel; Luquero, Francisco J.; Sakoba, Kéïta; Sylla, Souleymane; Haile, Melatwork; Grais, Rebecca F.; Ciglenecki, Iza; Quilici, Marie-Laure; Page, Anne-Laure

    2013-01-01

    Background During the 2012 cholera outbreak in the Republic of Guinea, the Ministry of Health, supported by Médecins Sans Frontières - Operational Center Geneva, used the oral cholera vaccine Shanchol as a part of the emergency response. The rapid diagnostic test (RDT) Crystal VC, widely used during outbreaks, detects lipopolysaccharide antigens of Vibrio cholerae O1 and O139, both included in Shanchol. In the context of reactive use of a whole-cell cholera vaccine in a region where cholera cases have been reported, it is essential to know what proportion of vaccinated individuals would be reactive to the RDT and for how long after vaccination. Methodology/Principal Findings A total of 108 vaccinated individuals, selected systematically among all persons older than one year, were included at vaccination sites and 106 were included in the analysis. Stools samples of this cohort of vaccinated participants were collected and tested with the RDT every day until the test was negative for two consecutive visits or for a maximum of 7 days. A total of 94.3% of cholera vaccine recipients had a positive test after vaccination; all except one of these positive results were reactive only with the O139 antigen. The mean time to become negative in those with an initial positive result after vaccination was 3.8 days, standard deviation 1.1 days. Conclusions/Significance The RDT Crystal VC becomes positive in persons recently vaccinated against cholera, although almost exclusively to the O139 antigen. This reactivity largely disappeared within five days after vaccination. These results suggest that the test can be used normally as soon as 24 hours after vaccination in a context of O1 epidemics, which represent the vast majority of cases, and after a period of five days in areas where V. cholerae O139 is present. The reason why only O139 test line became positive remains to be investigated. PMID:23967359

  12. The Performance of a Rapid Diagnostic Test in Detecting Malaria Infection in Pregnant Women and the Impact of Missed Infections

    PubMed Central

    Williams, John E.; Cairns, Matthew; Njie, Fanta; Laryea Quaye, Stephen; Awine, Timothy; Oduro, Abraham; Tagbor, Harry; Bojang, Kalifa; Magnussen, Pascal; ter Kuile, Feiko O.; Woukeu, Arouna; Milligan, Paul; Chandramohan, Daniel; Greenwood, Brian

    2016-01-01

    Background. Intermittent screening and treatment in pregnancy (ISTp) is a potential strategy for the control of malaria during pregnancy. However, the frequency and consequences of malaria infections missed by a rapid diagnostic test (RDT) for malaria are a concern. Methods. Primigravidae and secundigravidae who participated in the ISTp arm of a noninferiority trial in 4 West African countries were screened with an HRP2/pLDH RDT on enrollment and, in Ghana, at subsequent antenatal clinic (ANC) visits. Blood samples were examined subsequently by microscopy and by a polymerase chain reaction (PCR) assay. Results. The sensitivity of the RDT to detect peripheral blood infections confirmed by microscopy and/or PCR at enrollment ranged from 91% (95% confidence interval [CI], 88%, 94%) in Burkina Faso to 59% (95% CI, 48%, 70% in The Gambia. In Ghana, RDT sensitivity was 89% (95% CI, 85%, 92%), 83% (95% CI, 76%, 90%) and 77% (95% CI, 67%, 86%) at enrollment, second and third ANC visits respectively but only 49% (95% CI, 31%, 66%) at delivery. Screening at enrollment detected 56% of all infections detected throughout pregnancy. Seventy-five RDT negative PCR or microscopy positive infections were detected in 540 women; these were not associated with maternal anemia, placental malaria, or low birth weight. Conclusions. The sensitivity of an RDT to detect malaria in primigravidae and secundigravidae was high at enrollment in 3 of 4 countries and, in Ghana, at subsequent ANC visits. In Ghana, RDT negative malaria infections were not associated with adverse birth outcomes but missed infections were uncommon. PMID:26721833

  13. Laboratory demonstration of a prozone-like effect in HRP2-detecting malaria rapid diagnostic tests: implications for clinical management

    PubMed Central

    2011-01-01

    Background Malaria rapid diagnostic tests (RDTs) are now widely used for prompt on-site diagnosis in remote endemic areas where reliable microscopy is absent. Aberrant results, whereby negative test results occur at high parasite densities, have been variously reported for over a decade and have led to questions regarding the reliability of the tests in clinical use. Methods In the first trial, serial dilutions of recombinant HRP2 antigen were tested on an HRP2-detectiing RDT. In a second trial, serial dilutions of culture-derived Plasmodium falciparum parasites were tested against three HRP2-detecting RDTs. Results A prozone-like effect occurred in RDTs at a high concentration of the target antigen, histidine-rich protein-2 (above 15,000 ng/ml), a level that corresponds to more than 312000 parasites per μL. Similar results were noted on three RDT products using dilutions of cultured parasites up to a parasite density of 25%. While reduced line intensity was observed, no false negative results occurred. Conclusions These results suggest that false-negative malaria RDT results will rarely occur due to a prozone-like effect in high-density infections, and other causes are more likely. However, RDT line intensity is poorly indicative of parasite density in high-density infections and RDTs should, therefore, not be considered quantitative. Immediate management of suspected severe malaria should rely on clinical assessment or microscopy. Evaluation against high concentrations of antigen should be considered in malaria RDT product development and lot-release testing, to ensure that very weak or false negative results will not occur at antigen concentrations that might be seen clinically. PMID:21957869

  14. An evaluation of the New Roche Diagnostics Kit for the rapid identification of clinically important non-dextrose, non-fastidious gram-negative rods.

    PubMed

    Elegbe, I A

    1980-01-01

    The evaluation of the new Roche Diagnostics Commercial kit (Roche Diagnostics, 1975) for the identification of non-dextrose fermenting, non-fastidious gram-negative rods has been compared with conventional methods in the recognition and identification of these non-dextrose, non-fastidious gram-negative bacteria. This new kit has definite advantages over and above the conventional methods in a number of ways. It is cheaper to run, and above all it is less cumbersome, less time consuming and it is accurate. Apart from all these, the new method makes use of the odour test (Roche Diagnostics, 1975) and other additional conventional tests recommended by the Oxi/ferm manufacturer. PMID:6283862

  15. MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

    PubMed

    Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

    2016-08-01

    All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species. PMID:27296834

  16. The impact of providing rapid diagnostic malaria tests on fever management in the private retail sector in Ghana: a cluster randomized trial

    PubMed Central

    Narh-Bana, Solomon; Affran-Bonful, Harriet; Bart-Plange, Constance; Cundill, Bonnie; Gyapong, Margaret; Whitty, Christopher J M

    2015-01-01

    Objective To examine the impact of providing rapid diagnostic tests for malaria on fever management in private drug retail shops where most poor rural people with fever present, with the aim of reducing current massive overdiagnosis and overtreatment of malaria. Design Cluster randomized trial of 24 clusters of shops. Setting Dangme West, a poor rural district of Ghana. Participants Shops and their clients, both adults and children. Interventions Providing rapid diagnostic tests with realistic training. Main outcome measures The primary outcome was the proportion of clients testing negative for malaria by a double-read research blood slide who received an artemisinin combination therapy or other antimalarial. Secondary outcomes were use of antibiotics and antipyretics, and safety. Results Of 4603 clients, 3424 (74.4%) tested negative by double-read research slides. The proportion of slide-negative clients who received any antimalarial was 590/1854 (32%) in the intervention arm and 1378/1570 (88%) in the control arm (adjusted risk ratio 0.41 (95% CI 0.29 to 0.58), P<0.0001). Treatment was in high agreement with rapid diagnostic test result. Of those who were slide-positive, 690/787 (87.8%) in the intervention arm and 347/392 (88.5%) in the control arm received an artemisinin combination therapy (adjusted risk ratio 0.96 (0.84 to 1.09)). There was no evidence of antibiotics being substituted for antimalarials. Overall, 1954/2641 (74%) clients in the intervention arm and 539/1962 (27%) in the control arm received appropriate treatment (adjusted risk ratio 2.39 (1.69 to 3.39), P<0.0001). No safety concerns were identified. Conclusions Most patients with fever in Africa present to the private sector. In this trial, providing rapid diagnostic tests for malaria in the private drug retail sector significantly reduced dispensing of antimalarials to patients without malaria, did not reduce prescribing of antimalarials to true malaria cases, and appeared safe. Rapid

  17. A Rapid Diagnostic Technique to Discriminate between Two Pests of Palms, Brontispa longissima and Octodonta nipae (Coleoptera: Chrysomelidae), for Quarantine Applications.

    PubMed

    Zhang, X; Tang, B; Hou, Y

    2015-02-01

    Octodonta nipae (Maulik) is morphologically and biologically similar to Brontispa longissima (Gestro), one of the most damaging pests of coconut. The two species share several palm hosts and produce similar symptoms. They are easily confused when they invade a new area, and without professional taxonomic expertise accurate identification is arduous and time-consuming. Thus, a method of rapidly distinguishing these two invasive insects rapidly is critical for quarantine. Based on the first internal transcribed spacer and the mitochondrial cytochrome oxidase I gene, two pairs of special primers and corresponding polymerase chain reaction processes have been developed to enhance a single objective band only from the O. nipae DNA template. This will quickly discriminate between these two species. The present results provide a rapid method of distinguishing O. nipae from B. longissima to help avoid misidentification, and furthermore, to facilitate rapid and appropriate quarantine decisions and effective treatments to the pest. PMID:26470108

  18. Immediate-Early Gene Transcriptional Activation in Hippocampus Ca1 and Ca3 Does Not Accurately Reflect Rapid, Pattern Completion-Based Retrieval of Context Memory

    ERIC Educational Resources Information Center

    Pevzner, Aleksandr; Guzowski, John F.

    2015-01-01

    No studies to date have examined whether immediate-early gene (IEG) activation is driven by context memory recall. To address this question, we utilized the context preexposure facilitation effect (CPFE) paradigm. In CPFE, animals acquire contextual fear conditioning through hippocampus-dependent rapid retrieval of a previously formed contextual…

  19. Evaluation of three parasite lactate dehydrogenase-based rapid diagnostic tests for the diagnosis of falciparum and vivax malaria

    PubMed Central

    Ashley, Elizabeth A; Touabi, Malek; Ahrer, Margareta; Hutagalung, Robert; Htun, Khayae; Luchavez, Jennifer; Dureza, Christine; Proux, Stephane; Leimanis, Mara; Lwin, Myo Min; Koscalova, Alena; Comte, Eric; Hamade, Prudence; Page, Anne-Laure; Nosten, François; Guerin, Philippe J

    2009-01-01

    Background In areas where non-falciparum malaria is common rapid diagnostic tests (RDTs) capable of distinguishing malaria species reliably are needed. Such tests are often based on the detection of parasite lactate dehydrogenase (pLDH). Methods In Dawei, southern Myanmar, three pLDH based RDTs (CareStart™ Malaria pLDH (Pan), CareStart™ Malaria pLDH (Pan, Pf) and OptiMAL-IT®)were evaluated in patients presenting with clinically suspected malaria. Each RDT was read independently by two readers. A subset of patients with microscopically confirmed malaria had their RDTs repeated on days 2, 7 and then weekly until negative. At the end of the study, samples of study batches were sent for heat stability testing. Results Between August and November 2007, 1004 patients aged between 1 and 93 years were enrolled in the study. Slide microscopy (the reference standard) diagnosed 213 Plasmodium vivax (Pv) monoinfections, 98 Plasmodium falciparum (Pf) mono-infections and no malaria in 650 cases. The sensitivities (sens) and specificities (spec), of the RDTs for the detection of malaria were- CareStart Malaria™ pLDH (Pan) test: sens 89.1% [CI95 84.2-92.6], spec 97.6% [CI95 96.5-98.4] OptiMal-IT®: Pf+/- other species detection: sens 95.2% [CI95 87.5-98.2], spec 94.7% [CI95 93.3-95.8]; non-Pf detection alone: sens 89.6% [CI95 83.6-93.6], spec 96.5% [CI95 94.8-97.7] CareStart Malaria™ pLDH (Pan, Pf): Pf+/- other species: sens 93.5% [CI9585.4-97.3], spec 97.4% [95.9-98.3]; non-Pf: sens 78.5% [CI9571.1-84.4], spec 97.8% [CI95 96.3-98.7] Inter-observer agreement was excellent for all tests (kappa > 0.9). The median time for the RDTs to become negative was two days for the CareStart™ Malaria tests and seven days for OptiMAL-IT®. Tests were heat stable up to 90 days except for OptiMAL-IT® (Pf specific pLDH stable to day 20 at 35°C). Conclusion None of the pLDH-based RDTs evaluated was able to detect non-falciparum malaria with high sensitivity, particularly at low

  20. Cotton-based diagnostic devices.

    PubMed

    Lin, Shang-Chi; Hsu, Min-Yen; Kuan, Chen-Meng; Wang, Hsi-Kai; Chang, Chia-Ling; Tseng, Fan-Gang; Cheng, Chao-Min

    2014-01-01

    A good diagnostic procedure avoids wasting medical resources, is easy to use, resists contamination, and provides accurate information quickly to allow for rapid follow-up therapies. We developed a novel diagnostic procedure using a "cotton-based diagnostic device" capable of real-time detection, i.e., in vitro diagnostics (IVD), which avoids reagent contamination problems common to existing biomedical devices and achieves the abovementioned goals of economy, efficiency, ease of use, and speed. Our research reinforces the advantages of an easy-to-use, highly accurate diagnostic device created from an inexpensive and readily available U.S. FDA-approved material (i.e., cotton as flow channel and chromatography paper as reaction zone) that adopts a standard calibration curve method in a buffer system (i.e., nitrite, BSA, urobilinogen and uric acid assays) to accurately obtain semi-quantitative information and limit the cross-contamination common to multiple-use tools. Our system, which specifically targets urinalysis diagnostics and employs a multiple biomarker approach, requires no electricity, no professional training, and is exceptionally portable for use in remote or home settings. This could be particularly useful in less industrialized areas. PMID:25393975

  1. Integrated Community Case Management of Fever in Children under Five Using Rapid Diagnostic Tests and Respiratory Rate Counting: A Multi-Country Cluster Randomized Trial

    PubMed Central

    Mukanga, David; Tiono, Alfred B.; Anyorigiya, Thomas; Källander, Karin; Konaté, Amadou T.; Oduro, Abraham R.; Tibenderana, James K.; Amenga-Etego, Lucas; Sirima, Sodiomon B.; Cousens, Simon; Barnish, Guy; Pagnoni, Franco

    2012-01-01

    Evidence on the impact of using diagnostic tests in community case management of febrile children is limited. This effectiveness trial conducted in Burkina Faso, Ghana, and Uganda, compared a diagnostic and treatment package for malaria and pneumonia with presumptive treatment with anti-malarial drugs; artemisinin combination therapy (ACT). We enrolled 4,216 febrile children between 4 and 59 months of age in 2009–2010. Compliance with the malaria rapid diagnostic test (RDT) results was high in the intervention arm across the three countries, with only 4.9% (17 of 344) of RDT-negative children prescribed an ACT. Antibiotic overuse was more common: 0.9% (4 of 446) in Uganda, 38.5% (114 of 296) in Burkina Faso, and 44.6% (197 of 442) in Ghana. Fever clearance was high in both intervention and control arms at both Day 3 (97.8% versus 96.9%, P = 0.17) and Day 7 (99.2% versus 98.8%, P = 0.17). The use of diagnostic tests limits overuse of ACTs. Its impact on antibiotic overuse and on fever clearance is uncertain. PMID:23136274

  2. Study on the applicability of a precise, accurate method for rapid evaluation of engine and lubricant performance. [determination of wear metal in used lubricating oils

    NASA Technical Reports Server (NTRS)

    Kinard, J. T.

    1975-01-01

    The development of a procedure for obtaining data related to wear metal determinations in used lubricants is discussed. The procedure makes it possible to obtain rapid, simultaneous determinations of a number of wear metals at levels of parts per thousand to low parts per billion using a small amount of sample. The electrode assembly and instrumentation used in the process are described. Samples of data obtained from tests conducted under controlled conditions are tabulated.

  3. Helicopter Based Magnetic Detection Of Wells At The Teapot Dome (Naval Petroleum Reserve No. 3 Oilfield: Rapid And Accurate Geophysical Algorithms For Locating Wells

    NASA Astrophysics Data System (ADS)

    Harbert, W.; Hammack, R.; Veloski, G.; Hodge, G.

    2011-12-01

    In this study Airborne magnetic data was collected by Fugro Airborne Surveys from a helicopter platform (Figure 1) using the Midas II system over the 39 km2 NPR3 (Naval Petroleum Reserve No. 3) oilfield in east-central Wyoming. The Midas II system employs two Scintrex CS-2 cesium vapor magnetometers on opposite ends of a transversely mounted, 13.4-m long horizontal boom located amidships (Fig. 1). Each magnetic sensor had an in-flight sensitivity of 0.01 nT. Real time compensation of the magnetic data for magnetic noise induced by maneuvering of the aircraft was accomplished using two fluxgate magnetometers mounted just inboard of the cesium sensors. The total area surveyed was 40.5 km2 (NPR3) near Casper, Wyoming. The purpose of the survey was to accurately locate wells that had been drilled there during more than 90 years of continuous oilfield operation. The survey was conducted at low altitude and with closely spaced flight lines to improve the detection of wells with weak magnetic response and to increase the resolution of closely spaced wells. The survey was in preparation for a planned CO2 flood to enhance oil recovery, which requires a complete well inventory with accurate locations for all existing wells. The magnetic survey was intended to locate wells that are missing from the well database and to provide accurate locations for all wells. The well location method used combined an input dataset (for example, leveled total magnetic field reduced to the pole), combined with first and second horizontal spatial derivatives of this input dataset, which were then analyzed using focal statistics and finally combined using a fuzzy combination operation. Analytic signal and the Shi and Butt (2004) ZS attribute were also analyzed using this algorithm. A parameter could be adjusted to determine sensitivity. Depending on the input dataset 88% to 100% of the wells were located, with typical values being 95% to 99% for the NPR3 field site.

  4. Rapid-Response Parenting Intervention in Diagnostic Centers as a Patient-Centered Innovation for Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    McMillin, Stephen Edward; Bultas, Margaret W.; Wilmott, Jennifer; Grafeman, Sarah; Zand, Debra H.

    2015-01-01

    Parents of children newly diagnosed with autism spectrum disorders are a high-need population for whom skills-based parenting interventions likely help. Diagnostic centers are compelling locations to deliver parenting interventions because families are served in an accessible location and at a time they receive overwhelming treatment…

  5. Crystal Diagnostics Xpress™ E7 STEC Kit for the Rapid Multiplex Detection of E. coli O157 and non-O157 Shiga toxin-producing E. coli.

    PubMed

    Zhao, Weidong; Stumpf, Curtis H; Bullard, Brian; Kuzenko, Stephanie; Niehaus, Gary D

    2015-01-01

    The Crystal Diagnostics (CDx) Xpress E7 STEC kit is a rapid and sensitive detection assay for the detection of Escherichia coli O157 and six non-O157 Shiga toxin-producing E. coli (serogroups O26, O45, O1O3, O111, O121, and O145, collectively referred to as STEC) at 1 CFU/325 g of raw ground beef and raw beef trim, or 200 g of spinach. The system comprises an automatic Crystal Diagnostics Xpress System Reader that integrates immunochemical and optical processes for the liquid crystal-based detection of microorganisms, a CDx BioCassette that incorporates antibody-coupled microspheres and liquid crystal for selective identification of the intended microbe, and additional commercially available components. The Crystal Diagnostics Xpress System(TM) combines proprietary liquid crystal technology with antibody-coated paramagnetic microspheres to selectively capture and detect STEC from food matrixes. The Xpress System expeditiously (9.5 h enrichment) provides the sensitivity and specificity of the U. S. Department of Agriculture Food Safety and Inspection Service and the U. S. Food and Drug Administration reference methods in screening as low as 1 STEC CFU/test portion. The inclusivity validation demonstrated detection of 53 of 54 STEC test strains. Shelf life testing of the antibody-coated microspheres and other Crystal Diagnostic consumables indicated that all materials were stable for a minimum of 3 months (ongoing), and lot-to-lot testing demonstrated consistent results between lots (data not shown). The internal and independent laboratory tests demonstrate that the method is rapid and sensitive for screening of the target STEC. PMID:26651567

  6. Detection of 2009 pandemic influenza A(H1N1) virus Infection in different age groups by using rapid influenza diagnostic tests

    PubMed Central

    Gao, Fengxiang; Loring, Carol; Laviolette, Michael; Bolton, Denise; Daly, Elizabeth R.; Bean, Christine

    2011-01-01

    Please cite this paper as: Gao et al. (2011) Detection of 2009 pandemic influenza A(H1N1) virus Infection in different age groups by using rapid influenza diagnostic tests. Influenza and Other Respiratory Viruses 6(3), e30–e34. Background  The performance of rapid influenza diagnostic tests (RIDTs) in detecting influenza A(H1N1) 2009 has varied widely. Evaluations of RIDTs among infected individuals across all age groups have not been described in depth. Objectives  Determine RIDT clinical sensitivity in comparison with influenza detection using real‐time RT‐PCR among patients infected with influenza A(H1N1) 2009 across all age groups. Study design  This study analyzed respiratory specimens received by the New Hampshire Public Health Laboratories (NHPHL) from September 1, 2009, through December 31, 2009. RIDT performance was evaluated among different age groups of patients determined to be infected with influenza A (H1N1) 2009, and the association between age and RIDT sensitivity was determined. Results  Of 1373 specimens examined, 269 tested positive for influenza A(H1N1) 2009 by real‐time RT‐PCR (rRT‐PCR) and had RIDT results available. Overall clinical sensitivity and specificity of RIDTs were 53·9 and 98·5%, respectively. By age group, clinical sensitivity was 85·7% in patients <2 years old, 60·3% in patients between 2‐ and 39 years old, and 33·3% in patients aged 40 and older. Logistic regression analysis indicated that increasing age was negatively associated with RIDT performance. Conclusion  Rapid influenza diagnostic test sensitivity decreased significantly with increasing age. Findings from this study may impact a clinician’s interpretation of RIDT test results and ultimately have implications in clinical decision‐making. PMID:22114876

  7. A dual-plane co-RASOR technique for accurate and rapid tracking and position verification of an Ir-192 source for single fraction HDR brachytherapy

    NASA Astrophysics Data System (ADS)

    de Leeuw, Hendrik; Moerland, Marinus A.; van Vulpen, Marco; Seevinck, Peter R.; Bakker, Chris J. G.

    2013-11-01

    Effective high-dose-rate (HDR) treatment requires accurate and independent treatment verification to ensure that the treatment proceeds as prescribed, in particular if a high dose is given, as in single fraction therapy. Contrary to CT imaging and fluoroscopy, MR imaging provides high soft tissue contrast. Conventional MR techniques, however, do not offer the temporal resolution in combination with the 3D spatial resolution required for accurate brachytherapy source localization. We have developed an MR imaging method (center-out RAdial Sampling with Off-Resonance (co-RASOR)) that generates high positive contrast in the geometrical center of field perturbing objects, such as HDR brachytherapy sources. co-RASOR generates high positive contrast in the geometric center of an Ir-192 source by applying a frequency offset to center-out encoded data. To obtain high spatial accuracy in 3D with adequate temporal resolution, two orthogonal center-out encoded 2D images are applied instead of a full 3D acquisition. Its accuracy in 3D is demonstrated by 3D MRI and CT. The 2D images show high positive contrast in the geometric center of non-radioactive Ir-192 sources, with signal intensities up to 160% of the average signal intensity in the surrounding medium. The accuracy with which the center of the Ir-192 source is located by the dual-plane MRI acquisition corresponds closely to the accuracy obtained by 3D MRI and CT imaging. The positive contrast is shown to be obtained in homogeneous and in heterogeneous tissue. The dual-plane MRI technique allows the brachytherapy source to be tracked in 3D with millimeter accuracy with a temporal resolution of approximately 4 s.

  8. Evaluation of an in-house rapid diagnostic method for detection of Salmonella enterica serovar Typhi in fecal specimens.

    PubMed

    Vaishnavi, Chetana; Kaur, Sukhminderjit; Singh, Kartar

    2006-01-01

    Salmonella enterica serovar Typhi is the etiological agent of typhoid fever. Laboratory diagnosis requires isolation and identification of the organism from the patient's blood or feces. Feces is the specimen most commonly submitted to laboratories. Detection of bacterial antigens is an important adjunct to laboratory diagnosis. We carried out an in-house diagnostic method by preparing test reagents comprising of latex beads coated with specific antisera to detect Vi, O9 and H-d antigens of S. typhi. Fecal specimens from one hundred patients with diarrhea and fever as well as from twenty healthy controls were incubated for enrichment in Selenite F broth for 6 hours or overnight. Latex agglutination tests to detect antigens of S. typhi were carried out on centrifuged broth supernatants. Parallel cultures on media selective for S. typhi were also set up. Nine of the supernatants were positive for two or more specific antigens and S. typhi grew in three of the corresponding cultures. None of the samples from 20 healthy controls were positive by either the diagnostic method or by culture. The result of the in-house diagnostic assay can be obtained overnight and may help in directing immediate antimicrobial therapy. PMID:16910055

  9. Electrochemical-surface enhanced Raman spectroscopy (E-SERS) of uric acid: a potential rapid diagnostic method for early preeclampsia detection.

    PubMed

    Goodall, Barbara L; Robinson, Ashley M; Brosseau, Christa L

    2013-02-01

    An increased level of uric acid in urine and plasma is indicative of the development of preeclampsia, a hypertensive disorder that can occur during pregnancy. The preliminary steps towards developing a rapid tool for early diagnosis of preeclampsia using electrochemical SERS (E-SERS) for the detection of uric acid in urine are presented herein. Characterization of the uric acid species was completed using cyclic voltammetry, UV spectroscopy, Raman spectroscopy and electrochemical surface-enhanced Raman spectroscopy (E-SERS). E-SERS was capable of easily detecting uric acid directly at concentrations <1 mM in urine simulant, without the need for costly enzymes and bulky equipment, and thus demonstrates promise as a rapid point-of-care diagnostic tool for detection of early onset preeclampsia in developing nation settings. PMID:23187309

  10. Diagnostic value of a new myocardial perfusion agent, teboroxime (SQ 30,217), utilizing a rapid planar imaging protocol: Preliminary results

    SciTech Connect

    Hendel, R.C.; McSherry, B.; Karimeddini, M.; Leppo, J.A. )

    1990-10-01

    Technetium-99m-labeled agents have advantages over thallium-201 in terms of photon statistics, cost and clinical availability. They have been suggested as an alternative to thallium for myocardial perfusion imaging. Teboroxime is a new boronic acid adduct of technetium dioxime (BATO) compound that demonstrates favorable characteristics in preliminary studies. With use of a novel (seated) patient positioning technique and a rapid dynamic acquisition protocol, 30 patients underwent planar imaging with teboroxime while at rest and after maximal treadmill exercise. Postexercise scans were completed in an average time (mean +/- SD) of 4.4 +/- 1.6 min, with 4.8 +/- 1.5 min for the views at rest. These results were compared with coronary arteriography or thallium scintigraphy after treadmill exercise, or both. Diagnostic agreement (abnormal versus normal) was present in 28 of the 30 patients (p less than 0.001). Regarding physiologic assessment as compared with thallium scintigraphy, the finding of infarction and ischemia was concordant in 89% and 86% of patients, respectively. This report describes the initial use of teboroxime with a rapid dynamic planar imaging technique, resulting in a high correlation with exercise thallium scintigraphy. Delayed postexercise images obtained 5 to 10 min after exercise demonstrated rapid disappearance of exercise-induced defects noted on the initial (0 to 5 min) postexercise views. The rapid differential washout with teboroxime has not been previously described and the possible clinical significance is discussed.

  11. Diagnostic value of a new myocardial perfusion agent, teboroxime (SO 30,217), utilizing a rapid planar imaging protocol: Preliminary results

    SciTech Connect

    Hendel, R.C.; McSherry, B.; Karimeddini, M.; Leppo, J.A. )

    1990-11-01

    Technetium-99m-labeled agents have advantages over thallium-201 in terms of photon statistics, cost and clinical availability. They have been suggested as an alternative to thallium for myocardial perfusion imaging. Teboroxime is a new boronic acid adduct of technetium dioxime (BATO) compound that demonstrates favorable characteristics in preliminary studies. With use of a novel (seated) patient positioning technique and a rapid dynamic acquisition protocol, 30 patients underwent planar imaging with teboroxoime while at rest and after maximal treadmill exercise. Postexercise scans were completed in an average time (mean +/- SD) of 4.4 +/- 1.6 min, with 4.8 +/- 1.5 min for the views at rest. These results were compared with coronary arteriography or thallium scintigraphy after treadmill exercise, or both. Diagnostic agreement (abnormal versus normal) was present in 28 of the 30 patients (p less than 0.001). Regarding physiologic assessment as compared with thallium scintigraphy, the finding of infarction and ischemia was concordant in 89% and 86% of patients, respectively. This report describes the initial use of teboroxime with a rapid dynamic planar imaging technique, resulting in a high correlation with exercise thallium scintigraphy. Delayed postexercise images obtained 5 to 10 min after exercise demonstrated rapid disappearance of exercise-induced defects noted on the initial (0 to 5 min) postexercise views. The rapid differential washout with teboroxime has not been previously described and the possible clinical significance is discussed.

  12. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing

    PubMed Central

    2010-01-01

    Background In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiD™) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization. Results To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination

  13. A novel and rapid diagnostic method for discriminating between feces of sika deer and Japanese serow by loop-mediated isothermal amplification.

