Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens.

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Wong, Anita A; Pabbaraju, Kanti; Wong, Sallene; Tellier, Raymond

2016-03-01

Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here. Copyright © 2015 Elsevier B.V. All rights reserved.

Efficacy of an anaerobic swab transport system to maintain aerobic and anaerobic microorganism viability after storage at -80 degrees C.

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Musser, Jeffrey M B; Gonzalez, Rosa

2011-01-01

An Amies agar gel swab transport system was evaluated for its ability to maintain bacterial viability and relative quantity after freezing at -80°C. Nine American Type Culture Collection (ATCC) bacterial strains were used: 3 anaerobic strains (Propionibacterium acnes, Peptostreptococcus anaerobius, and Clostridium sporogenes) and 6 facultative or strict aerobic bacterial strains (Stenotrophomonas maltophilia, Escherichia coli ([ATCC 25922 and ATCC 11775], Salmonella enterica subsp. enterica serovar Typhimurium, Staphylococcus saprophyticus, and Lactobacillus casei). The bacterial species were chosen because they corresponded to bacteria identified in psittacine feces and cloacal samples. There were no significant differences between growth scores at baseline and after storage at -80°C for 40 days for any of the bacteria examined after 48 and 72 hr of incubation, with the exception of P. anaerobius. For P. anaerobius, there was a significant reduction (P < 0.001) in the growth score after storage at -80°C for 40 days from that of the baseline; however, the bacteria were still viable. The tested swab transport system may be useful when lengthy storage and transport times necessitate freezing samples prior to culture.

Development and evaluation of the quantitative real-time PCR assay in detection and typing of herpes simplex virus in swab specimens from patients with genital herpes.

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Liu, Junlian; Yi, Yong; Chen, Wei; Si, Shaoyan; Yin, Mengmeng; Jin, Hua; Liu, Jianjun; Zhou, Jinlian; Zhang, Jianzhong

2015-01-01

Genital herpes (GH), which is caused mainly by herpes simplex virus (HSV)-2 and HSV-1, remains a worldwide problem. Laboratory confirmation of GH is important, particularly as there are other conditions which present similarly to GH, while atypical presentations of GH also occur. Currently, virus culture is the classical method for diagnosis of GH, but it is time consuming and with low sensitivity. A major advance for diagnosis of GH is to use Real-time polymerase chain reaction (PCR). In this study, to evaluate the significance of the real-time PCR method in diagnosis and typing of genital HSV, the primers and probes targeted at HSV-1 DNA polymerase gene and HSV-2 glycoprotein D gene fraction were designed and applied to amplify DNA from HSV-1 or HSV-2 by employing the real-time PCR technique. Then the PCR reaction system was optimized and evaluated. HSV in swab specimens from patients with genital herpes was detected by real-time PCR. The real-time PCR assay showed good specificity for detection and typing of HSV, with good linear range (5×10(2)~5×10(8) copies/ml, r=0.997), a sensitivity of 5×10(2) copies/ml, and good reproducibility (intra-assay coefficients of variation 2.29% and inter-assay coefficients of variation 4.76%). 186 swab specimens were tested for HSV by real-time PCR, and the positive rate was 23.7% (44/186). Among the 44 positive specimens, 8 (18.2%) were positive for HSV-1 with a viral load of 8.5546×10(6) copies/ml and 36 (81.2%) were positive for HSV-2 with a viral load of 1.9861×10(6) copies/ml. It is concluded that the real-time PCR is a specific, sensitive and rapid method for the detection and typing of HSV, which can be widely used in clinical diagnosis of GH.

Pseudo-outbreak of Cupriavidus pauculus infection at an outpatient clinic related to rinsing culturette swabs in tap water.

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Balada-Llasat, Joan-Miquel; Elkins, Camille; Swyers, Lettie; Bannerman, Tammy; Pancholi, Preeti

2010-07-01

Cupriavidus pauculus is a water microorganism rarely isolated from clinical specimens. We describe a pseudo-outbreak in which multiple strains that were associated with moistening of culturette swabs with tap water were isolated from a single clinic before collecting the patient specimen.

Pseudo-Outbreak of Cupriavidus pauculus Infection at an Outpatient Clinic Related to Rinsing Culturette Swabs in Tap Water▿

OpenAIRE

Balada-Llasat, Joan-Miquel; Elkins, Camille; Swyers, Lettie; Bannerman, Tammy; Pancholi, Preeti

2010-01-01

Cupriavidus pauculus is a water microorganism rarely isolated from clinical specimens. We describe a pseudo-outbreak in which multiple strains that were associated with moistening of culturette swabs with tap water were isolated from a single clinic before collecting the patient specimen.

Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

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Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

2016-10-01

Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Pseudo-Outbreak of Cupriavidus pauculus Infection at an Outpatient Clinic Related to Rinsing Culturette Swabs in Tap Water▿

Science.gov (United States)

Balada-Llasat, Joan-Miquel; Elkins, Camille; Swyers, Lettie; Bannerman, Tammy; Pancholi, Preeti

2010-01-01

Cupriavidus pauculus is a water microorganism rarely isolated from clinical specimens. We describe a pseudo-outbreak in which multiple strains that were associated with moistening of culturette swabs with tap water were isolated from a single clinic before collecting the patient specimen. PMID:20444965

Randomized Comparison of Two Vaginal Self-Sampling Methods for Human Papillomavirus Detection: Dry Swab versus FTA Cartridge.

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Rosa Catarino

Full Text Available Human papillomavirus (HPV self-sampling (self-HPV is valuable in cervical cancer screening. HPV testing is usually performed on physician-collected cervical smears stored in liquid-based medium. Dry filters and swabs are an alternative. We evaluated the adequacy of self-HPV using two dry storage and transport devices, the FTA cartridge and swab.A total of 130 women performed two consecutive self-HPV samples. Randomization determined which of the two tests was performed first: self-HPV using dry swabs (s-DRY or vaginal specimen collection using a cytobrush applied to an FTA cartridge (s-FTA. After self-HPV, a physician collected a cervical sample using liquid-based medium (Dr-WET. HPV types were identified by real-time PCR. Agreement between collection methods was measured using the kappa statistic.HPV prevalence for high-risk types was 62.3% (95%CI: 53.7-70.2 detected by s-DRY, 56.2% (95%CI: 47.6-64.4 by Dr-WET, and 54.6% (95%CI: 46.1-62.9 by s-FTA. There was overall agreement of 70.8% between s-FTA and s-DRY samples (kappa = 0.34, and of 82.3% between self-HPV and Dr-WET samples (kappa = 0.56. Detection sensitivities for low-grade squamous intraepithelial lesion or worse (LSIL+ were: 64.0% (95%CI: 44.5-79.8 for s-FTA, 84.6% (95%CI: 66.5-93.9 for s-DRY, and 76.9% (95%CI: 58.0-89.0 for Dr-WET. The preferred self-collection method among patients was s-DRY (40.8% vs. 15.4%. Regarding costs, FTA card was five times more expensive than the swab (~5 US dollars (USD/per card vs. ~1 USD/per swab.Self-HPV using dry swabs is sensitive for detecting LSIL+ and less expensive than s-FTA.International Standard Randomized Controlled Trial Number (ISRCTN: 43310942.

