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Sample records for methods clinical specimens

  1. Method for thinning specimen

    Science.gov (United States)

    Follstaedt, David M.; Moran, Michael P.

    2005-03-15

    A method for thinning (such as in grinding and polishing) a material surface using an instrument means for moving an article with a discontinuous surface with an abrasive material dispersed between the material surface and the discontinuous surface where the discontinuous surface of the moving article provides an efficient means for maintaining contact of the abrasive with the material surface. When used to dimple specimens for microscopy analysis, a wheel with a surface that has been modified to produce a uniform or random discontinuous surface significantly improves the speed of the dimpling process without loss of quality of finish.

  2. Pretreatment of clinical specimens with sodium dodecyl (lauryl) sulfate is not suitable for the mycobacteria growth indicator tube cultivation method.

    OpenAIRE

    Pfyffer, G E; Welscher, H M; Kissling, P

    1997-01-01

    When using the Mycobacteria Growth Indicator Tube (MGIT), pretreatment of clinical specimens with N-acetyl-L-cysteine-NaOH is recommended by the manufacturer. Processing of clinical specimens (n = 1,000) with sodium dodecyl (lauryl) sulfate-NaOH resulted in both poor recovery and delayed mean time to detection of acid-fast bacilli. Values were comparable to those obtained on solid media.

  3. Evaluation and Comparison of Multiple Test Methods, Including Real-time PCR, for Legionella Detection in Clinical Specimens

    Science.gov (United States)

    Peci, Adriana; Winter, Anne-Luise; Gubbay, Jonathan B.

    2016-01-01

    Legionella is a Gram-negative bacterium that can cause Pontiac fever, a mild upper respiratory infection and Legionnaire’s disease, a more severe illness. We aimed to compare the performance of urine antigen, culture, and polymerase chain reaction (PCR) test methods and to determine if sputum is an acceptable alternative to the use of more invasive bronchoalveolar lavage (BAL). Data for this study included specimens tested for Legionella at Public Health Ontario Laboratories from 1st January, 2010 to 30th April, 2014, as part of routine clinical testing. We found sensitivity of urinary antigen test (UAT) compared to culture to be 87%, specificity 94.7%, positive predictive value (PPV) 63.8%, and negative predictive value (NPV) 98.5%. Sensitivity of UAT compared to PCR was 74.7%, specificity 98.3%, PPV 77.7%, and NPV 98.1%. Out of 146 patients who had a Legionella-positive result by PCR, only 66 (45.2%) also had a positive result by culture. Sensitivity for culture was the same using either sputum or BAL (13.6%); sensitivity for PCR was 10.3% for sputum and 12.8% for BAL. Both sputum and BAL yield similar results regardless testing methods (Fisher Exact p-values = 1.0, for each test). In summary, all test methods have inherent weaknesses in identifying Legionella; therefore, more than one testing method should be used. Obtaining a single specimen type from patients with pneumonia limits the ability to diagnose Legionella, particularly when urine is the specimen type submitted. Given ease of collection and similar sensitivity to BAL, clinicians are encouraged to submit sputum in addition to urine when BAL submission is not practical from patients being tested for Legionella. PMID:27630979

  4. Evaluation and comparison of multiple test methods, including real-time PCR, for Legionella detection in clinical specimens.

    Directory of Open Access Journals (Sweden)

    Adriana Peci

    2016-08-01

    Full Text Available Legionella is a gram-negative bacterium that can cause Pontiac fever, a mild upper respiratory infection and Legionnaire’s disease, a more severe illness. We aimed to compare the performance of urine antigen, culture and PCR test methods and to determine if sputum is an alternative to the use of more invasive bronchoalveolar lavage (BAL. Data for this study included specimens tested for Legionella at PHOL from January 1, 2010 to April 30, 2014, as part of routine clinical testing. We found sensitivity of UAT compared to culture to be 87%, specificity 94.7%, positive predictive value (PPV 63.8% and negative predictive value (NPV 98.5%. Sensitivity of UAT compared to PCR was 74.7%, specificity 98.3%, PPV 77.7% and NPV 98.1%. Of 146 patients who had a Legionella positive result by PCR, only 66(45.2% also had a positive result by culture. Sensitivity for culture was the same using either sputum or BAL (13.6%; sensitivity for PCR was 10.3% for sputum and 12.8% for BAL. Both sputum and BAL yield similar results despite testing methods (Fisher Exact p-values=1.0, for each test. In summary, all test methods have inherent weaknesses in identifying Legionella; thereforemore than one testing method should be used. Obtaining a single specimen type from patients with pneumonia limits the ability to diagnose Legionella, particularly when urine is the specimen type submitted. Given ease of collection, and similar sensitivity to BAL, clinicians are encouraged to submit sputum in addition to urine when BAL submission is not practical, from patients being tested for Legionella.

  5. [Identification of anaerobic gram-negative bacilli isolated from various clinical specimens and determination of antibiotic resistance profiles with E-test methods].

    Science.gov (United States)

    Demir, Cengiz; Keşli, Recep

    2018-01-01

    The aim of this study was to identify gram-negative anaerobic bacilli isolated from various clinical specimens that were obtained from patients with suspected anaerobic infections and to determine the antibiotic resistance profiles by using the antibiotic concentration gradient method. The study was performed in Afyon Kocatepe University Ahmet Necdet Sezer Research and Practice Hospital, Medical Microbiology Laboratory between 1 November 2014 and 30 October 2015. Two hundred and seventyeight clinical specimens accepted for anaerobic culture were enrolled in the study. All the samples were cultivated anaerobically by using Schaedler agar with 5% defibrinated sheep blood and Schaedler broth. The isolated anaerobic gram-negative bacilli were identified by using both the conventional methods and automated identification system (VITEK 2, bioMerieux, France). Antibiotic susceptibility tests were performed with antibiotic concentration gradient method (E-test, bioMerieux, France); against penicillin G, clindamycin, cefoxitin, metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem for each isolate. Of the 28 isolated anaerobic gram-negative bacilli; 14 were identified as Bacteroides fragilis group, 9 were Prevotella spp., and 5 were Fusobacterium spp. The highest resistance rate was found against penicillin (78.5%) and resistance rates against clindamycin and cefoxitin were found as 17.8% and 21.4%, respectively. No resistance was found against metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem. As a result, isolation and identification of anaerobic bacteria are difficult, time-consuming and more expensive when compared with the cost of aerobic culture. The rate of anaerobic bacteria isolation may be increased by obtaining the appropriate clinical specimen and appropriate transportation of these specimens. We believe that the data obtained from the study in our center may offer benefits for the follow up and treatment of infections

  6. Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

    Science.gov (United States)

    Page, Brent T; Shields, Christine E; Merz, William G; Kurtzman, Cletus P

    2006-09-01

    This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

  7. Clinical evaluation of a mobile digital specimen radiography system for intraoperative specimen verification.

    Science.gov (United States)

    Wang, Yingbing; Ebuoma, Lilian; Saksena, Mansi; Liu, Bob; Specht, Michelle; Rafferty, Elizabeth

    2014-08-01

    Use of mobile digital specimen radiography systems expedites intraoperative verification of excised breast specimens. The purpose of this study was to evaluate the performance of a such a system for verifying targets. A retrospective review included 100 consecutive pairs of breast specimen radiographs. Specimens were imaged in the operating room with a mobile digital specimen radiography system and then with a conventional digital mammography system in the radiology department. Two expert reviewers independently scored each image for image quality on a 3-point scale and confidence in target visualization on a 5-point scale. A target was considered confidently verified only if both reviewers declared the target to be confidently detected. The 100 specimens contained a total of 174 targets, including 85 clips (49%), 53 calcifications (30%), 35 masses (20%), and one architectural distortion (1%). Although a significantly higher percentage of mobile digital specimen radiographs were considered poor quality by at least one reviewer (25%) compared with conventional digital mammograms (1%), 169 targets (97%), were confidently verified with mobile specimen radiography; 172 targets (98%) were verified with conventional digital mammography. Three faint masses were not confidently verified with mobile specimen radiography, and conventional digital mammography was needed for confirmation. One faint mass and one architectural distortion were not confidently verified with either method. Mobile digital specimen radiography allows high diagnostic confidence for verification of target excision in breast specimens across target types, despite lower image quality. Substituting this modality for conventional digital mammography can eliminate delays associated with specimen transport, potentially decreasing surgical duration and increasing operating room throughput.

  8. Development of fatigue life evaluation method using small specimen

    International Nuclear Information System (INIS)

    Nogami, Shuhei; Nishimura, Arata; Wakai, Eichi; Tanigawa, Hiroyasu; Itoh, Takamoto; Hasegawa, Akira

    2013-01-01

    For developing the fatigue life evaluation method using small specimen, the effect of specimen size and shape on the fatigue life of the reduced activation ferritic/martensitic steels (F82H-IEA, F82H-BA07 and JLF-1) was investigated by the fatigue test at room temperature in air using round-bar and hourglass specimens with various specimen sizes (test section diameter: 0.85–10 mm). The round-bar specimen showed no specimen size and no specimen shape effects on the fatigue life, whereas the hourglass specimen showed no specimen size effect and obvious specimen shape effect on it. The shorter fatigue life of the hourglass specimen observed under low strain ranges could be attributed to the shorter micro-crack initiation life induced by the stress concentration dependent on the specimen shape. On the basis of this study, the small round-bar specimen was an acceptable candidate for evaluating the fatigue life using small specimen

  9. Sample handling of clinical specimens for ultratrace element analysis

    International Nuclear Information System (INIS)

    Cornelis, R.

    1987-01-01

    Some simple logistics to an improved sample handling of clinical specimens are presented. This comprises clean room conditions, clean laboratory ware, ultra-pure reagents and good analytical practice. Sample handling procedures for blood, urine, soft tissues and pharmaceuticals are briefly discussed. (author) 26 refs

  10. [Evaluation of four methods for detecting methicillin-resistant Staphylococcus aureus isolates from clinical specimens at a regional hospital in Mexico].

    Science.gov (United States)

    Acosta-Pérez, Gabriel; Rodríguez-Ábrego, Gabriela; Longoria-Revilla, Ernesto; Castro-Mussot, María Eugenia

    2012-01-01

    To estimate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in clinical isolates and to compare different methods for detection of MRSA in a lab with limited available personnel and resources. 140 Staphylococcus aureus strains isolated from patients in several departments were assayed for β-lactamase production, MIC-Vitek 2 oxacillin, ChromID MRSA, disk diffusion in agar for cefoxitin 30 μg and PBP2a detection. The results of conventional tests were compared with the "gold standard" PCR test for mecA gene. Cohen´s kappa index was also calculated in order to evaluate the intra assay agreement between the used methods. The found prevalence was 90.7%. Sensitivity and specificity were: disk diffusion for cefoxitin 97 and 92% respectively, MIC Vitek 2-XL 97 and 69%, ChromoID MRSA 97 and 85%, and PBP2a detection 98 and 100%. All methods are very good for detecting MRSA, choosing a method to use will depend on each laboratory infrastructure.

  11. Fusidic acid resistance among staphylococci strains isolated from clinical specimens

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    Özcan Deveci

    2012-03-01

    Full Text Available Objectives: The aim of this study was to investigate in vitrosusceptibility of fusidic acid to clinic isolates of staphylococci.Materials and methods: The forty-one coagulase negativestaphylococci (CNS and 18 Staphylococcus aureusstrains isolated from various clinical specimens were includedin this study. Staphylococci isolates were identifiedby conventional methods such as colony morphologyonto medium, gram staining, catalase and coagulasetests. According to “Clinical and Laboratory Standards Institute(CLSI” criteria, antimicrobial susceptibility testingof isolates was performed by Kirby-Bauer’s disk diffusionmethod.Results: The seventy-two percent of the isolated S.aureuswere defined as methicillin sensitive-S.aureus (MSSA,28% of the isolated S.aureus were defined as methicillinresistant-S.aureus (MRSA. The difference among fusidicacid susceptibility rates of MSSA and MRSA strains wasnot statistically significant (p=0.305. The twenty-nine percentof the isolated CNS were defined as methicillin sensitive-CNS (MS-CNS, 71% of the isolated CNS were definedas methicillin resistant-CNS (MR-CNS. There wasno statistically significant difference between MS-CNSand MR-CNS strains for fusidic acid susceptibility rates(p=0.490. But the difference among fusidic acid susceptibilityrates of CNS and S.aureus strains was statisticallysignificant (p<0.001. CNS strains were found more resistancethan S.aureus strains for fusidic acid.Conclusion: In this study, the resistance rates weredetected to increase for fusidic acid along with methicillinresistance. Among CNS isolates, fusidic acid resistancerates were significantly more elevated than that forS.aureus. Fusidic acid remains as an alternative in thetreatment of infections due to staphylococci.

  12. Centrifuge-operated specimen staining method and apparatus

    Science.gov (United States)

    Clarke, Mark S. F. (Inventor); Feeback, Daniel L. (Inventor)

    1999-01-01

    A method of staining preselected, mounted specimens of either biological or nonbiological material enclosed within a staining chamber where the liquid staining reagents are applied and removed from the staining chamber using hypergravity as the propelling force. In the preferred embodiment, a spacecraft-operated centrifuge and method of diagnosing biological specimens while in orbit, characterized by hermetically sealing a shell assembly. The assembly contains slide stain apparatus with computer control therefor, the operative effect of which is to overcome microgravity, for example on board an International Space Station.

  13. Method of 10B determination in biological specimens

    International Nuclear Information System (INIS)

    Nikitina, R.G.; Frolova, E.I.

    1981-01-01

    The paper is concerned with the methods of 10 B determination in biological specimens (blood, skin and tissues of rats). On the basis of investigations conducted there have been proposed films based on cellulose triacetate with optimal characteristics in terms of their possible utilization as solid detectors to record α-particles and recoil nuclei. The conditions of film staining are also discussed

  14. Vacuum sealing and cooling as methods to preserve surgical specimens

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Engvad, Birte; Nielsen, Ole

    2011-01-01

    Recently, vacuum-based preservation of surgical specimens has been proposed as a safe alternative to formalin fixation at the surgical theater. The method seems feasible from a practical point of view, but no systematic study has examined the effect of vacuum sealing alone with respect to tissue...

  15. Comparison of fastsure tb dna and mgit 960 for the detection of mycobacterium tuberculosis complex in clinical specimens

    International Nuclear Information System (INIS)

    Hussain, A.; Mirza, I.A.; Abbasi, S.A.; Ali, S.; Zia, F.; Ahmed, Z.

    2013-01-01

    Objective: To compare the efficacy of Fastsure TB DNA with fully automated MGIT 960 method for detection of Mycobacterium tuberculosis complex (MTB) in clinical specimens. Study Design: Comparative cross sectional study. Methodology: After decontamination procedure, the clinical specimens were subjected to DNA extraction and amplification. Extracted DNA was separated in a separate tube provided with fastsure TB DNA kit and was then inserted into the cartridge provided and results were observed within 30 minutes. For Processing in MGIT 960, OADC and PANTA were added to the clinical specimens after decontamination and then the tubes were processed in MGIT 960. Results: A total of 80 specimens were tested by both MGIT 960 and fastsure TB DNA. On MGIT 960 system, 57 specimens showed growth of MTB while 23 were negative. On Fastsure TB DNA, 47 Specimens were tested as positive and 33 specimens showed negative result. Sensitivity and specificity of Fastsure TB DNA method was calculated to be 82.45 % and 100 % respectively, while positive and negative predictive values were 100 % and 69.69 % respectively. Conclusion: Fast sure TB DNA is a rapid and accurate method for the detection of Mycobacterium tuberculosis complex (MTB) from clinical specimens. (author)

  16. Signal processing methods for in-situ creep specimen monitoring

    Science.gov (United States)

    Guers, Manton J.; Tittmann, Bernhard R.

    2018-04-01

    Previous work investigated using guided waves for monitoring creep deformation during accelerated life testing. The basic objective was to relate observed changes in the time-of-flight to changes in the environmental temperature and specimen gage length. The work presented in this paper investigated several signal processing strategies for possible application in the in-situ monitoring system. Signal processing methods for both group velocity (wave-packet envelope) and phase velocity (peak tracking) time-of-flight were considered. Although the Analytic Envelope found via the Hilbert transform is commonly applied for group velocity measurements, erratic behavior in the indicated time-of-flight was observed when this technique was applied to the in-situ data. The peak tracking strategies tested had generally linear trends, and tracking local minima in the raw waveform ultimately showed the most consistent results.

  17. Species identification of Candida isolated from clinical specimens in a tertiary care hospital

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    lsmet Nigar

    2016-07-01

    Full Text Available Background: Candida species are responsible for various clinical manifestations from mucocutaneous overgrowth to blood stream infections especially in immunocompromized situations. Although C. albicans is the most prevalent species, high incidence of non-albicans Candida species with antifungal resistance are emerging which is posing a serious threat to the patients care.Objective: This study aimed to isolate and identify different species of Candida from different clinical specimens. Methods: A total of 100 different clinical specimens were studied of which 35 were oral swab, 28 were high vaginal swab, 15 were urine, 14 were nail, 04 were bronchoalveolar lavage and peritoneal fluid were 04. Among 100 clinical specimens, Candida isolates were identified in 64 specimens. Isolation of Candida species was done by primary culture in SDA. Subsequent identification of species were performed by germ tube test, subculture in chromo­genic agar medium and carbohydrate assimilation test with commonly used twelve sugars.Results: Out of 64 isolated Candida species, Candida albicans were 51.56% and the non-albicans Candida species were 48.44%. The most prevalent Candida species was C. albicans 33 (51.53% followed by C. tropicalis 17 (26.56%. C. glabrata 4 (6.25%, C. parapsilo­sis 4 (6.25%, C. krusei 3 (4.68% and C. guilliermondii 2 (3.2%. One of the isolated Candida species was unidentified.Conclusion: Though Candida albicans was found as the most common species, but non-albicans Candida species are appearing as emerging pathogens as well. Exposure to chemotherapy appeared to be the commonest predisposing factor for Candida infection followed by indwelling urinary catheter in situ for prolong period.

  18. "Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment.

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    John J Farrell

    Full Text Available PCR coupled with electrospray ionization mass spectrometry (ESI-MS is a diagnostic approach that has demonstrated the capacity to detect pathogenic organisms from culture negative clinical samples after antibiotic treatment has been initiated. [1] We describe the application of PCR/ESI-MS for detection of bacteria in original patient specimens that were obtained after administration of antibiotic treatment in an open investigation analysis.We prospectively identified cases of suspected bacterial infection in which cultures were not obtained until after the initiation of antimicrobial treatment. PCR/ESI-MS was performed on 76 clinical specimens that were submitted for conventional microbiology testing from 47 patients receiving antimicrobial treatment.In our series, 72% (55/76 of cultures obtained following initiation of antimicrobial treatment were non-diagnostic (45 negative cultures; and 10 respiratory specimens with normal flora (5, yeast (4, or coagulase-negative staphylococcus (1. PCR/ESR-MS detected organisms in 83% (39/47 of cases and 76% (58/76 of the specimens. Bacterial pathogens were detected by PCR/ESI-MS in 60% (27/45 of the specimens in which cultures were negative. Notably, in two cases of relapse of prosthetic knee infections in patients on chronic suppressive antibiotics, the previous organism was not recovered in tissue cultures taken during extraction of the infected knee prostheses, but was detected by PCR/ESI-MS.Molecular methods that rely on nucleic acid amplification may offer a unique advantage in the detection of pathogens collected after initiation of antimicrobial treatment and may provide an opportunity to target antimicrobial therapy and "salvage" both individual treatment regimens as well as, in select cases, institutional antimicrobial stewardship efforts.

  19. 42 CFR 414.510 - Laboratory date of service for clinical laboratory and pathology specimens.

    Science.gov (United States)

    2010-10-01

    ... and pathology specimens. 414.510 Section 414.510 Public Health CENTERS FOR MEDICARE & MEDICAID... date of service for clinical laboratory and pathology specimens. The date of service for either a clinical laboratory test or the technical component of physician pathology service is as follows: (a...

  20. Synchrotron radiation microprobe quantitative analysis method for biomedical specimens

    International Nuclear Information System (INIS)

    Xu Qing; Shao Hanru

    1994-01-01

    Relative changes of trace elemental content in biomedical specimens are obtained easily by means of synchrotron radiation X-ray fluorescence microprobe analysis (SXRFM). However, the accurate assignment of concentration on a g/g basis is difficult. Because it is necessary to know both the trace elemental content and the specimen mass in the irradiated volume simultaneously. the specimen mass is a function of the spatial position and can not be weighed. It is possible to measure the specimen mass indirectly by measuring the intensity of Compton scattered peak for normal XRF analysis using a X-ray tube with Mo anode, if the matrix was consisted of light elements and the specimen was a thin sample. The Compton peak is not presented in fluorescence spectrum for white light SXRFM analysis. The continuous background in the spectrum was resulted from the Compton scattering with a linear polarization X-ray source. Biomedical specimens for SXRFM analysis, for example biological section and human hair, are always a thin sample for high energy X-ray, and they consist of H,C,N and O etc. light elements, which implies a linear relationship between the specimen mass and the Compton scattering background in the high energy region of spectrum. By this way , it is possible to carry out measurement of concentration for SXRFM analysis

  1. Patient safety in the clinical laboratory: a longitudinal analysis of specimen identification errors.

    Science.gov (United States)

    Wagar, Elizabeth A; Tamashiro, Lorraine; Yasin, Bushra; Hilborne, Lee; Bruckner, David A

    2006-11-01

    Patient safety is an increasingly visible and important mission for clinical laboratories. Attention to improving processes related to patient identification and specimen labeling is being paid by accreditation and regulatory organizations because errors in these areas that jeopardize patient safety are common and avoidable through improvement in the total testing process. To assess patient identification and specimen labeling improvement after multiple implementation projects using longitudinal statistical tools. Specimen errors were categorized by a multidisciplinary health care team. Patient identification errors were grouped into 3 categories: (1) specimen/requisition mismatch, (2) unlabeled specimens, and (3) mislabeled specimens. Specimens with these types of identification errors were compared preimplementation and postimplementation for 3 patient safety projects: (1) reorganization of phlebotomy (4 months); (2) introduction of an electronic event reporting system (10 months); and (3) activation of an automated processing system (14 months) for a 24-month period, using trend analysis and Student t test statistics. Of 16,632 total specimen errors, mislabeled specimens, requisition mismatches, and unlabeled specimens represented 1.0%, 6.3%, and 4.6% of errors, respectively. Student t test showed a significant decrease in the most serious error, mislabeled specimens (P patient safety projects. Trend analysis demonstrated decreases in all 3 error types for 26 months. Applying performance-improvement strategies that focus longitudinally on specimen labeling errors can significantly reduce errors, therefore improving patient safety. This is an important area in which laboratory professionals, working in interdisciplinary teams, can improve safety and outcomes of care.

  2. Prevalence of Nontuberculous Mycobacteria (NTM in Iranian Clinical Specimens: Systematic Review and Meta-Analysis

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    Azad Khaledi

    2017-01-01

    Full Text Available Background:    Although, nontuberculous mycobacteria can cause disease in different organisms, they usually are not reported in most countries because scientists in general consider them as non-pathogens. But, increasing nontuberculous mycobacteria diseases occurrence has changed this belief. Nevertheless, there is no meta-analysis review about prevalence of nontuberculous mycobacteria in Iran. Methods:   Any data about prevalence of nontuberculous mycobacteria in clinical specimens in Iran were retrieved by searching data bases such as Pub Med, MEDLINE, and Iranian data bases. Then the meta-analysis was performed by comprehensive meta-analysis software (CMA. Results:    The meta-analysis showed that the prevalence of nontuberculous mycobacteria in the clinical specimens in Iran was 1.3%. In the studies that had sample size less than 300, and in studies conducted after 2004, the prevalence was higher. Also, the prevalence of nontuberculous mycobacteria was higher in the West of Iran. In this study, the most prevalent rapid-growing mycobacterium was Mycobacterium. fortuitum and  most prevalent slow-growing mycobacterium was M. simiae with the prevalence 44.2% and 14.3%, respectively.Conclusion:   M. simiae is the most prevalent nontuberculous mycobacteria in the clinical specimens in Iran. As this species of nontuberculous mycobacteria has similar clinical and radiological manifestations with tuberculosis, it is often treated as tuberculosis. Unfortunately, M. simiae is resistant against first-line anti-TB drugs resulting in treatment failure after using routine anti-TB medication. Therefore, there is an urgent need for application of new diagnostic strategy for identification of nontuberculous mycobacteria species.

  3. Susceptibility pattern of extended spectrum beta-lactamase producing isolates in various clinical specimens

    International Nuclear Information System (INIS)

    Roshan, M.

    2011-01-01

    Objective: To determine the susceptibility pattern of extended spectrum beta-lactamase (ESBL) producing Gram negative isolates from various clinical specimens. Study Design: Descriptive study. Place and Duration of Study: Microbiology Department, Armed Forces Institute of Pathology, Rawalpindi, from January 2008 to January 2009. Methodology: A total of 308 ESBL producing isolates from various clinical specimens sent to AFIP for culture and sensitivity were identified using standard microbiological techniques and tested for antimicrobial susceptibility. At the same time screening for ESBL production was also done. ESBL production was confirmed by combination disc synergy method. The susceptibility pattern of isolates was then recorded in frequency percentages. Results: Out of the 308 ESBL producing isolates more than 99% were susceptible to carbapenems, 84% to tazobactam/ piperacillin, 81% to sulbactam/cefoperazone, 12% to fluoroquinolones, 13% to cotrimoxazole, 59% to amikacin and 18% to gentamicin. Among the urinary isolates 49% were susceptible to Nitrofurontoin and only 5% to Pipemidic acid. Conclusion: Antibiotic choices in case of ESBL producing isolates are limited and at present only carbapenems can be regarded as treatment of choice. As empirical agents, beta-lactam/beta lactamase inhibitor combinations should be used cautiously for serious infections. Fluoroquinolones showed very poor efficacy. Amikacin can be used alternatively in such cases. Nitrofurantoin is still a good oral agent for treating UTI. (author)

  4. Speciation and Biofilm Production of Coagulase Negative Staphylococcal Isolates from Clinically Significant Specimens and their Antibiogram

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    S. S. Vijayasri Badampudi

    2016-04-01

    Full Text Available Background: Coagulase Negative Staphylococci (CONS are increasingly recognized as significant nosocomial pathogens. Their ability of biofilm formation and multiple drug resistance are causing serious human infections. Aim and Objectives: To isolate, identify, speciate clinically significant CONS from various specimens, to study antibiotic resistance pattern and biofilm production. Material and Methods: Specimens were collected aseptically, processed and identified upto the species level by a simple scheme of tests urease, novobiocin resistance, mannose and mannitol fermentation, ornithine decarboxylase. Antibiotic sensitivity was done with special reference to methicillin resistance. Biofilm formation was detected by Congo Red Agar (CRA method and Tube Method (TM. Results: Study groupOf 100 isolates majority were pus (40, followed by urine (28, blood (16, CSF (5, body fluids (4 and catheter tips and implants (7. The most common species isolated was S. epidermidis (40% followed by S. haemolyticus (26%, S. saprophyticus (15%, S. schleiferi (13%, S. simulans (2%, S. cohnii (2% and S. warneri and S. capitis each 1%. Resistance to penicillin was 91% followed by ampicillin (79%, cotrimoxazole (67%. Methicillin resistance was 72%. Biofilm producers were 69% by CRAmethod and 33% by TM with majority species S. epidermidis (82.5%- CRA and 55%-TM. Biofilm production was significantly associated with MRCONS (p value 0.0036. Control group-Of 30 isolates were S. epidermidis 66.6% followed by S. haemolyticus (16.66%. Biofilm producers were 53.33% by CRA method and 26.65% by TM with majority species S. epidermidis (65%-CRA and 30%-TM.Methicillin resistance was 26.6%. Conclusion: Clinical significance of CONS is increasing day by day, so there is a need for accurate identification to species level and their antibiogram to avoid multidrug resistance. Biofilm producing CONS species pose a risk and CRA method for screening biofilm can be used in all conventional

  5. Fecal specimens preparation methods for PCR diagnosis of human taeniosis

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    Nunes Cáris Maroni

    2006-01-01

    Full Text Available Sample preparation and DNA extraction protocols for DNA amplification by PCR, which can be applied in human fecal samples for taeniasis diagnosis, are described. DNA extracted from fecal specimens with phenol/chloroform/isoamilic alcohol and DNAzol® reagent had to be first purified to generate fragments of 170 pb and 600 pb by HDP2-PCR. This purification step was not necessary with the use of QIAmp DNA stool mini kit®. Best DNA extraction results were achieved after eggs disruption with glass beads, either with phenol/chloroform/isoamilic alcohol, DNAzol® reagent or QIAmp DNA stool mini kit®.

  6. Methods and devices for small specimen testing at the Japan Atomic Energy Research Institute

    International Nuclear Information System (INIS)

    Jitsukawa, Shiro; Kizaki, Minoru; Umino, Akira; Shiba, Kiyoyuki; Hishinuma, Akimichi

    1993-01-01

    Devices for a punch test on annular notched specimens, small punch (SP) tests, and miniaturized tension tests in hot cells were developed. A micro-manipulator to handle small specimens and an electro-discharge machine (EDM) to extract miniaturized tension specimens and annular notched specimens from transmission electron microscopy (TEM) disks were also fabricated. These devices were designed and made for remote operation in hot cells. Preliminary tests to evaluate the applicability of test methods were carried out. Correlation between SP test results and tensile properties was not strong. Miniaturized tensile results were reasonably similar to the results with larger specimens. The ductile-brittle transition temperature (DBTT) by the punch test on annular notched specimens was higher than that obtained from the SP test. However, materials dependence of the DBTT was different from that measured by standard Charpy V-notch (CVN) tests. This may be due to a specimen size effect

  7. Acceptability and feasibility of repeated mucosal specimen collection in clinical trial participants in Kenya.

    Directory of Open Access Journals (Sweden)

    Gloria Omosa-Manyonyi

    Full Text Available Mucosal specimens are essential to evaluate compartmentalized immune responses to HIV vaccine candidates and other mucosally targeted investigational products. We studied the acceptability and feasibility of repeated mucosal sampling in East African clinical trial participants at low risk of HIV and other sexually transmitted infections.The Kenya AIDS Vaccine Initiative (KAVI enrolled participants into three Phase 1 trials of preventive HIV candidate vaccines in 2011-2012 at two clinical research centers in Nairobi. After informed consent to a mucosal sub-study, participants were asked to undergo collection of mucosal secretions (saliva, oral fluids, semen, cervico-vaginal and rectal, but could opt out of any collection at any visit. Specimens were collected at baseline and two additional time points. A tolerability questionnaire was administered at the final sub-study visit. Of 105 trial participants, 27 of 34 women (79% and 62 of 71 men (87% enrolled in the mucosal sub-study. Nearly all sub-study participants gave saliva and oral fluids at all visits. Semen was collected from about half the participating men (47-48% at all visits. Cervico-vaginal secretions were collected by Softcup from about two thirds of women (63% at baseline, increasing to 78% at the following visits, with similar numbers for cervical secretion collection by Merocel sponge; about half of women (52% gave cervico-vaginal samples at all visits. Rectal secretions were collected with Merocel sponge from about a quarter of both men and women (24% at all 3 visits, with 16% of men and 19% of women giving rectal samples at all visits.Repeated mucosal sampling in clinical trial participants in Kenya is feasible, with a good proportion of participants consenting to most sampling methods with the exception of rectal samples. Experienced staff members of both sexes and trained counselors with standardized messaging may improve acceptance of rectal sampling.

  8. Method for quantifying percentage wood failure in block-shear specimens by a laser scanning profilometer

    Science.gov (United States)

    C. T. Scott; R. Hernandez; C. Frihart; R. Gleisner; T. Tice

    2005-01-01

    A new method for quantifying percentage wood failure of an adhesively bonded block-shear specimen has been developed. This method incorporates a laser displacement gage with an automated two-axis positioning system that functions as a highly sensitive profilometer. The failed specimen is continuously scanned across its width to obtain a surface failure profile. The...

  9. Specimen holder for an electron microscope and device and method for mounting a specimen in an electron microscope

    NARCIS (Netherlands)

    Zandbergen, H.W.; Latenstein van Voorst, A.; Westra, C.; Hoveling, G.H.

    1996-01-01

    A specimen holder for an electron microscope, comprising a bar-shaped body provided adjacent one end with means for receiving a specimen, with means being present for screening the specimen from the environment at least temporarily in airtight and moisture-proof manner in a first position, which

  10. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    International Nuclear Information System (INIS)

    Sadi, Al Muktafi; Wang, Dong-Yu; Youngson, Bruce J; Miller, Naomi; Boerner, Scott; Done, Susan J; Leong, Wey L

    2011-01-01

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. We

  11. Detection of Enterovirus 71 gene from clinical specimens by reverse-transcription loop-mediated isothermal amplification

    OpenAIRE

    D Wang; X Wang; Y Geng; C An

    2014-01-01

    Purpose : The objective of this study was to develop a sensitive, specific and rapid approach to diagnose hand foot and mouth disease (HFMD) for an early treatment by using loop-mediated isothermal amplification (LAMP) technique. Materials and Methods : A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for detecting EV71 virus was developed, the specificity and sensitivity of RT-LAMP was tested, and the clinical specimens was assayed by the RT-LAMP comparing with conven...

  12. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

    Science.gov (United States)

    Nadeem, Sayyada Ghufrana; Hakim, Shazia Tabassum; Kazmi, Shahana Urooj

    2010-01-01

    Introduction Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. Material and methods A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX. Results The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. Conclusion The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients. PMID:21483597

  13. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

    Directory of Open Access Journals (Sweden)

    Sayyada Ghufrana Nadeem

    2010-02-01

    Full Text Available Introduction: Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. Material and methods: A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX. Results: The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. Conclusion: The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.

  14. Optimization of tensile method and specimen geometry in modified ring tensile test

    International Nuclear Information System (INIS)

    Kitano, Koji; Fuketa, Toyoshi; Sasajima, Hideo; Uetsuka, Hiroshi

    2001-03-01

    Several techniques in ring tensile test are proposed in order to evaluate mechanical properties of cladding under hoop loading condition caused by pellet/cladding mechanical interaction (PCMI). In the modified techniques, variety of tensile methods and specimen geometry are being proposed in order to limit deformation within the gauge section. However, the tensile method and the specimen geometry were not determined in the modified techniques. In the present study, we have investigated the tensile method and the specimen geometry through finite element method (FEM) analysis of specimen deformation and tensile test on specimens with various gauge section geometries. In using two-piece tensile tooling, the mechanical properties under hoop loading condition can be correctly evaluated when deformation part (gauge section) is put on the top of a half-mandrel, and friction between the specimen and the half-mandrel is reduced with Teflon tape. In addition, we have shown the optimum specimen geometry for PWR 17 by 17 type cladding. (author)

  15. Recommendations for Collection and Handling of Specimens From Group Breast Cancer Clinical Trials

    Science.gov (United States)

    Leyland-Jones, Brian R.; Ambrosone, Christine B.; Bartlett, John; Ellis, Matthew J.C.; Enos, Rebecca A.; Raji, Adekunle; Pins, Michael R.; Zujewski, Jo Anne; Hewitt, Stephen M.; Forbes, John F.; Abramovitz, Mark; Braga, Sofia; Cardoso, Fatima; Harbeck, Nadia; Denkert, Carsten; Jewell, Scott D.

    2008-01-01

    Recommendations for specimen collection and handling have been developed for adoption across breast cancer clinical trials conducted by the Breast International Group (BIG)-sponsored Groups and the National Cancer Institute (NCI)-sponsored North American Cooperative Groups. These recommendations are meant to promote identifiable standards for specimen collection and handling within and across breast cancer trials, such that the variability in collection/handling practices that currently exists is minimized and specimen condition and quality are enhanced, thereby maximizing results from specimen-based diagnostic testing and research. Three working groups were formed from the Cooperative Group Banking Committee, BIG groups, and North American breast cancer cooperative groups to identify standards for collection and handling of (1) formalin-fixed, paraffin-embedded (FFPE) tissue; (2) blood and its components; and (3) fresh/frozen tissue from breast cancer trials. The working groups collected standard operating procedures from multiple group specimen banks, administered a survey on banking practices to those banks, and engaged in a series of discussions from 2005 to 2007. Their contributions were synthesized into this document, which focuses primarily on collection and handling of specimens to the point of shipment to the central bank, although also offers some guidance to central banks. Major recommendations include submission of an FFPE block, whole blood, and serial serum or plasma from breast cancer clinical trials, and use of one fixative and buffer type (10% neutral phosphate-buffered formalin, pH 7) for FFPE tissue across trials. Recommendations for proper handling and shipping were developed for blood, serum, plasma, FFPE, and fresh/frozen tissue. PMID:18955459

  16. A simple method for the prevention of endometrial autolysis in hysterectomy specimens

    OpenAIRE

    Houghton, J P; Roddy, S; Carroll, S; McCluggage, W G

    2004-01-01

    Aims: Uteri are among the most common surgical pathology specimens. Assessment of the endometrium is often difficult because of pronounced tissue autolysis. This study describes a simple method to prevent endometrial autolysis and aid in interpretation of the endometrium.

  17. Method and Apparatus for Measuring Thermal Conductivity of Small, Highly Insulating Specimens

    Science.gov (United States)

    Miller, Robert A (Inventor); Kuczmarski, Maria A (Inventor)

    2013-01-01

    A method and apparatus for the measurement of thermal conductivity combines the following capabilities: 1) measurements of very small specimens; 2) measurements of specimens with thermal conductivity on the same order of that as air; and, 3) the ability to use air as a reference material. Care is taken to ensure that the heat flow through the test specimen is essentially one-dimensional. No attempt is made to use heated guards to minimize the flow of heat from the hot plate to the surroundings. Results indicate that since large correction factors must be applied to account for guard imperfections when specimen dimensions are small, simply measuring and correcting for heat from the heater disc that does not flow into the specimen is preferable.

  18. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings.

    Science.gov (United States)

    Nadeem, Sayyada Ghufrana; Hakim, Shazia Tabassum; Kazmi, Shahana Urooj

    2010-02-09

    Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal-tween 80 agar and biochemical methods by using API 20 C AUX. The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.

  19. Clinical value of IS6110-based loop-mediated isothermal amplification for detection of Mycobacterium tuberculosis complex in respiratory specimens.

    Science.gov (United States)

    Aryan, Ehsan; Makvandi, Manoochehr; Farajzadeh, Ahmad; Huygen, Kris; Alvandi, Amir-Hooshang; Gouya, Mohammad-Mehdi; Sadrizadeh, Ali; Romano, Marta

    2013-06-01

    A fundamental to global tuberculosis (TB) control is timely and accurate diagnosis of infectious cases of the disease. Among various methods, techniques based on nucleic acid amplification are the ones with promising prospects. The present study evaluates the diagnostic value of the recently developed IS6110-based loop-mediated isothermal amplification (LAMP) for detection of Mycobacterium tuberculosis complex (MTBC) in sputum specimens. In this cross-sectional study (2008-2009), IS6110-LAMP was evaluated on 101 sputum specimens from 93 highly suspected TB patients and compared to Amplicor MTB test and in-house IS6110-PCR and -nested PCR assays. Culture results or clinical recovery following anti-TB therapy was considered as a reference to prove the TB cases. The overall sensitivity of IS6110-LAMP, Amplicor, nPCR, and PCR were respectively 89.6% (69/77 specimens; 95% confidence interval [CI], 80.5-95.4%), 76.6% (59/77 specimens; CI, 65.6-85.5%), 79.2% (61/77 specimens; CI, 68.5-87.6%) and 59.7% (46/77 specimens; CI, 47.9-70.8%). The specificity and positive predictive value (PPV) were 100% for all the tests, and the negative predictive value (NPV) of IS6110-LAMP, Amplicor, nPCR, and PCR were respectively 75%, 57.1%, 60%, and 43.6%. There was an excellent overall agreement between LAMP and nPCR (k 0.828), and between LAMP and Amplicor (k 0.746), in addition to a better tolerance of IS6110-LAMP to inhibitors present in clinical specimens. The better diagnostic performance of IS6110-LAMP compared to Amplicor (p = 0.009), nPCR (p = 0.013) and PCR (p < 0.0001) besides its rapidity, simplicity, and cost-effectiveness makes it a valuable method for the detection of MTBC in clinical samples, particularly in resource-limited settings. Copyright © 2013 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  20. Comparison of Three Different Methods for Pile Integrity Testing on a Cylindrical Homogeneous Polyamide Specimen

    Science.gov (United States)

    Lugovtsova, Y. D.; Soldatov, A. I.

    2016-01-01

    Three different methods for pile integrity testing are proposed to compare on a cylindrical homogeneous polyamide specimen. The methods are low strain pile integrity testing, multichannel pile integrity testing and testing with a shaker system. Since the low strain pile integrity testing is well-established and standardized method, the results from it are used as a reference for other two methods.

  1. Correlation of clinical data with fallopian tube specimen immune cells and tissue culture capacity.

    Science.gov (United States)

    Ramraj, Satish Kumar; Smith, Katie M; Janakiram, Naveena B; Toal, Coralee; Raman, Ankita; Benbrook, Doris Mangiaracina

    2018-06-01

    Human fallopian tube fimbria secretory epithelial cells (hFTSECs) are considered an origin of ovarian cancer and methods for their culture from fallopian tube specimens have been reported. Our objective was to determine whether characteristics of the donors or surgeries were associated with the capacities of fimbria specimens to generate hFTSEC cultures or their immune profiles. There were no surgical complications attributable to fallopian tube removal. Attempts to establish primary hFTSEC cultures were successful in 37 of 55 specimens (67%). Success rates did not differ significantly between specimens grouped by patient or surgery characteristics. Established cultures could be revived after cryopreservation and none became contaminated with microorganisms. Two cultures evaluated for long term growth senesced between passages 10 and 15. M1 macrophages were the predominant cell type, while all other immune cells were present at much lower percentages. IL-10 and TGF-β exhibited opposing trends with M1 and M2 macrophages. Plasma IL-10 levels exhibited significant positive correlation with patient age. In conclusion, fallopian tube fimbria specimens exhibit a pro-inflammatory phenotype and can be used to provide a source of hFTSECs that can be cultured for a limited time regardless of the donor patient age or race, or the type of surgery performed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Development of Piezoelectric DNA-Based Biosensor for Direct Detection of Mycobacterium Tuberculosis in Clinical Specimens

    Directory of Open Access Journals (Sweden)

    Thongchai KAEWPHINIT

    2010-02-01

    Full Text Available This study was focused on establishment of piezoelectric biosensor for direct detection of Mycobacterium tuberculosis (MTB in clinical specimens. The quartz crystal immobilized via 3-mercaptopropionic acid (MPA/avidin/DNA biotinylated probe on gold surface and hybridization of the DNA target to DNA biotinylated probe. The optimal concentration of MPA, avidin and 5’-biotinylated DNA probe for immobilization of specific DNA probe on gold surface were 15 mM, 0.1 mg/ml and 1.5 μM, respectively. The detection of genomic DNA digestion in the range from 0.5 to 30 μg/ml. The fabricated biosensor was evaluated through an examination of 200 samples. No cross hybridization were observed against M. avium complex (MAC and other microorganism. This target DNA preparation without amplification will reduce time consuming, costs, and the tedious step of amplification. This study can be extended to develop the new method which is high sensitivity, specificity, cheap, easy to use, and rapid for detection of MTB in many fields.

  3. Practices for Identifying and Rejecting Hemolyzed Specimens Are Highly Variable in Clinical Laboratories.

    Science.gov (United States)

    Howanitz, Peter J; Lehman, Christopher M; Jones, Bruce A; Meier, Frederick A; Horowitz, Gary L

    2015-08-01

    Hemolysis is an important clinical laboratory quality attribute that influences result reliability. To determine hemolysis identification and rejection practices occurring in clinical laboratories. We used the College of American Pathologists Survey program to distribute a Q-Probes-type questionnaire about hemolysis practices to Chemistry Survey participants. Of 3495 participants sent the questionnaire, 846 (24%) responded. In 71% of 772 laboratories, the hemolysis rate was less than 3.0%, whereas in 5%, it was 6.0% or greater. A visual scale, an instrument scale, and combination of visual and instrument scales were used to identify hemolysis in 48%, 11%, and 41% of laboratories, respectively. A picture of the hemolysis level was used as an aid to technologists' visual interpretation of hemolysis levels in 40% of laboratories. In 7.0% of laboratories, all hemolyzed specimens were rejected; in 4% of laboratories, no hemolyzed specimens were rejected; and in 88% of laboratories, some specimens were rejected depending on hemolysis levels. Participants used 69 different terms to describe hemolysis scales, with 21 terms used in more than 10 laboratories. Slight and moderate were the terms used most commonly. Of 16 different cutoffs used to reject hemolyzed specimens, moderate was the most common, occurring in 30% of laboratories. For whole blood electrolyte measurements performed in 86 laboratories, 57% did not evaluate the presence of hemolysis, but for those that did, the most common practice in 21 laboratories (24%) was centrifuging and visually determining the presence of hemolysis in all specimens. Hemolysis practices vary widely. Standard assessment and consistent reporting are the first steps in reducing interlaboratory variability among results.

  4. Comparison of five methods for extraction of Legionella pneumophila from respiratory specimens.

    Science.gov (United States)

    Wilson, Deborah; Yen-Lieberman, Belinda; Reischl, Udo; Warshawsky, Ilka; Procop, Gary W

    2004-12-01

    The efficiencies of five commercially available nucleic acid extraction methods were evaluated for the recovery of a standardized inoculum of Legionella pneumophila in respiratory specimens (sputum and bronchoalveolar lavage [BAL] specimens). The concentrations of Legionella DNA recovered from sputa with the automated MagNA Pure (526,200 CFU/ml) and NucliSens (171,800 CFU/ml) extractors were greater than those recovered with the manual methods (i.e., Roche High Pure kit [133,900 CFU/ml], QIAamp DNA Mini kit [46,380 CFU/ml], and ViralXpress kit [13,635 CFU/ml]). The rank order was the same for extracts from BAL specimens, except that for this specimen type the QIAamp DNA Mini kit recovered more than the Roche High Pure kit.

  5. Development of reconstitution method for surveillance specimens using surface activated joining

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Terumi; Kaihara, Shoichiro; Yoshida, Kazuo; Sato, Akira [Ishikawajima-Harima Heavy Industries Co. Ltd., Tokyo (Japan); Onizawa, Kunio; Nishiyama, Yutaka; Fukaya, Kiyoshi; Suzuki, Masahide

    1996-03-01

    Evaluation of embrittlement of reactor vessel steel due to irradiation requires surveillance tests. However, many surveillance specimens are necessary for nuclear plants life extension. Therefore, a specimen reconstitution technique has become important to provide the many specimens for continued surveillance. A surface activated joining (SAJ) method has been developed to join various materials together at low temperatures with little deformation, and is useful to bond irradiated specimens. To assess the validity of this method, Charpy impact tests were carried out, and the characteristics caused by heating during joining were measured. The test results showed the Charpy impact values were almost the same as base materials, and surface activated joining reduced heat affected zone to less than 2 mm. (author).

  6. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

    OpenAIRE

    Hasan, Mohammad R.; Rawat, Arun; Tang, Patrick; Jithesh, Puthen V.; Thomas, Eva; Tan, Rusung; Tilley, Peter

    2016-01-01

    Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspi...

  7. Characterization of Burkholderia rhizoxinica and B. endofungorum isolated from clinical specimens.

    Directory of Open Access Journals (Sweden)

    Jay E Gee

    Full Text Available Eight isolates submitted to CDC from 1989 to 2006 from clinical specimens were initially identified as members of the genus Burkholderia based on preliminary cellular fatty acid analysis and/or 16S rRNA gene sequencing. With the recent descriptions of the new species B. rhizoxinica and B. endofungorum, which are considered endosymbiotic bacteria in Rhizopus microsporus fungi, we now identify seven of these clinical isolates as B. rhizoxinica and one as B. endofungorum based on biochemical testing, 16s rRNA, and DNA-DNA hybridization results. We also further characterize these isolates by assessing toxin production and/or by multiple locus sequence typing.

  8. Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization.

    Science.gov (United States)

    Botling, Johan; Micke, Patrick

    2011-01-01

    Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.

  9. Influence of Specimen Preparation and Test Methods on the Flexural Strength Results of Monolithic Zirconia Materials.

    Science.gov (United States)

    Schatz, Christine; Strickstrock, Monika; Roos, Malgorzata; Edelhoff, Daniel; Eichberger, Marlis; Zylla, Isabella-Maria; Stawarczyk, Bogna

    2016-03-09

    The aim of this work was to evaluate the influence of specimen preparation and test method on the flexural strength results of monolithic zirconia. Different monolithic zirconia materials (Ceramill Zolid (Amann Girrbach, Koblach, Austria), Zenostar ZrTranslucent (Wieland Dental, Pforzheim, Germany), and DD Bio zx² (Dental Direkt, Spenge, Germany)) were tested with three different methods: 3-point, 4-point, and biaxial flexural strength. Additionally, different specimen preparation methods were applied: either dry polishing before sintering or wet polishing after sintering. Each subgroup included 40 specimens. The surface roughness was assessed using scanning electron microscopy (SEM) and a profilometer whereas monoclinic phase transformation was investigated with X-ray diffraction. The data were analyzed using a three-way Analysis of Variance (ANOVA) with respect to the three factors: zirconia, specimen preparation, and test method. One-way ANOVA was conducted for the test method and zirconia factors within the combination of two other factors. A 2-parameter Weibull distribution assumption was applied to analyze the reliability under different testing conditions. In general, values measured using the 4-point test method presented the lowest flexural strength values. The flexural strength findings can be grouped in the following order: 4-point strength values than prepared before sintering. The Weibull moduli ranged from 5.1 to 16.5. Specimens polished before sintering showed higher surface roughness values than specimens polished after sintering. In contrast, no strong impact of the polishing procedures on the monoclinic surface layer was observed. No impact of zirconia material on flexural strength was found. The test method and the preparation method significantly influenced the flexural strength values.

  10. Anaerobic Bacteria in Clinical Specimens – Frequent, But a Neglected Lot: A Five Year Experience at a Tertiary Care Hospital

    Science.gov (United States)

    Shenoy, Padmaja Ananth; Gawda, Ashwini; Shetty, Seema; Anegundi, Renuka; Varma, Muralidhar; Mukhopadhyay, Chiranjay; Chawla, Kiran

    2017-01-01

    Introduction Anaerobic bacteria which constitute a significant proportion of the normal microbiota also cause variety of infections involving various anatomic sites. Considering the tedious culture techniques with longer turnaround time, anaerobic cultures are usually neglected by clinicians and microbiologists. Aim To study the frequency of isolation of different anaerobic bacteria from various clinical specimens. Materials and Methods A retrospective study to analyse the frequency of isolation of different anaerobic bacteria, was conducted over a period of five years from 2011 to 2015 including various clinical specimens submitted to anaerobic division of Microbiology laboratory. Anaerobic bacteria were isolated and identified following standard bacteriological techniques. Results Pathogenic anaerobes (n=336) were isolated from 278 (12.48%) of overall 2227 specimens processed with an average yield of 1.2 isolates. Anaerobes were isolated as polymicrobial flora with or without aerobic bacterial pathogens in 159 (57.2%) patients. Anaerobic Gram-negative bacilli (140, 41.7%) were the predominant isolates. B. fragilis group (67, 19.9%) were the most commonly isolated anaerobic pathogens. Anaerobes were predominantly isolated from deep seated abscess (23.9%). Conclusion Pathogenic anaerobes were isolated from various infection sites. Unless culture and susceptibility tests are performed as a routine, true magnitude of antimicrobial resistance among anaerobic pathogens will not be known. Knowledge of the distribution of these organisms may assist in the selection of appropriate empirical therapy for anaerobic infections. PMID:28892897

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

    Science.gov (United States)

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

    2000-09-01

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

  12. Four-hour processing of clinical/diagnostic specimens for electron microscopy using microwave technique.

    Science.gov (United States)

    Giberson, R T; Demaree, R S; Nordhausen, R W

    1997-01-01

    A protocol for routine 4-hour microwave tissue processing of clinical or other samples for electron microscopy was developed. Specimens are processed by using a temperature-restrictive probe that can be set to automatically cycle the magnetron to maintain any designated temperature restriction (temperature maximum). In addition, specimen processing during fixation is performed in 1.7-ml microcentrifuge tubes followed by subsequent processing in flow-through baskets. Quality control is made possible during each step through the addition of an RS232 port to the microwave, allowing direct connection of the microwave oven to any personal computer. The software provided with the temperature probe enables the user to monitor time and temperature on a real-time basis. Tissue specimens, goat placenta, mouse liver, mouse kidney, and deer esophagus were processed by conventional and microwave techniques in this study. In all instances, the results for the microwave-processed samples were equal to or better than those achieved by routine processing techniques.

  13. Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

    OpenAIRE

    Odugbemi, T; Nwofor, C; Joiner, K T

    1988-01-01

    An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

  14. Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

    Science.gov (United States)

    Odugbemi, T; Nwofor, C; Joiner, K T

    1988-05-01

    An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

  15. Development of stress relaxation measurement by a small size C-ring specimen method

    International Nuclear Information System (INIS)

    Shimanuki, Shizuka; Nakata, Kiyotomo; Kasahara, Shigeki; Kuniya, Jiro

    2002-01-01

    A stress relaxation measurement method has been developed by using C-ring specimens, and a specimen size effect has been evaluated taking radiation-induced stress relaxation into consideration. C-ring specimens were stressed by forcing a wedge in the gap. Giving an appropriate eccentric configuration in the half of the ring opposite the gap, the stress gradient along the circumference was eliminated in the section and the stress level could be varied by changing the gap spacing. The validity of the C-ring test method was confirmed by thermally stress relaxation experiments at annealing temperatures from 300 to 600degC for 1 min to 200 h in carbon steel: considerable stress relaxation could be measured for all levels of applied stress even at relatively low annealing temperatures. The relaxation results obtained from the C-ring test were in good agreement with those from a uniaxial tensile stress relaxation test. The smaller C-ring specimen with about 40 mm diameter, which is required for radiation-induced stress relaxation test, also showed adequate accuracy on stress relaxation at 600 to 830degC in stainless steel, compared with the large size C-ring specimen test. (author)

  16. Microbiological and biochemical studies on certain antibiotic-resistant bacteria isolated from certain clinical specimens

    International Nuclear Information System (INIS)

    Nada, H.M.AL.M.

    2008-01-01

    Infection is a dynamic process involving invasion of the body by pathogenic microorganisms and reactions of the tissues to microorganisms and their toxins. Pathogenic microorganisms isolated from clinical samples are of great threat to human health.The outcome of an infection depends on the virulence of the pathogen and the relative degree of resistance or susceptibility to antimicrobial chemotherapy. Antimicrobial agents interfere with specific processes that are essential for growth and division.Development of antibiotic resistance in bacteria is a problem of great concern. The high prevalence of resistant bacteria seems to be related to uncontrolled usage of antibiotics. B-lactamases are the most common cause of bacterial resistance to B-lactam antimicrobial agents, and it is one of the most important reason for increasing the resistance in pathogenic bacteria against some antibiotics especially those acting on inhibition of cell wall synthesis. One hundred and seven clinical samples and specimens were collected from public, private hospitals and National Cancer Institute (NCI) in Cairo, Egypt. Out of them 72 cases positive for microbial infection. Twelve cases were showed mixed infection. Eighty four isolates of pathogenic bacteria and yeast were collected from single and mixed culture. Susceptibilities of the isolates to 20 different antimicrobial agents were determined according to Kirby-Bauer method. Nine multi-drug resistant gram-negative bacterial strains were identified by (Micro Scan WalkAway 96 SI System). Six of them urine isolates, 2 wound (pus) isolates and one sputum isolate. The identified strains were exposed to in-vitro gamma irradiation at dose level of 24.4 Gy, which is biologically equivalent to the fractionated multiple therapeutic dose used in the protocol of cancer treatment of some patients. The antimicrobial susceptibility of the nine multi-drug resistant strains were carried out by disk diffusion method before and after irradiation

  17. Microbiological and biochemical studies on certain antibiotic-resistant bacteria isolated from certain clinical specimens

    Energy Technology Data Exchange (ETDEWEB)

    Nada, H M.AL.M. [National Center for Radiation Research and Technology, Atomic Energy Authority, Cairo (Egypt)

    2008-07-01

    Infection is a dynamic process involving invasion of the body by pathogenic microorganisms and reactions of the tissues to microorganisms and their toxins. Pathogenic microorganisms isolated from clinical samples are of great threat to human health.The outcome of an infection depends on the virulence of the pathogen and the relative degree of resistance or susceptibility to antimicrobial chemotherapy. Antimicrobial agents interfere with specific processes that are essential for growth and division.Development of antibiotic resistance in bacteria is a problem of great concern. The high prevalence of resistant bacteria seems to be related to uncontrolled usage of antibiotics. B-lactamases are the most common cause of bacterial resistance to B-lactam antimicrobial agents, and it is one of the most important reason for increasing the resistance in pathogenic bacteria against some antibiotics especially those acting on inhibition of cell wall synthesis. One hundred and seven clinical samples and specimens were collected from public, private hospitals and National Cancer Institute (NCI) in Cairo, Egypt. Out of them 72 cases positive for microbial infection. Twelve cases were showed mixed infection. Eighty four isolates of pathogenic bacteria and yeast were collected from single and mixed culture. Susceptibilities of the isolates to 20 different antimicrobial agents were determined according to Kirby-Bauer method. Nine multi-drug resistant gram-negative bacterial strains were identified by (Micro Scan WalkAway 96 SI System). Six of them urine isolates, 2 wound (pus) isolates and one sputum isolate. The identified strains were exposed to in-vitro gamma irradiation at dose level of 24.4 Gy, which is biologically equivalent to the fractionated multiple therapeutic dose used in the protocol of cancer treatment of some patients. The antimicrobial susceptibility of the nine multi-drug resistant strains were carried out by disk diffusion method before and after irradiation

  18. Characterization of specimens obtained by different sampling methods for evaluation of periodontal bacteria.

    Science.gov (United States)

    Okada, Ayako; Sogabe, Kaoru; Takeuchi, Hiroaki; Okamoto, Masaaki; Nomura, Yoshiaki; Hanada, Nobuhiro

    2017-12-27

    Quantitative analysis of periodontal bacteria is considered useful for clinical diagnosis, evaluation and assessment of the risk of periodontal disease. The purpose of this study was to compare the effectiveness of sampling of saliva, supragingival and subgingival plaque for evaluation of periodontal bacteria. From each of 12 subjects, i) subgingival plaque was collected from the deepest pocket using a sterile paper point, ii) stimulated whole saliva was collected after chewing gum, and iii) supragingival plaque was collected using a tooth brush. These samples were sent to the medical examination laboratory for quantitative analysis of the counts of three periodontal bacterial species: Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The proportions of these bacteria in subgingival plaque were higher than those in saliva or supragingival plaque, but lower in subgingival plaque than in saliva or supragingival plaque. In several cases, periodontal bacteria were below the levels of detection in subgingival plaque. We concluded that samples taken from subgingival plaque may be more useful for evaluating the proportion of periodontal bacteria in deep pockets than is the case for other samples. Therefore, for evaluation of periodontal bacteria, clinicians should consider the characteristics of the specimens obtained using different sampling methods.

  19. Detection of Enterovirus 71 gene from clinical specimens by reverse-transcription loop-mediated isothermal amplification

    Directory of Open Access Journals (Sweden)

    D Wang

    2014-01-01

    Full Text Available Purpose : The objective of this study was to develop a sensitive, specific and rapid approach to diagnose hand foot and mouth disease (HFMD for an early treatment by using loop-mediated isothermal amplification (LAMP technique. Materials and Methods : A reverse-transcription loop-mediated isothermal amplification (RT-LAMP for detecting EV71 virus was developed, the specificity and sensitivity of RT-LAMP was tested, and the clinical specimens was assayed by the RT-LAMP comparing with conventional reverse-transcription polymerase chain reaction (RT-PCR and real-time PCR. Results : A total of 116 clinical specimens from the suspected HFMD individual were detected with the RT-LAMP. The detection rate for EV71 was 56.89% by RT-LAMP, 41.38% by real-time PCR and 34.48% by RT-PCR. The minimum detection limit of RT-LAMP was 0.01 PFU, both of RT-PCR and real-time PCR was 0.1PFU. Non-cross-reactive amplification with other enteroviruses was detected in the survey reports. Conclusions : The effectiveness of RT-LAMP is higher than RT-PCR and real-time PCR. The protocol is easy to operate and time saving. It was not an expensive instrument, which was needed; it is an applicable method for rapid diagnosis of the disease, especially in resource-poor countries or in developing countries.

  20. Spectral isotopic methods of determining nitrogen and carbon in plant specimens with laser volatization

    International Nuclear Information System (INIS)

    Lazeeva, G.S.

    1986-01-01

    Methods have been devised for the local determination of nitrogen and carbon isotope compositions in plant specimens, which provide separate and joint determination. Local laser evaporation has been combined with spectroscopic determination of the isotope compositions in the gas phase. A continuous-wave CO 2 laser is preferable for the local evaporation; the carbon isotope composition may be determined directly on the sum of the evaporation products, whereas nitrogen must first be separated as N 2 . Methods have also been developed for the local determination of total nitrogen and carbon in a sample with isotope dilution on the basis of laser evaporation. In order to eliminate systematic errors in determining total carbon in plant material, an evaporation method free from a rim has been devised. These methods have been used in determining isotope concentration profiles in plant specimens grown in experiments employing labeled nitrogen and carbon

  1. Method for independent strain and temperature measurement in polymeric tensile test specimen using embedded FBG sensors

    DEFF Research Database (Denmark)

    Pereira, Gilmar Ferreira; McGugan, Malcolm; Mikkelsen, Lars Pilgaard

    2016-01-01

    to calculate independently the strain and temperature are presented in the article, together with a measurement resolution study. This multi-parameter measurement method was applied to an epoxy tensile specimen, tested in a unidirectional tensile test machine with a temperature controlled cabinet. A full......A novel method to obtain independent strain and temperature measurements using embedded Fibre Bragg Grating (FBG) in polymeric tensile test specimens is presented in this paper. The FBG strain and temperature cross-sensitivity was decoupled using two single mode FBG sensors, which were embedded...... of temperature, from 40 C to -10 C. The consistency of the expected theoretical results with the calibration procedure and the experimental validation shows that this proposed method is applicable to measure accurate strain and temperature in polymers during static or fatigue tensile testing. Two different...

  2. Detection of enterovirus 71 gene from clinical specimens by reverse-transcription loop-mediated isothermal amplification.

    Science.gov (United States)

    Wang, D; Wang, X; Geng, Y; An, C

    2014-01-01

    The objective of this study was to develop a sensitive, specific and rapid approach to diagnose hand foot and mouth disease (HFMD) for an early treatment by using loop-mediated isothermal amplification (LAMP) technique. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for detecting EV71 virus was developed, the specificity and sensitivity of RT-LAMP was tested, and the clinical specimens was assayed by the RT-LAMP comparing with conventional reverse-transcription polymerase chain reaction (RT-PCR) and real-time PCR. A total of 116 clinical specimens from the suspected HFMD individual were detected with the RT-LAMP. The detection rate for EV71 was 56.89% by RT-LAMP, 41.38% by real-time PCR and 34.48% by RT-PCR. The minimum detection limit of RT-LAMP was 0.01 PFU, both of RT-PCR and real-time PCR was 0.1PFU. Non-cross-reactive amplification with other enteroviruses was detected in the survey reports. The effectiveness of RT-LAMP is higher than RT-PCR and real-time PCR. The protocol is easy to operate and time saving. It was not an expensive instrument, which was needed; it is an applicable method for rapid diagnosis of the disease, especially in resource-poor countries or in developing countries.

  3. Collection, transport and general processing of clinical specimens in Microbiology laboratory.

    Science.gov (United States)

    Sánchez-Romero, M Isabel; García-Lechuz Moya, Juan Manuel; González López, Juan José; Orta Mira, Nieves

    2018-02-06

    The interpretation and the accuracy of the microbiological results still depend to a great extent on the quality of the samples and their processing within the Microbiology laboratory. The type of specimen, the appropriate time to obtain the sample, the way of sampling, the storage and transport are critical points in the diagnostic process. The availability of new laboratory techniques for unusual pathogens, makes necessary the review and update of all the steps involved in the processing of the samples. Nowadays, the laboratory automation and the availability of rapid techniques allow the precision and turn-around time necessary to help the clinicians in the decision making. In order to be efficient, it is very important to obtain clinical information to use the best diagnostic tools. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  4. Standard test method for laboratory evaluation of magnesium sacrificial anode test specimens for underground applications

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    1997-01-01

    1.1 This test method covers a laboratory procedure that measures the two fundamental performance properties of magnesium sacrificial anode test specimens operating in a saturated calcium sulfate, saturated magnesium hydroxide environment. The two fundamental properties are electrode (oxidation potential) and ampere hours (Ah) obtained per unit mass of specimen consumed. Magnesium anodes installed underground are usually surrounded by a backfill material that typically consists of 75 % gypsum (CaSO4·2H2O), 20 % bentonite clay, and 5 % sodium sulfate (Na2SO4). The calcium sulfate, magnesium hydroxide test electrolyte simulates the long term environment around an anode installed in the gypsum-bentonite-sodium sulfate backfill. 1.2 This test method is intended to be used for quality assurance by anode manufacturers or anode users. However, long term field performance properties may not be identical to property measurements obtained using this laboratory test. Note 1—Refer to Terminology G 15 for terms used ...

  5. Measurement of the Young's modulus of thin or flexible specimen with digital-image correlation method

    Science.gov (United States)

    Xu, Lianyun; Hou, Zhende; Qin, Yuwen

    2002-05-01

    Because some composite material, thin film material, and biomaterial, are very thin and some of them are flexible, the classical methods for measuring their Young's moduli, by mounting extensometers on specimens, are not available. A bi-image method based on image correlation for measuring Young's moduli is developed in this paper. The measuring precision achieved is one order enhanced with general digital image correlation or called single image method. By this way, the Young's modulus of a SS301 stainless steel thin tape, with thickness 0.067mm, is measured, and the moduli of polyester fiber films, a kind of flexible sheet with thickness 0.25 mm, are also measured.