    PubMed

    Aikawa, T; Horino, S; Ichihara, Y

    2015-08-01

    Severe damages to natural vegetation, agriculture, and forestry caused by overpopulation of sika deer (Cervus nippon) have markedly increased in Japan in recent years. To devise a population management plan of sika deer, information on the distribution and population size of the animal in each region is indispensable. An easy and effective method to obtain this information is to count the fecal pellets in the field. However, the habitat of sika deer in Japan overlaps that of Japanese serow (Capricornis crispus). Additionally, it is difficult to discriminate between the feces of both animals. Here, we present a rapid and precise diagnostic method for discriminating between the feces of sika deer and Japanese serow using loop-mediated isothermal amplification (LAMP) targeting cytochrome b gene in the mitochondrial DNA. Our results showed that the LAMP can discriminate between the feces of sika deer and Japanese serow, and the method is simpler and more sensitive than the conventional molecular diagnostic method. Since LAMP method does not require special skills for molecular biology techniques, even the field researchers who have never done a molecular experiment can easily carry out the protocol. In addition, the entire protocol, from DNA extraction from fecal pellet to identification of species, takes only about 75 min and does not require expensive equipment. Hence, this diagnostic method is simple, fast, and accessible to anyone. As such, the method can be a useful tool to estimate distribution and population size of sika deer. PMID:26084704

  14. Rational case management of malaria with a rapid diagnostic test, Paracheck Pf®, in antenatal health care in Bangui, Central African Republic

    PubMed Central

    2012-01-01

    Background Both treatment and prevention strategies are recommended by the World Health Organization for the control of malaria during pregnancy in tropical areas. The aim of this study was to assess use of a rapid diagnostic test for prompt management of malaria in pregnancy in Bangui, Central African Republic. Methods A cohort of 76 pregnant women was screened systematically for malaria with ParacheckPf® at each antenatal visit. The usefulness of the method was analysed by comparing the number of malaria episodes requiring treatment in the cohort with the number of prescriptions received by another group of pregnant women followed-up in routine antenatal care. Results In the cohort group, the proportion of positive ParacheckPf® episodes during antenatal clinics visits was 13.8%, while episodes of antimalarial prescriptions in the group which was followed-up routinely by antenatal personnel was estimated at 26.3%. Hence, the relative risk of the cohort for being prescribed an antimalarial drug was 0.53. Therefore, the attributable fraction of presumptive treatment avoided by systematic screening with ParacheckPf® was 47%. Conclusions Use of a rapid diagnostic test is useful, affordable and easy for adequate treatment of malaria in pregnant women. More powerful studies of the usefulness of introducing the test into antenatal care are needed in all heath centres in the country and in other tropical areas. PMID:22734602

  15. Rapid diagnostic imaging and pathologic evaluation of whole core biopsies at the point-of-care using structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Mei; Sholl, Andrew B.; Kimbrell, Hillary; Tulman, David B.; Elfer, Katherine N.; Brown, J. Quincy

    2015-07-01

    Video-rate structured illumination microscopy (VR-SIM) of fluorescently stained prostate biopsies is demonstrated as a potential tool for rapid diagnosis of prostate biopsies at the point of care. Images of entire biopsies at 1.3 micron lateral resolution are rendered in seconds, and pathologist review of the resulting images achieves 90% accuracy as compared to gold standard histopathology.

  16. Evaluation of a Density-Based Rapid Diagnostic Test for Sickle Cell Disease in a Clinical Setting in Zambia

    PubMed Central

    Hennek, Jonathan W.; Mantina, Hamakwa; Lee, S. Y. Ryan; Patton, Matthew R.; Sambo, Pauline; Sinyangwe, Silvester; Kankasa, Chipepo; Chintu, Chifumbe; Brugnara, Carlo; Stossel, Thomas P.; Whitesides, George M.

    2014-01-01

    Although simple and low-cost interventions for sickle cell disease (SCD) exist in many developing countries, child mortality associated with SCD remains high, in part, because of the lack of access to diagnostic tests for SCD. A density-based test using aqueous multiphase systems (SCD-AMPS) is a candidate for a low-cost, point-of-care diagnostic for SCD. In this paper, the field evaluation of SCD-AMPS in a large (n = 505) case-control study in Zambia is described. Of the two variations of the SCD-AMPS used, the best system (SCD-AMPS-2) demonstrated a sensitivity of 86% (82–90%) and a specificity of 60% (53–67%). Subsequent analysis identified potential sources of false positives that include clotting, variation between batches of SCD-AMPS, and shipping conditions. Importantly, SCD-AMPS-2 was 84% (62–94%) sensitive in detecting SCD in children between 6 months and 1 year old. In addition to an evaluation of performance, an assessment of end-user operability was done with health workers in rural clinics in Zambia. These health workers rated the SCD-AMPS tests to be as simple to use as lateral flow tests for malaria and HIV. PMID:25490722

  17. Polydimethylsiloxane-air partition ratios for semi-volatile organic compounds by GC-based measurement and COSMO-RS estimation: Rapid measurements and accurate modelling.

    PubMed

    Okeme, Joseph O; Parnis, J Mark; Poole, Justen; Diamond, Miriam L; Jantunen, Liisa M

    2016-08-01

    Polydimethylsiloxane (PDMS) shows promise for use as a passive air sampler (PAS) for semi-volatile organic compounds (SVOCs). To use PDMS as a PAS, knowledge of its chemical-specific partitioning behaviour and time to equilibrium is needed. Here we report on the effectiveness of two approaches for estimating the partitioning properties of polydimethylsiloxane (PDMS), values of PDMS-to-air partition ratios or coefficients (KPDMS-Air), and time to equilibrium of a range of SVOCs. Measured values of KPDMS-Air, Exp' at 25 °C obtained using the gas chromatography retention method (GC-RT) were compared with estimates from a poly-parameter free energy relationship (pp-FLER) and a COSMO-RS oligomer-based model. Target SVOCs included novel flame retardants (NFRs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), organophosphate flame retardants (OPFRs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs). Significant positive relationships were found between log KPDMS-Air, Exp' and estimates made using the pp-FLER model (log KPDMS-Air, pp-LFER) and the COSMOtherm program (log KPDMS-Air, COSMOtherm). The discrepancy and bias between measured and predicted values were much higher for COSMO-RS than the pp-LFER model, indicating the anticipated better performance of the pp-LFER model than COSMO-RS. Calculations made using measured KPDMS-Air, Exp' values show that a PDMS PAS of 0.1 cm thickness will reach 25% of its equilibrium capacity in ∼1 day for alpha-hexachlorocyclohexane (α-HCH) to ∼ 500 years for tris (4-tert-butylphenyl) phosphate (TTBPP), which brackets the volatility range of all compounds tested. The results presented show the utility of GC-RT method for rapid and precise measurements of KPDMS-Air. PMID:27179237

  18. Chronic Meningitis: Simplifying a Diagnostic Challenge.

    PubMed

    Baldwin, Kelly; Whiting, Chris

    2016-03-01

    Chronic meningitis can be a diagnostic dilemma for even the most experienced clinician. Many times, the differential diagnosis is broad and encompasses autoimmune, neoplastic, and infectious etiologies. This review will focus on a general approach to chronic meningitis to simplify the diagnostic challenges many clinicians face. The article will also review the most common etiologies of chronic meningitis in some detail including clinical presentation, diagnostic testing, treatment, and outcomes. By using a case-based approach, we will focus on the key elements of clinical presentation and laboratory analysis that will yield the most rapid and accurate diagnosis in these complicated cases. PMID:26888190

  19. Detection of human cytomegalovirus antigenaemia: a rapid diagnostic technique for predicting cytomegalovirus infection/pneumonitis in lung and heart transplant recipients.

    PubMed Central

    Egan, J. J.; Barber, L.; Lomax, J.; Fox, A.; Yonan, N.; Rahman, A. N.; Campbell, C. S.; Deiraniya, A. K.; Carroll, K. B.; Craske, J.

    1995-01-01

    BACKGROUND--New rapid diagnostic techniques offer the opportunity of early diagnosis of human cytomegalovirus (CMV) infection in immunocompromised patients at risk of developing CMV disease. The use of human CMV antigenaemia as a predictor of clinical CMV infection and disease in lung and heart transplant recipients was studied prospectively. METHODS--Twenty three heart and nine lung transplant recipients who survived 40 days were observed by standard CMV surveillance with serological testing, culture, and by sequential testing for CMV antigenaemia. CMV antigenaemia testing is a rapid and quantifiable technique in which a viral lower matrix protein is detected in cytospin preparations of peripheral blood polymorphonuclear leucocytes (PMNLs) by immunofluorescent staining. RESULTS--Eleven patients developed CMV infection and five developed CMV disease (four pneumonitis, one duodenitis). These clinical events occurred at a median of 65 days following transplantation. CMV antigenaemia occurred in 17 patients at a median of 35 days following transplantation. Detection of CMV antigenaemia had a sensitivity of 100%, a specificity of 93.7%, and a positive predictive value of 94.1% for CMV related illness. CMV antigenaemia was positive at a significant interval before the clinical event. High levels of CMV antigenaemia (> 50 CMV antigen positive cells/2 x 10(5) PMNLs) occurred in 11 patients and five of these developed disease. CMV antigenaemia of > 50 CMV antigen positive cells/2 x 10(5) PMNLs had a positive predictive value of 45.5% for disease but a negative predictive value of 100%. Patients with disease had higher levels of antigenaemia than those without disease. CONCLUSIONS--CMV antigenaemia is a rapid diagnostic technique which can identify patients likely to develop CMV disease, potentially allowing early treatment. Images PMID:7886659

  20. A reference substance free diagnostic fragment ion-based approach for rapid identification of non-target components in Pudilan Xiaoyan oral liquid by high resolution mass spectrometry.

    PubMed

    Dai, Chen; Wang, Chong; Zhang, Chunhua; Wang, Guoxiang; Wang, Jin; Chen, Jun; Guo, Bin; Yang, Tianshu; Cai, Bo

    2016-05-30

    Rapid and reliable identification of non-target components in herbal preparations remains a primary challenge, especially when corresponding reference substances are inaccessible. In this work, an efficient post-experiment data processing methodology, named reference substance free diagnostic fragment ion (RSFDFI), was developed based on ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry (UHPLC/LTQ-Orbitrap). The first step of this approach was to cluster the components that share common fragment ions into several groups. After querying the database using a predicted chemical formula, the component with the fewest primary hits was preferentially deduced based on its MS/MS spectrum. Once the structure was characterized, its common fragment ions could be used as the prior structural information to select the possible candidates that would facilitate the subsequent identification for each group. Taking Pudilan Xiaoyan oral liquid (PDL) as a model herbal preparation, which has been extensively used for the treatment of epidemic parotitis and children with hand-foot-mouth diseases, this strategy enables a nearly eight-fold narrowing of the database hits, with fifty-two components, including lignans, flavonoids, alkaloids and steroids, being rapidly identified. In conclusion, our work clearly demonstrates that integrating RSFDFI with high-resolution mass spectrometry is a powerful methodology for rapid identification of non-target components from herbal prescriptions and may open new avenues for chemical analysis in other complex mixtures. PMID:26938159

  1. Development and Diagnostic Evaluation of Loop-Mediated Isothermal Amplification Using a New Gene Target for Rapid Detection of Helicobacter pylori

    PubMed Central

    Bakhtiari, Somaye; Alvandi, Amirhooshang; Pajavand, Hamid; Navabi, Jafar; Najafi, Farid; Abiri, Ramin

    2016-01-01

    Background Helicobacter pylori cause chronic gastritis and subsequent diseases like gastric and duodenal ulcers and gastric adenocarcinoma. Current methods for detecting H. pylori have several disadvantages and it is of utmost importance to develop a simple, quick, accurate, and cost-effective diagnostic test. Objectives The aim of this study was to set up and evaluate a diagnostic value of loop- mediated isothermal amplification (LAMP) for detecting H. pylori. Patients and Methods The analytical sensitivity values (limit of detection) of LAMP and polymerase chain reaction (PCR) were determined using serial dilutions of H. pylori DNA. Analytical specificity of the methods using new designed primers targeted ureC gene was also determined. Results The detection limits of the LAMP and PCR assay were similar and were 10 fg of pure DNA of H. pylori, which is equal to 6 copy numbers of H. pylori genome. Analytical specificity of the tests was 100% because the tests were positive only with H. pylori DNA. Conclusions The analytical sensitivity of LAMP and PCR methods, using the designed primers, was 8 times more than any other reported methods. The designed methods are specific and sensitive for detection of H. pylori in different clinical and environmental samples. PMID:27540449

  2. Assessing the Public Health Risk of Shiga Toxin-Producing Escherichia coli by Use of a Rapid Diagnostic Screening Algorithm

    PubMed Central

    Ferdous, Mithila; Ott, Alewijn; Scheper, Henk R.; Wisselink, Guido J.; Heck, Max E.; Rossen, John W.; Kooistra-Smid, Anna M. D.

    2015-01-01

    Shiga toxin-producing Escherichia coli (STEC) is an enteropathogen of public health concern because of its ability to cause serious illness and outbreaks. In this prospective study, a diagnostic screening algorithm to categorize STEC infections into risk groups was evaluated. The algorithm consists of prescreening stool specimens with real-time PCR (qPCR) for the presence of stx genes. The qPCR-positive stool samples were cultured in enrichment broth and again screened for stx genes and additional virulence factors (escV, aggR, aat, bfpA) and O serogroups (O26, O103, O104, O111, O121, O145, O157). Also, PCR-guided culture was performed with sorbitol MacConkey agar (SMAC) and CHROMagar STEC medium. The presence of virulence factors and O serogroups was used for presumptive pathotype (PT) categorization in four PT groups. The potential risk for severe disease was categorized from high risk for PT group I to low risk for PT group III, whereas PT group IV consists of unconfirmed stx qPCR-positive samples. In total, 5,022 stool samples of patients with gastrointestinal symptoms were included. The qPCR detected stx genes in 1.8% of samples. Extensive screening for virulence factors and O serogroups was performed on 73 samples. After enrichment, the presence of stx genes was confirmed in 65 samples (89%). By culture on selective media, STEC was isolated in 36% (26/73 samples). Threshold cycle (CT) values for stx genes were significantly lower after enrichment compared to direct qPCR (P < 0.001). In total, 11 (15%), 19 (26%), 35 (48%), and 8 (11%) samples were categorized into PT groups I, II, III, and IV, respectively. Several virulence factors (stx2, stx2a, stx2f, toxB, eae, efa1, cif, espA, tccP, espP, nleA and/or nleB, tir cluster) were associated with PT groups I and II, while others (stx1, eaaA, mch cluster, ireA) were associated with PT group III. Furthermore, the number of virulence factors differed between PT groups (analysis of variance, P < 0.0001). In

  3. Rapid Diagnostic Device for Subclinical Mastitis Based on Electrochemical Detection of Superoxide Produced from Neutrophils in Fresh Milk

    NASA Astrophysics Data System (ADS)

    Okada, Kohei; Fukuda, Junji; Suzuki, Hiroaki

    Electrochemical microdevices were fabricated to identify mastitic cows based on the increased number of neutrophils in raw milk. Because neutrophils produce superoxide (O2·-), the amount of O2·- can be used as an early indicator for subclinical mastitis. In the microdevices, O2·- was detected on a gold electrode using superoxide dismutase immobilized via a self-assembled monolayer of cysteine. In a preliminary test using xanthine oxidase to produce O2·-, one of the devices detected the production and rapid extinction of O2·-. When neutrophils obtained from a mastitic cow were concentrated by centrifugation and introduced into the device, a current increase distinctly different from the background was observed. Furthermore, a micropillar structure was fabricated on the gold electrode to trap and collect neutrophils, thereby facilitating the concentration of these cells around the electrode. The measured current clearly depended on the number of neutrophils in raw milk samples, demonstrating the applicability of the device for rapid diagnosis of subclinical mastitis.

  4. Population screening for coeliac disease in primary care by district nurses using a rapid antibody test: diagnostic accuracy and feasibility study

    PubMed Central

    2007-01-01

    Objective To evaluate the feasibility and diagnostic accuracy of screening for coeliac disease by rapid detection of IgA antibodies to tissue transglutaminase performed in primary care. Design District nurses screened 6 year old children using rapid antibody testing of finger prick blood. They also collected capillary blood samples for laboratory determination of IgA and IgG antibodies to endomysium and IgA antibodies to tissue transglutaminase. Children with positive rapid test results were directly sent for biopsy of the small intestine. Setting Primary care in Jász-Nagykun-Szolnok county, Hungary. Participants 2690 children (77% of 6 year olds living in the county) and 120 nurses. Main outcome measures Positivity for antibodies to endomysium or transglutaminase in the laboratory and coeliac disease confirmed at biopsy. Results 37 children (1.4%, 95% confidence interval 0.9% to 1.8%) had biopsy confirmed coeliac disease. Only five of these children had been diagnosed clinically before screening. Rapid testing had a 78.1% sensitivity (70.0% to 89.3%) and 100% specificity (88.4% to 100%) for a final diagnosis of coeliac disease by biopsy. Sensitivity was 65.1% (50.2% to 77.6%) and specificity was 100% (99.8% to 100%) compared with combined results of IgA and IgG laboratory tests. Trained laboratory workers detected 30 of the 31 newly diagnosed IgA competent patients with the rapid test kit used blindly. Median time to biopsy after a positive rapid test result was significantly shorter (20 days, range 4-148) than after a positive laboratory result (142 days, 70-256; P<0.001). Children with coeliac disease detected at screening were smaller and had worse health status than their peers but they improved on a gluten-free diet. Conclusions A simple rapid antibody test enabled primary care nurses to detect patients with coeliac disease in the community who were not picked up in clinical care. Extra training is needed to improve sensitivity. PMID:18063612

  5. Rapid, low-cost and instrument-free CD4+ cell counting for HIV diagnostics in resource-poor settings.

    PubMed

    Glynn, Macdara T; Kinahan, David J; Ducrée, Jens

    2014-08-01

    We present a novel, user-friendly and widely autonomous point-of-care diagnostic to enable HIV monitoring in resource-poor regions where the current pandemic is most prevalent. To specifically isolate magnetically tagged CD4+ cells directly from patient blood, the low-cost and disposable microfluidic chip operates by dual-force CD4+ cell magnetophoresis; whereby the interplay of flow and magnetic fields governs the trajectory of target cells depending on whether the cell binds to a magnetic microbead. Instrument-free pumping is implemented by a finger-actuated elastic membrane; tagged beads are laterally deflected by a small and re-useable permanent magnet. The single-depth and monolithic microfluidic structure can easily be fabricated in a single casting step. After their magnetophoretic isolation from whole blood, estimation of CD4+ cell concentrations is then measured by bright-field inspection of the capture chamber. In addition, an optional fluorescence measurement can be used for confirmation of the bright-field result if required. On-chip CD4+ estimation produces a linear response over the full range of medically relevant CD4+ cell concentrations. Our technology combines high-efficiency capture (93.0 ± 3.3%) and cell enumeration. PMID:24911165

  6. Molecular diagnostics in a teacup: Non-Instrumented Nucleic Acid Amplification (NINA) for rapid, low cost detection of Salmonella enterica

    PubMed Central

    KUBOTA, Ryo; LABARRE, Paul; WEIGL, Bernhard H; LI, Yong; HAYDOCK, Paul; JENKINS, Daniel M

    2014-01-01

    We report on the use of a novel non-instrumented platform to enable a Loop Mediated isothermal Amplification (LAMP) based assay for Salmonella enterica. Heat energy is provided by addition of a small amount (<150 g) of boiling water, and the reaction temperature is regulated by storing latent energy at the melting temperature of a lipid-based engineered phase change material. Endpoint classification of the reaction is achieved without opening the reaction tube by observing the fluorescence of sequence-specific FRET-based assimilating probes with a simple handheld fluorometer. At or above 22°C ambient temperature the non-instrumented devices could maintain reactions above a threshold temperature of 61°C for over 90 min—significantly longer than the 60 min reaction time. Using the simple format, detection limits were less than 20 genome copies for reactions run at ambient temperatures ranging from 8 to 36°C. When used with a pre-enrichment step and non-instrumented DNA extraction device, trace contaminations of Salmonella in milk close to 1 CFU/mL could be reliably detected. These findings illustrate that the non- instrumented amplification approach is a simple, viable, low-cost alternative for field-based food and agricultural diagnostics or clinical applications in developing countries. PMID:25477717

  7. Enhanced performance of an innovative dengue IgG/IgM rapid diagnostic test using an anti-dengue EDI monoclonal antibody and dengue virus antigen.

    PubMed

    Lee, Jihoo; Kim, Young-Eun; Kim, Hak-Yong; Sinniah, Mangalam; Chong, Chom-Kyu; Song, Hyun-Ok

    2015-01-01

    High levels of anti-dengue IgM or IgG can be detected using numerous rapid diagnostic tests (RDTs). However, the sensitivity and specificity of these tests are reduced by changes in envelope glycoprotein antigenicity that inevitably occur in limited expression systems. A novel RDT was designed to enhance diagnostic sensitivity. Dengue viruses cultured in animal cells were used as antigens to retain the native viral coat protein. Monoclonal antibodies (mAbs) were then developed, for the first time, against domain I of envelope glycoprotein (EDI). The anti-dengue EDI mAb was employed as a capturer, and EDII and EDIII, which are mainly involved in the induction of neutralizing antibodies in patients, were fully available to bind to anti-dengue IgM or IgG in patients. A one-way automatic blood separation device prevented reverse migration of plasma and maximize the capture of anti-dengue antibodies at the test lines. A clinical evaluation in the field proved that the novel RDT (sensitivities of 96.5% and 96.7% for anti-dengue IgM and IgG) is more effective in detecting anti-dengue antibodies than two major commercial tests (sensitivities of 54.8% and 82% for SD BIOLINE; 50.4% and 75.3% for PanBio). The innovative format of RDT can be applied to other infectious viral diseases. PMID:26655854

  8. Enhanced performance of an innovative dengue IgG/IgM rapid diagnostic test using an anti-dengue EDI monoclonal antibody and dengue virus antigen

    PubMed Central

    Lee, Jihoo; Kim, Young-Eun; Kim, Hak-Yong; Sinniah, Mangalam; Chong, Chom-Kyu; Song, Hyun-Ok

    2015-01-01

    High levels of anti-dengue IgM or IgG can be detected using numerous rapid diagnostic tests (RDTs). However, the sensitivity and specificity of these tests are reduced by changes in envelope glycoprotein antigenicity that inevitably occur in limited expression systems. A novel RDT was designed to enhance diagnostic sensitivity. Dengue viruses cultured in animal cells were used as antigens to retain the native viral coat protein. Monoclonal antibodies (mAbs) were then developed, for the first time, against domain I of envelope glycoprotein (EDI). The anti-dengue EDI mAb was employed as a capturer, and EDII and EDIII, which are mainly involved in the induction of neutralizing antibodies in patients, were fully available to bind to anti-dengue IgM or IgG in patients. A one-way automatic blood separation device prevented reverse migration of plasma and maximize the capture of anti-dengue antibodies at the test lines. A clinical evaluation in the field proved that the novel RDT (sensitivities of 96.5% and 96.7% for anti-dengue IgM and IgG) is more effective in detecting anti-dengue antibodies than two major commercial tests (sensitivities of 54.8% and 82% for SD BIOLINE; 50.4% and 75.3% for PanBio). The innovative format of RDT can be applied to other infectious viral diseases. PMID:26655854

  9. Development of a rapid diagnostic assay for the detection of tomato chlorotic dwarf viroid based on isothermal reverse-transcription-recombinase polymerase amplification.

    PubMed

    Hammond, Rosemarie W; Zhang, Shulu

    2016-10-01

    A molecular diagnostic assay utilizing reverse transcription-recombinase polymerase amplification (RT-RPA) at an isothermal constant temperature of 39°C and target-specific primers and probe were developed for the rapid, sensitive, and specific detection of tomato chlorotic dwarf viroid (TCDVd) in infected leaf and seed tissues. The performance of the AmplifyRP(®) Acceler8™ RT-RPA diagnostic assay, utilizing a lateral flow strip contained within an amplicon detection chamber, was evaluated and the results were compared with a standard RT-PCR assay. The AmplifyRP(®) Acceler8™ assay was specific for TCDVd in leaf and seed tissues, its sensitivity was comparable to conventional RT-PCR in leaf tissues, and it does not require extensive sample purification, specialized equipment, or technical expertise. This is the first report utilizing an RT-RPA assay to detect viroids and the assay can be used both in the laboratory and in the field for TCDVd detection. PMID:27427473

  10. Isolation and identification of Duck tembusu virus strain lH and development of latex-agglutination diagnostic method for rapid detection of antibodies.

    PubMed

    Wang, Quanxi; Wen, Yaping; Yifan Huang; Wu, Yijian; Cai, Yilong; Xu, Lihui; Wang, Changkang; Li, Ang; Wu, Baocheng; Chen, Jilong

    2014-12-01

    SUMMARY. An outbreak of egg-drop syndrome occurred on a Sheldrake duck farm in Longhai in Fujian Province, China, in 2012. The main clinical symptoms were sharply reduced egg production, crooked necks, and death. We isolated the virus from the sick ducks, identified it, and observed the histopathologic changes after viral infection. We detected viral RNA in the blood and feces of the infected ducks and developed a latex-agglutination diagnostic method to detect anti-Tembusu-virus antibodies. Our results show that the pathogenic virus is a Tembusu virus. The histopathologic changes included follicular cell degeneration and necrosis, follicular cavity filled with blood cells, massive necrosis in the brain, and degeneration and necrosis of the nerve and glial cells. When the transmission of the virus in the infected ducks was studied, the duck blood was positive for viral nucleic acid for up to 29 days, and the feces were positive for viral nucleic acid for up to 13 days. We successfully established a simple, rapid, and easy- to-use latex-agglutination diagnostic method for the detection of antibodies against duck Tembusu virus. PMID:25619007

  11. A combined antral and corpus rapid urease testing protocol can increase diagnostic accuracy despite a low prevalence of Helicobacter pylori infection in patients undergoing routine gastroscopy

    PubMed Central

    Holleran, Grainne; Hall, Barry; Brennan, Denise; Crotty, Paul; McNamara, Deirdre

    2015-01-01

    Background The effects of an increased risk of sampling error and the lower prevalence of Helicobacter pylori infection on the diagnostic accuracy of standard invasive tests needs to be considered. Despite evidence of enhanced yield with additional biopsies, combined Rapid Urease Tests (RUTs) have not been widely adopted. We aimed to compare the diagnostic efficacy of a combined antral and corpus rapid urease test (RUT) to a single antral RUT in a low prevalence cohort. Methods Between August 2013 and April 2014 adult patients undergoing a scheduled gastroscopy were prospectively recruited. At endoscopy biopsies were taken and processed for single and combined RUTs, histology and culture using standard techniques. Infection was defined by positive culture or detection of Helicobacter like organisms on either antral or corpus samples. Results In all 123 patients were recruited. H. pylori prevalence was low at 36%, n = 44. There was a significant difference in positivity between single and combined RUTs, 20% (n = 25) versus 30% (n = 37), p = 0.0094, (95% CI 0.15–0.04). The number needed to treat (NNT) for an additional diagnosis of infection using a combined versus a single RUT is 4 (95% CI 2.2–11). The only factor associated with a reduction in RUT yield was regular proton pump inhibitor (PPI) use. Overall the sensitivity, specificity, positive and negative predictive value for any RUT test was 84%, 100%, 100% and 92% respectively. Conclusion Our data suggests taking routine antral and corpus biopsies in conjunction with a combined RUT appears to optimizing H. pylori detection and overcome sampling error in a low prevalence population. PMID:26535121

  12. Assessing the reliability of microscopy and rapid diagnostic tests in malaria diagnosis in areas with varying parasite density among older children and adult patients in Nigeria

    PubMed Central

    Ayogu, EE; Ukwe, CV; Nna, EO

    2016-01-01

    Background: Current malaria control strategies are based on early diagnosis and appropriate treatment of malaria cases. The study aimed at comparing the performance of blood film microscopy and rapid diagnostic test (RDT) in Plasmodium falciparum detection in patients ≥6 years of age. Materials and Methods: A total of 154 consecutive pyretic patients aged 6-62 years were enrolled, sampled, and tested for malaria using RDT (first response) and microscopy by Giemsa staining. Genomic DNA was extracted after saponin hemolysis and nested polymerase chain reaction (PCR) was used to detect Plasmodium falciparum. The endpoints were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Results: Of the 154 patients, 80 (51.9%) had fever of ≥37.5°C. 106 (68.8%) were positive by First response®, 132 (85.7%) by microscopy, and 121 (78.6%) by PCR. The sensitivity, specificity, PPV, and NPV of first response compared to microscopic method were 82.2%, 100.0%, 100.0%, and 34.3%, respectively, while it was 75.4%, 75.0%, 95.3%, and 31.2%, respectively, when compared to PCR. The sensitivity, specificity, PPV, and NPV of the microscopic method compared to PCR were 92.3%, 50.0%, 90.91%, and 54.5%, respectively. There was a significant difference in the performance of RDT and film microscopy methods (P ≤ 0.05). Conclusion: Microscopy performed better and is more reliable than first response (RDT) in areas with low parasite density among patients ≥6 years of age. Rapid diagnostic tests could be useful in aareas with high parasite density as an alternative to smear microscopy PMID:27241807

  13. Particle-size evidence of estuary evolution: A rapid and diagnostic tool for determining the nature of recent saltmarsh accretion

    NASA Astrophysics Data System (ADS)

    Rahman, Rubina; Plater, Andrew J.

    2014-05-01

    A conceptual model of saltmarsh sedimentation based on high-resolution particle-size analysis has been tested on short cores (c. 0.5 m) of known age from the Dee estuary, NW England, UK. Here, two components of the particle-size distribution (PSD) are interpreted as the traction load deposited by the faster tidal flow velocities ('fast tide') and the suspension load that settles during the turn of the tide ('slow tide'). The feasibility of this model for diagnosing the driving mechanism of estuary evolution in both time and space is tested with reference to historical evidence of saltmarsh accretion, up-core trends in dated saltmarsh cores, and the PSDs of present-day saltmarsh surface sediments. Cores that show an up-core progression from very fine-skewed to near symmetrical PSDs are interpreted in the context of estuary infilling due to a positive sediment budget (sediment surplus), whilst those that show a persistence of near-symmetrical, (very) poorly sorted, mesokurtic particle-size distributions in the fine to very fine silts size range are considered to be the result of 'slow tide' sedimentation. The influences of the two 'end-member' styles of saltmarsh accretion, i.e. (i) infilling due to sediment surplus and (ii) 'slow tide' settling linked to sea level, exhibit spatial and temporal trends as predicted, particularly in cores from mid- and lower saltmarsh locations. The upper saltmarsh cores also show evidence of estuary infilling due to 'slow tide' sedimentation at rates in excess of sea-level rise. The results confirm that the diagnostic approach can be applied as a 'pre-filtering' method for assessing the suitability of saltmarsh sediments for reconstructing sea-level trends, and for providing input data for improved estuary morphological modelling.