Randomized comparison of vaginal self-sampling by standard vs. dry swabs for Human papillomavirus testing

International Nuclear Information System (INIS)

Eperon, Isabelle; Vassilakos, Pierre; Navarria, Isabelle; Menoud, Pierre-Alain; Gauthier, Aude; Pache, Jean-Claude; Boulvain, Michel; Untiet, Sarah; Petignat, Patrick

2013-01-01

To evaluate if human papillomavirus (HPV) self-sampling (Self-HPV) using a dry vaginal swab is a valid alternative for HPV testing. Women attending colposcopy clinic were recruited to collect two consecutive Self-HPV samples: a Self-HPV using a dry swab (S-DRY) and a Self-HPV using a standard wet transport medium (S-WET). These samples were analyzed for HPV using real time PCR (Roche Cobas). Participants were randomized to determine the order of the tests. Questionnaires assessing preferences and acceptability for both tests were conducted. Subsequently, women were invited for colposcopic examination; a physician collected a cervical sample (physician-sampling) with a broom-type device and placed it into a liquid-based cytology medium. Specimens were then processed for the production of cytology slides and a Hybrid Capture HPV DNA test (Qiagen) was performed from the residual liquid. Biopsies were performed if indicated. Unweighted kappa statistics (κ) and McNemar tests were used to measure the agreement among the sampling methods. A total of 120 women were randomized. Overall HPV prevalence was 68.7% (95% Confidence Interval (CI) 59.3–77.2) by S-WET, 54.4% (95% CI 44.8–63.9) by S-DRY and 53.8% (95% CI 43.8–63.7) by HC. Among paired samples (S-WET and S-DRY), the overall agreement was good (85.7%; 95% CI 77.8–91.6) and the κ was substantial (0.70; 95% CI 0.57-0.70). The proportion of positive type-specific HPV agreement was also good (77.3%; 95% CI 68.2-84.9). No differences in sensitivity for cervical intraepithelial neoplasia grade one (CIN1) or worse between the two Self-HPV tests were observed. Women reported the two Self-HPV tests as highly acceptable. Self-HPV using dry swab transfer does not appear to compromise specimen integrity. Further study in a large screening population is needed. ClinicalTrials.gov: http://clinicaltrials.gov/show/NCT01316120

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

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

1994-04-01

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

Comparative study of the swabbing properties of seven commercially available swab materials for cleaning verification.

Science.gov (United States)

Corrigan, Damion K; Piletsky, Sergey; McCrossen, Sean

2009-01-01

This article compares the technical performances of several different commercially available swabbing materials for the purpose of cleaning verification. A steel surface was soiled with solutions of acetaminophen, nicotinic acid, diclofenac, and benzamidine and wiped with each swabbing material. The compounds were extracted with water or ethanol (depending on polarity of analyte) and their concentration in extract was quantified spectrophotometrically. The study also investigated swab debris on the wiped surface. The swab performances were compared and the best swab material was identified.

Instant Transport Media for Biopsied Soft Tissue Specimens: A Comparative Study

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Shankargouda Patil

2015-01-01

Full Text Available Background. Formalin, a traditionally preferred fixative in the field of pathology, has restricted usage in private settings. Since its toxicity violates the Occupational Safety and Health Administration regulations, an eco-friendly alternative would be the need of the hour. Hence an instant media which is economical and nontoxic and enables easy transport of biopsied soft tissue specimens in its original state is of vital importance. Materials and Methods. Commercially available fresh goat buccal mucosa specimens were sliced into smaller bits of equal dimensions and placed in six different containers containing 20% honey, 30% jaggery, milk, and ice for 1 hr, 6 hours, 12 hours, and 24 hours each with formalin as a positive control. After the set time interval, the specimens were fixed in 10% buffered formalin for 24 hours followed by routine processing and staining. The histologic interpretations were a blinded procedure and evaluated by two experts. Results were statistically analysed. Results. 30% jaggery proved to be an ideal transport media showing high quality preservation after 24 hours. 20% honey and ice showed optimal tissue preservation up to 6 hours following which quality deteriorated. Tissues transported in milk showed poor preservation. Conclusion. 30% jaggery can be endorsed in routine histopathological analysis as a transport media.

Comparison among performances of a ligase chain reaction-based assay and two enzyme immunoassays in detecting Chlamydia trachomatis in urine specimens from men with nongonococcal urethritis.

Science.gov (United States)

Deguchi, T; Yasuda, M; Uno, M; Tada, K; Iwata, H; Komeda, H; Maeda, S; Latila, V; Saito, I; Kawada, Y

1996-01-01

We evaluated the performances of a ligase chain reaction (LCR)-based assay and two enzyme immunoassays (Chlamydiazyme and IDEIA) in the detection of Chlamydia trachomatis in urine specimens. We compared the results of testing urine specimens by these assays with those of urethral swab culture by examining samples from 131 men with nongonococcal urethritis. Discrepant results were analyzed by testing urethral swab specimens for C. trachomatis by a PCR-based assay. After the resolution of discrepant results, the sensitivity of urethral swab culture was 85.3%, whereas those of the LCR assay, Chlamydiazyme, and IDEIA with urine specimens were 94.1, 82.4, and 94.1%, respectively. The LCR assay and IDEIA were more sensitive than was urethral swab culture. In addition, the LCR assay, with a sensitivity equal to that of IDEIA, was more specific. Overall, the LCR assay proved to be superior to the enzyme immunoassays in detecting C. trachomatis in urine specimens. Testing urine specimens by LCR assay should be a helpful alternative method for diagnosing C. trachomatis urethral infection in men with nongonococcal urethritis. PMID:8784574

Microchip capillary electrophoresis with laser-induced fluorescence combined with one-step duplex reverse-transcription polymerase chain reaction for the rapid detection of Enterovirus 71 and Coxsackievirus A16 in throat swab specimens.

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Jia, Ruan; Chengjun, Sun; Heng, Chen; Chen, Zhou; Yuanqian, Li; Yongxin, Li

2015-07-01

Enterovirus 71 and Coxsackievirus A16 are the main pathogens causing hand-foot-mouth disease. In this paper, microchip capillary electrophoresis with laser-induced fluorescence combined with one-step duplex reverse transcript-polymerase chain reaction has been developed for the detection of Enterovirus 71 and Coxsackievirus A16 in throat swab specimens. The specific reverse transcription-polymerase chain reaction amplicons labeled with SYBR Orange were separated by microchip capillary electrophoresis and detected by laser induced fluorescence detector within 7 min. The intraday and interday relative standard deviation of migration time for DNA Marker was in the range of 1.36-2.94 and 2.78-3.96%, respectively. The detection limits were as low as 2.06 × 10(3) copies/mL for Enterovirus 71 and 5 × 10(3) copies/mL for Coxsackievirus A16. No cross-reactivity was observed with rotavirus, astrovirus, norovirus, and adenovirus, which showed good specificity of the method. This assay was validated using 100 throat swab specimens that were detected by real-time reverse-transcript polymerase chain reaction in parallel and the two methods produced the same results. This study provided a rapid, sensitive and specific method for the detection of Enterovirus 71 and Coxsackievirus A16, which make a contribution to significant time and cost saving for the identification and treatment of patients. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

21 CFR 864.3250 - Specimen transport and storage container.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Specimen transport and storage container. 864.3250 Section 864.3250 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Pathology Instrumentation and Accessories § 864...

HIV-1 and herpes simplex virus type-2 genital shedding among co-infected women using self-collected swabs in Chiang Rai, Thailand.

Science.gov (United States)

Forhan, S E; Dunne, E F; Sternberg, M R; Whitehead, S J; Leelawiwat, W; Thepamnuay, S; Chen, C; Evans-Strickfaden, Tt; McNicholl, J M; Markowitz, L E

2012-08-01

We analysed 528 genital self-collected swabs (SCS) from 67 HIV-1 and herpes simplex virus type-2 (HSV-2) co-infected women collected during the placebo month of a randomized crossover clinical trial of suppressive acyclovir in Chiang Rai, Thailand. In this first longitudinal study of HIV-1 and HSV-2 co-infected women using genital SCS specimens, we found frequent mucosal HIV-1 shedding. Overall, 372 (70%) swabs had detectable HIV-1 RNA with median HIV-1 viral load of 2.61 log(10) copies/swab. We found no statistically significant association between detectable HIV-1 RNA and HSV-2 DNA in the same SCS specimen (adjusted odds ratio [aOR] 1.40; 95% confidence intervals [CI], 0.78-2.60, P = 0.25). Only baseline HIV-1 plasma viral load was independently associated with genital HIV-1 RNA shedding (aOR, 7.6; 95% CI, 3.3-17.2, P genital sampling, and inclusion of genital sites other than the cervix.