  6. Technical Note: Method to correlate whole-specimen histopathology of radical prostatectomy with diagnostic MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    McGrath, Deirdre M., E-mail: d.mcgrath@sheffield.ac.uk; Lee, Jenny; Foltz, Warren D. [Radiation Medicine Program, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2M9 (Canada); Samavati, Navid [Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9 (Canada); Jewett, Michael A. S. [Departments of Surgery (Urology) and Surgical Oncology, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Kwast, Theo van der [Pathology Department, University Health Network, Toronto, Ontario M5G 2C4 (Canada); Chung, Peter [Radiation Medicine Program, Princess Margaret Hospital, University Health Network and the University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Ménard, Cynthia [Radiation Medicine Program, Princess Margaret Hospital, University Health Network and the University of Toronto, Toronto, Ontario M5G 2M9, Canada and Centre Hospitalier de l’Université de Montréal, 1058 Rue Saint-Denis, Montréal, Québec H2X 3J4 (Canada); Brock, Kristy K. [Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48108 (United States)

    2016-03-15

    Purpose: Validation of MRI-guided tumor boundary delineation for targeted prostate cancer therapy is achieved via correlation with gold-standard histopathology of radical prostatectomy specimens. Challenges to accurate correlation include matching the pathology sectioning plane with the in vivo imaging slice plane and correction for the deformation that occurs between in vivo imaging and histology. A methodology is presented for matching of the histological sectioning angle and position to the in vivo imaging slices. Methods: Patients (n = 4) with biochemical failure following external beam radiotherapy underwent diagnostic MRI to confirm localized recurrence of prostate cancer, followed by salvage radical prostatectomy. High-resolution 3-D MRI of the ex vivo specimens was acquired to determine the pathology sectioning angle that best matched the in vivo imaging slice plane, using matching anatomical features and implanted fiducials. A novel sectioning device was developed to guide sectioning at the correct angle, and to assist the insertion of reference dye marks to aid in histopathology reconstruction. Results: The percentage difference in the positioning of the urethra in the ex vivo pathology sections compared to the positioning in in vivo images was reduced from 34% to 7% through slicing at the best match angle. Reference dye marks were generated, which were visible in ex vivo imaging, in the tissue sections before and after processing, and in histology sections. Conclusions: The method achieved an almost fivefold reduction in the slice-matching error and is readily implementable in combination with standard MRI technology. The technique will be employed to generate datasets for correlation of whole-specimen prostate histopathology with in vivo diagnostic MRI using 3-D deformable registration, allowing assessment of the sensitivity and specificity of MRI parameters for prostate cancer. Although developed specifically for prostate, the method is readily

  7. Technical Note: Method to correlate whole-specimen histopathology of radical prostatectomy with diagnostic MR imaging

    International Nuclear Information System (INIS)

    McGrath, Deirdre M.; Lee, Jenny; Foltz, Warren D.; Samavati, Navid; Jewett, Michael A. S.; Kwast, Theo van der; Chung, Peter; Ménard, Cynthia; Brock, Kristy K.

    2016-01-01

    Purpose: Validation of MRI-guided tumor boundary delineation for targeted prostate cancer therapy is achieved via correlation with gold-standard histopathology of radical prostatectomy specimens. Challenges to accurate correlation include matching the pathology sectioning plane with the in vivo imaging slice plane and correction for the deformation that occurs between in vivo imaging and histology. A methodology is presented for matching of the histological sectioning angle and position to the in vivo imaging slices. Methods: Patients (n = 4) with biochemical failure following external beam radiotherapy underwent diagnostic MRI to confirm localized recurrence of prostate cancer, followed by salvage radical prostatectomy. High-resolution 3-D MRI of the ex vivo specimens was acquired to determine the pathology sectioning angle that best matched the in vivo imaging slice plane, using matching anatomical features and implanted fiducials. A novel sectioning device was developed to guide sectioning at the correct angle, and to assist the insertion of reference dye marks to aid in histopathology reconstruction. Results: The percentage difference in the positioning of the urethra in the ex vivo pathology sections compared to the positioning in in vivo images was reduced from 34% to 7% through slicing at the best match angle. Reference dye marks were generated, which were visible in ex vivo imaging, in the tissue sections before and after processing, and in histology sections. Conclusions: The method achieved an almost fivefold reduction in the slice-matching error and is readily implementable in combination with standard MRI technology. The technique will be employed to generate datasets for correlation of whole-specimen prostate histopathology with in vivo diagnostic MRI using 3-D deformable registration, allowing assessment of the sensitivity and specificity of MRI parameters for prostate cancer. Although developed specifically for prostate, the method is readily

  8. Internet of Things technology-based management methods for environmental specimen banks.

    Science.gov (United States)

    Peng, Lihong; Wang, Qian; Yu, Ang

    2015-02-01

    The establishment and management of environmental specimen banks (ESBs) has long been a problem worldwide. The complexity of specimen environment has made the management of ESB likewise complex. Through an analysis of the development and management of ESBs worldwide and in light of the sophisticated Internet of Things (IOT) technology, this paper presents IOT technology-based ESB management methods. An IOT technology-based ESB management system can significantly facilitate ESB ingress and egress management as well as long-term storage management under quality control. This paper elaborates on the design of IOT technology-based modules, which can be used in ESB management to achieve standardized, smart, information-based ESB management. ESB management has far-reaching implications for environmental management and for research in environmental science.

  9. Evaluation of biological samples for specimen banking and biomonitoring by nuclear methods

    International Nuclear Information System (INIS)

    Stone, S.F.; Zeisler, R.

    1984-01-01

    In a pilot program for environmental specimen banking, human livers and marine mussels (Mytilus edulis) were sampled, analyzed and banked. Nuclear methods played a major role in the evaluation of the samples by providing concentration data for up to 37 major, mineral, and trace elements. Instrumental neutron activation analysis was complemented by neutron-capture prompt gamma activation analysis, radiochemical separations and, for the mussels, by instrumental X-ray fluorescence analysis. A cryogenic homogenization procedure was applied for sample preparation and evaluated. Assessment of accuracy was made by analyzing Standard Reference Materials and by intercomparing the techniques. Results are reported for 66 individual human liver specimens, collected at three locations in the United States, and for batches of 65 mussels from a collection made at Narragansett Bay, RI. 19 references, 23 figures, 4 tables

  10. A Multiplex PCR for Detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Bordetella pertussis in Clinical Specimens

    National Research Council Canada - National Science Library

    McDonough, E. A; Barrozo, C. P; Russell, K. L; Metzgar, D

    2005-01-01

    ..., and Bordetella pertussis in uncultured patient specimens. These organisms cause similar symptomologies and are often not diagnosed because they are difficult to identify with classical methods such as culture and serology...

  11. Antibiotic Resistance Profiling of Staphylococcus aureus Isolated from Clinical Specimens in a Tertiary Hospital from 2010 to 2012

    Directory of Open Access Journals (Sweden)

    Alain C. Juayang

    2014-01-01

    Full Text Available MRSA infection can affect a wide array of individuals that may lead to treatment failure. Also, the infection has the potential to spread from one area to another particularly health care facilities or communities eventually causing minor outbreaks. With this premise, the study aimed to describe MRSA infections using the hospital-based data of a tertiary hospital in Bacolod City, Philippines, from 2010 to 2012. Specifically, this study aimed to evaluate the antimicrobial resistance of S. aureus isolated from clinical specimens and to put emphasis on the prevalence of MRSA and Inducible Clindamycin Resistance. A total of 94 cases from 2010 to 2012 were diagnosed to have S. aureus infection using conventional bacteriologic methods. From these cases, 38 (40.6% were identified as MRSA and 37 (39.4% were inducible clindamycin resistant. Wounds and abscesses were considered to be the most common specimens with MRSA infections having 71.05% while blood was the least with 5.3%. For drug susceptibility, out of the 94 S. aureus cases, including MRSA, 100% were susceptible to linezolid making it the drug of choice for this study. It was then followed by tetracycline having a mean susceptibility of 95%;, while penicillin G was ineffective with 94 cases having 0% susceptibility.

  12. PREVALENCE OF ACINETOBACTER BAUMANNII ISOLATED FROM CLINICAL SPECIMENS IN ADAM MALIK HOSPITAL

    Directory of Open Access Journals (Sweden)

    Evita Mayasari

    2014-05-01

    Full Text Available AbstrakAcinetobacter baumannii merupakan spesies Acinetobacter spp. tersering diisolasi darimanusia, dan lebih sering dijumpai pada infeksi nosokomial dibandingkan dengan infeksi dikomunitas. Eksistensi bakteri ini di lingkungan terkait dengan keragaman reservoir, kemampuanmemperoleh gen pembawa sifat resisten antimikroba, dan sifat resisten terhadap pengeringan.Infeksi disebabkan strain A.baumannii yang resisten terhadap banyak antibiotik tidak mudahdikendalikan dan menjadi permasalahan di berbagai negara. Penelitian ini bertujuan untukmengetahui prevalensi A.baumannii dari spesimen klinis di instalasi mikrobiologi klinik RSUPHaji Adam Malik serta pola kepekaannya terhadap berbagai antibiotik. Identifikasi dan ujikepekaan menggunakan mesin otomatis Vitek 2 dengan Advanced Expert System (AES.Penelitian ini menemukan 644/3693 (17,44% isolat A.baumannii dari berbagai spesimen klinis.A.baumannii paling banyak diisolasi dari spesimen dahak. Penelitian ini menemukan 147/644(23% bahwa isolat carbapenem-resistent A.baumannii (imipenem dan meropenem. Sebagianbesar isolat sensitif terhadap colistin, amikacin dan tigecycline. Prevalensi A.baumanni yangditemukan pada penelitian ini adalah rendah namun resistensinya tinggi terhadap antibiotikterutama golongan penicillin, cephalosporin dan fluoroquinolon.AbstractAcinetobacter baumannii is the most frequent species of Acinetobacter spp. isolated fromhumans and more common in nosocomial infection than it is in community acquired infection.A.baumannii existence in environment is associated with the diversity of its reservoirs, itscapacity to accumulate genes of antimicrobial resistence, and its resistence to desiccation.Infection of Multidrug resistent (MDR strain of A.baumannii is not easy to manage and it hasbecome a problem in many countries. The aim of this retrospective study was to investigatethe prevalence of A.baumannii from routine clinical specimens sent to clinical microbiologylaboratory RSUP HAM

  13. Molecular epidemiology of Bordetella pertussis in Cambodia determined by direct genotyping of clinical specimens.

    Science.gov (United States)

    Moriuchi, Takumi; Vichit, Ork; Vutthikol, Yong; Hossain, Md Shafiqul; Samnang, Chham; Toda, Kohei; Grabovac, Varja; Hiramatsu, Yukihiro; Otsuka, Nao; Shibayama, Keigo; Kamachi, Kazunari

    2017-09-01

    This study sought to determine the genotypes of circulating Bordetella pertussis, the causative agent of pertussis, in Cambodia by direct molecular typing of clinical specimens. DNA extracts from nasopharyngeal swabs obtained from 82 pertussis patients in 2008-2016 were analyzed by multilocus variable-number tandem repeat analysis (MLVA). B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter ptxP were also investigated by DNA sequence-based typing. Forty-four DNA extracts (54%) yielded a complete MLVA profile, and these were sorted into 8 MLVA types (MT18, MT26, MT27, MT29, MT43, MT72, MT95, and MT200). MT27 and MT29, which are common in developed countries, were the predominant strain types (total 73%). The predominant profile of virulence-associated allelic genes was the combination of ptxP3/ptxA1/prn2/fim3A (48%). MT27 strains were detected during the entire study period, whereas MT29 strains were only found in 2014-2016. The B. pertussis population in Cambodia, where a whole-cell pertussis vaccine (WCV) has been continuously used, resembled those observed previously in developed countries where acellular pertussis vaccines are used. Circulating B. pertussis strains in Cambodia were distinct from those in other countries using WCVs. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  14. Feasibility of using microbeads with holographic barcodes to track DNA specimens in the clinical molecular laboratory

    Directory of Open Access Journals (Sweden)

    Jason D. Merker

    2013-07-01

    Full Text Available We demonstrate the feasibility of using glass microbeads with a holographic barcode identifier to track DNA specimens in the molecular pathology laboratory. These beads can be added to peripheral blood specimens and are carried through automated DNA extraction protocols that use magnetic glass particles. We found that an adequate number of microbeads are consistently carried over during genomic DNA extraction to allow specimen identification, that the beads do not interfere with the performance of several different molecular assays, and that the beads and genomic DNA remain stable when stored together under regular storage conditions in the molecular pathology laboratory. The beads function as an internal, easily readable specimen barcode. This approach may be useful for identifying DNA specimens and reducing errors associated with molecular laboratory testing.

  15. Transmission Electron Microscopy Specimen Preparation Method for Multiphase Porous Functional Ceramics

    DEFF Research Database (Denmark)

    Zhang, Wei; Kuhn, Luise Theil; Jørgensen, Peter Stanley

    2013-01-01

    An optimum method is proposed to prepare thin foil transmission electron microscopy (TEM) lamellae of multiphase porous functional ceramics: prefilling the pore space of these materials with an epoxy resin prior to focused ion beam milling. Several advantages of epoxy impregnation are demonstrated...... by successful preparation of TEM specimens that maintain the structural integrity of the entire lamella. Feasibility of the TEM alignment procedure is demonstrated, and ideal TEM analyses are illustrated on solid oxide fuel cell and solid oxide electrolysis cell materials. Some potential drawbacks of the TEM...

  16. Assessment of different methods of bovine oocytes collection, maturation and in vitro fertilization of abattoir specimens

    Directory of Open Access Journals (Sweden)

    W.M. Saleh

    2017-06-01

    Full Text Available The aim of this study is designed to evaluate the best methods for cow oocytes collection from abattoir specimens which is the cheapest, easily obtained and bulky number. Forty five fresh cow genitalia specimens and testicle were collected directly after slaughter from Al-Shoáalla abattoir north-west of Baghdad the capital early morning, transported in cool box under (4-8 °C to the laboratory of theriogenology in the College of Veterinary Medicine/Baghdad University during the period from November 2016 to February 2017. Ovaries were separated from the surrounding tissues, washed thoroughly with dis. water repeatedly, then with normal saline and finally with MEM medium containing Antibiotics and Nystatin for contaminant elimination. Oocytes were collected with four methods aspiration, slashing, slicing after aspiration and slicing. The result showed that; the collected oocytes were 55, 68, 87 and 106 oocytes respectively; slicing methods yield more oocytes count. Period of time between slaughtering and samples processing significantly affect oocytes collected percentage and quality, periods as 2, 6, 12 and 24 hours yield 75%, 68%, 61% and 55% oocytes counts of good, fair, poor to aged and bad quality oocytes respectively. Two hours period yield an elevated oocytes count with good quality. Maturation index of oocytes according to the type of collected methods showed 44, 37, 39 and 42 with 12, 8, 6 and 6 good oocyte quality for the four methods respectively. In conclusion slicing methods yield more oocytes count with a moderate quality and embryos production while aspiration methods yield a moderate oocytes count with an elevated quality and good embryos production.

  17. A Rapid and Cost-Effective Method for DNA Extraction from Archival Herbarium Specimens.

    Science.gov (United States)

    Krinitsina, A A; Sizova, T V; Zaika, M A; Speranskaya, A S; Sukhorukov, A P

    2015-11-01

    Here we report a rapid and cost-effective method for the extraction of total DNA from herbarium specimens up to 50-90-year-old. The method takes about 2 h, uses AMPure XP magnetic beads diluted by PEG-8000- containing buffer, and does not require use of traditional volatile components like chloroform, phenol, and liquid nitrogen. It yields up to 4 µg of total nucleic acid with high purity from about 30 mg of dry material. The quality of the extracted DNA was tested by PCR amplification of 5S rRNA and rbcL genes (nuclear and chloroplast DNA markers) and compared against the traditional chloroform/isoamyl alcohol method. Our results demonstrate that the use of the magnetic beads is crucial for extraction of DNA suitable for subsequent PCR from herbarium samples due to the decreasing inhibitor concentrations, reducing short fragments of degraded DNA, and increasing median DNA fragment sizes.

  18. Experimental study on variations in Charpy impact energies of low carbon steel, depending on welding and specimen cutting method

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhaorui; Kang, Hansaem; Lee, Young Seog [Chung-Ang University, Seoul (Korea, Republic of)

    2016-05-15

    This paper presents an experimental study that examines variations of Charpy impact energy of a welded steel plate, depending upon the welding method and the method for obtaining the Charpy specimens. Flux cored arc welding (FCAW) and Gas tungsten arc welding (GTAW) were employed to weld an SA516 Gr. 70 steel plate. The methods of wire cutting and water-jet cutting were adopted to take samples from the welded plate. The samples were machined according to the recommendations of ASTM SEC. II SA370, in order to fit the specimen dimension that the Charpy impact test requires. An X-ray diffraction (XRD) method was used to measure the as-weld residual stress and its redistribution after the samples were cut. The Charpy impact energy of specimens was considerably dependent on the cutting methods and locations in the welded plate where the specimens were taken. The specimens that were cut by water jet followed by FCAW have the greatest resistance-to-fracture (Charpy impact energy). Regardless of which welding method was used, redistributed transverse residual stress becomes compressive when the specimens are prepared using water-jet cutting. Meanwhile, redistributed transverse residual stress becomes tensile when the specimens are prepared using wire cutting.

  19. Detection of oral HPV infection - Comparison of two different specimen collection methods and two HPV detection methods.

    Science.gov (United States)

    de Souza, Marjorie M A; Hartel, Gunter; Whiteman, David C; Antonsson, Annika

    2018-04-01

    Very little is known about the natural history of oral HPV infection. Several different methods exist to collect oral specimens and detect HPV, but their respective performance characteristics are unknown. We compared two different methods for oral specimen collection (oral saline rinse and commercial saliva kit) from 96 individuals and then analyzed the samples for HPV by two different PCR detection methods (single GP5+/6+ PCR and nested MY09/11 and GP5+/6+ PCR). For the oral rinse samples, the oral HPV prevalence was 10.4% (GP+ PCR; 10% repeatability) vs 11.5% (nested PCR method; 100% repeatability). For the commercial saliva kit samples, the prevalences were 3.1% vs 16.7% with the GP+ PCR vs the nested PCR method (repeatability 100% for both detection methods). Overall the agreement was fair or poor between samples and methods (kappa 0.06-0.36). Standardizing methods of oral sample collection and HPV detection would ensure comparability between future oral HPV studies. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Line probe assay for differentiation within Mycobacterium tuberculosis complex. Evaluation on clinical specimens and isolates including Mycobacterium pinnipedii

    DEFF Research Database (Denmark)

    Kjeldsen, Marianne Kirstine; Bek, Dorte; Rasmussen, Erik Michael

    2009-01-01

    A line probe assay (GenoType MTBC) was evaluated for species differentiation within the Mycobacterium tuberculosis complex (MTBC). We included 387 MTBC isolates, 43 IS6110 low-copy MTBC isolates, 28 clinical specimens with varying microscopy grade, and 30 isolates of non-tuberculous mycobacteria...

  1. A simple method for the prevention of endometrial autolysis in hysterectomy specimens.

    Science.gov (United States)

    Houghton, J P; Roddy, S; Carroll, S; McCluggage, W G

    2004-03-01

    Uteri are among the most common surgical pathology specimens. Assessment of the endometrium is often difficult because of pronounced tissue autolysis. This study describes a simple method to prevent endometrial autolysis and aid in interpretation of the endometrium. Sixty uteri were injected with formalin using a needle and syringe directed alongside a probe, which was inserted through the external cervical os into the endometrial cavity. Injection was performed on the same day as removal of the uterus. As controls, 60 uteri that were not injected with formalin were examined. The degree of endometrial autolysis was assessed on a four point scale (0-3), with a score of 0 representing no or minimal autolysis and a score of 3 representing extensive autolysis, such that histological interpretation of the endometrium was impossible. In the injected group, the number of cases with scores of 0, 1, 2, and 3 was 42, 13, four, and one, respectively. The corresponding values for the control group were 17, 23, eight, and 12, respectively. This was highly significant (p autolysis in uteri injected with formalin. The use of this simple procedure should be encouraged in hysterectomy specimens.

  2. Method for efficient storage and transportation of sputum specimens for molecular testing of tuberculosis.

    Science.gov (United States)

    Guio, H; Okayama, H; Ashino, Y; Saitoh, H; Xiao, P; Miki, M; Yoshihara, N; Nakanowatari, S; Hattori, T

    2006-08-01

    The polymerase chain reaction (PCR) is a highly sensitive method for the detection of Mycobacterium tuberculosis and is available in most countries, though to a lesser extent in rural areas. To amplify M. tuberculosis DNA sequences of sputum spotted on FTA cards and compare them with the results of microscopic examination among culture-positive samples. A total of 102 sputum specimens of TB patients in treatment were spotted on FTA cards and stored at room temperature until DNA analysis. We assessed the IS6110 region of M. tuberculosis. The efficacy of the PCR assay for the direct detection of M. tuberculosis was evaluated and compared with the results of cultures (Middlebrook 7H9 broth) and smears of fresh sputum specimens. We were able to detect 10 fg/microl of mycobacterial DNA even after 6 months in storage. The PCR sensitivity and specificity using the FTA card system were 82% and 96%, while microscopic examination showed 41% and 95%, respectively. The FTA card system for the storage of bacterial DNA from sputum samples should be considered for the molecular diagnosis of tuberculosis. Samples can easily be obtained from geographically isolated populations and shipped by mail for accurate molecular diagnosis.

  3. Identification of non-tuberculous mycobacteria isolated from clinical specimens at a tertiary care hospital: a cross-sectional study.

    Science.gov (United States)

    Ahmed, Imran; Jabeen, Kauser; Hasan, Rumina

    2013-10-22

    Non-tuberculous mycobacteria (NTM) are opportunistic pathogens in immuno-compromised patients. They are also increasingly recognized as pathogens in immuno-competent individuals. Globally, an increase in NTM isolation is being reported with a varied geographic prevalence of different species around the world. There is lack of data on species distribution of these organisms from Pakistan. Treatment options differ according to the species isolated and its susceptibility profile. Knowledge of local species variation would help targeted therapy. This study was performed to determine frequencies of different NTM species isolated from various clinical specimens submitted at a tertiary care hospital laboratory. NTM isolated from 25955 clinical specimens over a period of two years (2010 to 2011) were included. All NTM were identified using conventional tests. Drug susceptibility testing (DST) was performed by broth microdilution and interpreted according to Clinical and Laboratory Standards Institute's document M24-A2. A total of 104 NTM were included in the study. Of these, 76% (54/71) rapidly growing mycobacteria (RGM) and 57.6% (19/33) slow growing mycobacteria (SGM) could be further identified. Mycobacterium fortuitum (21/54) was the commonest NTM identified among RGM followed by M. mucogenicum (12/54) and M. smegmatis (11/54). Among SGM, M. avium complex (MAC) was the most frequent (14/19). Clinical significance could be assessed in a limited number (52/104) of NTM isolates and MAC appeared to be the commonest significant NTM. Three extra-pulmonary cases were found to be healthcare associated infections. DST results for RGM showed susceptibility to amikacin (100%), clarithromycin (100%, except M. fortuitum where it is not reportable), linezolid (90%) and moxifloxacin (75%). Whereas SGM were susceptible to clarithromycin (100%), linezolid (58.8%) and moxifloxacin (64.7%). This is the first study reporting NTM species and their clinical significance isolated from

  4. Detection of bovine viral diarrhoea virus in specimens from cattle in South Africa and possible association with clinical disease

    Directory of Open Access Journals (Sweden)

    N. Kabongo

    2004-06-01

    Full Text Available Studies covering all aspects of bovine viral diarrhoea virus (BVDV have been conducted in several countries in Europe, Asia and America. In southern Africa, more information is required about the nature of BVDV infection, the prevalence of different strains and the economic importance of the disease. The presence of BVDV in southern Africa has been known since the early 1970s through serological surveys but few reports confirming its presence by virus isolation and correlation with clinical disease are available. Specimens (n = 312 collected in 1998/99, from live and dead cattle from different farming systems, were obtained from private practitioners, feedlot consultants and abattoirs throughout the country. Specimens (n=37 from African buffaloes (Syncerus caffer in the Kruger National Park were also included. All specimens were processed for virus isolation in cell culture with confirmation by means of immunofluorescent antibody tests and some also by means of an antigen capture ELISA. BVDV was isolated from 15 (4.7 % cattle and were all noncytopathic biotypes. BVDV was not detected in 37 lymph nodes obtained from buffaloes in the Kruger National Park. Of the clinical signs in cattle from which virus were isolated, respiratory signs was the most frequent (10/15, followed by diarrhoea (5/15. Abortion, congenital malformations, haemorrhagic diarrhoea and poor growth were also included as criteria for selection of animals for specimen collection, but no BVD viruses were isolated from cattle manifesting these clinical signs.

  5. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation

    Science.gov (United States)

    Panpradist, Nuttada; Beck, Ingrid A.; Chung, Michael H.; Kiarie, James N.; Frenkel, Lisa M.; Lutz, Barry R.

    2016-01-01

    Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories. PMID:26751207

  6. A multiplex PCR method for detection of Aspergillus spp. and Mycobacterium tuberculosis in BAL specimens.

    Science.gov (United States)

    Amini, F; Kachuei, R; Noorbakhsh, F; Imani Fooladi, A A

    2015-06-01

    The aim of this study was the detection of Aspergillus species and Mycobacterium tuberculosis together in bronchoalveolar lavage (BAL) using of multiplex PCR. In this study, from September 2012 until June 2013, 100 bronchoalveolar lavage (BAL) specimens were collected from patients suspected of tuberculosis (TB). After the direct and culture test, multiplex PCR were utilized in order to diagnose Aspergillus species and M. tuberculosis. Phenol-chloroform manual method was used in order to extract DNA from these microorganisms. Aspergillus specific primers, M. tuberculosis designed primers and beta actin primers were used for multiplex PCR. In this study, by multiplex PCR method, Aspergillus species were identified in 12 samples (12%), positive samples in direct and culture test were respectively 11% and 10%. Sensitivity and specificity of this method in comparison to direct test were respectively 100% and 98.8%, also sensitivity and specificity of this method in comparison to culture test were respectively 100% and 97.7%. In this assay, M. tuberculosis was identified in 8 samples (8%). Mycobacterium-positive samples in molecular method, direct and culture test were respectively 6%, 5% and 7%. Sensitivity and specificity of PCR method in comparison to direct test were 80% and 97.8% also sensitivity and specificity of this method in comparison to culture test was 71.4% and 98.9%. In the present study, multiplex PCR method had higher sensitivity than direct and culture test in order to identify and detect Aspergillus, also this method had lower sensitivity for identification of M. tuberculosis, suggesting that the method of DNA extraction was not suitable. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  7. Comparison of a radiometric method (BACTEC) and conventional culture media for recovery of mycobacteria from smear-negative specimens

    International Nuclear Information System (INIS)

    Morgan, M.A.; Horstmeier, C.D.; DeYoung, D.R.; Roberts, G.D.

    1983-01-01

    The BACTEC system and three conventional media (Middlebrook 7H10, selective Middlebrook 7H11 [S7H11], and Lowenstein-Jensen [LJ] were compared for their mean recovery times and recovery rates of mycobacteria from acid-fast, smear-negative clinical specimens. Of the 71 smear-negative, culture-positive specimens recovered from 2,165 submitted smear-negative cultures, the BACTEC system detected 71.8%, compared with 88.7% for the conventional three-medium system. When media were individually compared, BACTEC medium (Middlebrook 7H12) was more successful in recovering mycobacteria (71.8%) than was LJ (62%), Middlebrook medium 7H10 (55.9%), or Middlebrook S7H11 medium (52.1%). Middlebrook 7H11 medium containing sodium selenate was also evaluated and did not increase the recovery rate or decrease the recovery time of mycobacterial species when compared with LJ, Middlebrook 7H10, S7H11, and 7H12 media. The mean detection time for the BACTEC system was less than that by conventional methods for the seven species of mycobacteria recovered. Detection times for Mycobacterium tuberculosis on the BACTEC system and conventional cultural systems were 13.7 and 26.3 days, respectively

  8. Sensitivity patterns of pseudomonas aeruginosa isolates obtained from clinical specimens in peshawar

    International Nuclear Information System (INIS)

    Abbas, S.H.; Khan, M.Z.U.; Naeem, M.

    2015-01-01

    Pseudomonas aeruginosa (P. aeruginosa) is a highly virulent opportunistic pathogen and a leading cause of nosocomial infections.Affected patients are often hospitalized in an intensive care unit, and are immuno-compromised as a result of disease and treatment. Suspected P. aeruginosa require timely, adequate and empirical antibiotic therapy to ensure improved outcomes. The purpose of the study was to find the sensitivity and resistance pattern of P. aeruginosa to various groups of drugs, in clinical isolates collected from two major tertiary care hospitals of Peshawar. Methods: Different clinical isolate were taken from patients admitted in various wards of Khyber Teaching Hospital and Lady Reading Hospital Peshawar. Results: A total of 258 clinical isolates were positive for P. aeruginosa out of 2058 clinical isolates. Pseudomonas showed high degree of resistance to third generation Cephalosporins (Ceftazidime, and Ceftriaxone) and moderate degree of resistance to Quinolones and Aminoglycosides (Ofloxacin, Ciprofloxacin, Levofloxacin and Amikacin). Low resistance was observed to different combinations (Cefoperazone + Sulbactum, Piperacillin + Tazobactum). Meropenem and Imipenem had negligible resistance. Conclusion: There is growing resistance to different classes of antibiotics. Combination drugs are useful approach for empirical treatment in suspected Pseudomonas infection. Imipenem and Meropenem are extremely effective but should be in reserve. (author)

  9. USFDA-GUIDELINE BASED VALIDATION OF TESTING METHOD FOR RIFAMPICIN IN INDONESIAN SERUM SPECIMEN

    Directory of Open Access Journals (Sweden)

    Tri Joko Raharjo

    2010-06-01

    Full Text Available Regarding a new regulation from Indonesia FDA (Badan POM-RI, all new non patent drugs should show bioequivalence with the originator drug prior to registration. Bioequivalence testing (BE-testing has to be performed to the people that represented of population to which the drug to be administrated. BE testing need a valid bio-analytical method for certain drug target and group of population. This research report specific validation of bio-analysis of Rifampicin in Indonesian serum specimen in order to be used for BE testing. The extraction was performed using acetonitrile while the chromatographic separation was accomplished on a RP 18 column (250 × 4.6 mm i.d., 5 µm, with a mobile phase composed of KH2PO4 10 mM-Acetonitrile (40:60, v/v and UV detection was set at 333 nm. The method shown specificity compared to blank serum specimen with retention time of rifampicin at 2.1 min. Lower limit of quantification (LLOQ was 0.06 µg/mL with dynamic range up to 20 µg/mL (R>0.990. Precision of the method was very good with coefficient of variance (CV 0.58; 7.40 and 5.56% for concentration at 0.06, 5, 15 µg/mL, respectively. Accuracies of the method were 3.22; 1.94; 1.90% for concentration 0.06, 5 and 15 µg/mL respectively. The average recoveries were 97.82, 95.50 and 97.31% for concentration of rifampicin 1, 5 and 5 µg/mL, respectively. The method was also shown reliable result on stability test on freezing-thawing, short-term and long-term stability as well as post preparation stability. Validation result shown that the method was ready to be used for Rifampicin BE testing with Indonesian subject.   Keywords: Rifampicin, Validation, USFDA-Guideline

  10. Comparatively Studied Color Correction Methods for Color Calibration of Automated Microscopy Complex of Biomedical Specimens

    Directory of Open Access Journals (Sweden)

    T. A. Kravtsova

    2016-01-01

    Full Text Available The paper considers a task of generating the requirements and creating a calibration target for automated microscopy systems (AMS of biomedical specimens to provide the invariance of algorithms and software to the hardware configuration. The required number of color fields of the calibration target and their color coordinates are mostly determined by the color correction method, for which coefficients of the equations are estimated during the calibration process. The paper analyses existing color calibration techniques for digital imaging systems using an optical microscope and shows that there is a lack of published results of comparative studies to demonstrate a particular useful color correction method for microscopic images. A comparative study of ten image color correction methods in RGB space using polynomials and combinations of color coordinate of different orders was carried out. The method of conditioned least squares to estimate the coefficients in the color correction equations using captured images of 217 color fields of the calibration target Kodak Q60-E3 was applied. The regularization parameter in this method was chosen experimentally. It was demonstrated that the best color correction quality characteristics are provided by the method that uses a combination of color coordinates of the 3rd order. The study of the influence of the number and the set of color fields included in calibration target on color correction quality for microscopic images was performed. Six train sets containing 30, 35, 40, 50, 60 and 80 color fields, and test set of 47 color fields not included in any of the train sets were formed. It was found out that the train set of 60 color fields minimizes the color correction error values for both operating modes of digital camera: using "default" color settings and with automatic white balance. At the same time it was established that the use of color fields from the widely used now Kodak Q60-E3 target does not

  11. Analysis of radioactive corrosion test specimens by means of ICP-MS. Comparison with earlier methods

    International Nuclear Information System (INIS)

    Forsyth, Roy

    1997-07-01

    In June 1992, an ICP-MS instrument (Inductively Coupled Plasma-Mass Spectrometry) was commissioned for use with radioactive sample solutions at Studsvik Nuclear's Hot Cell Laboratory. For conventional environmental samples the instrument permits the simultaneous analysis of many trace elements, but the software used in evaluation of the mass spectra is based on a library of isotopic compositions relevant only for elements in the lithosphere. Fission products and actinides, however, have isotopic compositions which are significantly different from the natural elements, and which also vary with the burnup of the nuclear fuel specimen. Consequently, a spread-sheet had to be developed which could evaluate the mass spectra with these isotopic compositions. Following these preparations, a large number of samples (about 200) from SKB's experimental programme for the study of spent fuel corrosion have been analyzed by the ICP-MS technique. Many of these samples were archive solutions of samples which had been taken earlier in the programme. This report presents a comparison of the analytical results for uranium, plutonium, cesium, strontium and technetium by both the ICP-MS technique, and the previously used analytical methods. For three products, a satisfactory agreement between the results from the various methods was obtained, but for uranium and plutonium the ICP-MS method gave results which were 10-20% higher than the conventional methods. The comparison programme has also shown, not unexpectedly, that significant losses of plutonium from solution had occurred, by precipitation and/or absorption, in the archive solutions during storage. It can be expected that such losses also occur for the other actinides, and consequently, all the analytical results for actinides in older archive solutions must be treated with great caution. 9 refs

  12. Comparison of real-time and quantitative polymerase chain reaction assays in detection of cytomegalovirus DNA in clinical specimens

    International Nuclear Information System (INIS)

    Gokahmetoglu, S.; Deniz, E.

    2007-01-01

    To compare the real-time (RT) and qualitative (Q) polymerase chain reaction (PCR) assays for detection of Cytomegalovirus (CMV) DNA. The study took place in the Department of Microbiology, Erciyes University, Kayseri and in Iontek Laboratory, Istanbul, Turkey, from August to December 2006. One hundred and seven clinical specimens from 67 patients were included in the study. Cytomegalovirus DNA was investigated using RT-PCR kit (Fluorion Iontek, Turkey) and Q-PCR kit (Fluorion Iontek, Turkey). Deoxyribonucleic acid sequencing was applied to the samples that yielded discrepant results in both assays. Mac Nema's Chi Square test was used for statistical analysis. Of the specimens, 27 were found positive with both assays: 9 with only RT-PCR, and 11 with only Q-PCR assay. Both assays were found negative in 60 of the specimens. There was a good agreement between the 2 assays in 87(81.3%) of the specimens. There was no statistical significant difference between the assays (p>0.05). Two of the 11 samples that RT-PCR negative Q-PCR positive, and 3 of 9 samples that RT-PCR positive Q-PCR negative were found to be CMV DNA positive by DNA sequencing. A good level of concordance between RT-PCR and Q-PCR assays for CMV DNA detection has been found. (author)

  13. In vitro ciprofloxacin resistance patterns of gram positive bacteria isolated from clinical specimens in a teaching hospital in Saudi Arabia

    International Nuclear Information System (INIS)

    Akhtar, N.; Alzahrani, A.; Obeid, O.El-Treify; Dassal, D.

    2009-01-01

    Over the last few decades the ever-increasing level of bacterial resistance to antimicrobials has been a cause of worldwide concern. Fluoroquinolones, particularly ciprofloxacin has been used indiscriminately for both gram-positive and gram-negative bacterial infections. The increased use of ciprofloxacin has led to a progressive loss of bacterial susceptibility to this antibiotic. Therefore it is necessary to have update knowledge of resistance pattern of bacteria to this antibiotic so that alternate appropriate antibiotics can be used for ciprofloxacin-resistant bacterial infections. Objective: To evaluate the trends of ciprofloxacin resistance pattern in commonly isolated gram positive bacteria over time in a Saudi Arabian teaching hospital. Methods: A retrospective analysis was carried out for ciprofloxacin susceptibility patterns of 5534 isolates of gram-positive bacteria isolated from clinical specimens submitted to microbiology laboratories at King Fahd Hospital of the University (KFHU), Al-Khobar, Saudi Arabia during the period from January 2002 to August 2005. Results: Increase in ciprofloxacin resistance rates with some fluctuations, among these isolates, were observed. For Staphylococcus aureus, it varied from 4.62, 1.83, 7.01 and 3.98%, methicillin resistant Staphylococcus aureus (MRSA) 97.92, 97.75, 87.01 and 88.26%, Streptococcus pyogenes 5.35, 4.47, 14.44 and 3.53% during the years 2002, 2003, 2004 and 2005 respectively. Cirprofloxacin resistance during the years 2002, 2004 and 2005 for other isolates was as follows: Streptococcus pneumoniae, 30.23, 23.02 and 26.47%; enterococcus group D, 43.05, 20.68 and 57.03% and non-enterococcus group D, 62.96, 76.92 and 87.50% respectively. Conclusion: Ciprofloxacin resistance in gram positive bacterial clinical isolates particularly Staphylococcus aureus, methicillin resistant Staphylococcus aureus (MRSA) enterococcus group D, and non-enterococcus group D, has greatly increased and ciprofloxacin no more remains

  14. Anaerobic Bacteria in Clinical Specimens - Frequent, But a Neglected Lot: A Five Year Experience at a Tertiary Care Hospital.

    Science.gov (United States)

    Shenoy, Padmaja Ananth; Vishwanath, Shashidhar; Gawda, Ashwini; Shetty, Seema; Anegundi, Renuka; Varma, Muralidhar; Mukhopadhyay, Chiranjay; Chawla, Kiran

    2017-07-01

    Anaerobic bacteria which constitute a significant proportion of the normal microbiota also cause variety of infections involving various anatomic sites. Considering the tedious culture techniques with longer turnaround time, anaerobic cultures are usually neglected by clinicians and microbiologists. To study the frequency of isolation of different anaerobic bacteria from various clinical specimens. A retrospective study to analyse the frequency of isolation of different anaerobic bacteria, was conducted over a period of five years from 2011 to 2015 including various clinical specimens submitted to anaerobic division of Microbiology laboratory. Anaerobic bacteria were isolated and identified following standard bacteriological techniques. Pathogenic anaerobes (n=336) were isolated from 278 (12.48%) of overall 2227 specimens processed with an average yield of 1.2 isolates. Anaerobes were isolated as polymicrobial flora with or without aerobic bacterial pathogens in 159 (57.2%) patients. Anaerobic Gram-negative bacilli (140, 41.7%) were the predominant isolates. B. fragilis group (67, 19.9%) were the most commonly isolated anaerobic pathogens. Anaerobes were predominantly isolated from deep seated abscess (23.9%). Pathogenic anaerobes were isolated from various infection sites. Unless culture and susceptibility tests are performed as a routine, true magnitude of antimicrobial resistance among anaerobic pathogens will not be known. Knowledge of the distribution of these organisms may assist in the selection of appropriate empirical therapy for anaerobic infections.

  15. Material Stress Fringe Constant Measurement of Specimen under Pure Bending Load by Use of Photoelastic Phase Shifting Method

    International Nuclear Information System (INIS)

    Liu, Guan Yong; Kim, Myung Soo; Baek, Tae Hyun

    2014-01-01

    In a photoelastic experiment, it is necessary to know the material stress fringe constant of the photoelastic specimen to determine the stresses from the measured isochromatic fringe orders. The material stress fringe constant can be obtained using a simple tension specimen and/or a circular disk under diametric compression. In these methods, there is generally a need to apply numerous loads to the specimen in response to the relationship of the fringe order. Then, the least squares method is used to obtain the material constant. In this paper, the fringe orders that appear on a four-point bending specimen are used to determine the fringe constant. This method requires four photoelastic fringes obtained from a circular polariscope by rotating the analyzer to 0, π/4, π/2, and 3π/4 radians. Using the four-point bending specimen to determine the material stress fringe constant has an advantage because measurements can be made at different locations by applying a constant load. The stress fringe constant measured with this method is within the range suggested by the manufacturer of the photoelastic material

  16. Morphing methods to parameterize specimen-specific finite element model geometries.

    Science.gov (United States)

    Sigal, Ian A; Yang, Hongli; Roberts, Michael D; Downs, J Crawford

    2010-01-19

    Shape plays an important role in determining the biomechanical response of a structure. Specimen-specific finite element (FE) models have been developed to capture the details of the shape of biological structures and predict their biomechanics. Shape, however, can vary considerably across individuals or change due to aging or disease, and analysis of the sensitivity of specimen-specific models to these variations has proven challenging. An alternative to specimen-specific representation has been to develop generic models with simplified geometries whose shape is relatively easy to parameterize, and can therefore be readily used in sensitivity studies. Despite many successful applications, generic models are limited in that they cannot make predictions for individual specimens. We propose that it is possible to harness the detail available in specimen-specific models while leveraging the power of the parameterization techniques common in generic models. In this work we show that this can be accomplished by using morphing techniques to parameterize the geometry of specimen-specific FE models such that the model shape can be varied in a controlled and systematic way suitable for sensitivity analysis. We demonstrate three morphing techniques by using them on a model of the load-bearing tissues of the posterior pole of the eye. We show that using relatively straightforward procedures these morphing techniques can be combined, which allows the study of factor interactions. Finally, we illustrate that the techniques can be used in other systems by applying them to morph a femur. Morphing techniques provide an exciting new possibility for the analysis of the biomechanical role of shape, independently or in interaction with loading and material properties. Copyright 2009 Elsevier Ltd. All rights reserved.

  17. Antibacterial activity of amino- and amido- terminated poly (amidoamine)-G6 dendrimer on isolated bacteria from clinical specimens and standard strains

    Science.gov (United States)

    Rastegar, Ayoob; Nazari, Shahram; Allahabadi, Ahmad; Falanji, Farahnaz; Akbari Dourbash, Fakhreddin Akbari Dourbash; Rezai, Zahra; Alizadeh Matboo, Soudabeh; Hekmat-Shoar, Reza; Mohseni, Seyed Mohsen; Majidi, Gharib

    2017-01-01

    Background: Nanoscale poly (amidoamine) dendrimers have been investigated for their biological demands, but their antibacterial activity has not been widely discovered. Thus, the sixth generation of poly (amidoamine) dendrimer (PAMAM-G6) was synthesized and its antibacterial activities were evaluated on Gram-negative bacteria; P. aeruginosa, E. coli, A. baumannii, S. typhimurium, S. dysenteriae, K. pneumoniae, P. mirabilis, and Gram-positive bacteria, and S.aureus and B. subtilis, which were isolated from different clinical specimens and standard strains of these bacteria. Methods: In this study, 980 specimens including urine (47%), blood (27%), sputum (13%), wounds (8%), and burns (5%) were collected from clinical specimens of 16 hospitals and clinics in city of Sabzevar, Iran. Then, the target bacteria were isolated and identified using standard methods. Minimum inhibitory concentration and minimum bactericidal concentrations against Gram-positive and Gram-negative bacteria were determined according to guidelines described by clinical and laboratory standards institute (CLSI). Standard discs were prepared using 0.025, 0.25, 2.5, and 25 μg/mL concentrations of PAMAM-G6 on Mueller-Hinton agar plates to determinate the zone of inhibition. The cytotoxicity of PAMAM-G6 dendrimer was evaluated in HCT116 cells by MTT assay. Results: The most important isolated bacteria were E. coli (23.65%), S. aureus (24.7%), P. aeruginosa (10.49%), B. subtilis (7.7%), S. typhimurium (8.87%), A. baumannii (7.02%), K. pneumoniae (7.1%), P. mirabilis (6.46%), and S. dysenteriae (3.6%). Moreover, it was found that poly (amidoamine)–G6 exhibited more antibacterial efficacy on standard strains than isolated bacteria from clinical samples (p<0.05). The cytotoxicity of PAMAM-G6 to the cells showed that cytotoxicity depended on the concentration level and exposure time. Conclusion: The PAMAM-G6 dendrimer showed a positive impact on the removal of dominant bacterial isolated from clinical

  18. Comparison of HER2 and phospho-HER2 expression between biopsy and resected breast cancer specimens using a quantitative assessment method.

    Directory of Open Access Journals (Sweden)

    Yalai Bai

    Full Text Available BACKGROUND: HER2/Neu (ErbB-2 overexpression, which occurs in 15-20% of breast cancer cases, is associated with better response to treatment with the drug trastuzumab. PhosphoHER2 (pHER2 has been evaluated for prediction of response to trastuzumab. Both markers are heterogeneously detected and are potentially subject to loss as a consequence of delayed time to fixation. Here, we quantitatively assess both markers in core needle biopsies (CNBs and matched tumor resections to assess concordance between the core and the resection and between HER2 and pHER2. METHODS: A selected retrospective collection of archival breast cancer cases yielded 67 cases with both core and resection specimens. Both HER2 and pTyr(1248HER2 were analyzed by the AQUA® method of quantitative immunofluorescence on each specimen pair. RESULTS: Both HER2 immunoreactivity (P<0.0001 and pTyr(1248HER2 immunoreactivity (P<0.0001 were lower in resections relative to CNB specimens. However, clinical implications of this change may not be evident since no case changed from 3+ (CNB to negative (resection. Assessment of pTyr(1248HER2 showed no direct correlation with HER2 in either CNB or resection specimens. CONCLUSIONS: The data suggest that measurement of both HER2 and phospho- Tyr(1248HER2, in formalin-fixed tissue by immunological methods is significantly affected by pre-analytic variables. The current study warrants the adequate handling of resected specimens for the reproducible evaluation of HER2 and pHER2. The level of pTyr(1248HER2, was not correlated to total HER2 protein. Further studies are required to determine the significance of these observations with respect to response to HER2 directed therapies.

  19. Dried blood spot specimen quality and validation of a new pre-analytical processing method for qualitative HIV-1 PCR, KwaZulu-Natal, South Africa

    Science.gov (United States)

    Parboosing, Raveen; Siyaca, Ntombizandile; Moodley, Pravikrishnen

    2016-01-01

    Background Poor quality dried blood spot (DBS) specimens are usually rejected by virology laboratories, affecting early infant diagnosis of HIV. The practice of combining two incompletely-filled DBS in one specimen preparation tube during pre-analytical specimen processing (i.e., the two-spot method) has been implemented to reduce the number of specimens being rejected for insufficient volume. Objectives This study analysed laboratory data to describe the quality of DBS specimens and the use of the two-spot method over a one-year period, then validated the two-spot method against the standard (one-spot) method. Methods Data on HIV-1 PCR test requests submitted in 2014 to the Department of Virology at Inkosi Albert Luthuli Central Hospital in KwaZulu-Natal province, South Africa were analysed to describe reasons for specimen rejection, as well as results of the two-spot method. The accuracy, lower limit of detection and precision of the two-spot method were assessed. Results Of the 88 481 specimens received, 3.7% were rejected for pre-analytical problems. Of those, 48.9% were rejected as a result of insufficient specimen volume. Two health facilities had significantly more specimen rejections than other facilities. The two-spot method prevented 10 504 specimen rejections. The Pearson correlation coefficient comparing the standard to the two-spot method was 0.997. Conclusions The two-spot method was comparable with the standard method of pre-analytical specimen processing. Two health facilities were identified for targeted retraining on specimen quality. The two-spot method of DBS specimen processing can be used as an adjunct to retraining, to reduce the number of specimens rejected and improve linkage to care. PMID:28879108

  20. Dried blood spot specimen quality and validation of a new pre-analytical processing method for qualitative HIV-1 PCR, KwaZulu-Natal, South Africa.

    Science.gov (United States)

    Govender, Kerusha; Parboosing, Raveen; Siyaca, Ntombizandile; Moodley, Pravikrishnen

    2016-01-01

    Poor quality dried blood spot (DBS) specimens are usually rejected by virology laboratories, affecting early infant diagnosis of HIV. The practice of combining two incompletely-filled DBS in one specimen preparation tube during pre-analytical specimen processing (i.e., the two-spot method) has been implemented to reduce the number of specimens being rejected for insufficient volume. This study analysed laboratory data to describe the quality of DBS specimens and the use of the two-spot method over a one-year period, then validated the two-spot method against the standard (one-spot) method. Data on HIV-1 PCR test requests submitted in 2014 to the Department of Virology at Inkosi Albert Luthuli Central Hospital in KwaZulu-Natal province, South Africa were analysed to describe reasons for specimen rejection, as well as results of the two-spot method. The accuracy, lower limit of detection and precision of the two-spot method were assessed. Of the 88 481 specimens received, 3.7% were rejected for pre-analytical problems. Of those, 48.9% were rejected as a result of insufficient specimen volume. Two health facilities had significantly more specimen rejections than other facilities. The two-spot method prevented 10 504 specimen rejections. The Pearson correlation coefficient comparing the standard to the two-spot method was 0.997. The two-spot method was comparable with the standard method of pre-analytical specimen processing. Two health facilities were identified for targeted retraining on specimen quality. The two-spot method of DBS specimen processing can be used as an adjunct to retraining, to reduce the number of specimens rejected and improve linkage to care.

  1. [The in vitro antifungal activities of fluconazole against pathogenic yeasts recently isolated from clinical specimens].

    Science.gov (United States)

    Yamaguchi, H; Igari, J; Kume, H; Abe, M; Oguri, T; Kanno, H; Kawakami, S; Okuzumi, K; Fukayama, M; Ito, A; Kawata, K; Uchida, K

    1997-09-01

    The emergence of Candida albicans resistance to azole antifungal agents have been reported in the U. S. and Europe. We examined the in vitro antifungal activities of fluconazole against clinical isolates collected by seven investigators in three years to examine if a tendency existed toward the development of azole-resistance among fungal isolates in Japan. The following results were obtained: 1. Sensitivities to fluconazole (FLCZ) were determined for yeast-like fungi, including 113 strains isolated in 1993, 149 strains isolated in 1994 and 205 strains isolated in 1995. No significant differences in sensitivities in the three years were detected. 2. Minimum inhibitory concentrations of FLCZ were 0.1-0.78 microgram/ml for C. albicans and 3.13-25 micrograms/ml for C. glabrata. Strains with 25 micrograms/ml of FLCZ's MIC were detected; two strains of C. krusei and one strain each of C. krusei, Trichospron beigelii and Hansenula anomala. No strains with higher than 50 micrograms/ml MIC of FLCZ were detected. 3. In vitro activities of FLCZ were compared between clinical strains isolated between 1993 and 1995 and clinical strains isolated before the marketing of FLCZ (up to December 1987) or clinical yeasts isolated between 1991 and 1992. No significant differences were observed, suggesting that no tendency existed toward azole resistance among fungal strains examined.

  2. Frequency of Chlamydia trachomatis in genital specimens: kerman city, PCR method

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    Khalili M

    2008-06-01

    Full Text Available Background: Chlamydia trachomatis (CT is an obligate intracellular bacterium that causes genital disease and the most common sexually transmitted infection in the world. The most frequent risk factors associated with chlamydial infection are related to sexual behavior, multiple partners, and inconsistent condom use. Presenting primarily as urtheritis in men and cervicitis in women, CT a major cause of chronic pelvic inflammatory disease and subsequent infertility in women, eye and lung infection in newborns and other manifestations. Identification of CT-infected patients may prevent its spread and thereby reduce the high morbidity associated with CT infections. Polymerase chain reaction (PCR is a sensitive and specific method for the detection of small quantity of bacterial DNA in clinical samples. The aim of this study was to determine the frequency of C. trachomatis by PCR in genital samples from patients in the city of Kerman.Methods: A total of 130 genital samples including 64 endocervical and 66 urethral swab samples were collected by physicians. Nucleic acid was extracted from each sample using a commercial DNA extraction kit. PCR primers specific for a conserved region of the C. trachomatis omp2 gene, encoding an outer membrane protein, were used for amplification.  Results: A total of 9.2% (6.25% of cervicitis and 12.1% of urethritis of the samples were found positive for CT using this PCR method. Conclusions:  The present study shows a high prevalence of CT infection, especially in men with urethritis. Such patients should be referred to genitourinary clinics for treatment and partner notification. Given its worldwide prevalence, further CT studies on more populations are needed to assess potential public health implications of these infections.

  3. Microbiology specimens obtained at the time of surgical lung biopsy for interstitial lung disease: clinical yield and cost analysis.

    Science.gov (United States)

    Fibla, Juan J; Brunelli, Alessandro; Allen, Mark S; Wigle, Dennis; Shen, Robert; Nichols, Francis; Deschamps, Claude; Cassivi, Stephen D

    2012-01-01

    In efforts to obtain complete results, current practice in surgical lung biopsy (LB) for interstitial lung disease (ILD) recommends sending lung tissue samples for bacterial, mycobacterial, fungal, and viral cultures. This study assesses the value of this practice by evaluating the microbiology findings obtained from LB for ILD and their associated costs. A total of 296 consecutive patients (140 women, 156 men, median age=61 years) underwent LB for ILD from 2002 to 2009. All had lung tissue sent for microbiology examination. Microbiology results and resultant changes in patient management were analyzed retrospectively. A cost analysis was performed based upon nominal hospital charges adjusted on current inflation rates. Cost data included cultures, stains, smears, direct fluorescent antibody studies, and microbiologist consulting fees. As many as 25 patients (8.4%) underwent open LB and 271 (91.6%) underwent thoracoscopic LB. A total of 592 specimens were assessed (range 1-4 per patient). The most common pathologic diagnoses were idiopathic pulmonary fibrosis in 122 (41.2%), cryptogenic organizing pneumonia in 31 (10.5%), and respiratory bronchiolitis ILD in 16 (5.4%). Microbiology testing was negative in 174 patients (58.8%). A total of 118 of 122 (96.7%) positive results were clinically considered to be contaminants and resulted in no change in clinical management. The most common contaminants were Propionibacterium acnes (38 patients; 31%) and Penicillium fungus (16 patients; 13%). In only four patients (1.4%), the organism cultured (Nocardia one, Histoplasma one, and Aspergillus fumigatus two) resulted in a change in clinical management. The cost of microbiology studies per specimen was $984 (€709), with a total cost for the study cohort being $582,000 (€420,000). The yield and impact on clinical management of microbiology specimens from LB for ILD is very low. Its routine use in LB is questionable. We suggest it should be limited to those cases of ILD with

  4. Clinical map document based on XML (cMDX: document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens

    Directory of Open Access Journals (Sweden)

    Bettendorf Olaf

    2010-11-01

    Full Text Available Abstract Background The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa. The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed. For this purpose we developed cMDX. Methods The document architecture of cMDX was designed according to Open Packaging Conventions by separating the whole data into template data and patient data. Analogue custom XML elements were considered to harmonize the graphical representation (e.g. tumour extension with the textual data (e.g. histological patterns. The graphical documentation was based on the four-layer visualization model that forms the interaction between different custom XML elements. Sensible personal data were encrypted with a 256-bit cryptographic algorithm to avoid misuse. In order to assess the clinical value, we retrospectively analysed the tumour extension in 255 patients after radical prostatectomy. Results The pathology report with cMDX can represent pathological findings of the prostate in schematic styles. Such reports can be integrated into the hospital information system. "cMDX" documents can be converted into different data formats like text, graphics and PDF. Supplementary tools like cMDX Editor and an analyser tool were implemented. The graphical analysis of 255 prostatectomy specimens showed that PCa were mostly localized in the peripheral zone (Mean: 73% ± 25. 54% of PCa showed a multifocal growth pattern. Conclusions cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis.

  5. Improved Procedure for Transport of Dental Plaque Samples and Other Clinical Specimens Containing Anaerobic Bacteria

    Science.gov (United States)

    Spiegel, Carol A.; Minah, Glenn E.; Krywolap, George N.

    1979-01-01

    An improved transport system for samples containing anaerobic bacteria was developed. This system increased the recovery rate of anaerobic bacteria up to 28.8% as compared to a commonly used method. PMID:39087

  6. Metallo- β-lactamases among Multidrug Resistant (MDR Gram Negative Bacteria Isolated from Clinical Specimens during 2009 in Sanandaj, Kurdistan Province

    Directory of Open Access Journals (Sweden)

    Himen Salimizand

    2012-08-01

    Full Text Available Background: Today, there are numerous reports about emerging multi drug resistant gram negative bacteria all around the world, especially in ICUs. Rarely, Metallo-β-lactamase (MBL enzymes are responsible for these cases. Study of MBLs for diagnosing and preventing distribution of the origin of infection are critical issues. In addition, we would like to compare the efficacy of Iranian and foreign- made antibiotic disks. Materials and Methods: During 2009 all entered clinical specimens to the laboratory tested for detecting gram negative bacteria. Isolated bacteria were tested by Kirby-Bauer method to antibiotic susceptibility test by Iranian and foreign (MAST disks. For gram negative carbapenem resistant isolates, PCR technique used to detect VIM, GIM, and SIM variants of MBLs.Results: During one year, 17890 clinical specimens referred Besat laboratory. The most specimen was Urine (8172 followed by blood culture (5190 that in which 1110 gram negative and positives isolated. Out of which, 778 (70% of isolates were gram negatives. MDR gram negatives were 157 (20.2%. Imipenem and meropenem were the most efficient antibiotics (all susceptible and ceftriaxone was the least (19 % susceptible. E. coli was the most prevalent isolate. 79 Gram negative isolates (10.1% were resistant to Iranian-made discs but all susceptible for foreign ones. All 79 isolates were tested by PCR for MBL genes, that, all were negative. Besides, Iranian imipenem and cefepime disks have had distinguishable difference in susceptibility of isolates.Conclusion: Fortunately, none of gram negative isolates were MBL producer, which revealed no colonization of MBL producing bacteria. Iranian-made disks appear efficient except for imipenem and cefepime.

  7. Development of a strain measurement method for non-plane specimens by means of computer picture processing

    International Nuclear Information System (INIS)

    Yoshioka, Akira; Soneda, Naoki; Yagawa, Genki; Miyoshi, Akio.

    1988-01-01

    Integrity Tests of the Fast Breeder Reactor components are often conducted at an elevated temperature, say 550deg C. Since high-temperature strain measurement using special strain gauges is costly and unappropriate for large and repeated strains, the authors have developed an optical strain measurement method and system based on computer picture processing and the triangulation principle. The present method enables us to measure the strain in specimen with curved surfaces. Its operation is also easy, because of the automatic distinction of marks from noises. The verification tests with a plate specimen and a cylindrical one are performed under elevated temperatures. The results show that the present method is very suitable to the tests under elevated temperatures and that the measurement error of strain is within 0.2 % (2000μ), which is reasonable considering the limitation of hardware. (author)

  8. Donor Derived Candida stellimalicola in a Clinical Specimen: Preservation Fluid Contamination During Pancreas Procurement.

    Science.gov (United States)

    Dupont, Damien; Huguenin, Antoine; Tisserand, Elodie; Reiter, Véronique; Morelon, Emmanuel; Badet, Lionel; Villena, Isabelle; Wallon, Martine; Toubas, Dominique

    2017-07-05

    We report here a case of possible donor-derived Candida stellimalicola infection after pancreas transplantation. Candida stellimalicola, an environmental non-filamentous yeast, was isolated from both the peritoneal fluid of the graft donor and the preservation fluid of the transplanted pancreas. Interestingly, this strain exhibited high minimum inhibitory concentrations to azoles. These results justified the use of echinocandins as therapy instead of fluconazole. This switch permitted a favorable outcome. To our knowledge, this is the first report of C. stellimalicola from clinical samples and therefore the first reported case of a possible human infection. This case report highlights the need for standardized microbiological procedures in solid organ transplant settings. Moreover, it underlines the importance of using molecular identification technique when routine techniques do not allow successful identification of the pathogen. It is of utmost importance to determine sensitivity profile, even in the absence of species-level identification, because resistance to fluconazole is not uncommon, especially in emergent species.

  9. Various Statistical Methods in Use for Evaluating Human Malignant Gastric Specimens

    Directory of Open Access Journals (Sweden)

    Ventzeslav Enchev

    1998-01-01

    Full Text Available This paper presents the use of certain statistical methods (comparison of means – independent samples t‐test, multiple linear regression analysis, multiple logistic regression analysis, analysis of clusters, etc. included in the SPSS Statistical Package used to classify the patients quantitatively evaluated after a subtotal resection of their stomachs. The group consisted of 40 patients subdivided into two groups: primary neoplasia of the stomach (20 patients, and corresponding lymphogenic deposits in the abdominal perigastric lymph nodes (20 patients. Paraffin‐embedded tissue sections (thickness 4–5µm prepared as consecutive hematoxylin‐eosin‐stained slides were morphometrically measured by a rotation of a graduated eyepiece‐micrometer; thus, we obtained the minor and major axes’ lengths of the elliptic nuclear profiles and the minor and major caliper diameters of the corresponding cellular profiles. These four variables were used to determine the dynamic changes in quantitative features of human gastric lesions when passing from normal histological structures, through hyperplastic processes (chronic gastritis, gastric precancer (ulcers and polyps with or without malignancy till the development of primary carcinomas and their corresponding lymphogeneous metastases. Besides the increased cytomorphometrical measures, we also noted an opportunity to classify the patients according to these data as well as to add to the knowledge of our consultation system for clinical aid and use, recently published in the literature.

  10. Detection of hMPV antigen by EIA in clinical specimens.

    Science.gov (United States)

    Pancer, Katarzyna; Ciaćka, Agnieszka; Gut, Włodzimierz; Lipka, Bozena; Mierzejewska, Justyna; Milewska-Bobula, Bogumiła; Smorczewska-Kiljan, Anna; Jahnz-Rózyk, Karina; Litwińska, Bogumiła

    2011-01-01

    Human Metapneumovirus (hMPV) is one of the latest discovered viruses. It has been classified to Paramyxoviridae family. It is the second viral etiological agent, after RSV, which causes respiratory tract infections (RTI) in children, especially children below 5 years old. It is estimated that 5-25% of RTI in children is due to hMPV. In adults hMPV reinfections are bounded to upper respiratory tract infections. The aim of the study was to establish usefulness of ELISA test in detecting hMPV antigen and to analyze hMPV infection in connection to clinical diagnosis. 273 nasopharyngeal swabs from children (189 swabs) and adults (84 swabs) with respiratory tract infections collected from 2008 to 2010 were examined. Due to similarity of hMPV and RSV viruses and overlapping of their epidemic season rapid immunochromatographic test for RSV antigen detection was also performed in case of 120 samples, hMPV antigen was detected in 24.5% of all swabs (n = 67): in 0.0% probes in 2008, 29.0% in 2009 and 36.8% in first quarter of 2010. The highest rate ofhMPV infection was detected from summer of 2009 till the end of March 2010 (VIII-IX 2009 - 62.5%, X-XII 2009 - 44.1% and I-III 2010 -36.8%). We analyzed respiratory tract diseases reported in patients with hMPV infection. Infection due to hMPV was found in 26.5% of children and 24.0% of adults with recognized pneumonia, respectively in 28.4 and 17.6% of patients with bronchitis. Bronchiolitis was diagnosed in two children with hMPV. RSV and hMPV coinfections were confirmed in 15 out of 120 examined probes. Cross reaction pattern was excluded thanks to ELISA hMPV antigen test which was performed with suspension of RSV and thanks to statistical analysis. Coinfections were confirmed in 8% of pneumonia, 11% of bronchitis and 24.2% of the rest concomitant diagnoses. We found hMPV infection as the significant agent ofpneumonia not only in children but also in adults. ELISA hMPV antigen test can be used in diagnosis of etiological agent

  11. Molecular and antimicrobial susceptibility profiling of atypical Streptococcus species from porcine clinical specimens.

    Science.gov (United States)

    Moreno, Luisa Z; Matajira, Carlos E C; Gomes, Vasco T M; Silva, Ana Paula S; Mesquita, Renan E; Christ, Ana Paula G; Sato, Maria Inês Z; Moreno, Andrea M

    2016-10-01

    The Streptococcus species present broad phenotypic variation, making identification difficult using only traditional microbiological methods. Even though Streptococcus suis is the most important species for the worldwide swine industry, other Streptococcus species appear to be able to cause disease in swine and could represent a higher underestimated risk for porcine health. The aim of this study was to identify Streptococcus-like isolates by MALDI-TOF MS and 16S rRNA sequencing and further molecular and antibiotic susceptibility characterization of the atypical Streptococcus species capable of causing disease in swine. Fifty presumptive Streptococcus isolates from diseased pigs isolated from different Brazilian States between 2002 and 2014 were evaluated. Among the studied isolates, 26% were identified as Streptococcus hyovaginalis, 24% as Streptococcus plurianimalium, 12% as Streptococcus alactolyticus, 10% as Streptococcus hyointestinalis, and the remaining isolates belonged to Streptococcus henryi (6%), Streptococcus thoraltensis (6%), Streptococcus gallolyticus (6%), Streptococcus gallinaceus (4%), Streptococcus sanguinis (4%), and Streptococcus mitis (2%). The Streptococcus isolates were successfully identified by spectral cluster analysis and 16S rRNA sequencing with 96% of concordance between the techniques. The SE-AFLP analysis also supported Streptococcus species distinction and enabled further observation of higher genetic heterogeneity intra-species. The identified Streptococcus species presented variable MIC values to β-lactams, enrofloxacin and florfenicol, and high resistance rates to tetracyclines and macrolides, which appear to be directly related to the industry's antimicrobial usage and resistance selection. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Identification of mucorales from clinical specimens: a 4-year experience in a single institution.

    Science.gov (United States)

    Yang, Mina; Lee, Jang Ho; Kim, Young Kwon; Ki, Chang Seok; Huh, Hee Jae; Lee, Nam Yong

    2016-01-01

    Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales.

  13. Development of sandwich-form biosensor to detect Mycobacterium tuberculosis complex in clinical sputum specimens.

    Science.gov (United States)

    Shojaei, Taha Roodbar; Mohd Salleh, Mohamad Amran; Tabatabaei, Meisam; Ekrami, Alireza; Motallebi, Roya; Rahmani-Cherati, Tavoos; Hajalilou, Abdollah; Jorfi, Raheleh

    2014-01-01

    Mycobacterium tuberculosis, the causing agent of tuberculosis, comes second only after HIV on the list of infectious agents slaughtering many worldwide. Due to the limitations behind the conventional detection methods, it is therefore critical to develop new sensitive sensing systems capable of quick detection of the infectious agent. In the present study, the surface modified cadmium-telluride quantum dots and gold nanoparticles conjunct with two specific oligonucleotides against early secretory antigenic target 6 were used to develop a sandwich-form fluorescence resonance energy transfer-based biosensor to detect M. tuberculosis complex and differentiate M. tuberculosis and M. bovis Bacille Calmette-Guerin simultaneously. The sensitivity and specificity of the newly developed biosensor were 94.2% and 86.6%, respectively, while the sensitivity and specificity of polymerase chain reaction and nested polymerase chain reaction were considerably lower, 74.2%, 73.3% and 82.8%, 80%, respectively. The detection limits of the sandwich-form fluorescence resonance energy transfer-based biosensor were far lower (10 fg) than those of the polymerase chain reaction and nested polymerase chain reaction (100 fg). Although the cost of the developed nanobiosensor was slightly higher than those of the polymerase chain reaction-based techniques, its unique advantages in terms of turnaround time, higher sensitivity and specificity, as well as a 10-fold lower detection limit would clearly recommend this test as a more appropriate and cost-effective tool for large scale operations. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

  14. Detection of Histoplasma capsulatum from clinical specimens by cycling probe-based real-time PCR and nested real-time PCR.