  14. Development and Evaluation of a Rapid Diagnostic Test for Plasmodium falciparum, P. vivax, and Mixed-Species Malaria Antigens

    PubMed Central

    Lee, Gyu-Cheol; Jeon, Eun-Sung; Le, Dung Tien; Kim, Tong-Soo; Yoo, Jong-Ha; Kim, Hak Yong; Chong, Chom-Kyu

    2011-01-01

    Plasmodium falciparum and P. vivax malaria are endemic to many parts of the world and humans can be co-infected with both species. Because each Plasmodium species has different biological and clinical characteristics, accurate differentiation of the infecting species is essential for effective treatment. Therefore, we produced three monoclonal antibodies that recognize the lactate dehydrogenase of P. falciparum, P. vivax, or both to develop the first P. falciparum, P. vivax, and mixed-species infections malaria antigen detection kit. The detection limits of this kit were 150 and 250 parasites/μL for P. falciparum and P. vivax, respectively, and the kit was able to detect mixed-species infections. The sensitivity and specificity of this kit was assessed with 722 clinical specimens. Our results showed that its sensitivities for P. falciparum, P. vivax, and mixed-species infection were 96.5%, 95.3%, and 85.7%, respectively. In addition, its specificity was high (99.4%). PMID:22144432

  15. Clinical evaluation of the ZstatFlu-II test: a chemiluminescent rapid diagnostic test for influenza virus.

    PubMed

    Hamilton, Marilyn S; Abel, David M; Ballam, Yolanda J; Otto, Mary K; Nickell, Angela F; Pence, Lisa M; Appleman, James R; Shimasaki, Craig D; Achyuthan, Komandoor E

    2002-07-01

    Exploiting the high sensitivity of the chemiluminescence phenomenon, an accurate and sensitive point-of-care test, called the ZstatFlu-II test (ZymeTx, Inc., Oklahoma City, Okla.), was developed to detect influenza virus infections. The ZstatFlu-II test takes 20 min and requires approximately 2 min of "hands-on" time for operational steps. The ZstatFlu-II test does not distinguish between infections with influenza virus types A and B. ZstatFlu-II test results are printed on Polaroid High-Speed Detector Film, allowing test results to be archived. A prototype version of the ZstatFlu-II test was evaluated during the 2000-to-2001 flu season with 300 nasal aspirate specimens from children at a pediatric hospital. Compared to culture, the ZstatFlu-II test had 88% sensitivity and 92% specificity. The Directigen test had a sensitivity of 75% and a specificity of 93%. The sensitivity of the ZstatFlu-II test was significantly higher than that of the Directigen test (P < 0.0574). PMID:12089243

  16. How Do Patients and Health Workers Interact around Malaria Rapid Diagnostic Testing, and How Are the Tests Experienced by Patients in Practice? A Qualitative Study in Western Uganda

    PubMed Central

    Altaras, Robin; Nuwa, Anthony; Agaba, Bosco; Streat, Elizabeth; Tibenderana, James K.; Martin, Sandrine; Strachan, Clare E.

    2016-01-01

    Background Successful scale-up in the use of malaria rapid diagnostic tests (RDTs) requires that patients accept testing and treatment based on RDT results and that healthcare providers treat according to test results. Patient-provider communication is a key component of quality care, and leads to improved patient satisfaction, higher adherence to treatment and better health outcomes. Voiced or perceived patient expectations are also known to influence treatment decision-making among healthcare providers. While there has been a growth in literature on provider practices around rapid testing for malaria, there has been little analysis of inter-personal communication around the testing process. We investigated how healthcare providers and patients interact and engage throughout the diagnostic and treatment process, and how the testing service is experienced by patients in practice. Methods This research was conducted alongside a larger study which explored determinants of provider treatment decision-making following negative RDT results in a rural district (Kibaale) in mid-western Uganda, ten months after RDT introduction. Fifty-five patients presenting with fever were observed during routine outpatient visits at 12 low-level public health facilities. Observation captured communication practices relating to test purpose, results, diagnosis and treatment. All observed patients or caregivers were immediately followed up with in-depth interview. Analysis followed the ‘framework’ approach. A summative approach was also used to analyse observation data. Results Providers failed to consistently communicate the reasons for carrying out the test, and particularly to RDT-negative patients, a diagnostic outcome or the meaning of test results, also leading to confusion over what the test can detect. Patients appeared to value testing, but were frustrated by the lack of communication on outcomes. RDT-negative patients were dissatisfied by the absence of information on an

  17. Integrating Rapid Diagnostics and Antimicrobial Stewardship in Two Community Hospitals Improved Process Measures and Antibiotic Adjustment Time.

    PubMed

    Lockwood, Ashley M; Perez, Katherine K; Musick, William L; Ikwuagwu, Judy O; Attia, Engie; Fasoranti, Oyejoke O; Cernoch, Patricia L; Olsen, Randall J; Musser, James M

    2016-04-01

    OBJECTIVE To assess the impact of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry for rapid pathogen identification directly from early-positive blood cultures coupled with an antimicrobial stewardship program (ASP) in two community hospitals. Process measures and outcomes prior and after implementation of MALDI-TOF/ASP were evaluated. DESIGN Multicenter retrospective study. SETTING Two community hospitals in a system setting, Houston Methodist (HM) Sugar Land Hospital (235 beds) or HM Willowbrook Hospital (241 beds). PATIENTS Patients ≥ 18 years of age with culture-proven Gram-negative bacteremia. INTERVENTION Blood cultures from both hospitals were sent to and processed at our central microbiology laboratory. Clinical pharmacists at respective hospitals were notified of pathogen ID and susceptibility results. RESULTS We evaluated 572 patients for possible inclusion. After pre-defined exclusion criteria, 151 patients were included in the pre-intervention group and 242 were included in the intervention group. After MALDI-TOF/ASP implementation, the mean identification time after culture positivity was significantly reduced from 32 hours (±16 hours) to 6.5 hours (±5.4 hours) (P<.001); mean time to susceptibility results was significantly reduced from 48 (±22) hours to 23 (±14) hours (P<.001); and time to therapy adjustment was significantly reduced from 75 (±59) hours to 30 (±30) hours (P<.001). Mean hospital costs per patient were $3,411 less in the intervention group compared with the pre-intervention group ($18,645 vs $15,234; P=.04). CONCLUSION This study is the first to analyze the impact of MALDI-TOF coupled with an ASP in a community hospital setting. Time to results significantly differed with the use of MALDI-TOF, and time to appropriate therapy was significantly improved with the addition of ASP. PMID:26738993

  18. Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review.

    PubMed Central

    Warhurst, Geoffrey; Dunn, Graham; Chadwick, Paul; Blackwood, Bronagh; McAuley, Daniel; Perkins, Gavin D; McMullan, Ronan; Gates, Simon; Bentley, Andrew; Young, Duncan; Carlson, Gordon L; Dark, Paul

    2015-01-01

    -16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy. CONCLUSION SeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation

  19. A rapid and accurate method for the quantitative estimation of natural polysaccharides and their fractions using high performance size exclusion chromatography coupled with multi-angle laser light scattering and refractive index detector.

    PubMed

    Cheong, Kit-Leong; Wu, Ding-Tao; Zhao, Jing; Li, Shao-Ping

    2015-06-26

    In this study, a rapid and accurate method for quantitative analysis of natural polysaccharides and their different fractions was developed. Firstly, high performance size exclusion chromatography (HPSEC) was utilized to separate natural polysaccharides. And then the molecular masses of their fractions were determined by multi-angle laser light scattering (MALLS). Finally, quantification of polysaccharides or their fractions was performed based on their response to refractive index detector (RID) and their universal refractive index increment (dn/dc). Accuracy of the developed method for the quantification of individual and mixed polysaccharide standards, including konjac glucomannan, CM-arabinan, xyloglucan, larch arabinogalactan, oat β-glucan, dextran (410, 270, and 25 kDa), mixed xyloglucan and CM-arabinan, and mixed dextran 270 K and CM-arabinan was determined, and their average recoveries were between 90.6% and 98.3%. The limits of detection (LOD) and quantification (LOQ) were ranging from 10.68 to 20.25 μg/mL, and 42.70 to 68.85 μg/mL, respectively. Comparing to the conventional phenol sulfuric acid assay and HPSEC coupled with evaporative light scattering detection (HPSEC-ELSD) analysis, the developed HPSEC-MALLS-RID method based on universal dn/dc for the quantification of polysaccharides and their fractions is much more simple, rapid, and accurate with no need of individual polysaccharide standard, as well as free of calibration curve. The developed method was also successfully utilized for quantitative analysis of polysaccharides and their different fractions from three medicinal plants of Panax genus, Panax ginseng, Panax notoginseng and Panax quinquefolius. The results suggested that the HPSEC-MALLS-RID method based on universal dn/dc could be used as a routine technique for the quantification of polysaccharides and their fractions in natural resources. PMID:25990349

  20. Survey of the Diagnostic Retooling Process in National TB Reference Laboratories, with Special Focus on Rapid Speciation Tests Endorsed by WHO in 2007

    PubMed Central

    van Kampen, Sanne C.; Oskam, Linda; Tuijn, Coosje J.; Klatser, Paul R.

    2012-01-01

    Background Successful integration of new diagnostics in national tuberculosis (TB) control programs, also called ‘retooling’, is highly dependent on operational aspects related to test availability, accessibility and affordability. This survey aimed to find out whether recommendations to use new diagnostics lead to successful retooling in high TB endemic countries, using immunochromatographic tests (ICTs) for TB culture speciation as a case study. ICTs are recommended to accurately confirm the presence of bacteria of the Mycobacterium tuberculosis complex in liquid culture isolates. Methods and Findings Questionnaires were sent to national TB reference laboratories (NRLs) in 42 high TB endemic countries to address their access to information on ICT implementation, logistics related to availability, accessibility and affordability of ICTs, and testing algorithms. Results from 16 responding countries indicated that half of the NRLs were aware of the contents of WHO guidance documents on liquid culture and ICT implementation, as well as their eligibility for a negotiated pricing agreement for ICT procurement. No major issues with availability and accessibility of ICTs were raised. When asked about testing algorithms, ICTs were not used as stand-alone or first test for TB culture identification as recommended by WHO. Conclusions The low response rate was a limitation of this survey and together with NRLs managers' unawareness of global guidance, suggests a lack of effective communication between partners of the global laboratory network and NRLs. TB tests could become more affordable to high TB endemic countries, if the possibility to negotiate lower prices for commercial products is communicated to them more successfully. NRLs need additional guidance to identify where available technologies can be most usefully implemented and in what order, taking into account long-term laboratory strategies. PMID:22937050

  1. The lactate conundrum in wound healing: clinical and experimental findings indicate the requirement for a rapid point-of-care diagnostic.

    PubMed

    Britland, Stephen; Ross-Smith, Oliver; Jamil, Humzah; Smith, Annie G; Vowden, Kath; Vowden, Peter

    2012-07-01

    The increasing prevalence of chronic wounds has significant financial implications for nations with advanced healthcare provision. Although the diseases that predispose to hard-to-heal wounds are recognized, their etiology is less well understood, partly because practitioners in wound management lack specialized diagnostic support. Prognostic indicators for healing may be inherent to wound biochemistry but remain invisible under routine clinical investigation; lactate is an example of this. In this study, lactate concentration in exudate obtained from 20 patients undergoing wound management in hospital was variable but in some cases approached or exceeded 20 mM. In vitro viability studies indicated that fibroblasts and endothelial cells tolerated low levels of lactate (1-10 mM), but cell viability was severely compromised by high lactate concentrations (=20 mM). Scratched monolayer experiments revealed that cell migration was affected earlier than viability in response to increasing lactate dose, and this was shown by immunocytochemistry to be associated with cytoskeletal disruption. A prototype enzyme-based colorimetric assay for lactate generating a color change that was rapid in the context of clinical practise, and capable of functioning within a gel vehicle, was developed with point-of-care dipstick applications in mind. A randomized single-blinded trial involving 30 volunteers and using a color chart to calibrate the assay demonstrated that lactate concentration could be reliably estimated with 5 mM precision; this suggesting that "physiological" and "pathological" lactate concentration could be distinguished. The present data suggest that a dipstick-type colorimetric assay could comprise a viable diagnostic tool for identifying patients at-risk from high-wound lactate. PMID:22581665

  2. Ni(II)NTA AuNPs as a low-resource malarial diagnostic platform for the rapid colorimetric detection of Plasmodium falciparum Histidine-Rich Protein-2.

    PubMed

    Gulka, Christopher P; Swartz, Joshua D; Wright, David W

    2015-04-01

    Diagnosing infectious diseases remains a challenge in the developing world where there is a lack of dependable electricity, running water, and skilled technicians. Although rapid immunochromatographic tests (RDTs) have been deployed to diagnose diseases such as malaria, the extreme climate conditions encountered in these regions compounded with the discrepancies in test manufacturing have yielded varying results, so that more innovative and robust technologies are sought. Devoid of antibodies and thermally sensitive materials, we present a robust, colorimetric diagnostic platform for the detection of a malarial biomarker, Plasmodium falciparum Histidine-Rich Protein 2 (PfHRP-II). The assay exploits the optical properties of gold nanoparticles, covalently coupling them to a Ni(II)NTA recognition element specific for PfHRP-II. In the presence of the recombinant malarial biomarker (rcHRP-II), the Ni(II)NTA AuNPs begin to crosslink and aggregate in as little as one minute, triggering a red-to-purple color change in solution. To increase assay sensitivity and platform stability suitable for low-resource regions, the Ni(II)NTA AuNPs were assembled with varying spacer ligands in a mixed monolayer presentation. When assembled with a negatively charged Peg4-thiol ligand, the Ni(II)NTA AuNPs demonstrate low nanomolar limits of rcHRP-II detection in physiological concentrations of human serum albumin and maintain excellent stability at 37°C when stored for four weeks. Detection of the malaria biomarker is also measured by capturing and processing images of aggregated gold nanoparticles with a smartphone camera. By utilizing a smartphone camera and image processing application, there is no significant difference in assay sensitivity and rcHRP-II limit of detection in comparison to a spectrophotometer, further making this diagnostic platform applicable for use in low-resource regions. PMID:25640131

  3. Evaluation of Paracheck-PfTM rapid malaria diagnostic test for the diagnosis of malaria among HIV-positive patients in Ibadan, south-western Nigeria

    PubMed Central

    Falade, C O; Adesina-Adewole, B; Dada-Adegbola, H O; Ajayi, I O; Akinyemi, J O; Ademowo, O G; Adewole, I F; Kanki, P

    2013-01-01

    Febrile illnesses occur frequently among HIV positive patients and these are often treated presumptively as malaria in endemic areas. Parasite-based diagnosis of malaria will eliminate unnecessary treatment, reduce drug–drug interactions and the chances for the emergence of drug resistant Plasmodium. We evaluated finger prick blood samples from 387 people living with HIV (PLWHIV) and suspected of having malaria by expert microscopy and Paracheck-PfTM – a histidine-rich protein-II based malaria rapid diagnostic test. The study was conducted at the PEPFAR supported AIDS Prevention Initiative in Nigeria (APIN) Clinic of the University College Hospital Ibadan, southwest Nigeria. Outcome parameters were prevalence of malaria parasitemia, sensitivity and specificity of Paracheck-Pf as well as the positive and negative predictive values for Paracheck-Pf using microscopy of Giemsa-stained blood film as gold standard. Malaria parasites were detected in 19.1% (74/387) of enrollees by microscopy and 19.3% (74/383) by Paracheck-Pf. Geometric mean parasite density was 501/μl (range 39–749 202/μl). Sensitivity and specificity of Paracheck-Pf at all parasite densities were 55.4% and 89.3% while corresponding figures at parasite densities ≧200/μl were 90.9% and 90.3%. Sensitivity and specificity at parasite densities ≧500/μl was 97.6% and 90.3%. Positive and negative predictive values for parasite density ≧200/μl were 55.4% and 98.7%, respectively. Paracheck-pf was found to be a useful malaria diagnostic tool at parasite densities ≧200/μl facilitating appropriate clinical management. PMID:23683333

  4. A low cost, safe, disposable, rapid and self-sustainable paper-based platform for diagnostic testing: lab-on-paper.

    PubMed

    Costa, M N; Veigas, B; Jacob, J M; Santos, D S; Gomes, J; Baptista, P V; Martins, R; Inácio, J; Fortunato, E

    2014-03-01

    There is a strong interest in the use of biopolymers in the electronic and biomedical industries, mainly towards low-cost applications. The possibility of developing entirely new kinds of products based on cellulose is of current interest, in order to enhance and to add new functionalities to conventional paper-based products. We present our results towards the development of paper-based microfluidics for molecular diagnostic testing. Paper properties were evaluated and compared to nitrocellulose, the most commonly used material in lateral flow and other rapid tests. Focusing on the use of paper as a substrate for microfluidic applications, through an eco-friendly wax-printing technology, we present three main and distinct colorimetric approaches: (i) enzymatic reactions (glucose detection); (ii) immunoassays (antibodies anti-Leishmania detection); (iii) nucleic acid sequence identification (Mycobacterium tuberculosis complex detection). Colorimetric glucose quantification was achieved through enzymatic reactions performed within specific zones of the paper-based device. The colouration achieved increased with growing glucose concentration and was highly homogeneous, covering all the surface of the paper reaction zones in a 3D sensor format. These devices showed a major advantage when compared to the 2D lateral flow glucose sensors, where some carryover of the coloured products usually occurs. The detection of anti-Leishmania antibodies in canine sera was conceptually achieved using a paper-based 96-well enzyme-linked immunosorbent assay format. However, optimization is still needed for this test, regarding the efficiency of the immobilization of antigens on the cellulose fibres. The detection of Mycobacterium tuberculosis nucleic acids integrated with a non-cross-linking gold nanoprobe detection scheme was also achieved in a wax-printed 384-well paper-based microplate, by the hybridization with a species-specific probe. The obtained results with the above

  5. A low cost, safe, disposable, rapid and self-sustainable paper-based platform for diagnostic testing: lab-on-paper

    NASA Astrophysics Data System (ADS)

    Costa, M. N.; Veigas, B.; Jacob, J. M.; Santos, D. S.; Gomes, J.; Baptista, P. V.; Martins, R.; Inácio, J.; Fortunato, E.

    2014-03-01

    There is a strong interest in the use of biopolymers in the electronic and biomedical industries, mainly towards low-cost applications. The possibility of developing entirely new kinds of products based on cellulose is of current interest, in order to enhance and to add new functionalities to conventional paper-based products. We present our results towards the development of paper-based microfluidics for molecular diagnostic testing. Paper properties were evaluated and compared to nitrocellulose, the most commonly used material in lateral flow and other rapid tests. Focusing on the use of paper as a substrate for microfluidic applications, through an eco-friendly wax-printing technology, we present three main and distinct colorimetric approaches: (i) enzymatic reactions (glucose detection); (ii) immunoassays (antibodies anti-Leishmania detection); (iii) nucleic acid sequence identification (Mycobacterium tuberculosis complex detection). Colorimetric glucose quantification was achieved through enzymatic reactions performed within specific zones of the paper-based device. The colouration achieved increased with growing glucose concentration and was highly homogeneous, covering all the surface of the paper reaction zones in a 3D sensor format. These devices showed a major advantage when compared to the 2D lateral flow glucose sensors, where some carryover of the coloured products usually occurs. The detection of anti-Leishmania antibodies in canine sera was conceptually achieved using a paper-based 96-well enzyme-linked immunosorbent assay format. However, optimization is still needed for this test, regarding the efficiency of the immobilization of antigens on the cellulose fibres. The detection of Mycobacterium tuberculosis nucleic acids integrated with a non-cross-linking gold nanoprobe detection scheme was also achieved in a wax-printed 384-well paper-based microplate, by the hybridization with a species-specific probe. The obtained results with the above

  6. Using Rapid Diagnostic Tests as a Source of Viral RNA for Dengue Serotyping by RT-PCR - A Novel Epidemiological Tool

    PubMed Central

    Vongsouvath, Manivanh; Phommasone, Koukeo; Sengvilaipaseuth, Onanong; Kosoltanapiwat, Nathamon; Chantratita, Narisara; Blacksell, Stuart D.; Lee, Sue J.; de Lamballerie, Xavier; Mayxay, Mayfong; Keomany, Sommay; Newton, Paul N.; Dubot-Pérès, Audrey

    2016-01-01

    Background Dengue virus infection causes major public health problems in tropical and subtropical areas. In many endemic areas, including the Lao PDR, inadequate access to laboratory facilities is a major obstacle to surveillance and study of dengue epidemiology. Filter paper is widely used for blood collection for subsequent laboratory testing for antibody and nucleic acid detection. For the first time, we demonstrate that dengue viral RNA can be extracted from dengue rapid diagnostic tests (RDT) and then submitted to real-time RT-PCR for serotyping. Methodology/Principal Findings We evaluated the Standard Diagnostics (SD) Bioline Dengue Duo RDT, a commonly used test in dengue endemic areas. First, using the QIAamp RNA kit, dengue RNA was purified from the sample pad of the NS1 RDT loaded with virus isolates of the four serotypes, then quantified by RT-PCR. We observed greater recovery of virus, with a mean of 27 times more RNA recovered from RDT, than from filter paper. Second, we evaluated dengue NS1 RDTs from patients at Mahosot Hospital, Vientiane, (99 patients) and from rural Salavan Provincial Hospital (362 patients). There was good agreement between dengue RT-PCR from NS1 RDT with RT-PCR performed on RNA extracted from patient sera, either using RDT loaded with blood (82.8% and 91.4%, in Vientiane and Salavan, respectively) or serum (91.9% and 93.9%). There was 100% concordance between RDT and serum RT-PCR of infecting dengue serotype. Conclusions/Significance Therefore, the collection of NS1 positive RDTs, which do not require cold storage, may be a novel approach for dengue serotyping by RT-PCR and offers promising prospects for the collection of epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions. PMID:27159058

  7. The clinical diagnostic accuracy of rapid detection of healthcare-associated bloodstream infection in intensive care using multipathogen real-time PCR technology

    PubMed Central

    Dunn, Graham; Chadwick, Paul; Young, Duncan; Bentley, Andrew; Carlson, Gordon; Warhurst, Geoffrey

    2011-01-01

    Background There is growing interest in the potential utility of real-time PCR in diagnosing bloodstream infection by detecting pathogen DNA in blood samples within a few hours. SeptiFast is a multipathogen probe-based real-time PCR system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection and has European regulatory approval. The SeptiFast pathogen panel is suited to identifying healthcare-associated bloodstream infection acquired during complex healthcare, and the authors report here the protocol for the first detailed health-technology assessment of multiplex real-time PCR in this setting. Methods/design A Phase III multicentre double-blinded diagnostic study will determine the clinical validity of SeptiFast for the rapid detection of healthcare-associated bloodstream infection, against the current service standard of microbiological culture, in an adequately sized population of critically ill adult patients. Results from SeptiFast and standard microbiological culture procedures in each patient will be compared at study conclusion and the metrics of clinical diagnostic accuracy of SeptiFast determined in this population setting. In addition, this study aims to assess further the preliminary evidence that the detection of pathogen DNA in the bloodstream using SeptiFast may have value in identifying the presence of infection elsewhere in the body. Furthermore, differences in circulating immune-inflammatory markers in patient groups differentiated by the presence/absence of culturable pathogens and pathogen DNA will help elucidate further the patho-physiology of infection developing in the critically ill. Ethics and dissemination Ethical approval has been granted by the North West 6 Research Ethics Committee (09/H1003/109). Based on the results of this first non-commercial study, independent recommendations will be made to The Department of Health (open-access health technology

  8. Sensitivity and Specificity of a Prototype Rapid Diagnostic Test for the Detection of Trypanosoma brucei gambiense Infection: A Multi-centric Prospective Study

    PubMed Central

    Bisser, Sylvie; Lumbala, Crispin; Nguertoum, Etienne; Kande, Victor; Flevaud, Laurence; Vatunga, Gedeao; Boelaert, Marleen; Büscher, Philippe; Josenando, Theophile; Bessell, Paul R.; Biéler, Sylvain; Ndung’u, Joseph M.

    2016-01-01

    Background A major challenge in the control of human African trypanosomiasis (HAT) is lack of reliable diagnostic tests that are rapid and easy to use in remote areas where the disease occurs. In Trypanosoma brucei gambiense HAT, the Card Agglutination Test for Trypanosomiasis (CATT) has been the reference screening test since 1978, usually on whole blood, but also in a 1/8 dilution (CATT 1/8) to enhance specificity. However, the CATT is not available in a single format, requires a cold chain for storage, and uses equipment that requires electricity. A solution to these challenges has been provided by rapid diagnostic tests (RDT), which have recently become available. A prototype immunochromatographic test, the SD BIOLINE HAT, based on two native trypanosomal antigens (VSG LiTat 1.3 and VSG LiTat 1.5) has been developed. We carried out a non-inferiority study comparing this prototype to the CATT 1/8 in field settings. Methodology/Principal Findings The prototype SD BIOLINE HAT, the CATT Whole Blood and CATT 1/8 were systematically applied on fresh blood samples obtained from 14,818 subjects, who were prospectively enrolled through active and passive screening in clinical studies in three endemic countries of central Africa: Angola, the Democratic Republic of the Congo and the Central African Republic. One hundred and forty nine HAT cases were confirmed by parasitology. The sensitivity and specificity of the prototype SD BIOLINE HAT was 89.26% (95% confidence interval (CI) = 83.27–93.28) and 94.58% (95% CI = 94.20–94.94) respectively. The sensitivity and specificity of the CATT on whole blood were 93.96% (95% CI = 88.92–96.79) and 95.91% (95% CI = 95.58–96.22), and of the CATT 1/8 were 89.26% (95% CI = 83.27–93.28) and 98.88% (95% CI = 98.70–99.04) respectively. Conclusion/Significance After further optimization, the prototype SD BIOLINE HAT could become an alternative to current screening methods in primary healthcare settings in remote, resource

  9. Estimating the Influenza Vaccine Effectiveness against Medically Attended Influenza in Clinical Settings: A Hospital-Based Case-Control Study with a Rapid Diagnostic Test in Japan

    PubMed Central

    Suzuki, Motoi; Yoshimine, Hiroyuki; Harada, Yoshitaka; Tsuchiya, Naho; Shimada, Ikumi; Ariyoshi, Koya; Inoue, Kenichiro

    2013-01-01

    Background Influenza vaccine effectiveness (VE) studies are usually conducted by specialized agencies and require time and resources. The objective of this study was to estimate the influenza VE against medically attended influenza using a test-negative case-control design with rapid influenza diagnostic tests (RIDT) in a clinical setting. Methods A prospective study was conducted at a community hospital in Nagasaki, western Japan during the 2010/11 influenza season. All outpatients aged 15 years and older with influenza-like illnesses (ILI) who had undergone RIDT were enrolled. A test-negative case-control design was applied to estimate the VEs: the cases were ILI patients with positive RIDT results and the controls were ILI patients with negative RIDT results. Information on patient characteristics, including vaccination histories, was collected using questionnaires and medical records. Results Between December 2010 and April 2011, 526 ILI patients were tested with RIDT, and 476 were eligible for the analysis. The overall VE estimate against medically attended influenza was 47.6%, after adjusting for the patients' age groups, presence of chronic conditions, month of visit, and smoking and alcohol use. The seasonal influenza vaccine reduced the risk of medically attended influenza by 60.9% for patients less than 50 years of age, but a significant reduction was not observed for patients 50 years of age and older. A sensitivity analysis provided similar figures. Conclusion The test-negative case-control study using RIDT provided moderate influenza VE consistent with other reports. Utilizing the commonly used RIDT to estimate VE provides rapid assessment of VE; however, it may require validation with more specific endpoint. PMID:23326324

  10. Prospective assessment of rapid diagnostic tests for the detection of antibodies to hepatitis C virus, a tool for improving access to care.

    PubMed

    Chevaliez, S; Poiteau, L; Rosa, I; Soulier, A; Roudot-Thoraval, F; Laperche, S; Hézode, C; Pawlotsky, J-M

    2016-05-01

    Large-scale hepatitis C screening is required to prevent further spread of the infection, improve access to care in the context of new hepatitis C virus (HCV) drug regimens without interferon-alpha and subsequently reduce the risk of long-term complications of chronic liver disease. Rapid diagnostic tests (RDTs) represent an attractive alternative to enzyme immunoassay using blood from venepuncture. The aim of the present study was to prospectively assess the clinical performance of CE-marked RDTs detecting anti-HCV antibodies in fingerstick capillary whole blood and/or oral fluid. A total of 513 individuals, including 318 patients with chronic HCV infection, 25 patients with resolved HCV infection and 170 HCV-seronegative individuals, were prospectively enrolled. The specificity of RDTs with fingerstick whole blood varied from 98.8% to 100%. The clinical sensitivity was high for the OraQuick(®) and Toyo(®) tests (99.4% and 95.8%, respectively), but low for the Labmen(®) test (63.1%). The specificity and clinical sensitivity in crevicular fluid were both satisfactory for the OraQuick(®) test (100% and 97.6%, respectively). HCV antibody RDTs were easy and rapid to perform in the context of patient care. They were highly specific. Both the OraQuick(®) and Toyo(®) tests reached the expected level of performance for wide-scale use, with a performance advantage for the OraQuick(®) HCV test. RDTs appear to be a promising new tool for wide-scale screening of HCV infection in high-risk to medium-risk populations. Hence, careful assessment of the performance of HCV RDTs must be recommended before they can be implemented in clinical practice. PMID:26806260

  11. Irregular Migration as a Potential Source of Malaria Reintroduction in Sri Lanka and Use of Malaria Rapid Diagnostic Tests at Point-of-Entry Screening.

    PubMed

    Wickramage, Kolitha; Galappaththy, Gawrie N L; Dayarathne, D; Peiris, Sharika L; Basnayake, Rajeeka N; Mosca, Davide; Jacobs, Jan

    2013-01-01

    Background. We describe an irregular migrant who returned to Sri Lanka after a failed people smuggling operation from West Africa. Results. On-arrival screening by Anti-Malaria Campaign (AMC) officers using a rapid diagnostic test (RDT) (CareStart Malaria HRP2/PLDH) indicated a negative result. On day 3 after arrival, he presented with fever and chills but was managed as dengue (which is hyperendemic in Sri Lanka). Only on day 7, diagnosis of Plasmodium falciparum malaria was made by microcopy and CareStart RDT. The initially negative RDT was ascribed to a low parasite density. Irregular migration may be an unrecognized source of malaria reintroduction. Despite some limitations in detection, RDTs form an important point-of-entry assessment. As a consequence of this case, the AMC is now focused on repeat testing and close monitoring of all irregular migrants from malaria-endemic zones. Conclusion. The present case study highlights the effective collaboration and coordination between inter-governmental agencies such as IOM and the Ministry of Health towards the goals of malaria elimination in Sri Lanka. PMID:23861687

  12. Towards subsidized malaria rapid diagnostic tests. Lessons learned from programmes to subsidise artemisinin-based combination therapies in the private sector: a review.