Test performance and acceptability of self- versus provider-collected swabs for high-risk HPV DNA testing in female-to-male trans masculine patients.

Science.gov (United States)

Reisner, Sari L; Deutsch, Madeline B; Peitzmeier, Sarah M; White Hughto, Jaclyn M; Cavanaugh, Timothy P; Pardee, Dana J; McLean, Sarah A; Panther, Lori A; Gelman, Marcy; Mimiaga, Matthew J; Potter, Jennifer E

2018-01-01

High-risk human papillomavirus (hrHPV) causes virtually all cervical cancers. Trans masculine (TM) people (those assigned female at birth who identify with a gender other than female) have low uptake of conventional cervical cancer screening. Self-collected hrHPV DNA testing has high levels of acceptability among cisgender (non-transgender) females and may support increased cervical cancer screening uptake in TM individuals. To assess the test performance and acceptability of self-collected vaginal specimens in comparison to provider-collected cervical swabs for hrHPV DNA detection in TM individuals ages 21-64 years. Between March 2015-September 2016, 150 TM participants with a cervix (mean age = 27.5 years; SD = 5.7) completed a one-time study visit comprised of a self-report survey, self-collected vaginal HPV DNA swab, clinician-administered cervical HPV swab, and brief interview on acceptability of clinical procedures. Participants were randomized to complete either self- or provider-collection first to minimize ordering effects. Self- and provider-collected samples were tested for 13 hrHPV DNA types using a DNA Hybridization Assay. The primary outcome variable was the concordance (kappa statistic) and performance (sensitivity, specificity) of self-collected vaginal HPV DNA specimens versus provider-collected cervical HPV swabs as the gold standard. Of the 131 participants completing both the self- and provider-collected HPV tests, 21 cases of hrHPV were detected by the provider cervical swab (gold standard; 16.0% hrHPV prevalence); 15 of these cases were accurately detected by the self-collected vaginal swab (71.4% concordance) (Kappa = 0.75, 95% Confidence Interval [CI]: 0.59, 0.92; p<0.001). Compared to the provider-collected cervical hrHPV DNA sample (gold standard), the self-collected vaginal hrHPV DNA test demonstrated a sensitivity of 71.4% (95% CI: 0.52, 0.91; p = 0.0495) and specificity of 98.2% (95% CI: 0.96, 1.00; p<0.0001). Over 90% of participants

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

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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.

Improving the transport of urgent specimens to an off-site laboratory using a novel sticker-tracker.

Science.gov (United States)

Sepahzad, Afsoon; Ejiofor, Florence; Giles, Susan; Klaber, Robert

2013-01-01

Obtaining results for urgent microbiology specimens in an efficient manner is imperative to ensure that patients receive appropriate antibiotic therapy. A previous audit carried out in the Paediatric department of a central teaching hospital and a number of clinical incidents, highlighted a delay in transport of specimens (exceeding eight hours) and 'missing' specimens. This results in empirical antibiotic treatment of infection, with delay in confirming microbiology result and unnecessary, distressing repeat investigation. As an initial step we sought staff opinion to further explore the problem. A sticker was designed for the microbiology specimen bag to assign accountability, track each step in the transport process and to raise awareness of the problem. The sticker required the member of staff responsible at each stage of the process to time, date and sign it, to allow tracking of potential delays. The new sticker tracking system was promoted and launched in the Paediatric department. Initial challenges included lack of awareness of the protocol and lack of pods for sending urgent specimens. The team met regularly and completed stickers were analysed weekly to identify on-going issues and to devise solutions. Consequently total transport time was reduced to an average of 69 minutes by September (within four hr target). Our intervention improved the efficiency and reliability of urgent specimen transport. This is likely to result in safer antibiotic use and avoid the need for repeat investigation. The system is now also used in the Neonatal department and has lead to the development of a new 'Central Specimens Reception'.

Evaluation of self-swabbing coupled with a telephone health helpline as an adjunct tool for surveillance of influenza viruses in Ontario

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D. McGolrick

2016-09-01

Full Text Available Abstract Background Calls to a telephone health helpline (THHL have been previously evaluated for the ability to monitor specific syndromes, such as fever and influenza-like-illness or gastrointestinal illness. This method of surveillance has been shown to be highly correlated with traditional surveillance methods, and to have potential for early detection of community-based illness. Self-sampling, or having a person take his/her own nasal swab, has also proven successful as a useful method for obtaining a specimen, which may be used for respiratory virus detection. Methods This study describes a self-swabbing surveillance system mediated by a nurse-led THHL in Ontario whereby syndromic surveillance concepts are used to recruit and monitor participants with influenza-like illness. Once recruited, participants collect a nasal specimen obtained by self-swabbing and submit for testing and laboratory confirmation. Enumeration of weekly case counts was used to evaluate the timeliness of the self-swabbing surveillance system through comparison to other respiratory virus and influenza surveillance systems in Ontario. The operational efficiency of the system was also evaluated. Results The mean and median number of days between the day that a participant called the THHL, to the day a package was received at the laboratory for testing were approximately 10.4 and 8.6 days, respectively. The time between self-swab collection and package reception was 4.9 days on average, with a median of 4 days. The self-swabbing surveillance system adequately captured the 2014 influenza B season in a timely manner when compared to other Ontario-based sources of influenza surveillance data from the same year; however, the emergence of influenza B was not detected any earlier than with these other surveillance systems. Influenza A surveillance was also evaluated. Using the THHL self-swabbing system, a peak in the number of cases for influenza A was observed approximately

An evaluation of clinical performance of FTA cards for HPV 16/18 detection using cobas 4800 HPV Test compared to dry swab and liquid medium.

Science.gov (United States)

Dong, Li; Lin, Chunqing; Li, Li; Wang, Margaret; Cui, Jianfeng; Feng, Ruimei; Liu, Bin; Wu, Zeni; Lian, Jia; Liao, Guangdong; Chen, Wen; Qiao, Youlin

2017-09-01

Effective dry storage and transport media as an alternative to conventional liquid-based medium would facilitate the accessibility of women in the low-resource settings to human papillomavirus (HPV)- based cervical cancer screening. To evaluate analytical and clinical performance of indicating FTA™ Elute Cartridge (FTA card) for the detection of HPV16/18 and cervical precancerous lesions and cancer compared to dry swab and liquid medium. Ninety patients with abnormal cytology and/or HPV infection were included for analysis. Three specimens of cervical exfoliated cells from each woman were randomly collected by FTA card, dry swab or liquid-based medium prior to colposcopy examination. The subsequent HPV DNA tests were performed on cobas 4800 HPV platform. High-risk HPV (hrHPV) positivity rate was 63.3%, 62.2% and 65.6% for samples collected by FTA card, dry swab and liquid medium, respectively. The overall agreements and kappa values for the detection of hrHPV, HPV 16 and HPV 18 between FTA card and liquid-based medium were 88.9% (κ=0.76), 97.8% (κ=0.94) and 100% (κ=1.0),respectively; between FTA card and dry swab were 92.1% (κ=0.83), 94.5% (κ=0.87) and 100% (κ=1.0), respectively. The performances of hrHPV tested by FTA card, dry swab, and liquid-based medium for detecting CIN2+ were comparable in terms of the sensitivity and specificity. The specificity of detection of CIN2+ by HPV16/18 increased by approximately 40% compared to hrHPV for any medium albeit at cost of a moderate loss of sensitivity. Dry medium might offer an alternative to conventional liquid-based medium in the HPV-based cervical cancer screening program especially in low-resource settings but still needs further evaluation. Copyright © 2017. Published by Elsevier B.V.

Comparison of automated processing of flocked swabs with manual processing of fiber swabs for detection of nasal carriage of Staphylococcus aureus.