    Science.gov (United States)

    Muraosa, Yasunori; Toyotome, Takahito; Yahiro, Maki; Watanabe, Akira; Shikanai-Yasuda, Maria Aparecida; Kamei, Katsuhiko

    2016-05-01

    We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Improved detection of Burkholderia pseudomallei from non-blood clinical specimens using enrichment culture and PCR: narrowing diagnostic gap in resource-constrained settings.

    Science.gov (United States)

    Tellapragada, Chaitanya; Shaw, Tushar; D'Souza, Annet; Eshwara, Vandana Kalwaje; Mukhopadhyay, Chiranjay

    2017-07-01

    To evaluate the diagnostic utility of enrichment culture and PCR for improved case detection rates of non-bacteraemic form of melioidosis in limited resource settings. Clinical specimens (n = 525) obtained from patients presenting at a tertiary care hospital of South India with clinical symptoms suggestive of community-acquired pneumonia, lower respiratory tract infections, superficial or internal abscesses, chronic skin ulcers and bone or joint infections were tested for the presence of Burkholderia pseudomallei using conventional culture (CC), enrichment culture (EC) and PCR. Sensitivity, specificity, positive and negative predictive values of CC and PCR were initially deduced using EC as the gold standard method. Further, diagnostic accuracies of all the three methods were analysed using Bayesian latent class modelling (BLCM). Detection rates of B. pseudomallei using CC, EC and PCR were 3.8%, 5.3% and 6%, respectively. Diagnostic sensitivities and specificities of CC and PCR were 71.4, 98.4% and 100 and 99.4%, respectively in comparison with EC as the gold standard test. With Bayesian latent class modelling, EC and PCR demonstrated sensitivities of 98.7 and 99.3%, respectively, while CC showed a sensitivity of 70.3% for detection of B. pseudomallei. An increase of 1.6% (95% CI: 1.08-4.32%) in the case detection rate of melioidosis was observed in the study population when EC and/or PCR were used in adjunct to the conventional culture technique. Our study findings underscore the diagnostic superiority of enrichment culture and/or PCR over conventional microbiological culture for improved case detection of melioidosis from non-blood clinical specimens. © 2017 John Wiley & Sons Ltd.

  16. Clinical value of detection of HPL-expressing intermediate trophoblasts in abortion or curettage-obtained specimens for diagnosis of intrauterine or ectopic pregnancies

    International Nuclear Information System (INIS)

    He Xiaomei; Wang Yuping; Wang Lisha; Yang Jingxiu; Gao Xueyan

    2005-01-01

    Objective: To investigate the value of detection of HPL-expressing intermediate trophoblasts in endometrial specimens for diagnosis of intrauterine and ectopic pregnancies. Methods: The examined specimens included: (1) Group I, 35 specimens with suspected intermediate trophoblast in decidua (2) Group II, 30 specimens with decidua-like plump endometrial stroma cells and/ or A-S phenomena in glandular epithelium (3) 30 specimens from proven intrauterine pregnancies serving as controls. Histochemistry (SP method) was used for HPL detection in all these specimens. Results: In the 30 proven intrauterine pregnancies, decidua and villa were present in all the specimens. Only 24 of the 30 were found to be HPL(+) with 6 HPL negatives (20%). In Group I , 28 of the 35 specimens were found to be HPL(+) and all of 28 were from intrauterine pregnancies: Of the 7 HPL negative cases, 5 were later confirmed as with ectopic pregnancy, the remaining 2 were with intrauterine pregnancy. In Group II, 22 of 30 specimens were HPL(+) and all were from intrauterine pregnancy. Of the 8 HPL negative cases, 6 were later confirmed as with ectopic pregnancy and 2 were with intrauterine pregnancy. Combining the data from Group I and II, we could see that in the total 15 HPL negative cases, 11 were with ectopic pregnancy (11/15=73.3%) and 4 were with intrauterine pregnancy (4/15=26.7%). Conclusion: In specimens of intrauterine contents, demonstration of HPL (+) cells could be regarded as confirmative evidence of intrauterine pregnancy. However, the reverse did not hold true. Many of the HPL negative specimens were from intrauterine pregnancies (in this study 4/15 or 26.7%). Therefore, in HPL negative cases, there was a high possibility of ectopic pregnancy but further examinations were required to ascertain the diagnosis. (authors)

  17. An inexpensive and rapid method for extracting papilionoid genomic DNA from herbarium specimens.

    Science.gov (United States)

    Riahi, M; Zarre, S; Maassoumi, A A; Attar, F; Kazempour Osaloo, S

    2010-07-13

    Three DNA extraction protocols were compared for their ability to yield DNA from the leaves of herbarium specimens of nine species from nine genera of the Papilionoideae. We tested two protocols that use classic procedures for lysis and purification with cetyl trimethylammonium bromide (CTAB); a third protocol used a Nucleospin Plant kit. DNA obtained from all three procedures was quantified and tested by PCR. Test results indicated the superiority of one of the CTAB protocols. We made some modifications, developing a protocol that produced high-quality DNA from all nine species. The modification involved the use of a lower EDTA concentration (20 mM instead of 50 mM) and a higher beta-mercaptoethanol concentration (1% instead of 0.4%) in the extraction buffer. The modified protocol avoids the necessity for a second DNA precipitation step. This new CTAB protocol includes the use of 1.4 M NaCl, 20 mM EDTA and 1% beta-mercaptoethanol in the extraction; DNA precipitation time is reduced. A reduction in contaminating metabolites (such as PCR inhibitors) in the sample mixtures and lower costs for reagents are characteristics of this modified protocol; the cost of analysis per sample was lowered, compared to previous options. The quality of DNA was suitable for PCR amplification. This is a practical alternative to more difficult, time-consuming and expensive protocols.

  18. Biological specimens for community-based surveillance studies: Method of recruitment matters

    Directory of Open Access Journals (Sweden)

    Brenda L. Coleman

    2011-12-01

    Full Text Available Studies requiring the collection of biological specimens are often difficult to perform and costly. We compare face-to-face and telephone interviews to determine which is more effective for return of self-collected rectal swabs from subjects living in rural and semi-rural areas of Ontario, Canada. People interviewed face-to-face in 2006-2007 were asked to provide a rectal swab while the interviewer waited. Those interviewed by telephone were sent a package and asked to return the swab by mail, with one follow-up reminder call. Telephone interviewing resulted in a higher response rate for the completion of household and individual-level questionnaires. However, face-to-face interviews resulted in a significantly higher proportion of interviewees who returned swabs making the participation rate higher for this mode of contact (33.7 versus 25.0 percent. Using multivariable logistic regression, higher rates of rectal swab return were associated with face-to-face interviewing while adjusting for the impact of household size and respondent age and sex. For studies requiring the submission of intimate biological samples, face-to-face interviews can be expected to provide a higher rate of return than telephone interviews.

  19. Development of a method evaluation of deformation and fracture characteristics using small specimens

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, D. l.; Ahn, J. H.; Ju, J. B.; Choi, Y.; Lee, B. W. [Seoul National Univ., Seoul (Korea)

    2000-04-01

    In this study, the flow properties of various structural steels were estimated by analyzing the indentation load-depth curve obtained by ball indentation and the pile-up or sink-in phenomenon around indentation. The constraint factor {psi} was then related to the work-hardening characteristics of material. For various steels such as SA508, TMCP, SM50, SA213, SA106, and AISI1025, the results of indentation test were compared to those of tensile test, which shows that the present analysis can predict successfully the plastic flow properties of structural steels. In this study, in order to obtain more reliable fracture characteristics based on fracture mechanics, the pre-crack is introduced to SP specimen and acoustic emission is used to determine the crack initiation point. Using the load at crack initiation point, the fracture toughnesses of SA 508 Cl.3 steel, STS 304 stainless steel, SM 50 steel and TMCP steel were calculated successfully. 58 refs., 22 figs., 5 tabs. (Author)

  20. Comparison of immersion density and improved microstructural characterization methods for measuring swelling in small irradiated disk specimens

    International Nuclear Information System (INIS)

    Sawai, T.; Suzuki, M.; Hishinuma, A.; Maziasz, P.J.

    1992-01-01

    The procedure of obtaining microstructural data from reactor-irradiated specimens has been carefully checked for accuracy by comparison of swelling data obtained from transmission electron microscopy (TEM) observations of cavities with density-change data measured using the Precision Densitometer at Oak Ridge National Laboratory (ORNL). Comparison of data measured by both methods on duplicate or, in some cases, on the same specimen has shown some appreciable discrepancies for US/Japan collaborative experiments irradiated in the High Flux Isotope Reactor (HFIR). The contamination spot separation (CSS) method was used in the past to determine the thickness of a TEM foil. Recent work has revealed an appreciable error in this method that can result in an overestimation of the foil thickness. This error causes lower swelling values to be measured by TEM microstructural observation relative to the Precision Densitometer. An improved method is proposed for determining the foil thickness by the CSS method, which includes a correction for the systematic overestimation of foil thickness. (orig.)

  1. Evaluación de cuatro métodos para la detección de Staphylococcus aureus meticilino-resistente de muestras clínicas en un hospital regional Evaluation of four methods for detecting methicillin-resistant Staphylococcus aureus isolates from clinical specimens at a regional hospital in Mexico

    Directory of Open Access Journals (Sweden)

    Gabriel Acosta-Pérez

    2012-02-01

    Full Text Available OBJETIVO: Investigar la prevalencia de Staphylococcus aureus meticilino-resistente (MRSA en aislados clínicos y determinar la concordancia entre los métodos de detección de MRSA en un laboratorio con recursos y personal limitado. MATERIAL Y MÉTODOS: Se analizaron 140 cepas de Staphylococcus aureus aisladas de muestras clínicas de diferentes departamentos mediante pruebas convencionales: producción de β-lactamasa, sensibilidad a oxacilina con MIC-Vitek 2-XL, ChromID MRSA, difusión en agar para discos de 30 μg de cefoxitina, detección de PBP2a y PCR para el gen mecA. Se determinó el índice kappa de Cohen, para evaluar la concordancia entre los diferentes métodos utilizados. RESULTADOS: La prevalencia encontrada fue de 90.7%. La sensibilidad y especificidad para los diferentes métodos de detección fue: difusión en disco para cefoxitina 97 y 92% respectivamente, MIC Vitek 2-XL 97 y 69%, ChromoID MRSA 97 y 85% y detección de PBP2a 98 y 100%. CONCLUSIONES: Todos los métodos son muy buenos para la detección de MRSA; la elección en el uso de cada método dependerá de la infraestructura de cada laboratorio.OBJETIVE: To estimate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA in clinical isolates and to compare different methods for detection of MRSA in a lab with limited available personnel and resources. MATERIAL AND METHODS: 140 Staphylococcus aureus strains isolated from patients in several departments were assayed for β-lactamase production, MIC-Vitek 2 oxacillin, ChromID MRSA, disk diffusion in agar for cefoxitin 30 μg and PBP2a detection. The results of conventional tests were compared with the "gold standard" PCR test for mecA gene. Cohen´s kappa index was also calculated in order to evaluate the intra assay agreement between the used methods. RESULTS: The found prevalence was 90.7%. Sensitivity and specificity were: disk diffusion for cefoxitin 97 and 92% respectively, MIC Vitek 2-XL 97 and 69%, Chromo

  2. Qualitative risk assessment during polymer mortar test specimens preparation - methods comparison

    Science.gov (United States)

    Silva, F.; Sousa, S. P. B.; Arezes, P.; Swuste, P.; Ribeiro, M. C. S.; Baptista, J. S.

    2015-05-01

    Polymer binder modification with inorganic nanomaterials (NM) could be a potential and efficient solution to control matrix flammability of polymer concrete (PC) materials without sacrificing other important properties. Occupational exposures can occur all along the life cycle of a NM and “nanoproducts” from research through scale-up, product development, manufacturing, and end of life. The main objective of the present study is to analyse and compare different qualitative risk assessment methods during the production of polymer mortars (PM) with NM. The laboratory scale production process was divided in 3 main phases (pre-production, production and post-production), which allow testing the assessment methods in different situations. The risk assessment involved in the manufacturing process of PM was made by using the qualitative analyses based on: French Agency for Food, Environmental and Occupational Health & Safety method (ANSES); Control Banding Nanotool (CB Nanotool); Ecole Polytechnique Fédérale de Lausanne method (EPFL); Guidance working safely with nanomaterials and nanoproducts (GWSNN); Istituto Superiore per la Prevenzione e la Sicurezza del Lavoro, Italy method (ISPESL); Precautionary Matrix for Synthetic Nanomaterials (PMSN); and Stoffenmanager Nano. It was verified that the different methods applied also produce different final results. In phases 1 and 3 the risk assessment tends to be classified as medium-high risk, while for phase 2 the more common result is medium level. It is necessary to improve the use of qualitative methods by defining narrow criteria for the methods selection for each assessed situation, bearing in mind that the uncertainties are also a relevant factor when dealing with the risk related to nanotechnologies field.

  3. Qualitative risk assessment during polymer mortar test specimens preparation - methods comparison

    International Nuclear Information System (INIS)

    Silva, F; Sousa, S P B; Ribeiro, M C S; Arezes, P; Swuste, P; Baptista, J S

    2015-01-01

    Polymer binder modification with inorganic nanomaterials (NM) could be a potential and efficient solution to control matrix flammability of polymer concrete (PC) materials without sacrificing other important properties. Occupational exposures can occur all along the life cycle of a NM and “nanoproducts” from research through scale-up, product development, manufacturing, and end of life. The main objective of the present study is to analyse and compare different qualitative risk assessment methods during the production of polymer mortars (PM) with NM. The laboratory scale production process was divided in 3 main phases (pre-production, production and post-production), which allow testing the assessment methods in different situations. The risk assessment involved in the manufacturing process of PM was made by using the qualitative analyses based on: French Agency for Food, Environmental and Occupational Health and Safety method (ANSES); Control Banding Nanotool (CB Nanotool); Ecole Polytechnique Fédérale de Lausanne method (EPFL); Guidance working safely with nanomaterials and nanoproducts (GWSNN); Istituto Superiore per la Prevenzione e la Sicurezza del Lavoro, Italy method (ISPESL); Precautionary Matrix for Synthetic Nanomaterials (PMSN); and Stoffenmanager Nano. It was verified that the different methods applied also produce different final results. In phases 1 and 3 the risk assessment tends to be classified as medium-high risk, while for phase 2 the more common result is medium level. It is necessary to improve the use of qualitative methods by defining narrow criteria for the methods selection for each assessed situation, bearing in mind that the uncertainties are also a relevant factor when dealing with the risk related to nanotechnologies field. (paper)

  4. Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens.

    Science.gov (United States)

    Hage, Elias; Wilkie, Gavin S; Linnenweber-Held, Silvia; Dhingra, Akshay; Suárez, Nicolás M; Schmidt, Julius J; Kay-Fedorov, Penelope C; Mischak-Weissinger, Eva; Heim, Albert; Schwarz, Anke; Schulz, Thomas F; Davison, Andrew J; Ganzenmueller, Tina

    2017-06-01

    Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  5. Determination of antimicrobial resistance pattern and Extended-Spectrum Beta Lactamases producing Pseudomonas aeruginosa strains isolated from clinical specimens of Hajar and Kashani Hospitals,Shahrekord 1387

    Directory of Open Access Journals (Sweden)

    Mana Shojapour

    2011-09-01

    Full Text Available Background: Pseudomonas aeruginosa is one of the leading causes of hospital infections in patients hospitalized for a 10 day period or over. It is also considered to be the most important cause of the burn wound infection. Approximately 75% of deaths in burned patients are due to wound infection and the subsequent septicemia. Clinical use of antibiotics has increasingly led to the global distribution of P. aeruginosa isolates with multi-drug resistance. The study was launched to determine the antimicrobial susceptibility pattern and the presence of the extended-spectrum-beta lactamase (ESBL in P.aeruginosa strains isolated from clinical specimens. Methods: Totally, 175 P. aeruginosa strains were isolated from clinical samples and identified by standard methods. The pattern of antimicrobial resistance was then performed on the isolates using Disk Agar Diffusion (DAD according to CLSI Guideline. Primary screening test for ESBL producing strains was performed by ceftazidim antibiotic disk using disk diffusion method. Combined disk method was used to confirm ESBL producing bacteria. Results: The rate of antimicrobial resistance of P.aeruginosa isolates were 64% to ticarcillin, 52.2% to cefepime, 68.6% to ticarcillin/clavolanic acid, 68.6% to ceftazidime, 67.4% to amikacin, 68.6% to gentamicin, 48% to imipenem, 77.7% to ciprofloxacin and 5.1% to polymixcine B. In the primary screening test, 120 isolates of P.aeruginosa strains were resistant to ceftazidime. In the combined disk method, 66 isolates (55% were positive for ESBLs. Conclusion: Polymixcine B was found to be the most effective antimicrobial agent in this study. Bacteria carrying ESBL genes may increase mortality and morbidity. Thus, their accurate diagnosis is of extreme importance to prevent from the treatment failure resulted from improper antibiotic administration.

  6. Standard Test Method for Normal Spectral Emittance at Elevated Temperatures of Nonconducting Specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    1971-01-01

    1.1 This test method describes an accurate technique for measuring the normal spectral emittance of electrically nonconducting materials in the temperature range from 1000 to 1800 K, and at wavelengths from 1 to 35 μm. It is particularly suitable for measuring the normal spectral emittance of materials such as ceramic oxides, which have relatively low thermal conductivity and are translucent to appreciable depths (several millimetres) below the surface, but which become essentially opaque at thicknesses of 10 mm or less. 1.2 This test method requires expensive equipment and rather elaborate precautions, but produces data that are accurate to within a few percent. It is particularly suitable for research laboratories, where the highest precision and accuracy are desired, and is not recommended for routine production or acceptance testing. Because of its high accuracy, this test method may be used as a reference method to be applied to production and acceptance testing in case of dispute. 1.3 This test metho...

  7. Experimental Method for Plotting S-N Curve with a Small Number of Specimens

    Directory of Open Access Journals (Sweden)

    Strzelecki Przemysław

    2016-12-01

    Full Text Available The study presents two approaches to plotting an S-N curve based on the experimental results. The first approach is commonly used by researchers and presented in detail in many studies and standard documents. The model uses a linear regression whose parameters are estimated by using the least squares method. A staircase method is used for an unlimited fatigue life criterion. The second model combines the S-N curve defined as a straight line and the record of random occurrence of the fatigue limit. A maximum likelihood method is used to estimate the S-N curve parameters. Fatigue data for C45+C steel obtained in the torsional bending test were used to compare the estimated S-N curves. For pseudo-random numbers generated by using the Mersenne Twister algorithm, the estimated S-N curve for 10 experimental results plotted by using the second model, estimates the fatigue life in the scatter band of the factor 3. The result gives good approximation, especially regarding the time required to plot the S-N curve.

  8. Optimization of the graphical method of Swanepoel for characterization of thin film on substrate specimens from their transmittance spectrum

    International Nuclear Information System (INIS)

    Minkov, D A; Gavrilov, G M; Moreno, J M D; Vazquez, C G; Marquez, E

    2017-01-01

    The accuracy of the popular graphical method of Swanepoel (SGM) for the characterization of a thin film on a substrate specimen from its interference transmittance spectrum depends on the subjective choice of four characterization parameters: the slope of the graph, the order number for the longest wavelength extremum, and the two numbers of the extrema used for the calculation approximations of the average film thickness. Here, an error metric is introduced for estimating the accuracy of SGM characterization. An algorithm is proposed for the optimization of SGM, named the OGM algorithm, based on the minimization of this error metric. Its execution provides optimized values of the four characterization parameters, and the respective computation of the most accurate film characteristics achievable within the framework of SGM. Moreover, substrate absorption is accounted for, unlike in the classical SGM, which is beneficial when using modern UV/visible/NIR spectrophotometers due to the relatively larger amount of absorption in the commonly used glass substrates for wavelengths above 1700 nm. A significant increase in the accuracy of the film characteristics is obtained employing the OGM algorithm compared to the SGM algorithm for two model specimens. Such improvements in accuracy increase with increasing film absorption. The results of the film characterization by the OGM algorithm are presented for two specimens containing RF-magnetron-sputtered a -Si films with disparate film thicknesses. The computed average film thicknesses are within 1.1% of the respective film thicknesses measured by SEM for both films. Achieving such high film characterization accuracy is particularly significant for the film with a computed average thickness of 3934 nm, since we are not aware of any other film with such a large thickness that has been characterized by SGM. (paper)

  9. Optimization of the graphical method of Swanepoel for characterization of thin film on substrate specimens from their transmittance spectrum

    Science.gov (United States)

    Minkov, D. A.; Gavrilov, G. M.; Moreno, J. M. D.; Vazquez, C. G.; Marquez, E.

    2017-03-01

    The accuracy of the popular graphical method of Swanepoel (SGM) for the characterization of a thin film on a substrate specimen from its interference transmittance spectrum depends on the subjective choice of four characterization parameters: the slope of the graph, the order number for the longest wavelength extremum, and the two numbers of the extrema used for the calculation approximations of the average film thickness. Here, an error metric is introduced for estimating the accuracy of SGM characterization. An algorithm is proposed for the optimization of SGM, named the OGM algorithm, based on the minimization of this error metric. Its execution provides optimized values of the four characterization parameters, and the respective computation of the most accurate film characteristics achievable within the framework of SGM. Moreover, substrate absorption is accounted for, unlike in the classical SGM, which is beneficial when using modern UV/visible/NIR spectrophotometers due to the relatively larger amount of absorption in the commonly used glass substrates for wavelengths above 1700 nm. A significant increase in the accuracy of the film characteristics is obtained employing the OGM algorithm compared to the SGM algorithm for two model specimens. Such improvements in accuracy increase with increasing film absorption. The results of the film characterization by the OGM algorithm are presented for two specimens containing RF-magnetron-sputtered a-Si films with disparate film thicknesses. The computed average film thicknesses are within 1.1% of the respective film thicknesses measured by SEM for both films. Achieving such high film characterization accuracy is particularly significant for the film with a computed average thickness of 3934 nm, since we are not aware of any other film with such a large thickness that has been characterized by SGM.

  10. Potential methods for determination of crack length of specimens in fracture mechanics

    International Nuclear Information System (INIS)

    Russenberger, M.E.

    1979-01-01

    For a wide and general use of neutron radiography in materials testing, transportable neutron sources are required which are strong enough for satisfactory pictures at a permissible radiation exposure time. These neutron sources are still lacking, and this shartage must be met by the development of better sources and imaging techniques which make better use of the given neutron flux- A simple method is presented that provides a better image quality due to a better absorption of neutrons, a larger amount of conversion radiation detected by the film, and reduced intrinsic unshapness. (orig.) [de

  11. Investigation of the influence of different surface regularization methods for cylindrical concrete specimens in axial compression tests

    Directory of Open Access Journals (Sweden)

    R. MEDEIROS

    Full Text Available ABSTRACT This study was conducted with the aim of evaluating the influence of different methods for end surface preparation of compressive strength test specimens. Four different methods were compared: a mechanical wear method through grinding using a diamond wheel established by NBR 5738; a mechanical wear method using a diamond saw which is established by NM 77; an unbonded system using neoprene pads in metal retainer rings established by C1231 and a bonded capping method with sulfur mortar established by NBR 5738 and by NM 77. To develop this research, 4 concrete mixes were determined with different strength levels, 2 of group 1 and 2 of group 2 strength levels established by NBR 8953. Group 1 consists of classes C20 to C50, 5 in 5MPa, also known as normal strength concrete. Group 2 is comprised of class C55, C60 to C100, 10 in 10 MPa, also known as high strength concrete. Compression tests were carried out at 7 and 28 days for the 4 surface preparation methods. The results of this study indicate that the method established by NBR 5738 is the most effective among the 4 strengths considered, once it presents lower dispersion of values obtained from the tests, measured by the coefficient of variation and, in almost all cases, it demonstrates the highest mean of rupture test. The method described by NBR 5738 achieved the expected strength level in all tests.

  12. The development of underwater remote cutting method for the disassembling of rotary specimen rack KRR-1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    Lee, D. K.; Jung, K. H.; Lee, K. W.; Oh, W. J. [KAERI, Taejon (Korea, Republic of); Lee, K. Y. [Korea Institute of Industrial Technology, Kwangju (Korea, Republic of)

    2004-07-01

    The Rotary Specimen Racks (RSRs) were highly activated and then classified intermediate level radioactive waste for the decommissioning of KRR-1anel2. The RSR can be treated as low level radioactive waste after removing stainless steel parts. To reduce the volume of intermediate level radioactive waste, underwater cutting is required to separate stainless steel parts from RSR because of high radioactivity. In this study, the automatic remote cutting method was developed to disassemble RSR under water. For automatic remote cutting processes, a CAM (Computer Aided Manufacturing) system is employed. A computer inputs NC (Numerical Control) codes to the controller, which are based on CAM model, and the controller instructs the equipment to process according to NC codes automatically. And the cutting force model was improved to cut RSR stably. The automatic cutting was conducted using imitation of RSR and then it was resulted that the developed automatic cutting method can be safely disassemble stainless steel parts of RSR under water.

  13. Characterization of microbes in prosthetic joint specimens by culture-independent molecular methods

    DEFF Research Database (Denmark)

    Xu, Yijuan; Rudkjøbing, Vibeke Børsholt; Simonsen, Ole

    Prosthetic joint infection (PJI) is one of the most challenging complications of joint alloplasty. Formation of biofilm is a prominent feature of PJIs and constitutes a challenge to current sampling procedures and culture practices to obtain a reliable diagnosis. The aim of the study was to inves......Prosthetic joint infection (PJI) is one of the most challenging complications of joint alloplasty. Formation of biofilm is a prominent feature of PJIs and constitutes a challenge to current sampling procedures and culture practices to obtain a reliable diagnosis. The aim of the study...... was to investigate the microbial diversity in surgical samples (eg. synovial fluid, periprosthetic tissue, removed prosthesis) from 22 prosthetic patients using a range of culture-independent molecular methods including broad range 16S rRNA gene PCR, cloning, phylogeny, quantitative PCR (qPCR), and fluorescence...

  14. Methods in Clinical Pharmacology Series

    Science.gov (United States)

    Beaumont, Claire; Young, Graeme C; Cavalier, Tom; Young, Malcolm A

    2014-01-01

    Human radiolabel studies are traditionally conducted to provide a definitive understanding of the human absorption, distribution, metabolism and excretion (ADME) properties of a drug. However, advances in technology over the past decade have allowed alternative methods to be employed to obtain both clinical ADME and pharmacokinetic (PK) information. These include microdose and microtracer approaches using accelerator mass spectrometry, and the identification and quantification of metabolites in samples from classical human PK studies using technologies suitable for non-radiolabelled drug molecules, namely liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy. These recently developed approaches are described here together with relevant examples primarily from experiences gained in support of drug development projects at GlaxoSmithKline. The advantages of these study designs together with their limitations are described. We also discuss special considerations which should be made for a successful outcome to these new approaches and also to the more traditional human radiolabel study in order to maximize knowledge around the human ADME properties of drug molecules. PMID:25041729

  15. Apparatus and method for fatigue testing of a material specimen in a high-pressure fluid environment

    Science.gov (United States)

    Wang, Jy-An; Feng, Zhili; Anovitz, Lawrence M; Liu, Kenneth C

    2013-06-04

    The invention provides fatigue testing of a material specimen while the specimen is disposed in a high pressure fluid environment. A specimen is placed between receivers in an end cap of a vessel and a piston that is moveable within the vessel. Pressurized fluid is provided to compression and tension chambers defined between the piston and the vessel. When the pressure in the compression chamber is greater than the pressure in the tension chamber, the specimen is subjected to a compression force. When the pressure in the tension chamber is greater than the pressure in the compression chamber, the specimen is subjected to a tension force. While the specimen is subjected to either force, it is also surrounded by the pressurized fluid in the tension chamber. In some examples, the specimen is surrounded by hydrogen.

  16. Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens.

    Science.gov (United States)

    Rheem, Insoo; Park, Joowon; Kim, Tae-Hyun; Kim, Jong Wan

    2012-11-01

    In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea). Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses. The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%. The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.

  17. Evaluation of laboratory tests for dengue diagnosis in clinical specimens from consecutive patients with suspected dengue in Belo Horizonte, Brazil.

    Science.gov (United States)

    Ferraz, Fernanda Oliveira; Bomfim, Maria Rosa Quaresma; Totola, Antônio Helvécio; Ávila, Thiago Vinícius; Cisalpino, Daniel; Pessanha, José Eduardo Marques; da Glória de Souza, Danielle; Teixeira Júnior, Antônio Lúcio; Nogueira, Maurício Lacerda; Bruna-Romero, Oscar; Teixeira, Mauro Martins

    2013-09-01

    Dengue is a widely spread arboviral disease in tropical and subtropical regions of the world. Dengue fever presents clinical characteristics similar to other febrile illness. Thus laboratory diagnosis is important for adequate management of the disease. The present study was designed to evaluate the diagnostic performance of real-time PCR and serological methods for dengue in a real epidemic context. Clinical data and blood samples were collected from consecutive patients with suspected dengue who attended a primary health care unit in Belo Horizonte, Brazil. Serologic methods and real-time PCR were performed in serum samples to confirm dengue diagnosis. Among the 181 consecutive patients enrolled in this study with suspected dengue, 146 were considered positive by serological criteria (positive NS1 ELISA and/or anti-dengue IgM ELISA) and 138 were positive by real-time PCR. Clinical criteria were not sufficient for distinguishing between dengue and non-dengue febrile illness. The PCR reaction was pre-optimized using samples from patients with known viral infection. It had similar sensitivity compared to NS1 ELISA (88% and 89%, respectively). We also evaluated three commercial lateral flow immunochromatographic tests for NS1 detection (BIOEASY, BIORAD and PANBIO). All three tests showed high sensitivity (94%, 91% and 81%, respectively) for dengue diagnosis. According to our results it can be suggested that lateral flow tests for NS1 detection are the most feasible methods for early diagnosis of dengue. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens of dyspeptic patients

    Directory of Open Access Journals (Sweden)

    Ivy Bastos Ramis

    2012-09-01

    Full Text Available Helicobacter pylori infects nearly 50% of the world's population. This microorganism is accepted as the most important agent of gastritis and as a risk factor for peptic ulcer disease and gastric adenocarcinoma. Currently many diagnostic methods exist for detecting H. pylori, however they all have limitations, thus it is recommend a combination of at least two methods. The aim of this study was to evaluate diagnostic methods, such as in-house urease test, culture and Polymerase Chain Reaction (PCR, for the detection of the H. pylori in gastric biopsy specimens of 144 dyspeptic patients, using as gold standard the association between histology and rapid urease test. According to the gold standard used in this study, 48 (33.3% patients were infected with H. pylori, while 96 (66.7% were classified as not infected. The in-house urease test and the PCR were the most sensitive methods (100%, followed by culture (85.4%. However, the in-house urease test and the culture were the most specific (100%, followed by PCR (75%. In conclusion, this study showed that, in comparison with the combination of histology and rapid urease test, the in-house urease test and the PCR presented 100% of sensitivity in the diagnosis of gastric infection by H. pylori, while the in-house urease test and the culture reached 100% of specificity. These finding suggest that the combination of two or more methods may improve the accuracy of the H. pylori detection.

  19. Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

    Directory of Open Access Journals (Sweden)

    Sarah M Hykin

    Full Text Available For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles, attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp. We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens

  20. Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

    Science.gov (United States)

    Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

    2015-01-01

    For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for

  1. Performance evaluation of the Cobas TaqMan MTB assay on respiratory specimens according to clinical application

    Directory of Open Access Journals (Sweden)

    Jong Eun Park

    2017-11-01

    Full Text Available Objective: To evaluate the performance of the Cobas TaqMan MTB assay (Cobas assay with respect to its clinical application. Methods: This was a retrospective analysis of 1154 results from 1034 patients for whom mycobacterial cultures and the Cobas assay were performed simultaneously. Based on the patient medical records, two categories of clinical application were defined: (1 the diagnosis of patients with a high probability of pulmonary tuberculosis according to clinical and radiological features (n = 128, and (2 the exclusion of tuberculosis in clinically indeterminate patients (n = 1026. Standard culture was used as the reference method. Results: The sensitivity of the Cobas assay for the detection of Mycobacterium tuberculosis was 70.4% (95% confidence interval (CI 49.7–85.5% for category 1, but only 25.0% (95% CI 4.5–64.4% for category 2. The specificity was ≥95.0% for both categories. The positive predictive value was 79.2% (95% CI 57.3–92.1% for category 1 and 33.3% (95% CI 6.0–75.9% for category 2, while the negative predictive value was 92.3% (95% CI 85.0–96.4% for category 1 and 99.4% (95% CI 98.7–99.8% for category 2. Conclusions: The results of this study indicate that Cobas assay results must be interpreted carefully according to the clinical purpose of the assay. Keywords: Mycobacterium tuberculosis, Pulmonary tuberculosis, Cobas TaqMan MTB assay, Korea

  2. Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing.

    Science.gov (United States)

    Zhang, Liangxuan; Chen, Liangjing; Sah, Sachin; Latham, Gary J; Patel, Rajesh; Song, Qinghua; Koeppen, Hartmut; Tam, Rachel; Schleifman, Erica; Mashhedi, Haider; Chalasani, Sreedevi; Fu, Ling; Sumiyoshi, Teiko; Raja, Rajiv; Forrest, William; Hampton, Garret M; Lackner, Mark R; Hegde, Priti; Jia, Shidong

    2014-04-01

    The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology. We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls. Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA. AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.

  3. Proposal of an Appropriate Decalcification Method of Bone Marrow Biopsy Specimens in the Era of Expanding Genetic Molecular Study

    Directory of Open Access Journals (Sweden)

    Sung-Eun Choi

    2015-05-01

    Full Text Available Background: The conventional method for decalcification of bone specimens uses hydrochloric acid (HCl and is notorious for damaging cellular RNA, DNA, and proteins, thus complicating molecular and immunohistochemical analyses. A method that can effectively decalcify while preserving genetic material is necessary. Methods: Pairs of bilateral bone marrow biopsies sampled from 53 patients were decalcified according to protocols of two comparison groups: EDTA versus HCl and RDO GOLD (RDO versus HCl. Pairs of right and left bone marrow biopsy samples harvested from 28 cases were allocated into the EDTA versus HCl comparison group, and 25 cases to the RDO versus HCl comparison group. The decalcification protocols were compared with regards to histomorphology, immunohistochemistry, and molecular analysis. For molecular analysis, we randomly selected 5 cases from the EDTA versus HCl and RDO versus HCl groups. Results: The decalcification time for appropriate histomorphologic analysis was the longest in the EDTA method and the shortest in the RDO method. EDTA was superior to RDO or HCl in DNA yield and integrity, assessed via DNA extraction, polymerase chain reaction, and silver in situ hybridization using DNA probes. The EDTA method maintained intact nuclear protein staining on immunohistochemistry, while the HCl method produced poor quality images. Staining after the RDO method had equivocal results. RNA in situ hybridization using kappa and lambda RNA probes measured RNA integrity; the EDTA and RDO method had the best quality, followed by HCl. Conclusions: The EDTA protocol would be the best in preserving genetic material. RDO may be an acceptable alternative when rapid decalcification is necessary.

  4. Identification of Mycobacterium tuberculosis in Clinical Specimens of Patients Suspected of Having Extrapulmonary Tuberculosis by Application of Nested PCR on Five Different Genes.

    Science.gov (United States)

    Khosravi, Azar D; Alami, Ameneh; Meghdadi, Hossein; Hosseini, Atta A

    2017-01-01

    Definitive and rapid diagnosis of extrapulmonary tuberculosis (EPTB) is challenging since conventional techniques have limitations due to the paucibacillary nature of the disease. To increase the sensitivity of detection of Mycobacterium tuberculosis (MTB) in EPTB specimens, we performed a nested PCR assay targeting several genes of MTB on EPTB specimens. A total of 100 clinical specimens from suspected cases of EPTB were processed. Standard staining for acid fast bacilli (AFB) was performed as the preliminary screening test. Extracted DNAs from specimens were subjected to Nested PCR technique for the detection of five different MTB target genes of IS6110, IS1081, hsp65kd, mbp64 , and mtp40 . On performing AFB staining, only 13% of specimens were positive, of which ascites fluid (33.3%), followed by pleural effusion (30.8%) showed the greatest AFB positivity rate. We demonstrated slight improvement in yields in lymph node which comprised the majority of specimens in this study, by employing PCR targeted to IS6110 - and hsp65-genes in comparison to AFB staining. However, the yields in ascites fluid and pleural effusion were not substantially improved by PCR, but those from bone and wound were, as in nested PCR employing either gene, the same positivity rate were obtained for ascites fluid (33.3%), while for pleural effusion specimens only IS1081 based PCR showed identical positivity rate with AFB stain (30.8%). The results for bone and wound specimens, however, demonstrated an improved yield mainly by employing IS1081 gene. Here, we report higher detection rate of EPTB in clinical specimens using five different targeted MTB genes. This nested PCR approach facilitates the comparison and the selection of the most frequently detected genes. Of course this study demonstrated the priority of IS1081 followed by mtp40 and IS6110 , among the five tested genes and indicates the effectiveness of any of the three genes in the design of an efficient nested-PCR test that

  5. Application Anti Microbial Activity Test and Direct Inoculation of Urinary Specimen Test to Increase the Quality of Results and Decrease the Production Cost in Clinical Microbiology Laboratory, Sanglah General Hospital Hospital, Bali-Indonesia

    Directory of Open Access Journals (Sweden)

    Nyoman Sri-Budayanti

    2012-05-01

    Full Text Available Objective: Urinary tract infection (UTI is the most common bacterial infection in general practice and in hospitals. Fast and accurate urine culture and sensitivity test are needed for adequate therapy. Anti Microbial Activity test (AMA test that is used to detect the presence of antibiotics in urine specimens is not commonly used in clinical microbiology laboratories. Some laboratories are still using indirect inoculation technique using enriched media before inoculating onto the agar media. The aim of this research is to compare results of urinary examination of direct inoculation technique with AMA test with indirect inoculation technique without AMA test.Methods: A number of 210 urine specimens were collected in Clinical Microbiology Laboratory at Sanglah General Hospital within a time period between 16 June until 16 July 2009.Results: Antibiotics were detected in 40% of the urinary specimens; whereas 48.1% showed no evidence of UTI, that is negative AMA test and sterile urinary culture or colony growth < 105 CFU/ml. Only 11.9% of the specimens indicates urinary tract infections. The examination can be completed within 2-3 days which is shorter than indirect inoculation test which require 5-7 days. Direct inoculation technique can reduce the cost of production three-fold the costs require for an indirect inoculation test.Conclusions: Application of AMA test and direct inoculation technique can give results more rapidly, reliable and useful for clinicians. This also decrease the laboratory’s cost of production.

  6. qPCR-High resolution melt analysis for drug susceptibility testing of Mycobacterium leprae directly from clinical specimens of leprosy patients.

    Science.gov (United States)

    Araujo, Sergio; Goulart, Luiz Ricardo; Truman, Richard W; Goulart, Isabela Maria B; Vissa, Varalakshmi; Li, Wei; Matsuoka, Masanori; Suffys, Philip; Fontes, Amanda B; Rosa, Patricia S; Scollard, David M; Williams, Diana L

    2017-06-01

    Real-Time PCR-High Resolution Melting (qPCR-HRM) analysis has been recently described for rapid drug susceptibility testing (DST) of Mycobacterium leprae. The purpose of the current study was to further evaluate the validity, reliability, and accuracy of this assay for M. leprae DST in clinical specimens. The specificity and sensitivity for determining the presence and susceptibility of M. leprae to dapsone based on the folP1 drug resistance determining region (DRDR), rifampin (rpoB DRDR) and ofloxacin (gyrA DRDR) was evaluated using 211 clinical specimens from leprosy patients, including 156 multibacillary (MB) and 55 paucibacillary (PB) cases. When comparing the results of qPCR-HRM DST and PCR/direct DNA sequencing, 100% concordance was obtained. The effects of in-house phenol/chloroform extraction versus column-based DNA purification protocols, and that of storage and fixation protocols of specimens for qPCR-HRM DST, were also evaluated. qPCR-HRM results for all DRDR gene assays (folP1, rpoB, and gyrA) were obtained from both MB (154/156; 98.7%) and PB (35/55; 63.3%) patients. All PCR negative specimens were from patients with low numbers of bacilli enumerated by an M. leprae-specific qPCR. We observed that frozen and formalin-fixed paraffin embedded (FFPE) tissues or archival Fite's stained slides were suitable for HRM analysis. Among 20 mycobacterial and other skin bacterial species tested, only M. lepromatosis, highly related to M. leprae, generated amplicons in the qPCR-HRM DST assay for folP1 and rpoB DRDR targets. Both DNA purification protocols tested were efficient in recovering DNA suitable for HRM analysis. However, 3% of clinical specimens purified using the phenol/chloroform DNA purification protocol gave false drug resistant data. DNA obtained from freshly frozen (n = 172), formalin-fixed paraffin embedded (FFPE) tissues (n = 36) or archival Fite's stained slides (n = 3) were suitable for qPCR-HRM DST analysis. The HRM-based assay was also able to

  7. Detection and Differentiation of Leishmania spp. in Clinical Specimens by Use of a SYBR Green-Based Real-Time PCR Assay.

    Science.gov (United States)

    de Almeida, Marcos E; Koru, Ozgur; Steurer, Francis; Herwaldt, Barbara L; da Silva, Alexandre J

    2017-01-01

    Leishmaniasis in humans is caused by Leishmania spp. in the subgenera Leishmania and Viannia Species identification often has clinical relevance. Until recently, our laboratory relied on conventional PCR amplification of the internal transcribed spacer 2 (ITS2) region (ITS2-PCR) followed by sequencing analysis of the PCR product to differentiate Leishmania spp. Here we describe a novel real-time quantitative PCR (qPCR) approach based on the SYBR green technology (LSG-qPCR), which uses genus-specific primers that target the ITS1 region and amplify DNA from at least 10 Leishmania spp., followed by analysis of the melting temperature (T m ) of the amplicons on qPCR platforms (the Mx3000P qPCR system [Stratagene-Agilent] and the 7500 real-time PCR system [ABI Life Technologies]). We initially evaluated the assay by testing reference Leishmania isolates and comparing the results with those from the conventional ITS2-PCR approach. Then we compared the results from the real-time and conventional molecular approaches for clinical specimens from 1,051 patients submitted to the reference laboratory of the Centers for Disease Control and Prevention for Leishmania diagnostic testing. Specimens from 477 patients tested positive for Leishmania spp. with the LSG-qPCR assay, specimens from 465 of these 477 patients also tested positive with the conventional ITS2-PCR approach, and specimens from 10 of these 465 patients had positive results because of retesting prompted by LSG-qPCR positivity. On the basis of the T m values of the LSG-qPCR amplicons from reference and clinical specimens, we were able to differentiate four groups of Leishmania parasites: the Viannia subgenus in aggregate; the Leishmania (Leishmania) donovani complex in aggregate; the species L (L) tropica; and the species L (L) mexicana, L (L) amazonensis, L (L) major, and L (L) aethiopica in aggregate. Copyright © 2016 American Society for Microbiology.

  8. Utility of pooled urine specimens for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics in Mumbai, India, by PCR.

    Science.gov (United States)

    Lindan, Christina; Mathur, Meenakshi; Kumta, Sameer; Jerajani, Hermangi; Gogate, Alka; Schachter, Julius; Moncada, Jeanne

    2005-04-01

    Pooling urogenital specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification tests is an attractive alternative to individual testing. As pooling can reduce the costs of testing as well as labor, it has been advocated for use in resource-poor settings. However, it has neither been widely adopted nor evaluated for use in developing countries. We evaluated the practical use of pooling first-catch urine (FCU) specimens for the detection of C. trachomatis and N. gonorrhoeae from 690 men in Mumbai, India, by PCR. FCU, urethral smears, and swabs were collected from men seen at two sexually transmitted infection (STI) clinics. All laboratory testing was done at the Lokmanya Tilak General Hospital. Gram stain smears and culture isolation for N. gonorrhoeae were performed. Each FCU was tested individually and in pools using the Roche Amplicor PCR for C. trachomatis and N. gonorrhoeae with an internal control for inhibition. Specimen pools consisted of aliquots from five consecutively processed FCUs combined into an amplification tube. An optical density reading of > or =0.20 indicated a pool for which subsequent testing of individual samples was required. Prevalence by PCR on single specimens was 2.2% (15/690) for C. trachomatis and 5.4% (37/690) for N. gonorrhoeae. Compared to individual FCU results, pooling for C. trachomatis and N. gonorrhoeae had an overall sensitivity of 96.1% (50/52). Specificity was 96.5% (83/86) in that three pools required single testing that failed to identify a positive specimen. Pooling missed two positive specimens, decreased the inhibition rate, and saved 50.3% of reagent costs. In this resource-limited setting, the use of pooling to detect C. trachomatis and N. gonorrhoeae by PCR proved to be a simple, accurate, and cost-effective procedure compared to individual testing.

  9. Comparative Evaluation of Four Real-Time PCR Methods for the Quantitative Detection of Epstein-Barr Virus from Whole Blood Specimens.

    Science.gov (United States)

    Buelow, Daelynn; Sun, Yilun; Tang, Li; Gu, Zhengming; Pounds, Stanley; Hayden, Randall

    2016-07-01

    Monitoring of Epstein-Barr virus (EBV) load in immunocompromised patients has become integral to their care. An increasing number of reagents are available for quantitative detection of EBV; however, there are little published comparative data. Four real-time PCR systems (one using laboratory-developed reagents and three using analyte-specific reagents) were compared with one another for detection of EBV from whole blood. Whole blood specimens seeded with EBV were used to determine quantitative linearity, analytical measurement range, lower limit of detection, and CV for each assay. Retrospective testing of 198 clinical samples was performed in parallel with all methods; results were compared to determine relative quantitative and qualitative performance. All assays showed similar performance. No significant difference was found in limit of detection (3.12-3.49 log10 copies/mL; P = 0.37). A strong qualitative correlation was seen with all assays that used clinical samples (positive detection rates of 89.5%-95.8%). Quantitative correlation of clinical samples across assays was also seen in pairwise regression analysis, with R(2) ranging from 0.83 to 0.95. Normalizing clinical sample results to IU/mL did not alter the quantitative correlation between assays. Quantitative EBV detection by real-time PCR can be performed over a wide linear dynamic range, using three different commercially available reagents and laboratory-developed methods. EBV was detected with comparable sensitivity and quantitative correlation for all assays. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. Has the ThinPrep method of cervical screening maintained its improvement over conventional smears in terms of specimen adequacy?

    LENUS (Irish Health Repository)

    Treacy, A

    2009-04-01

    Liquid-based cytology (LBC) has replaced conventional smear assessment in many centers over recent years. In our laboratory this transfer took place in 1999. At that time we performed a split sample study comparing the conventional method of cervical smear evaluation with the ThinPrep system. This split sample study identified a dramatic improvement in specimen adequacy with LBC. While 11% of conventional preparations were reported as unsatisfactory and almost 9% were reported as suboptimal, evaluation of the same cases using LBC saw this combined figure reduced to 2.3%. AIM: To evaluate whether this dramatic fall in unsatisfactory smears has been maintained with the use of LBC. The database for all smears reported for 2005 (100% LBC) was interrogated. The number of unsatisfactory reports was calculated. The reason for an unsatisfactory report was recorded for each case. The overall unsatisfactory rate was compared with that reported in the 1999 split sample study. A total of 41,312 smear tests were reported in 2005. 1,342 (3.25%) were reported as unsatisfactory. Our findings support the ongoing value of LBC in a routine cervical screening laboratory in terms of continuing to maintain a low rate of unsatisfactory smears.

  11. Investigation of in-vitro susceptibility of multidrug-resistant Acinetobacter baumannii strains isolated from clinical specimens to tigecycline.

    Science.gov (United States)

    Tas, Tekin; Kocoglu, Esra; Mengeloglu, Zafer; Bucak, Ozlem; Karabörk, Seyda

    2013-11-01

    The management of infections due to A. baumannii is difficult because of rapidly developing resistance, however, tigecycline, a glycylcycline antimicrobial, is in use for several years. In the present study, it was aimed to determine the susceptibility rates of A. baumannii to tigecycline. A total of 90 A. baumanni isolates were tested using three methods such as disk diffusion, broth microdilution, and E-test. The MIC50 and MIC90 values and the MIC range were found as 2 µg/ml, 4 µg/ml, and 0.1-8 µg/ml by microdilution; and 2 µg/ml, 6 µg/ml, and 0.1-12 µg/ml by E-test, respectively. There were a few major errors as well as the minor rates were all high as between 35.7%-46.7%. The accuracy rates between the methods were low as 53.3% (48/90) between disk diffusion and E-test, 51.1% (46/90) between disk diffusion and microdilution, and 60.0% (54/90) between E-test and microdilution. In the ROC curve analysis, an inhibition zone diameter of susceptibility breakpoint of 21.5 mm had sensitivity between 68.8%-88.9%; specificity between 81.9%-87.9%; and accuracy between 80.0%-83.33%. An analysis based on EUCAST's non-species breakpoints, the MIC tests showed higher accuracy with a rate of 96.7%, however, performance of disk diffusion got worse as lower than 25%. In conclusion, we showed that the reliability of the methods even did not remain as high as the past. Our study presented that none of three methods revealed reliable results in determination of susceptibility of A. baumanni to tigecycline, so the clinical response should be followed up carefully in such cases.

  12. The detection of tightly closed flaws by nondestructive testing (NDT) methods. [fatigue crack formation in aluminum alloy test specimens

    Science.gov (United States)

    Rummel, W. D.; Rathke, R. A.; Todd, P. H., Jr.; Mullen, S. J.

    1975-01-01

    Liquid penetrant, ultrasonic, eddy current and X-radiographic techniques were optimized and applied to the evaluation of 2219-T87 aluminum alloy test specimens in integrally stiffened panel, and weld panel configurations. Fatigue cracks in integrally stiffened panels, lack-of-fusion in weld panels, and fatigue cracks in weld panels were the flaw types used for evaluation. A 2319 aluminum alloy weld filler rod was used for all welding to produce the test specimens. Forty seven integrally stiffened panels containing a total of 146 fatigue cracks, ninety three lack-of-penetration (LOP) specimens containing a total of 239 LOP flaws, and one-hundred seventeen welded specimens containing a total of 293 fatigue cracks were evaluated. Nondestructive test detection reliability enhancement was evaluated during separate inspection sequences in the specimens in the 'as-machined or as-welded', post etched and post proof loaded conditions. Results of the nondestructive test evaluations were compared to the actual flaw size obtained by measurement of the fracture specimens after completing all inspection sequences. Inspection data were then analyzed to provide a statistical basis for determining the flaw detection reliability.

  13. Bending moment evaluation of a long specimen using a radial speckle pattern interferometer in combination with relaxation methods

    Science.gov (United States)

    Pacheco, Anderson; Fontana, Filipe; Viotti, Matias R.; Veiga, Celso L. N.; Lothhammer, Lívia R.; Albertazzi G., Armando, Jr.

    2015-08-01

    The authors developed an achromatic speckle pattern interferometer able to measure in-plane displacements in polar coordinates. It has been used to measure combined stresses resulting from the superposition of mechanical loading and residual stresses. Relaxation methods have been applied to produce on the surface of the specimen a displacement field that can be used to determine the amount of combined stresses. Two relaxation methods are explored in this work: blind hole-drilling and indentation. The first one results from a blind hole drilled with a high-speed drilling unit in the area of interest. The measured displacement data is fitted in an appropriate model to quantify the stress level using an indirect approach based on a set of finite element coefficients. The second approach uses indentation, where a hard spherical tip is firmly pressed against the surface to be measured with a predetermined indentation load. A plastic flow occurs around the indentation mark producing a radial in-plane displacement field that is related to the amount of combined stresses. Also in this case, displacements are measured by the radial interferometer and used to determine the stresses by least square fitting it to a displacement field determined by calibration. Both approaches are used to quantify the amount of bending stresses and moment in eight sections of a 12 m long 200 mm diameter steel pipe submitted to a known transverse loading. Reference values of bending stresses are also determined by strain gauges. The comparison between the four results is discussed in the paper.

  14. The first report: An analysis of bacterial flora of the first voided urine specimens of patients with male urethritis using the 16S ribosomal RNA gene-based clone library method.

    Science.gov (United States)

    You, Chunlin; Hamasuna, Ryoichi; Ogawa, Midori; Fukuda, Kazumasa; Hachisuga, Toru; Matsumoto, Tetsuro; Taniguchi, Hatsumi

    2016-06-01

    To analyse the bacterial flora of urine from patients with male urethritis using the clone library method. Urine specimens from patients with urethritis were used. The bacterial flora was analysed according to the 16S ribosomal RNA gene-based clone library method. In addition, Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum or Ureaplasma parvum were detected by the conventional PCR methods (TMA or real-time PCR) and data from the clone library and conventional PCR methods were compared. Among 58 urine specimens, 38 were successfully analysed using the clone library method. From the specimens, 2427 clones were evaluated and 95 bacterial phylotypes were detected. N. gonorrhoeae was detected from 6 specimens and as the predominant bacterial species in 5 specimens. M. genitalium was detected from 5 specimens and as the predominant bacterial species in 3 specimens. C. trachomatis was detected from 15 specimens using the TMA method, but was detected from only 1 specimen using the clone library method. U. parvum was detected from only 2 specimens using the clone library method. In addition, Haemophilus influenzae and Neisseria meningitidis were also detected in 8 and 1 specimens, respectively. Gardnerella vaginalis, which is a potential pathogen for bacterial vaginitis in women, was detected in 10 specimens. The clone library method can detect the occupancy rate of each bacteria species among the bacterial flora and may be a new method for bacterial analyses in male urethritis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Survey of strain distribution and antibiotic resistance pattern of group B streptococci (Streptococcus agalactiae isolated from clinical specimens

    Directory of Open Access Journals (Sweden)

    Mousavi, Seyed Masoud

    2016-09-01

    Full Text Available Aim: The aims of the present study were to determine the antibiotic susceptibility profils with particular emphasis on susceptible or resistant strains to macrolides and lincosamids antibiotics and to determine possible antibiotic resistance mechanisms occurring in group B streptococci (GBS strains using PCR assay and disk diffusion method.Methods: A total of 62 clinical GBS strains were investigated. Antibacterial susceptibility testing was performed using the disk diffusion method and inducible resistance test for clindamycin by standard double disk diffusion or D-zone test for all isolates to differentiate macrolide resistance phenotype (M, constitutive macrolide-lincosamide-streptogramin B phenotype (cMLS and induced macrolide-lincosamide-streptogramin B phenotype (iMLS. In addition, minimum inhibitory concentrations (MIC of penicillin were determined for all isolates. Finally, possible existence of antibiotic resistance genes for erythromycin , and and for clindamycin were examined among isolates using PCR assay.Results: All 62 isolates were susceptible to penicillin, ampicillin, linezolid, cefazoline and vancomycin. However, 93.5% (n=58 of isolates showed an increased MIC to penicillin. The overall rate of erythromycin resistance was 35.5% (n=22. All erythromycin-resistant isolates displayed the M phenotype (100%, n=22. All three erythromycin resistance genes (i.e. , and were found in erythromycin-resistant isolates.Conclusion: It was concluded that prescribing antibiotic without antibacterial susceptibility tests should be prevented because of the high prevalence of erythromycin-resistant GBS strains and the fact that erythromycin-resistant GBS strains has shown an increased MIC to penicillin, as the drug of choice for treating GBS infections.

  16. A Comparative Study of the Retentive Strengths of Commercial and Indigenously Developed Luting Cements using Both Lathe-cut and Clinically Simulated Specimens.

    Science.gov (United States)

    Mathew, Joe; Kurian, Byju P; Philip, Biju; Mohammed, Sunil; Menon, Preetha; Raj, Rajan S

    2016-08-01

    Superior adhesive strength in luting agents is of paramount significance in fixed partial denture success. In this in vitro study five cements were tested for retentive qualities, using both lathe-cut and hand-prepared specimens. A total of 104 freshly extracted tooth specimens were prepared. Seventy of them were lathe-cut and 30 specimens were hand-prepared to simulate clinical conditions. Five different cements were tested, which included a compomer, a composite, a zinc phosphate, and 2 glass-ionomer luting cements. Of the 5, 2 trial cements were indigenously developed by Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, India - a glass-ionomer cement (Chitra GIC) and a chemical-cure composite (Chitra CCC). All cements were compared within each group and between groups (lathe-prepared and hand-prepared). GC Fuji 1 (GC America) exhibited superior retentive strengths in both lathe-cut and hand-prepared specimens, whereas the compomer cement displayed the lowest values when tested. In lathe-cut specimens, statistical analysis showed no significant difference between GC Fuji 1 and indigenously developed Chitra CCC. Both Chitra CCC and GC Fuji 1 have comparable strengths in lathe-cut samples, making Chitra CCC a potential luting agent. Statistical analysis reveals that all cements, except GC Fuji 1, exhibited a significant decrease in strength due to the change in design uniformity. The chemical bonding of GC Fuji 1 proves to be quite strong irrespective of shape and precision of the tooth crown. The indigenously developed Chitra GIC and Chitra CCC showed promising results to be used as a potential luting agent.

  17. Investigation of in-vitro susceptibility of multidrug-resistant Acinetobacter baumannii strains isolated from clinical specimens to tigecycline

    Directory of Open Access Journals (Sweden)

    Tekin Tas

    2013-11-01

    Full Text Available The management of infections due to A. baumannii is difficult because of rapidly developing resistance, however, tigecycline, a glycylcycline antimicrobial, is in use for several years. In the present study, it was aimed to determine the susceptibility rates of A. baumannii to tigecycline. A total of 90 A. baumanniisolates were tested using three methods such as disk diffusion, broth microdilution, and E-test. The MIC50and MIC90 values and the MIC range were found as 2 μg/ml, 4 μg/ml, and 0.1-8 μg/ml by microdilution; and 2 μg/ml, 6 μg/ml, and 0.1-12 μg/ml by E-test, respectively. There were a few major errors as well as the minor rates were all high as between 35.7%-46.7%. The accuracy rates between the methods were low as 53.3% (48/90 between disk diffusion and E-test, 51.1% (46/90 between disk diffusion and microdilution, and 60.0% (54/90 between E-test and microdilution. In the ROC curve analysis, an inhibition zone diameter of susceptibility breakpoint of 21.5 mm had sensitivity between 68.8%-88.9%; specificity between 81.9%-87.9%; and accuracy between 80.0%-83.33%. An analysis based on EUCAST’s non-species breakpoints, the MIC tests showed higher accuracy with a rate of 96.7%, however, performance of disk diffusion got worse as lower than 25%. In conclusion, we showed that the reliability of the methods even did not remain as high as the past. Our study presented that none of three methods revealed reliable results in determination of susceptibility of A. baumanni to tigecycline, so the clinical response should be followed up carefully in such cases.

  18. Compliance of clinical microbiology laboratories in the United States with current recommendations for processing respiratory tract specimens from patients with cystic fibrosis.

    Science.gov (United States)

    Zhou, Juyan; Garber, Elizabeth; Desai, Manisha; Saiman, Lisa

    2006-04-01

    Respiratory tract specimens from patients with cystic fibrosis (CF) require unique processing by clinical microbiology laboratories to ensure detection of all potential pathogens. The present study sought to determine the compliance of microbiology laboratories in the United States with recently published recommendations for CF respiratory specimens. Microbiology laboratory protocols from 150 of 190 (79%) CF care sites were reviewed. Most described the use of selective media for Burkholderia cepacia complex (99%), Staphylococcus aureus (82%), and Haemophilus influenzae (89%) and identified the species of all gram-negative bacilli (87%). Only 52% delineated the use of agar diffusion assays for susceptibility testing of Pseudomonas aeruginosa. Standardizing laboratory practices will improve treatment, infection control, and our understanding of the changing epidemiology of CF microbiology.

  19. Herbarium specimens can reveal impacts of climate change on plant phenology; a review of methods and applications.

    Science.gov (United States)

    Jones, Casey A; Daehler, Curtis C

    2018-01-01

    Studies in plant phenology have provided some of the best evidence for large-scale responses to recent climate change. Over the last decade, more than thirty studies have used herbarium specimens to analyze changes in flowering phenology over time, although studies from tropical environments are thus far generally lacking. In this review, we summarize the approaches and applications used to date. Reproductive plant phenology has primarily been analyzed using two summary statistics, the mean flowering day of year and first-flowering day of year, but mean flowering day has proven to be a more robust statistic. Two types of regression models have been applied to test for associations between flowering, temperature and time: flowering day regressed on year and flowering day regressed on temperature. Most studies analyzed the effect of temperature by averaging temperatures from three months prior to the date of flowering. On average, published studies have used 55 herbarium specimens per species to characterize changes in phenology over time, but in many cases fewer specimens were used. Geospatial grid data are increasingly being used for determining average temperatures at herbarium specimen collection locations, allowing testing for finer scale correspondence between phenology and climate. Multiple studies have shown that inferences from herbarium specimen data are comparable to findings from systematically collected field observations. Understanding phenological responses to climate change is a crucial step towards recognizing implications for higher trophic levels and large-scale ecosystem processes. As herbaria are increasingly being digitized worldwide, more data are becoming available for future studies. As temperatures continue to rise globally, herbarium specimens are expected to become an increasingly important resource for analyzing plant responses to climate change.

  20. A Demonstration using Low-kt Fatigue Specimens of a Method for Predicting the Fatigue Behaviour of Corroded Aircraft Components

    Science.gov (United States)

    2013-03-01

    predictions of infinite life, i.e. runouts . For this reason the NASGRO dataset was not used in the Criticality Model. UNCLASSIFIED DSTO-RR-0390...JSM-6490 SEM at DSTO. The fracture surfaces of the specimens were removed using an abrasive cut-off wheel , cleaned using water and analytical grade...Pitting Bolthole in NASA Space Shuttle wheels 7075-T6 EDM EDM Low-kt fatigue specimen Wei [133] 2024-T3/Thickness not stated 500 h in 0.5M

  1. Clinical map document based on XML (cMDX): document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens.

    Science.gov (United States)

    Eminaga, Okyaz; Hinkelammert, Reemt; Semjonow, Axel; Neumann, Joerg; Abbas, Mahmoud; Koepke, Thomas; Bettendorf, Olaf; Eltze, Elke; Dugas, Martin

    2010-11-15

    The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa). The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed. For this purpose we developed cMDX. The document architecture of cMDX was designed according to Open Packaging Conventions by separating the whole data into template data and patient data. Analogue custom XML elements were considered to harmonize the graphical representation (e.g. tumour extension) with the textual data (e.g. histological patterns). The graphical documentation was based on the four-layer visualization model that forms the interaction between different custom XML elements. Sensible personal data were encrypted with a 256-bit cryptographic algorithm to avoid misuse. In order to assess the clinical value, we retrospectively analysed the tumour extension in 255 patients after radical prostatectomy. The pathology report with cMDX can represent pathological findings of the prostate in schematic styles. Such reports can be integrated into the hospital information system. "cMDX" documents can be converted into different data formats like text, graphics and PDF. Supplementary tools like cMDX Editor and an analyser tool were implemented. The graphical analysis of 255 prostatectomy specimens showed that PCa were mostly localized in the peripheral zone (Mean: 73% ± 25). 54% of PCa showed a multifocal growth pattern. cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis.

  2. An inverse method based on finite element model to derive the plastic flow properties from non-standard tensile specimens of Eurofer97 steel

    Directory of Open Access Journals (Sweden)

    S. Knitel

    2016-12-01

    Full Text Available A new inverse method was developed to derive the plastic flow properties of non-standard disk tensile specimens, which were so designed to fit irradiation rods used for spallation irradiations in SINQ (Schweizer Spallations Neutronen Quelle target at Paul Scherrer Institute. The inverse method, which makes use of MATLAB and the finite element code ABAQUS, is based upon the reconstruction of the load-displacement curve by a succession of connected small linear segments. To do so, the experimental engineering stress/strain curve is divided into an elastic and a plastic section, and the plastic section is further divided into small segments. Each segment is then used to determine an associated pair of true stress/plastic strain values, representing the constitutive behavior. The main advantage of the method is that it does not rely on a hypothetic analytical expression of the constitutive behavior. To account for the stress/strain gradients that develop in the non-standard specimen, the stress and strain were weighted over the volume of the deforming elements. The method was validated with tensile tests carried out at room temperature on non-standard flat disk tensile specimens as well as on standard cylindrical specimens made of the reduced-activation tempered martensitic steel Eurofer97. While both specimen geometries presented a significant difference in terms of deformation localization during necking, the same true stress/strain curve was deduced from the inverse method. The potential and usefulness of the inverse method is outlined for irradiated materials that suffer from a large uniform elongation reduction.

  3. Immunohistochemical detection of VHS virus in paraffin-embedded specimens of rainbow trout (Oncorhynchus mykiss); The influence of primary antibody, fixative, and antigen unmasking on method sensitivity

    DEFF Research Database (Denmark)

    Evensen, O.; Olesen, Niels Jørgen

    1997-01-01

    performed on parallel specimens, and the virus titer (TCID50/ml) was determined. Purified nucleocapsid protein (N-protein) of the virus was incorporated in an artificial antigen substrate (polymerized bovine serum albumin), fixed as described above, and embedded in paraffin wax. Microwave unmasking...... was performed an formalin-, PLP-, and Bouin's fluid-fixed specimens. The presence of virus peptides in situ or N-protein in the artificial antigen substrates was Visualized using an immunohistochemical method based on alkaline phosphatase or peroxidase and one polyclonal and five monoclonal polypeptide......-specific antibodies. VHS virus was identified in situ in specimens with high virus titers (10(7-8) TCID50/ml) regardless of the fixative and without the need of an unmasking procedure. A pronounced masking effect was observed for the cross-linking formalin and PLP fixatives. Regardless of the primary antibodies used...

  4. Detection of Mycoplasma pneumoniae in simulated and true clinical throat swab specimens by nanorod array-surface-enhanced Raman spectroscopy.

    Directory of Open Access Journals (Sweden)

    Suzanne L Hennigan

    Full Text Available The prokaryote Mycoplasma pneumoniae is a major cause of respiratory disease in humans, accounting for 20% of all community-acquired pneumonia and the leading cause of pneumonia in older children and young adults. The limitations of existing options for mycoplasma diagnosis highlight a critical need for a new detection platform with high sensitivity, specificity, and expediency. Here we evaluated silver nanorod arrays (NA as a biosensing platform for detection and differentiation of M. pneumoniae in culture and in spiked and true clinical throat swab samples by surface-enhanced Raman spectroscopy (SERS. Three M. pneumoniae strains were reproducibly differentiated by NA-SERS with 95%-100% specificity and 94-100% sensitivity, and with a lower detection limit exceeding standard PCR. Analysis of throat swab samples spiked with M. pneumoniae yielded detection in a complex, clinically relevant background with >90% accuracy and high sensitivity. In addition, NA-SERS correctly classified with >97% accuracy, ten true clinical throat swab samples previously established by real-time PCR and culture to be positive or negative for M. pneumoniae. Our findings suggest that the unique biochemical specificity of Raman spectroscopy, combined with reproducible spectral enhancement by silver NA, holds great promise as a superior platform for rapid and sensitive detection and identification of M. pneumoniae, with potential for point-of-care application.