    PubMed

    Lussiana, Cristina

    2016-09-01

    The idea of a private sector subsidy programme of artemisinin-based combination therapies (ACTs) was first proposed in 2004. Since then, several countries around the world have hosted pilot projects or programmes on subsidized ACTs and/or the Affordable Medicines Facility-malaria programme (AMFm). Overall the private sector subsidy programmes of ACTs have been effective in increasing availability of ACTs in the private sector and driving down average prices but struggled to crowd out antimalarial monotherapies. The results obtained from this ambitious strategy should inform policy makers in the designing of future interventions aimed to control malaria morbidity and mortality. Among the interventions recently proposed, a subsidy of rapid diagnostic tests (RDTs) in the private sector has been recommended by governments and international donors to cope with over-treatment with ACTs and to delay the emergence of resistance to artemisinin. In order to improve the cost-effectiveness of co-paid RDTs, we should build on the lessons we learned from almost 10 years of private sector subsidy programmes of ACTs in malaria-endemic countries. PMID:25862732

  13. Towards subsidized malaria rapid diagnostic tests. Lessons learned from programmes to subsidise artemisinin-based combination therapies in the private sector: a review

    PubMed Central

    Lussiana, Cristina

    2016-01-01

    The idea of a private sector subsidy programme of artemisinin-based combination therapies (ACTs) was first proposed in 2004. Since then, several countries around the world have hosted pilot projects or programmes on subsidized ACTs and/or the Affordable Medicines Facility-malaria programme (AMFm). Overall the private sector subsidy programmes of ACTs have been effective in increasing availability of ACTs in the private sector and driving down average prices but struggled to crowd out antimalarial monotherapies. The results obtained from this ambitious strategy should inform policy makers in the designing of future interventions aimed to control malaria morbidity and mortality. Among the interventions recently proposed, a subsidy of rapid diagnostic tests (RDTs) in the private sector has been recommended by governments and international donors to cope with over-treatment with ACTs and to delay the emergence of resistance to artemisinin. In order to improve the cost-effectiveness of co-paid RDTs, we should build on the lessons we learned from almost 10 years of private sector subsidy programmes of ACTs in malaria-endemic countries. PMID:25862732

  14. Early experiences on the feasibility, acceptability, and use of malaria rapid diagnostic tests at peripheral health centres in Uganda-insights into some barriers and facilitators

    PubMed Central

    2012-01-01

    Background While feasibility of new health technologies in well-resourced healthcare settings is extensively documented, it is largely unknown in low-resourced settings. Uganda's decision to deploy and scale up malaria rapid diagnostic tests (mRDTs) in public health facilities and at the community level provides a useful entry point for documenting field experience, acceptance, and predictive variables for technology acceptance and use. These findings are important in informing implementation of new health technologies, plans, and budgets in low-resourced national disease control programmes. Methods A cross-sectional qualitative descriptive study at 21 health centres in Uganda was undertaken in 2007 to elucidate the barriers and facilitators in the introduction of mRDTs as a new diagnostic technology at lower-level health facilities. Pre-tested interview questionnaires were administered through pre-structured patient exit interviews and semi-structured health worker interviews to gain an understanding of the response to this implementation. A conceptual framework on technology acceptance and use was adapted for this study and used to prepare the questionnaires. Thematic analysis was used to generate themes from the data. Results A total of 52 of 57 health workers (92%) reported a belief that a positive mRDT result was true, although only 41 of 57 (64%) believed that treatment with anti-malarials was justified for every positive mRDT case. Of the same health workers, only 49% believed that a negative mRDT result was truly negative. Factors linked to these findings were related to mRDT acceptance and use, including the design and characteristics of the device, availability and quality of mRDT ancillary supplies, health worker capacity to investigate febrile cases testing negative with the device and provide appropriate treatment, availability of effective malaria treatments, reliability of the health commodity supply chain, existing national policy recommendations

  15. Rapid prenatal diagnosis of cytogenetic abnormalities by array CGH analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Array CGH analysis has been shown to be highly accurate for rapid detection of chromosomal aneuploidies and submicroscopic deletions or duplications on fetal DNA samples in a clinical prenatal diagnostic setting. The objective of this study is to present our "post-validation phase" experience with ...

  16. Microfluidic diagnostic technologies for global public health

    NASA Astrophysics Data System (ADS)

    Yager, Paul; Edwards, Thayne; Fu, Elain; Helton, Kristen; Nelson, Kjell; Tam, Milton R.; Weigl, Bernhard H.

    2006-07-01

    The developing world does not have access to many of the best medical diagnostic technologies; they were designed for air-conditioned laboratories, refrigerated storage of chemicals, a constant supply of calibrators and reagents, stable electrical power, highly trained personnel and rapid transportation of samples. Microfluidic systems allow miniaturization and integration of complex functions, which could move sophisticated diagnostic tools out of the developed-world laboratory. These systems must be inexpensive, but also accurate, reliable, rugged and well suited to the medical and social contexts of the developing world.

  17. Development of an ultra-rapid diagnostic method based on heart-type fatty acid binding protein levels in the CSF of CJD patients.

    PubMed

    Matsui, Yuki; Satoh, Katsuya; Mutsukura, Kazuo; Watanabe, Takuya; Nishida, Noriyuki; Matsuda, Hideo; Sugino, Masaichi; Shirabe, Susumu; Eguchi, Katsumi; Kataoka, Yasufumi

    2010-10-01

    Creutzfeldt-Jakob disease (CJD) is a transmissible, fatal, neurodegenerative disease in humans. Recently, various drugs have been reported to be useful in the treatment of CJD; however, for such treatments to be useful it is essential to rapidly and accurately diagnose CJD. 124 CJD patients and 87 with other diseases causing rapid progressive dementia were examined. Cerebral spinal fluid (CSF) from CJD patients was analyzed by 2D-PAGE and the protein expression pattern was compared with that from healthy subjects. One of three CJD-specific spots was found to be fatty acid binding protein (FABP), and heart-type FABP (H-FABP) was analyzed as a new biochemical marker for CJD. H-FABP ELISA results were compared between CJD patients and patients with other diseases (n = 211). Visual readout accuracy of the Rapicheck(®) H-FABP test panel for CSF was analyzed using an independent measure of CSF H-FABP concentration. The distribution of H-FABP in the brains of CJD patients was examined by immunohistochemistry. ELISA sensitivity and specificity were 90.3% and 92.9%, respectively, and Rapicheck(®) H-FABP sensitivity and specificity were 87.9% and 96.0%, respectively. ELISA and Rapicheck(®) H-FABP assays provided comparable results for 14-3-3 protein and total tau protein. Elevated H-FABP levels were associated with an accumulation of abnormal prion protein, astrocytic gliosis, and neuronal loss in the cerebral cortices of CJD patients. In conclusion, Rapicheck(®) H-FABP of CSF specimens enabled quick and frequent diagnosis of CJD. H-FABP represents a new biomarker for CJD distinct from 14-3-3 protein and total tau protein. PMID:20499272

  18. Willingness to use a rapid diagnostic test for malaria in a rural area of central Côte d’Ivoire

    PubMed Central

    2012-01-01

    Background Malaria mortality is mainly a direct consequence of inadequate and/or delayed diagnosis and case management. Some important control interventions (e.g. long-lasting insecticidal nests) have contributed to reduce malaria morbidity and mortality in different parts of the world. Moreover, the development and effective use of rapid diagnostic tests (RDTs) hold promise to further enhance the control and elimination of malaria, particularly in areas where health services are deficient. The aim of this study was to determine knowledge, attitudes, practices and beliefs in relation to RDTs for malaria in rural Côte d’Ivoire. Methods One hundred individuals from Bozi and Yoho who sought care at the health centre in Bozi and were offered an RDT for malaria were interviewed in April 2010 using a pre-tested questionnaire on practice and perceptions in relation to RDTs for malaria. The relationships between acceptance of RDTs and factors related to opinions were identified, using generalized linear mixed models. Qualitative data from open-ended questions complemented the quantitative analysis. Results Only 34 out of 100 patients who were offered an RDT for malaria were willing to undergo the test. People who perceived blood as a sacred body fluid were less likely to comply with an RDT. The concurrent availability and use of RDTs for HIV and malaria was associated with an unwilling attitude towards RDTs for malaria (Fisher’s exact test, p <0.001). The initial willingness of patients to accept malaria testing with RDTs was significantly related to general fear and wanting to know malaria infection status. For further and regular use of RDTs, a strong relationship was observed between acceptance and the idea that an RDT is a pretext used by health worker to know HIV status (odds ratio (OR) = 16.61, 95% confidence interval (CI) = 1.03-268.5). Those thinking that blood samples were useful for medical diagnoses were 8.31-times (95% CI = 2.22-31.1) more likely to

  19. Typical ultraviolet spectra in combination with diagnostic mass fragmentation analysis for the rapid and comprehensive profiling of chlorogenic acids in the buds of Lonicera macranthoides.

    PubMed

    Zhang, Shui-Han; Hu, Xin; Shi, Shu-Yun; Huang, Lu-Qi; Chen, Wei; Chen, Lin; Cai, Ping

    2016-05-01

    A major challenge of profiling chlorogenic acids (CGA) in natural products is to effectively detect unknown or minor isomeric compounds. Here, we developed an effective strategy, typical ultraviolet (UV) spectra in combination with diagnostic mass fragmentation analysis based on HPLC-DAD-QTOF-MS/MS, to comprehensively profile CGA in the buds of Lonicera macranthoides. First, three CGA UV patterns were obtained by UV spectra screening. Second, 13 types of CGA classified by molecular weights were found by thorough analysis of CGA peaks using high-resolution MS. Third, selected ion monitoring (SIM) was carried out for each type of CGA to avoid overlooking of minor ones. Fourth, MS/MS spectra of each CGA were investigated. Then 70 CGA were identified by matching their UV spectra, accurate mass signals and fragmentation patterns with standards or previously reported compounds, including six caffeoylquinic acids (CQA), six diCQA, one triCQA, three caffeoylshikimic acids (CSA), six diCSA, one triCSA, three p-coumaroylquinic acids (pCoQA), four p-coumaroylcaffeoylquinic acids (pCoCQA), four feruloylquinic acids (FQA), five methyl caffeoylquinates (MCQ), three ethyl caffeoylquinates (ECQ), three dimethoxycinnamoylquinic acids (DQA), six caffeoylferuloylquinic acids (CFQA), six methyl dicaffeoylquinates (MdiCQ), four FQA glycosides (FQAG), six MCQ glycosides (MCQG), and three ethyl dicaffeoylquinates (EdiCQ). Forty-five of them were discovered from Lonicera species for the first time, and it is noted that CGA profiles were investigated for the first time in L. macranthoides. Results indicated that the developed method was a useful approach to explore unknown and minor isomeric compounds from complex natural products. PMID:26970751

  20. Mapping of Schistosomiasis and Soil-Transmitted Helminths in Namibia: The First Large-Scale Protocol to Formally Include Rapid Diagnostic Tests

    PubMed Central

    Sousa-Figueiredo, José Carlos; Stanton, Michelle C.; Katokele, Stark; Arinaitwe, Moses; Adriko, Moses; Balfour, Lexi; Reiff, Mark; Lancaster, Warren; Noden, Bruce H.; Bock, Ronnie; Stothard, J. Russell

    2015-01-01

    Background Namibia is now ready to begin mass drug administration of praziquantel and albendazole against schistosomiasis and soil-transmitted helminths, respectively. Although historical data identifies areas of transmission of these neglected tropical diseases (NTDs), there is a need to update epidemiological data. For this reason, Namibia adopted a new protocol for mapping of schistosomiasis and geohelminths, formally integrating rapid diagnostic tests (RDTs) for infections and morbidity. In this article, we explain the protocol in detail, and introduce the concept of ‘mapping resolution’, as well as present results and treatment recommendations for northern Namibia. Methods/Findings/Interpretation This new protocol allowed a large sample to be surveyed (N = 17 896 children from 299 schools) at relatively low cost (7 USD per person mapped) and very quickly (28 working days). All children were analysed by RDTs, but only a sub-sample was also diagnosed by light microscopy. Overall prevalence of schistosomiasis in the surveyed areas was 9.0%, highly associated with poorer access to potable water (OR = 1.5, P<0.001) and defective (OR = 1.2, P<0.001) or absent sanitation infrastructure (OR = 2.0, P<0.001). Overall prevalence of geohelminths, more particularly hookworm infection, was 12.2%, highly associated with presence of faecal occult blood (OR = 1.9, P<0.001). Prevalence maps were produced and hot spots identified to better guide the national programme in drug administration, as well as targeted improvements in water, sanitation and hygiene. The RDTs employed (circulating cathodic antigen and microhaematuria for Schistosoma mansoni and S. haematobium, respectively) performed well, with sensitivities above 80% and specificities above 95%. Conclusion/Significance This protocol is cost-effective and sensitive to budget limitations and the potential economic and logistical strains placed on the national Ministries of Health. Here we present a high resolution map

  1. Effectiveness of Trivalent Inactivated Influenza Vaccine in Children Estimated by a Test-Negative Case-Control Design Study Based on Influenza Rapid Diagnostic Test Results

    PubMed Central

    Yamaguchi, Yoshio; Tomidokoro, Yuka; Sekiguchi, Shinichiro; Mitamura, Keiko; Fujino, Motoko; Shiro, Hiroyuki; Komiyama, Osamu; Taguchi, Nobuhiko; Nakata, Yuji; Yoshida, Naoko; Narabayashi, Atsushi; Myokai, Michiko; Sato, Masanori; Furuichi, Munehiro; Baba, Hiroaki; Fujita, Hisayo; Sato, Akihiro; Ookawara, Ichiro; Tsunematsu, Kenichiro; Yoshida, Makoto; Kono, Mio; Tanaka, Fumie; Kawakami, Chiharu; Kimiya, Takahisa; Takahashi, Takao; Iwata, Satoshi

    2015-01-01

    We assessed vaccine effectiveness (VE) against medically attended, laboratory-confirmed influenza in children 6 months to 15 years of age in 22 hospitals in Japan during the 2013–14 season. Our study was conducted according to a test-negative case-control design based on influenza rapid diagnostic test (IRDT) results. Outpatients who came to our clinics with a fever of 38°C or over and had undergone an IRDT were enrolled in this study. Patients with positive IRDT results were recorded as cases, and patients with negative results were recorded as controls. Between November 2013 and March 2014, a total of 4727 pediatric patients (6 months to 15 years of age) were enrolled: 876 were positive for influenza A, 66 for A(H1N1)pdm09 and in the other 810 the subtype was unknown; 1405 were positive for influenza B; and 2445 were negative for influenza. Overall VE was 46% (95% confidence interval [CI], 39–52). Adjusted VE against influenza A, influenza A(H1N1)pdm09, and influenza B was 63% (95% CI, 56–69), 77% (95% CI, 59–87), and 26% (95% CI, 14–36), respectively. Influenza vaccine was not effective against either influenza A or influenza B in infants 6 to 11 months of age. Two doses of influenza vaccine provided better protection against influenza A infection than a single dose did. VE against hospitalization influenza A infection was 76%. Influenza vaccine was effective against influenza A, especially against influenza A(H1N1)pdm09, but was much less effective against influenza B. PMID:26317334

  2. Diagnostic Value of Leukocyte Esterase Test Strip Reagents for Rapid Clinical Diagnosis of Spontaneous Bacterial Peritonitis in Patients Admitted to Hospital Emergency Departments in Iran

    PubMed Central

    Hashemian, Amir Masoud; Ahmadi, Koorosh; Zamani Moghaddam, Hamid; Zakeri, Hosein; Davoodi Navakh, Seyed Akbar; Sharifi, Mohammad Davood; Bahrami, Abdollah

    2015-01-01

    Background: Spontaneous bacterial peritonitis (SBP) is a common and important clinical problem and is life-threatening in decompensated liver disease. Ascites fluid test by leukocyte esterase test strip has been recently proposed as an effective and rapid method to diagnose SBP in patients with cirrhosis. Objectives: This study aimed to evaluate sensitivity and specificity of leukocyte esterase test strip in the diagnosis of SBP. Patients and Methods: The population of this research was all patients with cirrhosis and ascites admitted to the emergency room at Imam Reza (AS) hospital, Mashhad. A written consent was taken for inclusion in the study. 50 mL ascites sample was taken from all patients for use in a urine test strip (LER) (Urine Test Strips Convergys®Urine Matrix 11). The patient’s ascites samples were evaluated for cell counting. Positive dipstick test for LER in this study considered as grade 3 +. The values of WBC > 500 cell/mm3 or PMN > 250 cell/mm3 considered as positive result of the gold standard method for the diagnosis of SBP. Results: In this study, 100 patients with ascites due to cirrhosis, with an average age of 38.9 ± 6.54 years were evaluated. Twenty cases had positive results, of whom 17 cases were also detected based on the standard diagnostic criteria and other three cases were healthy individuals. Thus, sensitivity, specificity, positive and negative predictive values, and accuracy of the method were 95%, 96.3%, 85%, 97.5% and 95%, respectively. Conclusions: The use of leukocyte esterase urine dipstick test can be a quick and easy method in early diagnosis of SBP to start the treatment until preparation of SBP-cell count results. PMID:26568859

  3. Glycan-based diagnostic devices: current progress, challenges and perspectives.

    PubMed

    Wang, Sheng-Kai; Cheng, Chao-Min

    2015-12-01

    Diagnosis is an essential launching point for accurate medical treatment, and rapid and accurate diagnostic approaches have become the increasingly vital goal inspiring developments in a variety of analytical methods. With increasing attention in the area of glycosciences, the roles that carbohydrates play in many diseases have been elucidated, and the use of carbohydrates as disease biomarkers has become an emerging diagnostics strategy. This review article does not intend to comprehensively include all carbohydrate-related diagnostics studies. We do, however, wish to describe carbohydrate recognition and the design of sensitive detecting devices, especially those developed recently, so that readers might better grasp the principles behind such devices and relevant detection strategies, particularly those favoring inexpensive, rapid, and point-of-care (POC) approaches. PMID:26421872

  4. Novel, In-House, SYBR Green Based One-Step rRT-PCR: Rapid and Accurate Diagnosis of Crimean-Congo Hemorrhagic Fever Virus in Suspected Patients From Iran

    PubMed Central

    Zahraei, Bentolhoda; Hashemzadeh, Mohammad Sadegh; Najarasl, Mohammad; Zahiriyeganeh, Samaneh; Tat, Mahdi; Metanat, Maliheh; Sepehri Rad, Nahid; Khansari-nejad, Behzad; Zafari, Ehsan; Sharti, Mojtaba; Dorostkar, Ruhollah

    2016-01-01

    Background The Crimean-Congo hemorrhagic fever (CCHF) virus causes severe disease in humans, with a high mortality rate. Since, there is no approved vaccine or specific treatment for CCHF, an early and accurate diagnosis, as well as reliable surveillance, is essential for case management and patient improvement. Objectives For this research, our aim was to evaluate the application of a novel SYBR Green based one-step real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay for the in-house diagnosis of the CCHF virus. Patients and Methods In this experimental study, the highly conserved S-region sequence of the CCHF viral genome was first adapted from GenBank, and the specific primers targeting this region were designed. Then, the viral RNA was extracted from 75 serum samples from different patients in eastern Iran. The sensitivity and specificity of the primers were also evaluated in positive serum samples previously confirmed to have the CCHF virus, by this one-step rRT-PCR assay, as well as a DNA sequencing analysis. Results From a total of 75 suspected serum samples, 42 were confirmed to be positive for CCHF virus, with no false-positives detected by the sequencing results. After 40 amplification cycles, the melting curve analysis revealed a mean melting temperature (Tm) of 86.5 ± 0.6°C (quite different from those of the primer-dimers), and the positive samples showed only a small variation in the parameters. In all of the positive samples, the predicted length of 420 bp was confirmed by electrophoresis. Moreover, the sensitivity test showed that this assay can detect less than 20 copies of viral RNA per reaction. Conclusions This study showed that this novel one-step rRT-PCR assay is a rapid, reliable, repeatable, specific, sensitive, and simple tool for the detection of the CCHF virus. PMID:27099688

  5. Diagnostic Value of Animal-Side Antibody Assays for Rapid Detection of Mycobacterium bovis or Mycobacterium microti Infection in South American Camelids▿

    PubMed Central

    Lyashchenko, Konstantin P.; Greenwald, Rena; Esfandiari, Javan; Rhodes, Shelley; Dean, Gillian; de la Rua-Domenech, Ricardo; Meylan, Mireille; Vordermeier, HMartin; Zanolari, Patrik

    2011-01-01

    Tuberculosis (TB) in South American camelids (SAC) is caused by Mycobacterium bovis or Mycobacterium microti. Two serological methods, rapid testing (RT) and the dual-path platform (DPP) assay, were evaluated using naturally infected SAC. The study population included 156 alpacas and 175 llamas in Great Britain, Switzerland, and the United States. TB due to M. bovis (n = 44) or M. microti (n = 8) in 35 alpacas and 17 llamas was diagnosed by gross pathology examination and culture. Control animals were from herds with no TB history. The RT and the DPP assay showed sensitivities of 71% and 74%, respectively, for alpacas, while the sensitivity for llamas was 77% for both assays. The specificity of the DPP assay (98%) was higher than that of RT (94%) for llamas; the specificities of the two assays were identical (98%) for alpacas. When the two antibody tests were combined, the parallel-testing interpretation (applied when either assay produced a positive result) enhanced the sensitivities of antibody detection to 89% for alpacas and 88% for llamas but at the cost of lower specificities (97% and 93%, respectively), whereas the serial-testing interpretation (applied when both assays produced a positive result) maximized the specificity to 100% for both SAC species, although the sensitivities were 57% for alpacas and 65% for llamas. Over 95% of the animals with evidence of TB failed to produce skin test reactions, thus confirming concerns about the validity of this method for testing SAC. The findings suggest that serological assays may offer a more accurate and practical alternative for antemortem detection of camelid TB. PMID:22012976

  6. Rapid Detection of Pathogens

    SciTech Connect

    David Perlin

    2005-08-14

    Pathogen identification is a crucial first defense against bioterrorism. A major emphasis of our national biodefense strategy is to establish fast, accurate and sensitive assays for diagnosis of infectious diseases agents. Such assays will ensure early and appropriate treatment of infected patients. Rapid diagnostics can also support infection control measures, which monitor and limit the spread of infectious diseases agents. Many select agents are highly transmissible in the early stages of disease, and it is critical to identify infected patients and limit the risk to the remainder of the population and to stem potential panic in the general population. Nucleic acid-based molecular approaches for identification overcome many of the deficiencies associated with conventional culture methods by exploiting both large- and small-scale genomic differences between organisms. PCR-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for bacterial, fungal and many viral pathogenic agents. When combined with fluorescence-based oligonucleotide detection systems, this approach provides real-time, quantitative, high fidelity analysis capable of single nucleotide allelic discrimination (4). These probe systems offer rapid turn around time (<2 h) and are suitable for high throughput, automated multiplex operations that are critical for clinical diagnostic laboratories. In this pilot program, we have used molecular beacon technology invented at the Public health Research Institute to develop a new generation of molecular probes to rapidly detect important agents of infectious diseases. We have also developed protocols to rapidly extract nucleic acids from a variety of clinical specimen including and blood and tissue to for detection in the molecular assays. This work represented a cooperative research development program between the Kramer-Tyagi/Perlin labs on probe development

  7. Willingness to pay for rapid diagnostic tests for the diagnosis and treatment of malaria in southeast Nigeria: ex post and ex ante

    PubMed Central

    2010-01-01

    Background The introduction of rapid diagnostic tests (RDTs) has improved the diagnosis and treatment of malaria. However, any successful control of malaria will depend on socio-economic factors that influence its management in the community. Willingness to pay (WTP) is important because consumer responses to prices will influence utilization of services and revenues collected. Also the consumer's attitude can influence monetary valuation with respect to different conditions ex post and ex ante. Methods WTP for RDT for Malaria was assessed by the contingent valuation method using a bidding game approach in rural and urban communities in southeast Nigeria. The ex post WTP was assessed at the health centers on 618 patients immediately following diagnosis of malaria with RDT and the ex ante WTP was assessed by household interviews on 1020 householders with a prior history of malaria. Results For the ex ante WTP, 51% of the respondents in urban and 24.7% in rural areas were willing to pay for RDT. The mean WTP (235.49 naira) in urban is higher than WTP (182.05 Naira) in rural areas. For the ex post WTP, 89 and 90.7% of the respondents in urban and rural areas respectively were WTP. The mean WTP (372.30 naira) in urban is also higher than (296.28 naira) in rural areas. For the ex post scenario, the lower two Social Economic Status (SES) quartiles were more willing to pay and the mean WTP is higher than the higher two SES while in the ex ante scenario, the higher two SES quartiles were more WTP and with a higher WTP than the lower two SES quartile. Ex ante and ex post WTP were directly dependent on costs. Conclusion The ex post WTP is higher than the ex ante WTP and both are greater than the current cost of RDTs. Urban dwellers were more willing to pay than the rural dwellers. The mean WTP should be considered when designing suitable financial strategies for making RDTs available to communities. PMID:20148118

  8. Rapid diagnostic test supply chain and consumption study in Cabo Delgado, Mozambique: estimating stock shortages and identifying drivers of stock-outs

    PubMed Central

    2014-01-01

    Background Malaria rapid diagnostic tests (RDTs) are particularly useful in low-resource settings where follow-through on traditional laboratory diagnosis is challenging or lacking. The availability of these tests depends on supply chain processes within the distribution system. In Mozambique, stock-outs of malaria RDTs are fairly common at health facilities. A longitudinal cross-sectional study was conducted to evaluate drivers of stock shortages in the Cabo Delgado province. Methods Data were collected from purposively sampled health facilities, using monthly cross-sectional surveys between October 2011 and May 2012. Estimates of lost consumption (consumption not met due to stock-outs) served as the primary quantitative indicator of stock shortages. This is a better measure of the magnitude of stock-outs than binary indicators that only measure frequency of stock-outs at a given facility. Using a case study based methodology, distribution system characteristics were qualitatively analysed to examine causes of stock-outs at the provincial, district and health centre levels. Results 15 health facilities were surveyed over 120 time points. Stock-out patterns varied by data source; average monthly proportions of 59%, 17% and 17% of health centres reported a stock-out on stock cards, laboratory and pharmacy forms, respectively. Estimates of lost consumption percentage were significantly high; ranging from 0% to 149%; with a weighted average of 78%. Each ten-unit increase in monthly-observed consumption was associated with a nine-unit increase in lost consumption percentage indicating that higher rates of stock-outs occurred at higher levels of observed consumption. Causes of stock-outs included inaccurate tracking of lost consumption, insufficient sophistication in inventory management and replenishment, and poor process compliance by facility workers, all arguably stemming from inadequate attention to the design and implementation of the distribution system

  9. Performance of three multi-species rapid diagnostic tests for diagnosis of Plasmodium falciparum and Plasmodium vivax malaria in Oromia Regional State, Ethiopia

    PubMed Central

    2010-01-01

    Background Malaria transmission in Ethiopia is unstable and variable, caused by both Plasmodium falciparum and Plasmodium vivax. The Federal Ministry of Health (FMoH) is scaling up parasitological diagnosis of malaria at all levels of the health system; at peripheral health facilities this will be through use of rapid diagnostic tests (RDTs). The present study compared three RDT products to provide the FMoH with evidence to guide appropriate product selection. Methods Performance of three multi-species (pf-HRP2/pan-pLDH and pf-HRP2/aldolase) RDTs (CareStart®, ParaScreen® and ICT Combo®) was compared with 'gold standard' microscopy at three health centres in Jimma zone, Oromia Regional State. Ease of RDT use by health extension workers was assessed at community health posts. RDT heat stability was tested in a controlled laboratory setting according to WHO procedures. Results A total of 2,383 patients with suspected malaria were enrolled between May and July 2009, 23.2% of whom were found to be infected with Plasmodium parasites by microscopy. All three RDTs were equally sensitive in detecting P. falciparum or mixed infection: 85.6% (95% confidence interval 81.2-89.4). RDT specificity was similar for detection of P. falciparum or mixed infection at around 92%. For detecting P. vivax infection, all three RDTs had similar sensitivity in the range of 82.5 to 85.0%. CareStart had higher specificity in detecting P. vivax (97.2%) than both ParaScreen and ICT Combo (p < 0.001 and p = 0.05, respectively). Health extension workers preferred CareStart and ParaScreen to ICT Combo due to the clear labelling of bands on the cassette, while the 'lab in a pack' style of CareStart was the preferred design. ParaScreen and CareStart passed all heat stability testing, while ICT Combo did not perform as well. Conclusions CareStart appeared to be the most appropriate option for use at health posts in Ethiopia, considering the combination of quantitative performance, ease of use and

  10. Accuracy of malaria rapid diagnostic tests in community studies and their impact on treatment of malaria in an area with declining malaria burden in north-eastern Tanzania

    PubMed Central

    2011-01-01

    Background Despite some problems related to accuracy and applicability of malaria rapid diagnostic tests (RDTs), they are currently the best option in areas with limited laboratory services for improving case management through parasitological diagnosis and reducing over-treatment. This study was conducted in areas with declining malaria burden to assess; 1) the accuracy of RDTs when used at different community settings, 2) the impact of using RDTs on anti-malarial dispensing by community-owned resource persons (CORPs) and 3) adherence of CORPs to treatment guidelines by providing treatment based on RDT results. Methods Data were obtained from: 1) a longitudinal study of passive case detection of fevers using CORPs in six villages in Korogwe; and 2) cross-sectional surveys (CSS) in six villages of Korogwe and Muheza districts, north-eastern, Tanzania. Performance of RDTs was compared with microscopy as a gold standard, and factors affecting their accuracy were explored using a multivariate logistic regression model. Results Overall sensitivity and specificity of RDTs in the longitudinal study (of 23,793 febrile cases; 18,154 with microscopy and RDTs results) were 88.6% and 88.2%, respectively. In the CSS, the sensitivity was significantly lower (63.4%; χ2 = 367.7, p < 0.001), while the specificity was significantly higher (94.3%; χ2 = 143.1, p < 0.001) when compared to the longitudinal study. As determinants of sensitivity of RDTs in both studies, parasite density of < 200 asexual parasites/μl was significantly associated with high risk of false negative RDTs (OR≥16.60, p < 0.001), while the risk of false negative test was significantly lower among cases with fever (axillary temperature ≥37.5°C) (OR ≤ 0.63, p ≤ 0.027). The risk of false positive RDT (as a determinant of specificity) was significantly higher in cases with fever compared to afebrile cases (OR≥2.40, p < 0.001). Using RDTs reduced anti-malarials dispensing from 98.9% to 32.1% in cases

  11. Association between HRP–2/pLDH rapid diagnostic test band positivity and malaria–related anemia at a peripheral health facility in Western Uganda

    PubMed Central

    Boyce, Ross; Reyes, Raquel; Ntaro, Moses; Mulogo, Edgar; Matte, Michael; Boum, Yap; Siedner, Mark J.