Science.gov (United States)

Jones, Gillian; Matthews, Roger; Cunningham, Richard; Jenks, Peter

2011-07-01

The sensitivity of automated culture of Staphylococcus aureus from flocked swabs versus that of manual culture of fiber swabs was prospectively compared using nasal swabs from 867 patients. Automated culture from flocked swabs significantly increased the detection rate, by 13.1% for direct culture and 10.2% for enrichment culture.

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

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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.

Comparison of Automated Processing of Flocked Swabs with Manual Processing of Fiber Swabs for Detection of Nasal Carriage of Staphylococcus aureus▿‡

Science.gov (United States)

Jones, Gillian; Matthews, Roger; Cunningham, Richard; Jenks, Peter

2011-01-01

The sensitivity of automated culture of Staphylococcus aureus from flocked swabs versus that of manual culture of fiber swabs was prospectively compared using nasal swabs from 867 patients. Automated culture from flocked swabs significantly increased the detection rate, by 13.1% for direct culture and 10.2% for enrichment culture. PMID:21525218

Randomized Comparison of Two Vaginal Self-Sampling Methods for Human Papillomavirus Detection: Dry Swab versus FTA Cartridge

OpenAIRE

Catarino, Rosa; Vassilakos, Pierre; Bilancioni, Aline; Vanden Eynde, Mathieu; Meyer-Hamme, Ulrike; Menoud, Pierre-Alain; Guerry, Fr?d?ric; Petignat, Patrick

2015-01-01

Background Human papillomavirus (HPV) self-sampling (self-HPV) is valuable in cervical cancer screening. HPV testing is usually performed on physician-collected cervical smears stored in liquid-based medium. Dry filters and swabs are an alternative. We evaluated the adequacy of self-HPV using two dry storage and transport devices, the FTA cartridge and swab. Methods A total of 130 women performed two consecutive self-HPV samples. Randomization determined which of the two tests was performed f...

Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections

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Philip M. Giffard

2017-06-01

Full Text Available Background The microbiome of built environment surfaces is impacted by the presence of humans. In this study, we tested the hypothesis that analysis of surface swabs from clinic toilet/bathroom yields results correlated with sexually transmitted infection (STI notifications from corresponding human populations. We extended a previously reported study in which surfaces in toilet/bathroom facilities in primary health clinics in the Australian Northern Territory (NT were swabbed then tested for nucleic acid from the STI agents Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. This was in the context of assessing the potential for such nucleic acid to contaminate specimens collected in such facilities. STIs are notifiable in the NT, thus allowing comparison of swab and notification data. Methods An assumption in the design was that while absolute built environment loads of STI nucleic acids will be a function of patient traffic density and facility cleaning protocols, the relative loads of STI nucleic acids from different species will be largely unaffected by these processes. Another assumption was that the proportion of swabs testing positive for STIs provides a measure of surface contamination. Accordingly, “STI profiles” were calculated. These were the proportions that each of the three STIs of interest contributed to the summed STI positive swabs or notifications. Three comparisons were performed, using swab data from clinics in remote Indigenous communities, clinics in small-medium towns, and a single urban sexual health clinic. These data were compared with time and place-matched STI notifications. Results There were significant correlations between swab and notifications data for the both the remote Indigenous and regional data. For the remote Indigenous clinics the p values ranged from 0.041 to 0.0089, depending on data transformation and p value inference method. Further, the swab data appeared to strongly indicate

Comparison of air samples, nasal swabs, ear-skin swabs and environmental dust samples for detection of Methicillin Resistant Staphylococcus aureus (MRSA) in pig herds

DEFF Research Database (Denmark)

Agersø, Yvonne; Vigre, Håkan; Cavaco, Lina

2014-01-01

To identify a cost-effective and practical method for detection of methicillin-resistant Staphylococcus aureus (MRSA) in pig herds, the relative sensitivity of four sample types: nasal swabs, ear-skin (skin behind the ears) swabs, environmental dust swabs and air was compared. Moreover, dependency......-herd prevalence ⩾25%]. The results indicate that taking swabs of skin behind the ears (ten pools of five) was even more sensitive than taking nasal swabs (ten pools of five) at the herd level and detected significantly more positive samples. spa types t011, t034 and t4208 were observed. In conclusion, MRSA...... detection by air sampling is easy to perform, reduces costs and analytical time compared to existing methods, and is recommended for initial testing of herds. Ear-skin swab sampling may be more sensitive for MRSA detection than air sampling or nasal swab sampling....

'Swab racks are an old fashioned idea'.

Science.gov (United States)

Mumford, M

1991-12-01

Mary Mumford, theatre sister at the Princes of Wales Hospital, Bridgend, was asked to speak in a short debate at an NATN branch meeting, supporting the motion that 'swab racks are an old fashioned idea'. Although she did not like swab racks she had not attempted thus far to do anything about them. In the event, she actually lost the debate--not in principle but because she could offer no effective alternative method of checking swabs. Having been given the incentive, a trial is now being conducted in her hospital similar to that described by Paul Wicker. This is the case presented by Mary Mumford supporting the following motion ... 'that swab racks are an old fashioned idea, which cause more potential problems due to exposure of blood than is proven to be safe in today's theatre environment'.

Forensic analysis of explosive residues from hand swabs

International Nuclear Information System (INIS)

Umi Khairul Ahmad; Sumathy Rajendran; Syahidah Abu Hassan

2008-01-01

In the forensic examination of physical evidence for organic explosives, cotton swabs are often used to collect residue from surfaces, such as skin and post-blast debris. A preliminary study has been conducted to develop extraction method of a common energetic compound, pentaerythritol tetranitrate (PETN) from hand swabs followed by direct analysis of the resulting extract solution using high-performance liquid chromatography (HPLC) with ultraviolet (UV) detector. Analysis was performed on an octadecylsilane-based (C 18 ) column using acetonitrile-water mixture (55:45) as mobile phase. The mobile phase was pumped at 1.0 mL/ min and separation affected using an isocratic mode with the detection wavelength of 230 nm. The explosive residue was extracted from cotton swabs using acetone in an ultrasonic cold bath. The developed method was later applied to the real hand swabs samples, which were taken from three army personnel who handled PETN during a munition disposal operation at Asahan Camp Military Firing range. The acetone extract obtained using sonication method was found to be effective in recovering PETN from cotton swabs with relatively high recovery (89.5 %) and good sensitivity with detection limit as low as 2 ng. The content of PETN in the real hand swab samples were found to be in the range of 4.7-130 mg. (author)

Interpretation of nasal swab measurements following suspected releases of actinide aerosols

International Nuclear Information System (INIS)

Klumpp, John Allan; Bertelli, Luiz; Waters, Tom L.

2017-01-01

For radionuclides such as plutonium and americium, detection of removable activity in the nose (i.e., nasal swab measurements) are frequently used to determine whether follow-up bioassay measurements are warranted following a potential intake. For this paper, the authors analyzed 429 nasal swab measurements taken following incidents or suspicious circumstances (such as an air monitor alarming) at Los Alamos National Laboratory (LANL) for which the dose was later evaluated using in vitro bioassay. Nasal swab measurements were found to be very poor predictors of dose and should not be used as such in the field. However, nasal swab measurements can be indicative of whether a reliably detectable committed effective dose (CED) occurred. About 14% of nasal swab measurements between 1.25 and 16.7 Bq corresponded to CEDs greater than 1 mSv, so in general, positive nasal swabs always indicate that follow-up bioassay should be performed (positive nasal swabs less than 1.25 Bq are considered separately). This probability increased significantly for nasal swabs greater than 16.7 Bq. Only about 3% of nasal swabs with no detectable activity (NDA) corresponded to reliably detectable CEDs. As a result, a nasal swab with NDA is therefore necessary, but not sufficient, to negate the need for a follow-up bioassay if it was collected following other workplace indicators of a potential intake.

Consensus of microbiology reporting of ear swab results to primary care clinicians in patients with otitis externa.