  5. Cystic tumors of the pituitary infundibulum: seminal autopsy specimens (1899 to 1904) that allowed clinical-pathological craniopharyngioma characterization.

    Science.gov (United States)

    Pascual, José M; Prieto, Ruth; Rosdolsky, Maria; Strauss, Sewan; Castro-Dufourny, Inés; Hofecker, Verena; Winter, Eduard; Carrasco, Rodrigo; Ulrich, Walter

    2018-04-21

    A heterogeneous group of epithelial cystic tumors developed at the infundibulum and the third ventricle disconcerted pathologists at the dawn of the twentieth century. Very little was known at that time about the physiological role played by the pituitary gland, and there was almost complete ignorance regarding the function of the hypothalamus. Acromegaly, or enlargement of acral body parts, described in 1886 by Pierre Marie, was the only disease linked to primary hypertrophies of the pituitary gland, known as "pituitary strumas". A growing number of young patients manifesting an unexplained combination of physical and mental symptoms, including absent or delayed sexual maturation, progressive obesity, abnormal somnolence, and dementia-like changes in behavior were reported to present large solid-cystic tumors which characteristically expanded within the infundibulum and third ventricle, above an anatomically intact pituitary gland. Between 1899 and 1904, five seminal autopsy studies from different countries thoroughly described the anatomical relationships and histological features of this newly recognized type of infundibular tumors. These cases were instrumental in fostering the systematic investigation of similar lesions by the Austrian pathologist Jakob Erdheim (1874-1937), who in 1904 was able to classify these infundibulo-tuberal cysts under the common category of hypophyseal duct tumors. The pioneering American neurosurgeon Harvey Cushing (1869-1939) unsuccessfully attempted to surgically remove one of these cysts, for the first time in history, in 1902. The term "craniopharyngioma", chosen by Cushing in 1929 to designate these lesions, would eventually prevail over Erdheim's more accurate denomination, which linked their origin to squamous cell remnants derived from the embryological structures that give rise to the pituitary gland. This paper presents a comprehensive, renewed account of the five clinical-pathological reports which laid the groundwork for

  6. Mycobacterium grossiae sp. nov., a rapidly growing, scotochromogenic species isolated from human clinical respiratory and blood culture specimens.

    Science.gov (United States)

    Paniz-Mondolfi, Alberto Enrique; Greninger, Alexander L; Ladutko, Lynn; Brown-Elliott, Barbara A; Vasireddy, Ravikiran; Jakubiec, Wesley; Vasireddy, Sruthi; Wallace, Richard J; Simmon, Keith E; Dunn, Bruce E; Jackoway, Gary; Vora, Surabhi B; Quinn, Kevin K; Qin, Xuan; Campbell, Sheldon

    2017-11-01

    A previously undescribed, rapidly growing, scotochromogenic species of the genus Mycobacterium (represented by strains PB739 T and GK) was isolated from two clinical sources - the sputum of a 76-year-old patient with severe chronic obstructive pulmonary disease, history of tuberculosis exposure and Mycobacterium avium complex isolated years prior; and the blood of a 15-year-old male with B-cell acute lymphoblastic leukaemia status post bone marrow transplant. The isolates grew as dark orange colonies at 25-37 °C after 5 days, sharing features in common with other closely related species. Analysis of the complete 16S rRNA gene sequence (1492 bp) of strain PB739 T demonstrated that the isolate shared 98.8 % relatedness with Mycobacterium wolinskyi. Partial 429 bp hsp65 and 744 bp rpoB region V sequence analyses revealed that the sequences of the novel isolate shared 94.8 and 92.1 % similarity with those of Mycobacterium neoaurum and Mycobacterium aurum, respectively. Biochemical profiling, antimicrobial susceptibility testing, HPLC/gas-liquid chromatography analyses and multilocus sequence typing support the taxonomic status of these isolates (PB739 T and GK) as representatives of a novel species. Both isolates were susceptible to the Clinical and Laboratory Standards Institute recommended antimicrobials for susceptibility testing of rapidly growing mycobacteria including amikacin, ciprofloxacin, moxifloxacin, doxycycline/minocycline, imipenem, linezolid, clarithromycin and trimethropin/sulfamethoxazole. Both isolates PB739 T and GK showed intermediate susceptibility to cefoxitin. We propose the name Mycobacterium grossiae sp. nov. for this novel species and have deposited the type strain in the DSMZ and CIP culture collections. The type strain is PB739 T (=DSM 104744 T =CIP 111318 T ).

  7. Estimation of Surface Temperature and Heat Flux by Inverse Heat Transfer Methods Using Internal Temperatures Measured While Radiantly Heating a Carbon/Carbon Specimen up to 1920 F

    Science.gov (United States)

    Pizzo, Michelle; Daryabeigi, Kamran; Glass, David

    2015-01-01

    The ability to solve the heat conduction equation is needed when designing materials to be used on vehicles exposed to extremely high temperatures; e.g. vehicles used for atmospheric entry or hypersonic flight. When using test and flight data, computational methods such as finite difference schemes may be used to solve for both the direct heat conduction problem, i.e., solving between internal temperature measurements, and the inverse heat conduction problem, i.e., using the direct solution to march forward in space to the surface of the material to estimate both surface temperature and heat flux. The completed research first discusses the methods used in developing a computational code to solve both the direct and inverse heat transfer problems using one dimensional, centered, implicit finite volume schemes and one dimensional, centered, explicit space marching techniques. The developed code assumed the boundary conditions to be specified time varying temperatures and also considered temperature dependent thermal properties. The completed research then discusses the results of analyzing temperature data measured while radiantly heating a carbon/carbon specimen up to 1920 F. The temperature was measured using thermocouple (TC) plugs (small carbon/carbon material specimens) with four embedded TC plugs inserted into the larger carbon/carbon specimen. The purpose of analyzing the test data was to estimate the surface heat flux and temperature values from the internal temperature measurements using direct and inverse heat transfer methods, thus aiding in the thermal and structural design and analysis of high temperature vehicles.

  8. TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

    DEFF Research Database (Denmark)

    Marquard, Andrea Marion; Birkbak, Nicolai Juul; Thomas, Cecilia Engel

    2015-01-01

    A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations......-copy-number classifier on three independent data sets: 1669 newly available public tumors of various types, a cohort of 91 breast metastases, and a set of 24 specimens from 9 lung cancer patients subjected to multiregion sequencing. The cross-validation accuracy was highest when all three types of information were used...... detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2...

  9. Evaluation of BacT/Alert 3D Liquid Culture System for Recovery of Mycobacteria from Clinical Specimens Using Sodium Dodecyl (Lauryl) Sulfate-NaOH Decontamination

    Science.gov (United States)

    Carricajo, A.; Fonsale, N.; Vautrin, A. C.; Aubert, G.

    2001-01-01

    A total of 52 mycobacterial isolates were recovered from 1,197 clinical specimens decontaminated by a sodium dodecyl (lauryl) sulfate (SDS)-NaOH protocol. Of these, 94% were recovered with the BacT/Alert 3D system (Organon Teknika, Durham, N.C.) and 79% were recovered on Löwenstein-Jensen (LJ) medium. Mean times to detection of organisms of the Mycobacterium tuberculosis complex (n = 47) were 22.8 days with LJ medium and 16.2 days with the system. The BacT/Alert 3D system is a rapid and efficient detection system which can be used with an SDS-NaOH decontamination procedure. PMID:11574623

  10. Pneumocystis carinii pneumonia in AIDS patients: clinical course in relation to the parasite number found in routine specimens obtained by fiberoptic bronchoscopy

    DEFF Research Database (Denmark)

    Orholm, M; Nielsen, T L; Holten-Andersen, W

    1992-01-01

    The aim of this study was to evaluate whether the amount of Pneumocystis carinii organisms found at fiberoptic bronchoscopy (FB) performed on HIV-positive patients correlated to the character of the P. carinii pneumonia (PCP). A consecutive series of 105 patients presented with 131 episodes...... of pulmonary symptoms requiring FB, and in 75 of these episodes a diagnosis of PCP was made. Specimens were stained with Giemsa and methenamine silver nitrate and the number of parasites found was given as: numerous, many, few or none. The following signs and symptoms were registered: cough, dyspnoea, fever......, loss of weight, chest radiograph, haemoglobin, WBC, CD4 cell count, PO2 and HIV p24 antigen. The PCP was characterized by the clinical course: mild, moderate, severe, and by the outcome: pulmonary healthy, pulmonary insufficiency and death. No correlations between the number of P. carinii organisms...

  11. Urine culture - catheterized specimen

    Science.gov (United States)

    Culture - urine - catheterized specimen; Urine culture - catheterization; Catheterized urine specimen culture ... urinary tract infections may be found in the culture. This is called a contaminant. You may not ...

  12. Could home sexually transmitted infection specimen collection with e-prescription be a cost-effective strategy for clinical trials and clinical care?

    Science.gov (United States)

    Blake, Diane R; Spielberg, Freya; Levy, Vivian; Lensing, Shelly; Wolff, Peter A; Venkatasubramanian, Lalitha; Acevedo, Nincoshka; Padian, Nancy; Chattopadhyay, Ishita; Gaydos, Charlotte A

    2015-01-01

    Results of a recent demonstration project evaluating feasibility, acceptability, and cost of a Web-based sexually transmitted infection (STI) testing and e-prescription treatment program (eSTI) suggest that this approach could be a feasible alternative to clinic-based testing and treatment, but the results need to be confirmed by a randomized comparative effectiveness trial. We modeled a decision tree comparing (1) cost of eSTI screening using a home collection kit and an e-prescription for uncomplicated treatment versus (2) hypothetical costs derived from the literature for referral to standard clinic-based STI screening and treatment. Primary outcome was number of STIs detected. Analyses were conducted from the clinical trial perspective and the health care system perspective. The eSTI strategy detected 75 infections, and the clinic referral strategy detected 45 infections. Total cost of eSTI was $94,938 ($1266/STI detected) from the clinical trial perspective and $96,088 ($1281/STI detected) from the health care system perspective. Total cost of clinic referral was $87,367 ($1941/STI detected) from the clinical trial perspective and $71,668 ($1593/STI detected) from the health care system perspective. Results indicate that eSTI will likely be more cost-effective (lower cost/STI detected) than clinic-based STI screening, both in the context of clinical trials and in routine clinical care. Although our results are promising, they are based on a demonstration project and estimates from other small studies. A comparative effectiveness research trial is needed to determine actual cost and impact of the eSTI system on identification and treatment of new infections and prevention of their sequelae.

  13. The Sherlock Holmes method in clinical practice.

    Science.gov (United States)

    Sopeña, B

    2014-04-01

    This article lists the integral elements of the Sherlock Holmes method, which is based on the intelligent collection of information through detailed observation, careful listening and thorough examination. The information thus obtained is analyzed to develop the main and alternative hypotheses, which are shaped during the deductive process until the key leading to the solution is revealed. The Holmes investigative method applied to clinical practice highlights the advisability of having physicians reason through and seek out the causes of the disease with the data obtained from acute observation, a detailed review of the medical history and careful physical examination. Copyright © 2013 Elsevier España, S.L. All rights reserved.

  14. Automated processing, extraction and detection of herpes simplex virus types 1 and 2: A comparative evaluation of three commercial platforms using clinical specimens.

    Science.gov (United States)

    Binnicker, Matthew J; Espy, Mark J; Duresko, Brian; Irish, Cole; Mandrekar, Jay

    2017-04-01

    Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument. In this study, we compared three commercially-available systems; Aptima ® /Panther (Hologic, San Diego, CA), ARIES ® (Luminex Corporation, Austin, TX), and cobas ® 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples. Two-hundred seventy-seven specimens (genital [n=193], dermal [n=84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from ≥3 of the 4 assays. Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5h by the cobas 4800, 3.1h by Aptima/Panther, and 3.9h by ARIES. The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Analytic and clinical performance of cobas HPV testing in anal specimens from HIV-positive men who have sex with men.

    Science.gov (United States)

    Wentzensen, Nicolas; Follansbee, Stephen; Borgonovo, Sylvia; Tokugawa, Diane; Sahasrabuddhe, Vikrant V; Chen, Jie; Lorey, Thomas S; Gage, Julia C; Fetterman, Barbara; Boyle, Sean; Sadorra, Mark; Tang, Scott Dahai; Darragh, Teresa M; Castle, Philip E

    2014-08-01

    Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (P(trend) < 0.001), HPV18 (P(trend) = 0.07), and other carcinogenic types (P(trend) < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  16. Operational impact of using a vanadate oxidase method for direct bilirubin measurements at an academic medical center clinical laboratory

    Directory of Open Access Journals (Sweden)

    Neha Dhungana

    2017-08-01

    Full Text Available Objectives: The aim of this study was to compare the operational impact of using vanadate oxidase versus diazo direct bilirubin assays for an academic medical center patient population. Design and methods: Retrospective study was done over an approximately 3.5 year period. The main automated chemistry instrumentation was a Roche Diagnostics cobas 8000 line. The Roche Direct Bilirubin assay was compared to Diazyme Laboratories Direct Bilirubin Assay and Randox Laboratories Direct Bilirubin assay using manufacturer's guidelines for hemolysis index, lipemia index, and analytical measurement range (AMR. Results: Retrospective data was analyzed for 47,333 serum/plasma specimens that had clinical orders for direct bilirubin. A total of 5943 specimens (12.6% exceeded the hemolysis index limit for the Roche method compared to only 0.2% and 0.05% of specimens for the Diazyme and Randox methods, respectively. The impact was particularly large on patients less than 2 years old, for which 51.3% of specimens exceeded the hemolysis index for the Roche method. A total of 1671 specimens (3.5% exceeded the lipemia index limit for the Roche method compared to less than 0.1% for the Randox method. Lastly, 988 (2.1% of specimens had direct bilirubin concentrations exceeding the upper AMR limit of 10 mg/dL [171 µmol/L] for the Roche assay compared to less than 1% of specimens for the vanadate oxidase methods. Conclusions: Vanadate oxidase direct bilirubin methods offer advantages over diazo methods in terms of less interference by hemolysis and lipemia, as well as wider AMR. The advantages are particularly evident for neonatal and infant populations. Keywords: Bilirubin, Clinical chemistry tests, Hemolysis, Hyperlipidemias, Jaundice, Photometry

  17. A Real-Time PCR Assay to Identify and Discriminate Among Wild-Type and Vaccine Strains of Varicella-Zoster Virus and Herpes Simplex Virus in Clinical Specimens, and Comparison With the Clinical Diagnoses

    Science.gov (United States)

    Harbecke, Ruth; Oxman, Michael N.; Arnold, Beth A.; Ip, Charlotte; Johnson, Gary R.; Levin, Myron J.; Gelb, Lawrence D.; Schmader, Kenneth E.; Straus, Stephen E.; Wang, Hui; Wright, Peter F.; Pachucki, Constance T.; Gershon, Anne A.; Arbeit, Robert D.; Davis, Larry E.; Simberkoff, Michael S.; Weinberg, Adriana; Williams, Heather M.; Cheney, Carol; Petrukhin, Luba; Abraham, Katalin G.; Shaw, Alan; Manoff, Susan; Antonello, Joseph M.; Green, Tina; Wang, Yue; Tan, Charles; Keller, Paul M.

    2014-01-01

    A real-time PCR assay was developed to identify varicella-zoster virus (VZV) and herpes simplex virus (HSV) DNA in clinical specimens from subjects with suspected herpes zoster (HZ; shingles). Three sets of primers and probes were used in separate PCR reactions to detect and discriminate among wild-type VZV (VZV-WT), Oka vaccine strain VZV (VZV-Oka), and HSV DNA, and the reaction for each virus DNA was multiplexed with primers and probe specific for the human β-globin gene to assess specimen adequacy. Discrimination of all VZV-WT strains, including Japanese isolates and the Oka parent strain, from VZV-Oka was based upon a single nucleotide polymorphism at position 106262 in ORF 62, resulting in preferential amplification by the homologous primer pair. The assay was highly sensitive and specific for the target virus DNA, and no cross-reactions were detected with any other infectious agent. With the PCR assay as the gold standard, the sensitivity of virus culture was 53% for VZV and 77% for HSV. There was 92% agreement between the clinical diagnosis of HZ by the Clinical Evaluation Committee and the PCR assay results. PMID:19475609

  18. Evaluation of the crack initiation of curved compact tension specimens of a Zr-2.5Nb pressure tube using the unloading compliance and direct current potential drop methods

    International Nuclear Information System (INIS)

    Kim, Young Suk; Jeong, Hyeon Cheol; Ahn, Sang Bok

    2005-01-01

    The Direct Current Potential Drop(DCPD) method and the Unloading Compliance(UC) method with a crack opening displacement gauge were applied simultaneously to the Zr-2.5Nb Curved Compact Tension (CCT) specimens to determine which of the two methods can precisely determine the crack initiation point and hence the crack length for evaluation of their fracture toughness. The DCPD method detected the crack initiation at a smaller load-time displacement compared to the UC method. As a verification, a direct observation of the fracture surfaces on the curved compact tension specimens was made on the CCT specimens experiencing either 0.8 to 1.0 mm load line displacement or various loads from 50% to 80% of the maximum peak load, or P max . The DCPD method is concluded to be more precise in determining the crack initiation and fracture toughness, J in Zr-2.5Nb CCT specimens than the UC method

  19. Method for determining thermo-physical properties of specimens. [photographic recording of changes in thin film phase-change temperature indicating material in wind tunnel

    Science.gov (United States)

    Jones, R. A. (Inventor)

    1974-01-01

    The square root of the product of thermophysical properties q, c and k, where p is density, c is specific heat and k is thermal conductivity, is determined directly on a test specimen such as a wind tunnel model. The test specimen and a reference specimen of known specific heat are positioned at a given distance from a heat source. The specimens are provided with a coating, such as a phase change coating, to visually indicate that a given temperature was reached. A shutter interposed between the heat source and the specimens is opened and a motion picture camera is actuated to provide a time record of the heating step. The temperature of the reference specimen is recorded as a function of time. The heat rate to which both the test and reference specimens were subjected is determined from the temperature time response of the reference specimen by the conventional thin-skin calorimeter equation.

  20. DNA extraction from herbarium specimens.

    Science.gov (United States)

    Drábková, Lenka Záveská

    2014-01-01

    With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).

  1. Characterizing Ductile Damage and Failure: Application of the Direct Current Potential Drop Method to Uncracked Tensile Specimens

    OpenAIRE

    Brinnel, V.; Döbereiner, B.; Münstermann, Sebastian

    2014-01-01

    Modern high-strength steels exhibit excellent ductility properties but their application is hindered by traditional design rules. A characterization of necessary safety margins for the ductile failure of these steels is therefore required. Direct observation of ductile damage within tests is currently not possible, only limited measurements can be made with synchrotron or X-ray radiation facilities. The direct current potential drop (DCPD) method can determine ductile crack propagation with l...

  2. Comparison of group B streptococci colonization in vaginal and rectal specimens by culture method and polymerase chain reaction technique

    Directory of Open Access Journals (Sweden)

    Shahrokh Bidgani

    2016-03-01

    Conclusion: The frequency of GBS culture from rectal samples was higher than vaginal samples. However, the detection percentage of GBS using PCR from vaginal samples was higher than rectal samples. By contrast, the culture is a time-consuming method requiring at least 48 hours for GBS fully identification but PCR is a sensitive and rapid technique in detection of GBS, with the result was acquired during 3 hours.

  3. Optimization of high grade glioma cell culture from surgical specimens for use in clinically relevant animal models and 3D immunochemistry.

    Science.gov (United States)

    Hasselbach, Laura A; Irtenkauf, Susan M; Lemke, Nancy W; Nelson, Kevin K; Berezovsky, Artem D; Carlton, Enoch T; Transou, Andrea D; Mikkelsen, Tom; deCarvalho, Ana C

    2014-01-07

    Glioblastomas, the most common and aggressive form of astrocytoma, are refractory to therapy, and molecularly heterogeneous. The ability to establish cell cultures that preserve the genomic profile of the parental tumors, for use in patient specific in vitro and in vivo models, has the potential to revolutionize the preclinical development of new treatments for glioblastoma tailored to the molecular characteristics of each tumor. Starting with fresh high grade astrocytoma tumors dissociated into single cells, we use the neurosphere assay as an enrichment method for cells presenting cancer stem cell phenotype, including expression of neural stem cell markers, long term self-renewal in vitro, and the ability to form orthotopic xenograft tumors. This method has been previously proposed, and is now in use by several investigators. Based on our experience of dissociating and culturing 125 glioblastoma specimens, we arrived at the detailed protocol we present here, suitable for routine neurosphere culturing of high grade astrocytomas and large scale expansion of tumorigenic cells for preclinical studies. We report on the efficiency of successful long term cultures using this protocol and suggest affordable alternatives for culturing dissociated glioblastoma cells that fail to grow as neurospheres. We also describe in detail a protocol for preserving the neurospheres 3D architecture for immunohistochemistry. Cell cultures enriched in CSCs, capable of generating orthotopic xenograft models that preserve the molecular signatures and heterogeneity of GBMs, are becoming increasingly popular for the study of the biology of GBMs and for the improved design of preclinical testing of potential therapies.

  4. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens.

    Science.gov (United States)

    Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J; Rohan, Thomas; Ben-Dov, Iddo Z

    2017-03-14

    Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.

  5. A novel specimen-preparing method using epoxy resin as binding material for LIBS analysis of powder samples.

    Science.gov (United States)

    Shi, Linli; Lin, Qingyu; Duan, Yixiang

    2015-11-01

    In view of the inevitable preprocessing of powder samples for LIBS detection, epoxy resin glue was investigated for the first time as a binder of powder samples due to its superior property of improved performance in laser induced breakdown spectroscopy (LIBS) technique as a quantitative analytical tool. For comparative studies of the epoxy resin and traditional polyethylene (PE) pellets in soil, sample detection, the signal intensities of Fe (I) at 404.58 nm, Ca (I) at 443.57 nm, and Cr (I) at 453.52 nm, were studied and subsequently, the calibration curves for these elements were constructed using the standard samples with variable concentrations. The signal intensities of epoxy resin samples were, on average, about 2 times greater than those obtained with the traditional PE pellet samples. Meanwhile, the resin samples showed better R square values of 0.981, 0.985 and 0.979 for curves of Fe (I) 404.58 nm, Ca (I) 443.57 nm, and Cr (I) 453.52 nm, compared to the 0.974, 0.950 and 0.934, of the PE pellet samples. Furthermore, the former represented lower limits of detection (LOD) for Fe, Ca and Cr. These experimental results indicated that this proposed novel method based on epoxy resin can attach samples of properties of high homogeneity, cohesiveness, smoothness and hardness, which are conducive to system stability, testing accuracy and signal enhancement. This method can make LIBS more practical in powder sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Operational impact of using a vanadate oxidase method for direct bilirubin measurements at an academic medical center clinical laboratory.

    Science.gov (United States)

    Dhungana, Neha; Morris, Cory; Krasowski, Matthew D

    2017-08-01

    The aim of this study was to compare the operational impact of using vanadate oxidase versus diazo direct bilirubin assays for an academic medical center patient population. Retrospective study was done over an approximately 3.5 year period. The main automated chemistry instrumentation was a Roche Diagnostics cobas 8000 line. The Roche Direct Bilirubin assay was compared to Diazyme Laboratories Direct Bilirubin Assay and Randox Laboratories Direct Bilirubin assay using manufacturer's guidelines for hemolysis index, lipemia index, and analytical measurement range (AMR). Retrospective data was analyzed for 47,333 serum/plasma specimens that had clinical orders for direct bilirubin. A total of 5943 specimens (12.6%) exceeded the hemolysis index limit for the Roche method compared to only 0.2% and 0.05% of specimens for the Diazyme and Randox methods, respectively. The impact was particularly large on patients less than 2 years old, for which 51.3% of specimens exceeded the hemolysis index for the Roche method. A total of 1671 specimens (3.5%) exceeded the lipemia index limit for the Roche method compared to less than 0.1% for the Randox method. Lastly, 988 (2.1%) of specimens had direct bilirubin concentrations exceeding the upper AMR limit of 10 mg/dL [171 µmol/L] for the Roche assay compared to less than 1% of specimens for the vanadate oxidase methods. Vanadate oxidase direct bilirubin methods offer advantages over diazo methods in terms of less interference by hemolysis and lipemia, as well as wider AMR. The advantages are particularly evident for neonatal and infant populations.

  7. Evaluation of the ARCHITECT urine NGAL assay: Assay performance, specimen handling requirements and biological variability

    NARCIS (Netherlands)

    Grenier, F.C.; Ali, S.; Syed, H.; Workman, R.; Martens, F.; Liao, M.; Wang, Y.; Wong, P.Y.

    2010-01-01

    Objectives: NGAL (Neutrophil Gelatinase-Associated Lipocalin) has emerged as a new biomarker for the identification of acute kidney injury. Reliable clinical evaluations require a simple, robust test method for NGAL, and knowledge of specimen handling and specimen stability characteristics. We

  8. The frequency of Listeria monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR

    Directory of Open Access Journals (Sweden)

    abazar pournajaf

    2013-09-01

    Full Text Available Background: Listeria monocytogenes is a facultative intracellular pathogen that causes listeriosis which has extensive clinical manifestations. Infections with L. monocytogenes are a serious threat to immunocompromised persons. The aim of this study was to determine the frequency of L. monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR. Materials and Methods: In this study, 617 specimens were analyzed. All specimens were cultured in the specific PALCAM agar. Colonies were initially identified by routine biochemical tests. Finally, PCR assays using primers specific for inlA gene were performed. Results: In all, 46 (8.2% L. monocytogenes isolates were recovered from 617 specimens. Fourteen (8.2% strains, including 4 (7.5%, 2 (5.7%, 5 (14.2% and 3 (8.5% isolates were obtained from placental tissue, urine, vaginal and rectal swabs, respectively. In addition, 9 (7.4% strains of L. monocytogenes which were isolated from 107 different dairy products originated from cheese 5 (7.1%, cream 2 (10% and kashk 2 (11.7%, respectively. Among 11 (5.2% strains isolated from 210 different meat products, 5 (5.5%, 4 (7.2% and 2 (3% strains belonged to sausage, meat and poultry extracts, respectively. Finally, 12 (9.2% Listeria strains were recovered from 130 animal specimens that included 6 (10%, 4 (8% and 2 (10% strains from goat, sheep and cattle, respectively. Furthermore, all Listeria isolates (100% were found to be carriers of  inlA gene in PCR assay. Conclusion: The present study showed that the clinical and non-clinical specimens were contaminated with L. monocytogenes. So, it seems necessary to use a simple and standard technique such as PCR for rapid detection of this organism from various sources.

  9. Culturing Stool Specimens for Campylobacter spp., Pennsylvania, USA

    Science.gov (United States)

    M’ikanatha, Nkuchia M.; Dettinger, Lisa A.; Perry, Amanda; Rogers, Paul; Reynolds, Stanley M.

    2012-01-01

    In 2010, we surveyed 176 clinical laboratories in Pennsylvania regarding stool specimen testing practices for enteropathogens, including Campylobacter spp. Most (96.3%) routinely test for Campylobacter spp. In 17 (15.7%), a stool antigen test is the sole method for diagnosis. We recommend that laboratory practice guidelines for Campylobacter spp. testing be developed. PMID:22377086

  10. Pathologic diagnoses of appendectomy specimens: a 10-year review.

    African Journals Online (AJOL)

    A retrospective study was performed to see the pattern of histopathologic diagnoses in appendectomy specimens, their demographics, and the rate of negative appendectomy. Materials and methods: Records of resected appendices with a clinical diagnosis of acute appendicitis submitted to histopathology department of ...

  11. Laparoscopic specimen retrieval bags.

    Science.gov (United States)

    Smorgick, Noam

    2014-10-01

    Specimen retrieval bags have long been used in laparoscopic gynecologic surgery for contained removal of adnexal cysts and masses. More recently, the concerns regarding spread of malignant cells during mechanical morcellation of myoma have led to an additional use of specimen retrieval bags for contained "in-bag" morcellation. This review will discuss the indications for use retrieval bags in gynecologic endoscopy, and describe the different specimen bags available to date.

  12. Evaluation of Commercial Diagnostic Assays for the Specific Detection of Avian Influenza A (H7N9) Virus RNA Using a Quality-Control Panel and Clinical Specimens in China

    Science.gov (United States)

    Chen, Suhong; Wang, Dayan; Li, Changgui; Wu, Xing; Li, Lili; Bai, Dongting; Zhang, Chuntao; Wang, Junzhi

    2015-01-01

    A novel avian influenza A H7N9-subtype virus emerged in China in 2013 and threatened global public health. Commercial kits that specifically detect avian influenza A (H7N9) virus RNA are urgently required to prepare for the emergence and potential pandemic of this novel influenza virus. The safety and effectiveness of three commercial molecular diagnostic assays were evaluated using a quality-control panel and clinical specimens collected from over 90 patients with confirmed avian influenza A (H7N9) virus infections. The analytical performance evaluation showed that diverse influenza H7N9 viruses can be detected with high within- and between-lot reproducibility and without cross-reactivity to other influenza viruses (H1N1 pdm09, seasonal H1N1, H3N2, H5N1 and influenza B). The detection limit of all the commercial assays was 2.83 Log10 copies/μl [0.7 Log10TCID50/mL of avian influenza A (H7N9) virus strain A/Zhejiang/DTID-ZJU01/2013], which is comparable to the method recommended by the World Health Organization (WHO). In addition, using a WHO-Chinese National Influenza Center (CNIC) method as a reference for clinical evaluation, positive agreement of more than 98% was determined for all of the commercial kits, while negative agreement of more than 99% was observed. In conclusion, our findings provide comprehensive evidence for the high performance of three commercial diagnostic assays and suggest the application of these assays as rapid and effective diagnostic tools for avian influenza A (H7N9) virus in the routine clinical practice of medical laboratories. PMID:26361351

  13. Connecting clinical and actuarial prediction with rule-based methods

    NARCIS (Netherlands)

    Fokkema, M.; Smits, N.; Kelderman, H.; Penninx, B.W.J.H.

    2015-01-01

    Meta-analyses comparing the accuracy of clinical versus actuarial prediction have shown actuarial methods to outperform clinical methods, on average. However, actuarial methods are still not widely used in clinical practice, and there has been a call for the development of actuarial prediction

  14. Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens

    Directory of Open Access Journals (Sweden)

    Schirmacher Peter

    2008-09-01

    Full Text Available Abstract Background Invasion-related genes over-expressed by tumor cells as well as by reacting host cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. Results This study examined the suitability of a murine model (CT26/Balb/C of colorectal liver metastasis to represent clinical liver metastasis specimens using a global gene expression approach. Cross-species similarity was examined between pure liver, liver invasion, tumor invasion and pure tumor compartments through overlap of up-regulated genes and gene ontology (GO-based biological themes on the level of single GO-terms and of condensed GO-term families. Three out of four GO-term families were conserved in a compartment-specific way between the species: secondary metabolism (liver, invasion (invasion front, and immune response (invasion front and liver. Among the individual GO-terms over-represented in the invasion compartments in both species were "extracellular matrix", "cell motility", "cell adhesion" and "antigen presentation" indicating that typical invasion related processes are operating in both species. This was reflected on the single gene level as well, as cross-species overlap of potential target genes over-expressed in the combined invasion front compartments reached up to 36.5%. Generally, histopathology and gene expression correlated well as the highest single gene overlap was found to be 44% in syn-compartmental comparisons (liver versus liver whereas cross-compartmental overlaps were much lower (e.g. liver versus tumor: 9.7%. However, single gene overlap was surprisingly high in some cross-compartmental comparisons (e.g. human liver invasion compartment and murine tumor invasion compartment: 9.0% despite little histolopathologic similarity indicating that invasion relevant genes are not necessarily confined to histologically defined compartments. Conclusion In summary, cross

  15. Georeferencing Animal Specimen Datasets

    NARCIS (Netherlands)

    van Erp, M.G.J.; Hensel, R.; Ceolin, D.; van der Meij, M.

    2014-01-01

    For biodiversity research, the field of study that is concerned with the richness of species of our planet, it is of the utmost importance that the location of an animal specimen find is known with high precision. Due to specimens often having been collected over the course of many years, their

  16. Technical note: Discard the specimen collection swab directly at point of care to improve extensive automated processing in clinical microbiology laboratories.

    Science.gov (United States)

    Avolio, Manuela; Grosso, Shamanta; Bruschetta, Graziano; Camporese, Alessandro

    2016-10-01

    We compared, in terms of microorganisms recovery, the discard of specimen collection swab, after swirling into its medium, directly at point of care, with its placing into the medium and vortexing on arrival in the laboratory. Our results show that these two procedures are overlapped in terms of bacterial recovery. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Clinical Evaluation of the Cepheid Xpert TV Assay for Detection of Trichomonas vaginalis with Prospectively Collected Specimens from Men and Women.

    Science.gov (United States)

    Schwebke, Jane R; Gaydos, C A; Davis, T; Marrazzo, J; Furgerson, D; Taylor, S N; Smith, B; Bachmann, L H; Ackerman, R; Spurrell, T; Ferris, D; Burnham, C A; Reno, H; Lebed, J; Eisenberg, D; Kerndt, P; Philip, S; Jordan, J; Quigley, N

    2018-02-01

    Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and the acquisition and transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA cleared in the United States for detection of Trichomonas vaginalis in specimens from both women and men. This study reports the results of a multicenter study recently conducted using the Xpert TV ( T. vaginalis ) assay to test specimens from both men and women. On-demand results were available in as little as 40 min for positive specimens. A total of 1,867 women and 4,791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV assay was compared to the patient infected status (PIS) derived from the results of InPouch TV broth culture and Aptima NAAT for T. vaginalis The diagnostic sensitivities and specificities of the Xpert TV assay for the combined female specimens (urine samples, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 to 100% and 99.4 to 99.9%, respectively. For male urine samples, the diagnostic sensitivity and specificity were 97.2% and 99.9%, respectively, compared to PIS results derived from the results of broth culture for T. vaginalis and bidirectional gene sequencing of amplicons. Excellent performance characteristics were seen using both female and male specimens. The ease of using the Xpert TV assay should result in opportunities for enhanced screening for T. vaginalis in both men and women and, hopefully, improved control of this infection. Copyright © 2018 Schwebke et al.

  18. Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens.

    Science.gov (United States)

    Guan, Yaoyao; Gravitt, Patti E; Howard, Roslyn; Eby, Yolanda J; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E

    2013-04-01

    The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p=0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens

    Science.gov (United States)

    Guan, YaoYao; Gravitt, Patti E.; Howard, Roslyn; Eby, Yolanda J.; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E.

    2016-01-01

    The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p = 0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. PMID:23370404

  20. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    International Nuclear Information System (INIS)

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420 degrees C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs

  1. Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases.

    Science.gov (United States)

    Telle, Sabine; Thines, Marco

    2008-01-01

    During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm(2) of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; approximately 620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.

  2. Evaluating Antimicrobial Effects of Centaurea Plant’s Essential Oil on Pathogenic Bacteria: Staphylococcus Aureus, Staphylococcus Epidermidis, and Escherichia Coli Isolated from Clinical Specimens

    Directory of Open Access Journals (Sweden)

    Haedeh Mobaiyen

    2016-03-01

    Full Text Available Background & Objectives :Nowadays, development of drug resistance against chemical antimicrobial drugs has attracted attention using medicinal plants in treatment of infections. The aim of this study is to evaluate the antimicrobial effects of two species of Centaurea plant’s essential oil on drug resistant clinical isolates of three pathogenic isolates. Materials & Methods :The studied plants were collected from Marand city in East Azerbaijan, Iran and were confirmed as Centaurea Depressa M.B. and Centaurea Cyanus L. by botanists of Iran Agriculture Organization. The essential oil of these plants (Stems and leaf were extracted via steam distillation method by Clevenger, and their antimicrobial effects were studied by well diffusion method in the abovementioned bacteria. The components of essential oil were identified by injection to gas chromatography linked to mass spectrometry (GC/M. Results :The results of this study prove that the essential oils from the abovementioned plants have bactericidal effects. The most antibacterial effect is observed in Escherichia coli strains. The results of GC/MS chromatography reveal that the essential oils of Centaurea Depressa M.B. and Centaurea Cyanus L. have 28 and 32 compounds, respectively. Conclusion: This study confirmed that the grasses could be used in medicinal plants group with antibacterial properties. However, their effects in vivo must be evaluated and the most effective component of them must be identified carefully so that they can be applied commonly as an alternative synthetic drug in treating infections.

  3. Substrate optimization and clinical validation of reporter peptides for MS-based protease profiling in serum specimens: a new approach for diagnosis of malignant disease.

    Science.gov (United States)

    Yepes, Diego; Jacob, Anette; Dauber, Marc; Costina, Victor; Hofheinz, Ralf; Neumaier, Michael; Findeisen, Peter

    2011-07-01

    The progression of many solid tumors is characterized by the release of tumor-associated proteases, such as cancer procoagulant, MMP2 and MMP7. Consequently, the detection of tumor-specific proteolytic activity in serum specimens has recently been proposed as a new diagnostic tool in oncology. However, tumor-associated proteases are highly diluted in serum specimens and it is challenging to identify substrates that are specifically cleaved. In this study, we describe the systematic optimization of a synthetic peptide substrate using a positional scanning synthetic combinatorial library (PS-SCL) approach. The initial reporter peptide (RP) comprises of the cleavage site, WKPYDAAD, that is part of the coagulation factor X, the natural substrate of the tumor-associated cysteine protease cancer procoagulant (EC 3.4.22.26). Specifically, the amino acid substitution of aspartatic acid (D) in position P1' against asparagine (N) improved the processing of respective RPs in serum specimens from patients with colorectal tumors compared to healthy controls. Proteolytic fragments of RPs accumulated during prolonged incubation with serum specimens and were quantified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Finally, the optimized RP with the cleaved motif WKPYNAAD was combined with the RPs, VPLSLTMG and IPVSLRSG, that were cleaved by the tumor-associated proteases, MMP2 and MMP7, respectively. The diagnostic accuracy of MS-based protease profiling was evaluated for this triplex RP mix in a cohort of 50 serum specimens equally divided into colorectal cancer patients and healthy control individuals. Multiparametric analysis showed an AUC value of 0.90 for the receiver operating characteristic curve and was superior to the classification accuracy of the single markers. Our results demonstrate that RPs for MS-based protease profiling can systematically be optimized with a PS-SCL. Furthermore, the combination of different RPs can

  4. [Application of Delphi method in traditional Chinese medicine clinical research].

    Science.gov (United States)

    Bi, Ying-fei; Mao, Jing-yuan

    2012-03-01

    In recent years, Delphi method has been widely applied in traditional Chinese medicine (TCM) clinical research. This article analyzed the present application situation of Delphi method in TCM clinical research, and discussed some problems presented in the choice of evaluation method, classification of observation indexes and selection of survey items. On the basis of present application of Delphi method, the author analyzed the method on questionnaire making, selection of experts, evaluation of observation indexes and selection of survey items. Furthermore, the author summarized the steps of application of Delphi method in TCM clinical research.

  5. Clinical experimental stress studies: methods and assessment.

    Science.gov (United States)

    Bali, Anjana; Jaggi, Amteshwar Singh

    2015-01-01

    Stress is a state of threatened homeostasis during which a variety of adaptive processes are activated to produce physiological and behavioral changes. Stress induction methods are pivotal for understanding these physiological or pathophysiological changes in the body in response to stress. Furthermore, these methods are also important for the development of novel pharmacological agents for stress management. The well-described methods to induce stress in humans include the cold pressor test, Trier Social Stress Test, Montreal Imaging Stress Task, Maastricht Acute Stress Test, CO2 challenge test, Stroop test, Paced Auditory Serial Addition Task, noise stress, and Mannheim Multicomponent Stress Test. Stress assessment in humans is done by measuring biochemical markers such as cortisol, cortisol awakening response, dexamethasone suppression test, salivary α-amylase, plasma/urinary norepinephrine, norepinephrine spillover rate, and interleukins. Physiological and behavioral changes such as galvanic skin response, heart rate variability, pupil size, and muscle and/or skin sympathetic nerve activity (microneurography) and cardiovascular parameters such as heart rate, blood pressure, and self-reported anxiety are also monitored to assess stress response. This present review describes these commonly employed methods to induce stress in humans along with stress assessment methods.

  6. Simultaneous specimen and stage cleaning device for analytical electron microscope

    Science.gov (United States)

    Zaluzec, Nestor J.

    1996-01-01

    An improved method and apparatus are provided for cleaning both a specimen stage, a specimen and an interior of an analytical electron microscope (AEM). The apparatus for cleaning a specimen stage and specimen comprising a plasma chamber for containing a gas plasma and an air lock coupled to the plasma chamber for permitting passage of the specimen stage and specimen into the plasma chamber and maintaining an airtight chamber. The specimen stage and specimen are subjected to a reactive plasma gas that is either DC or RF excited. The apparatus can be mounted on the analytical electron microscope (AEM) for cleaning the interior of the microscope.

  7. Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex.

    Science.gov (United States)

    Liang, Xiao; Chigerwe, Munashe; Hietala, Sharon K; Crossley, Beate M

    2014-06-01

    In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI=0.89-0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (-27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P≥0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Determination of J-integral R-curves for the pressure vessel material A 533 B1 using the potential drop technique and the multi-specimen method

    International Nuclear Information System (INIS)

    Krompholz, K.; Ullrich, G.

    1985-01-01

    J-integral experiments at room temperature were performed on three point bend type specimens of the nuclear pressure vessel material A 533 B1 with a/w-ratios of 0.3 and 0.5. Following the ASTM-proposal for the multi-specimen technique a value is obtained close to the value obtained in the HSST round robin test. On the other hand, from the measurement of the Jsub(IC)-value by means of the potential drop technique there is an indication that a lower value of Jsub(IC) is correct. This is in agreement with the multi-specimen technique using linear regression lines without excluding 'invalid' points. That is reasonable if fractographic investigations gives clear indications that stable crack growth has occurred as is the case in this work. (Auth.)

  9. Specimen size effects in Charpy impact testing

    International Nuclear Information System (INIS)

    Alexander, D.J.; Klueh, R.L.

    1989-01-01

    Full-size , half-size, and third-size specimens from several different steels have been tested as part of an ongoing alloy development program. The smaller specimens permit more specimens to be made from small trail heats and are much more efficient for irradiation experiments. The results of several comparisons between the different specimen sizes have shown that the smaller specimens show qualitatively similar behavior to large specimens, although the upper-shelf energy level and ductile-to-ductile transition temperature are reduced. The upper-shelf energy levels from different specimen sizes can be compared by using a simple volume normalization method. The effect of specimen size and geometry on the ductile-to-ductile transition temperature is more difficult to predict, although the available data suggest a simple shift in the transition temperature due to specimen size changes.The relatively shallower notch used in smaller specimens alters the deformation pattern, and permits yielding to spread back to the notched surface as well as through to the back. This reduces the constraint and the peak stresses, and thus the initiation of cleavage is more difficult. A better understanding of the stress and strain distributions is needed. 19 refs., 3 figs., 3 tabs

  10. Evaluation of three automated nucleic acid extraction systems for identification of respiratory viruses in clinical specimens by multiplex real-time PCR.

    Science.gov (United States)

    Kim, Yoonjung; Han, Mi-Soon; Kim, Juwon; Kwon, Aerin; Lee, Kyung-A

    2014-01-01

    A total of 84 nasopharyngeal swab specimens were collected from 84 patients. Viral nucleic acid was extracted by three automated extraction systems: QIAcube (Qiagen, Germany), EZ1 Advanced XL (Qiagen), and MICROLAB Nimbus IVD (Hamilton, USA). Fourteen RNA viruses and two DNA viruses were detected using the Anyplex II RV16 Detection kit (Seegene, Republic of Korea). The EZ1 Advanced XL system demonstrated the best analytical sensitivity for all the three viral strains. The nucleic acids extracted by EZ1 Advanced XL showed higher positive rates for virus detection than the others. Meanwhile, the MICROLAB Nimbus IVD system was comprised of fully automated steps from nucleic extraction to PCR setup function that could reduce human errors. For the nucleic acids recovered from nasopharyngeal swab specimens, the QIAcube system showed the fewest false negative results and the best concordance rate, and it may be more suitable for detecting various viruses including RNA and DNA virus strains. Each system showed different sensitivity and specificity for detection of certain viral pathogens and demonstrated different characteristics such as turnaround time and sample capacity. Therefore, these factors should be considered when new nucleic acid extraction systems are introduced to the laboratory.

  11. Impact of specimen adequacy on the assessment of renal allograft biopsy specimens.

    Science.gov (United States)

    Cimen, S; Geldenhuys, L; Guler, S; Imamoglu, A; Molinari, M

    2016-01-01

    The Banff classification was introduced to achieve uniformity in the assessment of renal allograft biopsies. The primary aim of this study was to evaluate the impact of specimen adequacy on the Banff classification. All renal allograft biopsies obtained between July 2010 and June 2012 for suspicion of acute rejection were included. Pre-biopsy clinical data on suspected diagnosis and time from renal transplantation were provided to a nephropathologist who was blinded to the original pathological report. Second pathological readings were compared with the original to assess agreement stratified by specimen adequacy. Cohen's kappa test and Fisher's exact test were used for statistical analyses. Forty-nine specimens were reviewed. Among these specimens, 81.6% were classified as adequate, 6.12% as minimal, and 12.24% as unsatisfactory. The agreement analysis among the first and second readings revealed a kappa value of 0.97. Full agreement between readings was found in 75% of the adequate specimens, 66.7 and 50% for minimal and unsatisfactory specimens, respectively. There was no agreement between readings in 5% of the adequate specimens and 16.7% of the unsatisfactory specimens. For the entire sample full agreement was found in 71.4%, partial agreement in 20.4% and no agreement in 8.2% of the specimens. Statistical analysis using Fisher's exact test yielded a P value above 0.25 showing that - probably due to small sample size - the results were not statistically significant. Specimen adequacy may be a determinant of a diagnostic agreement in renal allograft specimen assessment. While additional studies including larger case numbers are required to further delineate the impact of specimen adequacy on the reliability of histopathological assessments, specimen quality must be considered during clinical decision making while dealing with biopsy reports based on minimal or unsatisfactory specimens.

  12. Controlled Environment Specimen Transfer

    DEFF Research Database (Denmark)

    Damsgaard, Christian Danvad; Zandbergen, Henny W.; Hansen, Thomas Willum

    2014-01-01

    an environmental transmission electron microscope to an in situ X-ray diffractometer through a dedicated transmission electron microscope specimen transfer holder, capable of sealing the specimen in a gaseous environment at elevated temperatures. Two catalyst material systems have been investigated; Cu/ZnO/Al2O3...... transferred in a reactive environment to the environmental transmission electron microscope where further analysis on the local scale were conducted. The Co/Al2O3 catalyst was reduced in the environmental microscope and successfully kept reduced outside the microscope in a reactive environment. The in situ......Specimen transfer under controlled environment conditions, such as temperature, pressure, and gas composition, is necessary to conduct successive complementary in situ characterization of materials sensitive to ambient conditions. The in situ transfer concept is introduced by linking...

  13. Preserve specimens for reproducibility

    Czech Academy of Sciences Publication Activity Database

    Krell, F.-T.; Klimeš, Petr; Rocha, L. A.; Fikáček, M.; Miller, S. E.

    2016-01-01

    Roč. 539, č. 7628 (2016), s. 168 ISSN 0028-0836 Institutional support: RVO:60077344 Keywords : reproducibility * specimen * biodiversity Subject RIV: EH - Ecology, Behaviour Impact factor: 40.137, year: 2016 http://www.nature.com/nature/journal/v539/n7628/full/539168b.html

  14. Monitoring of crack growth and crack mouth opening displacement in compact tension specimens at high temperatures : Development and implementation of the Direct Current Potential Drop (DCPD) method

    OpenAIRE

    Malmqvist, Philip

    2016-01-01

    The mechanical engineering department at the University of Idaho is conducting a project with the purpose of developing a complete system for investigating creep-, creep-fatigue- and fatigue properties of metallic materials at elevated temperatures up to 650 ˚C with Compact Tension (CT) specimens. Considerable efforts have been made to study and understand these phenomena, although numerous problems still exist. It is important to explore more extensively the complicated phenomena of creep, f...

  15. Biaxial Creep Specimen Fabrication

    International Nuclear Information System (INIS)

    JL Bump; RF Luther

    2006-01-01

    This report documents the results of the weld development and abbreviated weld qualification efforts performed by Pacific Northwest National Laboratory (PNNL) for refractory metal and superalloy biaxial creep specimens. Biaxial creep specimens were to be assembled, electron beam welded, laser-seal welded, and pressurized at PNNL for both in-pile (JOYO reactor, O-arai, Japan) and out-of-pile creep testing. The objective of this test campaign was to evaluate the creep behavior of primary cladding and structural alloys under consideration for the Prometheus space reactor. PNNL successfully developed electron beam weld parameters for six of these materials prior to the termination of the Naval Reactors program effort to deliver a space reactor for Project Prometheus. These materials were FS-85, ASTAR-811C, T-111, Alloy 617, Haynes 230, and Nirnonic PE16. Early termination of the NR space program precluded the development of laser welding parameters for post-pressurization seal weldments

  16. Biaxial Creep Specimen Fabrication

    Energy Technology Data Exchange (ETDEWEB)

    JL Bump; RF Luther

    2006-02-09

    This report documents the results of the weld development and abbreviated weld qualification efforts performed by Pacific Northwest National Laboratory (PNNL) for refractory metal and superalloy biaxial creep specimens. Biaxial creep specimens were to be assembled, electron beam welded, laser-seal welded, and pressurized at PNNL for both in-pile (JOYO reactor, O-arai, Japan) and out-of-pile creep testing. The objective of this test campaign was to evaluate the creep behavior of primary cladding and structural alloys under consideration for the Prometheus space reactor. PNNL successfully developed electron beam weld parameters for six of these materials prior to the termination of the Naval Reactors program effort to deliver a space reactor for Project Prometheus. These materials were FS-85, ASTAR-811C, T-111, Alloy 617, Haynes 230, and Nirnonic PE16. Early termination of the NR space program precluded the development of laser welding parameters for post-pressurization seal weldments.

  17. [Teaching methods for clinical settings: a literature review].

    Science.gov (United States)

    Brugnolli, Anna; Benaglio, Carla

    2017-01-01

    . Teaching Methods for clinical settings: a review. The teaching process during internship requires several methods to promote the acquisition of more complex technical skills such as relational, decisional and planning abilities. To describe effective teaching methods to promote the learning of relational, decisional and planning skills. A literature review of the teaching methods that have proven most effective, most appreciated by students, and most frequently used in Italian nursing schools. Clinical teaching is a central element to transform clinical experiences during internship in professional competences. The students are gradually brought to become more independent, because they are offered opportunities to practice in real contexts, to receive feedback, to have positive role models, to become more autonomous: all elements that facilitate and potentiate learning. Clinical teaching should be based on a variety of methods. The students value a gradual progression both in clinical experiences and teaching strategies from more supervised methods to methods more oriented towards reflecting on clinical practice and self-directed learning.

  18. Clinical simulation as an evaluation method in health informatics

    DEFF Research Database (Denmark)

    Jensen, Sanne

    2016-01-01

    Safe work processes and information systems are vital in health care. Methods for design of health IT focusing on patient safety are one of many initiatives trying to prevent adverse events. Possible patient safety hazards need to be investigated before health IT is integrated with local clinical...... work practice including other technology and organizational structure. Clinical simulation is ideal for proactive evaluation of new technology for clinical work practice. Clinical simulations involve real end-users as they simulate the use of technology in realistic environments performing realistic...... tasks. Clinical simulation study assesses effects on clinical workflow and enables identification and evaluation of patient safety hazards before implementation at a hospital. Clinical simulation also offers an opportunity to create a space in which healthcare professionals working in different...

  19. Legal clinic gender sensitive method for law students

    Directory of Open Access Journals (Sweden)

    Petrušić Nevena

    2008-01-01

    Full Text Available In this paper, the authors discuss models of integrating gender issues, gender perspective and some gender aspects into the university education. In that context, the authors particularly focus on the concept of clinical legal education in legal clinics offering a specific practical model of teaching gender studies. Legal clinics provide for an innovative approach to gender education of prospective legal professional. The teaching method used in these legal clinics is aimed at raising students' awareness of gender issues and common gender-related biases. In the recent period, the Legal Clinic at the Law Faculty in Niš has achieved excellent results in the Clinical legal education program on the women's rights protection, which clearly proves that legal clinics have good prospects in general legal education.

  20. Evaluation of the clinical implementation of a large-scale online e-learning program on venous blood specimen collection guideline practices.

    Science.gov (United States)

    Willman, Britta; Grankvist, Kjell; Bölenius, Karin

    2018-05-11

    When performed erroneously, the venous blood specimen collection (VBSC) practice steps patient identification, test request management and test tube labeling are at high risk to jeopardize patient safety. VBSC educational programs with the intention to minimize risk of harm to patients are therefore needed. In this study, we evaluate the efficiency of a large-scale online e-learning program on personnel's adherence to VBSC practices and their experience of the e-learning program. An interprofessional team transformed an implemented traditional VBSC education program to an online e-learning program developed to stimulate reflection with focus on the high-risk practice steps. We used questionnaires to evaluate the effect of the e-learning program on personnel's self-reported adherence to VBSC practices compared to questionnaire surveys before and after introduction of the traditional education program. We used content analysis to evaluate the participants free text experience of the VBSC e-learning program. Adherence to the VBSC guideline high-risk practice steps generally increased following the implementation of a traditional educational program followed by an e-learning program. We however found a negative trend over years regarding participation rates and the practice to always send/sign the request form following the introduction of an electronic request system. The participants were in general content with the VBSC e-learning program. Properly designed e-learning programs on VBSC practices supersedes traditional educational programs in usefulness and functionality. Inclusion of questionnaires in the e-learning program is necessary for follow-up of VBSC participant's practices and educational program efficiency.

  1. Enrichment methods to detect bone marrow micrometastases in breast carcinoma patients: clinical relevance

    International Nuclear Information System (INIS)

    Choesmel, Valérie; Pierga, Jean-Yves; Nos, Claude; Vincent-Salomon, Anne; Sigal-Zafrani, Brigitte; Thiery, Jean-Paul; Blin, Nathalie

    2004-01-01

    Improving technologies for the detection and purification of bone marrow (BM) micrometastatic cells in breast cancer patients should lead to earlier prognosis of the risk of relapse and should make it possible to design more appropriate therapies. The technique used has to overcome the challenges resulting from the small number of target cells (one per million hematopoietic cells) and the heterogeneous expression of micrometastatic cell markers. In the present study, we have assessed the clinical relevance of current methods aimed at detecting rare disseminated carcinoma cells. BM aspirates from 32 carcinoma patients were screened for the presence of micrometastatic cells positive for epithelial cell adhesion molecule and positive for cytokeratins, using optimized immunodetection methods. A comparison with data obtained for 46 control BM aspirates and a correlation with the clinical status of patients were performed. We developed a sensitive and efficient immunomagnetic protocol for the enrichment of BM micrometastases. This method was used to divide 32 breast carcinoma patients into three categories according to their epithelial cell adhesion molecule status. These categories were highly correlated with the recently revised American Joint Committee on Cancer staging system for breast cancer, demonstrating the clinical relevance of this simple and reliable immunomagnetic technique. We also evaluated immunocytochemical detection of cytokeratin-positive cells and cytomorphological parameters. Immunocytochemistry-based methods for the detection of BM micrometastases did not provide any information about the clinical status of patients, but helped to refine the immunomagnetic data by confirming the presence of micrometastases in some cases. We also tested a new density gradient centrifugation system, able to enrich the tumor fraction of BM specimens by twofold to threefold as compared with standard Ficoll methods. These improved methods for the detection of

  2. Development and implementation of real-time nucleic acid amplification for the detection of enterovirus infections in comparison to rapid culture of various clinical specimens

    NARCIS (Netherlands)

    van Doornum, G J J; Schutten, Martin; Voermans, J; Guldemeester, G J J; Niesters, H G M

    2007-01-01

    Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the

  3. Molecular Identification and Susceptibility of Trichosporon Species Isolated from Clinical Specimens in Qatar : Isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp nov.

    NARCIS (Netherlands)

    Taj-Aldeen, Saad J.; Al-Ansari, Nasser; El Shafei, Sittana; Meis, Jacques F.; Curfs-Breuker, Ilse; Theelen, Bart; Boekhout, Teun

    Trichosporon species have been reported as emerging pathogens and usually occur in severely immunocompromised patients. In the present work, 27 clinical isolates of Trichosporon species were recovered from 27 patients. The patients were not immunocompromised, except for one with acute myeloid

  4. Molecular identification and susceptibility of Trichosporon species isolated from clinical specimens in Qatar: isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp. nov

    NARCIS (Netherlands)

    Taj-Aldeen, S.J.; Al-Ansari, N.; El Shafei, S.; Meis, J.F.; Curfs-Breuker, I.; Theelen, B.J.F.; Boekhout, T.

    2009-01-01

    Trichosporon species have been reported as emerging pathogens and usually occur in severely immunocompromised patients. In the present work, 27 clinical isolates of Trichosporon species were recovered from 27 patients. The patients were not immunocompromised, except for one with acute myeloid

  5. Vaginal tampons as specimen collection device for the molecular diagnosis of non-ulcerative sexually transmitted infections in antenatal clinic attendees.

    NARCIS (Netherlands)

    Sturm, P.D.J.; Connolly, C.E.; Khan, N.; Ebrahim, S.; Sturm, A.W.

    2004-01-01

    Self-inserted vaginal tampons for the molecular diagnosis of non-ulcerative STIs were evaluated. Cervical and vaginal swabs, tampons and urines were collected from 185 first-time antenatal clinic attendees. Cultures and nucleic acid amplification assays (NAA) were performed. The sensitivity of PCR

  6. Nurse educators’ perceptions of OSCE as a clinical evaluation method

    Directory of Open Access Journals (Sweden)

    MM Chabeli

    2001-09-01

    Full Text Available The South African Qualifications Authority, and the South African Nursing Council are in pursuit of quality nursing education to enable the learners to practise as independent and autonomous practitioners. The educational programme should focus on the facilitation of critical and reflective thinking skills that will help the learner to make rational decisions and solve problems. A way of achieving this level of functioning is the use of assessment and evaluation methods that measure the learners’ clinical competence holistically. This article is focused on the perceptions of twenty nurse educators, purposively selected from three Nursing Colleges affiliated to a university in Gauteng, regarding the use of OSCE (Objective Structured Clinical Examination as a clinical evaluation method within a qualitative and descriptive research strategy. Three focus group interviews were conducted in different sessions. A descriptive content analysis was used. Trustworthiness was ensured by using Lincoln and Guba’s model (1985. The results revealed both positive and negative aspects of OSCE as a clinical evaluation method with regard to: administrative aspects; evaluators; learners; procedures/instruments and evaluation. The conclusion drawn from the related findings is that OSCE does not measure the learners’ clinical competence holistically. It is therefore recommended that the identified negative perception be taken as challenges faced by nurse educators and that the positive aspects be strengthened. One way of meeting these recommendations is the use of varied alternative methods for clinical assessment and evaluation that focus on the holistic measurement of the learners’ clinical competence.

  7. Frontiers of biostatistical methods and applications in clinical oncology

    CERN Document Server

    Crowley, John

    2017-01-01

    This book presents the state of the art of biostatistical methods and their applications in clinical oncology. Many methodologies established today in biostatistics have been brought about through its applications to the design and analysis of oncology clinical studies. This field of oncology, now in the midst of evolution owing to rapid advances in biotechnologies and cancer genomics, is becoming one of the most promising disease fields in the shift toward personalized medicine. Modern developments of diagnosis and therapeutics of cancer have also been continuously fueled by recent progress in establishing the infrastructure for conducting more complex, large-scale clinical trials and observational studies. The field of cancer clinical studies therefore will continue to provide many new statistical challenges that warrant further progress in the methodology and practice of biostatistics. This book provides a systematic coverage of various stages of cancer clinical studies. Topics from modern cancer clinical ...

  8. NASA Biological Specimen Repository

    Science.gov (United States)

    McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

    2010-01-01

    The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

  9. Rotating specimen rack repair

    International Nuclear Information System (INIS)

    Miller, G.E.; Rogers, P.J.; Nabor, W.G.; Bair, H.

    1984-01-01

    In 1980, an operator at the UCI TRIGA Reactor noticed difficulties with the rotation of the specimen rack. Investigations showed that the drive bearing in the rack had failed and allowed the bearings to enter the rack. After some time of operation in static mode it was decided that installation of a bearing substitute - a graphite sleeve - would be undertaken. Procedures were written and approved for removal of the rack, fabrication and installation of the sleeve, and re-installation of the rack. This paper describes these procedures in some detail. Detailed drawings of the necessary parts may be obtained from the authors

  10. Feasibility of Incorporating Alternative Teaching Methods into Clinical Clerkships.

    Science.gov (United States)

    Berman, Judith; And Others

    1990-01-01

    A study investigated the effectiveness of computer-assisted instruction, interactive video, and videotapes as alternative methods of instruction in clinical clerkship modules on diabetes and hypertension. The 17 participants were more interested in balancing time between patient contact and alternative teaching methods and had better knowledge,…

  11. SHOULD EVERY APPENDECECTOMY SPECIMEN BE SUBJECTED TO HISTOPATHOLOGICAL EXAMINATION? A RETROSPECTIVE STUDY OF HISTOLOGICAL FINDINGS IN APPENDICECTOMY SPECIMENS

    Directory of Open Access Journals (Sweden)

    Shahanuma Shaik

    2017-12-01

    Full Text Available BACKGROUND Appendicitis is one of the commonest surgical emergencies with a lifetime risk of 7-8%. The appendicectomy specimens operated upon clinically-suspected appendicitis often appear normal on gross examination, but histopathological evaluation may reveal a diverse underlying pathology. Therefore, for accurate diagnosis, histopathological examination of all appendicectomy specimens is mandatory. MATERIALS AND METHODS A retrospective study of 175 appendicectomy cases operated over a period of two years. The clinical data and histopathological reports were reviewed and various histopathological findings are categorised. RESULTS Out of the total 175 appendicectomies, 155 emergency appendicectomy cases were included in the study, while 20 cases of incidental appendicectomy were excluded. The peak incidence was found in the 2nd and 3rd decades with male predominance. Among the 155 specimens, 96.8% had histological features of appendicitis and 1.9% were normal appendix. The unusual histopathological findings were Carcinoid tumour and Enterobius vermicularis. CONCLUSION The definitive diagnoses of appendicitis as well as the unusual incidental findings that were missed intraoperatively are established by histopathological examination. The study supports the histological examination of all resected appendicectomy specimens.

  12. A sensitive duplex nanoparticle-assisted PCR assay for identifying porcine epidemic diarrhea virus and porcine transmissible gastroenteritis virus from clinical specimens.

    Science.gov (United States)

    Zhu, Yu; Liang, Lin; Luo, Yakun; Wang, Guihua; Wang, Chunren; Cui, Yudong; Ai, Xia; Cui, Shangjin

    2017-02-01

    In this study, a novel duplex nanoparticle-assisted polymerase chain reaction (nanoPCR) assay was developed to detect porcine epidemic diarrhea virus (PEDV) and porcine transmissible gastroenteritis virus (TGEV). Two pairs of primers were designed based on the conserved region within the N gene of PEDV and TGEV. In a screening of 114 clinical samples from four provinces in China for PEDV and TGEV, 48.2 and 3.5 % of the samples, respectively, tested positive. Under optimized conditions, the duplex nanoPCR assay had a detection limit of 7.6 × 10 1 and 8.5 × 10 1 copies μL -1 for PEDV and TGEV, respectively. The sensitivity of the duplex nanoPCR assay was ten times higher than that of a conventional PCR assay. Moreover, no fragments were amplified when the duplex nanoPCR assay was used to test samples containing other porcine viruses. Our results indicate that the duplex nanoPCR assay described here is useful for the rapid detection of PEDV and TGEV and can be applied in clinical diagnosis.

  13. A non-destructive DNA sampling technique for herbarium specimens.

    Science.gov (United States)

    Shepherd, Lara D

    2017-01-01

    Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of herbarium specimens up to 73 years old.

  14. Machine learning methods for clinical forms analysis in mental health.

    Science.gov (United States)

    Strauss, John; Peguero, Arturo Martinez; Hirst, Graeme

    2013-01-01

    In preparation for a clinical information system implementation, the Centre for Addiction and Mental Health (CAMH) Clinical Information Transformation project completed multiple preparation steps. An automated process was desired to supplement the onerous task of manual analysis of clinical forms. We used natural language processing (NLP) and machine learning (ML) methods for a series of 266 separate clinical forms. For the investigation, documents were represented by feature vectors. We used four ML algorithms for our examination of the forms: cluster analysis, k-nearest neigh-bours (kNN), decision trees and support vector machines (SVM). Parameters for each algorithm were optimized. SVM had the best performance with a precision of 64.6%. Though we did not find any method sufficiently accurate for practical use, to our knowledge this approach to forms has not been used previously in mental health.

  15. Self-consistent method for quantifying indium content from X-ray spectra of thick compound semiconductor specimens in a transmission electron microscope.

    Science.gov (United States)

    Walther, T; Wang, X

    2016-05-01

    Based on Monte Carlo simulations of X-ray generation by fast electrons we calculate curves of effective sensitivity factors for analytical transmission electron microscopy based energy-dispersive X-ray spectroscopy including absorption and fluorescence effects, as a function of Ga K/L ratio for different indium and gallium containing compound semiconductors. For the case of InGaN alloy thin films we show that experimental spectra can thus be quantified without the need to measure specimen thickness or density, yielding self-consistent values for quantification with Ga K and Ga L lines. The effect of uncertainties in the detector efficiency are also shown to be reduced. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  16. Analytical and clinical performance characteristics of the Abbott RealTime MTB RIF/INH Resistance, an assay for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis in pulmonary specimens.