    2015-01-01

    The detection of severe malaria in resource–constrained settings is often difficult because of requirements for laboratory infrastructure and/or clinical expertise. The aim of this study, therefore, was to explore the utility of a multiple antigen (HRP–2/pLDH) rapid diagnostic test (RDT) as a low–cost, surrogate marker of patients at high risk for complications of severe malaria. We reviewed programmatic data at a peripheral health center in Western Uganda. Available demographic and clinical data on all individuals presenting to the center who underwent an RDT for suspected malaria infection were reviewed. We fit logistic regression models to identify correlates of two outcomes of interest: 1) severe malaria–related anemia, defined here as hemoglobin ≤7g/dL and 2) receipt of parenteral quinine. 1509 patients underwent malaria testing with an SD FK60 RDT during the observation period. A total of 637 (42%) RDTs were positive for at least one species of malaria, of which 326 (51%) exhibited a single HRP–2 band and 307 (48%) exhibited both HRP–2 and pLDH bands, while 4 exhibited only a single pLDH band. There was a trend towards more severe anemia in patients with a HRP–2/pLDH positive RDT compared to a HRP–2 only RDT (β = –0.99 g/dl, 95% CI –1.99 to 0.02, P = 0.055). A HRP–2/pLDH positive RDT was associated with an increased risk of severe malaria–related anemia compared to a negative RDT (adjusted odds ratio (AOR) 18.8, 95% CI 4.32 to 82.0, P < 0.001) and to a HRP–2 only RDT (AOR 2.46, 95% CI 0.75 to 8.04, P = 0.14). There was no significant association between RDT result and the administration of parenteral quinine. These results offer preliminary evidence that specific patterns of antigen positivity on RDTs could be utilized to identify patients at an increased risk for complications of severe malaria. PMID:26207181

  12. IgG1 as a Potential Biomarker of Post-chemotherapeutic Relapse in Visceral Leishmaniasis, and Adaptation to a Rapid Diagnostic Test

    PubMed Central

    Bhattacharyya, Tapan; Ayandeh, Armon; Falconar, Andrew K.; Sundar, Shyam; El-Safi, Sayda; Gripenberg, Marissa A.; Bowes, Duncan E.; Thunissen, Caroline; Singh, Om Prakash; Kumar, Rajiv; Ahmed, Osman; Eisa, Osama; Saad, Alfarazdeg; Silva Pereira, Sara; Boelaert, Marleen; Mertens, Pascal; Miles, Michael A.

    2014-01-01

    Background Visceral leishmaniasis (VL), caused by protozoa of the Leishmania donovani complex, is a widespread parasitic disease of great public health importance; without effective chemotherapy symptomatic VL is usually fatal. Distinction of asymptomatic carriage from progressive disease and the prediction of relapse following treatment are hampered by the lack of prognostic biomarkers for use at point of care. Methodology/Principal Findings All IgG subclass and IgG isotype antibody levels were determined using unpaired serum samples from Indian and Sudanese patients with differing clinical status of VL, which included pre-treatment active VL, post-treatment cured, post-treatment relapsed, and post kala-azar dermal leishmaniasis (PKDL), as well as seropositive (DAT and/or rK39) endemic healthy controls (EHCs) and seronegative EHCs. L. donovani antigen-specific IgG1 levels were significantly elevated in relapsed versus cured VL patients (p<0.0001). Using paired Indian VL sera, consistent with the known IgG1 half-life, IgG1 levels had not decreased significantly at day 30 after the start of treatment (p = 0.8304), but were dramatically decreased by 6 months compared to day 0 (p = 0.0032) or day 15 (p<0.0001) after start of treatment. Similarly, Sudanese sera taken soon after treatment did not show a significant change in the IgG1 levels (p = 0.3939). Two prototype lateral flow immunochromatographic rapid diagnostic tests (RDTs) were developed to detect IgG1 levels following VL treatment: more than 80% of the relapsed VL patients were IgG1 positive; at least 80% of the cured VL patients were IgG1 negative (p<0.0001). Conclusions/Significance Six months after treatment of active VL, elevated levels of specific IgG1 were associated with treatment failure and relapse, whereas no IgG1 or low levels were detected in cured VL patients. A lateral flow RDT was successfully developed to detect anti-Leishmania IgG1 as a potential biomarker of post

  13. HRP2 and pLDH-Based Rapid Diagnostic Tests, Expert Microscopy, and PCR for Detection of Malaria Infection during Pregnancy and at Delivery in Areas of Varied Transmission: A Prospective Cohort Study in Burkina Faso and Uganda

    PubMed Central

    Cunningham, Jane; Angutoko, Patrick; Ategeka, John; Compaoré, Yves-Daniel; Muehlenbachs, Atis; Somé, Fabrice A.; Ouattara, Aminata; Rouamba, Noél; Ouédraogo, Jean-Bosco; Hopkins, Heidi

    2016-01-01

    Background Intermittent screening and treatment (IST) of malaria during pregnancy has been proposed as an alternative to intermittent preventive treatment in pregnancy (IPTp), where IPTp is failing due to drug resistance. However, the antenatal parasitaemias are frequently very low, and the most appropriate screening test for IST has not been defined. Methodology/Principal Findings We conducted a multi-center prospective study of 990 HIV-uninfected women attending ANC in two different malaria transmission settings at Tororo District Hospital, eastern Uganda and Colsama Health Center in western Burkina Faso. Women were enrolled in the study in the second or third trimester of pregnancy and followed to delivery, generating 2,597 blood samples for analysis. Screening tests included rapid diagnostic tests (RDTs) targeting histidine-rich protein 2 (HRP2) and parasite lactate dehydrogenase (pLDH) and microscopy, compared to nPCR as a reference standard. At enrolment, the proportion of pregnant women who were positive for P. falciparum by HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT, microscopy and PCR was 38%, 29%, 36% and 44% in Uganda and 21%, 16%, 15% and 35% in Burkina Faso, respectively. All test positivity rates declined during follow-up. In comparison to PCR, the sensitivity of the HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT and microscopy was 75.7%, 60.1% and 69.7% in Uganda, 55.8%, 42.6% and 55.8% in Burkina Faso respectively for all antenatal visits. Specificity was greater than 96% for all three tests. Comparison of accuracy using generalized estimating equation revealed that the HRP2- detecting RDT was the most accurate test in both settings. Conclusions/Significance The study suggests that HRP2-based RDTs are the most appropriate point-of-care test currently available for use during pregnancy especially for symptomatic women, but will still miss some PCR-positive women. The clinical significance of these very low density infections needs to be better defined. PMID

  14. Evaluating diagnostic tests.

    PubMed

    Kennedy, Ashley Graham

    2016-08-01

    Although much has been written on the role of randomized controlled trials and mechanistic reasoning in the evaluation of therapeutic treatments, philosophers of medicine have not yet turned their attention to the question of how diagnostic tests and procedures should be evaluated. I aim to begin to fill this gap by examining each of the following questions: What is the best way to determine the accuracy of a diagnostic test? What is the best way to determine the clinical effectiveness of a diagnostic test? Can an accurate diagnostic test be considered medically valuable even if it is not clinically effective? I argue that while diagnostic accuracy is a minimum requirement for both clinical effectiveness and medical value, accuracy and effectiveness are not sufficient for determining the value of a diagnostic test, because diagnostic value extends beyond patient outcomes. PMID:27091221

  15. DRG Watchdog highlights new financial dimensions of laboratory diagnostics.

    PubMed

    2003-01-01

    As nebulous as the details of the German diagnosis-oriented case reimbursement rate (G-DRGs) might be, one thing is obvious: rapid and accurate diagnostics will be vital in future to the reimbursement of standard cases that reflect the actual outlay. The laboratory that up to now has always been categorized as a potential for savings, now becomes a source of revenue for hospitals. A study initiated by the VDGH provides evidence for this (Clinical Laboratory 2002, 48, 327). PMID:14572206

  16. Array-based comparative genomic hybridization (array CGH) for rapid prenatal diagnosis of cytogenetic abnormalities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have shown in a prospective validation study that an array CGH test was highly accurate for rapid detection of chromosomal aneuploidies and deletions or duplications on fetal DNA samples in a clinical prenatal diagnostic setting. Here we present our updated "post-validation phase" experience with...

  17. A Survey on Use of Rapid Tests and Tuberculosis Diagnostic Practices by Primary Health Care Providers in South Africa: Implications for the Development of New Point-of-Care Tests

    PubMed Central

    Davids, Malika; Dheda, Keertan; Pant Pai, Nitika; Cogill, Dolphina; Pai, Madhukar; Engel, Nora

    2015-01-01

    Background Effective infectious disease control requires early diagnosis and treatment initiation. Point-of-care testing offers rapid turn-around-times, facilitating same day clinical management decisions. To maximize the benefits of such POC testing programs, we need to understand how rapid tests are used in everyday clinical practice. Methods In this cross-sectional survey study, 400 primary healthcare providers in two cities in South Africa were interviewed on their use of rapid tests in general, and tuberculosis diagnostic practices, between September 2012 and June 2013. Public healthcare facilities were selected using probability-sampling techniques and private healthcare providers were randomly selected from the Health Professional Council of South Africa list. To ascertain differences between the two healthcare sectors 2-sample z-tests were used to compare sample proportions. Results The numbers of providers interviewed were equally distributed between the public (n = 200) and private sector (n = 200). The most frequently reported tests in the private sector include blood pressure (99.5%), glucose finger prick (89.5%) and urine dipstick (38.5%); and in the public sector were pregnancy (100%), urine dipstick (100%), blood pressure (100%), glucose finger prick (99%) and HIV rapid test (98%). The majority of TB testing occurs in the public sector, where significantly more providers prefer Xpert MTB/RIF assay, the designated clinical TB diagnostic tool by the national TB program, as compared to the private sector (87% versus 71%, p-value >0.0001). Challenges with regard to TB diagnosis included the long laboratory turn-around-time, difficulty in obtaining sputum samples and lost results. All providers indicated that a new POC test for TB should be rapid and cheap, have good sensitivity and specificity, ease of sample acquisition, detect drug-resistance and work in HIV-infected persons. Conclusion/significance The existing centralized laboratory services, poor

  18. Integrating the Xpert MTB/RIF Assay into a Diagnostic Workflow for Rapid Detection of Mycobacterium tuberculosis in a Low-Prevalence Area

    PubMed Central

    Deggim, Vanessa; Somoskovi, Akos; Voit, Antje; Böttger, Erik C.

    2013-01-01

    The Xpert MTB/RIF assay is a rapid and fully automated real-time PCR assay. The performance of the Xpert MTB/RIF assay as a primary screening test for urgent clinical specimens was evaluated during a 2-year period. The results showed that replacing smear microscopy with the Xpert MTB/RIF assay facilitates laboratory handling and improves the sensitivity and specificity of Mycobacterium tuberculosis detection. PMID:23616455

  19. Rapidly enlarging cutaneous nodules on a full-thickness skin graft following an excision of a squamous cell carcinoma – a diagnostic clue for multiple myeloma

    PubMed Central

    Sugrue, Conor M.; McInerney, Niall M.; Aalto, Laura; Joyce, Cormac W.; Kelly, Jack L.

    2014-01-01

    Abstract Cutaneous extramedullary plasmacytomas (EMPs) are rare plasma cell neoplasms of the skin occurring in 2–4% of patients with multiple myeloma (MM). We describe a man diagnosed with IgA lambda MM (Stage III) after rapidly enlarging cutaneous nodules developed in the surgical site of recently excised skin malignancies. Cutaneous EMP must be considered for expanding cutaneous nodules at sites of surgery or trauma.

  20. Recent advances in the use of laser-induced breakdown spectroscopy (LIBS) as a rapid point-of-care pathogen diagnostic

    NASA Astrophysics Data System (ADS)

    Rehse, Steven; Trojand, Daniel; Putnam, Russell; Gillies, Derek; Woodman, Ryan; Sheikh, Khadija; Daabous, Andrew

    2013-05-01

    There is a well-known and urgent need in the fields of medicine, environmental health and safety, food-processing, and defense/security to develop new 21st Century technologies for the rapid and sensitive identification of bacterial pathogens. In only the last five years, the use of a real-time elemental (atomic) analysis performed with laser-induced breakdown spectroscopy (LIBS) has made tremendous progress in becoming a viable technology for rapid bacterial pathogen detection and identification. In this talk we will show how this laser-based optical emission spectroscopic technique is able to sensitively assay the elemental composition of bacterial cells in situ. We will also present the latest achievements of our lab to fully develop LIBS-based bacterial sensing including simulation of a rapid urinary tract infection diagnosis and investigation of a variety of autonomous multivariate analysis algorithms. Lastly, we will show how this technology is now ready to be transitioned from the laboratory to field-portable and potentially man-portable instrumentation. The introduction of such a technology into popular use could very well transform the field of bacterial biosensing - a market valued at approximately 10 billion/year world-wide. Funding for this project was provided in part by a Natural Sciences and Engineering Research Council of Canada Discovery Grant.

  1. Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

    PubMed

    Segerman, Bo; De Medici, Dario; Ehling Schulz, Monika; Fach, Patrick; Fenicia, Lucia; Fricker, Martina; Wielinga, Peter; Van Rotterdam, Bart; Knutsson, Rickard

    2011-03-01

    The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams. PMID:20826036

  2. Comparison of laboratory costs of rapid molecular tests and conventional diagnostics for detection of tuberculosis and drug-resistant tuberculosis in South Africa

    PubMed Central

    2013-01-01

    Background The World Health Organization has endorsed the use of molecular methods for the detection of TB and drug-resistant TB as a rapid alternative to culture-based systems. In South Africa, the Xpert MTB/Rif assay and the GenoType MTBDRplus have been implemented into reference laboratories for diagnosis of TB and drug-resistance, but their costs have not been fully elucidated. Methods We conducted a detailed reference laboratory cost analysis of new rapid molecular assays (Xpert and MTBDRplus) for tuberculosis testing and drug-resistance testing in South Africa, and compared with the costs of conventional approaches involving sputum microscopy, liquid mycobacterial culture, and phenotypic drug sensitivity testing. Results From a laboratory perspective, Xpert MTB/RIF cost $14.93/sample and the MTBDRplus line probe assay cost $23.46/sample, compared to $16.88/sample using conventional automated liquid culture-based methods. Laboratory costs of Xpert and MTBDRplus were most influenced by cost of consumables (60-80%). Conclusions At current public sector pricing, Xpert MTB/RIF and MTBDRplus are comparable in cost to mycobacterial culture and conventional drug sensitivity testing. Overall, reference laboratories must balance costs with performance characteristics and the need for rapid results. PMID:23895665

  3. Fast and accurate automated cell boundary determination for fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Arce, Stephen Hugo; Wu, Pei-Hsun; Tseng, Yiider

    2013-07-01

    Detailed measurement of cell phenotype information from digital fluorescence images has the potential to greatly advance biomedicine in various disciplines such as patient diagnostics or drug screening. Yet, the complexity of cell conformations presents a major barrier preventing effective determination of cell boundaries, and introduces measurement error that propagates throughout subsequent assessment of cellular parameters and statistical analysis. State-of-the-art image segmentation techniques that require user-interaction, prolonged computation time and specialized training cannot adequately provide the support for high content platforms, which often sacrifice resolution to foster the speedy collection of massive amounts of cellular data. This work introduces a strategy that allows us to rapidly obtain accurate cell boundaries from digital fluorescent images in an automated format. Hence, this new method has broad applicability to promote biotechnology.

  4. Diagnostics for pulmonary tuberculosis.

    PubMed

    Cudahy, Patrick; Shenoi, Sheela V

    2016-04-01

    Tuberculosis (TB) remains a leading cause of human suffering and mortality despite decades of effective treatment being available. Accurate and timely diagnosis remains an unmet goal. The HIV epidemic has also led to new challenges in the diagnosis of TB. Several new developments in TB diagnostics have the potential to positively influence the global campaign against TB. We aim to review the performance of both established as well as new diagnostics for pulmonary TB in adults, and discuss the ongoing challenges. PMID:27005271

  5. Diagnostics for pulmonary tuberculosis

    PubMed Central

    Cudahy, Patrick

    2016-01-01

    Tuberculosis (TB) remains a leading cause of human suffering and mortality despite decades of effective treatment being available. Accurate and timely diagnosis remains an unmet goal. The HIV epidemic has also led to new challenges in the diagnosis of TB. Several new developments in TB diagnostics have the potential to positively influence the global campaign against TB. We aim to review the performance of both established as well as new diagnostics for pulmonary TB in adults, and discuss the ongoing challenges. PMID:27005271

  6. Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia

    PubMed Central

    Ofori-Anyinam, Boatema; Kanuteh, Fatoumatta; Okoi, Catherine; Dolganov, Gregory; Schoolnik, Gary; Secka, Ousman; Antonio, Martin; de Jong, Bouke C.; Gehre, Florian

    2016-01-01

    Background MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis (TB). Mycobacterium africanum West Africa 2 (Maf 2) remains an important cause of TB in West Africa and causes one third of disease in The Gambia. Since the introduction of MPT64 antigen tests, a higher than expected rate of suspected non-tuberculous mycobacteria (NTM) was seen among AFB smear positive TB suspects, which led us to prospectively assess sensitivity of the MPT64 antigen test in our setting. Methodology/Principal Findings We compared the abundance of mRNA encoded by the mpt64 gene in sputa of patients with untreated pulmonary TB caused by Maf 2 and Mycobacterium tuberculosis (Mtb). Subsequently, prospectively collected sputum samples from presumptive TB patients were inoculated in the BACTEC MGIT 960 System. One hundred and seventy-three acid fast bacilli (AFB)-positive and blood agar negative MGIT cultures were included in the study. Cultures were tested on the day of MGIT positivity with the BD MGIT TBc Identification Test. A random set of positives and all negatives were additionally tested with the SD Bioline Ag MPT64 Rapid. MPT64 negative cultures were further incubated at 37°C and retested until positive. Bacteria were spoligotyped and assigned to different lineages. Maf 2 isolates were 2.52-fold less likely to produce a positive test result and sensitivity ranged from 78.4% to 84.3% at the beginning and end of the recommended 10 day testing window, respectively. There was no significant difference between the tests. We further showed that the decreased rapid test sensitivity was attributable to variations in mycobacterial growth behavior and the smear grades of the patient. Conclusions/Significance In areas where Maf 2 is endemic MPT64 tests should be cautiously used and MPT64 negative results confirmed by a second technique, such as nucleic acid amplification tests, to avoid their misclassification as NTMs. PMID:27387550

  7. Development of a rapid diagnostic method for identification of Staphylococcus aureus and antimicrobial resistance in positive blood culture bottles using a PCR-DNA-chromatography method.

    PubMed

    Ohshiro, Takeya; Miyagi, Chihiro; Tamaki, Yoshikazu; Mizuno, Takuya; Ezaki, Takayuki

    2016-06-01

    Blood culturing and the rapid reporting of results are essential for infectious disease clinics to obtain bacterial information that can affect patient prognosis. When gram-positive coccoid cells are observed in blood culture bottles, it is important to determine whether the strain is Staphylococcus aureus and whether the strain has resistance genes, such as mecA and blaZ, for proper antibiotic selection. Previous work led to the development of a PCR method that is useful for rapid identification of bacterial species and antimicrobial susceptibility. However, that method has not yet been adopted in community hospitals due to the high cost and methodological complexity. We report here the development of a quick PCR and DNA-chromatography test, based on single-tag hybridization chromatography, that permits detection of S. aureus and the mecA and blaZ genes; results can be obtained within 1 h for positive blood culture bottles. We evaluated this method using 42 clinical isolates. Detection of S. aureus and the resistance genes by the PCR-DNA-chromatography method was compared with that obtained via the conventional identification method and actual antimicrobial susceptibility testing. Our method had a sensitivity of 97.0% and a specificity of 100% for the identification of the bacterial species. For the detection of the mecA gene of S. aureus, the sensitivity was 100% and the specificity was 95.2%. For the detection of the blaZ gene of S. aureus, the sensitivity was 100% and the specificity was 88.9%. The speed and simplicity of this PCR-DNA-chromatography method suggest that our method will facilitate rapid diagnoses. PMID:27056092

  8. Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP(®) using reverse transcription-recombinase polymerase amplification.

    PubMed

    Zhang, Shulu; Ravelonandro, Michel; Russell, Paul; McOwen, Nathan; Briard, Pascal; Bohannon, Seven; Vrient, Albert

    2014-10-01

    Plum pox virus (PPV) causes the most destructive viral disease known as plum pox or Sharka disease in stone fruit trees. As an important regulated pathogen, detection of PPV is thus of critical importance to quarantine and eradication of the spreading disease. In this study, the innovative development of two AmplifyRP(®) tests is reported for a rapid isothermal detection of PPV using reverse transcription-recombinase polymerase amplification. In an AmplifyRP(®) test, all specific recombination and amplification reactions occur at a constant temperature without thermal cycling and the test results are either recorded in real-time with a portable fluorescence reader or displayed using a lateral flow strip contained inside an amplicon detection chamber. The major improvement of this assay is that the entire test from sample preparation to result can be completed in as little as 20min and can be performed easily both in laboratories and in the field. The results from this study demonstrated the ability of the AmplifyRP(®) technique to detect all nine PPV strains (An, C, CR, D, EA, M, Rec, T, or W). Among the economic benefits to pathogen surveys is the higher sensitivity of the AmplifyRP(®) to detect PPV when compared to the conventional ELISA and ImmunoStrip(®) assays. This is the first report describing the use of such an innovative technique to detect rapidly plant viruses affecting perennial crops. PMID:25010790

  9. The Use of NS1 Rapid Diagnostic Test and qRT-PCR to Complement IgM ELISA for Improved Dengue Diagnosis from Single Specimen.

    PubMed

    Teoh, Boon-Teong; Sam, Sing-Sin; Tan, Kim-Kee; Johari, Jefree; Abd-Jamil, Juraina; Hooi, Poh-Sim; AbuBakar, Sazaly

    2016-01-01

    Timely and accurate dengue diagnosis is important for differential diagnosis and immediate implementation of appropriate disease control measures. In this study, we compared the usefulness and applicability of NS1 RDT (NS1 Ag Strip) and qRT-PCR tests in complementing the IgM ELISA for dengue diagnosis on single serum specimen (n = 375). The NS1 Ag Strip and qRT-PCR showed a fair concordance (κ = 0.207, p = 0.001). While the NS1 Ag Strip showed higher positivity than qRT-PCR for acute (97.8% vs. 84.8%) and post-acute samples (94.8% vs. 71.8%) of primary infection, qRT-PCR showed higher positivity for acute (58.1% vs. 48.4%) and post-acute (50.0% vs.41.4%) samples in secondary infection. IgM ELISA showed higher positivity in samples from secondary dengue (74.2-94.8%) than in those from primary dengue (21.7-64.1%). More primary dengue samples showed positive with combined NS1 Ag Strip/IgM ELISA (99.0% vs. 92.8%) whereas more secondary samples showed positive with combined qRT-PCR/IgM ELISA (99.4% vs. 96.2%). Combined NS1 Ag Strip/IgM ELISA is a suitable combination tests for timely and accurate dengue diagnosis on single serum specimen. If complemented with qRT-PCR, combined NS1 Ag Strip/IgM ELISA would improve detection of secondary dengue samples. PMID:27278716

  10. The Use of NS1 Rapid Diagnostic Test and qRT-PCR to Complement IgM ELISA for Improved Dengue Diagnosis from Single Specimen

    PubMed Central

    Teoh, Boon-Teong; Sam, Sing-Sin; Tan, Kim-Kee; Johari, Jefree; Abd-Jamil, Juraina; Hooi, Poh-Sim; AbuBakar, Sazaly

    2016-01-01

    Timely and accurate dengue diagnosis is important for differential diagnosis and immediate implementation of appropriate disease control measures. In this study, we compared the usefulness and applicability of NS1 RDT (NS1 Ag Strip) and qRT-PCR tests in complementing the IgM ELISA for dengue diagnosis on single serum specimen (n = 375). The NS1 Ag Strip and qRT-PCR showed a fair concordance (κ = 0.207, p = 0.001). While the NS1 Ag Strip showed higher positivity than qRT-PCR for acute (97.8% vs. 84.8%) and post-acute samples (94.8% vs. 71.8%) of primary infection, qRT-PCR showed higher positivity for acute (58.1% vs. 48.4%) and post-acute (50.0% vs.41.4%) samples in secondary infection. IgM ELISA showed higher positivity in samples from secondary dengue (74.2–94.8%) than in those from primary dengue (21.7–64.1%). More primary dengue samples showed positive with combined NS1 Ag Strip/IgM ELISA (99.0% vs. 92.8%) whereas more secondary samples showed positive with combined qRT-PCR/IgM ELISA (99.4% vs. 96.2%). Combined NS1 Ag Strip/IgM ELISA is a suitable combination tests for timely and accurate dengue diagnosis on single serum specimen. If complemented with qRT-PCR, combined NS1 Ag Strip/IgM ELISA would improve detection of secondary dengue samples. PMID:27278716

  11. Diagnostic Accuracy Assessment of Immunochromatographic Tests for the Rapid Detection of Antibodies against Orientia tsutsugamushi Using Paired Acute and Convalescent Specimens

    PubMed Central

    Watthanaworawit, Wanitda; Turner, Paul; Turner, Claudia; Tanganuchitcharnchai, Ampai; Jintaworn, Suthatip; Hanboonkunupakarn, Borimas; Richards, Allen L.; Day, Nicholas P. J.; Blacksell, Stuart D.; Nosten, François

    2015-01-01

    We assessed the diagnostic accuracy of two immunochromatographic tests (ICTs), the Access Bio CareStart Scrub Typhus test (Somerset, NJ) (IgM), and the SD BIOLINE Tsutsugamushi test (Kyonggi-do, Republic of Korea) (IgG, IgM, or IgA) compared with indirect immunofluorescence assay (IFA) and real-time PCR results as reference tests using 86 paired acute and convalescent specimens from febrile patients. The sensitivity and specificity of the CareStart test were 23.3% (95% confidence interval [CI]: 11.8–38.6) and 81.4% (95% CI: 66.6–91.6), respectively, for acute specimens and 32.6% (95% CI: 19.1–48.5) and 79.1% (95% CI: 64.0–90.0), respectively, for convalescent specimens. For the SD BIOLINE test, sensitivity and specificity were 20.9% (95% CI: 10.0–36.0) and 74.4% (95% CI: 58.8–86.5), respectively, for acute specimens and 76.7% (95% CI: 61.4–88.2) and 76.7% (95% CI: 61.4–88.2), respectively, for convalescent specimens. The poor sensitivity obtained for both ICTs during this study when performed on acute specimens highlights the difficulties in prompt diagnosis of scrub typhus. PMID:26458778

  12. Field Evaluation and Impact on Clinical Management of a Rapid Diagnostic Kit That Detects Dengue NS1, IgM and IgG

    PubMed Central

    Andries, Anne-Claire; Duong, Veasna; Ngan, Chantha; Ong, Sivuth; Huy, Rekol; Sroin, Kim Kim; Te, Vantha; Y, Bunthin; Try, Patrich Lorn; Buchy, Philippe

    2012-01-01

    Background Dengue diagnosis is complex and until recently only specialized laboratories were able to definitively confirm dengue infection. Rapid tests are now available commercially making biological diagnosis possible in the field. The aim of this study was to evaluate a combined dengue rapid test for the detection of NS1 and IgM/IgG antibodies. The evaluation was made prospectively in the field conditions and included the study of the impact of its use as a point-of-care test for case management as well as retrospectively against a panel of well-characterized samples in a reference laboratory. Methodology/Principal Findings During the prospective study, 157 patients hospitalized for a suspicion of dengue were enrolled. In the hospital laboratories, the overall sensitivity, specificity, PPV and NPV of the NS1/IgM/IgG combination tests were 85.7%, 83.9%, 95.6% and 59.1% respectively, whereas they were 94,4%, 90.0%, 97.5% and 77.1% respectively in the national reference laboratory at Institut Pasteur in Cambodia. These results demonstrate that optimal performances require adequate training and quality assurance. The retrospective study showed that the sensitivity of the combined kit did not vary significantly between the serotypes and was not affected by the immune status or by the interval of time between onset of fever and sample collection. The analysis of the medical records indicates that the physicians did not take into consideration the results obtained with the rapid test including for care management and use of antibiotic therapy. Conclusions In the context of our prospective field study, we demonstrated that if the SD Bioline Dengue Duo kit is correctly used, a positive result highly suggests a dengue case but a negative result doesn't rule out a dengue infection. Nevertheless, Cambodian pediatricians in their daily practice relied on their clinical diagnosis and thus the false negative results obtained did not directly impact on the clinical management

  13. BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System.

    PubMed

    Janku, Filip; Huang, Helen J; Claes, Bart; Falchook, Gerald S; Fu, Siqing; Hong, David; Ramzanali, Nishma M; Nitti, Giovanni; Cabrilo, Goran; Tsimberidou, Apostolia M; Naing, Aung; Piha-Paul, Sarina A; Wheler, Jennifer J; Karp, Daniel D; Holley, Veronica R; Zinner, Ralph G; Subbiah, Vivek; Luthra, Rajyalakshmi; Kopetz, Scott; Overman, Michael J; Kee, Bryan K; Patel, Sapna; Devogelaere, Benoit; Sablon, Erwin; Maertens, Geert; Mills, Gordon B; Kurzrock, Razelle; Meric-Bernstam, Funda