Science.gov (United States)

Geyer, M; Howell-Jones, R; Cunningham, R; McNulty, C

2011-01-01

Otitis externa is a ubiquitous inflammatory disease; although it arises most commonly from an infection, there is no consensus in the UK for the reporting of ear swab culture results. This study aims to review current microbiology laboratory reporting of ear swab specimens to primary care and reach an evidence-based consensus for a reporting policy. Fifty consecutive ear swab reports were reviewed from each of 12 laboratories in the South West region to determine and discuss reporting practice. The Health Protection Agency (HPA) GP Microbiology Laboratory Use Group reviewed the underlying evidence and worked towards a consensus of expert microbiology opinion for laboratory reporting of ear swab results using a modified version of the Delphi technique. A total of 487 reports from primary care were reviewed (54% female; 46% male). Cultures most commonly yielded Pseudomonas species (36%), Staphylococcus species (21%), Streptococcus species (15%) and fungi (11%). Five reporting policies were agreed: Policy 1: Common pathogens such as group A beta-haemolytic streptococci, Streptococcus pneumoniae, Staphylococcus aureus - Always reported by name with antibiotic susceptibilities. Policy 2: Pseudomonas species - Always reported, but antibiotic susceptibilities only reported in severe disease. Policy 3: Aspergillus, Candida, coliforms and Proteus species, as well as non-group A streptococci and anaerobes - Only reported if moderate numbers of colonies and it is the predominant organism present; if appropriate report antibiotic susceptibilities. Policy 4: Coagulase-negative staphylococci, diphtheroids and enterococci - Not reported by name; generic terms used and antibiotic susceptibilities not reported. Policy 5: When antibiotic susceptibilities reported these must include susceptibility to a topical antibiotic. It is suggested that laboratories should consider adopting this evidence-based reporting consensus for ear swab culture results from primary care patients with

A simple and novel method for retrieval of Pasteurellaceae from swab samples collected in the field

DEFF Research Database (Denmark)

Hansen, Mie J; Bertelsen, Mads F; Dietz, Rune

2013-01-01

and stored at -20°C. As a control study, 15 samples were collected from the oral cavity of a captive brown bear. One was immediately plated, while the remaining 12 swabs were stored at -20°C for 7 days and multiples of 30 days up to 330 days prior to plating. Two samples were stored without the medium for 7......Traditionally it has been difficult or impossible to collect and preserve bacterial samples of especially fastidious bacteria in mixed primary cultures, unless the samples could be transported to a laboratory within approximately 24 h. Therefore, a simple novel method for preserving swab samples...... until bacterial isolation can be completed in the laboratory was developed and evaluated. Pasteurellaceae bacteria were used as a representative for fastidious bacteria. A 7.5% glucose serum medium was used as freeze medium. Swab samples were soaked in the medium a maximum of 2 h after collection...

A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs.

Science.gov (United States)

Manage, Dammika P; Lauzon, Jana; Atrazhev, Alexey; Morrissey, Yuen C; Edwards, Ann L; Stickel, Alexander J; Crabtree, H John; Pabbaraju, Kanti; Zahariadis, George; Yanow, Stephanie K; Pilarski, Linda M

2012-05-07

Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.

Development of an ELISA for evaluation of swab recovery efficiencies of bovine serum albumin.

Directory of Open Access Journals (Sweden)

Nadja Sparding

Full Text Available After a potential biological incident the sampling strategy and sample analysis are crucial for the outcome of the investigation and identification. In this study, we have developed a simple sandwich ELISA based on commercial components to quantify BSA (used as a surrogate for ricin with a detection range of 1.32-80 ng/mL. We used the ELISA to evaluate different protein swabbing procedures (swabbing techniques and after-swabbing treatments for two swab types: a cotton gauze swab and a flocked nylon swab. The optimal swabbing procedure for each swab type was used to obtain recovery efficiencies from different surface materials. The surface recoveries using the optimal swabbing procedure ranged from 0-60% and were significantly higher from nonporous surfaces compared to porous surfaces. In conclusion, this study presents a swabbing procedure evaluation and a simple BSA ELISA based on commercial components, which are easy to perform in a laboratory with basic facilities. The data indicate that different swabbing procedures were optimal for each of the tested swab types, and the particular swab preference depends on the surface material to be swabbed.

Seeking responsibility for the lost swab? Search elsewhere.

Science.gov (United States)

Wheeler, R; Blackburn, S; Biggs, H

2014-04-01

This article explores the possibility that the surgeon's control over his or her environment is not complete and that, in certain circumstances, the final swab count can be distinguished from the 'normal course of events'. We readily accept that most swabs and instruments are left inside patients simply as a result of substandard care but we cannot accept that this is invariably the case, and lessons from the common law are cited to illustrate the reasons why. We hope to persuade defendant lawyers that it might be worthwhile to tease out from surgeons under scrutiny how these factors may have influenced their practice on the day that a swab was retained.

Comparação entre dois meios de coleta e transporte para estudo da microbiota conjuntival de indivíduos normais Comparison of two transportation media for study of normal individual conjunctival microbiota

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Daniel Cruz Nogueira

2007-12-01

Casa Misericórdia de São Paulo, in August of 2006. Eighty normal eyes of 40 healthy individuals were analyzed. Samples were collected in the right eye with a dry swab and stored in Stuart's medium, where all microbiological material is kept immersed in the medium and the tube is hermetically sealed. In the left eye, the conjunctival material was collected using a swab embedded in saline solution 0.9%, and stored in dry and sterile test tubes sealed with cotton. The samples were analyzed within 2 hours at most after collection. RESULTS: Out of 40 samples collected with wet swab and transported in dry tube, bacteria were observed in 10 (25%, whereas of 40 samples collected with dry swab and transported in Stuart's medium, 12 (30% had bacteria. CONCLUSION: The results of the microbiological profile of normal conjunctival microbiota using dry swab in Stuart's medium were statistically similar (p=0.85 to those obtained in wet swab in dry tube for spreading performed within 2 hours after collection of conjunctival specimen.

Differential contributions of specimen types, culturing, and 16S rRNA sequencing in diagnosis of prosthetic joint infections

DEFF Research Database (Denmark)

Larsen, Lone Heimann; Khalid, Vesal; Xu, Yijuan

2018-01-01

Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due...... to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint...... fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study...

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.

EVA Swab Tool to Support Planetary Protection and Astrobiology Evaluations

Science.gov (United States)

Rucker, Michelle A.; Hood, Drew; Walker, Mary; Venkateswaran, Kasthuri J.; Schuerger, Andrew C.

2018-01-01

When we send humans to search for life on other planets, we'll need to know what we brought with us versus what may already be there. To ensure our crewed systems meet planetary protection requirements-and to protect our science from human contamination-we'll need to assess whether microorganisms may be leaking or venting from our spacecraft. Microbial sample collection outside of a pressurized spacecraft is complicated by temperature extremes, low pressures that preclude the use of laboratory standard (wetted) swabs, and operation either in bulky spacesuits or with robotic assistance. A team at the National Aeronautics and Space Administration (NASA) recently developed a swab kit for use in collecting microbial samples from the external surfaces of crewed spacecraft, including spacesuits. The Extravehicular Activity (EVA) Swab Kit consists of a single swab tool handle and an eight-canister sample caddy. The design team minimized development cost by re-purposing a heritage Space Shuttle tile repair handle that was designed to quickly snap into different tool attachments by engaging a mating device in each end effector. This allowed the tool handle to snap onto a fresh swab end effector much like popular shaving razor handles can snap onto a disposable blade cartridge. To disengage the handle from a swab, the user performs two independent functions, which can be done with a single hand. This dual operation mitigates the risk that a swab will be inadvertently released and lost in microgravity. Each swab end effector is fitted with commercially available foam swab tips, vendor-certified to be sterile for Deoxyribonucleic Acid (DNA). A microbial filter installed in the bottom of each sample container allows the container to outgas and re-pressurize without introducing microbial contaminants to internal void spaces. Extensive ground testing, post-test handling, and sample analysis confirmed the design is able to maintain sterile conditions as the canister moves between

A simplified field protocol for genetic sampling of birds using buccal swabs

Science.gov (United States)

Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.