    Science.gov (United States)

    Kostera, Joshua; Leckie, Gregor; Tang, Ning; Lampinen, John; Szostak, Magdalena; Abravaya, Klara; Wang, Hong

    2016-12-01

    Clinical management of drug-resistant tuberculosis patients continues to present significant challenges to global health. To tackle these challenges, the Abbott RealTime MTB RIF/INH Resistance assay was developed to accelerate the diagnosis of rifampicin and/or isoniazid resistant tuberculosis to within a day. This article summarizes the performance of the Abbott RealTime MTB RIF/INH Resistance assay; including reliability, analytical sensitivity, and clinical sensitivity/specificity as compared to Cepheid GeneXpert MTB/RIF version 1.0 and Hain MTBDRplus version 2.0. The limit of detection (LOD) of the Abbott RealTime MTB RIF/INH Resistance assay was determined to be 32 colony forming units/milliliter (cfu/mL) using the Mycobacterium tuberculosis (MTB) strain H37Rv cell line. For rifampicin resistance detection, the Abbott RealTime MTB RIF/INH Resistance assay demonstrated statistically equivalent clinical sensitivity and specificity as compared to Cepheid GeneXpert MTB/RIF. For isoniazid resistance detection, the assay demonstrated statistically equivalent clinical sensitivity and specificity as compared to Hain MTBDRplus. The performance data presented herein demonstrate that the Abbott RealTime MTB RIF/INH Resistance assay is a sensitive, robust, and reliable test for realtime simultaneous detection of first line anti-tuberculosis antibiotics rifampicin and isoniazid in patient specimens. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

  17. Analytic performance studies and clinical reproducibility of a real-time PCR assay for the detection of epidermal growth factor receptor gene mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer

    International Nuclear Information System (INIS)

    O’Donnell, Patrick; Shieh, Felice; Wei, Wen; Lawrence, H Jeffrey; Wu, Lin; Schilling, Robert; Bloom, Kenneth; Maltzman, Warren; Anderson, Steven; Soviero, Stephen; Ferguson, Jane; Shyu, Johnny; Current, Robert; Rehage, Taraneh; Tsai, Julie; Christensen, Mari; Tran, Ha Bich; Chien, Sean Shih-Chang

    2013-01-01

    Epidermal growth factor receptor (EGFR) gene mutations identify patients with non-small cell lung cancer (NSCLC) who have a high likelihood of benefiting from treatment with anti-EGFR tyrosine kinase inhibitors. Sanger sequencing is widely used for mutation detection but can be technically challenging, resulting in longer turn-around-time, with limited sensitivity for low levels of mutations. This manuscript details the technical performance verification studies and external clinical reproducibility studies of the cobas EGFR Mutation Test, a rapid multiplex real-time PCR assay designed to detect 41 mutations in exons 18, 19, 20 and 21. The assay’s limit of detection was determined using 25 formalin-fixed paraffin-embedded tissue (FFPET)-derived and plasmid DNA blends. Assay performance for a panel of 201 specimens was compared against Sanger sequencing with resolution of discordant specimens by quantitative massively parallel pyrosequencing (MPP). Internal and external reproducibility was assessed using specimens tested in duplicate by different operators, using different reagent lots, instruments and at different sites. The effects on the performance of the cobas EGFR test of endogenous substances and nine therapeutic drugs were evaluated in ten FFPET specimens. Other tests included an evaluation of the effects of necrosis, micro-organisms and homologous DNA sequences on assay performance, and the inclusivity of the assay for less frequent mutations. A >95% hit rate was obtained in blends with >5% mutant alleles, as determined by MPP analysis, at a total DNA input of 150 ng. The overall percent agreement between Sanger sequencing and the cobas test was 96.7% (negative percent agreement 97.5%; positive percent agreement 95.8%). Assay repeatability was 98% when tested with two operators, instruments, and reagent lots. In the external reproducibility study, the agreement was > 99% across all sites, all operators and all reagent lots for 11/12 tumors tested. Test

  18. Improved modeling of clinical data with kernel methods.

    Science.gov (United States)

    Daemen, Anneleen; Timmerman, Dirk; Van den Bosch, Thierry; Bottomley, Cecilia; Kirk, Emma; Van Holsbeke, Caroline; Valentin, Lil; Bourne, Tom; De Moor, Bart

    2012-02-01

    Despite the rise of high-throughput technologies, clinical data such as age, gender and medical history guide clinical management for most diseases and examinations. To improve clinical management, available patient information should be fully exploited. This requires appropriate modeling of relevant parameters. When kernel methods are used, traditional kernel functions such as the linear kernel are often applied to the set of clinical parameters. These kernel functions, however, have their disadvantages due to the specific characteristics of clinical data, being a mix of variable types with each variable its own range. We propose a new kernel function specifically adapted to the characteristics of clinical data. The clinical kernel function provides a better representation of patients' similarity by equalizing the influence of all variables and taking into account the range r of the variables. Moreover, it is robust with respect to changes in r. Incorporated in a least squares support vector machine, the new kernel function results in significantly improved diagnosis, prognosis and prediction of therapy response. This is illustrated on four clinical data sets within gynecology, with an average increase in test area under the ROC curve (AUC) of 0.023, 0.021, 0.122 and 0.019, respectively. Moreover, when combining clinical parameters and expression data in three case studies on breast cancer, results improved overall with use of the new kernel function and when considering both data types in a weighted fashion, with a larger weight assigned to the clinical parameters. The increase in AUC with respect to a standard kernel function and/or unweighted data combination was maximum 0.127, 0.042 and 0.118 for the three case studies. For clinical data consisting of variables of different types, the proposed kernel function--which takes into account the type and range of each variable--has shown to be a better alternative for linear and non-linear classification problems

  19. EGFR Mutations in Surgically Resected Fresh Specimens from 697 Consecutive Chinese Patients with Non-Small Cell Lung Cancer and Their Relationships with Clinical Features

    Directory of Open Access Journals (Sweden)

    Yuanyang Lai

    2013-12-01

    Full Text Available We aimed to reveal the true status of epidermal growth factor receptor (EGFR mutations in Chinese patients with non-small cell lung cancer (NSCLC after lung resections. EGFR mutations of surgically resected fresh tumor samples from 697 Chinese NSCLC patients were analyzed by Amplification Refractory Mutation System (ARMS. Correlations between EGFR mutation hotspots and clinical features were also explored. Of the 697 NSCLC patients, 235 (33.7% patients had tyrosine kinase inhibitor (TKIs sensitive EGFR mutations in 41 (14.5% of the 282 squamous carcinomas, 155 (52.9% of the 293 adenocarcinomas, 34 (39.5% of the 86 adenosquamous carcinomas, one (9.1% of the 11 large-cell carcinomas, 2 (11.1% of the 18 sarcomatoid carcinomas, and 2 (28.6% of the 7 mucoepidermoid carcinomas. TKIs sensitive EGFR mutations were more frequently found in female patients (p < 0.001, non-smokers (p = 0.047 and adenocarcinomas (p < 0.001. The rates of exon 19 deletion mutation (19-del, exon 21 L858R point mutation (L858R, exon 21 L861Q point mutation (L861Q, exon 18 G719X point mutations (G719X, including G719C, G719S, G719A were 43.4%, 48.1%, 1.7% and 6.8%, respectively. Exon 20 T790M point mutation (T790M was detected in 3 squamous carcinomas and 3 adenocarcinomas and exon 20 insertion mutation (20-ins was detected in 2 patients with adenocarcinoma. Our results show the rates of EGFR mutations are higher in all types of NSCLC in Chinese patients. 19-del and L858R are two of the more frequent mutations. EGFR mutation detection should be performed as a routine postoperative examination in Chinese NSCLC patients.

  20. Connecting clinical and actuarial prediction with rule-based methods.

    Science.gov (United States)

    Fokkema, Marjolein; Smits, Niels; Kelderman, Henk; Penninx, Brenda W J H

    2015-06-01

    Meta-analyses comparing the accuracy of clinical versus actuarial prediction have shown actuarial methods to outperform clinical methods, on average. However, actuarial methods are still not widely used in clinical practice, and there has been a call for the development of actuarial prediction methods for clinical practice. We argue that rule-based methods may be more useful than the linear main effect models usually employed in prediction studies, from a data and decision analytic as well as a practical perspective. In addition, decision rules derived with rule-based methods can be represented as fast and frugal trees, which, unlike main effects models, can be used in a sequential fashion, reducing the number of cues that have to be evaluated before making a prediction. We illustrate the usability of rule-based methods by applying RuleFit, an algorithm for deriving decision rules for classification and regression problems, to a dataset on prediction of the course of depressive and anxiety disorders from Penninx et al. (2011). The RuleFit algorithm provided a model consisting of 2 simple decision rules, requiring evaluation of only 2 to 4 cues. Predictive accuracy of the 2-rule model was very similar to that of a logistic regression model incorporating 20 predictor variables, originally applied to the dataset. In addition, the 2-rule model required, on average, evaluation of only 3 cues. Therefore, the RuleFit algorithm appears to be a promising method for creating decision tools that are less time consuming and easier to apply in psychological practice, and with accuracy comparable to traditional actuarial methods. (c) 2015 APA, all rights reserved).

  1. Compass: A hybrid method for clinical and biobank data mining

    DEFF Research Database (Denmark)

    Krysiak-Baltyn, Konrad; Petersen, Thomas Nordahl; Audouze, Karine Marie Laure

    2014-01-01

    We describe a new method for identification of confident associations within large clinical data sets. The method is a hybrid of two existing methods; Self-Organizing Maps and Association Mining. We utilize Self-Organizing Maps as the initial step to reduce the search space, and then apply...... Association Mining in order to find association rules. We demonstrate that this procedure has a number of advantages compared to traditional Association Mining; it allows for handling numerical variables without a priori binning and is able to generate variable groups which act as “hotspots” for statistically...... significant associations. We showcase the method on infertility-related data from Danish military conscripts. The clinical data we analyzed contained both categorical type questionnaire data and continuous variables generated from biological measurements, including missing values. From this data set, we...

  2. Evaluation of a clinically intuitive quality assurance method

    International Nuclear Information System (INIS)

    Norris, H; Thomas, A; Oldham, M

    2013-01-01

    There is a pressing need for clinically intuitive quality assurance methods that report metrics of relevance to the likely impact on tumor control of normal tissue injury. This paper presents a preliminary investigation into the accuracy of a novel ''transform method'' which enables a clinically relevant analysis through dose-volume-histograms (DVHs) and dose overlays on the patient's CT data. The transform method was tested by inducing a series of known mechanical and delivery errors onto simulated 3D dosimetry measurements of six different head-and-neck IMRT treatment plans. Accuracy was then examined through the comparison of the transformed patient dose distributions and the known actual patient dose distributions through dose-volume histograms and normalized dose difference analysis. Through these metrics, the transform method was found to be highly accurate in predicting measured patient dose distributions for these types of errors.

  3. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

    Science.gov (United States)

    Sproul, John S; Maddison, David R

    2017-11-01

    Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens. © 2017 John Wiley & Sons Ltd.

  4. Clinical value of different detection methods in blunt ocular trauma

    Directory of Open Access Journals (Sweden)

    Yang Li

    2018-02-01

    Full Text Available Blunt ocular can cause persistent change of eye structure and function, the method of detection which is closely related to eye injury including B-can ultrasonography, UBM, OCT, FFA, scanning laser polarimetry, fundus autofluorescence, each examination with particular emphasis. This paper aims to review the advantages and disadvantages of different inspection methods in order to provide reference for clinical diagnosis and treatment of blunt ocular trauma.

  5. Collagen Quantification in Tissue Specimens.

    Science.gov (United States)

    Coentro, João Quintas; Capella-Monsonís, Héctor; Graceffa, Valeria; Wu, Zhuning; Mullen, Anne Maria; Raghunath, Michael; Zeugolis, Dimitrios I

    2017-01-01

    Collagen is the major extracellular protein in mammals. Accurate quantification of collagen is essential in the biomaterials (e.g., reproducible collagen scaffold fabrication), drug discovery (e.g., assessment of collagen in pathophysiologies, such as fibrosis), and tissue engineering (e.g., quantification of cell-synthesized collagen) fields. Although measuring hydroxyproline content is the most widely used method to quantify collagen in biological specimens, the process is very laborious. To this end, the Sircol™ Collagen Assay is widely used due to its inherent simplicity and convenience. However, this method leads to overestimation of collagen content due to the interaction of Sirius red with basic amino acids of non-collagenous proteins. Herein, we describe the addition of an ultrafiltration purification step in the process to accurately determine collagen content in tissues.

  6. The early evolution of Jean Piaget's clinical method.

    Science.gov (United States)

    Mayer, Susan Jean

    2005-11-01

    This article analyzes the early evolution of Jean Piaget's renowned "clinical method" in order to investigate the method's strikingly original and generative character. Throughout his 1st decade in the field, Piaget frequently discussed and justified the many different approaches to data collection he used. Analysis of his methodological progression during this period reveals that Piaget's determination to access the genuine convictions of children eventually led him to combine 3 distinct traditions in which he had been trained-naturalistic observation, psychometrics, and the psychiatric clinical examination. It was in this amalgam, first evident in his 4th text, that Piaget discovered the clinical dynamic that would drive the classic experiments for which he is most well known.

  7. Statistical methods for mass spectrometry-based clinical proteomics

    NARCIS (Netherlands)

    Kakourou, A.

    2018-01-01

    The work presented in this thesis focuses on methods for the construction of diagnostic rules based on clinical mass spectrometry proteomic data. Mass spectrometry has become one of the key technologies for jointly measuring the expression of thousands of proteins in biological samples.

  8. Counseling Psychology Doctoral Trainees' Satisfaction with Clinical Methods Training

    Science.gov (United States)

    Menke, Kristen Ann

    2015-01-01

    Counseling psychology doctoral trainees' satisfaction with their clinical methods training is an important predictor of their self-efficacy as counselors, persistence in graduate programs, and probability of practicing psychotherapy in their careers (Fernando & Hulse-Killacky, 2005; Hadjipavlou & Ogrodniczuk, 2007; Morton & Worthley,…

  9. Assessing Clinical Significance: Does it Matter which Method we Use?

    Science.gov (United States)

    Atkins, David C.; Bedics, Jamie D.; Mcglinchey, Joseph B.; Beauchaine, Theodore P.

    2005-01-01

    Measures of clinical significance are frequently used to evaluate client change during therapy. Several alternatives to the original method devised by N. S. Jacobson, W. C. Follette, & D. Revenstorf (1984) have been proposed, each purporting to increase accuracy. However, researchers have had little systematic guidance in choosing among…

  10. Multicenter evaluation of resistance patterns of Klebsiella pneumoniae, Escherichia coli, Salmonella spp and Shigella spp isolated from clinical specimens in Brazil: RESISTNET surveillance program

    Directory of Open Access Journals (Sweden)

    Carmen Paz Oplustil

    Full Text Available Surveillance programs are essential to detect the increase of antimicrobial resistance, and several different programs are being conducted in many countries. The RESISTNET is a surveillance program for bacterial resistance against several antimicrobial agents initiated in 1998 among Latin American countries. In Brazil, several centers were invited to join this surveillance and a total of 11 centers (6 from São Paulo and 5 from other states participated in the study. All results were analyzed using the WHONET program. A total of 894 Escherichia coli, 386 Klebsiella pneumoniae, 70 Shigella spp and 57 Salmonella spp strains were analyzed in this study from April, 1998, to April, 1999. Susceptibility testing was performed by the disk diffusion method using NCCLS 1998 guidelines for several different drugs. For all strains, imipenem was the most effective drug (100% of the strains were susceptible. Klebsiella pneumoniae presented a high resistance rate to ampicillin (96.4%. The rate of probable ESBL producers among K. pneumoniae strains was 36.3%, most of them being isolated from catheters (58.8%. Among all Escherichia coli strains analyzed, the highest resistance rate was found for trimethoprim/sulfamethoxazole (46.9% and the majority of the resistant strains were isolated from urine samples (47.8%. Among Salmonella spp, the resistance rates were low for all antibiotics tested. For Shigella spp strains there was a high resistance to trimethoprim/sulfamethoxazole (80.0%. No resistance to ceftriaxone was observed in these strains. Surveillance of antimicrobial resistance is critical for the successful management of infectious diseases. The results of this survey show significant resistance rates among these bacteria which are responsible for several types of human infections.

  11. Adaptive design methods in clinical trials – a review

    Directory of Open Access Journals (Sweden)

    Chang Mark

    2008-05-01

    Full Text Available Abstract In recent years, the use of adaptive design methods in clinical research and development based on accrued data has become very popular due to its flexibility and efficiency. Based on adaptations applied, adaptive designs can be classified into three categories: prospective, concurrent (ad hoc, and retrospective adaptive designs. An adaptive design allows modifications made to trial and/or statistical procedures of ongoing clinical trials. However, it is a concern that the actual patient population after the adaptations could deviate from the originally target patient population and consequently the overall type I error (to erroneously claim efficacy for an infective drug rate may not be controlled. In addition, major adaptations of trial and/or statistical procedures of on-going trials may result in a totally different trial that is unable to address the scientific/medical questions the trial intends to answer. In this article, several commonly considered adaptive designs in clinical trials are reviewed. Impacts of ad hoc adaptations (protocol amendments, challenges in by design (prospective adaptations, and obstacles of retrospective adaptations are described. Strategies for the use of adaptive design in clinical development of rare diseases are discussed. Some examples concerning the development of Velcade intended for multiple myeloma and non-Hodgkin's lymphoma are given. Practical issues that are commonly encountered when implementing adaptive design methods in clinical trials are also discussed.

  12. LC-MS (/MS) in clinical toxicology screening methods.

    Science.gov (United States)

    Viette, Véronique; Hochstrasser, Denis; Fathi, Marc

    2012-01-01

    Toxicological screening is the analysis of biological samples to detect and identify unknown compounds. The high selectivity and sensitivity of liquid chromatography (LC) coupled to mass spectrometry (MS) or tandem mass spectrometry (MS/MS) technology provide an attractive alternative to the current methods (LC-UV, GC/MS, etc.). For these reasons, an increasing number of applications are being published. This paper is a brief overview of LC-MS(/MS) screening methods developed for clinical toxicology in recent years. Various sample treatments, chromatographic separations and detection by mass spectrometry can be combined to obtain screening methods adapted to the constraints and needs of clinical toxicology laboratories. Currently the techniques are in the hands of specialists, mainly in academic institutions. However, the evolution in technology should allow application of these techniques as a tool in toxicology laboratories, thus allowing a more widespread exploitation of their potential.

  13. Current role of liquid chromatography coupled to mass spectrometry in clinical toxicology screening methods.

    Science.gov (United States)

    Viette, Véronique; Fathi, Marc; Rudaz, Serge; Hochstrasser, Denis; Veuthey, Jean-Luc

    2011-07-01

    Abstract Toxicological screening is the analysis of a biological specimen to detect and identify compounds in patients admitted to the hospital with acute intoxication of unknown origin. The screening of a wide range of toxicologically relevant compounds in biological samples is a serious challenge for clinical laboratories. The high selectivity and sensitivity of liquid chromatography coupled to mass spectrometry or tandem mass spectrometry technology provides an attractive alternative to the current methods. For these reasons, an increasing number of applications for multi-target screening or general screening of unknown compounds in biological matrices are being published. This paper is an overview of sample clean-up, chromatographic separation and mass spectrometry detection procedures which can be combined to obtain screening methods adapted to the constraints and needs of various laboratories, and none specifically in clinical toxicology. Currently the techniques are in the hands of specialists, principally in academic institutes. However, the evolution in technology should allow application of the techniques as a tool in toxicology laboratories and thus more widespread exploitation of their potential.

  14. Platelet function testing: methods of assessment and clinical utility.

    LENUS (Irish Health Repository)

    Mylotte, Darren

    2012-02-01

    Platelets play a central role in the regulation of both thrombosis and haemostasis yet tests of platelet function have, until recently, been exclusively used in the diagnosis and management of bleeding disorders. Recent advances have demonstrated the clinical utility of platelet function testing in patients with cardiovascular disease. The ex vivo measurement of response to antiplatelet therapies (aspirin and clopidogrel), by an ever-increasing array of platelet function tests, is with some assays, predictive of adverse clinical events and thus, represents an emerging area of interest for both the clinician and basic scientist. This review article will describe the advantages and disadvantages of the currently available methods of measuring platelet function and discuss both the limitations and emerging data supporting the role of platelet function studies in clinical practice.

  15. Platelet function testing: methods of assessment and clinical utility.

    LENUS (Irish Health Repository)

    Mylotte, Darren

    2011-01-01

    Platelets play a central role in the regulation of both thrombosis and haemostasis yet tests of platelet function have, until recently, been exclusively used in the diagnosis and management of bleeding disorders. Recent advances have demonstrated the clinical utility of platelet function testing in patients with cardiovascular disease. The ex vivo measurement of response to antiplatelet therapies (aspirin and clopidogrel), by an ever-increasing array of platelet function tests, is with some assays, predictive of adverse clinical events and thus, represents an emerging area of interest for both the clinician and basic scientist. This review article will describe the advantages and disadvantages of the currently available methods of measuring platelet function and discuss both the limitations and emerging data supporting the role of platelet function studies in clinical practice.

  16. Design of specimen for weld residual stress simulation

    International Nuclear Information System (INIS)

    Kim, Jin Weon; Park, Jong Sun; Lee, Kyung Soo

    2008-01-01

    The objective of this study is to design a laboratory specimen for simulating residual stress of circumferential butt welding of pipe. Specimen type and method for residual stress generation were proposed based on the review of prior studies and parametric finite element simulation. To prove the proposed specimen type and loading method, the residual stress was generated using the designed specimen by applying proposed method and was measured. The measured residual stress using X-ray diffraction reasonably agreed with the results of finite element simulation considered in the specimen design. Comparison of residual strains measured at several locations of specimen and given by finite element simulation also showed good agreement. Therefore, it is indicated that the designed specimen can reasonably simulate the residual stress of circumferential butt welding of pipe

  17. Comparative study on Charpy specimen reconstitution techniques

    International Nuclear Information System (INIS)

    Bourdiliau, B.; Decroix, G.-M.; Averty, X.; Wident, P.; Bienvenu, Y.

    2011-01-01

    Highlights: → Welding processes are used to reconstitute previously tested Charpy specimens. → Stud welding is preferred for a quick installation, almost immediately operational. → Friction welding produces better quality welds, but requires a development effort. - Abstract: Reconstitution techniques are often used to allow material from previously fractured Charpy-V specimens to be reused for additional experiments. This paper presents a comparative experimental study of various reconstitution techniques and evaluates the feasibility of these methods for future use in shielded cells. The following techniques were investigated: arc stud welding, 6.0 kW CO 2 continuous wave laser welding, 4.5 kW YAG continuous wave laser welding and friction welding. Subsize Charpy specimens were reconstituted using a 400 W YAG pulsed wave laser. The best result was obtained with arc stud welding; the resilience of the reconstituted specimens and the load-displacement curves agreed well with the reference specimens, and the temperature elevation caused by the welding process was limited to the vicinity of the weld. Good results were also obtained with friction welding; this process led to the best quality welds. Laser welding seems to have affected the central part of the specimens, thus leading to different resilience values and load-displacement curves.

  18. Automated patient and medication payment method for clinical trials

    Directory of Open Access Journals (Sweden)

    Yawn BP

    2013-01-01

    Full Text Available Barbara P Yawn,1 Suzanne Madison,1 Susan Bertram,1 Wilson D Pace,2 Anne Fuhlbrigge,3 Elliot Israel,3 Dawn Littlefield,1 Margary Kurland,1 Michael E Wechsler41Olmsted Medical Center, Department of Research, Rochester, MN, 2UCDHSC, Department of Family Medicine, University of Colorado Health Science Centre, Aurora, CO, 3Brigham and Women's Hospital, Pulmonary and Critical Care Division, Boston, MA, 4National Jewish Medical Center, Division of Pulmonology, Denver, CO, USABackground: Published reports and studies related to patient compensation for clinical trials focus primarily on the ethical issues related to appropriate amounts to reimburse for patient's time and risk burden. Little has been published regarding the method of payment for patient participation. As clinical trials move into widely dispersed community practices and more complex designs, the method of payment also becomes more complex. Here we review the decision process and payment method selected for a primary care-based randomized clinical trial of asthma management in Black Americans.Methods: The method selected is a credit card system designed specifically for clinical trials that allows both fixed and variable real-time payments. We operationalized the study design by providing each patient with two cards, one for reimbursement for study visits and one for payment of medication costs directly to the pharmacies.Results: Of the 1015 patients enrolled, only two refused use of the ClinCard, requesting cash payments for visits and only rarely a weekend or fill-in pharmacist refused to use the card system for payment directly to the pharmacy. Overall, the system has been well accepted by patients and local study teams. The ClinCard administrative system facilitates the fiscal accounting and medication adherence record-keeping by the central teams. Monthly fees are modest, and all 12 study institutional review boards approved use of the system without concern for patient

  19. Splitting tests on rock specimens

    Energy Technology Data Exchange (ETDEWEB)

    Davies, J D; Stagg, K G

    1970-01-01

    Splitting tests are described for a square-section sandstone specimens line loaded through steel or timber packings on the top face and supported on the bottom face either on similar packings (type A specimen) or directly on the lower platen plate of the testing machine (type B specimens). The stress distribution across the vertical central plane and the horizontal central plane were determined from a linear elastic finite element analysis for both types. Two solutions were obtained for the type B specimen: one assuming no friction between the base of the specimen and the platen plate and the other assuming no relative slip between the surfaces. Vertical and horizontal strains were measured at the center of the specimens for all loads up to failure.

  20. Janka hardness using nonstandard specimens

    Science.gov (United States)

    David W. Green; Marshall Begel; William Nelson

    2006-01-01

    Janka hardness determined on 1.5- by 3.5-in. specimens (2×4s) was found to be equivalent to that determined using the 2- by 2-in. specimen specified in ASTM D 143. Data are presented on the relationship between Janka hardness and the strength of clear wood. Analysis of historical data determined using standard specimens indicated no difference between side hardness...

  1. Clinical experience with the objective symmetry detector method for gammaencephalography

    International Nuclear Information System (INIS)

    Sachs, C.; Ericson, K.; Lind, M.

    1982-01-01

    The objective symmetry detector method for gammaencephalography previously described has been further developed. A rapid micro-computerized automatic measuring device has been constructed and the method used in screening of neurologic patients. The previously chosen classification boundaries between normal and pathologic isotope distributions were not entirely satisfactory for clinical screening of patients with neurologic symptoms. By use of new classification boundaries, 87 per cent of patients with brain tumours could be separated from patients with neurologic symptoms but without gross brain lesions and from neurologically healthy subjects. (Auth.)

  2. A simple and low-toxic method of preparing small specimens of bacteria, flagellates and their likes for Scanning Electron Microscopy

    DEFF Research Database (Denmark)

    Møller, O. S.; Buchman, K.; Dalsgaard, Inger

    2013-01-01

    The preparation of samples of bacteria and other very small organisms (Electron Microscopy is often complex and intricate, which typically involve the use of specialized filter systems, complex handling and toxic chemicals. Based on the methods described in the literature...

  3. Clinical tooth preparations and associated measuring methods: a systematic review.

    Science.gov (United States)

    Tiu, Janine; Al-Amleh, Basil; Waddell, J Neil; Duncan, Warwick J

    2015-03-01

    The geometries of tooth preparations are important features that aid in the retention and resistance of cemented complete crowns. The clinically relevant values and the methods used to measure these are not clear. The purpose of this systematic review was to retrieve, organize, and critically appraise studies measuring clinical tooth preparation parameters, specifically the methodology used to measure the preparation geometry. A database search was performed in Scopus, PubMed, and ScienceDirect with an additional hand search on December 5, 2013. The articles were screened for inclusion and exclusion criteria and information regarding the total occlusal convergence (TOC) angle, margin design, and associated measuring methods were extracted. The values and associated measuring methods were tabulated. A total of 1006 publications were initially retrieved. After removing duplicates and filtering by using exclusion and inclusion criteria, 983 articles were excluded. Twenty-three articles reported clinical tooth preparation values. Twenty articles reported the TOC, 4 articles reported margin designs, 4 articles reported margin angles, and 3 articles reported the abutment height of preparations. A variety of methods were used to measure these parameters. TOC values seem to be the most important preparation parameter. Recommended TOC values have increased over the past 4 decades from an unachievable 2- to 5-degree taper to a more realistic 10 to 22 degrees. Recommended values are more likely to be achieved under experimental conditions if crown preparations are performed outside of the mouth. We recommend that a standardized measurement method based on the cross sections of crown preparations and standardized reporting be developed for future studies analyzing preparation geometry. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

  4. A comparison of cosegregation analysis methods for the clinical setting.

    Science.gov (United States)

    Rañola, John Michael O; Liu, Quanhui; Rosenthal, Elisabeth A; Shirts, Brian H

    2018-04-01

    Quantitative cosegregation analysis can help evaluate the pathogenicity of genetic variants. However, genetics professionals without statistical training often use simple methods, reporting only qualitative findings. We evaluate the potential utility of quantitative cosegregation in the clinical setting by comparing three methods. One thousand pedigrees each were simulated for benign and pathogenic variants in BRCA1 and MLH1 using United States historical demographic data to produce pedigrees similar to those seen in the clinic. These pedigrees were analyzed using two robust methods, full likelihood Bayes factors (FLB) and cosegregation likelihood ratios (CSLR), and a simpler method, counting meioses. Both FLB and CSLR outperform counting meioses when dealing with pathogenic variants, though counting meioses is not far behind. For benign variants, FLB and CSLR greatly outperform as counting meioses is unable to generate evidence for benign variants. Comparing FLB and CSLR, we find that the two methods perform similarly, indicating that quantitative results from either of these methods could be combined in multifactorial calculations. Combining quantitative information will be important as isolated use of cosegregation in single families will yield classification for less than 1% of variants. To encourage wider use of robust cosegregation analysis, we present a website ( http://www.analyze.myvariant.org ) which implements the CSLR, FLB, and Counting Meioses methods for ATM, BRCA1, BRCA2, CHEK2, MEN1, MLH1, MSH2, MSH6, and PMS2. We also present an R package, CoSeg, which performs the CSLR analysis on any gene with user supplied parameters. Future variant classification guidelines should allow nuanced inclusion of cosegregation evidence against pathogenicity.

  5. Evaluation of clinical methods for peroneal muscle testing.

    Science.gov (United States)

    Sarig-Bahat, Hilla; Krasovsky, Andrei; Sprecher, Elliot

    2013-03-01

    Manual muscle testing of the peroneal muscles is well accepted as a testing method in musculoskeletal physiotherapy for the assessment of the foot and ankle. The peroneus longus and brevis are primary evertors and secondary plantar flexors of the ankle joint. However, some international textbooks describe them as dorsi flexors, when instructing peroneal muscle testing. The identified variability raised a question whether these educational texts are reflected in the clinical field. The purposes of this study were to investigate what are the methods commonly used in the clinical field for peroneal muscle testing and to evaluate their compatibility with functional anatomy. A cross-sectional study was conducted, using an electronic questionnaire sent to 143 Israeli physiotherapists in the musculoskeletal field. The survey questioned on the anatomical location of manual resistance and the combination of motions resisted. Ninety-seven responses were received. The majority (69%) of respondents related correctly to the peronei as evertors, but asserted that resistance should be located over the dorsal aspect of the fifth metatarsus, thereby disregarding the peroneus longus. Moreover, 38% of the respondents described the peronei as dorsi flexors, rather than plantar flexors. Only 2% selected the correct method of resisting plantarflexion and eversion at the base of the first metatarsus. We consider this technique to be the most compatible with the anatomy of the peroneus longus and brevis. The Fisher-Freeman-Halton test indicated that there was a significant relationship between responses on the questions (P = 0.0253, 95% CI 0.0249-0.0257), thus justifying further correspondence analysis. The correspondence analysis found no clustering of the answers that were compatible with anatomical evidence and were applied in the correct technique, but did demonstrate a common error, resisting dorsiflexion rather than plantarflexion, which was in agreement with the described

  6. An easy, rapid, and cost-effective method for DNA extraction from various lichen taxa and specimens suitable for analysis of fungal and algal strains.

    Science.gov (United States)

    Park, Sook-Young; Jang, Seol-Hwa; Oh, Soon-Ok; Kim, Jung A; Hur, Jae-Seoun

    2014-12-01

    Lichen studies, including biodiversity, phylogenetic relationships, and conservation concerns require definitive species identification, however many lichens can be challenging to identify at the species level. Molecular techniques have shown efficacy in discriminating among lichen taxa, however, obtaining genomic DNA from herbarium and fresh lichen thalli by conventional methods has been difficult, because lichens contain high proteins, polysaccharides, and other complex compounds in their cell walls. Here we report a rapid, easy, and inexpensive protocol for extracting PCR-quality DNA from various lichen species. This method involves the following two steps: first, cell breakage using a beadbeater; and second, extraction, isolation, and precipitation of genomic DNA. The procedure requires approximately 10 mg of lichen thalli and can be completed within 20 min. The obtained DNAs were of sufficient quality and quantity to amplify the internal transcribed spacer region from the fungal and algal lichen components, as well as to sequence the amplified products. In addition, 26 different lichen taxa were tested, resulting in successful PCR products. The results of this study validated the experimental protocols, and clearly demonstrated the efficacy and value of our KCl extraction method applied in the fungal and algal samples.

  7. Dose escalation methods in phase I cancer clinical trials.

    Science.gov (United States)

    Le Tourneau, Christophe; Lee, J Jack; Siu, Lillian L

    2009-05-20

    Phase I clinical trials are an essential step in the development of anticancer drugs. The main goal of these studies is to establish the recommended dose and/or schedule of new drugs or drug combinations for phase II trials. The guiding principle for dose escalation in phase I trials is to avoid exposing too many patients to subtherapeutic doses while preserving safety and maintaining rapid accrual. Here we review dose escalation methods for phase I trials, including the rule-based and model-based dose escalation methods that have been developed to evaluate new anticancer agents. Toxicity has traditionally been the primary endpoint for phase I trials involving cytotoxic agents. However, with the emergence of molecularly targeted anticancer agents, potential alternative endpoints to delineate optimal biological activity, such as plasma drug concentration and target inhibition in tumor or surrogate tissues, have been proposed along with new trial designs. We also describe specific methods for drug combinations as well as methods that use a time-to-event endpoint or both toxicity and efficacy as endpoints. Finally, we present the advantages and drawbacks of the various dose escalation methods and discuss specific applications of the methods in developmental oncotherapeutics.

  8. Identification of Echinococcus Granulosus Strains in Isolated Hydatid Cyst Specimens from Animals by PCR-RFLP Method in West Azerbaijan – Iran

    Directory of Open Access Journals (Sweden)

    Haleh Hanifian

    2013-09-01

    Full Text Available Background: The aim of this study was DNA extraction from protosco­lecses of Echinococcus granulosus and identification of these strains in West-Azerbai­jan Province, north western Iran.Methods: Thirty one livestock isolates from sheep and cattle were collected from abattoirs of the province. To investigate the genetic variation of the isolates, after DNA extraction by Glass beads-phenol chloroform method; PCR-RLFP analysis of rDNA-ITS1 was performed using three different restric­tion enzymes of Taq 1, Rsa 1 and Alu 1.Result: Amplified PCR products for all isolates were 1000bp band which is expected band in sheep strains (G1-G3 complex. The results of RFLP analy­sis also were the same for all isolates. PCR-RFLP patterns restriction en­zymes were identical as follows, Rsa1 bands under UV showed two bands approximately 655bp and 345bp. Alu1 bands were as follows: two approx­imately 800bp and 200bp and Taq1 did not cut any region and bands were approximately 1000 bp in all samples.Conclusions: Based on PCR-RFLP patterns of ITS1 fragment produced with endonucleases enzyme digestion in animal isolates, it can be concluded that a single strain of E. granulosus (sheep strain or G1-G3 complex is domi­nant genotype in this province

  9. Dose Escalation Methods in Phase I Cancer Clinical Trials

    OpenAIRE

    Le Tourneau, Christophe; Lee, J. Jack; Siu, Lillian L.

    2009-01-01

    Phase I clinical trials are an essential step in the development of anticancer drugs. The main goal of these studies is to establish the recommended dose and/or schedule of new drugs or drug combinations for phase II trials. The guiding principle for dose escalation in phase I trials is to avoid exposing too many patients to subtherapeutic doses while preserving safety and maintaining rapid accrual. Here we review dose escalation methods for phase I trials, including the rule-based and model-...

  10. Nuclear morphometry in histological specimens of canine prostate cancer: Correlation with histological subtypes, Gleason score, methods of collection and survival time.

    Science.gov (United States)

    Di Donato, Guido; Laufer-Amorim, Renée; Palmieri, Chiara

    2017-10-01

    Ten normal prostates, 22 benign prostatic hyperplasia (BPH) and 29 prostate cancer (PC) were morphometrically analyzed with regard to mean nuclear area (MNA), mean nuclear perimeter (MNP), mean nuclear diameter (MND), coefficient of variation of the nuclear area (NACV), mean nuclear diameter maximum (MDx), mean nuclear diameter minimum (MDm), mean nuclear form ellipse (MNFe) and form factor (FF). The relationship between nuclear morphometric parameters and histological type, Gleason score, methods of sample collection, presence of metastases and survival time of canine PC were also investigated. Overall, nuclei from neoplastic cells were larger, with greater variation in nuclear size and shape compared to normal and hyperplastic cells. Significant differences were found between more (small acinar/ductal) and less (cribriform, solid) differentiated PCs with regard to FF (pnuclear morphometric analysis in combination with Gleason score can help in canine prostate cancer grading, thus contributing to the establishment of a more precise prognosis and patient's management. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Methods to Succeed in Effective Knowledge Translation in Clinical Practice.

    Science.gov (United States)

    Kitson, Alison L; Harvey, Gillian

    2016-05-01

    To explore the evidence around facilitation as an intervention for the successful implementation of new knowledge into clinical practice. The revised version of the Promoting Action on Research Implementation in Health Services (PARIHS) framework, called the integrated or i-PARIHS framework, is used as the explanatory framework. This framework posits that evidence is a multidimensional construct embedded within innovation and operationalized by clinicians (individuals and within teams), working across multiple layers of context. Facilitation is the active ingredient that promotes successful implementation. An emerging body of evidence supports facilitation as a mechanism to getting new knowledge into clinical practice. Facilitation roles are divided into beginner, experienced, and expert facilitators. Facilitators can be internal or external to the organization they work in, and their skills and attributes complement other knowledge translation (KT) roles. Complex KT projects require facilitators who are experienced in implementation methods. Facilitation is positioned as the active ingredient to effectively introduce new knowledge into a clinical setting. Levels of facilitation experience are assessed in relation to the complexity of the KT task. Three core facilitation roles are identified, and structured interventions are established taking into account the nature and novelty of the evidence, the receptiveness of the clinicians, and the context or setting where the new evidence is to be introduced. Roles such as novice, experienced, and expert facilitators have important and complementary parts to play in enabling the successful translation of evidence into everyday practice in order to provide effective care for patients. © 2016 Sigma Theta Tau International.

  12. Rehydration of forensically important larval Diptera specimens.

    Science.gov (United States)

    Sanford, Michelle R; Pechal, Jennifer L; Tomberlin, Jeffery K

    2011-01-01

    Established procedures for collecting and preserving evidence are essential for all forensic disciplines to be accepted in court and by the forensic community at large. Entomological evidence, such as Diptera larvae, are primarily preserved in ethanol, which can evaporate over time, resulting in the dehydration of specimens. In this study, methods used for rehydrating specimens were compared. The changes in larval specimens with respect to larval length and weight for three forensically important blow fly (Diptera: Calliphoridae) species in North America were quantified. Phormia regina (Meigen), Cochliomyia macellaria (F.), and Chrysomya rufifacies (Macquart) third-instar larvae were collected from various decomposing animals and preserved with three preservation methods (80% ethanol, 70% isopropyl alcohol, and hot-water kill then 80% ethanol). Preservative solutions were allowed to evaporate. Rehydration was attempted with either of the following: 80% ethanol, commercial trisodium phosphate substitute solution, or 0.5% trisodium phosphate solution. All three methods partially restored weight and length of specimens recorded before preservation. Analysis of variance results indicated that effects of preservation, rehydration treatment, and collection animal were different in each species. The interaction between preservative method and rehydration treatment had a significant effect on both P. regina and C. macellaria larval length and weight. In addition, there was a significant interaction effect of collection animal on larval C. macellaria measurements. No significant effect was observed in C. rufifacies larval length or weight among the preservatives or treatments. These methods could be used to establish a standard operating procedure for dealing with dehydrated larval specimens in forensic investigations.

  13. SurePath Specimens Versus ThinPrep Specimen Types on the COBAS 4800 Platform: High-Risk HPV Status and Cytology Correlation in an Ethnically Diverse Bronx Population.

    Science.gov (United States)

    Naeem, R C; Goldstein, D Y; Einstein, Mark H; Ramos Rivera, G; Schlesinger, K; Khader, S N; Suhrland, M; Fox, A S

    2017-08-01

    To compare the cytologic preparations of 130 cervical specimens (from women of various ethnicities at high risk for human papillomavirus [HPV] infection) using the SurePath (SP) collection system with specimens gathered using the ThinPrep (TP) system, as processed on the Cobas 4800 analyzer, to determine which collection method more accurately identifies HPV infection. In our prospective study, specimens were collected from 130 women of various ethnicities residing in or near Bronx County, NY. The SP-collected specimen was first processed for cytologic findings; if clinical HPV testing was requested on that specimen, it was tested using Hybrid Capture II (HC2) methodology. We tested the remnant SP-collected cell concentrate using the Cobas analyzer. Then, the TP-collected and SP-collected specimens were tested in the same run on that analyzer, and the results were compared. We also compared the results with the concurrent cytologic findings. The results were concordant for overall HR-HPV status in 93.8% of cases. Also, a statistically significant lower cycle threshold value was observed with Cobas testing of specimen concentrates tested via the BD SurePath Pap Test (P = .001), suggesting higher sensitivity compared with specimens tested via the ThinPrep Pap Test. Cobas 4800 HPV testing of SP-collected specimen concentrates yields comparable results to TP-collected specimen concentrates. Based on the limited data that we derived, SP collection may be a more favorable methodology than TP collection for HPV testing of individuals at high risk in our ethnically diverse, urban patient population. © American Society for Clinical Pathology, 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  14. Screen-film specimen radiography

    International Nuclear Information System (INIS)

    Shepard, S.J.; Hogan, J.; Schreck, B.

    1990-01-01

    This paper reports on the reproducibility and quality of biopsy specimen radiographs, a unique phototimed cabinet x-ray system is being developed. The system utilizes specially modified Kodal Min-R cassettes and will be compatible with current mammographic films. Tube voltages are in the 14-20-kVp range with 0.1-1.0-second exposure times. A top-hat type compression device is used (1) to compress the specimen to uniform thickness, (2) to measure the specimen thickness and determine optimum kVp, and (3) to superimpose a grid over the specimen for identification of objects of radiographic interest. The phototiming circuit developed specifically for this purpose will be described along with the modified Min-R cassette. Characteristics of the generator and cabinet will also be described. Tests will be performed on phantoms to evaluate the system limitations

  15. Location specific in situ TEM straining specimens made using FIB

    International Nuclear Information System (INIS)

    Field, R.D.; Papin, P.A.

    2004-01-01

    A method has been devised and demonstrated for producing in situ straining specimens for the transmission electron microscope (TEM) from specific locations in a sample using a dual-beam focused ion beam (FIB) instrument. The specimen is removed from a polished surface in the FIB using normal methods and then attached to a pre-fabricated substrate in the form of a modified TEM tensile specimen. In this manner, specific features of the microstructure of a polished optical mount can be selected for in situ tensile straining. With the use of electron backscattered diffraction (EBSD), this technique could be extended to select specific orientations of the specimen as well

  16. Polymeric LabChip real-time PCR as a point-of-care-potential diagnostic tool for rapid detection of influenza A/H1N1 virus in human clinical specimens.

    Directory of Open Access Journals (Sweden)

    Hyun-Ok Song

    Full Text Available It is clinically important to be able to detect influenza A/H1N1 virus using a fast, portable, and accurate system that has high specificity and sensitivity. To achieve this goal, it is necessary to develop a highly specific primer set that recognizes only influenza A viral genes and a rapid real-time PCR system that can detect even a single copy of the viral gene. In this study, we developed and validated a novel fluidic chip-type real-time PCR (LabChip real-time PCR system that is sensitive and specific for the detection of influenza A/H1N1, including the pandemic influenza strain A/H1N1 of 2009. This LabChip real-time PCR system has several remarkable features: (1 It allows rapid quantitative analysis, requiring only 15 min to perform 30 cycles of real-time PCR. (2 It is portable, with a weight of only 5.5 kg. (3 The reaction cost is low, since it uses disposable plastic chips. (4 Its high efficiency is equivalent to that of commercially available tube-type real-time PCR systems. The developed disposable LabChip is an economic, heat-transferable, light-transparent, and easy-to-fabricate polymeric chip compared to conventional silicon- or glass-based labchip. In addition, our LabChip has large surface-to-volume ratios in micro channels that are required for overcoming time consumed for temperature control during real-time PCR. The efficiency of the LabChip real-time PCR system was confirmed using novel primer sets specifically targeted to the hemagglutinin (HA gene of influenza A/H1N1 and clinical specimens. Eighty-five human clinical swab samples were tested using the LabChip real-time PCR. The results demonstrated 100% sensitivity and specificity, showing 72 positive and 13 negative cases. These results were identical to those from a tube-type real-time PCR system. This indicates that the novel LabChip real-time PCR may be an ultra-fast, quantitative, point-of-care-potential diagnostic tool for influenza A/H1N1 with a high sensitivity and

  17. Comparison of measurement results between cervical pedicle specimens and CT images

    International Nuclear Information System (INIS)

    Zhang Guangjian; Li Hua; Liu Haiyan; Gao Zhenping

    2011-01-01

    Objective: To compare the difference between the measurement results of the cervical pedicle specimens and CT image, and provide the basis for clinical cervical screw internal fixation operation. Methods: Twenty-seven Chinese adult cadaver cervical specimens including C3 to C7 vertebrae were measured by a digital calipers and CT image, containing pedicle height (PH, PH'), pedicle width(PW, PW'), total pedicle length (TL, TL') and two pedicle lengths(PL1, PL2; PL1', PL2'). The results of specimens and CT image were compared. Results: Different cervical vertebra in the same side of specimens or CT images, PW (PW'): C3, C4< C5, C6 (P<0.05), C5, C6< C7 (P<0.01); PH (PH'): there were no significant differences; TL, PL1, PL2 (TL', PL1', PL2'): there were no marked differences. In the same cervical vertebra of the specimens or CT images, PW (PW')< PH (PH') (P<0.01), PL1 (PL1') < PL2 (PL2') (P<0.01). Conclusion: The results of measurement by CT images are not markedly different from that of specimens. CT image measurement is available before cervical screw internal fixation operation. (authors)

  18. Production and use of plastinated anatomical specimens as teaching and learning tools in veterinary gross anatomy in the Caribbean

    Directory of Open Access Journals (Sweden)

    Reda Mohamed

    2018-03-01

    Full Text Available Objective: Veterinary Anatomy is considered as the backbone subject in the veterinary medicine program. Formalized specimens were not very much accepted by the veterinary students due to their wetness, bad smell and potential harmful effects. Plastination has evolved as a new technique for prolonged preservation of specimens by replacing the water and fat by a curable plastic polymer. Material and methods: The process of plastination involved fixation, dehydration, impregnation and curing. The plastinated specimens were used for teaching and learning of veterinary gross anatomy courses for veterinary students. Results: Plastinated specimens were appreciated by the staff and students as they were odorless, non-toxic and durable, needed less space for storage and they were used in teaching the veterinary anatomy courses. Plastinated specimens were used for studying not only in the dissection hall but also in the lecture room, both individually and in groups. Conclusion: The plastinated specimens were excellent for demonstration but they could not completely replace the traditional dissection because students learn best by exploratory and hands-on dissection. Moreover, the wet specimens provided a more accurate visual representation of the body parts and skills to aid in dealing with actual clinical cases in the future. Therefore, the plastinated and wet specimens were used simultaneously depending on the topic being taught at the time. [J Adv Vet Anim Res 2018; 5(1.000: 44-52

  19. Quantitative X-ray microanalysis of biological specimens

    International Nuclear Information System (INIS)

    Roomans, G.M.

    1988-01-01

    Qualitative X-ray microanalysis of biological specimens requires an approach that is somewhat different from that used in the materials sciences. The first step is deconvolution and background subtraction on the obtained spectrum. The further treatment depends on the type of specimen: thin, thick, or semithick. For thin sections, the continuum method of quantitation is most often used, but it should be combined with an accurate correction for extraneous background. However, alternative methods to determine local mass should also be considered. In the analysis of biological bulk specimens, the ZAF-correction method appears to be less useful, primarily because of the uneven surface of biological specimens. The peak-to-local background model may be a more adequate method for thick specimens that are not mounted on a thick substrate. Quantitative X-ray microanalysis of biological specimens generally requires the use of standards that preferably should resemble the specimen in chemical and physical properties. Special problems in biological microanalysis include low count rates, specimen instability and mass loss, extraneous contributions to the spectrum, and preparative artifacts affecting quantitation. A relatively recent development in X-ray microanalysis of biological specimens is the quantitative determination of local water content

  20. Mechanomyographic Parameter Extraction Methods: An Appraisal for Clinical Applications

    Directory of Open Access Journals (Sweden)

    Morufu Olusola Ibitoye

    2014-12-01

    Full Text Available The research conducted in the last three decades has collectively demonstrated that the skeletal muscle performance can be alternatively assessed by mechanomyographic signal (MMG parameters. Indices of muscle performance, not limited to force, power, work, endurance and the related physiological processes underlying muscle activities during contraction have been evaluated in the light of the signal features. As a non-stationary signal that reflects several distinctive patterns of muscle actions, the illustrations obtained from the literature support the reliability of MMG in the analysis of muscles under voluntary and stimulus evoked contractions. An appraisal of the standard practice including the measurement theories of the methods used to extract parameters of the signal is vital to the application of the signal during experimental and clinical practices, especially in areas where electromyograms are contraindicated or have limited application. As we highlight the underpinning technical guidelines and domains where each method is well-suited, the limitations of the methods are also presented to position the state of the art in MMG parameters extraction, thus providing the theoretical framework for improvement on the current practices to widen the opportunity for new insights and discoveries. Since the signal modality has not been widely deployed due partly to the limited information extractable from the signals when compared with other classical techniques used to assess muscle performance, this survey is particularly relevant to the projected future of MMG applications in the realm of musculoskeletal assessments and in the real time detection of muscle activity.

  1. Porphyromonas pogonae sp. nov., an anaerobic but low concentration oxygen adapted coccobacillus isolated from lizards (Pogona vitticeps) or human clinical specimens, and emended description of the genus Porphyromonas Shah and Collins 1988.

    Science.gov (United States)

    Kawamura, Yoshiaki; Kuwabara, Saki; Kania, Stephen A; Kato, Hisayuki; Hamagishi, Manami; Fujiwara, Nagatoshi; Sato, Takuichi; Tomida, Junko; Tanaka, Kaori; Bemis, David A

    2015-03-01

    During the process of identifying a Gram-negative coccobacillus isolated from a human clinical specimen, we found that the isolate's 16S rRNA gene had very close sequence identity with that of a variant Porphyromonas isolated from polymicrobial infections in the central bearded dragon, a species of lizard [2]. The 16S rRNA gene sequences of the human isolate and of six isolates from lizards were nearly identical (99.9-100%). Phylogenetic analysis placed all of these isolates in a single phylogenetic cluster well separated from other species in the genus Porphyromonas. The closest species was Porphyromonas catoniae with 90.7-90.9% sequence identity, although there was less than 6% DNA similarity between the P. catoniae type strain and our representative isolates from lizards (PAGU 1787(T)) and human (PAGU 1776). These isolates could grow under anaerobic or microaerobic conditions (6% O2 atmosphere). The isolates were positive for catalase and very strong β-hemolytic activity, but did not show black or brown pigmentation. Biochemically, the isolates could be differentiated from closely related species by pyroglutamic acid arylamidase and glycine arylamidase activity, and some others. The fermentation products mainly included succinic acid and propionic acid. The major fatty acids detected in cells of the isolates were iso-C15:0, anteiso-C15:0, and 3OH-iso-C17:0. The G+C content was 43.0 ± 0.62 mol%. The species name Porphyromonas pogonae sp. nov. is proposed for these isolates with the type strain of PAGU 1787(T) (=MI 10-1288(T)=JCM 19732(T)=ATCC BAA-2643(T)). Copyright © 2014 Elsevier GmbH. All rights reserved.

  2. Enzymatic detection of formalin-fixed museum specimens for DNA analysis and enzymatic maceration of formalin-fixed specimens

    DEFF Research Database (Denmark)

    Sørensen, Margrethe; Redsted Rasmussen, Arne; Simonsen, Kim Pilkjær

    2016-01-01

    % ethanol. The method was subsequently tested on wild-living preserved specimens and an archived specimen. The protease enzyme used was SavinaseH 16 L, Type EX from Novozymes A/S. The enzymatic screening test demands only simple laboratory equipment. The method is useful for natural history collections...

  3. Detecting Rickettsia parkeri Infection from Eschar Swab Specimens

    Science.gov (United States)

    2013-05-01

    Detecting Rickettsia parkeri Infection from Eschar Swab Specimens Todd Myers, Tahaniyat Lalani, Mike Dent, Ju Jiang, Patrick L. Daly, Jason D...Maguire, and Allen L. Richards The typical clinical presentation of several spotted fever group Rickettsia infections includes eschars. Clinical...diagnosis by using an eschar swab specimen from patients infected with Rickettsia parkeri. Until 2004, all confirmed cases of tick-borne spotted

  4. Technique of manufacturing specimen of irradiated fuel rods

    International Nuclear Information System (INIS)

    Min, Duck Seok; Seo, Hang Seok; Min, Duck Kee; Koo, Dae Seo; Lee, Eun Pyo; Yang, Song Yeol

    1999-04-01

    Technique of manufacturing specimen of irradiated fuel rods to perform efficient PIE is developed by analyzing the relation between requiring time of manufacturing specimen and manufacturing method in irradiated fuel rods. It takes within an hour to grind 1 mm of specimen thickness under 150 rpm in speed of grinding, 600 g gravity in force using no.120, no.240, no.320 of grinding paper. In case of no.400 of grinding paper, it takes more an hour to grind the same thickness as above. It takes up to a quarter to grind 80-130 μm in specimen thickness using no.400 of grinding paper. When grinding time goes beyond 15 minutes, the grinding thickness of specimen does not exist. The polishing of specimen with 150 Rpms in speed of grinding machine, 600 g gravity in force, 10 minutes in polishing time using diamond paste 15 μm on polishing cloths amounts to 50 μm in specimen thickness. In case of diamond paste 9 μm on polishing cloth, the polishing of specimen amounts to 20 μm. The polishing thickness of specimen with 15 minutes in polishing time using 6 μm, 3 μm, 1 μm, 1/4 μm does not exist. Technique of manufacturing specimen of irradiated fuel rods will have application to the destructive examination of PIE. (author). 6 refs., 1 tab., 10 figs

  5. [Methods of investigation in clinical cardiology. VIII. Socioeconomic evaluation of clinical cardiology practice].

    Science.gov (United States)

    Lázaro de Mercado, P

    1997-06-01

    Health services are systems whose mission is to improve the health status of both individuals and society in general. In recent decades, these systems have faced challenges such as their increasing complexity, limited resources, rapid innovation and diffusion of medical technologies, pressures on demand from society and professionals, and the lack of knowledge of the effects of these factors on costs and society's health. In addition, health care expenditures have grown twice as fast as wealth in industrialized countries during the last 25 years. These problems have prompted cost containment as a key issue in health policy and, at the same time, have promoted the development of socioeconomic evaluation as a scientific activity in the frame of health services research. Socioeconomic evaluation tries to determine if the sacrifice made by society, which devotes part of its limited resources to health care, maximizes the outcomes for population. This article describes basic concepts and methods of economic appraisal in health services which are illustrated with examples of clinical practice in cardiology. Common methods of evaluation are described; the relation between the clinical outcome of a procedure and its associated costs is emphasized in explaining the types of efficiency analysis (cost-efficacy, cost-effectiveness, cost-utility, and cost-benefit); and finally a guide for socioeconomic evaluation is provided.

  6. Detection of PCR inhibitors in cervical specimens by using the AMPLICOR Chlamydia trachomatis assay

    NARCIS (Netherlands)

    R.P.A.J. Verkooyen (Roel); A. Luijendijk (Ad); W.M. Huisman; W.H.F. Goessens (Wil); J.A.J.W. Kluytmans (Jan); J.H. van Rijsoort-Vos; H.A. Verbrugh (Henri)

    1996-01-01

    textabstractTo determine that susceptibility of AMPLICOR Chlamydia trachomatis PCR to inhibitory factors possibly present in cervical specimens, we obtained cervical specimens from 200 gynecology patients attending our outpatient clinic. The prevalence of C. trachomatis

  7. Histopathologic analysis of appendectomy specimens

    Directory of Open Access Journals (Sweden)

    R Shrestha

    2012-03-01

    Full Text Available Background: Acute appendicitis is one of the common conditions requiring emergency surgery. A retrospective study was performed to determine various histopathological diagnoses, their demographics and the rates of perforated appendicitis, negative appendectomy and incidental appendectomy. Materials and Methods: Histopathological records of resected appendices submitted to histopathology department Chitwan medical college teaching hospital over the period of 2 yrs from May, 2009 to April 2011 were reviewed retrospectively. Results: Out of 930 specimens of appendix, appendicitis accounted for 88.8% with peak age incidence in the age group of 11 to 30 yrs in both sexes. Histopathologic diagnoses included acute appendicitis (45.6%, acute suppurative (20.8%, gangrenous (16.3%, perforated (1.7%, resolving /recurrent/non specific chronic appendicitis (2.5%, acute eosinophilic appendicitis (1.2%, periappendicitis (0.2%, and carcinoid tumour (0.1%. Other important coexisting pathologies were parasitic infestation (0.2% and Meckel’s diverticulum (0.2%. Negative appendectomy rate was 10.8% and three times more common in females with peak occurrence in the age group of 21-30 yrs. There were 10 cases of acute appendicitis in incidental appendectomies (2.5%, 24 cases with 7 times more common in females of age group of 31- 60 yrs. Conclusion: There is a high incidence of appendicitis in adolescents and young adults in central south region of Nepal. Negative appendectomy is also very common in females. Incidental appendectomy in elderly females may have preventive value. DOI: http://dx.doi.org/10.3126/jpn.v2i3.6025 JPN 2012; 2(3: 215-219

  8. Resource costing for multinational neurologic clinical trials: methods and results.

    Science.gov (United States)

    Schulman, K; Burke, J; Drummond, M; Davies, L; Carlsson, P; Gruger, J; Harris, A; Lucioni, C; Gisbert, R; Llana, T; Tom, E; Bloom, B; Willke, R; Glick, H

    1998-11-01

    We present the results of a multinational resource costing study for a prospective economic evaluation of a new medical technology for treatment of subarachnoid hemorrhage within a clinical trial. The study describes a framework for the collection and analysis of international resource cost data that can contribute to a consistent and accurate intercountry estimation of cost. Of the 15 countries that participated in the clinical trial, we collected cost information in the following seven: Australia, France, Germany, the UK, Italy, Spain, and Sweden. The collection of cost data in these countries was structured through the use of worksheets to provide accurate and efficient cost reporting. We converted total average costs to average variable costs and then aggregated the data to develop study unit costs. When unit costs were unavailable, we developed an index table, based on a market-basket approach, to estimate unit costs. To estimate the cost of a given procedure, the market-basket estimation process required that cost information be available for at least one country. When cost information was unavailable in all countries for a given procedure, we estimated costs using a method based on physician-work and practice-expense resource-based relative value units. Finally, we converted study unit costs to a common currency using purchasing power parity measures. Through this costing exercise we developed a set of unit costs for patient services and per diem hospital services. We conclude by discussing the implications of our costing exercise and suggest guidelines to facilitate more effective multinational costing exercises.

  9. Evaluation of the crack initiation of curved compact tension specimens of a Zr-2.5Nb pressure tube using the unloading compliance and direct current potential drop methods

    International Nuclear Information System (INIS)

    Jeong, Hyeon Cheol; Ahn, Sang Bok; Park, Joong Chul; Kim, Young Suk

    2005-01-01

    Zr-2.5Nb pressure tubes, carrying fuel bundles and heavy water coolant inside, degrade due to neutron irradiation and hydrogen embrittlement during their operation in heavy water reactors. The safety criterion for the Zr-2.5Nb tubes to meet is a leak-before-break (LBB) requirement. To evaluate a safety margin related to the LBB criterion, facture toughness of the pressure tubes are to be determined periodically with their operational time. For a reliable evaluation of the LBB safety criterion of the pressure tubes, it is required to precisely determine their fracture toughness. Since the fracture toughness or J of the pressure tubes is determined only by the extended crack length, it is important to reliably and precisely evaluate the advanced crack length. However, the problem lies with the detection of the crack opening point because prior plastic deformation before a start of the crack makes it difficult. The aim of this work is to evaluate which method can define the crack initiation point in the Zr- 2.5Nb compact tension specimens more precisely between the unloading compliance method with a crack opening displacement (COD) gauge and the direct current potential drop (DCPD) methods

  10. Clinicopathologic features of incidental prostatic adenocarcinoma in radical cystoprostatectomy specimens

    Directory of Open Access Journals (Sweden)

    Vuruskan Hakan

    2011-07-01

    Full Text Available Abstract Background The aim of this study is to review all features of incidentally discovered prostate adenocarcinoma in patients undergoing radical cystoprostatectomy for bladder cancer. Methods The medical charts of 300 male patients who underwent radical cystoprostatectomy for bladder cancer between 1997 and 2005 were retrospectively reviewed. The mean age of the patients was 62 (range 51-75 years. Results Prostate adenocarcinoma was present in 60 (20% of 300 specimens. All were acinar adenocarcinoma. Of these, 40 (66.7% were located in peripheral zone, 20 (33.3% had pT2a tumor, 12 (20% had pT2b tumor, 22(36.7% had pT2c and, 6 (10% had pT3a tumor. Gleason score was 6 or less in 48 (80% patients. Surgical margins were negative in 54 (90% patients, and tumor volume was less than 0.5 cc in 23 (38.3% patients. Of the 60 incidentally detected cases of prostate adenocarcinoma 40 (66.7% were considered clinically significant. Conclusion Incidentally detected prostate adenocarcinoma is frequently observed in radical cystoprostatectomy specimens. The majority are clinically significant.

  11. [Hysteroscopy clinic: diagnostic and therapeutic method in abnormal uterine bleeding].

    Science.gov (United States)

    Alanis Fuentes, José; Obregón Zegarra, Eva Haydee

    2012-12-01

    Abnormal uterine bleeding is a public health problem prevalence exceeded only by abnormal vaginal discharge as a reason for medical consultation. To describe the findings reported by the Hysteroscopy clinic of the Hospital GEA Gonzalez on patients with Abnormal Uterine bleeding diagnosis. Retrospective, transversal, descriptive study. The total 2546 records of those patient that were evaluated by Office Hysteroscopic between January 2007 and December 2008 on the Hysteroscopy Clinic of Hospital Manuel GEA Gonzalez, then we selected the 1482 records of those patients that were sended because of an Abnormal Uterine bleeding condition. We descrive the frequencies of the diagnosis and its interrelation with the age of the patients. We also report the therapeutical interventions during office hysteroscopy. The mean age of the patients was 42.15 +/- 9.30 years (from 12 a 92 years); the age groups of patients that belonged to 40-44 years and 45-49 years are the most frequent patient and they represent the 25% y el 23.3% of the records. The abnormal findings occurred on the 66% de of the patients. Those patients of 65 years old and older do not have any report of normal cavities, all of then have abnormal findings. The leiomyoma (26.9%) and the endometrial polyps (27.3%) were the most frequent findings. The postmenopausal bleeding had a rate of 90.9% abnormal findings and in this group of patients the most frequent diagnosis was atrophic endometrium (32.2%) and polyps (24.3%). Besides that the office hysteroscopy show its therapeutical usefulness because of the 67% and 77.5% of polipectomy perform for endometrial and cervical polyps respectively The office Hysteroscopy is a well tolerated diagnosis and therapeutic method that is useful for any women with abnormal uterine bleeding condition and it is the ideal technique for the examination of abnormal uterine bleeding in postmenopausal women... The office hysteroscopy is a efficient cost-effective and cost-benefic method for

  12. Specimen-specific modeling of hip fracture pattern and repair.

    Science.gov (United States)

    Ali, Azhar A; Cristofolini, Luca; Schileo, Enrico; Hu, Haixiang; Taddei, Fulvia; Kim, Raymond H; Rullkoetter, Paul J; Laz, Peter J

    2014-01-22

    Hip fracture remains a major health problem for the elderly. Clinical studies have assessed fracture risk based on bone quality in the aging population and cadaveric testing has quantified bone strength and fracture loads. Prior modeling has primarily focused on quantifying the strain distribution in bone as an indicator of fracture risk. Recent advances in the extended finite element method (XFEM) enable prediction of the initiation and propagation of cracks without requiring a priori knowledge of the crack path. Accordingly, the objectives of this study were to predict femoral fracture in specimen-specific models using the XFEM approach, to perform one-to-one comparisons of predicted and in vitro fracture patterns, and to develop a framework to assess the mechanics and load transfer in the fractured femur when it is repaired with an osteosynthesis implant. Five specimen-specific femur models were developed from in vitro experiments under a simulated stance loading condition. Predicted fracture patterns closely matched the in vitro patterns; however, predictions of fracture load differed by approximately 50% due to sensitivity to local material properties. Specimen-specific intertrochanteric fractures were induced by subjecting the femur models to a sideways fall and repaired with a contemporary implant. Under a post-surgical stance loading, model-predicted load sharing between the implant and bone across the fracture surface varied from 59%:41% to 89%:11%, underscoring the importance of considering anatomic and fracture variability in the evaluation of implants. XFEM modeling shows potential as a macro-level analysis enabling fracture investigations of clinical cohorts, including at-risk groups, and the design of robust implants. © 2013 Published by Elsevier Ltd.

  13. Quantitative Clinical Imaging Methods for Monitoring Intratumoral Evolution.

    Science.gov (United States)

    Kim, Joo Yeun; Gatenby, Robert A

    2017-01-01

    images in landscape ecology and, with appropriate application of Darwinian first principles and sophisticated image analytic methods, can be used to estimate regional variations in the molecular properties of cancer cells.We have initially examined this technique in glioblastoma, a malignant brain neoplasm which is morphologically complex and notorious for a fast progression from diagnosis to recurrence and death, making a suitable subject of noninvasive, rapidly repeated assessment of intratumoral evolution. Quantitative imaging analysis of routine clinical MRIs from glioblastoma has identified macroscopic morphologic characteristics which correlate with proteogenomics and prognosis. The key to the accurate detection and forecasting of intratumoral evolution using quantitative imaging analysis is likely to be in the understanding of the synergistic interactions between observable intratumoral subregions and the resulting tumor behavior.