    2016-06-01

    Cell-free (cf) DNA from plasma offers an easily obtainable material for BRAF mutation analysis for diagnostics and response monitoring. In this study, plasma-derived cfDNA samples from patients with progressing advanced cancers or malignant histiocytosis with known BRAF(V600) status from formalin-fixed paraffin-embedded (FFPE) tumors were tested using a prototype version of the Idylla BRAF Mutation Test, a fully integrated real-time PCR-based test with turnaround time about 90 minutes. Of 160 patients, BRAF(V600) mutations were detected in 62 (39%) archival FFPE tumor samples and 47 (29%) plasma cfDNA samples. The two methods had overall agreement in 141 patients [88%; κ, 0.74; SE, 0.06; 95% confidence interval (CI), 0.63-0.85]. Idylla had a sensitivity of 73% (95% CI, 0.60-0.83) and specificity of 98% (95% CI, 0.93-1.00). A higher percentage, but not concentration, of BRAF(V600) cfDNA in the wild-type background (>2% vs. ≤ 2%) was associated with shorter overall survival (OS; P = 0.005) and in patients with BRAF mutations in the tissue, who were receiving BRAF/MEK inhibitors, shorter time to treatment failure (TTF; P = 0.001). Longitudinal monitoring demonstrated that decreasing levels of BRAF(V600) cfDNA were associated with longer TTF (P = 0.045). In conclusion, testing for BRAF(V600) mutations in plasma cfDNA using the Idylla BRAF Mutation Test has acceptable concordance with standard testing of tumor tissue. A higher percentage of mutant BRAF(V600) in cfDNA corresponded with shorter OS and in patients receiving BRAF/MEK inhibitors also with shorter TTF. Mol Cancer Ther; 15(6); 1397-404. ©2016 AACR. PMID:27207774

  14. TB diagnostic tests: how do we figure out their costs?

    PubMed

    Sohn, Hojoon; Minion, Jessica; Albert, Heidi; Dheda, Keertan; Pai, Madhukar

    2009-08-01

    Tuberculosis continues to be a major global health problem. Lack of accurate, rapid and cost-effective diagnostic tests poses a huge obstacle to global TB control. While several new diagnostic tools are being developed and evaluated for TB, it is important that new tools are introduced for widespread use only after careful validation of accuracy, impact as well as cost-effectiveness in real-world settings. While there are large numbers of studies on the accuracy of TB diagnostic tests, there are few studies that are focused on cost and cost-effectiveness. There are currently no widely accepted standards on how to evaluate costs of a TB test. In this review, we describe the basic approach for computing the costs of TB diagnostic tests, and provide templates for various data elements and parameters that go into the costing analysis. We hope this will pave the way for a standardized methodology for costing of TB diagnostic tests. Such a tool would enable improved and more generalizable costing analyses that can provide a strong foundation for more sophisticated economic analyses that evaluate the full economic and epidemiological impact resulting from the implementation and routine use of performance-verified new and innovative diagnostic tools. This, in turn, will facilitate evidence-based adoption and use of new diagnostics, especially in resource-limited settings. PMID:19681700

  15. Evaluation of an Automated Rapid Diagnostic Assay for Detection of Gram-Negative Bacteria and Their Drug-Resistance Genes in Positive Blood Cultures

    PubMed Central

    Tojo, Masayoshi; Fujita, Takahiro; Ainoda, Yusuke; Nagamatsu, Maki; Hayakawa, Kayoko; Mezaki, Kazuhisa; Sakurai, Aki; Masui, Yoshinori; Yazaki, Hirohisa; Takahashi, Hiroshi; Miyoshi-Akiyama, Tohru; Totsuka, Kyoichi; Kirikae, Teruo; Ohmagari, Norio

    2014-01-01

    We evaluated the performance of the Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN; Nanosphere, Northbrook, IL, USA), an automated multiplex assay for rapid identification of positive blood cultures caused by 9 Gram-negative bacteria (GNB) and for detection of 9 genes associated with β-lactam resistance. The BC-GN assay can be performed directly from positive blood cultures with 5 minutes of hands-on and 2 hours of run time per sample. A total of 397 GNB positive blood cultures were analyzed using the BC-GN assay. Of the 397 samples, 295 were simulated samples prepared by inoculating GNB into blood culture bottles, and the remaining were clinical samples from 102 patients with positive blood cultures. Aliquots of the positive blood cultures were tested by the BC-GN assay. The results of bacterial identification between the BC-GN assay and standard laboratory methods were as follows: Acinetobacter spp. (39 isolates for the BC-GN assay/39 for the standard methods), Citrobacter spp. (7/7), Escherichia coli (87/87), Klebsiella oxytoca (13/13), and Proteus spp. (11/11); Enterobacter spp. (29/30); Klebsiella pneumoniae (62/72); Pseudomonas aeruginosa (124/125); and Serratia marcescens (18/21); respectively. From the 102 clinical samples, 104 bacterial species were identified with the BC-GN assay, whereas 110 were identified with the standard methods. The BC-GN assay also detected all β-lactam resistance genes tested (233 genes), including 54 blaCTX-M, 119 blaIMP, 8 blaKPC, 16 blaNDM, 24 blaOXA-23, 1 blaOXA-24/40, 1 blaOXA-48, 4 blaOXA-58, and 6 blaVIM. The data shows that the BC-GN assay provides rapid detection of GNB and β-lactam resistance genes in positive blood cultures and has the potential to contributing to optimal patient management by earlier detection of major antimicrobial resistance genes. PMID:24705449

  16. Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using the Vitek MS System for Rapid and Accurate Identification of Dermatophytes on Solid Cultures

    PubMed Central

    Monnin, Valérie; Girard, Victoria; Welker, Martin; Arsac, Maud; Cellière, Béatrice; Durand, Géraldine; Bosshard, Philipp P.; Farina, Claudio; Passera, Marco; Van Belkum, Alex; Petrini, Orlando; Tonolla, Mauro

    2014-01-01

    The objective of this research was to extend the Vitek MS fungal knowledge base version 2.0.0 to allow the robust identification of clinically relevant dermatophytes, using a variety of strains, incubation times, and growth conditions. First, we established a quick and reliable method for sample preparation to obtain a reliable and reproducible identification independently of the growth conditions. The Vitek MS V2.0.0 fungal knowledge base was then expanded using 134 well-characterized strains belonging to 17 species in the genera Epidermophyton, Microsporum, and Trichophyton. Cluster analysis based on mass spectrum similarity indicated good species discrimination independently of the culture conditions. We achieved a good separation of the subpopulations of the Trichophyton anamorph of Arthroderma benhamiae and of anthropophilic and zoophilic strains of Trichophyton interdigitale. Overall, the 1,130 mass spectra obtained for dermatophytes gave an estimated identification performance of 98.4%. The expanded fungal knowledge base was then validated using 131 clinical isolates of dermatophytes belonging to 13 taxa. For 8 taxa all strains were correctly identified, and for 3 the rate of successful identification was >90%; 75% (6/8) of the M. gypseum strains were correctly identified, whereas only 47% (18/38) of the African T. rubrum population (also called T. soudanense) were recognized accurately, with a large quantity of strains misidentified as T. violaceum, demonstrating the close relationship of these two taxa. The method of sample preparation was fast and efficient and the expanded Vitek MS fungal knowledge base reliable and robust, allowing reproducible dermatophyte identifications in the routine laboratory. PMID:25297329

  17. Leptospirosis in Kuala Lumpur and the comparative evaluation of two rapid commercial diagnostic kits against the MAT test for the detection of antibodies to leptospira interrogans.

    PubMed

    Sekhar, W Y; Soo, E H; Gopalakrishnan, V; Devi, S

    2000-08-01

    The aim of the study was to look into the epidemiology of serodiagnosed cases of leptospirosis at the University Hospital and compare two commercial ELISA Assays to the Microscopic Agglutination Test (MAT). Demographic data for all serodiagnosed cases for the years 1991-1997 were collected. From this data, 104 sera (n = 104) were selected as samples for comparative evaluation of the commercial ELISAs (INDX Dip-S-Ticks and PanBio ELISA) to the MAT test. Thirty two (n = 32) negative control sera were selected from serodiagnosed cases of other differential diagnosis of leptospira infection. The MAT test is a standard test that detects agglutination antibodies to leptospira biflexa, while the INDX Dip-S-Ticks is an ELISA dot test assaying for total anti-leptospira antibodies. The PanBio ELISA is a colorometric assay in test well strips to detect anti-leptospira IgM. The sensitivity, specificity, and efficiency of tests were calculated at a MAT cut-off value of 1:320. Demographic data showed that leptospirosis peaks during March-May and Aug-Nov coinciding with the inter-monsoon period with more men being infected than women and more adults than children. The sensitivity, specificity, and efficiency of test for the INDX Dip-S-Ticks were 83.3%, 93.8% and 87.5% while the values for the PanBio ELISA were 54.2%, 96.9% and 71.3%. The suboptimal PanBio result could be related to the blocking effect of high IgG titres or could be related to the diagnostic MAT cut-off values used in this study. The data hence reflects a pattern of transmission that is related to "wet" occupational risk factors. The commercial assays evaluated, are easier to perform but interpretation of results should be based on level of endemicity. The INDX Dip-S-Ticks allows this flexibility and is a practical alternative to the MAT test. PMID:11256343

  18. Diagnostic accuracy of the genotype MTBDRsl assay for rapid diagnosis of extensively drug-resistant tuberculosis in HIV-coinfected patients.

    PubMed

    Kontsevaya, Irina; Ignatyeva, Olga; Nikolayevskyy, Vladyslav; Balabanova, Yanina; Kovalyov, Alexander; Kritsky, Andrey; Matskevich, Olesya; Drobniewski, Francis

    2013-01-01

    The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of Mycobacterium tuberculosis multidrug resistance (MDR) and extensive drug resistance (XDR), especially in HIV-coinfected patients. Rapid and reliable diagnosis for detection of resistance to second-line drugs is vital for adequate patient management. We evaluated the performance of the GenoType MTBDRsl (Hain Lifescience GmbH, Nehren, Germany) assay on smear-positive sputum specimens obtained from 90 HIV-infected MDR TB patients from Russia. Test interpretability was over 98%. Specificity was over 86% for all drugs, while sensitivity varied, being the highest (71.4%) for capreomycin and lowest (9.4%) for kanamycin, probably due to the presence of mutations in the eis gene. The sensitivity of detection of XDR TB was 13.6%, increasing to 42.9% if kanamycin (not commonly used in Western Europe) was excluded. The assay is a highly specific screening tool for XDR detection in direct specimens from HIV-coinfected TB patients but cannot be used to rule out XDR TB. PMID:23152552

  19. Diagnostic Accuracy of the GenoType MTBDRsl Assay for Rapid Diagnosis of Extensively Drug-Resistant Tuberculosis in HIV-Coinfected Patients

    PubMed Central

    Kontsevaya, Irina; Ignatyeva, Olga; Nikolayevskyy, Vladyslav; Balabanova, Yanina; Kovalyov, Alexander; Kritsky, Andrey; Matskevich, Olesya

    2013-01-01

    The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of Mycobacterium tuberculosis multidrug resistance (MDR) and extensive drug resistance (XDR), especially in HIV-coinfected patients. Rapid and reliable diagnosis for detection of resistance to second-line drugs is vital for adequate patient management. We evaluated the performance of the GenoType MTBDRsl (Hain Lifescience GmbH, Nehren, Germany) assay on smear-positive sputum specimens obtained from 90 HIV-infected MDR TB patients from Russia. Test interpretability was over 98%. Specificity was over 86% for all drugs, while sensitivity varied, being the highest (71.4%) for capreomycin and lowest (9.4%) for kanamycin, probably due to the presence of mutations in the eis gene. The sensitivity of detection of XDR TB was 13.6%, increasing to 42.9% if kanamycin (not commonly used in Western Europe) was excluded. The assay is a highly specific screening tool for XDR detection in direct specimens from HIV-coinfected TB patients but cannot be used to rule out XDR TB. PMID:23152552

  20. Rapid, Simultaneous Detection of Clostridium sordellii and Clostridium perfringens in Archived Tissues by a Novel PCR-Based Microsphere Assay: Diagnostic Implications for Pregnancy-Associated Toxic Shock Syndrome Cases

    PubMed Central

    Bhatnagar, Julu; DeLeon-Carnes, Marlene; Kellar, Kathryn L.; Bandyopadhyay, Kakali; Antoniadou, Zoi-Anna; Shieh, Wun-Ju; Paddock, Christopher D.; Zaki, Sherif R.

    2012-01-01

    Clostridium sordellii and Clostridium perfringens are infrequent human pathogens; however, the case-fatality rates for the infections are very high, particularly in obstetric C. sordellii infections (>90%). Deaths from Clostridium sordellii and Clostridium perfringens toxic shock (CTS) are sudden, and diagnosis is often challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues usually are the only specimens available for sudden fatal cases, and immunohistochemistry (IHC) for Clostridia is generally performed but it cannot identify species. A clear need exists for a rapid, species-specific diagnostic assay for FFPE tissues. We developed a duplex PCR-based microsphere assay for simultaneous detection of C. sordellii and C. perfringens and evaluated DNA extracted from 42 Clostridium isolates and FFPE tissues of 28 patients with toxic shock/endometritis (20 CTS, 8 non-CTS, as confirmed by PCR and sequencing). The microsphere assay correctly identified C. sordellii and C. perfringens in all known isolates and in all CTS patients (10 C. sordellii, 8 C. perfringens, 2 both) and showed 100% concordance with PCR and sequencing results. The microsphere assay is a rapid, specific, and cost-effective method for the diagnosis of CTS and offers the advantage of simultaneous testing for C. sordellii and C. perfringens in FFPE tissues using a limited amount of DNA. PMID:22536012

  1. Reusable, robust, and accurate laser-generated photonic nanosensor.

    PubMed

    Yetisen, Ali K; Montelongo, Yunuen; da Cruz Vasconcellos, Fernando; Martinez-Hurtado, J L; Neupane, Sankalpa; Butt, Haider; Qasim, Malik M; Blyth, Jeffrey; Burling, Keith; Carmody, J Bryan; Evans, Mark; Wilkinson, Timothy D; Kubota, Lauro T; Monteiro, Michael J; Lowe, Christopher R

    2014-06-11

    Developing noninvasive and accurate diagnostics that are easily manufactured, robust, and reusable will provide monitoring of high-risk individuals in any clinical or point-of-care environment. We have developed a clinically relevant optical glucose nanosensor that can be reused at least 400 times without a compromise in accuracy. The use of a single 6 ns laser (λ = 532 nm, 200 mJ) pulse rapidly produced off-axis Bragg diffraction gratings consisting of ordered silver nanoparticles embedded within a phenylboronic acid-functionalized hydrogel. This sensor exhibited reversible large wavelength shifts and diffracted the spectrum of narrow-band light over the wavelength range λpeak ≈ 510-1100 nm. The experimental sensitivity of the sensor permits diagnosis of glucosuria in the urine samples of diabetic patients with an improved performance compared to commercial high-throughput urinalysis devices. The sensor response was achieved within 5 min, reset to baseline in ∼10 s. It is anticipated that this sensing platform will have implications for the development of reusable, equipment-free colorimetric point-of-care diagnostic devices for diabetes screening. PMID:24844116

  2. Grading More Accurately

    ERIC Educational Resources Information Center

    Rom, Mark Carl

    2011-01-01

    Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

  3. Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics.

    PubMed

    Mishra, Saswat; Saadat, Darius; Kwon, Ohjin; Lee, Yongkuk; Choi, Woon-Seop; Kim, Jong-Hoon; Yeo, Woon-Hong

    2016-07-15

    There is a high demand for a non-invasive, rapid, and highly accurate tool for disease diagnostics. Recently, saliva based diagnostics for the detection of specific biomarkers has drawn significant attention since the sample extraction is simple, cost-effective, and precise. Compared to blood, saliva contains a similar variety of DNA, RNA, proteins, metabolites, and microbiota that can be compiled into a multiplex of cancer detection markers. The salivary diagnostic method holds great potential for early-stage cancer diagnostics without any complicated and expensive procedures. Here, we review various cancer biomarkers in saliva and compare the biomarkers efficacy with traditional diagnostics and state-of-the-art bioelectronics. We summarize biomarkers in four major groups: genomics, transcriptomics, proteomics, and metabolomics/microbiota. Representative bioelectronic systems for each group are summarized based on various stages of a cancer. Systematic study of oxidative stress establishes the relationship between macromolecules and cancer biomarkers in saliva. We also introduce the most recent examples of salivary diagnostic electronics based on nanotechnologies that can offer rapid, yet highly accurate detection of biomarkers. A concluding section highlights areas of opportunity in the further development and applications of these technologies. PMID:26946257

  4. ROM Plus®: accurate point-of-care detection of ruptured fetal membranes

    PubMed Central

    McQuivey, Ross W; Block, Jon E

    2016-01-01

    Accurate and timely diagnosis of rupture of fetal membranes is imperative to inform and guide gestational age-specific interventions to optimize perinatal outcomes and reduce the risk of serious complications, including preterm delivery and infections. The ROM Plus is a rapid, point-of-care, qualitative immunochromatographic diagnostic test that uses a unique monoclonal/polyclonal antibody approach to detect two different proteins found in amniotic fluid at high concentrations: alpha-fetoprotein and insulin-like growth factor binding protein-1. Clinical study results have uniformly demonstrated high diagnostic accuracy and performance characteristics with this point-of-care test that exceeds conventional clinical testing with external laboratory evaluation. The description, indications for use, procedural steps, and laboratory and clinical characterization of this assay are presented in this article. PMID:27274316

  5. ROM Plus(®): accurate point-of-care detection of ruptured fetal membranes.

    PubMed

    McQuivey, Ross W; Block, Jon E

    2016-01-01

    Accurate and timely diagnosis of rupture of fetal membranes is imperative to inform and guide gestational age-specific interventions to optimize perinatal outcomes and reduce the risk of serious complications, including preterm delivery and infections. The ROM Plus is a rapid, point-of-care, qualitative immunochromatographic diagnostic test that uses a unique monoclonal/polyclonal antibody approach to detect two different proteins found in amniotic fluid at high concentrations: alpha-fetoprotein and insulin-like growth factor binding protein-1. Clinical study results have uniformly demonstrated high diagnostic accuracy and performance characteristics with this point-of-care test that exceeds conventional clinical testing with external laboratory evaluation. The description, indications for use, procedural steps, and laboratory and clinical characterization of this assay are presented in this article. PMID:27274316

  6. Accurate and Accidental Empathy.

    ERIC Educational Resources Information Center

    Chandler, Michael

    The author offers two controversial criticisms of what are rapidly becoming standard assessment procedures for the measurement of empathic skill. First, he asserts that assessment procedures which attend exclusively to the accuracy with which subjects are able to characterize other people's feelings provide little or no useful information about…

  7. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  8. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  9. ‘It puts life in us and we feel big’: shifts in the local health care system during the introduction of rapid diagnostic tests for malaria into drug shops in Uganda

    PubMed Central

    Hutchinson, Eleanor; Chandler, Clare; Clarke, Siân; Lal, Sham; Magnussen, Pascal; Kayendeke, Miriam; Nabirye, Christine; Kizito, James; Mbonye, Anthony

    2015-01-01

    This paper is an analysis of the social interaction between drug sellers, their clients and local health care workers within a medical trial that introduced rapid diagnostic tests for malaria into private sector drug shops in Mukono District, Uganda. It locates the introduction of a new technology to test blood and a system of referral within the context of local concerns about the choice and evaluation of treatment; and the socially legitimated statuses, roles and hierarchies within the local health care system. Based on the multi-layered interpretation of 21 focus group discussions, we describe three key aspects of the trial central to local interpretation: openly testing blood, supervisory visits to drug shops and a new referral form. Each had the potential to shift drug shop vendors from outsider to insider of the formal health service. The responses of the different groups of participants reflect their situation within the health care system. The clients and patients welcomed the local availability of new diagnostic technology and the apparent involvement of the government in securing good quality health services for them from providers with often uncertain credentials. The drug shop vendors welcomed the authorization to openly test blood, enabling the demonstration of a new skill and newfound legitimacy as a health worker rather than simple drug seller. Formal sector health workers were less enthusiastic about the trial, raising concerns about professional hierarchies and the maintenance of a boundary around the formal health service to ensure the exclusion of those they considered untrained, unprofessional and untrustworthy personnel. PMID:25632175

  10. Integrated diagnostics

    NASA Technical Reports Server (NTRS)

    Hunthausen, Roger J.

    1988-01-01

    Recently completed projects in which advanced diagnostic concepts were explored and/or demonstrated are summarized. The projects begin with the design of integrated diagnostics for the Army's new gas turbine engines, and advance to the application of integrated diagnostics to other aircraft subsystems. Finally, a recent project is discussed which ties together subsystem fault monitoring and diagnostics with a more complete picture of flight domain knowledge.

  11. Integrated diagnostics: proceedings from the 9th biennial symposium of the International Society for Strategic Studies in Radiology.

    PubMed

    Krestin, G P; Grenier, P A; Hricak, H; Jackson, V P; Khong, P L; Miller, J C; Muellner, A; Schwaiger, M; Thrall, J H

    2012-11-01

    The International Society for Strategic Studies in Radiology held its 9th biennial meeting in August 2011. The focus of the programme was integrated diagnostics and massive computing. Participants discussed the opportunities, challenges, and consequences for the discipline of radiology that will likely arise from the integration of diagnostic technologies. Diagnostic technologies are increasing in scope, including advanced imaging techniques, new molecular imaging agents, and sophisticated point-of-use devices. Advanced information technology (IT), which is increasingly influencing the practice of medicine, will aid clinical communication and the development of "population images" that represent the phenotype of particular diseases, which will aid the development of diagnostic algorithms. Integrated diagnostics offer increased operational efficiency and benefits to patients through quicker and more accurate diagnoses. As physicians with the most expertise in IT, radiologists are well placed to take the lead in introducing IT solutions and cloud computing to promote integrated diagnostics. To achieve this, radiologists must adapt to include quantitative data on biomarkers in their reports. Radiologists must also increase their role as participating physicians, collaborating with other medical specialties, not only to avoid being sidelined by other specialties but also to better prepare as leaders in the selection and sequence of diagnostic procedures. Key Points • New diagnostic technologies are yielding unprecedented amounts of diagnostic information.• Advanced IT/cloud computing will aid integration and analysis of diagnostic data.• Better diagnostic algorithms will lead to faster diagnosis and more rapid treatment. PMID:22699871

  12. A rapid and accurate solar tracker (notice of removal)

    NASA Astrophysics Data System (ADS)

    Xiao, Baoping; Xu, Lijun

    2008-12-01

    This paper (713043) was removed from the SPIE Digital Library on 13 April 2010 due to discovery of plagiarism. As stated in the SPIE Guidelines for Professional Conduct and Publishing Ethics, SPIE defines plagiarism as the reuse of someone else's prior ideas, processes, results, or words without explicit attribution of the original author and source, or falsely representing someone else's work as one's own. SPIE considers plagiarism in any form, at any level, to be unacceptable and a serious breach of professional conduct. It is SPIE policy to remove such papers and to take appropriate corrective or disciplinary action against the offending author(s).

  13. Accurate and rapid micromixer for integrated microfluidic devices

    SciTech Connect

    Van Dam, R. Michael; Liu, Kan; Shen, Kwang -Fu Clifton; Tseng, Hsian -Rong

    2015-09-22

    The invention may provide a microfluidic mixer having a droplet generator and a droplet mixer in selective fluid connection with the droplet generator. The droplet generator comprises first and second fluid chambers that are structured to be filled with respective first and second fluids that can each be held in isolation for a selectable period of time. The first and second fluid chambers are further structured to be reconfigured into a single combined chamber to allow the first and second fluids in the first and second fluid chambers to come into fluid contact with each other in the combined chamber for a selectable period of time prior to being brought into the droplet mixer.

  14. Accurate measurement of time

    NASA Astrophysics Data System (ADS)

    Itano, Wayne M.; Ramsey, Norman F.

    1993-07-01

    The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

  15. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  16. Advanced clinical monitoring: considerations for real-time hemodynamic diagnostics.

    PubMed Central

    Goldman, J. M.; Cordova, M. J.

    1994-01-01

    In an effort to ease staffing burdens and potentially improve patient outcome in an intensive care unit (ICU) environment, we are developing a real-time system to accurately and efficiently diagnose cardiopulmonary emergencies. The system is being designed to utilize all relevant routinely-monitored physiological data in order to automatically diagnose potentially fatal events. The initial stage of this project involved formulating the overall system design and appropriate methods for real-time data acquisition, data storage, data trending, waveform analysis, and implementing diagnostic rules. Initially, we defined a conceptual analysis of the minimum physiologic data set, and the monitoring time-frames (trends) which would be required to diagnose cardiopulmonary emergencies. Following that analysis, we used a fuzzy logic diagnostic engine to analyze physiological data during a simulated arrhythmic cardiac arrest (ACA) in order to assess the validity of our diagnostic methodology. We used rate, trend, and morphologic data extracted from the following signals: expired CO2 time-concentration curve (capnogram), electrocardiogram, and arterial blood pressure. The system performed well: The fuzzy logic engine effectively diagnosed the likelihood of ACA from the subtle hemodynamic trends which preceded the complete arrest. As the clinical picture worsened, the fuzzy logic-based system accurately indicated the change in patient condition. Termination of the simulated arrest was rapidly detected by the diagnostic engine. In view of the effectiveness of this fuzzy logic implementation, we plan to develop additional fuzzy logic modules to diagnose other cardiopulmonary emergencies. PMID:7950025

  17. Cell-Free DNA as a Diagnostic Tool for Human Parasitic Infections.

    PubMed

    Weerakoon, Kosala G; McManus, Donald P

    2016-05-01

    Parasites often cause devastating diseases and represent a significant public health and economic burden. More accurate and convenient diagnostic tools are needed in support of parasite control programmes in endemic regions, and for rapid point-of-care diagnosis in nonendemic areas. The detection of cell-free DNA (cfDNA) is a relatively new concept that is being applied in the current armamentarium of diagnostics. Here, we review the application of cfDNA detection with nucleic acid amplification tests for the diagnosis and evaluation of different human parasitic infections and highlight the significant benefits of the approach using non-invasive clinical samples. PMID:26847654

  18. Rapid improvement in passive tuberculosis case detection and tuberculosis treatment outcomes after implementation of a bundled laboratory diagnostic and on-site training intervention targeting mid-level providers.

    PubMed

    Manabe, Yukari C; Zawedde-Muyanja, Stella; Burnett, Sarah M; Mugabe, Frank; Naikoba, Sarah; Coutinho, Alex

    2015-01-01

    Background.  Tuberculosis (TB) control is a public health priority with 3 million cases unrecognized by the public health system each year. We assessed the impact of improved TB diagnostics and on-site training on TB case detection and treatment outcomes in rural healthcare facilities. Methods.  Fluorescence microscopy, Xpert MTB/RIF, and on-site training were introduced at 10 healthcare facilities. Using quasi-experimental methods, these 10 intervention healthcare facilities were compared with 2 controls and their own performance the previous year. Results.  From January to October 2012, 186 357 and 32 886 outpatients were seen in the 10 intervention and 2 control facilities, respectively. The intervention facilities had a 52.04% higher proportion of presumptive TB cases with a sputum examination (odds ratio [OR] = 12.65; 95% confidence interval [CI], 5.60-28.55). After adjusting for age group and gender, the proportion of smear-positive patients initiated on treatment was 37.76% higher in the intervention than in the control facilities (adjusted OR [AOR], 7.59; 95% CI, 2.19-26.33). After adjusting for the factors above, as well as human immunodeficiency virus and TB retreatment status, the proportion of TB cases who completed treatment was 29.16% higher (AOR, 4.89; 95% CI, 2.24-10.67) and the proportion of TB cases who were lost to follow-up was 66.98% lower (AOR, 0.04; 95% CI, 0.01-0.09). When compared with baseline performance, the intervention facilities had a significantly higher proportion of presumptive TB cases with a sputum examination (64.70% vs 3.44%; OR, 23.95; 95% CI, 12.96-44.25), and these facilities started 56.25% more smear-positive TB cases on treatment during the project period (AOR, 15.36; 95% CI, 6.57-35.91). Conclusions.  Optimizing the existing healthcare workforce through a bundled diagnostics and on-site training intervention for nonphysician healthcare workers will rapidly improve TB case detection and outcomes towards global

  19. Rapid Improvement in Passive Tuberculosis Case Detection and Tuberculosis Treatment Outcomes After Implementation of a Bundled Laboratory Diagnostic and On-Site Training Intervention Targeting Mid-Level Providers

    PubMed Central

    Manabe, Yukari C.; Zawedde-Muyanja, Stella; Burnett, Sarah M.; Mugabe, Frank; Naikoba, Sarah; Coutinho, Alex

    2015-01-01

    Background. Tuberculosis (TB) control is a public health priority with 3 million cases unrecognized by the public health system each year. We assessed the impact of improved TB diagnostics and on-site training on TB case detection and treatment outcomes in rural healthcare facilities. Methods. Fluorescence microscopy, Xpert MTB/RIF, and on-site training were introduced at 10 healthcare facilities. Using quasi-experimental methods, these 10 intervention healthcare facilities were compared with 2 controls and their own performance the previous year. Results. From January to October 2012, 186 357 and 32 886 outpatients were seen in the 10 intervention and 2 control facilities, respectively. The intervention facilities had a 52.04% higher proportion of presumptive TB cases with a sputum examination (odds ratio [OR] = 12.65; 95% confidence interval [CI], 5.60–28.55). After adjusting for age group and gender, the proportion of smear-positive patients initiated on treatment was 37.76% higher in the intervention than in the control facilities (adjusted OR [AOR], 7.59; 95% CI, 2.19–26.33). After adjusting for the factors above, as well as human immunodeficiency virus and TB retreatment status, the proportion of TB cases who completed treatment was 29.16% higher (AOR, 4.89; 95% CI, 2.24–10.67) and the proportion of TB cases who were lost to follow-up was 66.98% lower (AOR, 0.04; 95% CI, 0.01–0.09). When compared with baseline performance, the intervention facilities had a significantly higher proportion of presumptive TB cases with a sputum examination (64.70% vs 3.44%; OR, 23.95; 95% CI, 12.96–44.25), and these facilities started 56.25% more smear-positive TB cases on treatment during the project period (AOR, 15.36; 95% CI, 6.57–35.91). Conclusions. Optimizing the existing healthcare workforce through a bundled diagnostics and on-site training intervention for nonphysician healthcare workers will rapidly improve TB case detection and outcomes towards

  20. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    PubMed

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs. PMID:26141269

  1. Beamlet laser diagnostics

    SciTech Connect

    Burkhart, S.C.; Behrendt, W.C.; Smith, I.