2018-01-01

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

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

Isolation and identification of female DNA on postcoital penile swabs.

Science.gov (United States)

Cina, S J; Collins, K A; Pettenati, M J; Fitts, M

2000-06-01

After sexual assault, cells originating from the assailant may be recovered from the victim. Through polymerase chain reaction (PCR)-based technology, positive scientific identification of the assailant may be made from these cells. Described is a prospective study describing a method for positively identifying cells from a female sex partner obtained from postcoital swabs of the penis of the male sex partner. Swabs were taken from the penis of a man at 1- to 24-hour intervals after coitus. DNA was isolated from each swab through standard organic extraction methods. The presence of female DNA was detected using the gender-specific amelogenin marker. Extracted DNA was amplified for eight different genetic loci using the Promega PowerPlex kit (Promega) and Amplitaq Gold (Perkin Elmer). Amplified samples were electrophoresed on precast sequencing gels (Hitachi) and were analyzed fluorescently using Hitachi's FMBIO 2 fluorescent scanner and software. Each sample obtained from a penile swab or condom was compared to male and female buccal controls. Female DNA was isolated from all postcoital penile swabs as determined by exclusive amplification of the X-chromosome specific 212 base pair amelogenin marker. In all cases, scientific identification of the female DNA from the swabs was determined by coamplification of eight STR loci (PowerPlex) and was compared to female and male control profiles. Cells shed from a female victim during sexual intercourse can be retrieved from the penis of a male offender after sexual intercourse during a 1- to 24-hour postcoital interval. DNA can be extracted from these cells and can be used to scientifically identify the female sexual participant through PCR-based technology. It is suggested that penile swabs be taken from alleged perpetrators of sexual assaults to associate them with a female victim.

Detection and Serogrouping of Dichelobacter nodosus Infection by Use of Direct PCR from Lesion Swabs To Support Outbreak-Specific Vaccination for Virulent Footrot in Sheep.

Science.gov (United States)

McPherson, Andrew S; Dhungyel, Om P; Whittington, Richard J

2018-04-01

Virulent footrot is an economically significant disease in most sheep-rearing countries. The disease can be controlled with vaccine targeting the fimbriae of virulent strains of the essential causative agent, Dichelobacter nodosus However, the bacterium is immunologically heterogeneous, and 10 distinct fimbrial serogroups have been identified. Ideally, in each outbreak the infecting strains would be cultured and serogrouped so that the appropriate serogroup-specific mono- or bivalent vaccine could be administered, because multivalent vaccines lack efficacy due to antigenic competition. If clinical disease expression is suspected to be incomplete, culture-based virulence tests are required to confirm the diagnosis, because control of benign footrot is economically unjustifiable. Both diagnosis and vaccination are conducted at the flock level. The aims of this study were to develop a PCR-based procedure for detecting and serogrouping D. nodosus directly from foot swabs and to determine whether this could be done accurately from the same cultured swab. A total of 269 swabs from the active margins of foot lesions of 261 sheep in 12 Merino sheep flocks in southeastern Australia were evaluated. DNA extracts taken from putative pure cultures of D. nodosus and directly from the swabs were evaluated in PCR assays for the 16S rRNA and fimA genes of D. nodosus Pure cultures were tested also by the slide agglutination test. Direct PCR using extracts from swabs was more sensitive than culture for detecting and serogrouping D. nodosus strains. Using the most sensitive sample collection method of the use of swabs in lysis buffer, D. nodosus was more likely to be detected by PCR in active than in inactive lesions, and in lesions with low levels of fecal contamination, but lesion score was not a significant factor. PCR conducted on extracts from swabs in modified Stuart's transport medium that had already been used to inoculate culture plates had lower sensitivity. Therefore, if

Improving communication at handover and transfer reduces retained swabs in maternity services.

Science.gov (United States)

Lean, Katie; Page, Bethan F; Vincent, Charles

2018-01-01

To reduce the incidence of retained vaginal swabs and near misses. A review of previous retained swab incidents and near misses in a large maternity unit identified handovers and transfers as a key point of vulnerability. Interventions were introduced to improve communication at handover from the delivery suite to theatre and from theatre to the high dependency unit. Process data was collected to monitor compliance. The outcome measures were the incidence of retained swab never events and the incidence of near misses. Chi-squared analysis was used to test the significance of the results. For transfers from delivery suite to theatre, verbal handover significantly increased from 28.8% to 75.6% (ptransfers to theatre post-intervention: in 88 (30.2%) of these transfers a vaginal swab was already in situ. In 70/88 (79.5%) of cases the presence of the swab was communicated to theatre staff in three ways (verbally, written and transfer of opened swab packets) according to the new policy. In the post-intervention period there were 56 women transferred from theatre to the high-dependency unit with a vaginal pack in situ: 52 (92.9%) of these women had a sticker in place serving as a constant reminder of the presence of the vaginal pack to staff. Following a baseline of four near misses in two months, there has been only one near miss in the 15 months since the interventions were implemented, (33.3% vs. 1.1%, pcommunication at handover and transfer can reduce the incidence of retained vaginal swabs and near misses. Further work is needed to raise the profile of swab counting in maternity settings: swab counting needs to be the responsibility of all disciplines, not just the responsibility of theatre staff. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Peyronie's disease after urethral swab, an unusual complication: a case report

Directory of Open Access Journals (Sweden)

Paulis G

2015-11-01

Full Text Available Gianni Paulis,1,2 Davide Barletta3 1Andrology Center, Regina Apostolorum Hospital, Albano Laziale, Rome, Italy; 2Castelfidardo Medical Team, Peyronie's Disease Care Center, Rome, Italy; 3Department of Urology, Andrology Center, San Matteo Hospital, Pavia, Italy Abstract: Urethral swabs are still currently used as a diagnostic tool when urethritis or prostatitis are suspected. Urologists are certainly aware that Peyronie's disease may occur after traumatic urethral instrumentation (catheterization, urethrocystoscopy, etc, but onset of Peyronie's disease after urethral swab for diagnostic purposes has never been reported in the literature. This paper presents the case of a patient who developed Peyronie's disease after a clumsy urethral swab insertion. It is an unusual, and to date unreported, complication which we would like to call attention to. In the case of our patient, the swab had been inserted to a greater depth than normally required and strong pressure had also been applied. During the procedure, the patient experienced severe urethral and penile pain, which was followed by urethrorrhagia, and later penile curvature. The patient was treated conservatively with good results, partly because the disease was still in its active stage and not yet stable. In the light of what we report, when ordering a urethral swab, physicians should always recommend that it be performed at testing centers that follow accurate, rigorous standards. Patients should also be informed that the test they are to undergo consists of a swab being inserted into the urethra for a short distance, not more than 2–3 cm. Keywords: genitourinary trauma, penile curvature, Peyronie, urethral swab

Differential contributions of specimen types, culturing, and 16S rRNA sequencing in diagnosis of prosthetic joint infections

DEFF Research Database (Denmark)

Larsen, Lone Heimann; Khalid, Vesal; Xu, Yijuan

2018-01-01

to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint...... fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study...... completion. Of the 156 patients enrolled, 111 underwent 114 surgical revisions (cases) due to indications of either PJI (n = 43) or AF (n = 71). Conventional tissue biopsy cultures confirmed PJI in 28/43 (65%) cases and refuted AF in 3/71 (4%) cases; one case was not evaluable. Based on these results, minor...

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.