  14. Clinical observation of two operation methods for neovascular glaucoma

    Directory of Open Access Journals (Sweden)

    Peng Zhang

    2013-11-01

    Full Text Available AIM: To evaluate the clinical effect of two different surgical treatments for neovascular glaucoma(NVG.METHODS: A total of 30 NVG inpatients(30 eyesat our hospital from April 2008 to December 2011 were reviewed. Patients were divided into two groups according to the different surgical treatments. In group A, 12 cases(12 eyeswere treated with Ahmed glaucoma valve(AGVimplantation and in group B, 18 cases(18 eyeswere treated with semiconductor diode laser photocoagulation transscleral cyclophotocoagulation(TSCPC. Intraocular pressure, visual acuity and complications were compared between two groups postoperatively.RESULTS: The postoperative IOP was significantly lower in each group(PPP>0.05in IOP 1 month after surgery. Visual acuity: in group A, the visual acuity was improved in 3 eyes, unchanged in 7 eyes and worsened in 2 eyes.; in group B, the visual acuity was improved in 3 eyes, unchanged in 12 eyes and worsened in 3 eyes. Postoperative complications: in group A, eyeball pain and corneal edema were found in 5 cases(41.7%, shallow anterior chamber in 3 cases(25%, anterior chamber fibroid exudation in 2 cases(16.7%, hyphema in 3 cases(25%; in group B, eyeball pain atearly stage after surgery were found in 10 cases(55.6% , corneal edema in 11 cases(61.1%, anterior chamber fibroid exudation in 5 cases(27.8%, hyphema in 6 cases(33.3%.CONCLUSION: AGV implantation and TSCPC are both effective surgical treatment methods for NVG. AGV implantation is a filtration surgery, which is relatively safe. TSCPC is more economical and suitable for glaucoma of advanced or absolute stage.

  15. [Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

    Science.gov (United States)

    Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

    2006-01-01

    Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory.

  16. Observation and control of hepatic specimens with MRI and MRS

    International Nuclear Information System (INIS)

    Ludescher, B.; Wietek, B.; Machann, J.; Graf, H.; Schick, F.; Subke, J.; Claussen, C.D.

    2004-01-01

    Purpose: The purpose of this study was to observe the process of fixation in liver specimens non-invasively by means of magnetic resonance. The fixation process of several formaldehyde-containing solutions was monitored with MRI and MRS at two different temperatures. Materials and Methods: Liver specimens were conserved in aqueous fixative solutions containing formaldehyde concentrations of 0.7, 1.8, 4 and 7.2% and at different temperatures of 5 C and 20 C. MRI was performed with T1-, T2- and PD-weighted TSE sequences, a 2D FLASH-sequence with and without magnetization transfer, and a FISP 3D-sequence on a clinical 1.5 Tesla MR whole-body unit, and MRS with 1 H-spectroscopic methods (STEAM-sequence) on a 3 Tesla MR whole-body unit. Results: The diffusion of formaldehyde into the tissue was best identified on PD- and T1-weighted images as a band under the liver surface with increasing thickness, penetrating especially fast during the first three days. Spectroscopic measurements revealed the rising formaldehyde concentration in the inner part of the organs. Temperature had no significant influence on the velocity of immersing, but cooling conditions produced less gas-filled caverns due to reduced undesired decomposition processes. Conclusion: The spatial and temporal process of ongoing fixation in the liver can be monitored by MRI. MRS confirms a rising concentration of formaldehyde during ongoing fixation. (orig.) [de

  17. An introduction to clinical microeconomic analysis: purposes and analytic methods.

    Science.gov (United States)

    Weintraub, W S; Mauldin, P D; Becker, E R

    1994-06-01

    The recent concern with health care economics has fostered the development of a new discipline that is generally called clinical microeconomics. This is a discipline in which microeconomic methods are used to study the economics of specific medical therapies. It is possible to perform stand alone cost analyses, but more profound insight into the medical decision making process may be accomplished by combining cost studies with measures of outcome. This is most often accomplished with cost-effectiveness or cost-utility studies. In cost-effectiveness studies there is one measure of outcome, often death. In cost-utility studies there are multiple measures of outcome, which must be grouped together to give an overall picture of outcome or utility. There are theoretical limitations to the determination of utility that must be accepted to perform this type of analysis. A summary statement of outcome is quality adjusted life years (QALYs), which is utility time socially discounted survival. Discounting is used because people value a year of future life less than a year of present life. Costs are made up of in-hospital direct, professional, follow-up direct, and follow-up indirect costs. Direct costs are for medical services. Indirect costs reflect opportunity costs such as lost time at work. Cost estimates are often based on marginal costs, or the cost for one additional procedure of the same type. Finally an overall statistic may be generated as cost per unit increase in effectiveness, such as dollars per QALY.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Standard guide for preparation of metallographic specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2011-01-01

    1.1 The primary objective of metallographic examinations is to reveal the constituents and structure of metals and their alloys by means of a light optical or scanning electron microscope. In special cases, the objective of the examination may require the development of less detail than in other cases but, under nearly all conditions, the proper selection and preparation of the specimen is of major importance. Because of the diversity in available equipment and the wide variety of problems encountered, the following text presents for the guidance of the metallographer only those practices which experience has shown are generally satisfactory; it cannot and does not describe the variations in technique required to solve individual specimen preparation problems. Note 1—For a more extensive description of various metallographic techniques, refer to Samuels, L. E., Metallographic Polishing by Mechanical Methods, American Society for Metals (ASM) Metals Park, OH, 3rd Ed., 1982; Petzow, G., Metallographic Etchin...

  19. Blood specimen labelling errors: Implications for nephrology nursing practice.

    Science.gov (United States)

    Duteau, Jennifer

    2014-01-01

    Patient safety is the foundation of high-quality health care, as recognized both nationally and worldwide. Patient blood specimen identification is critical in ensuring the delivery of safe and appropriate care. The practice of nephrology nursing involves frequent patient blood specimen withdrawals to treat and monitor kidney disease. A critical review of the literature reveals that incorrect patient identification is one of the major causes of blood specimen labelling errors. Misidentified samples create a serious risk to patient safety leading to multiple specimen withdrawals, delay in diagnosis, misdiagnosis, incorrect treatment, transfusion reactions, increased length of stay and other negative patient outcomes. Barcode technology has been identified as a preferred method for positive patient identification leading to a definitive decrease in blood specimen labelling errors by as much as 83% (Askeland, et al., 2008). The use of a root cause analysis followed by an action plan is one approach to decreasing the occurrence of blood specimen labelling errors. This article will present a review of the evidence-based literature surrounding blood specimen labelling errors, followed by author recommendations for completing a root cause analysis and action plan. A failure modes and effects analysis (FMEA) will be presented as one method to determine root cause, followed by the Ottawa Model of Research Use (OMRU) as a framework for implementation of strategies to reduce blood specimen labelling errors.

  20. A novel rapid genotyping technique for Collie eye anomaly: SYBR Green-based real-time polymerase chain reaction method applicable to blood and saliva specimens on Flinders Technology Associates filter paper.

    Science.gov (United States)

    Chang, Hye-Sook; Mizukami, Keijiro; Yabuki, Akira; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Arai, Toshiro; Yamato, Osamu

    2010-09-01

    Collie eye anomaly (CEA) is a canine inherited ocular disease that shows a wide variety of manifestations and severity of clinical lesions. Recently, a CEA-associated mutation was reported, and a DNA test that uses conventional polymerase chain reaction (PCR) has now become available. The objective of the current study was to develop a novel rapid genotyping technique by using SYBR Green-based real-time PCR for future large-scale surveys as a key part in the strategy to eradicate CEA by selective breeding. First, a SYBR Green-based real-time PCR assay for genotyping of CEA was developed and evaluated by using purified DNA samples from normal, carrier, and affected Border Collies in which genotypes had previously been determined by conventional PCR. This real-time PCR assay demonstrated appropriate amplifications in all genotypes, and the results were consistent with those of conventional PCR. Second, the availability of Flinders Technology Associates filter paper (FTA card) as DNA templates for the real-time PCR assay was evaluated by using blood and saliva specimens to determine suitability for CEA screening. DNA-containing solution prepared from a disc of blood- or saliva-spotted FTA cards was available directly as templates for the real-time PCR assay when the volume of solution was 2.5% of the PCR mixture. In conclusion, SYBR Green-based real-time PCR combined with FTA cards is a rapid genotyping technique for CEA that can markedly shorten the overall time required for genotyping as well as simplify the sample preparation. Therefore, this newly developed technique suits large-scale screening in breeding populations of Collie-related breeds.

  1. Wildlife specimen collection, preservation, and shipment

    Science.gov (United States)

    White, C. LeAnn; Dusek, Robert J.; Franson, J. Christian; Friend, Milton; Gibbs, Samantha E.J.; Wild, Margaret A.

    2015-01-01

    Specimens are used to provide supporting information leading to the determination of the cause of disease or death in wildlife and for disease monitoring or surveillance. Commonly used specimens for wildlife disease investigations include intact carcasses, tissues from carcasses, euthanized or moribund animals, parasites, ingested food, feces, or environmental samples. Samples from live animals or the environment (e.g., contaminated feed) in the same vicinity as a mortality event also may be helpful. The type of specimen collected is determined by availability of samples and biological objectives. Multiple fresh, intact carcasses from affected species are the most useful in establishing a cause for a mortality event. Submission of entire carcasses allows observation of gross lesions and abnormalities, as well as disease testing of multiple tissues. Samples from live animals may be more appropriate when sick animals cannot be euthanized (e.g., threatened or endangered species) or for research and monitoring projects examining disease or agents circulating in apparently healthy animals or those not exhibiting clinical signs. Samples from live animals may include collections of blood, hair, feathers, feces, or ectoparasites, or samples obtained by swabbing lesions or orifices. Photographs and videos are useful additions for recording field and clinical signs and conveying conditions at the site. Collection of environmental samples (e.g., feces, water, feed, or soil) may be appropriate when animals cannot be captured for sampling or the disease agent may persist in the environment. If lethal collection is considered necessary, biologists should refer to the policies, procedures, and permit requirements of their institution/facility and the agency responsible for species management (U.S. Fish and Wildlife Service or State natural resource agency) prior to use in the field. If threatened or endangered species are found dead, or there is evidence of illegal take, field

  2. Clinical evaluation of β-tubulin real-time PCR for rapid diagnosis of dermatophytosis, a comparison with mycological methods.

    Science.gov (United States)

    Motamedi, Marjan; Mirhendi, Hossein; Zomorodian, Kamiar; Khodadadi, Hossein; Kharazi, Mahboobeh; Ghasemi, Zeinab; Shidfar, Mohammad Reza; Makimura, Koichi

    2017-10-01

    Following our previous report on evaluation of the beta tubulin real-time PCR for detection of dermatophytosis, this study aimed to compare the real-time PCR assay with conventional methods for the clinical assessment of its diagnostic performance. Samples from a total of 853 patients with suspected dermatophyte lesions were subjected to direct examination (all samples), culture (499 samples) and real-time PCR (all samples). Fungal DNA was extracted directly from clinical samples using a conical steel bullet, followed by purification with a commercial kit and subjected to the Taq-Man probe-based real-time PCR. The study showed that among the 499 specimens for which all three methods were used, 156 (31.2%), 128 (25.6%) and 205 (41.0%) were found to be positive by direct microscopy, culture and real-time PCR respectively. Real-time PCR significantly increased the detection rate of dermatophytes compared with microscopy (288 vs 229) with 87% concordance between the two methods. The sensitivity, specificity, positive predictive value, and negative predictive value of the real-time PCR was 87.5%, 85%, 66.5% and 95.2% respectively. Although real-time PCR performed better on skin than on nail samples, it should not yet fully replace conventional diagnosis. © 2017 Blackwell Verlag GmbH.

  3. The effect of specimen and flaw dimensions on fracture toughness

    International Nuclear Information System (INIS)

    Nevalainen, M.J.

    1997-06-01

    The effect of the specimen size and geometry on fracture toughness has been investigated both by experimental tests and computational analyses. The methods for constraint description, namely T-stress, Q-parameter and Small-Scale Yielding Correction (SSYC) have been compared and applied for various geometries. A statistical treatment for the specimen thickness effect on cleavage fracture toughness has been investigated. Elliptical surface cracks were compared with straight-thickness cracks and a method for crack shape correction was presented. Based on the results, the differences in apparent fracture toughness values obtained from various specimen configurations can be better understood and taken into account

  4. Caries assessment: establishing mathematical link of clinical and benchtop method

    Science.gov (United States)

    Amaechi, Bennett T.

    2009-02-01

    It is well established that the development of new technologies for early detection and quantitative monitoring of dental caries at its early stage could provide health and economic benefits ranging from timely preventive interventions to reduction of the time required for clinical trials of anti-caries agents. However, the new technologies currently used in clinical setting cannot assess and monitor caries using the actual mineral concentration within the lesion, while a laboratory-based microcomputed tomography (MCT) has been shown to possess this capability. Thus we envision the establishment of mathematical equations relating the measurements of each of the clinical technologies to that of MCT will enable the mineral concentration of lesions detected and assessed in clinical practice to be extrapolated from the equation, and this will facilitate preventitive care in dentistry to lower treatment cost. We utilize MCT and the two prominent clinical caries assessment devices (Quantitative Light-induced Fluorescence [QLF] and Diagnodent) to longitudinally monitor the development of caries in a continuous flow mixed-organisms biofilm model (artificial mouth), and then used the collected data to establish mathematical equation relating the measurements of each of the clinical technologies to that of MCT. A linear correlation was observed between the measurements of MicroCT and that of QLF and Diagnodent. Thus mineral density in a carious lesion detected and measured using QLF or Diagnodent can be extrapolated using the developed equation. This highlights the usefulness of MCT for monitoring the progress of an early caries being treated with therapeutic agents in clinical practice or trials.

  5. A cylindrical specimen holder for electron cryo-tomography

    International Nuclear Information System (INIS)

    Palmer, Colin M.; Löwe, Jan

    2014-01-01

    The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the “missing wedge” problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. - Highlights: • The missing wedge is a serious problem for electron cryo-tomography. • Cylindrical specimens allow the missing wedge to be eliminated. • Carbon nanopipettes can be used as cylindrical holders for tomography of frozen-hydrated specimens. • Cryo-tomography of cylindrical biological samples demonstrates a reduction of deleterious effects associated with the missing wedge

  6. A new concept and a comprehensive evaluation of SYSMEX UF-1000i  flow cytometer to identify culture-negative urine specimens in patients with UTI.

    Science.gov (United States)

    Monsen, T; Ryden, P

    2017-09-01

    Urinary tract infections (UTIs) are among the most common bacterial infections in men and urine culture is gold standard for diagnosis. Considering the high prevalence of culture-negative specimens, any method that identifies such specimens is of interest. The aim was to evaluate a new screening concept for flow cytometry analysis (FCA). The outcomes were evaluated against urine culture, uropathogen species and three conventional screening methods. A prospective, consecutive study examined 1,312 urine specimens, collected during January and February 2012. The specimens were analyzed using the Sysmex UF1000i FCA. Based on the FCA data culture negative specimens were identified in a new model by use of linear discriminant analysis (FCA-LDA). In total 1,312 patients were included. In- and outpatients represented 19.6% and 79.4%, respectively; 68.3% of the specimens originated from women. Of the 610 culture-positive specimens, Escherichia coli represented 64%, enterococci 8% and Klebsiella spp. 7%. Screening with FCA-LDA at 95% sensitivity identified 42% (552/1312) as culture negative specimens when UTI was defined according to European guidelines. The proposed screening method was either superior or similar in comparison to the three conventional screening methods. In conclusion, the proposed/suggested and new FCA-LDA screening method was superior or similar to three conventional screening methods. We recommend the proposed screening method to be used in clinic to exclude culture negative specimens, to reduce workload, costs and the turnaround time. In addition, the FCA data may add information that enhance handling and support diagnosis of patients with suspected UTI pending urine culture [corrected].

  7. Clinical study of Whole Heart MRCA. Evaluation of acquisition method

    International Nuclear Information System (INIS)

    Iwai, Mitsuhiro; Tateishi, Toshiki; Takeda, Soji; Hayashi, Ryuji

    2006-01-01

    In CT coronary angiography (CTCA), image reconstruction is performed using the optimal phase with either the relative or the absolute delaying methods. Whole Heart MRCA is generally considered to set up the signal acquisition time when is only the middle-diastolic phase in the standstill state of the right coronary artery per cardiac beat as the conventional method. However, in the case of high cardiac beats, such as arrhythmia respiratory instability, etc., image acquisition can take long time and a good quality image may not be maintained. We use not only the middle-diastolic acquisition (conventional method) but also the systolic phase acquisition (systolic phase method) and the shortening method (total acquisition shortening (TASH) method). The aim of this study was to examine the depiction ability and the image quality in the images of 585 Whole Heart MRCA(s) acquired by three methods described above. Seventy percent of all exhibited good quality images in the middle of extension. The remaining images obtained by the systolic phase (at the time of high cardiac beats) and the TASH methods (respiratory instability etc.) were better than those obtained using the conventional method. The sensitivity and the specificity of coronary stenosis (75%) in the TASH, systolic-phase and the conventional methods were 90% and 96%, 96% and 97%, and 87% and 96%, respectively. These findings proved that no significant differences in the depiction of the coronary stenosis were apparent using the three methods. It was concluded that it was necessary to establish suitable signal time acquisition and to change the acquisition method depending on cardiac beats or the state of breathing for Whole Heart MRCA. (author)

  8. Milestones: a rapid assessment method for the Clinical Competency Committee

    OpenAIRE

    Nabors, Christopher; Forman, Leanne; Peterson, Stephen J.; Gennarelli, Melissa; Aronow, Wilbert S.; DeLorenzo, Lawrence; Chandy, Dipak; Ahn, Chul; Sule, Sachin; Stallings, Gary W.; Khera, Sahil; Palaniswamy, Chandrasekar; Frishman, William H.

    2016-01-01

    Introduction Educational milestones are now used to assess the developmental progress of all U.S. graduate medical residents during training. Twice annually, each program?s Clinical Competency Committee (CCC) makes these determinations and reports its findings to the Accreditation Council for Graduate Medical Education (ACGME). The ideal way to conduct the CCC is not known. After finding that deliberations reliant upon the new milestones were time intensive, our internal medicine residency pr...

  9. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Directory of Open Access Journals (Sweden)

    Roberta Zappacosta

    2013-01-01

    Full Text Available Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+. p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure.

  10. Chromogenic In Situ Hybridization and p16/Ki67 Dual Staining on Formalin-Fixed Paraffin-Embedded Cervical Specimens: Correlation with HPV-DNA Test, E6/E7 mRNA Test, and Potential Clinical Applications

    Science.gov (United States)

    Zappacosta, Roberta; Colasante, Antonella; Viola, Patrizia; D'Antuono, Tommaso; Lattanzio, Giuseppe; Capanna, Serena; Gatta, Daniela Maria Pia; Rosini, Sandra

    2013-01-01

    Although HPV-DNA test and E6/E7 mRNA analyses remain the current standard for the confirmation of human papillomavirus (HPV) infections in cytological specimens, no universally adopted techniques exist for the detection of HPV in formalin-fixed paraffin-embedded samples. Particularly, in routine laboratories, molecular assays are still time-consuming and would require a high level of expertise. In this study, we investigated the possible use of a novel HPV tyramide-based chromogenic in situ hybridization (CISH) technology to locate HPV on tissue specimens. Then, we evaluate the potential usefulness of p16INK4a/Ki-67 double stain on histological samples, to identify cervical cells expressing HPV E6/E7 oncogenes. In our series, CISH showed a clear signal in 95.2% of the specimens and reached a sensitivity of 86.5%. CISH positivity always matched with HPV-DNA positivity, while 100% of cases with punctated signal joined with cervical intraepithelial neoplasia grade 2 or worse (CIN2+). p16/Ki67 immunohistochemistry gave an interpretable result in 100% of the cases. The use of dual stain significantly increased the agreement between pathologists, which reached 100%. Concordance between dual stain and E6/E7 mRNA test was 89%. In our series, both CISH and p16INK4a/Ki67 dual stain demonstrated high grade of performances. In particular, CISH would help to distinguish episomal from integrated HPV, in order to allow conclusions regarding the prognosis of the lesion, while p16INK4a/Ki67 dual stain approach would confer a high level of standardization to the diagnostic procedure. PMID:24369532

  11. Advances in Probes and Methods for Clinical EPR Oximetry

    Science.gov (United States)

    Hou, Huagang; Khan, Nadeem; Jarvis, Lesley A.; Chen, Eunice Y.; Williams, Benjamin B.; Kuppusamy, Periannan

    2015-01-01

    EPR oximetry, which enables reliable, accurate, and repeated measurements of the partial pressure of oxygen in tissues, provides a unique opportunity to investigate the role of oxygen in the pathogenesis and treatment of several diseases including cancer, stroke, and heart failure. Building on significant advances in the in vivo application of EPR oximetry for small animal models of disease, we are developing suitable probes and instrumentation required for use in human subjects. Our laboratory has established the feasibility of clinical EPR oximetry in cancer patients using India ink, the only material presently approved for clinical use. We now are developing the next generation of probes, which are both superior in terms of oxygen sensitivity and biocompatibility including an excellent safety profile for use in humans. Further advances include the development of implantable oxygen sensors linked to an external coupling loop for measurements of deep-tissue oxygenations at any depth, overcoming the current limitation of 10 mm. This paper presents an overview of recent developments in our ability to make meaningful measurements of oxygen partial pressures in human subjects under clinical settings. PMID:24729217

  12. Bibliography of clinical research in malaysia: methods and brief results.

    Science.gov (United States)

    Teng, C L; Zuhanariah, M N; Ng, C S; Goh, C C

    2014-08-01

    This article describes the methodology of this bibliography. A search was conducted on the following: (1) bibliographic databases (PubMed, Scopus, and other databases) using search terms that maximize the retrieval of Malaysian publications; (2) Individual journal search of Malaysian healthrelated journals; (3) A targeted search of Google and Google Scholar; (4) Searching of Malaysian institutional repositories; (5) Searching of Ministry of Health and Clinical Research Centre website. The publication years were limited to 2000- 2013. The citations were imported or manually entered into bibliographic software Refworks. After removing duplicates, and correcting data entry errors, PubMed's Medical Subject Headings (MeSH terms) were added. Clinical research is coded using the definition "patient-oriented-research or research conducted with human subjects (or on material of human origin) for which the investigator directly interacts with the human subjects at some point during the study." A bibliography of citations [n=2056] that fit the criteria of clinical research in Malaysia in selected topics within five domains was generated: Cancers [589], Cardiovascular diseases [432], Infections [795], Injuries [142], and Mental Health [582]. This is done by retrieving citations with the appropriate MESH terms, as follow: For cancers (Breast Neoplasms; Colorectal Neoplasms; Uterine Cervical Neoplasms), for cardiovascular diseases (Coronary Disease; Hypertension; Stroke), for infections (Dengue; Enterovirus Infections, HIV Infections; Malaria; Nipah Virus; Tuberculosis), for injuries (Accidents, Occupational; Accidents, Traffic; Child Abuse; Occupational Injuries), for mental health (Depression; Depressive Disorder; Depressive Disorder, Major; Drug Users; Psychotic Disorders; Suicide; Suicide, Attempted; Suicidal Ideation; Substance- Related Disorders).

  13. Applications of mixed-methods methodology in clinical pharmacy research.

    Science.gov (United States)

    Hadi, Muhammad Abdul; Closs, S José

    2016-06-01

    Introduction Mixed-methods methodology, as the name suggests refers to mixing of elements of both qualitative and quantitative methodologies in a single study. In the past decade, mixed-methods methodology has gained popularity among healthcare researchers as it promises to bring together the strengths of both qualitative and quantitative approaches. Methodology A number of mixed-methods designs are available in the literature and the four most commonly used designs in healthcare research are: the convergent parallel design, the embedded design, the exploratory design, and the explanatory design. Each has its own unique advantages, challenges and procedures and selection of a particular design should be guided by the research question. Guidance on designing, conducting and reporting mixed-methods research is available in the literature, so it is advisable to adhere to this to ensure methodological rigour. When to use it is best suited when the research questions require: triangulating findings from different methodologies to explain a single phenomenon; clarifying the results of one method using another method; informing the design of one method based on the findings of another method, development of a scale/questionnaire and answering different research questions within a single study. Two case studies have been presented to illustrate possible applications of mixed-methods methodology. Limitations Possessing the necessary knowledge and skills to undertake qualitative and quantitative data collection, analysis, interpretation and integration remains the biggest challenge for researchers conducting mixed-methods studies. Sequential study designs are often time consuming, being in two (or more) phases whereas concurrent study designs may require more than one data collector to collect both qualitative and quantitative data at the same time.

  14. Molecular markers: Implications for cytopathology and specimen collection.

    Science.gov (United States)

    VanderLaan, Paul A

    2015-08-01

    Cytologic specimens obtained through minimally invasive biopsy techniques are increasingly being used as principle diagnostic specimens for tumors arising in multiple sites. The number and scope of ancillary tests performed on these specimens have grown substantially over the past decade, including many molecular markers that not only can aid in formulating accurate and specific diagnoses but also can provide prognostic or therapeutic information to help direct clinical decisions. Thus, the cytopathologist needs to ensure that adequate material is collected and appropriately processed for the study of relevant molecular markers, many of which are specific to tumor site. This brief review covers considerations for effective cytologic specimen collection and processing to ensure diagnostic and testing success. In addition, a general overview is provided of molecular markers pertinent to tumors from a variety of sites. The recognition of these established and emerging molecular markers by cytopathologists is an important step toward realizing the promise of personalized medicine. © 2015 American Cancer Society.

  15. Fracture toughness measurements with subsize disk compact specimens

    International Nuclear Information System (INIS)

    Alexander, D.J.

    1992-01-01

    Special fixtures and test methods are necessary to facilitate the fracture toughness testing of small disk compact specimens of irradiated candidate materials for first-wall fusion applications. New methods have been developed for both the unloading compliance and potential drop techniques of monitoring crack growth. Provisions have been made to allow the necessary probes and instrumentation to be installed remotely using manipulators for testing of irradiated specimens in a hot cell. Laboratory trials showed that both unloading compliance and potential drop gave useful results. Both techniques gave similar data, and predicted the final crack extension within allowable limits. The results from the small disk compact specimens were similar to results from conventional compact specimen 12.7 mm thick. However, the slopes of the J-R curves from the larger specimens were lower, suggesting that the smaller disk compact specimens may have lost some constraint due to their size. The testing shows that it should be possible to generate useful J-R curve fracture toughness data from the small disk compact specimens

  16. Fracture toughness measurements with subsize disk compact specimens

    International Nuclear Information System (INIS)

    Alexander, D.J.

    1992-01-01

    Special fixtures and test methods have been developed for testing small disk compact specimens (12.5 mm diam by 4.6 mm thick). Both unloading compliance and potential drop methods have been used to monitor crack extension during the J-integral resistance (J-R) curve testing. Provisions have been made to allow the necessary probes and instrumentation to be installed remotely using manipulators for testing of irradiated specimens in a hat cell. Laboratory trials showed that both unloading compliance and potential drop gave useful results. Both techniques gave similar data, and predicted the final crack extension within allowable limits. The results from the small disk compact specimens were similar to results from conventional compact specimens 12.7-mm thick. However, the slopes of the J-R curves from the larger specimens were lower, suggesting that the smaller disk compact specimens may have lost some constraint due to their size. The testing shows that it should be possible to generate useful J-R curve fracture toughness data from the small disk compact specimens

  17. COMPARATIVE ANALYSIS OF METHODS FOR IDENTIFICATION OF NONTUBERCULOUS MYCOBACTERIA ISOLATED FROM CLINICAL MATERIAL

    Directory of Open Access Journals (Sweden)

    A. V. Lyamin

    2017-01-01

    Full Text Available Recently there has been a significant increase in the incidence of mycobacteriosis, which is due to an increase in the proportion of immunosuppressed patients, the presence of these various comorbid conditions, as well as the improvement of diagnostic methods. Selecting the most accurate method of identification is extremely important in determining treatment strategy of patients. The aim of the study was to conduct a comparative analysis of modern methods of identification NTMB isolated from clinical specimens in 2015 in the Samara region. The work was carried out identification of 78 strains of microorganisms. Laboratory diagnosis was carried out using the DNA hybridization method and MALDI-ToF mass spectrometry. When microbial identification using MALDI-ToF mass spectrometry was isolated 16 strains (20.5% M. kansasii; 11 strains (14.1% M. avium and M. fortuitum; 9 strains (11.5% M. gordonae; strain 3 (3.8% M. peregrinum, M. szulgai, M. chimera intracellulare group, strain 2 (2.6% M. abscessus, M. septicum, M. paragordonae, M. senegalence, 1 strain (1.3% M. chelonae, M. frederiksbergense, M. monacense, M. lentiflavum. By using mass spectrometry, it was identified 15 types NTMB compared with 9 types — by DNA hybridization. Full match identification results was observed only in 45 (57.7% strains of divergent strains were found in 16 (20.5%. Most often when using the DNA hybridization method, discrepancy was detected in slow-growing cultures (9 strains with a predominance of microorganisms identified as M. gordonae. Among the representatives of fast-growing NTMB, seven investigations were identified in the identification, more often among representatives of the M. fortuitum and M. peregrinum groups. Particular attention should be paid to the identification of the M. kansasii strain by a molecular genetic method, which mass spectrometry was defined as M. bovis. Both cultures of M. tuberculosis complex, which were identified by MALDI

  18. Clinical evaluation and validation of laboratory methods for the diagnosis of Bordetella pertussis infection: Culture, polymerase chain reaction (PCR) and anti-pertussis toxin IgG serology (IgG-PT).

    Science.gov (United States)

    Lee, Adria D; Cassiday, Pamela K; Pawloski, Lucia C; Tatti, Kathleen M; Martin, Monte D; Briere, Elizabeth C; Tondella, M Lucia; Martin, Stacey W

    2018-01-01

    The appropriate use of clinically accurate diagnostic tests is essential for the detection of pertussis, a poorly controlled vaccine-preventable disease. The purpose of this study was to estimate the sensitivity and specificity of different diagnostic criteria including culture, multi-target polymerase chain reaction (PCR), anti-pertussis toxin IgG (IgG-PT) serology, and the use of a clinical case definition. An additional objective was to describe the optimal timing of specimen collection for the various tests. Clinical specimens were collected from patients with cough illness at seven locations across the United States between 2007 and 2011. Nasopharyngeal and blood specimens were collected from each patient during the enrollment visit. Patients who had been coughing for ≤ 2 weeks were asked to return in 2-4 weeks for collection of a second, convalescent blood specimen. Sensitivity and specificity of each diagnostic test were estimated using three methods-pertussis culture as the "gold standard," composite reference standard analysis (CRS), and latent class analysis (LCA). Overall, 868 patients were enrolled and 13.6% were B. pertussis positive by at least one diagnostic test. In a sample of 545 participants with non-missing data on all four diagnostic criteria, culture was 64.0% sensitive, PCR was 90.6% sensitive, and both were 100% specific by LCA. CRS and LCA methods increased the sensitivity estimates for convalescent serology and the clinical case definition over the culture-based estimates. Culture and PCR were most sensitive when performed during the first two weeks of cough; serology was optimally sensitive after the second week of cough. Timing of specimen collection in relation to onset of illness should be considered when ordering diagnostic tests for pertussis. Consideration should be given to including IgG-PT serology as a confirmatory test in the Council of State and Territorial Epidemiologists (CSTE) case definition for pertussis.

  19. Is one sputum specimen as good as two during follow-up cultures for monitoring multi drug resistant tuberculosis patients in India?

    Directory of Open Access Journals (Sweden)

    Sharath Burugina Nagaraja

    Full Text Available BACKGROUND: In India, the Revised National Tuberculosis Control Programme (RNTCP has adopted the strategy of examining two specimens during follow-up culture examinations to monitor the treatment response of multi-drug resistant tuberculosis (MDR-TB patients. OBJECTIVES: To determine the incremental yield of the second sputum specimen during follow-up culture examinations among patients with MDR-TB and the effect on case management on changing from two to one specimen follow-up strategy. METHODS: A cross sectional record review of MDR-TB patients registered during 2008-09 under RNTCP was undertaken in three MDR-TB treatment sites of India. RESULTS: Of 1721 pairs of follow-up sputum culture examinations done among 220 MDR-TB patients, 451(26% were positive with either of the two specimens; 29(1.7% were culture positive only on the second specimen indicating the incremental yield. To detect one additional culture positive result on the second specimen, 59 specimens needed to be processed. If we had examined only one specimen, we would have missed 29 culture-positive results. By current RNTCP guidelines, however, a single specimen policy would have altered case management in only 3(0.2% instances, where patients would have missed a one month extension of the intensive phase of MDR-TB treatment. There is no meaningful advantage in using two specimens for the monitoring of MDR-TB patients. A single specimen policy could be safely implemented with negligible clinical effect on MDR-TB patients and favourable resource implications for RNTCP.

  20. Notch effects in uniaxial tension specimens

    International Nuclear Information System (INIS)

    Delph, T.J.

    1979-03-01

    Results of a literature survey on the effect of notches on the time-dependent failure of uniaxial tension specimens at elevated temperatures are presented. Particular attention is paid to the failure of notched specimens containing weldments

  1. Measurements and Counts for Notacanthidae Specimens

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Taxonomic data were collected for specimens of deep-sea spiny eels (Notacanthidae) from the Hawaiian Ridge by Bruce C. Mundy. Specimens were collected off the north...

  2. Improved PID control for triaxial testing liquefied specimen

    DEFF Research Database (Denmark)

    Sabaliauskas, Tomas; Ibsen, Lars Bo

    Using a frictionless triaxial apparatus, sand specimens can be tested at relatively high axial strains, even while liquefying. However, liquefying specimens have extremely nonlinear stiffness, thus standard PID control does not perform well. To maintain control over applied loads, the PID...... controller was modified to adapt to disturbed soil states. The proposed methods expand the scope of testing towards options which are otherwise inaccessible by triaxial testing....

  3. The assessment of irritation using clinical methods and questionnaires

    DEFF Research Database (Denmark)

    Kjærgaard, Søren K.; Hogdson, M.

    2001-01-01

    , and hyperemia. Methods for detecting nasal mucosa irritation include measuring swelling of the nasal mucosa, peak airflows through the nose, acoustic rhinometry, and rhinostereometry, which measures thickness of the anterior nasal turbinate. Questionnaires are useful for defining a set of symptoms in an attempt...

  4. Investigation of the clinical features and therapeutic methods for the ...

    African Journals Online (AJOL)

    Purpose: To establish if there are different classes of inflammatory lacrimal punctum diseases (ILPDs) and to examine the various strategies by which they can be managed therapeutically. Methods: Two hundred and fifty nine (259) patients with inflammatory punctum lacrimal disease were identified and used as subjects for ...

  5. Interleaved Carbon Minibeams: An Experimental Radiosurgery Method With Clinical Potential

    Energy Technology Data Exchange (ETDEWEB)

    Dilmanian, F. Avraham, E-mail: dilmanian@bnl.gov [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); Department of Radiation Oncology, Stony Brook University Medical Center, NY (United States); Department of Neurology, Stony Brook University Medical Center, NY (United States); Rusek, Adam [NASA Space Radiation Laboratory, Brookhaven National Laboratory, Upton, NY (United States); Fois, Giovanna R. [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); Physics Department, University of Cagliari, Sardinia (Italy); Olschowka, John [Department of Neurobiology and Anatomy, University of Rochester, Rochester, NY (United States); Desnoyers, Nicolle R. [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies (Country Unknown); Park, Jane Y. [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); College of Veterinary Medicine, Cornell University, Ithaca, NY (United States); Dioszegi, Istvan [Nonproliferation and National Security Department, Brookhaven National Laboratory, Upton, NY (United States); Dane, Bari; Wang Ruiliang [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); Tomasi, Dardo [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); National Institute on Alcoholism and Alcohol Abuse, Bethesda, MD (United States); Lee, Hedok [Medical Department, Brookhaven National Laboratory, Upton, NY (United States); Hurley, Sean D. [Department of Neurobiology and Anatomy, University of Rochester, Rochester, NY (United States); Coyle, Patricia K. [Department of Neurology, Stony Brook University Medical Center, NY (United States); Meek, Allen G. [Department of Radiation Oncology, Stony Brook University Medical Center, NY (United States); O' Banion, M. Kerry [Department of Neurobiology and Anatomy, University of Rochester, Rochester, NY (United States)

    2012-10-01

    Purpose: To evaluate the efficacy of 'interleaved carbon minibeams' for ablating a 6.5-mm target in a rabbit brain with little damage to the surrounding brain. The method is based on the well-established tissue-sparing effect of arrays of thin planes of radiation. Methods and Materials: Broad carbon beams from the National Aeronautics and Space Agency Space Radiation Facility at Brookhaven National Laboratory were segmented into arrays of parallel, horizontal, 0.3-mm-thick planar beams (minibeams). The minibeams' gradual broadening in tissues resulted in 0.525-mm beam thickness at the target's proximal side in the spread-out Bragg peak. Interleaving was therefore implemented by choosing a 1.05 mm beam spacing on-center. The anesthetized rabbit, positioned vertically on a stage capable of rotating about a vertical axis, was exposed to arrays from four 90 Degree-Sign angles, with the stage moving up by 0.525 mm in between. This produced a solid radiation field at the target while exposing the nontargeted tissues to single minibeam arrays. The target 'physical' absorbed dose was 40.2 Gy. Results: The rabbit behaved normally during the 6-month observation period. Contrast magnetic resonance imaging and hematoxylin and eosin histology at 6 months showed substantial focal target damage with little damage to the surrounding brain. Conclusion: We plan to evaluate the method's therapeutic efficacy by comparing it with broad-beam carbon therapy in animal models. The method's merits would combine those of carbon therapy (i.e., tight target dose because of the carbon's Bragg-peak, sharp dose falloff, and high relative biological effectiveness at the target), together with the method's low impact on the nontargeted tissues. The method's smaller impact on the nontargeted brain might allow carbon therapy at higher target doses and/or lower normal tissue impact, thus leading to a more effective treatment of radioresistant

  6. Instrumented impact testing machine with reduced specimen oscillation effects

    International Nuclear Information System (INIS)

    Rintamaa, R.; Rahka, K.; Wallin, K.

    1984-07-01

    Owing to small and inexpensive specimens the Charpy impact test is widely used in quality control and alloy development. Limitations in power reactor survellance capsules it is also widely used for safety analysis purposes. Instrumenting the tup and computerizing data acquisition, makes dynamic fracture mechanics data measurement possible and convenient. However, the dynamic effects (inertia forces, specimen oscillations) in the impact test cause inaccuracies in the recorded load-time diagram and hence diminish the reliability of the calculated dynamic fracture mechanics parameters. To decrease inaccuracies a new pendulum type of instrumented impact test apparatus has been developed and constructed in the Metals Laboratory of the Technical Research Centre of Finland. This tester is based on a new principle involving inverted test geometry. The purpose of the geometry inversion is to reduce inertia load and specimen oscillation effects. Further, the new impact tester has some other novel features: e.g. the available initia impact energy is about double compared to the conventional standard (300 J) impact tester allowing the use of larger (10 x 20 x 110 mm) bend specimens than normal Charpy specimens. Also, the rotation asix in the three point bending is nearly stationary making COD-measurements possible. An experimental test series is described in which the inertia effects and specimen oscillations are compared in the conventional and new impact tester utilizing Charpy V-notch specimens. Comparison of the two test geometries is also made with the aid of an analytical model using finite element method (FEM) analysis. (author)

  7. Histological evaluation of 400 cholecystectomy specimens

    Directory of Open Access Journals (Sweden)

    H Kumar

    2015-09-01

    Full Text Available Background: A majority of gallbladder specimens show changes associated with chronic cholecystitis; however few harbour a highly lethal carcinoma. This study was conducted to review the significant histopathological findings encountered in gallbladder specimens received in our laboratory.Materials and Methods: Four hundred cholecystectomy specimens were studied over a period of five years (May, 2002 to April, 2007 received at department of pathology, Kasturba Medical College, Mangalore, India. Results: Gallstones and associated diseases were more common in women in the 4th to 5th decade as compared to men with M: F ratio of 1:1.33. Maximum number of patients (28.25% being 41 to 50 years old. Histopathologically, the most common diagnosis was chronic cholecystitis (66.75%, followed by chronic active cholecystitis (20.25%, acute cholecystitis (6%, gangrenous cholecystitis (2.25%,xanthogranulomatous cholecystitis (0.50%, empyema (1%, mucocele (0.25%, choledochal cyst (0.25%, adenocarcinoma gallbladder (1.25% and  normal  gallbladders (1%.Conclusion: All lesions were found more frequently in women except chronic active cholecystitis. Gallstones were present in (80.25% cases, and significantly associated with various lesions (P value 0.009. Pigment stones were most common, followed by cholesterol stones and mixed stones. Adequate  sectioning  is  mandatory  in  all  cases  to  assess  epithelial changes arising from cholelithiasis and chronic cholecystitis as it has been known to progress to malignancy in some cases.

  8. Bright field electron microscopy of biological specimens

    International Nuclear Information System (INIS)

    Johansen, B.V.

    1976-01-01

    A preirradiation procedure is described which preserves negatively stained morphological features in bright field electron micrographs to a resolution of about 1.2 nm. Prior to microscopy the pre-irradiation dose (1.6 x 10 -3 C cm -2 ) is given at low electron optical magnification at five different areas on the grid (the centre plus four 'corners'). This pre-irradiation can be measured either with a Faraday cage or through controlled exposure-developing conditions. Uranyl formate stained T2 bacteriophages and stacked disk aggregates of Tobacco Mosaic Virus (TMV) protein served as test objects. A comparative study was performed on specimens using either the pre-irradiation procedure or direct irradiation by the 'minimum beam exposure' technique. Changes in the electron diffraction pattern of the stain-protein complex and the disappearance of certain morphological features in the specimens were both used in order to compare the pre-irradiation method with the direct exposure technique. After identical electron exposures the pre-irradiation approach gave a far better preservation of specimen morphology. Consequently this procedure gives the microscopist more time to select and focus appropriate areas for imaging before deteriorations take place. The investigation also suggested that microscopy should be carried out between 60,000 and 100,000 times magnification. Within this magnification range, it is possible to take advantage of the phase contrast transfer characteristics of the objective lens while the electron load on the object is kept at a moderate level. Using the pre-irradiation procedure special features of the T2 bacteriophage morphology could be established. (author)

  9. Whole-cell protein profiles are useful for distinguishing enterococcal species recovered from clinical specimens Los perfiles de proteínas totales son útiles para distinguir especies de enterococos recuperados de muestras clínicas

    Directory of Open Access Journals (Sweden)

    R. Massa

    2007-12-01

    Full Text Available Whole-cell protein analysis was performed for differentiating 150 enterococcal isolates to the species level, which had previously been identified by extended phenotypic conventional tests. Whole-cell protein profile (WCPP showed a high degree of similarity within species and comparison between species revealed important differences in band profiles. All Enterococcus faecalis and Enterococcus faecium isolates were properly located into their corresponding species, regardless of their clinical source and susceptibility pattern. Moreover, WCPP allowed relocation of some isolates that had erroneously been identified by the usual conventional scheme (i.e. two atypical arginine-negative E. faecalis isolates. WCPP proved to be a simple method to ascertain the various enterococcal species, especially those other than E. faecalis, and may be a suitable tool for high-complexity or reference clinical laboratories.La comparación del perfil de proteínas totales permitió agrupar 150 aislamientos de enterococos dentro de la especie en la que habían sido ubicados por el esquema convencional de pruebas bioquímicas. Los patrones de proteínas totales, comparados visualmente, se mantuvieron con alto grado de similitud intraespecie y revelaron diferencias notorias en la comparación interespecie. Todos los aislamientos de Enterococcus faecalis y Enterococcus faecium, independientemente de los sitios de aislamiento, cuadro clínico del paciente, biotipo o antibiotipo, fueron fácilmente encuadrados en su especie. Asimismo, el estudio del perfil de proteínas totales de enterococos permitió reubicar taxonómicamente aislamientos que habían sido incorrectamente identificados por los métodos bioquímicos convencionales, como por ejemplo dos aislamientos atípicos de E. faecalis arginina negativos. Dado que la metodología empleada es económica y rápida, la comparación de perfiles de proteínas totales en SDS-PAGE podría ser considerada una herramienta

  10. Clinical application of DSA and evaluation of its methods

    International Nuclear Information System (INIS)

    Ouyang, Yong; Ma, Heping; Gu, Shubing; Zhou, Qunhui; Zhang, Shulan; Liu, Pengzni; Zhang, Junyi.

    1990-01-01

    A total of 160 patients of two hospitals received 192 DSA examinations with different contrast administrations, and techniques of performing DSA were analyzed, compared, and evaluated with reference to the literature. It was concluded that (1) the peripheral injection of contrast material for IVDSA via cannula is simpler than that via a short catheter, but the incidences of contrast extravasation in both cases are higher than with central injection. (2) Both the lower part of the superior vena cava and the right atrial cavity are safe sites for central injection. With central injection for IVDSA, the arterial iodine concentration is approximately double that of peripheral injection, and consistent high quality examinations of the intracranial vessels may be obtained. However, neither peripheral nor central injections can visualize the small vessels clearly. (3) IVDSA may be substituted for conventional angiography only in examinations of the aorta and its main branches. (4) IADSA is becoming a superior angiographic technique and its clinical application is increasing. In addition, means of avoiding contrast extravasation during IVDSA and the main points of selecting the optimal technique for DSA are described in this paper. (author)

  11. CT appearances of emphysema and clinical application

    International Nuclear Information System (INIS)

    Wang Xinlian; Ma Daqing; Chen Budong; He Wen; Guan Yansheng; Zhang Yansong; Tang Hongqu; Wang Zhenguang

    2006-01-01

    Objective: To investigate CT appearances of different types of emphysema and to determine the clinic value for differential diagnosis. Methods: Twenty-three specimens with emphysema selected from 33 autopsy specimens were included in this study. All specimens were inflated and fixed by Heitzman's method, then examined by spiral CT scan. The CT appearances of different types of emphysema in every specimen were analyzed. After the specimens were cut into 10 mm thickness slices, the CT- pathologic correlation was done. Fifteen clinical cases confirmed by pathology or clinical process were all performed spiral CT scan and analyzed, including emphysema-accompanying pneumonia 11 cases, emphysema-accompanying nodule 4 cases. Result: Centriacinar emphysema (CAE)can be seen in 21 of 23 specimens, pancinar emphysema(PAE) can be seen in 5 of 23 specimens, all coexisting with CAE. Distal acinar emphysema(DAE) can be seen in 19 of 23 specimens, irregular emphysema can be seen in 3 of 23 specimens. In all specimens, emphysema can be seen in bilateral lung fields, distributing similarly. Seventeen of 23 eases (17/23) showed no less than two types of emphysema. Fourteen cases of emphysema- accompanying pneumonia (clinic: 11 cases, specimen: 3 cases) showed 'pseudocavity' or 'pseudohoneycombing' (emphysema lesion that had not been filled in the consolidation). Four eases of emphysema-accompanying nodule showed 'pseudopleuralhollow' (wall of DAE or bulla connecting with nodule). Conclusion: The CT manifestations of emphysema, the characteristics of distribution and multi- type of emphysema coexisting can help differentiate cystic air space diseases. The characteristics of complications of emphysema, the 'pseudocavity', 'pseudohoneycombing' and 'pseudopleuralhollow', may be help for differential diagnosis. (authors)

  12. Clinical evaluation of right ventricular function using radionuclide method

    International Nuclear Information System (INIS)

    Ishii, Yasushi; Tamaki, Nagayoshi; Mukai, Takao; Motohara, Seiichito; Ikekubo, Katsuji.

    1982-01-01

    Essential thing to evaluate the right ventricular (RV) function is its volumetric measurement. However, its geometrical complexity has hampered this even with the contrast ventriculography, unlike left ventricle (LV). Meanwhile, the radionuclide time-activity curve from the first pass of a tracer through RV in the RAO view provides the most reliable data of the RV ejection fraction (RVEF), same data from the multigated equilibrium study in the LAO view is necessitated for a repeated intervention study, but the latter imposes a critical problem to locate ROI separately in the LAO view. Finally, three dimensional location of RV should be mandatory using new method as the dynamic SPECT in the future. (author)

  13. LEFT ATRIAL FUNCTION: MODERN ASSESSMENT METHODS AND CLINICAL SIGNIFICANCE

    Directory of Open Access Journals (Sweden)

    E. N. Pavlyukova

    2017-01-01

    Full Text Available Assessment of the left atrial (LA function is important aspect of comprehensive cardiovascular system estimation. Many cardiac diseases make an impact to LA work either by direct affect on myocardium or hemodynamic condition changing. It is considered, LA and left ventricle diastolic pressure is interrelated, thus without mitral valve disease LA expanding is a sign of LV filling pressure augmentation. Examination of LA size and function by analysis of atrial reservoir, conduit, and booster pump can predict cardiovascular outcomes in patients with cardiomyopathy, ischemic heart disease and valvular heart disease. The last two decades gave new technologies to accurate and comprehensive LA mechanics estimation, in the first place related to tissue Doppler imaging. Atrial strain and strain rate obtained using two-dimensional speckle-tracking echocardiography have proved to be feasible and reproducible techniques to evaluate LA mechanics.In physiological settings, LA is a highly expandable chamber with relatively low pressures. However in the presence of acute and chronic injury, LA wall stretches. LA stretching is a hallmark of structure changing with myocardial fibrosis and has influence on LA strain and strain rate. LA strain estimation could be useful in the prediction of sinus rhythm restoration and maintenance after cardioversion and catheter ablation. Low values of global longitudinal LA strain indicate irreversible LA remodeling and are related to the atrial fibrillation progression from paroxysmal to permanent forms. The most interesting in these circumstances is the potential contribution of echocardiography to thromboembolic risk stratification in atrial fibrillation and invasive procedures such as atrial ablation. Therefore, at present, the main task is to understand the ways of clinical application of data  obtained during the LA study.

  14. Methods and application of bone densitometry in clinical diagnosis

    International Nuclear Information System (INIS)

    Wahner, H.W.; Riggs, B.L.

    1986-01-01

    With the awareness of osteoporosis as a major health problem for an aging population, there is great interest in early recognition and treatment of abnormal bone loss. Effective prevention of bone loss has to occur prior to the occurrence of irreparable damage. Standard radiographic procedures are not sensitive enough for the task. Therefore, a number of alternative procedures to estimate bone loss have been developed over the years, ranging from efforts to quantitate information obtained from radiographic images to sophisticated procedures such as neutron activation analysis or procedures based on the Compton scatter phenomenon. Only two procedures, photon absorptiometry and computed tomography (CT), have emerged as applicable for routine clinical use. In photon absorptiometry the entire bone mineral (cortical and trabecular bone) of a specific skeletal site is measured. CT allows measuring of bone mineral of trabecular or cortical bone alone. Normally, bone mass reaches a maximum in the third decade and then continuously declines. This age-related bone loss is greater in women in whom an accelerated rate of loss occurs at the menopause. When bone density reaches a critical fracture threshold, skeletal fractures occur (spine, hip, and distal long bones). The age at which this critical fracture threshold is reached depends on the maximal bone mass achieved in early adulthood and the rate of loss with increasing age. With the exception of NaF, present-day therapeutic efforts only retard or prevent bone loss but do not significantly add bone mineral to the skeleton. Recognition of high-risk groups and early treatment are therefore required. 79 references

  15. An Enzymatic Clinical Chemistry Laboratory Experiment Incorporating an Introduction to Mathematical Method Comparison Techniques

    Science.gov (United States)

    Duxbury, Mark

    2004-01-01

    An enzymatic laboratory experiment based on the analysis of serum is described that is suitable for students of clinical chemistry. The experiment incorporates an introduction to mathematical method-comparison techniques in which three different clinical glucose analysis methods are compared using linear regression and Bland-Altman difference…

  16. A method to adjust radiation dose-response relationships for clinical risk factors

    DEFF Research Database (Denmark)

    Appelt, Ane Lindegaard; Vogelius, Ivan R

    2012-01-01

    Several clinical risk factors for radiation induced toxicity have been identified in the literature. Here, we present a method to quantify the effect of clinical risk factors on radiation dose-response curves and apply the method to adjust the dose-response for radiation pneumonitis for patients...

  17. Clinical relevance of liquid chromatography tandem mass spectrometry as an analytical method in microdose clinical studies.

    Science.gov (United States)

    Yamane, Naoe; Tozuka, Zenzaburo; Kusama, Makiko; Maeda, Kazuya; Ikeda, Toshihiko; Sugiyama, Yuichi

    2011-08-01

    To investigate the potency of LC-MS/MS by means of sensitivity and the applicability for cassette dosing in microdose clinical trials. Thirty one top-selling 31 drugs were spiked to human plasma, extracted, and analyzed by LC-MS/MS. The lower limits of quantification for each drug varied from 0.08 to 50 pg/mL, and were lower than one eighth of the assumed maximum plasma concentration at microdose in all drugs except for losartan, indicating the high performance in acquisition of full pharmacokinetic profiles at microdose. We also succeeded in simultaneous analysis of multiple compounds, assuming a situation of cassette dosing in which multiple drug candidates would be administrated simultaneously. Together with the features of LC-MS/MS, such as immediate verification, the utilization of non-radiolabeled drugs and no special facilities, we suppose that LC-MS/MS analysis would be widely applicable in conducting microdose clinical studies.

  18. Interleaved Carbon Minibeams: An Experimental Radiosurgery Method With Clinical Potential

    International Nuclear Information System (INIS)

    Dilmanian, F. Avraham; Rusek, Adam; Fois, Giovanna R.; Olschowka, John; Desnoyers, Nicolle R.; Park, Jane Y.; Dioszegi, Istvan; Dane, Bari; Wang Ruiliang; Tomasi, Dardo; Lee, Hedok; Hurley, Sean D.; Coyle, Patricia K.; Meek, Allen G.; O’Banion, M. Kerry

    2012-01-01

    Purpose: To evaluate the efficacy of “interleaved carbon minibeams” for ablating a 6.5-mm target in a rabbit brain with little damage to the surrounding brain. The method is based on the well-established tissue-sparing effect of arrays of thin planes of radiation. Methods and Materials: Broad carbon beams from the National Aeronautics and Space Agency Space Radiation Facility at Brookhaven National Laboratory were segmented into arrays of parallel, horizontal, 0.3-mm-thick planar beams (minibeams). The minibeams’ gradual broadening in tissues resulted in 0.525-mm beam thickness at the target’s proximal side in the spread-out Bragg peak. Interleaving was therefore implemented by choosing a 1.05 mm beam spacing on-center. The anesthetized rabbit, positioned vertically on a stage capable of rotating about a vertical axis, was exposed to arrays from four 90° angles, with the stage moving up by 0.525 mm in between. This produced a solid radiation field at the target while exposing the nontargeted tissues to single minibeam arrays. The target “physical” absorbed dose was 40.2 Gy. Results: The rabbit behaved normally during the 6-month observation period. Contrast magnetic resonance imaging and hematoxylin and eosin histology at 6 months showed substantial focal target damage with little damage to the surrounding brain. Conclusion: We plan to evaluate the method’s therapeutic efficacy by comparing it with broad-beam carbon therapy in animal models. The method’s merits would combine those of carbon therapy (i.e., tight target dose because of the carbon’s Bragg-peak, sharp dose falloff, and high relative biological effectiveness at the target), together with the method’s low impact on the nontargeted tissues. The method’s smaller impact on the nontargeted brain might allow carbon therapy at higher target doses and/or lower normal tissue impact, thus leading to a more effective treatment of radioresistant tumors. It should also make the method more

  19. Examination of the fatigue life under combined loading of specimens

    Directory of Open Access Journals (Sweden)

    Fojtík F.

    2008-11-01

    Full Text Available This contribution describes experimental results under combined loading of specimens manufactured from common construction steel 11523. Specimens were gradually loaded by amplitude of the torque, then by combination of torque and tension prestress. The last set of specimens was loaded in combination of torque and inner overpressure. To obtain the required input values the stress-strain analysis of specimens by finite element method in software Ansys was performed within the last experiment. For evaluation of the results the Fuxa's criterion was applied. The performed experiments and their results embody a good agreement with bellow mentioned conjugated strength criterion. The experiments were performed on reconstructed testing machine equipped by pressure chamber.

  20. Development of Reconstitution Technology for Surveillance Specimens

    International Nuclear Information System (INIS)

    Yasushi Atago; Shunichi Hatano; Eiichiro Otsuka

    2002-01-01

    The Japan Power Engineering and Inspection Corporation (JAPEIC) has been carrying out the project titled 'Nuclear Power Plant Integrated Management Technology (PLIM)' consigned by Japanese Ministry of Economy, Trade and Industry (METI) since 1996FY as a 10-years project. As one of the project themes, development of reconstitution technology for reactor pressure vessel (RPV/RV) surveillance specimens, which are installed in RPVs to monitor the neutron irradiation embrittlement on RPV/RV materials, is now on being carried out to deal with the long-term operation of nuclear power plants. The target of this theme is to establish the technical standard for applicability of reconstituted surveillance specimens including the reconstitution of the Charpy specimens and Compact Tension (CT) specimens. With the Charpy specimen reconstitution, application of 10 mm length inserts is used, which enables the conversion of tests from the LT-direction to the TL-direction. This paper presents the basic data from Charpy and CT specimens of RPV materials using the surveillance specimens obtained for un-irradiated materials including the following. 1) Reconstitution Technology of Charpy Specimens. a) The interaction between plastic zone and Heat Affected Zone (HAZ). b) The effects of the possible deviations from the standard specimens for the reconstituted specimens. 2) Reconstitution Technology of CT specimens. a) The correlation between fracture toughness and plastic zone width. Because the project is now in progress, this paper describes the outline of the results obtained as of the end of 2000 FY. (authors)

  1. Clinical management methods for out-patients with alcohol dependence

    Directory of Open Access Journals (Sweden)

    Boulze Isabelle

    2006-02-01

    Full Text Available Abstract Background In France outpatient centres for the care of alcoholics are healthcare establishments providing medical, psychological and social support. Although they meet the practical needs of these patients, their degree of use in each of these domains and the respective mobilisation of different skills by the care team are not well understood. Our aim was therefore to determine in detail the management involved as a function of the severity of alcohol dependence. For this purpose, all the procedures involved were compiled in a thesaurus describing its type (psychological, medical, social, reception, its scheduled or unscheduled nature, its method (face-to-face, telephone, letter and its duration. The severity of dependence was evaluated using the Addiction Severity Index (ASI. Results 45 patients were included and followed-up during 291 ± 114 days. The mean initial ASI scores (± SD were: medical (M = 0.39 ± 0.3, working-income (ER = 0.5 ± 0.3, alcohol (A = 0.51 ± 0.2, illicit drugs (D = 0.07 ± 0.08, legal (L = 0.06 ± 0.13, familial and social environment (FS = 0.34 ± 0.26, psychological (P = 0.39 ± 0.22. The total number of procedures was 1341 (29.8 per patient corresponding to 754.4 hours (16.7 per patient. The intensity of management peaked during the first month of treatment, and then declined rapidly; the maximum incidence of abstinence was observed during the 3rd month of management. Interviews with patients, group therapy and staff meetings represented 68.7%, 9.9% and 13.9% of all procedures, respectively. In patients with severe dependence, as compared to moderate, management was twice as intense in the psychological and social domains, but not in the medical domain. The ASI questionnaire was completed a second time by 24 patients, after an average of 3.2 months. The improvement was significant in the M, A, D and P domains only. Conclusion This study provided an overview of the methods employed in managing a sample of

  2. Onychomycosis: Clinical findings, etiological agents and evaluation of laboratory methods

    Directory of Open Access Journals (Sweden)

    Dubljanin Eleonora

    2014-01-01

    Full Text Available The aim of this study was to identify the etiological agents in patients with suspected onychomycosis, and to carry out comparative testing of individual or combinations of tests: direct microscopy with KOH and Blankophor (BP, culturing on Sabouraud’s dextrose agar (SDA, diluted Sabouraud’s dextrose agar (D-SDA and dermatophyte test medium (DTM. From 70 nail samples (65 toenails, 5 fingernails, 46 (60.5% had at least one of five positive tests. Isolation was possible in 41, while in 5 samples the presence of fungi was observed by KOH and/or BP. Dermatophytes were most frequently isolated (80.5% where Trichophyton rubrum was predominant. Candida spp. was isolated in 9.8%, Aspergillus spp. 4.9%, Alternaria spp. 2.4% and Fusarium spp. 2.4%. Application of BP as an individual test was the most sensitive method. The combination of BP with DTM or D-SDA provides the best sensitivity and allows the identification of fungi to the species/genus level.

  3. Influence of thermal conditioning media on Charpy specimen test temperature

    International Nuclear Information System (INIS)

    Nanstad, R.K.; Swain, R.L.; Berggren, R.G.

    1989-01-01

    The Charpy V-notch (CVN) impact test is used extensively for determining the toughness of structural materials. Research programs in many technologies concerned with structural integrity perform such testing to obtain Charpy energy vs temperature curves. American Society for Testing and Materials Method E 23 includes rather strict requirements regarding determination and control of specimen test temperature. It specifies minimum soaking times dependent on the use of liquids or gases as the medium for thermally conditioning the specimen. The method also requires that impact of the specimen occur within 5 s removal from the conditioning medium. It does not, however, provide guidance regarding choice of conditioning media. This investigation was primarily conducted to investigate the changes in specimen temperature which occur when water is used for thermal conditioning. A standard CVN impact specimen of low-alloy steel was instrumented with surface-mounted and embedded thermocouples. Dependent on the media used, the specimen was heated or cooled to selected temperatures in the range -100 to 100 degree C using cold nitrogen gas, heated air, acetone and dry ice, methanol and dry ice, heated oil, or heated water. After temperature stabilization, the specimen was removed from the conditioning medium while the temperatures were recorded four times per second from all thermocouples using a data acquisition system and a computer. The results show that evaporative cooling causes significant changes in the specimen temperatures when water is used for conditioning. Conditioning in the other media did not result in such significant changes. The results demonstrate that, even within the guidelines of E 23, significant test temperature changes can occur which may substantially affect the Charpy impact test results if water is used for temperature conditioning. 7 refs., 11 figs

  4. The STAR score: a method for auditing clinical records

    Science.gov (United States)

    Tuffaha, H

    2012-01-01

    INTRODUCTION Adequate medical note keeping is critical in delivering high quality healthcare. However, there are few robust tools available for the auditing of notes. The aim of this paper was to describe the design, validation and implementation of a novel scoring tool to objectively assess surgical notes. METHODS An initial ‘path finding’ study was performed to evaluate the quality of note keeping using the CRABEL scoring tool. The findings prompted the development of the Surgical Tool for Auditing Records (STAR) as an alternative. STAR was validated using inter-rater reliability analysis. An audit cycle of surgical notes using STAR was performed. The results were analysed and a structured form for the completion of surgical notes was introduced to see if the quality improved in the next audit cycle using STAR. An education exercise was conducted and all participants said the exercise would change their practice, with 25% implementing major changes. RESULTS Statistical analysis of STAR showed that it is reliable (Cronbach’s a = 0.959). On completing the audit cycle, there was an overall increase in the STAR score from 83.344% to 97.675% (p<0.001) with significant improvements in the documentation of the initial clerking from 59.0% to 96.5% (p<0.001) and subsequent entries from 78.4% to 96.1% (p<0.001). CONCLUSIONS The authors believe in the value of STAR as an effective, reliable and reproducible tool. Coupled with the application of structured forms to note keeping, it can significantly improve the quality of surgical documentation and can be implemented universally. PMID:22613300

  5. [On academic thought and clinical application of LI Yan-Fang's middle-warmer energy method].

    Science.gov (United States)

    Li, Li-Jun

    2010-10-01

    The present paper introduces LI Yan-Fang's middle-warmer energy method from acupoint selection, needling methods, treatment principle and his clinical experiences in treatment of stroke and insomnia etc. The acupuncture prescription of this method consist of Shangwan (CV 13), Zhongwan (CV 12), Jianli (CV 11), Xiawan (CV 10), Shuifen (CV 9), Huangshu (KI 16) and Qihai (CV 6) etc as the main acupoints combined with strict manipulation and depth of needling to treat clinical diseases.

  6. Single specimen fracture toughness determination procedure using instrumented impact test

    International Nuclear Information System (INIS)

    Rintamaa, R.

    1993-04-01

    In the study a new single specimen test method and testing facility for evaluating dynamic fracture toughness has been developed. The method is based on the application of a new pendulum type instrumented impact tester equipped with and optical crack mouth opening displacement (COD) extensometer. The fracture toughness measurement technique uses the Double Displacement Ratio (DDR) method, which is based on the assumption that the specimen is deformed as two rigid arms that rotate around an apparent centre of rotation. This apparent moves as the crack grows, and the ratio of COD versus specimen displacement changes. As a consequence the onset ductile crack initiation can be detected on the load-displacement curve. Thus, an energy-based fracture toughness can be calculated. In addition the testing apparatus can use specimens with the Double ligament size as compared with the standard Charpy specimen which makes the impact testing more appropriate from the fracture mechanics point of view. The novel features of the testing facility and the feasibility of the new DDR method has been verified by performing an extensive experimental and analytical study. (99 refs., 91 figs., 27 tabs.)

  7. Monolithic integration of nanoscale tensile specimens and MEMS structures

    International Nuclear Information System (INIS)

    Yilmaz, Mehmet; Kysar, Jeffrey W

    2013-01-01

    Nanoscale materials often have stochastic material properties due to a random distribution of material defects and an insufficient number of defects to ensure a consistent average mechanical response. Current methods to measure the mechanical properties employ MEMS-based actuators. The nanoscale specimens are typically mounted manually onto the load platform, so the boundary conditions have random variations, complicating the experimental measurement of the intrinsic stochasticity of the material properties. Here we show methods for monolithic integration of a nanoscale specimen co-fabricated with the loading platform. The nanoscale specimen is gold with dimensions of ∼40 nm thickness, 350 ± 50 nm width, and 7 μm length and the loading platform is an interdigitated electrode electrostatic actuator. The experiment is performed in a scanning electron microscope and digital image correlation is employed to measure displacements to determine stress and strain. The ultimate tensile strength of the nanocrystalline nanoscale specimen approaches 1 GPa, consistent with measurements made by other nanometer scale sample characterization methods on other material samples at the nanometer scale, as well as gold samples at the nanometer scale. The batch-compatible microfabrication method can be used to create nominally identical nanoscale specimens and boundary conditions for a broad range of materials. (paper)

  8. The glenoid track: a review of the clinical relevance, method of calculation and current evidence behind this method

    Energy Technology Data Exchange (ETDEWEB)

    Younan, Yara; Wong, Philip K.; Umpierrez, Monica; Gonzalez, Felix; Singer, Adam Daniel [Emory University Hospital, Department of Radiology and Imaging Sciences, Section of Musculoskeletal Imaging, Atlanta, GA (United States); Karas, Spero [Emory University Hospital, Department of Orthopedic Surgery, Atlanta, GA (United States); Jose, Jean [University of Miami, Department of Radiology, Miami, FL (United States)

    2017-12-15

    In the setting of bipolar bone injury, orthopedic surgeons are currently making use of the glenoid track method to guide surgical management. Using preoperative CT or MR imaging, this method allows the identification of patients who are more likely to fail a primary capsuloligamentous Bankart repair. As the glenoid track method becomes increasingly used in preoperative planning, it is important for the radiologist to become familiar with its concept and method of calculation. This review article aims to concisely summarize the current literature and the clinical implications of the glenoid track method. (orig.)