    1996-06-01

    Beamlet is instrumented extensively to monitor the performance of the overall laser system and many of its subsystems. Beam diagnostics, installed in key locations, are used to fully characterize the beam during its propagation through the multipass cavity and the laser`s output section. This article describes the diagnostics stations located on Beamlet and discusses the design, calibration, and performance of the Beamlet calorimeters. The authors used Nova`s diagnostics packages to develop the Beamlet design to determine beam energy, spatial profile, temporal profile, and other beam parameters. Technologic improvements within the last several years in controls, charge-coupled device (CCD) cameras, and fast oscilloscopes have allowed the authors to obtain more accurate measurements on the Beamlet laser system. They briefly cover some of these techniques, including a description of their LabVIEW based data acquisition system.

  2. Combining rapid diagnostic tests and dried blood spot assays for point-of-care testing of human immunodeficiency virus, hepatitis B and hepatitis C infections in Burkina Faso, West Africa.

    PubMed

    Kania, D; Bekalé, A M; Nagot, N; Mondain, A-M; Ottomani, L; Meda, N; Traoré, M; Ouédraogo, J B; Ducos, J; Van de Perre, P; Tuaillon, E

    2013-12-01

    People screened for human immunodeficiency virus (HIV) using rapid diagnostic tests (RDTs) in Africa remain generally unaware of their status for hepatitis B (HBV) and hepatitis C (HCV) infections. We evaluated a two-step screening strategy in Burkina Faso, using both HIV RDTs and Dried Blood Spot (DBS) assays to confirm an HIV-positive test, and to test for HBV and HCV infections. HIV counselling and point-of-care testing were performed at a voluntary counselling and testing centre with HBV, HCV status and HIV confirmation using DBS specimens, being assessed at a central laboratory. Serological testing on plasma was used as the reference standard assay to control for the performance of DBS assays. Nineteen out of 218 participants included in the study were positive for HIV using RDTs. A fourth-generation HIV ELISA and immunoblot assays on DBS confirmed HIV status. Twenty-four out of 25 participants infected with HBV were found positive for hepatitis B surface antigen (HBsAg) using DBS. One sample with a low HBsAg concentration on plasma was not detected on DBS. Five participants tested positive for HCV antibodies were confirmed positive with an immunoblot assay using DBS specimens. Laboratory results were communicated within 7 days to participants with no loss to follow up of participants between the first and second post-test counselling sessions. In conclusion, DBS collection during HIV point-of-care testing enables screening and confirmation of HBV, HCV and HIV infections. Diagnosis using DBS may assist with implementation of national programmes for HBV, HCV and HIV screening and clinical care in middle- to low-income countries. PMID:23902574

  3. External Quality Assessment of Reading and Interpretation of Malaria Rapid Diagnostic Tests among 1849 End-Users in the Democratic Republic of the Congo through Short Message Service (SMS)

    PubMed Central

    Mukadi, Pierre; Gillet, Philippe; Lukuka, Albert; Mbatshi, Joêl; Otshudiema, John; Muyembe, Jean-Jacques; Buyze, Jozefien; Jacobs, Jan; Lejon, Veerle

    2013-01-01

    Background Although malaria rapid diagnostic tests (RDT) are simple to perform, they remain subject to errors, mainly related to the post-analytical phase. We organized the first large scale SMS based external quality assessment (EQA) on correct reading and interpretation of photographs of a three-band malaria RDT among laboratory health workers in the Democratic Republic of the Congo (DR Congo). Methods and Findings High resolution EQA photographs of 10 RDT results together with a questionnaire were distributed to health facilities in 9 out of 11 provinces in DR Congo. Each laboratory health worker answered the EQA by Short Message Service (SMS). Filled-in questionnaires from each health facility were sent back to Kinshasa. A total of 1849 laboratory health workers in 1014 health facilities participated. Most frequent errors in RDT reading were i) failure to recognize invalid (13.2–32.5% ) or negative test results (9.8–12.8%), (ii) overlooking faint test lines (4.1–31.2%) and (iii) incorrect identification of the malaria species (12.1–17.4%). No uniform strategy for diagnosis of malaria at the health facility was present. Stock outs of RDTs occurred frequently. Half of the health facilities had not received an RDT training. Only two thirds used the RDT recommended by the National Malaria Control Program. Performance of RDT reading was positively associated with training and the technical level of health facility. Facilities with RDT positivity rates >50% and located in Eastern DR Congo performed worse. Conclusions Our study confirmed that errors in reading and interpretation of malaria RDTs are widespread and highlighted the problem of stock outs of RDTs. Adequate training of end-users in the application of malaria RDTs associated with regular EQAs is recommended. PMID:23967211

  4. Companion diagnostics and molecular imaging-enhanced approaches for oncology clinical trials

    PubMed Central

    Van Heertum, Ronald L; Scarimbolo, Robert; Ford, Robert; Berdougo, Eli; O’Neal, Michael

    2015-01-01

    In the era of personalized medicine, diagnostic approaches are helping pharmaceutical and biotechnology sponsors streamline the clinical trial process. Molecular assays and diagnostic imaging are routinely being used to stratify patients for treatment, monitor disease, and provide reliable early clinical phase assessments. The importance of diagnostic approaches in drug development is highlighted by the rapidly expanding global cancer diagnostics market and the emergent attention of regulatory agencies worldwide, who are beginning to offer more structured platforms and guidance for this area. In this paper, we highlight the key benefits of using companion diagnostics and diagnostic imaging with a focus on oncology clinical trials. Nuclear imaging using widely available radiopharmaceuticals in conjunction with molecular imaging of oncology targets has opened the door to more accurate disease assessment and the modernization of standard criteria for the evaluation, staging, and treatment responses of cancer patients. Furthermore, the introduction and validation of quantitative molecular imaging continues to drive and optimize the field of oncology diagnostics. Given their pivotal role in disease assessment and treatment, the validation and commercialization of diagnostic tools will continue to advance oncology clinical trials, support new oncology drugs, and promote better patient outcomes. PMID:26392755

  5. New Diagnostic Aides for Melanoma

    PubMed Central

    Ferris, Laura K.; Harris, Ryan J.

    2012-01-01

    Synopsis Detection of melanoma at an early stage is crucial to improving survival rates in melanoma. Accurate diagnosis by current techniques including dermatoscopy remains difficult, and new tools are needed to improve our diagnostic abilities. This article discusses recent advances in diagnostic techniques including confocal scanning laser microscopy, MelaFind, Siascopy, noninvasive genomic detection, as well as other future possibilities to aid in diagnosing melanoma. Advantages and barriers to implementation of the various technologies are discussed as well. PMID:22800557

  6. Optical Imaging Techniques for Point-of-care Diagnostics

    PubMed Central

    Zhu, Hongying; Isikman, Serhan O.; Mudanyali, Onur; Greenbaum, Alon; Ozcan, Aydogan

    2012-01-01

    Improving the access to effective and affordable healthcare has long been a global endeavor. In this quest, the development of cost-effective and easy-to-use medical testing equipment that enable rapid and accurate diagnosis is essential to reduce the time and costs associated with healthcare services. To this end, point-of-care (POC) diagnostics plays a crucial role in healthcare delivery in both the developed and developing countries by bringing medical testing to patients, or to sites near patients. As the diagnosis of a wide range of diseases, including various types of cancers and many endemics relies on optical techniques, numerous compact and cost-effective optical imaging platforms have been developed in recent years for use at the POC. Here, we review the state-of-the-art optical imaging techniques that can have significant impact on global health by facilitating effective and affordable POC diagnostics. PMID:23044793

  7. Current developments in salivary diagnostics

    PubMed Central

    Foley, Joseph D; Bailey, Alison L; Campell, Charles L; Humphries, Roger L; Christodoulides, Nicolaos; Floriano, Pierre N; Simmons, Glennon; Bhagwandin, Bryon; Jacobson, James W; Redding, Spencer W; Ebersole, Jeffrey L; McDevitt, John T

    2010-01-01

    Salivary diagnostics is an emerging field that has progressed through several important developments in the past decade, including the publication of the human salivary proteome and the infusion of federal funds to integrate nanotechnologies and microfluidic engineering concepts into developing compact point-of-care devices for rapid analysis of this secretion. In this article, we discuss some of these developments and their relevance to the prognosis, diagnosis and management of periodontitis, as an oral target, and cardiovascular disease, as a systemic example for the potential of these biodiagnostics. Our findings suggest that several biomarkers are associated with distinct biological stages of these diseases and demonstrate promise as practical biomarkers in identifying and managing periodontal disease, and acute myocardial infarction. The majority of these studies have progressed through biomarker discovery, with the identified molecules requiring more robust clinical studies to enable substantive validation for disease diagnosis. It is predicted that with continued advances in this field the use of a combination of biomarkers in multiplex panels is likely to yield accurate screening tools for these diagnoses in the near future. PMID:20387312

  8. Current developments in salivary diagnostics.

    PubMed

    Miller, Craig S; Foley, Joseph D; Bailey, Alison L; Campell, Charles L; Humphries, Roger L; Christodoulides, Nicolaos; Floriano, Pierre N; Simmons, Glennon; Bhagwandin, Bryon; Jacobson, James W; Redding, Spencer W; Ebersole, Jeffrey L; McDevitt, John T

    2010-02-01

    Salivary diagnostics is an emerging field that has progressed through several important developments in the past decade, including the publication of the human salivary proteome and the infusion of federal funds to integrate nanotechnologies and microfluidic engineering concepts into developing compact point-of-care devices for rapid analysis of this secretion. In this article, we discuss some of these developments and their relevance to the prognosis, diagnosis and management of periodontitis, as an oral target, and cardiovascular disease, as a systemic example for the potential of these biodiagnostics. Our findings suggest that several biomarkers are associated with distinct biological stages of these diseases and demonstrate promise as practical biomarkers in identifying and managing periodontal disease, and acute myocardial infarction. The majority of these studies have progressed through biomarker discovery, with the identified molecules requiring more robust clinical studies to enable substantive validation for disease diagnosis. It is predicted that with continued advances in this field the use of a combination of biomarkers in multiplex panels is likely to yield accurate screening tools for these diagnoses in the near future. PMID:20387312

  9. Accurate Detection of Rifampicin-Resistant Mycobacterium Tuberculosis Strains.

    PubMed

    Song, Keum-Soo; Nimse, Satish Balasaheb; Kim, Hee Jin; Yang, Jeongseong; Kim, Taisun

    2016-01-01

    In 2013 alone, the death rate among the 9.0 million people infected with Mycobacterium tuberculosis (TB) worldwide was around 14%, which is unacceptably high. An empiric treatment of patients infected with TB or drug-resistant Mycobacterium tuberculosis (MDR-TB) strain can also result in the spread of MDR-TB. The diagnostic tools which are rapid, reliable, and have simple experimental protocols can significantly help in decreasing the prevalence rate of MDR-TB strain. We report the evaluation of the 9G technology based 9G DNAChips that allow accurate detection and discrimination of TB and MDR-TB-RIF. One hundred and thirteen known cultured samples were used to evaluate the ability of 9G DNAChip in the detection and discrimination of TB and MDR-TB-RIF strains. Hybridization of immobilized probes with the PCR products of TB and MDR-TB-RIF strains allow their detection and discrimination. The accuracy of 9G DNAChip was determined by comparing its results with sequencing analysis and drug susceptibility testing. Sequencing analysis showed 100% agreement with the results of 9G DNAChip. The 9G DNAChip showed very high sensitivity (95.4%) and specificity (100%). PMID:26999135

  10. Accurate Detection of Rifampicin-Resistant Mycobacterium Tuberculosis Strains

    PubMed Central

    Song, Keum-Soo; Nimse, Satish Balasaheb; Kim, Hee Jin; Yang, Jeongseong; Kim, Taisun

    2016-01-01

    In 2013 alone, the death rate among the 9.0 million people infected with Mycobacterium tuberculosis (TB) worldwide was around 14%, which is unacceptably high. An empiric treatment of patients infected with TB or drug-resistant Mycobacterium tuberculosis (MDR-TB) strain can also result in the spread of MDR-TB. The diagnostic tools which are rapid, reliable, and have simple experimental protocols can significantly help in decreasing the prevalence rate of MDR-TB strain. We report the evaluation of the 9G technology based 9G DNAChips that allow accurate detection and discrimination of TB and MDR-TB-RIF. One hundred and thirteen known cultured samples were used to evaluate the ability of 9G DNAChip in the detection and discrimination of TB and MDR-TB-RIF strains. Hybridization of immobilized probes with the PCR products of TB and MDR-TB-RIF strains allow their detection and discrimination. The accuracy of 9G DNAChip was determined by comparing its results with sequencing analysis and drug susceptibility testing. Sequencing analysis showed 100% agreement with the results of 9G DNAChip. The 9G DNAChip showed very high sensitivity (95.4%) and specificity (100%). PMID:26999135

  11. Diagnostic Imaging

    MedlinePlus

    Diagnostic imaging lets doctors look inside your body for clues about a medical condition. A variety of machines and ... and activities inside your body. The type of imaging your doctor uses depends on your symptoms and ...

  12. Diagnostic radiology

    SciTech Connect

    Leeds, N.E.; Jacobson, H.G.

    1986-10-17

    Developments in the burgeoning field of diagnostic radiology have continued apace. Four areas that represent either subspecialities or technological advances in diagnostic radiology will be considered in this report: ultrasonography, interventional radiology, nuclear radiology, and magnetic resonance. In no sense is the exclusion of other subdisciplines and modalities (eg, pediatric radiology, computed tomography) and indication of their of importance or their failure to include innovative concepts.

  13. Rapid and quantitative detection of hepatitis B virus

    PubMed Central

    Liu, Yue-Ping; Yao, Chun-Yan

    2015-01-01

    Despite availability of a universal vaccine, hepatitis B virus (HBV) infection has a huge impact on public health worldwide. Accurate and timely diagnosis of HBV infection is needed. Rapid developments have been made in the diagnostic and monitoring methods for HBV infection, including serological and molecular assays. In clinical practice, qualitative hepatitis B surface antigen (HBsAg) testing has long served as a diagnostic marker for individuals infected with HBV. More recently, HBsAg level has been used to predict treatment outcome when determined early during treatment or at baseline. However, identification of HBV DNA positive cases that do not have detectable HBsAg has encouraged the application of molecular tests. Hence, combination of quantitative detection of HBV DNA and HBsAg can be used to discriminate patients during the course of HBV infection and to monitor therapy. This article reviews the most commonly used quantitative methods for HBsAg and HBV DNA. PMID:26576084

  14. Advanced tests for early and accurate diagnosis of Creutzfeldt-Jakob disease.

    PubMed

    Zanusso, Gianluigi; Monaco, Salvatore; Pocchiari, Maurizio; Caughey, Byron

    2016-06-01

    Early and accurate diagnosis of Creutzfeldt-Jakob disease (CJD) is a necessary to distinguish this untreatable disease from treatable rapidly progressive dementias, and to prevent iatrogenic transmission. Currently, definitive diagnosis of CJD requires detection of the abnormally folded, CJD-specific form of protease-resistant prion protein (PrP(CJD)) in brain tissue obtained postmortem or via biopsy; therefore, diagnosis of sporadic CJD in clinical practice is often challenging. Supporting investigations, including MRI, EEG and conventional analyses of cerebrospinal fluid (CSF) biomarkers, are helpful in the diagnostic work-up, but do not allow definitive diagnosis. Recently, novel ultrasensitive seeding assays, based on the amplified detection of PrP(CJD), have improved the diagnostic process; for example, real-time quaking-induced conversion (RT-QuIC) is a sensitive method to detect prion-seeding activity in brain homogenate from humans with any subtype of sporadic CJD. RT-QuIC can also be used for in vivo diagnosis of CJD: its diagnostic sensitivity in detecting PrP(CJD) in CSF samples is 96%, and its specificity is 100%. Recently, we provided evidence that RT-QuIC of olfactory mucosa brushings is a 97% sensitive and 100% specific for sporadic CJD. These assays provide a basis for definitive antemortem diagnosis of prion diseases and, in doing so, improve prospects for reducing the risk of prion transmission. Moreover, they can be used to evaluate outcome measures in therapeutic trials for these as yet untreatable infections. PMID:27174240

  15. A new sample preparation and separation combination for precise, accurate, rapid, and simultaneous determination of vitamins B1, B2, B3, B5, B6, B7, and B9 in infant formula and related nutritionals by LC-MS/MS.

    PubMed

    Cellar, Nicholas A; McClure, Sean C; Salvati, Louis M; Reddy, Todime M

    2016-08-31

    An improved method was developed for simultaneous determination of the fortified forms of thiamine (B1), riboflavin (B2), nicotinamide and nicotinic acid (B3), pantothenic acid (B5), pyridoxine (B6), biotin (B7), and folic acid (B9) in infant formulas and related nutritionals. The method employed a simple, effective, and rapid sample preparation followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). It improved upon previous methodologies by offering facile and rugged sample preparation with improved chromatographic conditions, which culminated in a highly accurate and precise method for water-soluble vitamin determination in a wide range of formulas. The method was validated over six days in ten unique matrices with two analysts and on instruments in two different labs. Intermediate precision averaged 3.4 ± 2.6% relative standard deviation and over-spike recovery averaged 100.2 ± 2.4% (n = 160). Due to refinements in sample preparation, the method had high sample throughput capacity. PMID:27506358

  16. Confirmed Zika virus infection in a Belgian traveler returning from Guatemala, and the diagnostic challenges of imported cases into Europe.

    PubMed

    De Smet, Birgit; Van den Bossche, Dorien; van de Werve, Charlotte; Mairesse, Jacques; Schmidt-Chanasit, Jonas; Michiels, Jo; Ariën, Kevin K; Van Esbroeck, Marjan; Cnops, Lieselotte

    2016-07-01

    We report the first laboratory-confirmed Zika virus (ZIKV) infection in a Belgian traveler after a three week holiday in Guatemala, December 2015. This case along with other imported cases into Europe emphases once again the need for accurate diagnostic tools for this rapidly emerging virus. The challenge is to diagnose patients in the acute phase, which appears short, as serological testing is complicated by cross-reactivity, vaccination status and scarce availability of specific ZIKV tests. PMID:27128355

  17. Fungal Diagnostics

    PubMed Central

    Kozel, Thomas R.; Wickes, Brian

    2014-01-01

    Early diagnosis of fungal infection is critical to effective treatment. There are many impediments to diagnosis such as a diminishing number of clinical mycologists, cost, time to result, and requirements for sensitivity and specificity. In addition, fungal diagnostics must meet the contrasting needs presented by the increasing diversity of fungi found in association with the use of immunosuppressive agents in countries with high levels of medical care and the need for diagnostics in resource-limited countries where large numbers of opportunistic infections occur in patients with AIDS. Traditional approaches to diagnosis include direct microscopic examination of clinical samples, histopathology, culture, and serology. Emerging technologies include molecular diagnostics and antigen detection in clinical samples. Innovative new technologies that use molecular and immunoassay platforms have the potential to meet the needs of both resource-rich and resource-limited clinical environments. PMID:24692193

  18. DIAGNOSTICS OF BNL ERL

    SciTech Connect

    POZDEYEV,E.; BEN-ZVI, I.; CAMERON, P.; GASSNER, D.; KAYRAN, D.; ET AL.

    2007-06-25

    The ERL Prototype project is currently under development at the Brookhaven National Laboratory. The ERL is expected to demonstrate energy recovery of high-intensity beams with a current of up to a few hundred milliamps, while preserving the emittance of bunches with a charge of a few nanocoulombs produced by a high-current SRF gun. To successfully accomplish this task the machine will include beam diagnostics that will be used for accurate characterization of the three dimensional beam phase space at the injection and recirculation energies, transverse and longitudinal beam matching, orbit alignment, beam current measurement, and machine protection. This paper outlines requirements on the ERL diagnostics and describes its setup and modes of operation.

  19. Template tailoring: Accurate determination of heterozygous alleles using peptide nucleic acid and dideoxyNTP

    PubMed Central

    Tariq, Muhammad Akram; Pourmand, Nader

    2010-01-01

    Measurement of the length of DNA fragments plays a pivotal role in genetic mapping, disease diagnostics, human identification and forensic applications. PCR followed by electrophoresis is used for DNA length measurement of STRs, a process that requires labeled primers and allelic ladders as standards to avoid machine error. Sequencing-based approaches can be used for STR analysis to eliminate the requirement of labeled primers and allelic ladder. However, the limiting factor with this approach is unsynchronized polymerization in heterozygous sample analysis, in which alleles with different lengths can lead to imbalanced heterozygote peak height ratios. We have developed a rapid DNA length measurement method using peptide nucleic acid and dideoxy dNTPs to “tailor” DNA templates for accurate sequencing to overcome this hurdle. We also devised an accelerated “dyad” pyrosequencing strategy, such that the combined approach can be used as a faster, more accurate alternative to de novo sequencing. Dyad sequencing interrogates two bases at a time by allowing the polymerase to incorporate two nucleotides to DNA template, cutting the analysis time in half. In addition, for the first time, we show the effect of peptide nucleic acid as a blocking probe to stop polymerization, which is essential to analyze the heterozygous samples by sequencing. This approach provides a new platform for rapid and cost-effective DNA length measurement for STRs and resequencing of small DNA fragments. PMID:20408144

  20. New model accurately predicts reformate composition

    SciTech Connect

    Ancheyta-Juarez, J.; Aguilar-Rodriguez, E. )

    1994-01-31

    Although naphtha reforming is a well-known process, the evolution of catalyst formulation, as well as new trends in gasoline specifications, have led to rapid evolution of the process, including: reactor design, regeneration mode, and operating conditions. Mathematical modeling of the reforming process is an increasingly important tool. It is fundamental to the proper design of new reactors and revamp of existing ones. Modeling can be used to optimize operating conditions, analyze the effects of process variables, and enhance unit performance. Instituto Mexicano del Petroleo has developed a model of the catalytic reforming process that accurately predicts reformate composition at the higher-severity conditions at which new reformers are being designed. The new AA model is more accurate than previous proposals because it takes into account the effects of temperature and pressure on the rate constants of each chemical reaction.

  1. Diagnostic imaging.

    PubMed

    Morris, Peter; Perkins, Alan

    2012-04-21

    Physical techniques have always had a key role in medicine, and the second half of the 20th century in particular saw a revolution in medical diagnostic techniques with the development of key imaging instruments: x-ray imaging and emission tomography (nuclear imaging and PET), MRI, and ultrasound. These techniques use the full width of the electromagnetic spectrum, from gamma rays to radio waves, and sound. In most cases, the development of a medical imaging device was opportunistic; many scientists in physics laboratories were experimenting with simple x-ray images within the first year of the discovery of such rays, the development of the cyclotron and later nuclear reactors created the opportunity for nuclear medicine, and one of the co-inventors of MRI was initially attempting to develop an alternative to x-ray diffraction for the analysis of crystal structures. What all these techniques have in common is the brilliant insight of a few pioneering physical scientists and engineers who had the tenacity to develop their inventions, followed by a series of technical innovations that enabled the full diagnostic potential of these instruments to be realised. In this report, we focus on the key part played by these scientists and engineers and the new imaging instruments and diagnostic procedures that they developed. By bringing the key developments and applications together we hope to show the true legacy of physics and engineering in diagnostic medicine. PMID:22516558

  2. Point of care diagnostics for sexually transmitted infections: perspectives and advances

    PubMed Central

    Gaydos, Charlotte; Hardick, Justin

    2014-01-01

    Accurate and inexpensive point-of-care (POC) tests are urgently needed to control sexually transmitted infection (STI) epidemics, so that patients can receive immediate diagnoses and treatment. Current POC assays for Chlamydia trachomatis and Neisseria gonorrhoeae perform inadequately and require better assays. Diagnostics for Trichomonas vaginalis rely on wet preparation, with some notable advances. Serological POC assays for syphilis can impact resource-poor settings, with many assays available, but only one available in the U.S. HIV POC diagnostics demonstrate the best performance, with excellent assays available. There is a rapid assay for HSV lesion detection; but no POC serological assays are available. Despite the inadequacy of POC assays for treatable bacterial infections, application of technological advances offers the promise of advancing POC diagnostics for all STIs. PMID:24484215

  3. Point-of-Care Diagnostics in Low Resource Settings: Present Status and Future Role of Microfluidics

    PubMed Central

    Sharma, Shikha; Zapatero-Rodríguez, Julia; Estrela, Pedro; O’Kennedy, Richard

    2015-01-01

    The inability to diagnose numerous diseases rapidly is a significant cause of the disparity of deaths resulting from both communicable and non-communicable diseases in the developing world in comparison to the developed world. Existing diagnostic instrumentation usually requires sophisticated infrastructure, stable electrical power, expensive reagents, long assay times, and highly trained personnel which is not often available in limited resource settings. This review will critically survey and analyse the current lateral flow-based point-of-care (POC) technologies, which have made a major impact on diagnostic testing in developing countries over the last 50 years. The future of POC technologies including the applications of microfluidics, which allows miniaturisation and integration of complex functions that facilitate their usage in limited resource settings, is discussed The advantages offered by such systems, including low cost, ruggedness and the capacity to generate accurate and reliable results rapidly, are well suited to the clinical and social settings of the developing world. PMID:26287254

  4. Point-of-Care Diagnostics in Low Resource Settings: Present Status and Future Role of Microfluidics.

    PubMed

    Sharma, Shikha; Zapatero-Rodríguez, Julia; Estrela, Pedro; O'Kennedy, Richard

    2015-01-01

    The inability to diagnose numerous diseases rapidly is a significant cause of the disparity of deaths resulting from both communicable and non-communicable diseases in the developing world in comparison to the developed world. Existing diagnostic instrumentation usually requires sophisticated infrastructure, stable electrical power, expensive reagents, long assay times, and highly trained personnel which is not often available in limited resource settings. This review will critically survey and analyse the current lateral flow-based point-of-care (POC) technologies, which have made a major impact on diagnostic testing in developing countries over the last 50 years. The future of POC technologies including the applications of microfluidics, which allows miniaturisation and integration of complex functions that facilitate their usage in limited resource settings, is discussed The advantages offered by such systems, including low cost, ruggedness and the capacity to generate accurate and reliable results rapidly, are well suited to the clinical and social settings of the developing world. PMID:26287254

  5. Molecular diagnostics for tuberculosis.

    PubMed

    Noor, K M; Shephard, L; Bastian, I

    2015-04-01

    The phenotypic methods of smear microscopy, culture and indirect drug susceptibility testing (DST) remain the 'gold standard' diagnostics for tuberculosis (TB) in 2015. However, this review demonstrates that genotypic methods are in the ascendancy. Current-generation nucleic acid amplification tests (NAATs) are important supplementary tests for the rapid direct detection of (multidrug-resistant) TB in specific clinical settings. Genotypic detection is already the preferred method of detecting rifampicin and pyrazinamide resistance. Next-generation NAATs able to detect about 10 colony forming units/mL of sputum could replace culture as the initial test for detecting TB. Whole genome sequencing could also plausibly replace phenotypic DST but much work is required in method standardisation, database development and elucidation of all resistance gene determinants. The challenge then will be to rollout these increasingly complex and expensive diagnostics in the low-income countries where TB is prevalent. PMID:25719854

  6. Viral Hemorrhagic Fever Diagnostics.

    PubMed

    Racsa, Lori D; Kraft, Colleen S; Olinger, Gene G; Hensley, Lisa E

    2016-01-15

    There are 4 families of viruses that cause viral hemorrhagic fever (VHF), including Filoviridae. Ebola virus is one virus within the family Filoviridae and the cause of the current outbreak of VHF in West Africa. VHF-endemic areas are found throughout the world, yet traditional diagnosis of VHF has been performed in large reference laboratories centered in Europe and the United States. The large amount of capital needed, as well as highly trained and skilled personnel, has limited the availability of diagnostics in endemic areas except in conjunction with governmental and nongovernmental entities. However, rapid diagnosis of VHF is essential to efforts that will limit outbreaks. In addition, increased global travel suggests VHF diagnoses may be made outside of the endemic areas. Thus, understanding how to diagnose VHF is imperative for laboratories worldwide. This article reviews traditional and current diagnostic modalities for VHF. PMID:26354968

  7. FEL-accelerator related diagnostics

    SciTech Connect

    Kevin Jordan; David Douglas; Stephen V. Benson; Pavel Evtuschenko

    2007-08-02

    Free Electron Lasers (FEL) present a unique set of beam parameters to the diagnostics suite. The FEL requires characterization of the full six dimensional phase space of the electron beam at the wiggler and accurate alignment of the electron beam to the optical mode of the laser. In addition to the FEL requirements on the diagnostics suite, the Jefferson Lab FEL is operated as an Energy Recovered Linac (ERL) which imposes additional requirements on the diagnostics. The ERL aspect of the Jefferson Lab FEL requires that diagnostics operate over a unique dynamic range and operate with simultaneous transport of the accelerated and energy recovered beams. This talk will present how these challenges are addressed at the Jefferson Lab FEL.

  8. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  9. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  10. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, David C.; Goorvitch, D.

    1994-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  11. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139

  12. Accurate Molecular Polarizabilities Based on Continuum Electrostatics

    PubMed Central

    Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034

  13. Accurate phase-shift velocimetry in rock

    NASA Astrophysics Data System (ADS)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  14. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  15. Diagnostic Accuracy of Xpert Test in Tuberculosis Detection: A Systematic Review and Meta-analysis

    PubMed Central

    Kaur, Ravdeep; Kachroo, Kavita; Sharma, Jitendar Kumar; Vatturi, Satyanarayana Murthy; Dang, Amit

    2016-01-01

    Background: World Health Organization (WHO) recommends the use of Xpert MTB/RIF assay for rapid diagnosis of tuberculosis (TB) and detection of rifampicin resistance. This systematic review was done to know about the diagnostic accuracy and cost-effectiveness of the Xpert MTB/RIF assay. Methods: A systematic literature search was conducted in following databases: Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews, MEDLINE, PUBMED, Scopus, Science Direct and Google Scholar for relevant studies for studies published between 2010 and December 2014. Studies given in the systematic reviews were accessed separately and used for analysis. Selection of studies, data extraction and assessment of quality of included studies was performed independently by two reviewers. Studies evaluating the diagnostic accuracy of Xpert MTB/RIF assay among adult or predominantly adult patients (≥14 years), presumed to have pulmonary TB with or without HIV infection were included in the review. Also, studies that had assessed the diagnostic accuracy of Xpert MTB/RIF assay using sputum and other respiratory specimens were included. Results: The included studies had a low risk of any form of bias, showing that findings are of high scientific validity and credibility. Quantitative analysis of 37 included studies shows that Xpert MTB/RIF is an accurate diagnostic test for TB and detection of rifampicin resistance. Conclusion: Xpert MTB/RIF assay is a robust, sensitive and specific test for accurate diagnosis of tuberculosis as compared to conventional tests like culture and microscopic examination. PMID:27013842

  16. Novel molecular diagnostic tools for malaria elimination: a review of options from the point of view of high-throughput and applicability in resource limited settings.