Effects of saliva collection using cotton swabs on melatonin enzyme immunoassay

Directory of Open Access Journals (Sweden)

Katsuura Tetsuo

2011-01-01

Full Text Available Abstract Background Although various acceptable and easy-to-use devices have been used for saliva collection, cotton swabs are among the most common ones. Previous studies reported that cotton swabs yield a lower level of melatonin detection. However, this statistical method is not adequate for detecting an agreement between cotton saliva collection and passive saliva collection, and a test for bias is needed. Furthermore, the effects of cotton swabs have not been examined at lower melatonin level, a level at which melatonin is used for assessment of circadian rhythms, namely dim light melatonin onset (DLMO. In the present study, we estimated the effect of cotton swabs on the results of salivary melatonin assay using the Bland-Altman plot at lower level. Methods Nine healthy males were recruited and each provided four saliva samples on a single day to yield a total of 36 samples. Saliva samples were directly collected in plastic tubes using plastic straws, and subsequently pipetted onto cotton swabs (cotton saliva collection and into clear sterile tubes (passive saliva collection. The melatonin levels were analyzed in duplicate using commercially available ELISA kits. Results The mean melatonin concentration in cotton saliva collection samples was significantly lower than that in passive saliva collection samples at higher melatonin level (>6 pg/mL. The Bland-Altman plot indicated that cotton swabs causes relative and proportional biases in the assay results. For lower melatonin level ( Conclusion Our findings indicate an interference effect of cotton swabs on the assay result of salivary melatonin at lower melatonin level. Cotton-based collection devices might, thus, not be suitable for assessment of DLMO.

Equivalence of self- and staff-collected nasal swabs for the detection of viral respiratory pathogens.

Directory of Open Access Journals (Sweden)

Manas K Akmatov

Full Text Available BACKGROUND: The need for the timely collection of diagnostic biosamples during symptomatic episodes represents a major obstacle to large-scale studies on acute respiratory infection (ARI epidemiology. This may be circumvented by having the participants collect their own nasal swabs. We compared self- and staff-collected swabs in terms of swabbing quality and detection of viral respiratory pathogens. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective study among employees of our institution during the ARI season 2010/2011 (December-March. Weekly emails were sent to the participants (n = 84, reminding them to come to the study center in case of new symptoms. The participants self-collected an anterior nasal swab from one nostril, and trained study personnel collected one from the other nostril. The participants self-collected another two swabs (one from each nostril on a subsequent day. Human β-actin DNA concentration was determined in the swabs as a quality control. Viral respiratory pathogens were detected by multiplex RT-PCR (Seeplex RV15 kit, Seegene, Eschborn, Germany. Of 84 participants, 56 (67% reported at least one ARI episode, 18 participants two, and one participant three. Self-swabbing was highly accepted by the participants. The amount of β-actin DNA per swab was higher in the self- than in the staff-collected swabs (p = 0.008. β-actin concentration was lower in the self-swabs collected on day 1 than in those collected on a subsequent day (p<0.0001. A respiratory viral pathogen was detected in 31% (23/75 of staff- and in 35% (26/75 of self-collected swabs (p = 0.36. With both approaches, the most frequently identified pathogens were human rhinoviruses A/B/C (12/75 swabs, 16% and human coronavirus OC43 (4/75 swabs, 5%. There was almost perfect agreement between self- and staff-collected swabs in terms of pathogen detection (agreement = 93%, kappa = 0.85, p<0.0001. CONCLUSIONS/SIGNIFICANCE: Nasal self-swabbing

Effects of saliva collection using cotton swabs on melatonin enzyme immunoassay.

Science.gov (United States)

Kozaki, Tomoaki; Lee, Soomin; Nishimura, Takayuki; Katsuura, Tetsuo; Yasukouchi, Akira

2011-01-10

Although various acceptable and easy-to-use devices have been used for saliva collection, cotton swabs are among the most common ones. Previous studies reported that cotton swabs yield a lower level of melatonin detection. However, this statistical method is not adequate for detecting an agreement between cotton saliva collection and passive saliva collection, and a test for bias is needed. Furthermore, the effects of cotton swabs have not been examined at lower melatonin level, a level at which melatonin is used for assessment of circadian rhythms, namely dim light melatonin onset (DLMO). In the present study, we estimated the effect of cotton swabs on the results of salivary melatonin assay using the Bland-Altman plot at lower level. Nine healthy males were recruited and each provided four saliva samples on a single day to yield a total of 36 samples. Saliva samples were directly collected in plastic tubes using plastic straws, and subsequently pipetted onto cotton swabs (cotton saliva collection) and into clear sterile tubes (passive saliva collection). The melatonin levels were analyzed in duplicate using commercially available ELISA kits. The mean melatonin concentration in cotton saliva collection samples was significantly lower than that in passive saliva collection samples at higher melatonin level (>6 pg/mL). The Bland-Altman plot indicated that cotton swabs causes relative and proportional biases in the assay results. For lower melatonin level (<6 pg/mL), although the BA plots didn't show proportional and relative biases, there was no significant correlation between passive and cotton saliva collection samples. Our findings indicate an interference effect of cotton swabs on the assay result of salivary melatonin at lower melatonin level. Cotton-based collection devices might, thus, not be suitable for assessment of DLMO.

Rapid diagnosis of diarrhea caused by Shigella sonnei using dipsticks; comparison of rectal swabs, direct stool and stool culture.

Directory of Open Access Journals (Sweden)

Claudia Duran

Full Text Available BACKGROUND: We evaluated a dipstick test for rapid detection of Shigella sonnei on bacterial colonies, directly on stools and from rectal swabs because in actual field situations, most pathologic specimens for diagnosis correspond to stool samples or rectal swabs. METHODOLOGY/PRINCIPAL FINDINGS: The test is based on the detection of S. sonnei lipopolysaccharide (LPS O-side chains using phase I-specific monoclonal antibodies coupled to gold particles, and displayed on a one-step immunochromatographic dipstick. A concentration as low as 5 ng/ml of LPS was detected in distilled water and in reconstituted stools in 6 minutes. This is the optimal time for lecture to avoid errors of interpretation. In distilled water and in reconstituted stools, an unequivocal positive reaction was obtained with 4 x 10(6 CFU/ml of S. sonnei. The specificity was 100% when tested with a battery of Shigella and different unrelated strains. When tested on 342 rectal swabs in Chile, specificity (281/295 was 95.3% (95% CI: 92.9% - 97.7% and sensitivity (47/47 was 100%. Stool cultures and the immunochromatographic test showed concordant results in 95.5 % of cases (328/342 in comparative studies. Positive and negative predictive values were 77% (95% CI: 65% - 86.5% and 100% respectively. When tested on 219 stools in Chile, Vietnam, India and France, specificity (190/198 was 96% (95% CI 92%-98% and sensitivity (21/21 was 100%. Stool cultures and the immunochromatographic test showed concordant results in 96.3 % of cases (211/219 in comparative studies. Positive and negative predictive values were 72.4% (95% CI 56.1%-88.6% and 100 %, respectively. CONCLUSION: This one-step dipstick test performed well for diagnosis of S. sonnei both on stools and on rectal swabs. These data confirm a preliminary study done in Chile.

Effects of saliva collection using cotton swab on cortisol enzyme immunoassay.

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Kozaki, Tomoaki; Hashiguchi, Nobuko; Kaji, Yumi; Yasukouchi, Akira; Tochihara, Yutaka

2009-12-01

Cotton swabs are among the most commonly used devices for collecting saliva, but various studies have reported that their use impacts the results of salivary cortisol assays. These studies, however, estimated this impact by comparing the average of the concentration and/or scatter plots. In the present study, we estimated the impact of cotton swabs on the results of salivary cortisol enzyme immunoassay (EIA) by Bland-Altman plot. Eight healthy males (aged 20-23 years) provided four saliva samples on different days to yield a total of 32 samples. Saliva samples were collected directly in plastic tubes using plastic straws and then pipetted onto cotton swabs (cotton saliva collection) and into clear sterile tubes (passive saliva collection). There was a lower correlation between cotton and passive saliva collection. Individually, four subjects showed a negative correlation between passive and cotton saliva collection. A Bland-Altman plot indicated that cotton swabs causes a proportional bias on the EIA assay result. Our findings indicate a considerable effect of using cotton swabs for saliva collection, and subject-specific variability in the impact. A Bland-Altman plot further suggests possible reasons for this effect.