  9. Preliminary investigation of candidate specimens for the Egyptian environmental specimen bank

    International Nuclear Information System (INIS)

    Shawky, S.; Amer, H.; Schladot, J.D.; Ostapczuk, P.; Emons, H.; Abou El-Nour, F.

    2000-01-01

    In the frame of establishing an environmental monitoring program related to environmental specimen banking in egypt, some candidate specimens from the aquatic environment (Fish muscle, fish liver; mussels) were investigated. The selection of specimens and sampling sites is described. Specimens are chemically characterised with respect to some major and trace elements and the results are compared with data obtained from comparable specimens collected in aquatic ecosystems of germany

  10. Impregnation of soft biological specimens with thermosetting resins and elastomers.

    Science.gov (United States)

    von Hagens, G

    1979-06-01

    A new method for impregnation of biological specimens with thermosetting resins and elastomers is described. The method has the advantage that the original relief of the surface is retained. The impregnation is carried out by utilizing the difference between the high vapor tension of the intermedium (e.g., methylene chloride) and the low vapor tension of the solution to be polymerized. After impregnation, the specimen is subject to polymerization conditions without surrounding embedding material. The optical and mechanical properties can be selected by proper choice from various kinds of resins and different procedures, for example, by complete or incomplete impregnation. Acrylic resins, polyester resins, epoxy resins, polyurethanes and silicone rubber have been found suitable for the method. Excellent results have been obtained using transparent silicone rubber since after treatment the specimens are still flexible and resilient, and have retained their natural appearance.

  11. Evaluation of the Ortho-Clinical Diagnostics Vitros ECi Anti-HCV test: comparison with three other methods.

    Science.gov (United States)

    Watterson, Jeannette M; Stallcup, Paulina; Escamilla, David; Chernay, Patrick; Reyes, Alfred; Trevino, Sylvia C

    2007-01-01

    After observing a high incidence of low positive hepatitis C virus (HCV) antibody screens by the Ortho-Clinical Vitros ECi test (Orthoclinical Diagnostics, Raritan, NJ), we compared results against those obtained using another chemiluminescent analyzer, as well as two U.S. Food and Drug Administration (FDA)-approved confirmatory methodologies. To ascertain the true anti-HCV status of samples deemed low-positive by the Ortho-Clinical Vitros ECi test, we tested samples using the ADVIA Centaur HCV screen test (Siemens Medical Solutions Diagnostics), the Chiron recombinant immunoblot assay (RIBA) test (Chiron Corp., Emeryville, CA), and the Roche COBAS Amplicor HCV qualitative test (Roche Diagnostics, Indianapolis, IN) in a series of studies. Of 94 specimens positive by Vitros ECi, 19% were observed to be negative by Centaur. A separate study of 91 samples with signal-to-cutoff (s/co) values less than 8.0 showed that all but one was negative for HCV ribonucleic acid (RNA). In comparison with RIBA, 100% (77) samples positive by the Vitros ECi test with s/co values less than 12.0 were negative or indeterminate by RIBA. A final study comparing all four methods side-by-side showed 63% disagreement by Centaur for Vitros ECi low-positive samples, 75% disagreement by RIBA, and 97% disagreement by polymerase chain reaction (PCR). In conclusion, the Ortho-Clinical Vitros ECi Anti-HCV test yields a high rate of false-positive results in the low s/co range in our patient population. (c) 2007 Wiley-Liss, Inc.

  12. Intraoperative specimen radiography in patients with nonpalpable malignant breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Schmachtenberg, C.; Engelken, F.; Fischer, T.; Bick, U.; Poellinger, A.; Fallenberg, E.M. [Charite, Berlin (Germany). Radiology

    2012-07-15

    Purpose: Specimen mammography of nonpalpable wire-localized breast lesions is the standard in breast-conserving surgery. The aim of this study was to evaluate the reliability of intraoperative 2-view specimen mammography in different cancer types. Materials and Methods: After ethics approval, 3 readers retrospectively evaluated margins on 266 2-view specimen radiographs. They determined the closest margin and the orientation. The results were correlated with the histopathology (intra-class correlation coefficient [ICC] and contingency coefficient [CC]) and compared (Wilcoxon test). Results: Invasive ductal carcinoma (IDC) with ductal carcinoma in situ (DCIS) was present in 115 (43 %), IDC in 75 (28 %), invasive lobular carcinoma (ILC) in 57 (22 %) and rare cancers (CA) in 19 specimens (7 %). The sensitivity/specificity and positive/negative predictive value (P/NPV) of specimen mammography were 0.50/0.86 and 0.86/0.50 for CA, 0.42/0.68 and 0.48/0.63 for IDC, 0.36/0.81 and 0.69/0.51 for ILC, and 0.22/0.78 and 0.68/0.32 for IDC+DCIS. Readers correctly identified the orientation of the closest margin in at least one view in an average of 149 specimens (56 %). CCs were between 0.680 (IDC) and 0.912 (CA), suggesting a moderate correlation between radiographic and histological orientation. The correlations were worse for the radiographic and histological distances, with ICC ranging from 0.238 (ILC) to 0.475 (CA). The Wilcoxon test revealed overestimation of the radiographic margins compared to the histological ones for DCIS. Conclusion: Our results suggest that specimen radiography has relatively good overall specificity and good PPV, while the sensitivity and NPV are low for DCIS. A negative result on specimen radiography does not rule out histologically involved margins. (orig.)

  13. Intraoperative specimen radiography in patients with nonpalpable malignant breast lesions

    International Nuclear Information System (INIS)

    Schmachtenberg, C.; Engelken, F.; Fischer, T.; Bick, U.; Poellinger, A.; Fallenberg, E.M.

    2012-01-01

    Purpose: Specimen mammography of nonpalpable wire-localized breast lesions is the standard in breast-conserving surgery. The aim of this study was to evaluate the reliability of intraoperative 2-view specimen mammography in different cancer types. Materials and Methods: After ethics approval, 3 readers retrospectively evaluated margins on 266 2-view specimen radiographs. They determined the closest margin and the orientation. The results were correlated with the histopathology (intra-class correlation coefficient [ICC] and contingency coefficient [CC]) and compared (Wilcoxon test). Results: Invasive ductal carcinoma (IDC) with ductal carcinoma in situ (DCIS) was present in 115 (43 %), IDC in 75 (28 %), invasive lobular carcinoma (ILC) in 57 (22 %) and rare cancers (CA) in 19 specimens (7 %). The sensitivity/specificity and positive/negative predictive value (P/NPV) of specimen mammography were 0.50/0.86 and 0.86/0.50 for CA, 0.42/0.68 and 0.48/0.63 for IDC, 0.36/0.81 and 0.69/0.51 for ILC, and 0.22/0.78 and 0.68/0.32 for IDC+DCIS. Readers correctly identified the orientation of the closest margin in at least one view in an average of 149 specimens (56 %). CCs were between 0.680 (IDC) and 0.912 (CA), suggesting a moderate correlation between radiographic and histological orientation. The correlations were worse for the radiographic and histological distances, with ICC ranging from 0.238 (ILC) to 0.475 (CA). The Wilcoxon test revealed overestimation of the radiographic margins compared to the histological ones for DCIS. Conclusion: Our results suggest that specimen radiography has relatively good overall specificity and good PPV, while the sensitivity and NPV are low for DCIS. A negative result on specimen radiography does not rule out histologically involved margins. (orig.)

  14. Significance of microscopic extention from 1162 esophageal carcinoma specimens

    International Nuclear Information System (INIS)

    Wang Jun; Zhu Shuchai; Han Chun; Zhang Xin; Xiao Aiqin; Ma Guoxin

    2007-01-01

    Objective: To examine the subclinical microscopic tumor extention along the long axis in 1162 specimens of esophageal carcinoma so as to help define the clinical target volume(CTV) according to the degree of microscopic extention(ME) for radiotherapy for esophageal carcinoma. Methods: 1162 resected esophageal carcinoma specimens originally located in the neck and thorax were studied with special reference to the correlation between upper and lower resection length from the tumor and positive microscopic margin. Another 52 resected esophageal carcinoma specimens were made into pathological giant sections: the actual resection length of upper and para-esophageal normal tissues was compared with that of the lower nor- mal tissues from the tumor, there by, the ratio of shrinkage was obtained and compared. Results: After fixation, microscopic positive margin ratio of the upper resection border in length ≤0.5 cm group was higher than that in length > 0.5 cm group (16.4% vs 4.1%, P=0.000). Microscopic positive margin ratio of the lower resection border in length ≤1.5 cm group was higher than that in length > 1.5 cm group( 8.1% vs 0.4%, P = 0.000). This showed that the positive margin ratio of the upper border was higher than that of the lower border in resection length > 1.5 cm group(3.5% vs 0.4%, P=0. 000). The actual length of upper and lower normal esophageal tissue after having been made into pathological giant sections in 52 patients, was 30% ± 14% and 44% ± 19% of that measured in the operation. Conclusions: Considering the shrinkage of the normal esophagus during fixation, a CTV margin of 2.0 cm along the upper long axis and 3.5 cm along the lower long axis should be chosen for radiotherapy for esophageal carcinoma, according to the ratio of shrinkage. Ascending invasion proportion is higher than the descending invasion in that tumor. (authors)

  15. Techniques for the recovery and identification of Cryptosporidium oocysts from stool specimens.

    Science.gov (United States)

    Garcia, L S; Bruckner, D A; Brewer, T C; Shimizu, R Y

    1983-07-01

    Due to increasing numbers of patients with documented infections with Cryptosporidium and other coccidia, it is important for the physician and clinical laboratory to be aware of the appropriate diagnostic techniques necessary for organism recovery and identification. Although Cryptosporidium is found in the gastrointestinal tract, tissue biopsies may be insufficient for organism recovery; the examination of stool specimens is a noninvasive procedure and will provide better overall opportunities for organism recovery. Human clinical specimens were examined from 45 patients with confirmed cryptosporidiosis or suspected of having the infection. Tissue biopsy sections, fecal wet preparations, and permanent stained smears were examined. Stool specimens were submitted in 10% Formalin, 2.5% potassium dichromate, and polyvinyl alcohol and were examined for oocysts by using 15 different methods: phase-contrast and light microscopy; Sheather's sugar flotation; Formalin concentration techniques; 10% potassium hydroxide; Giemsa; trichrome; periodic acid-Schiff; modified periodic acid-Schiff; silver methenamine; acridine orange; auramine-rhodamine; Kinyoun acid-fast; Ziehl-Neelsen carbolfuchsin; and a modified acid-fast procedure. Each technique or combination of techniques was assessed by organism quantitation, organism morphology, and ease of visual recognition. Based on these comparative studies, the modified Ziehl-Neelsen carbolfuchsin stain on 10% Formalin-preserved stool is recommended for the recovery and identification of Cryptosporidium.

  16. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations

    Directory of Open Access Journals (Sweden)

    Stürenburg, Enno

    2009-07-01

    Full Text Available Methicillin-resistant Staphylococcus aureus (MRSA isolates is a serious public health problem whose ever-increasing rate is commensurate with the pressure it is exerting on the healthcare system. At present, more than 20% of clinical S. aureus isolates in German hospitals are methicillin resistant. Strategies from low-prevalence countries show that this development is not necessarily inevitable. In the Scandinavian countries and the Netherlands, thanks to a rigorous prevention programme, MRSA prevalence has been kept at an acceptably low level (<1–3%. Central to these ‘search and destroy’ control strategies is an admission screening using several MRSA swabs taken from mucocutaneous colonisation sites of high-risk patients (‘MRSA surveillance’. It has also been reported that the speed with which MRSA carriage is detected has an important role to play, as it is a key component of any effective strategy to prevent the pathogen from spreading. Since MRSA culturing involves a 2–3 day delay before the final results are available, rapid detection techniques (commonly referred to as ‘MRSA rapid tests’ using PCR methods and, most recently, rapid culturing methods have been developed. The implementation of rapid tests reduces the time of detection of MRSA carriers from 48–72 to 2–5 h. Clinical evaluation data have shown that MRSA can thus be detected with very high sensitivity. Specificity however is sometimes impaired due to false-positive PCR signals occurring in mixed flora specimens. In order to rule out any false-positive PCR results, a culture screen must always be carried out simultaneously.The data provide preliminary evidence that a PCR assay can reduce nosocomial MRSA transmission in high-risk patients or high-risk areas, whereas an approach that screens all patients admitted to the hospital is probably not effective. Information concerning the cost-effectiveness of rapid MRSA tests is still sparse and thus the issue remains

  17. An investigation on clinical, radiological and biochemical methods for assessing periodontitis activity

    International Nuclear Information System (INIS)

    Janssen, P.T.M.

    1987-01-01

    In order to recognize in which stage rapidly progressing destruction of periodontal ligament fibers occurs, a number of diagnostic methods are studied in this thesis. It turns out that the actual much utilized clinical methods can not be improved while radiological and biochemical diagnositic methods are much more promising. 106 refs.; 20 figs.; 36 tabs

  18. Translating Basic Behavioral and Social Science Research to Clinical Application: The EVOLVE Mixed Methods Approach

    Science.gov (United States)

    Peterson, Janey C.; Czajkowski, Susan; Charlson, Mary E.; Link, Alissa R.; Wells, Martin T.; Isen, Alice M.; Mancuso, Carol A.; Allegrante, John P.; Boutin-Foster, Carla; Ogedegbe, Gbenga; Jobe, Jared B.

    2013-01-01

    Objective: To describe a mixed-methods approach to develop and test a basic behavioral science-informed intervention to motivate behavior change in 3 high-risk clinical populations. Our theoretically derived intervention comprised a combination of positive affect and self-affirmation (PA/SA), which we applied to 3 clinical chronic disease…

  19. [Predictive methods versus clinical titration for the initiation of lithium therapy. A systematic review].

    Science.gov (United States)

    Geeraerts, I; Sienaert, P

    2013-01-01

    When lithium is administered, the clinician needs to know when the lithium in the patient’s blood has reached a therapeutic level. At the initiation of treatment the level is usually achieved gradually through the application of the titration method. In order to increase the efficacy of this procedure several methods for dosing lithium and for predicting lithium levels have been developed. To conduct a systematic review of the publications relating to the various methods for dosing lithium or predicting lithium levels at the initiation of therapy. We searched Medline systematically for articles published in English, French or Dutch between 1966 and April 2012 which described or studied a method for dosing lithium or for predicting the lithium level reached following a specific dosage. We screened the reference lists of relevant articles in order to locate additional papers. We found 38 lithium prediction methods, in addition to the clinical titration method. These methods can be divided into two categories: the ‘a priori’ methods and the ‘test-dose’ methods, the latter requiring the administration of a test dose of lithium. The lithium prediction methods generally achieve a therapeutic blood level faster than the clinical titration method, but none of the methods achieves convincing results. On the basis of our review, we propose that the titration method should be used as the standard method in clinical practice.

  20. HER2 testing on core needle biopsy specimens from primary breast cancers: interobserver reproducibility and concordance with surgically resected specimens

    Directory of Open Access Journals (Sweden)

    Yamamoto Sohei

    2010-10-01

    Full Text Available Abstract Background Accurate evaluation of human epidermal growth factor receptor type-2 (HER2 status based on core needle biopsy (CNB specimens is mandatory for identification of patients with primary breast cancer who will benefit from primary systemic therapy with trastuzumab. The aim of the present study was to validate the application of HER2 testing with CNB specimens from primary breast cancers in terms of interobserver reproducibility and comparison with surgically resected specimens. Methods A total of 100 pairs of archival formalin-fixed paraffin-embedded CNB and surgically resected specimens of invasive breast carcinomas were cut into sections. All 100 paired sections were subjected to HER2 testing by immunohistochemistry (IHC and 27 paired sections were subjected to that by fluorescence in situ hybridization (FISH, the results being evaluated by three and two observers, respectively. Interobserver agreement levels in terms of judgment and the concordance of consensus scores between CNB samples and the corresponding surgically resected specimens were estimated as the percentage agreement and κ statistic. Results In CNB specimens, the percentage interobserver agreement of HER2 scoring by IHC was 76% (κ = 0.71 for 3 × 3 categories (0-1+ versus 2+ versus 3+ and 90% (κ = 0.80 for 2 × 2 categories (0-2+ versus 3+. These levels were close to the corresponding ones for the surgically resected specimens: 80% (κ = 0.77 for 3 × 3 categories and 92% (κ = 0.88 for 2 × 2 categories. Concordance of consensus for HER2 scores determined by IHC between CNB and the corresponding surgical specimens was 87% (κ = 0.77 for 3 × 3 categories, and 94% (κ = 0.83 for 2 × 2 categories. Among the 13 tumors showing discordance in the mean IHC scores between the CNB and surgical specimens, the results of consensus for FISH results were concordant in 11. The rate of successful FISH analysis and the FISH positivity rate in cases with a HER2 IHC score of

  1. Measurement of deformation field in CT specimen using laser speckle

    International Nuclear Information System (INIS)

    Jeon, Moon Chang; Kang, Ki Ju

    2001-01-01

    To obtain A 2 experimentally in the J-A 2 theory, deformation field on the lateral surface of a CT specimen was to be determined using laser speckle method. The crack growth was measured using direct current potential drop method and most procedure of experimental and data reduction was performed according to ASTM Standard E1737-96. Laser speckle images during crack propagation were monitored by two CCD cameras to cancel the effect of rotation and translation of the specimen. An algorithm to pursue displacement of a point from each image was developed and successfully used to measure A 2 continuously as the crack tip was propagated. The effects of specimen thickness on J-R curve and A 2 were explored

  2. The effect of specimen and flaw dimensions on fracture toughness

    Energy Technology Data Exchange (ETDEWEB)

    Nevalainen, M.J. [VTT Manufacturing Technology, Espoo (Finland)

    1997-06-01

    The effect of the specimen size and geometry on fracture toughness has been investigated both by experimental tests and computational analyses. The methods for constraint description, namely T-stress, Q-parameter and Small-Scale Yielding Correction (SSYC) have been compared and applied for various geometries. A statistical treatment for the specimen thickness effect on cleavage fracture toughness has been investigated. Elliptical surface cracks were compared with straight-thickness cracks and a method for crack shape correction was presented. Based on the results, the differences in apparent fracture toughness values obtained from various specimen configurations can be better understood and taken into account. 64 refs. The thesis includes also four previous publications by author.

  3. Assessing data quality and the variability of source data verification auditing methods in clinical research settings.

    Science.gov (United States)

    Houston, Lauren; Probst, Yasmine; Martin, Allison

    2018-05-18

    Data audits within clinical settings are extensively used as a major strategy to identify errors, monitor study operations and ensure high-quality data. However, clinical trial guidelines are non-specific in regards to recommended frequency, timing and nature of data audits. The absence of a well-defined data quality definition and method to measure error undermines the reliability of data quality assessment. This review aimed to assess the variability of source data verification (SDV) auditing methods to monitor data quality in a clinical research setting. The scientific databases MEDLINE, Scopus and Science Direct were searched for English language publications, with no date limits applied. Studies were considered if they included data from a clinical trial or clinical research setting and measured and/or reported data quality using a SDV auditing method. In total 15 publications were included. The nature and extent of SDV audit methods in the articles varied widely, depending upon the complexity of the source document, type of study, variables measured (primary or secondary), data audit proportion (3-100%) and collection frequency (6-24 months). Methods for coding, classifying and calculating error were also inconsistent. Transcription errors and inexperienced personnel were the main source of reported error. Repeated SDV audits using the same dataset demonstrated ∼40% improvement in data accuracy and completeness over time. No description was given in regards to what determines poor data quality in clinical trials. A wide range of SDV auditing methods are reported in the published literature though no uniform SDV auditing method could be determined for "best practice" in clinical trials. Published audit methodology articles are warranted for the development of a standardised SDV auditing method to monitor data quality in clinical research settings. Copyright © 2018. Published by Elsevier Inc.

  4. A new shape specimens determined the J1c value of nuclear pressure vessel steel

    International Nuclear Information System (INIS)

    Xu, W.Q.

    1989-01-01

    The J integral has two basic definitions, a two-dimensional energy line integral definition and an energy rate definition. The line integral definition cannot be used for this experimental determination. The energy rate definition can be used but the procedure is somewhat laborious. Methods were developed for more easily determining J by approximation formulas. The first of these were where J could be estimated with reasonable accuracy for a deeply cracked bend-type specimen. This method is slightly inaccurate. This paper is concerned with a new shape specimen. It is called the W-shape specimen. The W-shape specimens are smaller volume than the compact specimens. It is convenient to operate the W-shape specimens in hot cell. It can be put into surveillance capsules and can also do specimen irradiation in engineering test reactor

  5. Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods.

    OpenAIRE

    Shawar, R M; el-Zaatari, F A; Nataraj, A; Clarridge, J E

    1993-01-01

    Detection of Mycobacterium tuberculosis in clinical specimens by the polymerase chain reaction (PCR) was compared with detection by culture. A 317-bp segment within the M. tuberculosis-specific insertion sequence IS6110 was amplified. The detection limit of the PCR assay for cultured mycobacteria was 50 cells per reaction by ethidium bromide-stained agarose gel electrophoresis and 5 cells per reaction by hybridization with an oligonucleotide probe conjugated with either digoxigenin or alkalin...

  6. Consistency of direct microscopic examination and ELISA in detection of Giardia in stool specimen among children

    Directory of Open Access Journals (Sweden)

    Zohreh Torabi

    2014-09-01

    Full Text Available Objective: To investigate the consistency of direct microscopic examination and ELISA for determination of Giadia in stool specimen. Method: Study population consisted of children with any clinical symptoms of Giardia infestation since last two weeks. Fresh stool specimen was collected from each child. The stools specimens were assessed by two methods of direct microscopic examination and ELISA.The degree of agreement between direct stool exam and ELISA was calculated by Cohen's kappa coefficient. Results: In this study, 124 children with age range 2-12 years were investigated. A total of 64 (61.7% and 79 (65.7% of children had Giardia by direct stool exam and ELISA test respectively. There was association between frequency of constipation and Giardia infection (P=0.036. The Cohen's kappa coefficient calculated for degree of agreement between direct stool exam and ELISA showed κ=0.756 (P<0.001. Conclusions: The frequency of Giardia infection in symptomatic children was high and there was high agreement rate between ELISA and direct stool smear.

  7. An analysis of clinical transition stresses experienced by dental students: A qualitative methods approach.

    Science.gov (United States)

    Botelho, M; Gao, X; Bhuyan, S Y

    2018-04-17

    Stress in dental students is well established with potential psychological distress, emotional exhaustion and burnout-related symptoms. Little attention has been given to the problems encountered by dental students during the transition from theoretical or paraclinical training to the clinical environment. The aim of this study was to adopt a qualitative research methods approach to understand the perceived stressors during students' clinical transition and provide insights for curriculum planners to enhance learning. This study analysed four groups of 2nd- and 3rd-year BDS students' experiences in focus group interviews relating to their pre-clinical and clinical transitions. The interviews were recorded and transcribed verbatim, and a thematic analysis was performed using an inductive qualitative approach. Key overlapping domains identified were the transition gap and stresses. The transition gap was subclassified into knowledge and skill (hard and soft), and stresses was subcategorised into internal and external stresses. On first coming to clinics, students experienced knowledge gaps of unfamiliar clinical treatments with mismatches between knowledge acquisition and clinical exposure. Students felt incompetent owing to the stresses attributable to curriculum design, staff and the patient. This negatively affected their confidence and clinical performance. A range of challenges have been identified that will allow curriculum designer's to plan a more supportive learning experience to help students during their transition to clinical practice giving them timely knowledge, confidence and clinical performance to better prepare them for entering clinics. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Medical school clinical placements - the optimal method for assessing the clinical educational environment from a graduate entry perspective.

    Science.gov (United States)

    Hyde, Sarah; Hannigan, Ailish; Dornan, Tim; McGrath, Deirdre

    2018-01-05

    Educational environment is a strong determinant of student satisfaction and achievement. The learning environments of medical students on clinical placements are busy workplaces, composed of many variables. There is no universally accepted method of evaluating the clinical learning environment, nor is there consensus on what concepts or aspects should be measured. The aims of this study were to compare the Dundee ready educational environment measure (DREEM - the current de facto standard) and the more recently developed Manchester clinical placement index (MCPI) for the assessment of the clinical learning environment in a graduate entry medical student cohort by correlating the scores of each and analysing free text comments. This study also explored student perceptionof how the clinical educational environment is assessed. An online, anonymous survey comprising of both the DREEM and MCPI instruments was delivered to students on clinical placement in a graduate entry medical school. Additional questions explored students' perceptions of instruments for giving feedback. Numeric variables (DREEM score, MCPI score, ratings) were tested for normality and summarised. Pearson's correlation coefficient was used to measure the strength of the association between total DREEM score and total MCPI scores. Thematic analysis was used to analyse the free text comments. The overall response rate to the questionnaire was 67% (n = 180), with a completed response rate for the MCPI of 60% (n = 161) and for the DREEM of 58% (n = 154). There was a strong, positive correlation between total DREEM and MCPI scores (r = 0.71, p < 0.001). On a scale of 0 to 7, the mean rating for how worthwhile students found completing the DREEM was 3.27 (SD 1.41) and for the MCPI was 3.49 (SD 1.57). 'Finding balance' and 'learning at work' were among the themes to emerge from analysis of free text comments. The present study confirms that DREEM and MCPI total scores are strongly correlated

  9. Measurement properties of existing clinical assessment methods evaluating scapular positioning and function. A systematic review

    DEFF Research Database (Denmark)

    Larsen, Camilla Marie; Juul-Kristensen, Birgit; Lund, Hans

    2014-01-01

    a substantially larger number of clinical scapular assessment methods than previously reported. Using the COSMIN checklist the methodological quality of the included measurement properties in the reliability and validity domains were in general ‘‘fair’’ to ‘‘poor’’. None were examined for all three domains: (1...... utility for clinical practice.......The aims were to compile a schematic overview of clinical scapular assessment methods and critically appraise the methodological quality of the involved studies. A systematic, computerassisted literature search using Medline, CINAHL, SportDiscus and EMBASE was performed from inception to October...

  10. 7 CFR 97.8 - Specimen requirements.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Specimen requirements. 97.8 Section 97.8 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... required by the examiner to furnish representative specimens of the variety, or its flower, fruit, or seeds...

  11. Advantages and disadvantages of technologies for HER2 testing in breast cancer specimens.

    Science.gov (United States)

    Furrer, Daniela; Sanschagrin, François; Jacob, Simon; Diorio, Caroline

    2015-11-01

    Human epidermal growth factor receptor 2 (HER2) plays a central role as a prognostic and predictive marker in breast cancer specimens. Reliable HER2 evaluation is central to determine the eligibility of patients with breast cancer to targeted anti-HER2 therapies such as trastuzumab and lapatinib. Presently, several methods exist for the determination of HER2 status at different levels (protein, RNA, and DNA level). In this review, we discuss the main advantages and disadvantages of the techniques developed so far for the evaluation of HER2 status in breast cancer specimens. Each technique has its own advantages and disadvantages. It is therefore not surprising that no consensus has been reached so far on which technique is the best for the determination of HER2 status. Currently, emphasis must be put on standardization of procedures, internal and external quality control assessment, and competency evaluation of already existing methods to ensure accurate, reliable, and clinically meaningful test results. Development of new robust and accurate diagnostic assays should also be encouraged. In addition, large clinical trials are warranted to identify the technique that most reliably predicts a positive response to anti-HER2 drugs. Copyright© by the American Society for Clinical Pathology.

  12. Recent advances on Charpy specimen reconstitution techniques

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Arnaldo H.P.; Lobo, Raquel M.; Miranda, Carlos Alexandre J., E-mail: aandrade@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-07-01

    Charpy specimen reconstitution is widely used around the world as a tool to enhance or supplement surveillance programs of nuclear reactor pressure vessels. The reconstitution technique consists in the incorporation of a small piece from a previously tested specimen into a compound specimen, allowing to increase the number of tests. This is especially important if the available materials is restricted and fracture mechanics parameter have to be determined. The reconstitution technique must fulfill some demands, among them tests results like the original standard specimens and the loaded material of the insert must not be influenced by the welding and machining procedure. It is known that reconstitution of Charpy specimens may affect the impact energy in a consequence of the constraint of plastic deformation by the hardened weldment and HAZ. This paper reviews some recent advances of the reconstitution technique and its applications. (author)

  13. Recent advances on Charpy specimen reconstitution techniques

    International Nuclear Information System (INIS)

    Andrade, Arnaldo H.P.; Lobo, Raquel M.; Miranda, Carlos Alexandre J.

    2017-01-01

    Charpy specimen reconstitution is widely used around the world as a tool to enhance or supplement surveillance programs of nuclear reactor pressure vessels. The reconstitution technique consists in the incorporation of a small piece from a previously tested specimen into a compound specimen, allowing to increase the number of tests. This is especially important if the available materials is restricted and fracture mechanics parameter have to be determined. The reconstitution technique must fulfill some demands, among them tests results like the original standard specimens and the loaded material of the insert must not be influenced by the welding and machining procedure. It is known that reconstitution of Charpy specimens may affect the impact energy in a consequence of the constraint of plastic deformation by the hardened weldment and HAZ. This paper reviews some recent advances of the reconstitution technique and its applications. (author)

  14. Limited Utility of Polymerase Chain Reaction in Induced Sputum Specimens for Determining the Causes of Childhood Pneumonia in Resource-Poor Settings: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study.

    Science.gov (United States)

    Thea, Donald M; Seidenberg, Phil; Park, Daniel E; Mwananyanda, Lawrence; Fu, Wei; Shi, Qiyuan; Baggett, Henry C; Brooks, W Abdullah; Feikin, Daniel R; Howie, Stephen R C; Knoll, Maria Deloria; Kotloff, Karen L; Levine, Orin S; Madhi, Shabir A; O'Brien, Katherine L; Scott, J Anthony G; Antonio, Martin; Awori, Juliet O; Baillie, Vicky L; DeLuca, Andrea N; Driscoll, Amanda J; Higdon, Melissa M; Hossain, Lokman; Jahan, Yasmin; Karron, Ruth A; Kazungu, Sidi; Li, Mengying; Moore, David P; Morpeth, Susan C; Ofordile, Ogochukwu; Prosperi, Christine; Sangwichian, Ornuma; Sawatwong, Pongpun; Sylla, Mamadou; Tapia, Milagritos D; Zeger, Scott L; Murdoch, David R; Hammitt, Laura L

    2017-06-15

    Sputum examination can be useful in diagnosing the cause of pneumonia in adults but is less well established in children. We sought to assess the diagnostic utility of polymerase chain reaction (PCR) for detection of respiratory viruses and bacteria in induced sputum (IS) specimens from children hospitalized with severe or very severe pneumonia. Among children aged 1-59 months, we compared organism detection by multiplex PCR in IS and nasopharyngeal/oropharyngeal (NP/OP) specimens. To assess whether organism presence or density in IS specimens was associated with chest radiographic evidence of pneumonia (radiographic pneumonia), we compared prevalence and density in IS specimens from children with radiographic pneumonia and children with suspected pneumonia but without chest radiographic changes or clinical or laboratory findings suggestive of pneumonia (nonpneumonia group). Among 4232 cases with World Health Organization-defined severe or very severe pneumonia, we identified 1935 (45.7%) with radiographic pneumonia and 573 (13.5%) with nonpneumonia. The organism detection yield was marginally improved with IS specimens (96.2% vs 92.4% for NP/OP specimens for all viruses combined [P = .41]; 96.9% vs 93.3% for all bacteria combined [P = .01]). After accounting for presence in NP/OP specimens, no organism was detected more frequently in the IS specimens from the radiographic pneumonia compared with the nonpneumonia cases. Among high-quality IS specimens, there were no statistically significant differences in organism density, except with cytomegalovirus, for which there was a higher quantity in the IS specimens from cases with radiographic pneumonia compared with the nonpneumonia cases (median cycle threshold value, 27.9 vs 28.5, respectively; P = .01). Using advanced molecular methods with IS specimens provided little additional diagnostic information beyond that obtained with NP/OP swab specimens. © The Author 2017. Published by Oxford University Press for the

  15. Research methods to change clinical practice for patients with rare cancers.

    Science.gov (United States)

    Billingham, Lucinda; Malottki, Kinga; Steven, Neil

    2016-02-01

    Rare cancers are a growing group as a result of reclassification of common cancers by molecular markers. There is therefore an increasing need to identify methods to assess interventions that are sufficiently robust to potentially affect clinical practice in this setting. Methods advocated for clinical trials in rare diseases are not necessarily applicable in rare cancers. This Series paper describes research methods that are relevant for rare cancers in relation to the range of incidence levels. Strategies that maximise recruitment, minimise sample size, or maximise the usefulness of the evidence could enable the application of conventional clinical trial design to rare cancer populations. Alternative designs that address specific challenges for rare cancers with the aim of potentially changing clinical practice include Bayesian designs, uncontrolled n-of-1 trials, and umbrella and basket trials. Pragmatic solutions must be sought to enable some level of evidence-based health care for patients with rare cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. LPTR irradiation of LLL vanadium tensile specimens and LLL Nb--1Zr tensile specimens

    International Nuclear Information System (INIS)

    MacLean, S.C.; Rowe, C.L.

    1977-01-01

    The LPTR irradiation of 14 LLL vanadium tensile specimens and 14 LLL Nb-1Zr tensile specimens is described. Sample packaging, the irradiation schedule and neutron fluences for three energy ranges are given

  17. Small specimen technique for assessing mechanical properties of metallic components

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, Raquel M.; Andrade, Arnaldo H.P.; Morcelli, Aparecido E., E-mail: rmlobo@ipen.br, E-mail: morcelliae@gmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-11-01

    Small Punch Test (SPT) is one of the most promising techniques of small specimen test, which was originally applied in testing of irradiated materials in nuclear engineering. Then it was introduced to other fields as an almost nondestructive method to measure the local mechanical properties that are difficult to be obtained using conventional mechanical tests. Most studies to date are focused on metallic materials, although SPT applications are recently spreading to other materials. The small punch test (SPT) employs small-sized specimens (for example, samples measuring 8 mm in diameter and 0.5 mm thick). The specimen is firmly clamped between two circular dies and is bi-axially strained until failure into a circular hole using a hemispherical punch. The 'load-punch displacement' record can be used to estimate the yield strength, the ultimate tensile strength, the tensile elongation, and the temperature of the ductile-to-brittle transition. Recently, some researchers are working on the use of miniature notched or pre-cracked specimens (denoted as p-SPT) to validate its geometry and dimensions for obtaining the fracture properties of metallic materials. In a first approach, the technique makes it possible to convert primary experimental data into conventional mechanical properties of a massive specimen. In this paper a comprehensive review of the different STP applications is presented with the aim of clarifying its usefulness. (author)

  18. Small specimen technique for assessing mechanical properties of metallic components

    International Nuclear Information System (INIS)

    Lobo, Raquel M.; Andrade, Arnaldo H.P.; Morcelli, Aparecido E.

    2017-01-01

    Small Punch Test (SPT) is one of the most promising techniques of small specimen test, which was originally applied in testing of irradiated materials in nuclear engineering. Then it was introduced to other fields as an almost nondestructive method to measure the local mechanical properties that are difficult to be obtained using conventional mechanical tests. Most studies to date are focused on metallic materials, although SPT applications are recently spreading to other materials. The small punch test (SPT) employs small-sized specimens (for example, samples measuring 8 mm in diameter and 0.5 mm thick). The specimen is firmly clamped between two circular dies and is bi-axially strained until failure into a circular hole using a hemispherical punch. The 'load-punch displacement' record can be used to estimate the yield strength, the ultimate tensile strength, the tensile elongation, and the temperature of the ductile-to-brittle transition. Recently, some researchers are working on the use of miniature notched or pre-cracked specimens (denoted as p-SPT) to validate its geometry and dimensions for obtaining the fracture properties of metallic materials. In a first approach, the technique makes it possible to convert primary experimental data into conventional mechanical properties of a massive specimen. In this paper a comprehensive review of the different STP applications is presented with the aim of clarifying its usefulness. (author)

  19. [Theory analysis and clinical application of spirit-regulating and pain-relieving acupuncture method].

    Science.gov (United States)

    Chen, Liang; Tang, Lewei; Du, Huaibin; Zheng, Hui; Liang, Fanrong

    2015-04-01

    The theoretical foundation and scientific connotation of spirit-regulating and pain-relieving acupuncture method as well as its clinical application for pain are discussed. During spirit regulation, attention should be paid on regulating heart and brain, while acupoints should be selected mainly from the Heart Meridian, Pericardium Meridian and Governor Vessel. It has significant efficacy for refractory pain in clinical treatment. Spirit-regulating and pain-relieving acupuncture method is development of acupuncture treating spirit, and it is an important method for pain in clinic. Improvement on sensitization of pain center and brain function is considered as one of the mechanisms in spirit-regulating and pain-relieving acupuncture method.

  20. Measurement properties of existing clinical assessment methods evaluating scapular positioning and function. A systematic review

    DEFF Research Database (Denmark)

    Larsen, Camilla Marie; Juul-Kristensen, Birgit; Lund, Hans

    %), with only one study rated as ‘good’. The reliability domain was most often investigated. Fewof the assessment methods in the included studies that had ‘fair’ or ‘good’ measurement properties demonstrated acceptable results for both reliability and validity.ConclusionWe found a substantially larger number......ABSTRACT OARSI Measurement properties of existing clinical assessment methods evaluating scapular positioning and function. A systematic review Larsen CM1, Juul-Kristensen B1,2 Lund H1,2, Søgaard K11University of Southern Denmark, Institute of Sports Science and Clinical Biomechanics2Institute...... assessment methods have measured the degree of scapular dyskinesis, subjectively by visual evaluation and objectively by measurements of static and dynamic scapular positioning, by either a 3-dimensional electromagnetic device or 2-dimensional clinically applicable methods. Since advanced equipment (i.e. 3D...

  1. 16 CFR Figure 3 to Part 1610 - Specimen Holder Supported in Specimen Rack

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Specimen Holder Supported in Specimen Rack 3 Figure 3 to Part 1610 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT... Holder Supported in Specimen Rack ER25MR08.002 ...

  2. A comparison of photographic, replication and direct clinical examination methods for detecting developmental defects of enamel

    Directory of Open Access Journals (Sweden)

    Pakshir Hamid-Reza

    2011-04-01

    Full Text Available Abstract Background Different methods have been used for detecting developmental defects of enamel (DDE. This study aimed to compare photographic and replication methods with the direct clinical examination method for detecting DDE in children's permanent incisors. Methods 110 8-10-year-old schoolchildren were randomly selected from an examined sample of 335 primary Shiraz school children. Modified DDE index was used in all three methods. Direct examinations were conducted by two calibrated examiners using flat oral mirrors and tongue blades. Photographs were taken using a digital SLR camera (Nikon D-80, macro lens, macro flashes, and matt flash filters. Impressions were taken using additional-curing silicon material and casts made in orthodontic stone. Impressions and models were both assessed using dental loupes (magnification=x3.5. Each photograph/impression/cast was assessed by two calibrated examiners. Reliability of methods was assessed using kappa agreement tests. Kappa agreement, McNemar's and two-sample proportion tests were used to compare results obtained by the photographic and replication methods with those obtained by the direct examination method. Results Of the 110 invited children, 90 were photographed and 73 had impressions taken. The photographic method had higher reliability levels than the other two methods, and compared to the direct clinical examination detected significantly more subjects with DDE (P = 0.002, 3.1 times more DDE (P Conclusion The photographic method was much more sensitive than direct clinical examination in detecting DDE and was the best of the three methods for epidemiological studies. The replication method provided less information about DDE compared to photography. Results of this study have implications for both epidemiological and detailed clinical studies on DDE.

  3. Analysis of Investigational Drugs in Biological Fluids - Method Development and Analysis of Pre-Clinical Samples

    National Research Council Canada - National Science Library

    Lin, Emil

    2001-01-01

    ... (and metabolites and artesunate). Work on routine analyses of biological specimens during this period was performed for studies that required determination of concentrations of artelinic acid, choroquine...

  4. Friction Compensation in the Upsetting of Cylindrical Test Specimens

    DEFF Research Database (Denmark)

    Christiansen, Peter; Martins, P. A. F.; Bay, Niels Oluf

    2016-01-01

    This manuscript presents a combined numerical andexperimental methodology for determining the stress-straincurve of metallic materials from the measurements of forceand displacement obtained in the axial compression of cylindrical test specimens with friction between the specimens and the platens....... The methodology is based on minimizing the errorbetween the average surface pressure obtained from the experimental measurements of the force and displacement and thatobtained from the slab method of analysis of metal plasticity.Three different friction models based on Coulomb friction, the constant friction...... model or combined friction models are utilized .Experimental results obtained from cylindrical and Rastegaev test specimens with different lubricants combined with the experimental determination of friction by means of ring compression tests allows compensating the effect of friction...

  5. Extraction of ultrashort DNA molecules from herbarium specimens.

    Science.gov (United States)

    Gutaker, Rafal M; Reiter, Ella; Furtwängler, Anja; Schuenemann, Verena J; Burbano, Hernán A

    2017-02-01

    DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.

  6. Strip specimen tests for pipeline materials and girth welds

    Energy Technology Data Exchange (ETDEWEB)

    Mohr, William C. [Edison Welding Institute (EWI), Columbus, Ohio (United States)

    2009-07-01

    Strip specimen testing of pipeline materials has been widely applied as a method of getting data relevant to the performance of pipelines under axial direction loading. Comparisons of strip specimen against smaller standard tests (round tensile bar, fracture toughness specimens, polished round bars) and against full-scale or large-scale testing will be explored. Data from early-generation pipe welds from the 1920's to the 1940's to the most recent materials for offshore reeled pipe will be used for examples. Strip samples can provide full thickness information to take account of varying material properties or imperfection distribution through the thickness. Strip samples can also accommodate measurement of effects of the original surface finish or weld surface shape. Strip samples have more design flexibility than standard tests, but must be designed to limit stress concentrations and effects of local bending. (author)

  7. Fracture toughness measurements with subsize disk compact specimens

    International Nuclear Information System (INIS)

    Alexander, D.J.

    1994-01-01

    Special fixtures and test methods have been developed for testing small disk compact specimens (1.25 mm diam by 4.6 mm thick). Specimens of European type 316L austenitic stainless steel were irradiated to damage levels of about 3 dpa at nominal irradiation temperatures of either 90 or 250 C and tested over a temperature range from 20 to 250 C. Results show that irradiation to this dose level at these temperatures reduces the fracture toughness but the toughness remains quite high. The toughness decreases as the test temperature increases. Irradiation at 250 C is more damaging than at 90 C, causing larger decreases in the fracture toughness. The testing shows that it is possible to generate useful fracture toughness data with a small disk compact specimens

  8. Catalogue of test specimens for non-destructive examination

    International Nuclear Information System (INIS)

    1985-05-01

    One of the key elements in assuring the integrity of reactor primary circuits is the availability of trustworthy non-destructive methods for detecting dangerous defects that may be present. Various approaches to making such examinations are being developed, including the use of ultrasonic and radiographic techniques. To demonstrate their capability and reliability, they must be tested on steel specimens reproducing the various types of faults which may arise in real primary circuit vessels and piping. Such specimens are costly to fabricate. It is therefore clearly desirable that existing specimens should be made accessible to as many organisations as possible for testing. This catalogue contains detailed Information on forty-odd deliberately flawed plates, blocks, vessels, etc. which have been produced in OECD countries, along with the name of a contact person to whom inquiries should be directed in each case

  9. cp-R, an interface the R programming language for clinical laboratory method comparisons.

    Science.gov (United States)

    Holmes, Daniel T

    2015-02-01

    Clinical scientists frequently need to compare two different bioanalytical methods as part of assay validation/monitoring. As a matter necessity, regression methods for quantitative comparison in clinical chemistry, hematology and other clinical laboratory disciplines must allow for error in both the x and y variables. Traditionally the methods popularized by 1) Deming and 2) Passing and Bablok have been recommended. While commercial tools exist, no simple open source tool is available. The purpose of this work was to develop and entirely open-source GUI-driven program for bioanalytical method comparisons capable of performing these regression methods and able to produce highly customized graphical output. The GUI is written in python and PyQt4 with R scripts performing regression and graphical functions. The program can be run from source code or as a pre-compiled binary executable. The software performs three forms of regression and offers weighting where applicable. Confidence bands of the regression are calculated using bootstrapping for Deming and Passing Bablok methods. Users can customize regression plots according to the tools available in R and can produced output in any of: jpg, png, tiff, bmp at any desired resolution or ps and pdf vector formats. Bland Altman plots and some regression diagnostic plots are also generated. Correctness of regression parameter estimates was confirmed against existing R packages. The program allows for rapid and highly customizable graphical output capable of conforming to the publication requirements of any clinical chemistry journal. Quick method comparisons can also be performed and cut and paste into spreadsheet or word processing applications. We present a simple and intuitive open source tool for quantitative method comparison in a clinical laboratory environment. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  10. The clinically-integrated randomized trial: proposed novel method for conducting large trials at low cost

    Directory of Open Access Journals (Sweden)

    Scardino Peter T

    2009-03-01

    Full Text Available Abstract Introduction Randomized controlled trials provide the best method of determining which of two comparable treatments is preferable. Unfortunately, contemporary randomized trials have become increasingly expensive, complex and burdened by regulation, so much so that many trials are of doubtful feasibility. Discussion Here we present a proposal for a novel, streamlined approach to randomized trials: the "clinically-integrated randomized trial". The key aspect of our methodology is that the clinical experience of the patient and doctor is virtually indistinguishable whether or not the patient is randomized, primarily because outcome data are obtained from routine clinical data, or from short, web-based questionnaires. Integration of a randomized trial into routine clinical practice also implies that there should be an attempt to randomize every patient, a corollary of which is that eligibility criteria are minimized. The similar clinical experience of patients on- and off-study also entails that the marginal cost of putting an additional patient on trial is negligible. We propose examples of how the clinically-integrated randomized trial might be applied in four distinct areas of medicine: comparisons of surgical techniques, "me too" drugs, rare diseases and lifestyle interventions. Barriers to implementing clinically-integrated randomized trials are discussed. Conclusion The proposed clinically-integrated randomized trial may allow us to enlarge dramatically the number of clinical questions that can be addressed by randomization.

  11. Handling of biological specimens for electron microscopy

    International Nuclear Information System (INIS)

    Bullock, G.

    1987-01-01

    There are many different aspects of specimen preparation procedure which need to be considered in order to achieve good results. Whether using the scanning or transmission microscope, the initial handling procedures are very similar and are selected for the information required. Handling procedures and techniques described are: structural preservation; immuno-and histo-chemistry; x-ray microanalysis and autoradiography; dehydration and embedding; mounting and coating specimens for scanning electron microscopy; and sectioning of resin embedded material. With attention to detail and careful choice of the best available technique, excellent results should be obtainable whatever the specimen. 6 refs

  12. Evaluation of irradiated coating material specimens

    International Nuclear Information System (INIS)

    Lee, Yong Jin; Nam, Seok Woo; Cho, Lee Moon

    2007-12-01

    Evaluation result of irradiated coating material specimens - Coating material specimens radiated Gamma Energy(Co 60) in air condition. - Evaluation conditions was above 1 X 10 4 Gy/hr, and radiated TID 2.0 X 10 6 Gy. - The radiated coating material specimens, No Checking, Cracking, Flaking, Delamination, Peeling and Blistering. - Coating system at the Kori no. 1 and APR 1400 Nuclear power plant, evaluation of irradiated coating materials is in accordance with owner's requirement(2.0 X 10 6 Gy)

  13. Personal computer based system to evaluate J-integral by a single specimen unloading compliance method: Pt. 2. Results on A533B Class I steel and CORONA-5

    Energy Technology Data Exchange (ETDEWEB)

    Narendrnath, K R; Margolin, H; Jung, Y H; Godavarti, P S; Murty, K L

    1988-01-01

    A personal computer based single specimen unloading technique has been demonstrated using a nuclear grade pressure vessel material, A533B Class I steel, and an ..cap alpha..-..beta.. titanium alloy, CORONA-5. Experimental parameters investigated in the case of steel include the effect of test temperature, loading rate and neutron irradiation. Results revealed the effect of dynamic strain aging (DSA) as a drop in the critical crack initiation fracture toughness (Jsub(q)); the minimum in Jsub(q) shifts to higher temperatures at higher test speeds as predicted from DSA models. In CORONA-5, the effects of microstructure and heat treatment for two different sizes of equiaxed ..cap alpha.. morphology in a ..beta..-matrix heat treated to different yield strengths were investigated. It is found that the observed higher values of Jsub(q) and tearing modulus result from a greater tortuosity of the crack path and ease of crack blunting. The largest increase in Jsub(q) occurred in fine equiaxed ..cap alpha.. microstructure aged to a nominal yield strength of 896 MPa. Results reveal potential application of the low cost technique for determining fracture toughness of engineering materials.

  14. Methodical principles of assessment of financial compensation for clinical trial volunteer participants

    Directory of Open Access Journals (Sweden)

    V. Ye. Dobrova

    2013-10-01

    Full Text Available Introduction. Due to the necessity to obtain the reliable results of a clinical trial and to distribute it to the general population of patients the problem of recruiting the adequate number of individuals to participate in the study as objects of observation in the group receiving the investigational medicinal product or as a member of the control group should to be solved. Aim of study. The aim of our study was to research and to justify practically the methodological approaches to determining financial compensation for participation of volunteers in the clinical trials and the appropriate methods of its calculation. Material and methods. For the purpose of determining the baseline factors for calculating the hourly compensation the survey of healthy volunteers and of expert professionals as well as the analysis of its results have been done. Questioning healthy volunteers regarding their attitudes towards inconvenience and discomfort during participation in clinical trials was held at the Ukrainian clinical research centers. Survey participants number was 99, they were healthy volunteers who took part in the first phase clinical trial or bioequivalence studies. The expert survey included questioning of the 193 professionals from Ukrainian clinical research centers, CRO, pharmaceutical manufacturers – research sponsors and collaborators State Expert Center Ministry of Health of Ukraine, who were involved in the planning, organization, implementation and evaluation of clinical trials as well as their regulatory control. Results of study. Using the method of pairwise comparisons and iterative refinement procedures the collective estimate of experts questionnaire results has been performed, by the results of which the nine indicators have been identified and the importance of each of them as units of discomfort have been established. Motivational factors of voluntary participation in clinical trials have been studied. Motivation system for

  15. Laparoscopic sleeve gastrectomy for morbid obesity with natural orifice specimen extraction (NOSE).

    Science.gov (United States)

    Gunkova, P; Gunka, I; Zonca, P; Dostalik, J; Ihnat, P

    2015-01-01

    An experience with laparoscopic sleeve gastrectomy using the natural orifice specimen extraction (NOSE) technique. Bariatric surgery is nowadays the only long term effective obesity treatment method. Twenty one consecutive patients underwent laparoscopic sleeve gastrectomy with the use of natural orifice specimen extraction (NOSE) in the Surgical Clinic of Faculty Hospital Ostrava between May 2012 and August 2012. Inclusion criteria were the body mass index (BMI) higher than 35 kg/m2 or higher than 32 kg/m2 accompanied with relevant comorbidities. Among 21 patients in this series, there were three men (14.3%) and 18 women (85.7%). Their mean age was 40.9±10.2 years. Their mean preoperative BMI was 40.4±4.6 kg/m2. No patient had previous bariatric surgery, one patient had laparoscopic fundoplication. All operations were completed laparoscopically with no conversions to an open procedure. In two cases, laparoscopic cholecystectomy was performed and the gallbladder was extracted along with the gastric specimen by transgastric approach. Laparoscopic sleeve gastrectomy is a safe and effective bariatric procedure with low morbidity and mortality. Based on our initial experiences it could be an indication for NOSE with transgastric approach. Obese patients would benefit from this approach due to the elimination of wound complications (Tab. 2, Fig. 3, Ref. 22).

  16. A simple method for plasma total vitamin C analysis suitable for routine clinical laboratory use.

    Science.gov (United States)

    Robitaille, Line; Hoffer, L John

    2016-04-21

    In-hospital hypovitaminosis C is highly prevalent but almost completely unrecognized. Medical awareness of this potentially important disorder is hindered by the inability of most hospital laboratories to determine plasma vitamin C concentrations. The availability of a simple, reliable method for analyzing plasma vitamin C could increase opportunities for routine plasma vitamin C analysis in clinical medicine. Plasma vitamin C can be analyzed by high performance liquid chromatography (HPLC) with electrochemical (EC) or ultraviolet (UV) light detection. We modified existing UV-HPLC methods for plasma total vitamin C analysis (the sum of ascorbic and dehydroascorbic acid) to develop a simple, constant-low-pH sample reduction procedure followed by isocratic reverse-phase HPLC separation using a purely aqueous low-pH non-buffered mobile phase. Although EC-HPLC is widely recommended over UV-HPLC for plasma total vitamin C analysis, the two methods have never been directly compared. We formally compared the simplified UV-HPLC method with EC-HPLC in 80 consecutive clinical samples. The simplified UV-HPLC method was less expensive, easier to set up, required fewer reagents and no pH adjustments, and demonstrated greater sample stability than many existing methods for plasma vitamin C analysis. When compared with the gold-standard EC-HPLC method in 80 consecutive clinical samples exhibiting a wide range of plasma vitamin C concentrations, it performed equivalently. The easy set up, simplicity and sensitivity of the plasma vitamin C analysis method described here could make it practical in a normally equipped hospital laboratory. Unlike any prior UV-HPLC method for plasma total vitamin C analysis, it was rigorously compared with the gold-standard EC-HPLC method and performed equivalently. Adoption of this method could increase the availability of plasma vitamin C analysis in clinical medicine.

  17. Helen Flanders Dunbar, John Dewey, and clinical pragmatism: reflections on method in psychosomatic medicine and bioethics.

    Science.gov (United States)

    Hart, Curtis W

    2002-01-01

    This article outlines the method utilized by physicians and major figures in the founding of Clinical Pastoral Education, Helen Flanders Dunbar, in her work of 1943, Psychosomatic Diagnosis, and relates it to the currently evolving approach in bioethics known as clinical pragmatism. It assesses Dewey's influence on both Dunbar in psychosomatic medicine and clinical pragmatism in bioethics, and illustrates the breadth of influence of the school of philosophical thought known as pragmatism with which Dewey's name and those of William James and Charles Sanders Pierce are most often identified.

  18. The analysis of verbal interaction sequences in dyadic clinical communication: a review of methods.

    Science.gov (United States)

    Connor, Martin; Fletcher, Ian; Salmon, Peter

    2009-05-01

    To identify methods available for sequential analysis of dyadic verbal clinical communication and to review their methodological and conceptual differences. Critical review, based on literature describing sequential analyses of clinical and other relevant social interaction. Dominant approaches are based on analysis of communication according to its precise position in the series of utterances that constitute event-coded dialogue. For practical reasons, methods focus on very short-term processes, typically the influence of one party's speech on what the other says next. Studies of longer-term influences are rare. Some analyses have statistical limitations, particularly in disregarding heterogeneity between consultations, patients or practitioners. Additional techniques, including ones that can use information about timing and duration of speech from interval-coding are becoming available. There is a danger that constraints of commonly used methods shape research questions and divert researchers from potentially important communication processes including ones that operate over a longer-term than one or two speech turns. Given that no one method can model the complexity of clinical communication, multiple methods, both quantitative and qualitative, are necessary. Broadening the range of methods will allow the current emphasis on exploratory studies to be balanced by tests of hypotheses about clinically important communication processes.

  19. Breast surgical specimen radiographs: How reliable are they?

    International Nuclear Information System (INIS)

    Britton, P.D.; Sonoda, L.I.; Yamamoto, A.K.; Koo, B.; Soh, E.; Goud, A.

    2011-01-01

    Radiography of the excised surgical specimen following wire guided localisation of impalpable breast lesions is standard surgical practice. The aims of the study were to establish the reliability of the breast specimen radiograph (SR) in determining lesion excision and to determine whether the radiographic margin correlated with the histological margin. The clinical, imaging, SR and pathological details of 106 patients with a pre-operative diagnosis of breast cancer were retrospectively reviewed. The reliability of orientation was estimated and the appearance and distance from the mammographic abnormality to each radial margin were measured and correlated with surgical histological findings. The overall accuracy of the specimen radiograph in determining whether the mammographic lesion was present was 99%. The SR could be orientated 'very reliably' or 'reliably' in 80% of patients however in only 48% of patients did the closest margin on the SR correspond with the same nearest margin at final histology. A maximum measurement of 11 mm or more from the lesion to the specimen edge was associated with a 77% likelihood of having a clear final histological margin (taken as 5 mm or more) and if <11 mm a 58% chance of having involved final histological margins. There was however a wide overlap in the results with patients having an apparently wide SR margin but histologically involved margins and vice versa. The SR is reliable at determining whether the target lesion has been removed. The correlation of SR margin orientation and measurement with final histological measurement is however far less reliable.

  20. Clinical way method in treatment of out-patients with ischemic heart disease after cardiosurgery

    Directory of Open Access Journals (Sweden)

    Vardosanidze S.L.

    2010-12-01

    Full Text Available 158 patients with ischemic heart disease (IHD have been understudy during the period of 12 months in out-patient conditions. After completion of the primary examination all the patients of basic group (118 patients received clinical way method of treatment. Patients of the comparison group (40 patients after provided treatment were cared by their local therapeutists (cardiologists. The findings proved the fact that treatment of patients after cardiosurgery by clinical way method in out-patient conditions enabled to raise patient motivation to treatment, thereby assisting them to feel better, promoting normalization of arterial pressure data. The research results stated that clinical way method of treatment may be considered as rational and effective

  1. 50 CFR 14.24 - Scientific specimens.

    Science.gov (United States)

    2010-10-01

    ..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS... international mail system. Provided, that this exception will not apply to any specimens or parts thereof taken...

  2. Tremor Detection Using Parametric and Non-Parametric Spectral Estimation Methods: A Comparison with Clinical Assessment

    Science.gov (United States)

    Martinez Manzanera, Octavio; Elting, Jan Willem; van der Hoeven, Johannes H.; Maurits, Natasha M.

    2016-01-01

    In the clinic, tremor is diagnosed during a time-limited process in which patients are observed and the characteristics of tremor are visually assessed. For some tremor disorders, a more detailed analysis of these characteristics is needed. Accelerometry and electromyography can be used to obtain a better insight into tremor. Typically, routine clinical assessment of accelerometry and electromyography data involves visual inspection by clinicians and occasionally computational analysis to obtain objective characteristics of tremor. However, for some tremor disorders these characteristics may be different during daily activity. This variability in presentation between the clinic and daily life makes a differential diagnosis more difficult. A long-term recording of tremor by accelerometry and/or electromyography in the home environment could help to give a better insight into the tremor disorder. However, an evaluation of such recordings using routine clinical standards would take too much time. We evaluated a range of techniques that automatically detect tremor segments in accelerometer data, as accelerometer data is more easily obtained in the home environment than electromyography data. Time can be saved if clinicians only have to evaluate the tremor characteristics of segments that have been automatically detected in longer daily activity recordings. We tested four non-parametric methods and five parametric methods on clinical accelerometer data from 14 patients with different tremor disorders. The consensus between two clinicians regarding the presence or absence of tremor on 3943 segments of accelerometer data was employed as reference. The nine methods were tested against this reference to identify their optimal parameters. Non-parametric methods generally performed better than parametric methods on our dataset when optimal parameters were used. However, one parametric method, employing the high frequency content of the tremor bandwidth under consideration

  3. Thick Concrete Specimen Construction, Testing, and Preliminary Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Clayton, Dwight A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hoegh, Kyle [Univ. of Minnesota, Minneapolis, MN (United States); Khazanovich, Lev [Univ. of Minnesota, Minneapolis, MN (United States)

    2015-03-01

    The purpose of the U.S. Department of Energy Office of Nuclear Energy’s Light Water Reactor Sustainability (LWRS) Program is to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the operating lifetimes of nuclear power plants (NPPs) beyond 60 years. Since many important safety structures in an NPP are constructed of concrete, inspection techniques must be developed and tested to evaluate the internal condition. In-service containment structures generally do not allow for the destructive measures necessary to validate the accuracy of these inspection techniques. This creates a need for comparative testing of the various nondestructive evaluation (NDE) measurement techniques on concrete specimens with known material properties, voids, internal microstructure flaws, and reinforcement locations. A preliminary report detailed some of the challenges associated with thick reinforced concrete sections and prioritized conceptual designs of specimens that could be fabricated to represent NPP concrete structures for using in NDE evaluation comparisons. This led to the construction of the concrete specimen presented in this report, which has sufficient reinforcement density and cross-sectional size to represent an NPP containment wall. Details on how a suitably thick concrete specimen was constructed are presented, including the construction materials, final nominal design schematic, as well as formwork and rigging required to safely meet the desired dimensions of the concrete structure. The report also details the type and methods of forming the concrete specimen as well as information on how the rebar and simulated defects were embedded. Details on how the resulting specimen was transported, safely anchored, and marked to allow access for systematic comparative NDE testing of defects in a representative NPP containment wall concrete specimen are also given. Data collection using the MIRA Ultrasonic NDE equipment and

  4. Specimen environments in thermal neutron scattering experiments

    International Nuclear Information System (INIS)

    Cebula, D.J.

    1980-11-01

    This report is an attempt to collect into one place outline information concerning the techniques used and basic design of sample environment apparatus employed in neutron scattering experiments. Preliminary recommendations for the specimen environment programme of the SNS are presented. The general conclusion reached is that effort should be devoted towards improving reliability and efficiency of operation of specimen environment apparatus and developing systems which are robust and easy to use, rather than achieving performance at the limits of technology. (author)

  5. Prediction of multiaxial fatigue life for notched specimens of titanium alloy TC4

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Z. R.; Li, Z. X. [Southeast University, Nanjing (China); Hu, X. T.; Song, Y. D. [Nanjing University, Nanjing (China)

    2016-05-15

    Both the proportional and nonproportional multiaxial fatigue tests were conducted on two kinds of notched specimens of titanium alloy TC4. The multiaxial fatigue critical area of notched specimen is considered as the location experiencing the maximum damage. It is unsatisfactory to predict the multiaxial fatigue life with the local stress and strain in the fatigue critical area. The critical distance concepts are employed in the multiaxial life prediction method for notched specimens. The proposed method was checked by the test data of TC4 notched specimens. The prediction results are almost within a factor of three scatter band of the test results.

  6. Thermal property testing technique on micro specimen

    International Nuclear Information System (INIS)

    Baba, Tetsuya; Kishimoto, Isao; Taketoshi, Naoyuki

    2000-01-01

    This study aims at establishment of further development on some testing techniques on the nuclear advanced basic research accumulated by the National Research Laboratory of Metrology for ten years. For this purpose, a technology to test heat diffusion ratio and specific heat capacity of less than 3 mm in diameter and 1 mm in thickness of micro specimen and technology to test heat diffusion ratio at micro area of less than 1 mm in area along cross section of less than 10 mm in diameter of column specimen were developed to contribute to common basic technology supporting the nuclear power field. As a result, as an element technology to test heat diffusion ratio and specific heat capacity of the micro specimen, a specimen holding technique stably to hold a micro specimen with 3 mm in diameter could be developed. And, for testing the specific heat capacity by using the laser flush differential calorimetry, a technique to hold two specimen of 5 mm in diameter at their proximities was also developed. In addition, by promoting development of thermal property data base capable of storing thermal property data obtained in this study and with excellent workability in this 1998 fiscal year a data in/out-put program with graphical user interface could be prepared. (G.K.)

  7. Comparative effectiveness and acceptability of home-based and clinic-based sampling methods for sexually transmissible infections screening in females aged 14-50 years: a systematic review and meta-analysis.

    Science.gov (United States)

    Odesanmi, Tolulope Y; Wasti, Sharada P; Odesanmi, Omolola S; Adegbola, Omololu; Oguntuase, Olubukola O; Mahmood, Sajid

    2013-12-01

    Home-based sampling is a strategy to enhance uptake of sexually transmissible infection (STI) screening. This review aimed to compare the screening uptake levels of home-based self-sampling and clinic-based specimen collection for STIs (chlamydia (Chlamydia trachomatis), gonorrhoea (Neisseria gonorrhoeae) and trichomoniasis) in females aged 14-50 years. Acceptability and effect on specimen quality were determined. Sixteen electronic databases were searched from inception to September 2012. Randomised controlled trials (RCTs) comparing the uptake levels of home-based self-sampling and clinic-based sampling for chlamydia, gonorrhoea and trichomoniasis in females aged 14-50 years were eligible for inclusion. The risk of bias in the trials was assessed. Risk ratios (RRs) for dichotomous outcomes were meta-analysed. Of 3065 papers, six studies with seven RCTs contributed to the final review. Compared with clinic-based methods, home-based screening increased uptake significantly (P=0.001-0.05) in five trials and was substantiated in a meta-analysis (RR: 1.55; 95% confidence interval: 1.30-1.85; P=0.00001) of two trials. In three trials, a significant preference for home-based testing (P=0.001-0.05) was expressed. No significant difference was observed in specimen quality. Sampling was rated as easy by a significantly higher number of women (P=0.01) in the clinic group in one trial. The review provides evidence that home-based testing results in greater uptake of STI screening in females (14-50 years) than clinic-based testing without compromising quality in the developed world. Home collection strategies should be added to clinic-based screening programs to enhance uptake.

  8. How useful are delta checks in the 21st century? A stochastic-dynamic model of specimen mix-up and detection

    Directory of Open Access Journals (Sweden)

    Katie Ovens

    2012-01-01

    Full Text Available Introduction: Delta checks use two specimen test results taken in succession in order to detect test result changes greater than expected physiological variation. One of the most common and serious errors detected by delta checks is specimen mix-up errors. The positive and negative predictive values of delta checks for detecting specimen mix-up errors, however, are largely unknown. Materials and Methods: We addressed this question by first constructing a stochastic dynamic model using repeat test values for five analytes from approximately 8000 inpatients in Calgary, Alberta, Canada. The analytes examined were sodium, potassium, chloride, bicarbonate, and creatinine. The model simulated specimen mix-up errors by randomly switching a set number of pairs of second test results. Sensitivities and specificities were then calculated for each analyte for six combinations of delta check equations and cut-off values from the published literature. Results: Delta check specificities obtained from this model ranged from 50% to 99%; however the sensitivities were generally below 20% with the exception of creatinine for which the best performing delta check had a sensitivity of 82.8%. Within a plausible incidence range of specimen mix-ups the positive predictive values of even the best performing delta check equation and analyte became negligible. Conclusion: This finding casts doubt on the ongoing clinical utility of delta checks in the setting of low rates of specimen mix-ups.