    PubMed

    Britton, Sumudu; Cheng, Qin; McCarthy, James S

    2016-01-01

    As malaria transmission continues to decrease, an increasing number of countries will enter pre-elimination and elimination. To interrupt transmission, changes in control strategies are likely to require more accurate identification of all carriers of Plasmodium parasites, both symptomatic and asymptomatic, using diagnostic tools that are highly sensitive, high throughput and with fast turnaround times preferably performed in local health service settings. Currently available immunochromatographic lateral flow rapid diagnostic tests and field microscopy are unlikely to consistently detect infections at parasite densities less than 100 parasites/µL making them insufficiently sensitive for detecting all carriers. Molecular diagnostic platforms, such as PCR and LAMP, are currently available in reference laboratories, but at a cost both financially and in turnaround time. This review describes the recent progress in developing molecular diagnostic tools in terms of their capacity for high throughput and potential for performance in non-reference laboratories for malaria elimination. PMID:26879936

  17. Rotorcraft Diagnostics

    NASA Technical Reports Server (NTRS)

    Haste, Deepak; Azam, Mohammad; Ghoshal, Sudipto; Monte, James

    2012-01-01

    Health management (HM) in any engineering systems requires adequate understanding about the system s functioning; a sufficient amount of monitored data; the capability to extract, analyze, and collate information; and the capability to combine understanding and information for HM-related estimation and decision-making. Rotorcraft systems are, in general, highly complex. Obtaining adequate understanding about functioning of such systems is quite difficult, because of the proprietary (restricted access) nature of their designs and dynamic models. Development of an EIM (exact inverse map) solution for rotorcraft requires a process that can overcome the abovementioned difficulties and maximally utilize monitored information for HM facilitation via employing advanced analytic techniques. The goal was to develop a versatile HM solution for rotorcraft for facilitation of the Condition Based Maintenance Plus (CBM+) capabilities. The effort was geared towards developing analytic and reasoning techniques, and proving the ability to embed the required capabilities on a rotorcraft platform, paving the way for implementing the solution on an aircraft-level system for consolidation and reporting. The solution for rotorcraft can he used offboard or embedded directly onto a rotorcraft system. The envisioned solution utilizes available monitored and archived data for real-time fault detection and identification, failure precursor identification, and offline fault detection and diagnostics, health condition forecasting, optimal guided troubleshooting, and maintenance decision support. A variant of the onboard version is a self-contained hardware and software (HW+SW) package that can be embedded on rotorcraft systems. The HM solution comprises components that gather/ingest data and information, perform information/feature extraction, analyze information in conjunction with the dependency/diagnostic model of the target system, facilitate optimal guided troubleshooting, and offer

  18. Personalized nutrition diagnostics at the point-of-need.

    PubMed

    Lee, Seoho; Srinivasan, Balaji; Vemulapati, Sasank; Mehta, Saurabh; Erickson, David

    2016-07-01

    Micronutrient deficiency is widespread and negatively impacts morbidity, mortality, and quality of life globally. On-going advancements in nutritional biomarker discovery are enabling objective and accurate assessment of an individual's micronutrient and broader nutritional status. The vast majority of such assessment however still needs to be conducted in traditional centralized laboratory facilities which are not readily accessible in terms of cost and time in both the developed and developing countries. Lab-on-a-chip (LOC) technologies are enabling an increasing number of biochemical reactions at the point-of-need (PON) settings, and can significantly improve the current predicament in nutrition diagnostics by allowing rapid evaluation of one's nutritional status and providing an easy feedback mechanism for tracking changes in diet or supplementation. We believe that nutrition diagnostics represents a particularly appealing opportunity over other PON applications for two reasons: (1) healthy ranges for many micronutrients are well defined which allows for an unbiased diagnosis, and (2) many deficiencies can be reversed through changes in diet or supplementation before they become severe. In this paper, we provide background on nutritional biomarkers used in nutrition diagnostics and review the emerging technologies that exploit them at the point-of-need. PMID:27272753

  19. Study of Spatially Resolved Temperature Diagnostics for High Explosives

    SciTech Connect

    Lee, H

    2000-04-05

    The next generation of 2-D and 3-D weapon-simulation codes will require marked advances in the spatial and temporal resolution of the various diagnostics to verify the complex physics predicted from these calculations. This is particularly true for the complicated physics of high-explosive (HE) detonation and burn, of which a detailed understanding is crucial to nuclear weapons performance and integrity. The processes involved in the detonation of HEs occur very rapidly and lead to extremely high pressures (several GPa) and temperatures (several thousand Kelvin). A key diagnostic that has so far eluded experimentalists is a temperature diagnostic for burning HE. Temperature is a basic thermodynamic property that enables a fundamental understanding of important HE physics such as the chemical processes involved in the shock-to-detonation transition, and to assess the thermal part of the equation-of-state of the detonation products. Accurate, spatially localized temperature measurements with high temporal resolution are thus crucial, but are unfortunately lacking. Our work address this important problem.

  20. Pathogenesis and Diagnostic Approaches of Avian Infectious Bronchitis

    PubMed Central

    Bande, Faruku; Arshad, Siti Suri; Omar, Abdul Rahman; Bejo, Mohd Hair; Abubakar, Muhammad Salisu; Abba, Yusuf

    2016-01-01

    Infectious bronchitis (IB) is one of the major economically important poultry diseases distributed worldwide. It is caused by infectious bronchitis virus (IBV) and affects both galliform and nongalliform birds. Its economic impact includes decreased egg production and poor egg quality in layers, stunted growth, poor carcass weight, and mortality in broiler chickens. Although primarily affecting the respiratory tract, IBV demonstrates a wide range of tissues tropism, including the renal and reproductive systems. Thus, disease outcome may be influenced by the organ or tissue involved as well as pathotypes or strain of the infecting virus. Knowledge on the epidemiology of the prevalent IBV strains in a particular region is therefore important to guide control and preventions. Meanwhile previous diagnostic methods such as serology and virus isolations are less sensitive and time consuming, respectively; current methods, such as reverse transcription polymerase chain reaction (RT-PCR), Restriction Fragment Length Polymorphism (RFLP), and sequencing, offer highly sensitive, rapid, and accurate diagnostic results, thus enabling the genotyping of new viral strains within the shortest possible time. This review discusses aspects on pathogenesis and diagnostic methods for IBV infection. PMID:26955391

  1. Pathogenesis and Diagnostic Approaches of Avian Infectious Bronchitis.

    PubMed

    Bande, Faruku; Arshad, Siti Suri; Omar, Abdul Rahman; Bejo, Mohd Hair; Abubakar, Muhammad Salisu; Abba, Yusuf

    2016-01-01

    Infectious bronchitis (IB) is one of the major economically important poultry diseases distributed worldwide. It is caused by infectious bronchitis virus (IBV) and affects both galliform and nongalliform birds. Its economic impact includes decreased egg production and poor egg quality in layers, stunted growth, poor carcass weight, and mortality in broiler chickens. Although primarily affecting the respiratory tract, IBV demonstrates a wide range of tissues tropism, including the renal and reproductive systems. Thus, disease outcome may be influenced by the organ or tissue involved as well as pathotypes or strain of the infecting virus. Knowledge on the epidemiology of the prevalent IBV strains in a particular region is therefore important to guide control and preventions. Meanwhile previous diagnostic methods such as serology and virus isolations are less sensitive and time consuming, respectively; current methods, such as reverse transcription polymerase chain reaction (RT-PCR), Restriction Fragment Length Polymorphism (RFLP), and sequencing, offer highly sensitive, rapid, and accurate diagnostic results, thus enabling the genotyping of new viral strains within the shortest possible time. This review discusses aspects on pathogenesis and diagnostic methods for IBV infection. PMID:26955391

  2. Investigating rapid eye movement sleep without atonia in Parkinson's disease using the rapid eye movement sleep behavior disorder screening questionnaire.

    PubMed

    Bolitho, Samuel J; Naismith, Sharon L; Terpening, Zoe; Grunstein, Ron R; Melehan, Kerri; Yee, Brendon J; Coeytaux, Alessandra; Gilat, Moran; Lewis, Simon J G

    2014-05-01

    Rapid eye movement (REM) sleep behavior disorder (RBD) is frequently observed in patients with Parkinson's disease (PD). Accurate diagnosis is essential for managing this condition. Furthermore, the emergence of idiopathic RBD in later life can represent a premotor feature, heralding the development of PD. Reliable, accurate methods for identifying RBD may offer a window for early intervention. This study sought to identify whether the RBD screening questionnaire (RBDSQ) and three questionnaires focused on dream enactment were able to correctly identify patients with REM without atonia (RWA), the neurophysiological hallmark of RBD. Forty-six patients with PD underwent neurological and sleep assessment in addition to completing the RBDSQ, the RBD single question (RBD1Q), and the Mayo Sleep Questionnaire (MSQ). The REM atonia index was derived for all participants as an objective measure of RWA. Patients identified to be RBD positive on the RBDSQ did not show increased RWA on polysomnography (80% sensitivity and 55% specificity). However, patients positive for RBD on questionnaires specific to dream enactment correctly identified higher degrees of RWA and improved the diagnostic accuracy of these questionnaires. This study suggests that the RBDSQ does not accurately identify RWA, essential for diagnosing RBD in PD. Furthermore, the results suggest that self-report measures of RBD need to focus questions on dream enactment behavior to better identify RWA and RBD. Further studies are needed to develop accurate determination and quantification of RWA in RBD to improve management of patients with PD in the future. PMID:24619826

  3. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  4. Rapid Identification of Candida Species and Other Clinically Important Yeast Species by Flow Cytometry†

    PubMed Central

    Page, Brent T.; Kurtzman, Cletus P.

    2005-01-01

    Two rapid diagnostic assays, utilizing two different Luminex flow cytometry methods, were developed for identification of clinically important ascomycetous yeast species. Direct hybridization and allele-specific primer extension methods were both successful in establishing a DNA-based assay that can rapidly and accurately identify Candida albicans, Candida krusei, Candida parapsilosis, Candida glabrata, and Candida tropicalis as well as other clinical species. The direct hybridization assay was designed to identify a total of 19 ascomycetous yeast species, and the allele-specific primer extension assay was designed to identify a total of 34 species. Probes were validated against 438 strains representing 303 species. From culture to identification, the allele-specific primer extension method takes 8 h and the direct hybridization method takes less than 5 h to complete. These assays represent comprehensive, rapid tests that are well suited for the clinical laboratory. PMID:16145099

  5. Instrumentation and diagnostics

    SciTech Connect

    Nakaishi, C.V.; Bedick, R.C.

    1990-12-01

    This Technology Status Report describes research and accomplishments for the Instrumentation and Diagnostics (I D) Projects within the Advanced Research and Technology Development (AR TD) Program of the United States Department of Energy (DOE) Office of Fossil Energy (FE). Process understanding and control can be improved through the development of advanced instrumentation and diagnostics. The thrust of the I D Projects is to further develop existing measurement and control techniques for application to advanced coal-based technologies. Project highlights are: an inductively coupled plasma (ICP) instrument has been developed to analyze trace elements in gasification and combustion process streams. An in situ two-color Mie scattering technique with LSS can simultaneously measure the size, velocity, and elemental composition of coal particles during combustion. A high-temperature, fluorescence thermometry technique has accurately measured gas temperatures during field testing in combustion and gasification environments. Expert systems have been developed to improve the control of advanced coal-based processes. Capacitance flowmeters were developed to determine the mass flowrate, solid volume fraction, and particle velocities of coal slurries. 32 refs., 9 figs.

  6. Additive manufacture (3d printing) of plasma diagnostic components and assemblies for fusion experiments

    NASA Astrophysics Data System (ADS)

    Sieck, Paul; Woodruff, Simon; Stuber, James; Romero-Talamas, Carlos; Rivera, William; You, Setthivoine; Card, Alexander

    2015-11-01

    Additive manufacturing (or 3D printing) is now becoming sufficiently accurate with a large range of materials for use in printing sensors needed universally in fusion energy research. Decreasing production cost and significantly lowering design time of energy subsystems would realize significant cost reduction for standard diagnostics commonly obtained through research grants. There is now a well-established set of plasma diagnostics, but these expensive since they are often highly complex and require customization, sometimes pace the project. Additive manufacturing (3D printing) is developing rapidly, including open source designs. Basic components can be printed for (in some cases) less than 1/100th costs of conventional manufacturing. We have examined the impact that AM can have on plasma diagnostic cost by taking 15 separate diagnostics through an engineering design using Conventional Manufacturing (CM) techniques to determine costs of components and labor costs associated with getting the diagnostic to work as intended. With that information in hand, we set about optimizing the design to exploit the benefits of AM. Work performed under DOE Contract DE-SC0011858.

  7. Case Studies Illustrating Focal Alzheimer's, Fluent Aphasia, Late-Onset Memory Loss, and Rapid Dementia.

    PubMed

    Camsari, Gamze Balci; Murray, Melissa E; Graff-Radford, Neill R

    2016-08-01

    Many dementia subtypes have more shared signs and symptoms than defining ones. We review 8 cases with 4 overlapping syndromes and demonstrate how to distinguish the cases. These include focal cortical presentations of Alzheimer's disease (AD; posterior cortical atrophy and corticobasal syndrome [CBS]), fluent aphasia (semantic dementia and logopenic aphasia), late-onset slowly progressive dementia (hippocampal sclerosis and limbic predominant AD) and rapidly progressive dementia (Creutzfeldt-Jakob disease and limbic encephalitis). Recognizing the different syndromes can help the clinician to improve their diagnostic skills, leading to improved patient outcomes by early and accurate diagnosis, prompt treatment, and appropriate counseling and guidance. PMID:27445249

  8. A comparative study of the diagnostic methods for Group A streptococcal sore throat in two reference hospitals in Yaounde, Cameroon

    PubMed Central

    Gonsu, Hortense Kamga; Bomki, Cynthia Mbimenyuy; Djomou, François; Toukam, Michel; Ndze, Valantine Ngum; Lyonga, Emilia Enjema; Mbakop, Calixte Didier; Koulla-Shiro, Sinata

    2015-01-01

    Introduction Sore throat is a common complaint in general practice which is more frequent in children. The most frequent pathogenic bacteria associated with this infection is Streptococcus pyogenes. Rapid Antigen Diagnostic Test (RADT) facilitates the rapid identification and consequently prompt treatment of patients, prevents complications, and also reduces the risk of spread of Group A Streptococcus (GAS). The main objective of this study was to assess the diagnostic value of a rapid streptococcal antigen detection test in patients with sore throat. Methods A cross-sectional descriptive study was carried out from January to April 2011 on patients aged 3 to 72 years consulting for pharyngitis or sore throat at the paediatric and Ear, Nose and Throat units of the University Teaching Hospital Yaounde and the Central Hospital Yaounde. Two throat swabs were collected per patient. One was used for the rapid test and the other for standard bacteriological analysis. Results The prevalence of GAS in the study population was 22.5%. Out of the 71 samples collected, the RADT detected group A streptococcal antigens in 12 of 16 positive cultures giving a sensitivity of 75%. The specificity of the rapid test was 96%, with positive predictive value of 85.7%, and negative predictive value of 93% respectively. Conclusion Rapid test may have an additional value in the management of patients with high risk of having GAS infection. However, tests with a higher sensitivity are needed for accurate and reliable results for early diagnosis of patients with sore throat caused by GAS.

  9. Rig Diagnostic Tools

    NASA Technical Reports Server (NTRS)

    Soileau, Kerry M.; Baicy, John W.

    2008-01-01

    Rig Diagnostic Tools is a suite of applications designed to allow an operator to monitor the status and health of complex networked systems using a unique interface between Java applications and UNIX scripts. The suite consists of Java applications, C scripts, Vx- Works applications, UNIX utilities, C programs, and configuration files. The UNIX scripts retrieve data from the system and write them to a certain set of files. The Java side monitors these files and presents the data in user-friendly formats for operators to use in making troubleshooting decisions. This design allows for rapid prototyping and expansion of higher-level displays without affecting the basic data-gathering applications. The suite is designed to be extensible, with the ability to add new system components in building block fashion without affecting existing system applications. This allows for monitoring of complex systems for which unplanned shutdown time comes at a prohibitive cost.

  10. Diagnostic paediatric imaging

    SciTech Connect

    Hall, C.M.; Lingam, S.

    1986-01-01

    This book is a case study teaching manual presenting radiographs and examples of other imaging modalities from 100 paediatric patients. The material comes from the radiological teaching collection at the Hospital for Sick Children at Great Ormond Street in London and was compiled over a ten year period. With each case a short clinical history is given and a series of questions posed, similar to those encountered in postgraduate medical examinations. Sample answers with comments and more illustrations are presented on the following page. The last decade has seen a rapid expansion in the range and sophistication of diagnostic imaging modalities which are available to clinicians. Since it is impossible to achieve comprehensive coverage in a book of this size, the authors have selected examples of cases which illustrate the range of imaging modalities currently available and which may be encountered in both clinical practice and in examinations.

  11. Understanding the spectrum of haemophagocytic lymphohistiocytosis: update on diagnostic challenges and therapeutic options.

    PubMed

    Brisse, Ellen; Matthys, Patrick; Wouters, Carine H

    2016-07-01

    The cytokine storm syndrome 'haemophagocytic lymphohistiocytosis' (HLH) is an under-recognized hyperinflammatory disorder, causing high morbidity and mortality risk in children and adults. It can be subdivided into a primary, genetic form and a secondary, acquired form that complicates diverse infections, malignancies and autoimmune or autoinflammatory disorders. Both subtypes present with the same spectrum of non-specific symptoms, making accurate diagnosis and rapid treatment initiation challenging. In the last decade, increased awareness and international collaborative efforts fuelled a marked progress in diagnostic protocols and novel treatment strategies for HLH and new diagnostic guidelines are being tailored to specific secondary HLH subtypes. Therapy is gradually shifting its focus from overall immunosuppression towards targeting specific cytokines, cell types or signalling pathways underlying pathophysiology. Nevertheless, continued research efforts remain indispensable to customize therapy to individual patient needs. PMID:27292929

  12. Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains.

    PubMed

    Lewandowska, Dagmara W; Zagordi, Osvaldo; Zbinden, Andrea; Schuurmans, Macé M; Schreiber, Peter; Geissberger, Fabienne-Desirée; Huder, Jon B; Böni, Jürg; Benden, Christian; Mueller, Nicolas J; Trkola, Alexandra; Huber, Michael

    2015-10-01

    Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations. PMID:26231254

  13. Principles and applications of polymerase chain reaction in medical diagnostic fields: a review

    PubMed Central

    Valones, Marcela Agne Alves; Guimarães, Rafael Lima; Brandão, Lucas André Cavalcanti; de Souza, Paulo Roberto Eleutério; de Albuquerque Tavares Carvalho, Alessandra; Crovela, Sergio

    2009-01-01

    Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology, microbiology and dentistry. Among these methods, Polymerase Chain Reaction (PCR) has generated great benefits and allowed scientific advancements. PCR is an excellent technique for the rapid detection of pathogens, including those difficult to culture. Along with conventional PCR techniques, Real-Time PCR has emerged as a technological innovation and is playing an ever-increasing role in clinical diagnostics and research laboratories. Due to its capacity to generate both qualitative and quantitative results, Real-Time PCR is considered a fast and accurate platform. The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances. PMID:24031310

  14. Introduction to DNA-Based Genetic Diagnostics

    PubMed Central

    Glickman, Richard M.; Phillips, M. Ann; Glickman, Barry W.

    1988-01-01

    Molecular biology and recombinant DNA technology are beginning to have an effect on the medical health care field, particularly in the area of clinical genetics. Dramatic improvements in the prerequisite technology are in the process of being transferred from the research lab to routine clinical laboratories. The general practitioner, along with his genetic diagnostic colleagues, can soon expect to have access to accurate and reliable diagnostic assays for a wide variety of genetic disorders. This article introduces the basic technologies involved in genetic diagnostics and provides an indication both of their limitations and their future potential. PMID:21253094

  15. [An ultra-high-pressure liquid chromatography/linear ion trap-Orbitrap mass spectrometry method coupled with a diagnostic fragment ions-searching-based strategy for rapid identification and characterization of chemical components in Polygonum cuspidatum].

    PubMed

    Pan, Zhiran; Liang, Hailong; Liang, Chabhufi; Xu, Wen

    2015-01-01

    A method for qualitative analysis of constituents in Polygonum cuspidatum by ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MS) has been established. The methanol extract of Polygonum cuspidatumrn was separated on a Waters UPLC C18 column using acetonitrile-water (containing formic acid) eluting system and detected by LTQ-Orbitrap hybrid mass spectrometer in negative mode. The targeted components were further fragmented in LTQ and high accuracy data were acquired by Orbitrap MS. The summarized fragmentation pathways of typical reference components and a diagnostic fragment ions-searching-based strategy were used for detection and identification of the main phenolic components in Polygonum cuspidatum. Other clues such as nitrogen rule, even electron rule, degree of unsaturation rule and isotopic peak data were included for the structural elucidation as well. The whole analytical procedure was within 10 min and more than 30 components were identified or tentatively identified. This method is helpful for further phytochemical research and quality control on Polygonum cuspidatum and related preparations. PMID:25958663

  16. Diagnostic vitrectomy for infectious uveitis

    PubMed Central

    Jeroudi, Abdallah; Yeh, Steven

    2014-01-01

    The identification of an infectious or noninfectious uveitis syndrome is important to determine the range of therapeutic and prognostic implications of that disease entity. Diagnostic dilemmas arise with atypical history, atypical clinical presentations, inconclusive diagnostic workup, and persistent or worsened inflammation despite appropriate immunosuppression. More invasive intraocular testing is indicated in these situations particularly in infectious uveitis where a delay in treatment may result in worsening of the patient’s disease and a poor visual outcome. Laboratory analysis of vitreous fluid via diagnostic pars plana vitrectomy is an important technique in the diagnostic armamentarium, but the most important aspects of sample collection include rapid processing, close coordination with an ophthalmic pathology laboratory, and directed testing on this limited collected sample. Culture and staining has utility in bacterial, fungal, and nocardial infection. Polymerase chain reaction (PCR) analysis has shown promising results for bacterial endophthalmitis and infection with mycobacterium tuberculosis whereas PCR testing for viral retinitides and ocular toxoplasmosis has a more established role. Antibody testing is appropriate for toxoplasmosis and toxocariasis, and may be complementary to PCR for viral retinitis. Masquerade syndromes represent neoplastic conditions that clinically appear as infectious or inflammatory conditions and should be considered as part of the differential diagnosis. Diagnostic vitrectomy and chorioretinal biopsy are thus critical tools for the management of patients in whom an infectious etiology of uveitis is suspected. PMID:24613892

  17. Review of Two Decades of Cholera Diagnostics – How Far Have We Really Come?

    PubMed Central

    Dick, Michal H.; Guillerm, Martine; Moussy, Francis; Chaignat, Claire-Lise

    2012-01-01

    Background Cholera, an ancient scourge, continues to inflict high rates of mortality today. The rising incidence of epidemics in areas of poor sanitation and crowding highlight the need for better epidemic prevention and early response. Such interventions require the availability of rapid and accurate diagnostic techniques to trigger timely response and mitigate the scale of the outbreak. The current gold standard of bacterial culture is inadequate for rapid diagnosis, highlighting the overarching neglect of field diagnostic needs. This paper was written to support the World Health Organisation's Global Task Force on Cholera Control mandated Cholera and diarrhoeal disease laboratory Network (CholdiNet) in devising a protocol for the validation of Rapid Diagnostic Tests (RDTs) for Vibrio cholerae. The status of diagnostic tools for Vibrio cholerae is assessed, describing products that have been commercialised over the last two decades and discussing their peer-reviewed evaluation. Method Review of post-1990 peer-reviewed and grey literature on rapid diagnostic tests for Vibrio cholerae. Results Since 1990, twenty four diagnostic tests have been developed for the detection of Vibrio cholerae in human faecal samples. Fourteen of these have also been described in the literature, with rapid chromatographic-immuno assays (CIA) featuring strongly. Polymerase chain reaction (PCR) assays maintain the ability to detect the lowest amount of bacteria; however CIAs achieve both low detection thresholds and high sensitivity and specificity, making them possible candidates for use in field conditions. Field and laboratory studies were performed in a wide range of settings demonstrating variability in performance, however only a few of these studies were sufficiently stringent, highlighting five RDTs that showed promise in field conditions; COAT, IP cholera dipstick, SMART, IP dipstick and Medicos. In light of non-independent reporting, the authors would like to see these five

  18. Predict amine solution properties accurately

    SciTech Connect

    Cheng, S.; Meisen, A.; Chakma, A.

    1996-02-01

    Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

  19. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  20. Advantages of Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry as a Rapid Diagnostic Tool for Identification of Yeasts and Mycobacteria in the Clinical Microbiological Laboratory

    PubMed Central

    Chen, Jonathan H. K.; Yam, Wing-Cheong; Ngan, Antonio H. Y.; Fung, Ami M. Y.; Woo, Wai-Lan; Yan, Mei-Kum; Choi, Garnet K. Y.; Ho, Pak-Leung; Cheng, Vincent C. C.

    2013-01-01

    Yeast and mycobacteria can cause infections in immunocompromised patients and normal hosts. The rapid identification of these organisms can significantly improve patient care. There has been an increasing number of studies on using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for rapid yeast and mycobacterial identifications. However, studies on direct comparisons between the Bruker Biotyper and bioMérieux Vitek MS systems for the identification of yeast and mycobacteria have been limited. This study compared the performance of the two systems in their identification of 98 yeast and 102 mycobacteria isolates. Among the 98 yeast isolates, both systems generated species-level identifications in >70% of the specimens, of which Candida albicans was the most commonly cultured species. At a genus-level identification, the Biotyper system identified more isolates than the Vitek MS system for Candida (75/78 [96.2%]versus 68/78 [87.2%], respectively; P = 0.0426) and non-Candida yeasts (18/20 [90.0%]versus 7/20 [35.0%], respectively; P = 0.0008). For mycobacterial identification, the Biotyper system generated reliable identifications for 89 (87.3%) and 64 (62.8%) clinical isolates at the genus and species levels, respectively, from solid culture media, whereas the Vitek MS system did not generate any reliable identification. The MS method differentiated 12/21 clinical species, despite the fact that no differentiation between Mycobacterium abscessus and Mycobacterium chelonae was found by using 16S rRNA gene sequencing. In summary, the MALDI-TOF MS method provides short turnaround times and a standardized working protocol for the identification of yeast and mycobacteria. Our study demonstrates that MALDI-TOF MS is suitable as a first-line test for the identification of yeast and mycobacteria in clinical laboratories. PMID:24048537

  1. Rapid Prototyping

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Javelin, a Lone Peak Engineering Inc. Company has introduced the SteamRoller(TM) System as a commercial product. The system was designed by Javelin during a Phase II NASA funded small commercial product. The purpose of the invention was to allow automated-feed of flexible ceramic tapes to the Laminated Object Manufacturing rapid prototyping equipment. The ceramic material that Javelin was working with during the Phase II project is silicon nitride. This engineered ceramic material is of interest for space-based component.

  2. Accurate, meshless methods for magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Hopkins, Philip F.; Raives, Matthias J.

    2016-01-01

    Recently, we explored new meshless finite-volume Lagrangian methods for hydrodynamics: the `meshless finite mass' (MFM) and `meshless finite volume' (MFV) methods; these capture advantages of both smoothed particle hydrodynamics (SPH) and adaptive mesh refinement (AMR) schemes. We extend these to include ideal magnetohydrodynamics (MHD). The MHD equations are second-order consistent and conservative. We augment these with a divergence-cleaning scheme, which maintains nabla \\cdot B≈ 0. We implement these in the code GIZMO, together with state-of-the-art SPH MHD. We consider a large test suite, and show that on all problems the new methods are competitive with AMR using constrained transport (CT) to ensure nabla \\cdot B=0. They correctly capture the growth/structure of the magnetorotational instability, MHD turbulence, and launching of magnetic jets, in some cases converging more rapidly than state-of-the-art AMR. Compared to SPH, the MFM/MFV methods exhibit convergence at fixed neighbour number, sharp shock-capturing, and dramatically reduced noise, divergence errors, and diffusion. Still, `modern' SPH can handle most test problems, at the cost of larger kernels and `by hand' adjustment of artificial diffusion. Compared to non-moving meshes, the new methods exhibit enhanced `grid noise' but reduced advection errors and diffusion, easily include self-gravity, and feature velocity-independent errors and superior angular momentum conservation. They converge more slowly on some problems (smooth, slow-moving flows), but more rapidly on others (involving advection/rotation). In all cases, we show divergence control beyond the Powell 8-wave approach is necessary, or all methods can converge to unphysical answers even at high resolution.

  3. Advances in rapid prototyping

    SciTech Connect

    Atwood, C.L.; McCarty, G.D.; Pardo, B.T.; Bryce, E.A.

    1993-12-31

    Recent advances in stereolithography and selective laser sintering have had a significant impact on the overall quality of parts produced using these rapid prototyping processes. The development and implementation of 3D System`s QuickCast{trademark} resin and software for building investment casting patterns have proven to be major steps toward fabricating highly accurate patterns with very good surface finishes. Sandia uses patterns generated from rapid prototyping processes to reduce the cycle time and cost of fabricating prototype parts in support of a Sandia National Laboratories managed program called FASTCAST. As participants in the Beta test program for QuickCast{trademark} resin and software, they experienced a steep learning curve and were able to build accurate parts in a short period of time. It is now possible, using this technology, to produce highly accurate prototype parts as well as acceptable firs article and small lots size production parts. They use the Selective Laser Sintering (SLS) process to fabricate prototype wax patterns for investment casting. DTM Corporation recently introduced the use of their polycarbonate material for fabricating investment casting patterns. The polycarbonate material is processed significantly faster, with improved strength, dimensional stability, and without a support structure during the build process. Sandia is currently changing from investment casting wax to polycarbonate for the fabrication of investment casting patterns using the SLS process. This presentation will focus on the successes with these new materials from the standpoints of application, accuracy, surface finish, and post processing. Also presented will be examples of parts manufactured by these processes.