  9. Gleason Score Correlation Between Prostate Biopsy and Radical Prostatectomy Specimens

    Directory of Open Access Journals (Sweden)

    Erdem Öztürk

    2018-04-01

    Full Text Available Objective: Prostate cancer is the most common malignancy in men and the second cause of cancer-related mortality. Prostate biopsy and the Gleason score guide treatment decisions in prostate cancer. Several studies have investigated the correlation between biopsy scores and radical prostatectomy specimen scores. We also evaluated the correlation of Gleason scores of these specimens in our patient series. Materials and Methods: We retrospectively reviewed the data of 468 men who were diagnosed with prostate cancer and underwent radical prostatectomy between 2008 and 2017. Patients’ age, prostate-specific antigen levels at diagnosis, and prostate biopsy and radical prostatectomy specimen Gleason scores were recorded. Upgrading and downgrading were defined as increase or decrease of Gleason score of radical prostate specimen compared to Gleason score of prostate biopsy. Results: A total of 442 men diagnosed with prostate cancer were included in the study. The mean age of the patients was 62.62±6.26 years (44-84 years and mean prostate specific antigen level was 9.01±6.84 ng/mL (1.09-49 ng/mL. Prostate biopsy Gleason score was 7 in 27 (6.1% men. Radical prostatectomy specimen Gleason score was 7 in 62 (14% men. Gleason correlation was highest in the 240 patients (71.6% with score <7 and was lowest in the 31 (38.75% patients with score =7. Conclusion: This study demonstrated that the discordance rate between Gleason scores of prostate biopsy and radical prostatectomy specimens was 35.7%.

  10. Imaging of concrete specimens using inverse synthetic aperture radar

    International Nuclear Information System (INIS)

    Rhim, Hong C.; Buyukozturk, Oral

    2000-01-01

    Radar Measurement results of laboratory size concrete specimens are presented in this paper. The purpose of this research work is to study various aspects of the radar method in an effort to develop an improved radar system for nondestructive testing of concrete structures. The radar system used for the study is an Inverse Synthetic Aperture Radar (ISAR), which is capable of transmitting microwaves at three different frequency ranges of 2-3.4, 3.4-5.8, and 8-12 GHz. Radar measurement setup is such that the radar is locates 14.4 m away from a concrete target to satisfy a far-field criterion. The concrete target is rotated for 20 degrees during the measurements for the generation of two-dimensional (cross-range) imagery. Concrete targets used for the measurements have the dimensions of 305 mm (width)x305 mm (height)x92 mm (thickness) with different inside configurations. Comparisons are made for dry and wet specimens, specimens with and without inclusions. Each specimen is made to model various situations that a concrete structure can have in reality. Results show that center frequency, frequency bandwidth, and polarization of the incident wave have different effects on identifying the thickness or inclusions inside concrete specimens. Results also suggest that a certain combination of measurement parameters is suitable for a specific application area. Thus, measurement parameters can be optimized for a specific problem. The findings are presented and discussed in details in the paper. Signal processing schemes implemented for imaging of the specimens are also discussed

  11. Development of piezoelectric ceramics driven fatigue testing machine for small specimens

    International Nuclear Information System (INIS)

    Saito, S.; Kikuchi, K.; Onishi, Y.; Nishino, T.

    2002-01-01

    A new fatigue testing machine with piezoelectric ceramics actuators was developed and a prototype was manufactured for high-cycle fatigue tests with small specimens. The machine has a simple mechanism and is compact. These features make it easy to set up and to maintain the machine in a hot cell. The excitation of the actuator can be transmitted to the specimen using a lever-type testing jig. More than 100 μm of displacement could be prescribed precisely to the specimen at a frequency of 50 Hz. This was sufficient performance for high-cycle bend fatigue tests on specimens irradiated at the SINQ target in Paul Scherrer Institute. The relationship of a displacement applied to the specimen and the strain of the necking part were obtained by experimental methods and by finite element method (FEM) calculations. Both results showed good agreement. This fact makes it possible to evaluate the strain of irradiated specimens by FEM simulations

  12. Fracture toughness of Charpy-size compound specimens and its application in engineering

    International Nuclear Information System (INIS)

    Zhang, X.P.; Shi, Y.W.

    1994-01-01

    The use of a pre-cracked Charpy-size specimen with a side-groove to evaluate the fracture toughness of materials has been researched and considered. This method not only satisfies the demand for small-size specimens in surveillance tests of fracture toughness but also avoids using complicated physical methods to monitor the initial conditions of crack propagation. For most materials this method has solved the problem in which the small-size specimen did not satisfy the valid conditions of a fracture toughness measurement. In order to obtain more information from neutron-irradiated sample specimens and raise the reliability of fracture toughness surveillance tests, it has been considered more important to repeatedly exploit the broken Charpy-size specimen tested in the surveillance test, and to make it renewable. In this work, on the renewing design and utilization of Charpy-size specimens, nine data on fracture toughness can be obtained from one pre-cracked side-grooved Charpy-size specimen, while at present usually only one to three data on fracture toughness can be obtained from one Charpy-size specimen. Thus, it is found that the new method would improve the reliability of fracture toughness surveillance testing and evaluation. In addition, some factors that affect the optimum design of pre-cracked deep side-groove Charpy-size compound specimens have also been discussed. (author)

  13. Contribution of flow cytometry to the diagnosis of gastric lymphomas in endoscopic biopsy specimens.

    Science.gov (United States)

    Almasri, N M; Zaer, F S; Iturraspe, J A; Braylan, R C

    1997-07-01

    Gastric lymphomas seem to have unique clinical, pathologic, and immunophenotypic features that set them apart from nodal lymphomas. Microscopic examination of endoscopic biopsy specimens is the most frequent procedure used to diagnose gastric tumors, but it is very difficult, and sometimes impossible, to recognize lymphomas in endoscopic samples by histologic or even immunohistologic methods. Because most gastric lymphomas are of B-cell origin, we used flow cytometry to assess B-cell clonality in gastric biopsy specimens containing dense lymphocytic infiltrates thought to represent lymphoma. We prepared viable cell suspensions from unfixed specimens obtained from 29 consecutive patients who had a previous microscopic diagnosis of suspicious gastric lymphoid infiltrates. We performed immunophenotypic studies with multicolor flow cytometry, and we assessed clonality by examination of immunoglobulin (Ig) light-chain expression analyzed exclusively on B cells identified by anti-CD20 or CD19 antibodies. The mean number of cells recovered was 1.04 x 10(6), from an average of 5.5 gastric biopsy fragments per patient. In 26 of the 29 patients, the number of cells was adequate for analysis. We detected B-cell monoclonality in 16 cases, including 5 in which the percentage of clonal B cells was less than 5%. Of the 16 cases, only 8 could be diagnosed as lymphomas on morphologic grounds alone; the remaining 8 patients had either suspicious lymphoid infiltrates or chronic gastritis. The three cases with an insufficient number of cells were considered non-neoplastic either on histologic grounds alone or in conjunction with Southern analysis of Ig genes. We conclude that flow cytometric immunophenotypic analysis of freshly prepared cell suspensions obtained from endoscopic biopsy specimens can be used to evaluate gastric lymphocytic infiltrates. Specifically, the analysis of surface Ig light-chain expression on B cells distinguishes between monoclonal (lymphoma) and polyclonal

  14. Performance assessment of two lysis methods for direct identification of yeasts from clinical blood cultures using MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Jeddi, Fakhri; Yapo-Kouadio, Gisèle Cha; Normand, Anne-Cécile; Cassagne, Carole; Marty, Pierre; Piarroux, Renaud

    2017-02-01

    In cases of fungal infection of the bloodstream, rapid species identification is crucial to provide adapted therapy and thereby ameliorate patient outcome. Currently, the commercial Sepsityper kit and the sodium-dodecyl sulfate (SDS) method coupled with MALDI-TOF mass spectrometry are the most commonly reported lysis protocols for direct identification of fungi from positive blood culture vials. However, the performance of these two protocols has never been compared on clinical samples. Accordingly, we performed a two-step survey on two distinct panels of clinical positive blood culture vials to identify the most efficient protocol, establish an appropriate log score (LS) cut-off, and validate the best method. We first compared the performance of the Sepsityper and the SDS protocols on 71 clinical samples. For 69 monomicrobial samples, mass spectrometry LS values were significantly higher with the SDS protocol than with the Sepsityper method (P < .0001), especially when the best score of four deposited spots was considered. Next, we established the LS cut-off for accurate identification at 1.7, based on specimen DNA sequence data. Using this LS cut-off, 66 (95.6%) and 46 (66.6%) isolates were correctly identified at the species level with the SDS and the Sepsityper protocols, respectively. In the second arm of the survey, we validated the SDS protocol on an additional panel of 94 clinical samples. Ninety-two (98.9%) of 93 monomicrobial samples were correctly identified at the species level (median LS = 2.061). Overall, our data suggest that the SDS method yields more accurate species identification of yeasts, than the Sepsityper protocol. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. The development of IRMA method of hepatocarcinoma ferritin and its preliminary clinical application

    International Nuclear Information System (INIS)

    Ying Jilin; Deng Jinglan; Lin Guocheng; Fu Chenghua; Liu Yanfang; Xu Liqing

    1993-01-01

    The double antibody sandwich IRMA method using human hepatocarcinoma ferritin (HF) and anti-HF monoclonal antibody has been established. The intra-assay or inter-assay CV value (%) is 4.1 ∼ 7.3 or 5.1 ∼ 10.9 respectively. The effective assay range of HF is 5 ∼ 640 μg/L. The mean value of recovery rate is 102.5%. The serum HF specimen were measured in 75 cases of normal persons and 230 cases of carcinoma patients. The results showed that the normal value of male or female was 14.3 +- 10.9 μg/L or 11.6 +- 7.0 μg/L, and there was no statistical difference. The serum HF levels in patients of hepatocarcinoma and pulmonary carcinoma were strikingly higher than normal (P<0.001), and also HF levels in patients of breast and pancreas cancer were apparently higher than normal (P<0.05). It has suggested that HF IRMA method has diagnostic significance in above related tumors

  16. The development of IRMA method of hepatocarcinoma ferritin and its preliminary clinical application

    Energy Technology Data Exchange (ETDEWEB)

    Jilin, Ying; Jinglan, Deng; Guocheng, Lin; Chenghua, Fu; Yanfang, Liu; Liqing, Xu [Fourth Military Medical Coll., Xi' an (China). First Affiliated Hospital

    1993-08-01

    The double antibody sandwich IRMA method using human hepatocarcinoma ferritin (HF) and anti-HF monoclonal antibody has been established. The intra-assay or inter-assay CV value (%) is 4.1 [approx] 7.3 or 5.1 [approx] 10.9 respectively. The effective assay range of HF is 5 [approx] 640 [mu]g/L. The mean value of recovery rate is 102.5%. The serum HF specimen were measured in 75 cases of normal persons and 230 cases of carcinoma patients. The results showed that the normal value of male or female was 14.3 +- 10.9 [mu]g/L or 11.6 +- 7.0 [mu]g/L, and there was no statistical difference. The serum HF levels in patients of hepatocarcinoma and pulmonary carcinoma were strikingly higher than normal (P<0.001), and also HF levels in patients of breast and pancreas cancer were apparently higher than normal (P<0.05). It has suggested that HF IRMA method has diagnostic significance in above related tumors.

  17. High resolution SAW elastography for ex-vivo porcine skin specimen

    Science.gov (United States)

    Zhou, Kanheng; Feng, Kairui; Wang, Mingkai; Jamera, Tanatswa; Li, Chunhui; Huang, Zhihong

    2018-02-01

    Surface acoustic wave (SAW) elastography has been proven to be a non-invasive, non-destructive method for accurately characterizing tissue elastic properties. Current SAW elastography technique tracks generated surface acoustic wave impulse point by point which are a few millimeters away. Thus, reconstructed elastography has low lateral resolution. To improve the lateral resolution of current SAW elastography, a new method was proposed in this research. A M-B scan mode, high spatial resolution phase sensitive optical coherence tomography (PhS-OCT) system was employed to track the ultrasonically induced SAW impulse. Ex-vivo porcine skin specimen was tested using this proposed method. A 2D fast Fourier transform based algorithm was applied to process the acquired data for estimating the surface acoustic wave dispersion curve and its corresponding penetration depth. Then, the ex-vivo porcine skin elastogram was established by relating the surface acoustic wave dispersion curve and its corresponding penetration depth. The result from the proposed method shows higher lateral resolution than that from current SAW elastography technique, and the approximated skin elastogram could also distinguish the different layers in the skin specimen, i.e. epidermis, dermis and fat layer. This proposed SAW elastography technique may have a large potential to be widely applied in clinical use for skin disease diagnosis and treatment monitoring.

  18. Measurement properties of clinical assessment methods for classifying generalized joint hypermobility

    DEFF Research Database (Denmark)

    Juul-Kristensen, Birgit; Schmedling, Karoline; Rombaut, Lies

    2017-01-01

    methods. For BS-self, the validity showed unknown evidence compared with test assessment methods. In conclusion, following recommended uniformity of testing procedures, the recommendation for clinical use in adults is BS with cut-point of 5 of 9 including historical information, while in children it is BS...... with cut-point of at least 6 of 9. However, more studies are needed to conclude on the validity properties of these assessment methods, and before evidence-based recommendations can be made for clinical use on the "best" assessment method for classifying GJH. © 2017 Wiley Periodicals, Inc....... for evaluating the methodological quality of the identified studies, all included studies were rated "fair" or "poor." Most studies were using BS, and for BS the reliability most of the studies showed limited positive to conflicting evidence, with some shortcomings on studies for the validity. The three other...

  19. Method to integrate clinical guidelines into the electronic health record (EHR) by applying the archetypes approach.

    Science.gov (United States)

    Garcia, Diego; Moro, Claudia Maria Cabral; Cicogna, Paulo Eduardo; Carvalho, Deborah Ribeiro

    2013-01-01

    Clinical guidelines are documents that assist healthcare professionals, facilitating and standardizing diagnosis, management, and treatment in specific areas. Computerized guidelines as decision support systems (DSS) attempt to increase the performance of tasks and facilitate the use of guidelines. Most DSS are not integrated into the electronic health record (EHR), ordering some degree of rework especially related to data collection. This study's objective was to present a method for integrating clinical guidelines into the EHR. The study developed first a way to identify data and rules contained in the guidelines, and then incorporate rules into an archetype-based EHR. The proposed method tested was anemia treatment in the Chronic Kidney Disease Guideline. The phases of the method are: data and rules identification; archetypes elaboration; rules definition and inclusion in inference engine; and DSS-EHR integration and validation. The main feature of the proposed method is that it is generic and can be applied toany type of guideline.

  20. Action research as a method for changing patient education practice in a clinical diabetes setting

    DEFF Research Database (Denmark)

    Voigt, Jane Rohde; Hansen, Ulla M.; Glindorf, Mette

    2014-01-01

    with researchers developed and implemented a participatory, group-based diabetes education program in a diabetes clinic in the Danish health care system. The research process included a variety of qualitative methods: workshops, classroom observations, video recordings and semi-structured interviews. These methods......Action research is potentially a useful method for changing clinical practice by involving practitioners in the process of change. The aim of this study was to explore the utility of action research in bridging the gap between research and practice. Diabetes educators in collaboration...... aimed at obtaining contextual sensitivity, allowing dynamic interactions with educators and people with diabetes. Despite challenges, the study demonstrates how action research methods contribute to development and change of diabetes education practice while simultaneously adding knowledge to the action...

  1. Changes in nursing students' expectations of nursing clinical faculties' competences: A longitudinal, mixed methods study.

    Science.gov (United States)

    Lovrić, Robert; Prlić, Nada; Milutinović, Dragana; Marjanac, Igor; Žvanut, Boštjan

    2017-12-01

    Changes in nursing students' expectations of their clinical nursing faculty competences over the course of time are an insufficiently researched phenomenon. To explore what competences BSc nursing students expect from their clinical faculties during their clinical training, and whether their expectations changed during their three-year studies. Furthermore, to survey factors which influenced their expectations and whether the fulfilment levels of their expectations influenced their feelings, learning, and behaviour. A two-phase, mixed-methods design was used. The Higher Nursing Education Institution in Osijek, Croatia, European Union. A cohort of 34 BSc nursing students, who were followed over the course of their three-year studies. In Phase I, in each year, prior to their clinical training, participants responded to the same modified Nursing Clinical Teacher Effectiveness Inventory questionnaire about their expectations of clinical faculties' competences (52 items representing six categories of competences). In Phase II, seven days after their graduation, participants wrote reflections on the aforementioned expectations during their studies. The results show that Clinical faculties' evaluation of student was the category in which participants had the highest expectations in all three years. Results of Wilcoxon signed rank test indicate a significant increase of participants' expectations in all categories of clinical nursing faculties' competences during their study. Participants' reflections confirm these results and indicate that actual competences of clinical faculties and behaviour have the most significant effects on the change in these expectations. Participants reported that expectations, if fulfilled, facilitate their learning and motivation for better performance. BSc nursing students' expectations of clinical nursing faculty competences represent an important concept, as they obviously determine the quality of faculty practice. Hence, they should be

  2. A study of active learning methods for named entity recognition in clinical text.

    Science.gov (United States)

    Chen, Yukun; Lasko, Thomas A; Mei, Qiaozhu; Denny, Joshua C; Xu, Hua

    2015-12-01

    Named entity recognition (NER), a sequential labeling task, is one of the fundamental tasks for building clinical natural language processing (NLP) systems. Machine learning (ML) based approaches can achieve good performance, but they often require large amounts of annotated samples, which are expensive to build due to the requirement of domain experts in annotation. Active learning (AL), a sample selection approach integrated with supervised ML, aims to minimize the annotation cost while maximizing the performance of ML-based models. In this study, our goal was to develop and evaluate both existing and new AL methods for a clinical NER task to identify concepts of medical problems, treatments, and lab tests from the clinical notes. Using the annotated NER corpus from the 2010 i2b2/VA NLP challenge that contained 349 clinical documents with 20,423 unique sentences, we simulated AL experiments using a number of existing and novel algorithms in three different categories including uncertainty-based, diversity-based, and baseline sampling strategies. They were compared with the passive learning that uses random sampling. Learning curves that plot performance of the NER model against the estimated annotation cost (based on number of sentences or words in the training set) were generated to evaluate different active learning and the passive learning methods and the area under the learning curve (ALC) score was computed. Based on the learning curves of F-measure vs. number of sentences, uncertainty sampling algorithms outperformed all other methods in ALC. Most diversity-based methods also performed better than random sampling in ALC. To achieve an F-measure of 0.80, the best method based on uncertainty sampling could save 66% annotations in sentences, as compared to random sampling. For the learning curves of F-measure vs. number of words, uncertainty sampling methods again outperformed all other methods in ALC. To achieve 0.80 in F-measure, in comparison to random

  3. The Impact of Storage Times of Museum Insect Specimens on PCR Success: Case Study on Moth Collections in Indonesia

    Directory of Open Access Journals (Sweden)

    HARI SUTRISNO

    2012-06-01

    Full Text Available Museum specimens are vast repositories of genetic information of interests to biological researchers. Since a new method in DNA extraction, a non destructive method, has been reported to be successful in extracting DNA of museum specimens even fossils without any morphological damages, using museum specimens as resources of genetic information for molecular studies is becoming popular recently. However, the PCR success depends on the quality of the specimens. To evaluate the impact of the storage times of museum specimens on PCR success, we conducted DNA extraction of 14 dry museum specimens of the moths collected from 1992 to 2010 by using a non destructive method. The results showed that the DNA specimens museum were fragmented into various sizes (100-1000 bp depend on the storage times. On the other hand, fresh specimens which were preserved within absolute ethanol were almost not fragmented. The specimens of < 6 years old (2005-2010 succeed to amplify in 650 bp amplicon but for some specimens of 7 years old (2 of 3 specimens resulted in a very weak amplification. These specimens, however, were able to amplify strongly in 300 bp amplicon. The results also showed that specimens of 1-19 years old were success to amplify in 100 bp amplicon.

  4. Label-free reflectance hyperspectral imaging for tumor margin assessment: a pilot study on surgical specimens of cancer patients

    Science.gov (United States)

    Fei, Baowei; Lu, Guolan; Wang, Xu; Zhang, Hongzheng; Little, James V.; Patel, Mihir R.; Griffith, Christopher C.; El-Diery, Mark W.; Chen, Amy Y.

    2017-08-01

    A label-free, hyperspectral imaging (HSI) approach has been proposed for tumor margin assessment. HSI data, i.e., hypercube (x,y,λ), consist of a series of high-resolution images of the same field of view that are acquired at different wavelengths. Every pixel on an HSI image has an optical spectrum. In this pilot clinical study, a pipeline of a machine-learning-based quantification method for HSI data was implemented and evaluated in patient specimens. Spectral features from HSI data were used for the classification of cancer and normal tissue. Surgical tissue specimens were collected from 16 human patients who underwent head and neck (H&N) cancer surgery. HSI, autofluorescence images, and fluorescence images with 2-deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-D-glucose (2-NBDG) and proflavine were acquired from each specimen. Digitized histologic slides were examined by an H&N pathologist. The HSI and classification method were able to distinguish between cancer and normal tissue from the oral cavity with an average accuracy of 90%±8%, sensitivity of 89%±9%, and specificity of 91%±6%. For tissue specimens from the thyroid, the method achieved an average accuracy of 94%±6%, sensitivity of 94%±6%, and specificity of 95%±6%. HSI outperformed autofluorescence imaging or fluorescence imaging with vital dye (2-NBDG or proflavine). This study demonstrated the feasibility of label-free, HSI for tumor margin assessment in surgical tissue specimens of H&N cancer patients. Further development of the HSI technology is warranted for its application in image-guided surgery.

  5. A simple method for plasma total vitamin C analysis suitable for routine clinical laboratory use

    OpenAIRE

    Robitaille, Line; Hoffer, L. John

    2016-01-01

    Background In-hospital hypovitaminosis C is highly prevalent but almost completely unrecognized. Medical awareness of this potentially important disorder is hindered by the inability of most hospital laboratories to determine plasma vitamin C concentrations. The availability of a simple, reliable method for analyzing plasma vitamin C could increase opportunities for routine plasma vitamin C analysis in clinical medicine. Methods Plasma vitamin C can be analyzed by high performance liquid chro...

  6. Comparison of two interpolative background subtraction methods using phantom and clinical data

    International Nuclear Information System (INIS)

    Houston, A.S.; Sampson, W.F.D.

    1989-01-01

    Two interpolative background subtraction methods used in scintigraphy are tested using both phantom and clinical data. Cauchy integral subtraction was found to be relatively free of artefacts but required more computing time than bilinear interpolation. Both methods may be used with reasonable confidence for the quantification of relative measurements such as left ventricular ejection fraction and myocardial perfusion index but should be avoided if at all possible in the quantification of absolute measurements such as glomerular filtration rate. (author)

  7. Closeout of JOYO-1 Specimen Fabrication Efforts

    International Nuclear Information System (INIS)

    ME Petrichek; JL Bump; RF Luther

    2005-01-01

    Fabrication was well under way for the JOYO biaxial creep and tensile specimens when the NR Space program was canceled. Tubes of FS-85, ASTAR-811C, and T-111 for biaxial creep specimens had been drawn at True Tube (Paso Robles, CA), while tubes of Mo-47.5 Re were being drawn at Rhenium Alloys (Cleveland, OH). The Mo-47.5 Re tubes are now approximately 95% complete. Their fabrication and the quantities produced will be documented at a later date. End cap material for FS-85, ASTAR-811C, and T-111 had been swaged at Pittsburgh Materials Technology, Inc. (PMTI) (Large, PA) and machined at Vangura (Clairton, PA). Cutting of tubes, pickling, annealing, and laser engraving were in process at PMTI. Several biaxial creep specimen sets of FS-85, ASTAR-811C, and T-111 had already been sent to Pacific Northwest National Laboratory (PNNL) for weld development. In addition, tensile specimens of FS-85, ASTAR-811C, T-111, and Mo-47.5 Re had been machined at Kin-Tech (North Huntington, PA). Actual machining of the other specimen types had not been initiated. Flowcharts 1-3 detail the major processing steps each piece of material has experienced. A more detailed description of processing will be provided in a separate document [B-MT(SRME)-51]. Table 1 lists the in-process materials and finished specimens. Also included are current metallurgical condition of these materials and specimens. The available chemical analyses for these alloys at various points in the process are provided in Table 2

  8. Clinical effect comparison of different surgical methods for treating diabetic retinopathy

    Directory of Open Access Journals (Sweden)

    Qing Wu

    2014-12-01

    Full Text Available AIM: To compare the clinical results of different surgical methods for diabetic antipathy. METHODS: Eighty cases(102 eyeswith diabetic antipathy were selected in our hospital from January 2012 to December 2013. Thirty-eight cases(48 eyesin group A received joint surgical treatment, 42 cases(54 eyesin group B took staging of surgical treatment. The clinical effect was observed in both groups.RESULTS: The vision after surgery was improved than that of before surgery in two groups, there were no significant differences(P>0.05. A postoperative complication rate was 16.7% in group A and 22.2% in group B, showed no significant difference(P>0.05. CONCLUSION: Surgery and staging joint surgery are both feasible for diabetic retinopathy patients, can, improve the visionr. Both of them are worthy of clinical application.

  9. The summer institute in clinical dental research methods: still going and growing after twenty years.

    Science.gov (United States)

    Derouen, Timothy A; Wiesenbach, Carol

    2012-11-01

    The first Summer Institute in Clinical Dental Research Methods, a faculty development program at the University of Washington, was offered in the summer of 1992 for sixteen participants. The primary objective of the program was to give clinical faculty members in dentistry an introduction to and an understanding of the fundamental principles and methods used in good clinical research. In the twentieth offering of the institute in 2011, there were thirty-five participants, and over the twenty institutes, there has been a cumulative total of 463 participants who have come from thirty U.S. states as well as forty-three countries outside the United States. The curriculum has expanded from the initial offering of biostatistics, clinical epidemiology, behavioral research methods, and ethics in clinical research to now include clinical trials, grantsmanship, data analysis, an elective in molecular biology, and a team project that provides participants with hands-on experience in research proposal development as members of an interdisciplinary team. Enrollment has doubled since the first year, yet exit evaluations of the program content have remained consistently high (rated as very good to excellent). One of the indicators of program quality is that at least 50 percent of recent participants indicated that they attended because the program was recommended by colleagues who had attended. There seems to be an ever-increasing pool of dental faculty members who are eager to learn more about clinical research methodology through the institute despite the intensive demands of full-time participation in a six-week program.

  10. Protein Profile study of clinical samples using Laser Induced Fluorescence as the detection method

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Raja, Sujatha N.; Rai, Lavanya

    2009-01-01

      Protein profiles of tissue homogenates were recorded using HPLC separation and LIF detection method. The samples were collected from volunteers with clinically normal or cervical cancer conditions. It is shown that the protein profile can be classified as belonging to malignant or normal state ...

  11. [Adequate application of quantitative and qualitative statistic analytic methods in acupuncture clinical trials].

    Science.gov (United States)

    Tan, Ming T; Liu, Jian-ping; Lao, Lixing

    2012-08-01

    Recently, proper use of the statistical methods in traditional Chinese medicine (TCM) randomized controlled trials (RCTs) has received increased attention. Statistical inference based on hypothesis testing is the foundation of clinical trials and evidence-based medicine. In this article, the authors described the methodological differences between literature published in Chinese and Western journals in the design and analysis of acupuncture RCTs and the application of basic statistical principles. In China, qualitative analysis method has been widely used in acupuncture and TCM clinical trials, while the between-group quantitative analysis methods on clinical symptom scores are commonly used in the West. The evidence for and against these analytical differences were discussed based on the data of RCTs assessing acupuncture for pain relief. The authors concluded that although both methods have their unique advantages, quantitative analysis should be used as the primary analysis while qualitative analysis can be a secondary criterion for analysis. The purpose of this paper is to inspire further discussion of such special issues in clinical research design and thus contribute to the increased scientific rigor of TCM research.

  12. "Unscrambling what's in your head": A mixed method evaluation of clinical supervision for midwives.

    Science.gov (United States)

    Love, Bev; Sidebotham, Mary; Fenwick, Jennifer; Harvey, Susan; Fairbrother, Greg

    2017-08-01

    As a strategy to promote workforce sustainability a number of midwives working in one health district in New South Wales, Australia were trained to offer a reflective model of clinical supervision. The expectation was that these midwives would then be equipped to facilitate clinical supervision for their colleagues with the organisational aim of supporting professional development and promoting emotional well-being. To identify understanding, uptake, perceptions of impact, and the experiences of midwives accessing clinical supervision. Mixed Methods. In phase one 225 midwives were invited to complete a self-administered survey. Descriptive and inferential statistics were used to analyse the data. In phase two 12 midwives were interviewed. Thematic analysis was used to deepen understanding of midwives' experiences of receiving clinical supervision. Sixty percent of midwives responding in phase one had some experience of clinical supervision. Findings from both phases were complementary with midwives reporting a positive impact on their work, interpersonal skills, situational responses and career goals. Midwives described clinical supervision as a formal, structured and confidential space for 'safe reflection' that was valued as an opportunity for self-care. Barriers included misconceptions, perceived work related pressures and a sense that taking time out was unjustifiable. Education, awareness raising and further research into reflective clinical supervision, to support emotional well-being and professional midwifery practice is needed. In addition, health organisations need to design, implement and evaluate strategies that support the embedding of clinical supervision within midwives' clinical practice. Copyright © 2016 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

  13. Uptake of novel statistical methods for early-phase clinical studies in the UK public sector.

    Science.gov (United States)

    Jaki, Thomas

    2013-04-01

    In recent years, the success rate of confirmatory studies has been poor resulting in more emphasis on the conduct of exploratory studies. As one possibility to improve decision-making during the early stages of development, adaptive and Bayesian methods have been recommended. To investigate the current practice in designing early-phase studies in UK public sector research institutions and the use of adaptive and Bayesian methods in particular and to determine factors that hinder the penetration of methodological advances into practice. A questionnaire was sent to all UK clinical trials units (CTUs) to gauge their involvement in early-phase studies and to learn about the designs used in these studies. Follow-up visits to units conducting early-phase studies with round-table discussions around the methods used and the obstacles faced when using adaptive methods were undertaken. More than half of the CTUs are involved in early-phase studies, but conservatism in the methods used in these studies is present. Reasons for novel methodology not being used include a lack of expertise, incompatible funding and unit structure, and a lack of software. Information is collected from UK CTUs, which undertake a large portion (but not all) publicly funded trials. The use of adaptive and Bayesian methods for early-phase clinical studies in the UK public sector is at present limited. Various different initiatives aim to support and facilitate the use of these methods, however, so that an increased use of these methods can be anticipated in the future.

  14. Field theoretical finite element method to provide theoretical calibration curves for the electrical direct-current potential crack-monitoring system as applied to a three-dimensional fracture mechanics specimen with surface crack

    International Nuclear Information System (INIS)

    Dietrich, R.

    1984-01-01

    The basic concepts of the finite element method are explained. The results are compared to existing calibration curves for such test piece geometries derived using experimental procedures. (orig./HP) [de

  15. Fracture toughness evaluation of Eurofer'97 by testing small specimens

    International Nuclear Information System (INIS)

    Serrano, M.; Fernandez, P.; Lapena, J.

    2006-01-01

    The Eurofer'97 is the structural reference material that will be tested in the ITER modules. Its metallurgical properties have been well characterized during the last years. However, more investigations related with the fracture toughness of this material are necessary because this property is one of the most important to design structural components and to study their integrity assessment. In the case of structural materials for fusion reactor the small specimen technology (SSTT) are being actively developed to investigate the fracture toughness among other mechanical properties. The use of small specimens is due to the small available irradiation volume of IFMIF and also due to the high fluence expected in the fusion reactor. The aim of this paper is to determine the fracture toughness of the Eurofer'97 steel by testing small specimens of different geometry in the ductile to brittle transition region, with the application of the Master Curve methodology, and to evaluate this method to assess the decrease in fracture toughness due to neutron irradiation. The tests and data analysis have been performed following the Master Curve approach included in the ASTM Standard E1921-05. Specimen size effect and comparison of the fracture toughness results with data available in the literature are also considered. (author)

  16. [Clinical evaluation of TANDEM PSA in Japanese cases and comparison with other methods].

    Science.gov (United States)

    Kuriyama, M; Yamamoto, N; Shinoda, I; Kawada, Y; Akimoto, S; Shimazaki, J

    1995-01-01

    Clinical evaluation of TANDEM PSA which is the most frequently used prostate specific antigen (PSA) assay method in the world and a comparison with other methods were performed in Japanese cases in a cooperative research fashion. The minimum detectable level of the method was found to be 0.50 ng of PSA in one ml of serum and 1.9 ng/ml was regarded as the upper normal value in Japanese males. The distribution of serum PSA showed a significant difference between the benign prostate hypertrophy (BPH) cases and patients with stage C or D prostate cancer. The sero-diagnosis prostate cancer at an early stage with the TANDEM PSA was difficult. The correlation to other methods of PSA detection was very high. Furthermore, the clinical use of the method in following-up the clinical course of prostate cancer patients was very useful. These findings suggested that the PSA detection using TANDEM PSA is applicable even in Japanese cases although the upper cut-off level is decreased.

  17. The mass angular scattering power method for determining the kinetic energies of clinical electron beams

    International Nuclear Information System (INIS)

    Blais, N.; Podgorsak, E.B.

    1992-01-01

    A method for determining the kinetic energy of clinical electron beams is described, based on the measurement in air of the spatial spread of a pencil electron beam which is produced from the broad clinical electron beam. As predicted by the Fermi-Eyges theory, the dose distribution measured in air on a plane, perpendicular to the incident direction of the initial pencil electron beam, is Gaussian. The square of its spatial spread is related to the mass angular scattering power which in turn is related to the kinetic energy of the electron beam. The measured spatial spread may thus be used to determine the mass angular scattering power, which is then used to determine the kinetic energy of the electron beam from the known relationship between mass angular scattering power and kinetic energy. Energies obtained with the mass angular scattering power method agree with those obtained with the electron range method. (author)

  18. Applying Process Improvement Methods to Clinical and Translational Research: Conceptual Framework and Case Examples.

    Science.gov (United States)

    Daudelin, Denise H; Selker, Harry P; Leslie, Laurel K

    2015-12-01

    There is growing appreciation that process improvement holds promise for improving quality and efficiency across the translational research continuum but frameworks for such programs are not often described. The purpose of this paper is to present a framework and case examples of a Research Process Improvement Program implemented at Tufts CTSI. To promote research process improvement, we developed online training seminars, workshops, and in-person consultation models to describe core process improvement principles and methods, demonstrate the use of improvement tools, and illustrate the application of these methods in case examples. We implemented these methods, as well as relational coordination theory, with junior researchers, pilot funding awardees, our CTRC, and CTSI resource and service providers. The program focuses on capacity building to address common process problems and quality gaps that threaten the efficient, timely and successful completion of clinical and translational studies. © 2015 The Authors. Clinical and Translational Science published by Wiley Periodicals, Inc.

  19. Measurement properties of exsisting clinical assessment methods evaluating scapular positioning and function. A systematic review

    DEFF Research Database (Denmark)

    Larsen, Camilla Marie; Juul-Kristensen, B; Lund, H

    (COSMIN checklist), the methodological quality in the reliability and validity domains was ‘fair’ (57%) to ‘poor’ (43%), with only one study rated as ‘good’. The reliability domain was most often investigated. Fewof the assessment methods in the included studies that had ‘fair’ or ‘good’ measurement......MEASUREMENT PROPERTIES OF EXISTING CLINICAL ASSESSMENT METHODS EVALUATING SCAPULAR POSITIONING AND FUNCTION. A SYSTEMATIC REVIEW1,2Camilla Marie Larsen, 1,3Birgit Juul-Kristensen, 1,3Hans Lund, 1Karen Søgaard1Institute of Sports Science and Clinical Biomechanics, University of Southern Denmark2......,2]. Rehabilitation exercises are aiming at altering abnormal/asymmetric scapular positioning and/or function. Numerous assessment methods have measured the degree of scapular dyskinesis, subjectively by visual evaluation and objectively by measurements of static and dynamic scapular positioning, by either a 3...

  20. Determination of electron clinical spectra from percentage depth dose (PDD) curves by classical simulated annealing method

    International Nuclear Information System (INIS)

    Visbal, Jorge H. Wilches; Costa, Alessandro M.

    2016-01-01

    Percentage depth dose of electron beams represents an important item of data in radiation therapy treatment since it describes the dosimetric properties of these. Using an accurate transport theory, or the Monte Carlo method, has been shown obvious differences between the dose distribution of electron beams of a clinical accelerator in a water simulator object and the dose distribution of monoenergetic electrons of nominal energy of the clinical accelerator in water. In radiotherapy, the electron spectra should be considered to improve the accuracy of dose calculation since the shape of PDP curve depends of way how radiation particles deposit their energy in patient/phantom, that is, the spectrum. Exist three principal approaches to obtain electron energy spectra from central PDP: Monte Carlo Method, Direct Measurement and Inverse Reconstruction. In this work it will be presented the Simulated Annealing method as a practical, reliable and simple approach of inverse reconstruction as being an optimal alternative to other options. (author)

  1. Detection and genotyping of human papilloma virus in cervical cancer specimens from Saudi patients.

    Science.gov (United States)

    Al-Badawi, Ismail A; Al-Suwaine, Abdulrahman; Al-Aker, Murad; Asaad, Lina; Alaidan, Alwaleed; Tulbah, Asma; Fe Bohol, Marie; Munkarah, Adnan R

    2011-07-01

    To determine the rates and types of human papilloma virus (HPV) infection in cervical cancer specimens from Saudi patients. One hundred specimens were randomly selected and retrieved from the achieved samples stored in the pathology department accessioned under the diagnosis of cervical cancer and carcinoma in situ between the years 1997 and 2007. Human papilloma virus in the clinical samples was detected using polymerase chain reaction amplification methods. Two primer systems are commonly used: the MY09-MY11 primers and the GP5+-GP6+ that amplify a wide range of HPV genotypes. Human papilloma virus isolates were genotyped using DNA sequencing and reverse line blot hybridization assay to identify the high-risk HPV genotypes. Ninety cases fulfilled the diagnostic criteria and were analyzed. The rate of HPV genotype detection among cervical cancer samples was 95.5%. The most common HPV genotype detected by both methods was HPV-16 (63.4%), followed by HPV-18 (11.1%), HPV-45 (4.5%), HPV-33 (3.3%), and HPV-31, HPV-52, HPV-53, HPV-58, HPV-59, and HPV-66 with 2.2% prevalence rate each. Prevalence of HPV genotypes among patients with cervical cancer in Saudi Arabia is comparable to the international rates. The use of the reverse line blot hybridization assay genotyping method could be useful for classifying oncogenic HPV-positive women. It is relatively inexpensive and reliable and can be performed in routine practice or epidemiological study compared with the available standard commercial kits.

  2. Asian Americans and Cancer Clinical Trials: A Mixed-Methods Approach to Understanding Awareness and Experience

    Science.gov (United States)

    Paterniti, Debora A.; Chen, Moon S.; Chiechi, Christine; Beckett, Laurel A.; Horan, Nora; Turrell, Corinne; Smith, Ligaya; Morain, Claudia; Montell, Lisa; Gonzalez, Jose Luis; Davis, Sharon; Lara, Primo N.

    2006-01-01

    Cancer clinical trials have been based on low accrual rates. Barriers to recruitment of minority populations affect the generalizability and impact of trial findings for those populations. The authors undertook a mixed-methods approach to understanding levels of awareness and experiences with cancer clinical trials. A survey was administered to new cancer patients and their caretakers (family, close friends, or other social support) at outpatient oncology clinics. Field observations of the trial accrual process also were conducted by employing the grounded theory approach in qualitative methods. Comparison of survey results for Asian-American respondents and non-Asian respondents indicated that Asians were less likely to have heard the term “clinical trial” and were more likely to define a clinical trial as “an experiment” or “a test procedure in a clinic” than non-Asians. Asians were more likely to have employer-based insurance and to report understanding issues related to cost reimbursement. Asians were less likely to have been involved in or to know someone in a trial and reported less willingness than white respondents to consider trial participation. Qualitative observations suggested that Asians who presented for a potential trial were interested in the availability of a novel cancer therapy but were not eligible for available trials. Multiple strategies will be necessary to enhance awareness of and experience with accrual to cancer clinical trials for Asians, including richer understanding and increased involvement of Asians in cancer clinical trials and greater attention to the location and diversity of the Asian population in structuring study centers and evaluating trial results. PMID:16247795

  3. Feasibility study of structured diagnosis methods for functional dyspepsia in Korean medicine clinics

    Directory of Open Access Journals (Sweden)

    Jeong Hwan Park

    2017-12-01

    Full Text Available Background: Functional dyspepsia (FD is the seventh most common disease encountered in Korean medicine (KM clinics. Despite the large number of FD patients visiting KM clinics, the accumulated medical records have no utility in evidence development, due to being unstructured. This study aimed to construct a standard operating procedure (SOP with appropriate structured diagnostic methods for FD, and assess the feasibility for use in KM clinics. Methods: Two rounds of professional surveys were conducted by 10 Korean internal medicine professors to select the representative diagnostic methods. A feasibility study was conducted to evaluate compliance and time required for using the structured diagnostic methods by three specialists in two hospitals. Results: As per the results of the professional survey, five questionnaires and one basic diagnostic method were selected. An SOP was constructed based on the survey results, and a feasibility study showed that the SOP compliance score (out of 5 was 3.45 among the subjects, and 3.25 among the practitioners. The SOP was acceptable and was not deemed difficult to execute. The total execution time was 136.5 minutes, out of which the gastric emptying test time was 129 minutes. Conclusion: This feasibility study of the SOP with structured diagnostic methods for FD confirmed it was adequate for use in KM clinics. It is expected that these study findings will be helpful to clinicians who wish to conduct observational studies as well as to generate quantitative medical records to facilitate Big Data research. Keywords: Big Data, Dyspepsia, Korean medicine, Feasibility studies, Observational study

  4. The effect of residual stresses induced by prestraining on fatigue life of notched specimens

    Science.gov (United States)

    Sadeler, R.; Ozel, A.; Kaymaz, I.; Totik, Y.

    2005-06-01

    The effect of tensile prestraining-induced residual stress on the fatigue life of notched steel parts was investigated. The study was performed on AISI 4140 steel. Rotating bending fatigue tests were carried out on semicircular notched specimens with different notch radii in the as-quenched and tempered conditions. Metallography of the specimens was performed by means of light optical microscopy. The finite-element method was used to evaluate the residual stress distribution near the notch region. Fatigue tests revealed fatigue life improvement for notched specimens, which changes depending on the notch radii and applied stress. Scanning electron microscopy was used to examine the fracture surfaces of the specimens.

  5. Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes.

    Science.gov (United States)

    Hughey, Jeffery R; Gabrielson, Paul W; Rohmer, Laurence; Tortolani, Jacquie; Silva, Mayra; Miller, Kathy Ann; Young, Joel D; Martell, Craig; Ruediger, Erik

    2014-06-04

    Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm(2) of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19(th) and early 20(th) century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

  6. Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

    Science.gov (United States)

    Hughey, Jeffery R.; Gabrielson, Paul W.; Rohmer, Laurence; Tortolani, Jacquie; Silva, Mayra; Miller, Kathy Ann; Young, Joel D.; Martell, Craig; Ruediger, Erik

    2014-01-01

    Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm2 of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method. PMID:24894641

  7. Flipped clinical training: a structured training method for undergraduates in complete denture prosthesis.

    Science.gov (United States)

    K, Anbarasi; K, Kasim Mohamed; Vijayaraghavan, Phagalvarthy; Kandaswamy, Deivanayagam

    2016-12-01

    To design and implement flipped clinical training for undergraduate dental students in removable complete denture treatment and predict its effectiveness by comparing the assessment results of students trained by flipped and traditional methods. Flipped training was designed by shifting the learning from clinics to learning center (phase I) and by preserving the practice in clinics (phase II). In phase I, student-faculty interactive session was arranged to recap prior knowledge. This is followed by a display of audio synchronized video demonstration of the procedure in a repeatable way and subsequent display of possible errors that may occur in treatment with guidelines to overcome such errors. In phase II, live demonstration of the procedure was given. Students were asked to treat three patients under instructor's supervision. The summative assessment was conducted by applying the same checklist criterion and rubric scoring used for the traditional method. Assessment results of three batches of students trained by flipped method (study group) and three traditionally trained previous batches (control group) were taken for comparison by chi-square test. The sum of traditionally trained three batch students who prepared acceptable dentures (score: 2 and 3) and unacceptable dentures (score: 1) was compared with the same of flipped trained three batch students revealed that the number of students who demonstrated competency by preparing acceptable dentures was higher for flipped training (χ 2 =30.996 with p<0.001). The results reveal the supremacy of flipped training in enhancing students competency and hence recommended for training various clinical procedures.

  8. Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

    Directory of Open Access Journals (Sweden)

    Brett E. Etchebarne

    2017-12-01

    Full Text Available Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70–120 min genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx. The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1 real-time thermocycler fluorescent detection of LAMP amplification and (2 visual discrimination of color change in the presence of Eriochrome Black T (EBT dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp was 97.3%, with a positive predictive value (PPV of 53.7% and a negative predictive value (NPV of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a

  9. Novel joint selection methods can reduce sample size for rheumatoid arthritis clinical trials with ultrasound endpoints.

    Science.gov (United States)

    Allen, John C; Thumboo, Julian; Lye, Weng Kit; Conaghan, Philip G; Chew, Li-Ching; Tan, York Kiat

    2018-03-01

    To determine whether novel methods of selecting joints through (i) ultrasonography (individualized-ultrasound [IUS] method), or (ii) ultrasonography and clinical examination (individualized-composite-ultrasound [ICUS] method) translate into smaller rheumatoid arthritis (RA) clinical trial sample sizes when compared to existing methods utilizing predetermined joint sites for ultrasonography. Cohen's effect size (ES) was estimated (ES^) and a 95% CI (ES^L, ES^U) calculated on a mean change in 3-month total inflammatory score for each method. Corresponding 95% CIs [nL(ES^U), nU(ES^L)] were obtained on a post hoc sample size reflecting the uncertainty in ES^. Sample size calculations were based on a one-sample t-test as the patient numbers needed to provide 80% power at α = 0.05 to reject a null hypothesis H 0 : ES = 0 versus alternative hypotheses H 1 : ES = ES^, ES = ES^L and ES = ES^U. We aimed to provide point and interval estimates on projected sample sizes for future studies reflecting the uncertainty in our study ES^S. Twenty-four treated RA patients were followed up for 3 months. Utilizing the 12-joint approach and existing methods, the post hoc sample size (95% CI) was 22 (10-245). Corresponding sample sizes using ICUS and IUS were 11 (7-40) and 11 (6-38), respectively. Utilizing a seven-joint approach, the corresponding sample sizes using ICUS and IUS methods were nine (6-24) and 11 (6-35), respectively. Our pilot study suggests that sample size for RA clinical trials with ultrasound endpoints may be reduced using the novel methods, providing justification for larger studies to confirm these observations. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  10. Stress-deformed state of cylindrical specimens during indirect tensile strength testing

    Directory of Open Access Journals (Sweden)

    Levan Japaridze

    2015-10-01

    Full Text Available In this study, the interaction between cylindrical specimen made of homogeneous, isotropic, and linearly elastic material and loading jaws of any curvature is considered in the Brazilian test. It is assumed that the specimen is diametrically compressed by elliptic normal contact stresses. The frictional contact stresses between the specimen and platens are neglected. The analytical solution starts from the contact problem of the loading jaws of any curvature and cylindrical specimen. The contact width, corresponding loading angle (2θ0, and elliptical stresses obtained through solution of the contact problems are used as boundary conditions for a cylindrical specimen. The problem of the theory of elasticity for a cylinder is solved using Muskhelishvili's method. In this method, the displacements and stresses are represented in terms of two analytical functions of a complex variable. In the main approaches, the nonlinear interaction between the loading bearing blocks and the specimen as well as the curvature of their surfaces and the elastic parameters of their materials are taken into account. Numerical examples are solved using MATLAB to demonstrate the influence of deformability, curvature of the specimen and platens on the distribution of the normal contact stresses as well as on the tensile and compressive stresses acting across the loaded diameter. Derived equations also allow calculating the modulus of elasticity, total deformation modulus and creep parameters of the specimen material based on the experimental data of radial contraction of the specimen.

  11. Use of miniature tensile specimen and video extensometer for measurement of mechanical properties

    International Nuclear Information System (INIS)

    Kumar, Kundan; Pooleery, Arun; Madhusoodanan, K.

    2014-08-01

    Miniaturisation of the tensile test specimen below the sub-size level poses various challenges, such as conformity of specimen to various acceptance criteria as per standard test specimen, aspect ratio, minimum number of grains required in a gauge cross-section, fabrication for uniformity in metrological values, etc. Apart from these, measurement of strain over a very limited available space on the test specimen is another practical challenge. Despite these limitations, miniature specimen testing is increasingly being used worldwide these days. The driving forces behind increasing use of miniature test techniques are new material development, assuring fitness of component after in-service-inspection, low dose of radiation exposure due to smaller dimensions of test specimens etc. However, the evaluation of mechanical properties from a miniature tensile test has a greater advantage over the other miniature novel test techniques, such as small punch test, ABI, miniature fatigue and impact tests etc., as it is a direct method of measurement of mechanical properties. This report covers various aspects of miniature tensile test methodologies, which include geometrical design of specimen having gauge length of 3-5 mm, fabrication, development of special fixtures for gripping the test specimens, and use of optical method for strain measurement. The geometrical design of the specimen and its behaviour over application of tensile load has been established using FEM analysis. A good agreement between conventional and miniature test results exemplifies the potential of the miniature tensile test technique. (author)

  12. Doctors' use of mobile devices in the clinical setting: a mixed methods study.

    Science.gov (United States)

    Nerminathan, Arany; Harrison, Amanda; Phelps, Megan; Alexander, Shirley; Scott, Karen M

    2017-03-01

    Mobile device use has become almost ubiquitous in daily life and therefore includes use by doctors in clinical settings. There has been little study as to the patterns of use and impact this has on doctors in the workplace and how negatively or positively it impacts at the point of care. To explore how doctors use mobile devices in the clinical setting and understand drivers for use. A mixed methods study was used with doctors in a paediatric and adult teaching hospital in 2013. A paper-based survey examined mobile device usage data by doctors in the clinical setting. Focus groups explored doctors' reasons for using or refraining from using mobile devices in the clinical setting, and their attitudes about others' use. The survey, completed by 109 doctors, showed that 91% owned a smartphone and 88% used their mobile devices frequently in the clinical setting. Trainees were more likely than consultants to use their mobile devices for learning and accessing information related to patient care, as well as for personal communication unrelated to work. Focus group data highlighted a range of factors that influenced doctors to use personal mobile devices in the clinical setting, including convenience for medical photography, and factors that limited use. Distraction in the clinical setting due to use of mobile devices was a key issue. Personal experience and confidence in using mobile devices affected their use, and was guided by role modelling and expectations within a medical team. Doctors use mobile devices to enhance efficiency in the workplace. In the current environment, doctors are making their own decisions based on balancing the risks and benefits of using mobile devices in the clinical setting. There is a need for guidelines around acceptable and ethical use that is patient-centred and that respects patient privacy. © 2016 Royal Australasian College of Physicians.

  13. Evaluating current automatic de-identification methods with Veteran’s health administration clinical documents

    Directory of Open Access Journals (Sweden)

    Ferrández Oscar

    2012-07-01

    Full Text Available Abstract Background The increased use and adoption of Electronic Health Records (EHR causes a tremendous growth in digital information useful for clinicians, researchers and many other operational purposes. However, this information is rich in Protected Health Information (PHI, which severely restricts its access and possible uses. A number of investigators have developed methods for automatically de-identifying EHR documents by removing PHI, as specified in the Health Insurance Portability and Accountability Act “Safe Harbor” method. This study focuses on the evaluation of existing automated text de-identification methods and tools, as applied to Veterans Health Administration (VHA clinical documents, to assess which methods perform better with each category of PHI found in our clinical notes; and when new methods are needed to improve performance. Methods We installed and evaluated five text de-identification systems “out-of-the-box” using a corpus of VHA clinical documents. The systems based on machine learning methods were trained with the 2006 i2b2 de-identification corpora and evaluated with our VHA corpus, and also evaluated with a ten-fold cross-validation experiment using our VHA corpus. We counted exact, partial, and fully contained matches with reference annotations, considering each PHI type separately, or only one unique ‘PHI’ category. Performance of the systems was assessed using recall (equivalent to sensitivity and precision (equivalent to positive predictive value metrics, as well as the F2-measure. Results Overall, systems based on rules and pattern matching achieved better recall, and precision was always better with systems based on machine learning approaches. The highest “out-of-the-box” F2-measure was 67% for partial matches; the best precision and recall were 95% and 78%, respectively. Finally, the ten-fold cross validation experiment allowed for an increase of the F2-measure to 79% with partial matches

  14. Preparation of specimens for analysis by: X-ray diffraction and X-ray fluorescence analysis

    International Nuclear Information System (INIS)

    Banos L, L.

    2004-01-01

    Specimen preparation is one of the most important requirements in the analysis of samples by X-ray Diffraction and X-ray Fluorescence. This statement is especially true for samples containing different types of materials. There are many forms of specimen suitable for X-ray analysis and the type of the sample as received will generally determine the method of pretreatment. It is convenient to refer to the material received for analysis as the sample, and that, which is actually analyzed as the specimen. The powder Diffraction method assumes that the particles in the specimen are ideally random orientation and that there are enough crystallites in the specimen to achieve a representative intensity distribution for these crystallites. X ray Fluorescence is essentially a comparative method of analysis, it is vital that all standards and unknowns be presented to the spectrometer in a reproducible and identical manner. (Author) 3 refs., 6 figs

  15. A comparison of three clustering methods for finding subgroups in MRI, SMS or clinical data

    DEFF Research Database (Denmark)

    Kent, Peter; Jensen, Rikke K; Kongsted, Alice

    2014-01-01

    ). There is a scarcity of head-to-head comparisons that can inform the choice of which clustering method might be suitable for particular clinical datasets and research questions. Therefore, the aim of this study was to perform a head-to-head comparison of three commonly available methods (SPSS TwoStep CA, Latent Gold...... LCA and SNOB LCA). METHODS: The performance of these three methods was compared: (i) quantitatively using the number of subgroups detected, the classification probability of individuals into subgroups, the reproducibility of results, and (ii) qualitatively using subjective judgments about each program...... classify individuals into those subgroups. CONCLUSIONS: Our subjective judgement was that Latent Gold offered the best balance of sensitivity to subgroups, ease of use and presentation of results with these datasets but we recognise that different clustering methods may suit other types of data...

  16. Effectiveness of Plastinated Anatomical Specimens Depicting Common Sports Injuries to Enhance Musculoskeletal Injury Evaluation Education

    Science.gov (United States)

    Tamura, Kaori; Stickley, Christopher D.; Labrash, Steven J.; Lozanoff, Scott

    2014-01-01

    Context: Plastination techniques have emerged as effective methods for preserving human tissue and enabling human specimens to be utilized in a fashion similar to anatomical models with much greater accuracy. Opportunities to observe and experience human specimens in classroom settings should be beneficial to undergraduate and graduate students in…

  17. Small specimen measurements of dynamic fracture toughness of heavy section steels for nuclear pressure vessel

    International Nuclear Information System (INIS)

    Tanaka, Y.; Iwadate, T.; Suzuki, K.

    1987-01-01

    This study presents the dynamic fracture toughness properties (KId) of 12 heats of RPV steels measured using small specimens and analysed based on the current research. The correlation between the KId test and other engineering small specimen tests such as Charpy test and drop weight test are also discussed and a method to predict the KId value is presented. (orig./HP)

  18. Preparation of transmission electron microscopy cross-section specimens using focused ion beam milling

    International Nuclear Information System (INIS)

    Langford, R.M.; Petford-Long, A.K.

    2001-01-01

    The preparation of transmission electron microscopy cross-section specimens using focused ion beam milling is outlined. The 'liftout' and 'trench' techniques are both described in detail, and their relative advantages and disadvantages are discussed. Artifacts such as ion damage to the top surface and sidewalls of the cross-section specimens, and methods of reducing them, are addressed

  19. Sem-observation of developing plant organs using deep-frozen specimens

    NARCIS (Netherlands)

    NN,

    1982-01-01

    The SEM-observation of plant material normally requires dehydrated, dry specimens coated with carbon or metal. Unfortunately, the standard drying methods (including the critical-point-drying-technique) often cause shrinking and deformation of the specimen surface; therefore, SEMstudies on plant

  20. Study of brittle fracture in thick walled structures using small and large specimens

    International Nuclear Information System (INIS)

    Norrthon, J.-O.; Carlsson, J.

    1979-01-01

    A Russian pressure vessel steel has been investigated for fracture toughness data, Ksub(Ic) and Jsub(Ic). Four large specimens have been tested and the results correlated to data from several smaller specimens. Onset of crack growth has been detected by a high frequency electric method. (author)

  1. Bedside Teaching: Is it Effective Methods in Clinical Nursing Students Learning?

    Directory of Open Access Journals (Sweden)

    Fatikhu Yatuni Asmara

    2017-01-01

    Full Text Available Introduction: Clinical learning is the centre of medical students education. Students not only learn about practical skills but also communication with patient and other health care givers which both competencies are useful for students when they come into working world (Spencer, 2003. There are variations of methods applied in clinical learning process; one of them is bedside teaching. The aim of this study was to observe the bedside teaching process which is held in group of students, teacher, and patient. Another aim was to know responses of students, teacher, and patients to the bedside teaching process. Method: The method which was applied in this study is observation in which bedside teaching process was observed related to the roles and function of each component of bedside teaching: students, teacher, and patient in each phase: preparation, process, and evaluation. Then it was continued by interview to know the responses of students, teacher, and patient related to bedside teaching process. Result: The result showed that both students and teacher felt that bedside teaching is an effective method since it helped students to achieve their competences in clinical setting and develop their communication skill. Furthermore teacher stated that bedside teaching facilitated her to be a good role model for students. As well as students and teacher, patient got advantage from the bedside teaching process that she got information related to her case; however the time to discuss was limited. During the observation, each component of bedside teaching did their roles and function, such as: during the preparation teacher asked inform consent from patient, and patient gave inform consent as well while students prepared the material. Discussions: Suggestion for next research is conducting a deeper study about perception of students, teacher, and patient about bedside teaching process and the strategies to develop it to be better method. Keywords: bedside

  2. Resampling Approach for Determination of the Method for Reference Interval Calculation in Clinical Laboratory Practice▿

    Science.gov (United States)

    Pavlov, Igor Y.; Wilson, Andrew R.; Delgado, Julio C.

    2010-01-01

    Reference intervals (RI) play a key role in clinical interpretation of laboratory test results. Numerous articles are devoted to analyzing and discussing various methods of RI determination. The two most widely used approaches are the parametric method, which assumes data normality, and a nonparametric, rank-based procedure. The decision about which method to use is usually made arbitrarily. The goal of this study was to demonstrate that using a resampling approach for the comparison of RI determination techniques could help researchers select the right procedure. Three methods of RI calculation—parametric, transformed parametric, and quantile-based bootstrapping—were applied to multiple random samples drawn from 81 values of complement factor B observations and from a computer-simulated normally distributed population. It was shown that differences in RI between legitimate methods could be up to 20% and even more. The transformed parametric method was found to be the best method for the calculation of RI of non-normally distributed factor B estimations, producing an unbiased RI and the lowest confidence limits and interquartile ranges. For a simulated Gaussian population, parametric calculations, as expected, were the best; quantile-based bootstrapping produced biased results at low sample sizes, and the transformed parametric method generated heavily biased RI. The resampling approach could help compare different RI calculation methods. An algorithm showing a resampling procedure for choosing the appropriate method for RI calculations is included. PMID:20554803

  3. Differences in quantitative methods for measuring subjective cognitive decline - results from a prospective memory clinic study

    DEFF Research Database (Denmark)

    Vogel, Asmus; Salem, Lise Cronberg; Andersen, Birgitte Bo

    2016-01-01

    influence reports of cognitive decline. METHODS: The Subjective Memory Complaints Scale (SMC) and The Memory Complaint Questionnaire (MAC-Q) were applied in 121 mixed memory clinic patients with mild cognitive symptoms (mean MMSE = 26.8, SD 2.7). The scales were applied independently and raters were blinded...... decline. Depression scores were significantly correlated to both scales measuring subjective decline. Linear regression models showed that age did not have a significant contribution to the variance in subjective memory beyond that of depressive symptoms. CONCLUSIONS: Measures for subjective cognitive...... decline are not interchangeable when used in memory clinics and the application of different scales in previous studies is an important factor as to why studies show variability in the association between subjective cognitive decline and background data and/or clinical results. Careful consideration...

  4. Preparation of TEM specimen by cross-section technique

    International Nuclear Information System (INIS)

    Hamada, Shozo

    1986-01-01

    Transmission electron microscopy (TEM) is applied to the direct observation of the depth dependent damage structure in ion-irradiated stainless steel by using the cross-section technique; obtaining the TEM specimen from a slice of the irradiated stainless steel with thick Ni plating. Here has been developed the specimen preparation method of cross-section technique without heat treatment, which was necessary in the conventional method to strengthen the bonding between Ni and stainless steel. Nickel plating with good bonding to stainless steel is enabled by the following manner. First, the irradiated stainless steel is immersed in the Wood's nickel solution at room temperature for 60s to activate the surface, followed by the stricking for 300s at a current density of 300 A/m 2 in the solution to make fine and homogeneous nucleation of Ni on the stainless steel. Then, the sample is plated with Ni in the Watt's nickel plating solution at 333 K with current density of 900 ∼ 1,000 A/m 2 . The TEM disc is obtained by mechanical slicing from the specimen with Ni plating of more than 3 mm thickness. Electropolishing is accomplished by using both Ballmann method and jet electropolishing to perforate the disc accurately at the aimed point for the observation of the damage structure. (author)

  5. 3D printing from microfocus computed tomography (micro-CT) in human specimens: education and future implications.

    Science.gov (United States)

    Shelmerdine, Susan C; Simcock, Ian C; Hutchinson, John Ciaran; Aughwane, Rosalind; Melbourne, Andrew; Nikitichev, Daniil I; Ong, Ju-Ling; Borghi, Alessandro; Cole, Garrard; Kingham, Emilia; Calder, Alistair D; Capelli, Claudio; Akhtar, Aadam; Cook, Andrew C; Schievano, Silvia; David, Anna; Ourselin, Sebastian; Sebire, Neil J; Arthurs, Owen J

    2018-06-14

    Microfocus CT (micro-CT) is an imaging method that provides three-dimensional digital data sets with comparable resolution to light microscopy. Although it has traditionally been used for non-destructive testing in engineering, aerospace industries and in preclinical animal studies, new applications are rapidly becoming available in the clinical setting including post-mortem fetal imaging and pathological specimen analysis. Printing three-dimensional models from imaging data sets for educational purposes is well established in the medical literature, but typically using low resolution (0.7 mm voxel size) data acquired from CT or MR examinations. With higher resolution imaging (voxel sizes below 1 micron, printing of micro-CT imaged specimens can provide insight into craniofacial surgical applications, developmental cardiac anatomy, placental imaging, archaeological remains and high-resolution bone imaging. We conclude with other potential future usages of this emerging technique.

  6. Comparative evaluation of uniplex, nested, semi-nested, multiplex and nested multiplex PCR methods in the identification of microbial etiology of clinically suspected infectious endophthalmitis.

    Science.gov (United States)

    Bharathi, Madasamy Jayahar; Murugan, Nandagopal; Rameshkumar, Gunasekaran; Ramakrishnan, Rengappa; Venugopal Reddy, Yerahaia Chinna; Shivkumar, Chandrasekar; Ramesh, Srinivasan

    2013-05-01

    This study is aimed to determine the utility of various polymerase chain reaction (PCR) methods in vitreous fluids (VFs) for detecting the infectious genomes in the diagnosis of infectious endophthalmitis in terms of sensitivity and specificity. This prospective and consecutive analysis included a total of 66 VFs that were submitted for the microbiological evaluation, which were obtained from 66 clinically diagnosed endophthalmitis patients presented between November 2010 and October 2011 at the tertiary eye care referral centre in South India. Part of the collected VFs were subjected to cultures and smears, and the remaining parts were utilized for five PCR methods: uniplex, nested, semi-nested, multiplex and nested multiplex after extracting DNA, using universal eubacterial and Propionibacterium acnes species-specific primer sets targeting 16S rRNA gene in all bacteria and P. acnes, and panfungal primers, targeting 28S rRNA gene in all fungi. Of the 66 VFs, five (7.5%) showed positive results in smears, 16 (24%) in cultures and 43 (65%) showed positive results in PCRs. Among the 43 positively amplified VFs, 10 (15%) were positive for P. acnes genome, one for panfungal genome and 42 (62%) for eubacterial genome (including 10 P. acnes positives). Among 42 eubacterial-positive VFs, 36 were positive by both uniplex (first round) and multiplex (first round) PCRs, while nested (second round) and nested multiplex (second round) PCRs produced positive results in 42 and 41 VFs, respectively. Of the 43 PCR-positive specimens, 16 (37%) had positive growth (15 bacterial and one fungal) in culture. Of 50 culture-negative specimens, 27 (54%) were showed positive amplification, of which 10 were amplified for both P. acnes and eubacterial genomes and the remaining 17 were for eubacterial genome alone. Nested PCRs are superior than uniplex and multiplex PCR. PCRs proved to be a powerful tool in the diagnosis of endophthalmitis, especially for detecting uncultured microbes.

  7. Effect of ultraviolet light on creatinine measurement in jaundiced specimens

    International Nuclear Information System (INIS)

    Nisbet, J.A.; D'Souza, R.

    1986-01-01

    During initial evaluation of a creatinine method using the RA-1000 analyser, experiments with addition of bilirubin indicated negligible interference. However the finding of a 'zero' creatinine value in an extremely jaundiced specimen prompted to re-examine the method. In contrast to earlier findings with normal plasma containing added bilirubin, the authors found that plasma from moderately or severely jaundiced patients gave creatinine values lower than those obtained with a reference method. Since bilirubin has been implicated in the interference, the authors studied the effect of destroying bilirubin with ultraviolet light to see if this provided a practical solution to the problem. (Auth.)

  8. Virus isolation: Specimen type and probable transmission

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Virus isolation: Specimen type and probable transmission. Over 500 CHIK virus isolations were made. 4 from male Ae. Aegypti (?TOT). 6 from CSF (neurological involvement). 1 from a 4-day old child (transplacental transmission.

  9. Some recent innovations in small specimen testing

    International Nuclear Information System (INIS)

    Odette, G.R.; He, M.; Gragg, D.; Klingensmith, D.; Lucas, G.E.

    2002-01-01

    New innovative small specimen test techniques are described. Finite element simulations show that combinations of cone indentation pile-up geometry and load-penetration depth relations can be used to determine both the yield stress and strain-hardening behavior of a material. Techniques for pre-cracking and testing sub-miniaturized fracture toughness bend bars, with dimensions of 1.65x1.65x9 mm 3 , or less, are described. The corresponding toughness-temperature curves have a very steep transition slope, primarily due to rapid loss of constraint, which has advantages in some experiments to characterize the effects of specified irradiation variables. As one example of using composite specimens, an approach to evaluating helium effects is proposed, involving diffusion bonding small wires of a 54 Fe-based ferritic-martensitic alloy to a surrounding fracture specimen composed of an elemental Fe-based alloy. Finally, we briefly outline some potential approaches to multipurpose specimens and test automation

  10. Comparative study among calibration methods of clinical applicators of beta radiation

    International Nuclear Information System (INIS)

    Antoni