Real-Time Detection and Identification of Chlamydophila Species in Veterinary Specimens by Using SYBR Green-Based PCR Assays

DEFF Research Database (Denmark)

Nordentoft, Steen; Kabell, Susanne; Pedersen, Karl

2011-01-01

of Chlamydiaceae and differentiate the most prevalent veterinary Chlamydophila species: Cp. psittaci, Cp. abortus, Cp. felis, and Cp. caviae. By adding bovine serum albumin to the master mixes, target DNA could be detected directly in crude lysates of enzymatically digested conjunctival or pharyngeal swabs...... or tissue specimens from heart, liver, and spleen without further purification. The assays were evaluated on veterinary specimens where all samples were screened using a family-specific PCR, and positive samples were further tested using species-specific PCRs. Cp. psittaci was detected in 47 birds, Cp...... with a highly sensitive family-specific PCR, we were able to screen for Chlamydiaceae in veterinary specimens and confirm the species in positive samples with additional PCR assays....

Effect of lingual gauze swab placement on pulse oximeter readings in anaesthetised dogs and cats.

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Mair, A; Martinez-Taboada, F; Nitzan, M

2017-01-14

This study aimed to evaluate the effect of lingual gauze swab placement on pulse oximeter readings in anaesthetised dogs and cats. Following anaesthetic induction, the following pulse oximeter probe configurations were performed: no gauze swab (control), placement of a gauze swab between the tongue and the probe, placement of different thicknesses of gauze swab, placement of red cotton fabric, placement of a sheet of white paper and placement of the probe and gauze swab on different locations on the tongue. Oxygen saturation (SpO 2 ) and peripheral perfusion index (PI) were recorded. Placement of a gauze swab between the pulse oximeter probe and the tongue in anaesthetised dogs and cats resulted in significantly higher SpO 2 values compared with the control group. In dogs, PI values were significantly higher than the control in all groups except the quarter thickness swab group. In cats, PI was significantly higher in the double thickness swab and white paper groups compared with the control. Cats had significantly higher SpO 2 and lower PI values than dogs. The authors propose that increased contact pressure is responsible for significantly higher SpO 2 and PI readings with the use of a lingual gauze swab resulting from changes in transmural pressure and arterial compliance. British Veterinary Association.

Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control.

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Glisovic, Sanja; Eintracht, Shaun; Longtin, Yves; Oughton, Matthew; Brukner, Ivan

Rectal swabs are routinely used by public health authorities to screen for multi-drug resistant enteric bacteria including vancomycin-resistant enterococci (VRE) and carbapenem-resistant enterobacteriaceae (CRE). Screening sensitivity can be influenced by the quality of the swabbing, whether performed by the patient (self-swabbing) or a healthcare practitioner. One common exclusion criterion for rectal swabs is absence of "visible soiling" from fecal matter. In our institution, this criterion excludes almost 10% of rectal swabs received in the microbiology laboratory. Furthermore, over 30% of patients in whom rectal swabs are cancelled will not be re-screened within the next 48h, resulting in delays in removing infection prevention measures. We describe two quantitative polymerase chain reaction (qPCR)-based assays, human RNAse P and eubacterial 16S rDNA, which might serve as suitable controls for sampling adequacy. However, lower amounts of amplifiable human DNA make the 16s rDNA assay a better candidate for sample adequacy control. Copyright © 2017. Published by Elsevier Ltd.

Differences of detection efficiency among several nasal swab samples simulated for nuclear emergency accident

International Nuclear Information System (INIS)

Fukutsu, Kumiko; Yamada, Yuji; Kurihara, Osamu; Akashi, Makoto; Momose, Takumaro; Miyabe, Kenjiro

2008-01-01

At nuclear emergency accident such as inhalation intake of alpha nuclide, an indispensable nasal swab method has not been used for the precise internal dose estimation. One of the reasons is uncertainty in its radiation measurement, so that precise measurement with alpha spectrometry was examined for filter samples simulating nasal swab. It was confirmed that the alpha spectrometry made possible the distinction between solution and particulate in addition to the nuclide identification. The alpha activity in swab sample was precisely evaluated only when the detection efficiency was determined considering the self-absorption with filter fibers. Another big problem of wiping efficiency in nasal swabbing is still remain, but this study certainly raised the usefulness of the nasal swab method for rapid response in emergency. (author)

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

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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.

A comparative evaluation of feathers, oropharyngeal swabs, and cloacal swabs for the detection of H5N1 highly pathogenic avian influenza virus infection in experimentally infected chickens and ducks.

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Nuradji, Harimurti; Bingham, John; Lowther, Sue; Wibawa, Hendra; Colling, Axel; Long, Ngo Thanh; Meers, Joanne

2015-11-01

Oropharyngeal and cloacal swabs have been widely used for the detection of H5N1 highly pathogenic avian Influenza A virus (HPAI virus) in birds. Previous studies have shown that the feather calamus is a site of H5N1 virus replication and therefore has potential for diagnosis of avian influenza. However, studies characterizing the value of feathers for this purpose are not available, to our knowledge; herein we present a study investigating feathers for detection of H5N1 virus. Ducks and chickens were experimentally infected with H5N1 HPAI virus belonging to 1 of 3 clades (Indonesian clades 2.1.1 and 2.1.3, Vietnamese clade 1). Different types of feathers and oropharyngeal and cloacal swab samples were compared by virus isolation. In chickens, virus was detected from all sample types: oral and cloacal swabs, and immature pectorosternal, flight, and tail feathers. During clinical disease, the viral titers were higher in feathers than swabs. In ducks, the proportion of virus-positive samples was variable depending on viral strain and time from challenge; cloacal swabs and mature pectorosternal feathers were clearly inferior to oral swabs and immature pectorosternal, tail, and flight feathers. In ducks infected with Indonesian strains, in which most birds did not develop clinical signs, all sampling methods gave intermittent positive results; 3-23% of immature pectorosternal feathers were positive during the acute infection period; oropharyngeal swabs had slightly higher positivity during early infection, while feathers performed better during late infection. Our results indicate that immature feathers are an alternative sample for the diagnosis of HPAI in chickens and ducks. © 2015 The Author(s).

Buccal DNA collection: comparison of buccal swabs with FTA cards.

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Milne, Elizabeth; van Bockxmeer, Frank M; Robertson, Laila; Brisbane, Joanna M; Ashton, Lesley J; Scott, Rodney J; Armstrong, Bruce K

2006-04-01

Collection and analysis of DNA, most commonly from blood or buccal cells, is becoming more common in epidemiologic studies. Buccal samples, which are painless to take and relatively easily collected, are often the preferred source. There are several buccal cell collection methods: swabs, brushes, mouthwash, and treated cards, such as FTA or IsoCode cards. Few studies have systematically compared methods of buccal cell collection with respect to DNA yield and amplification success under similar conditions. We compared buccal DNA collection and amplification using buccal swabs and FTA cards in 122 control subjects from our Australian case-control study of childhood acute lymphoblastic leukaemia. Buccal DNA was quantified using a real-time PCR for beta-actin and genotyped at the loci of three polymorphisms (MTHFR 677C>T, ACE I/D, and XPD 1012G>A). PCR was successful with DNA from buccal swabs for 62% to 89% of subjects and from FTA cards for 83% to 100% of subjects, depending on the locus. The matched pair odds ratios (95% confidence interval) comparing success of FTA cards with buccal swabs are as follows: MTHFR 677C>T using PCR-RFLP, 12.5 (11.6-13.5) and using real-time PCR, 130.0 (113.1-152.8); ACE I/D using PCR-amplified fragment length polymorphism, 3.36 (3.2-3.5); XPD 1012G>A using real-time PCR, 150.0 (132.7-172.3). FTA cards are a robust DNA collection method and generally produce DNA suitable for PCR more reliably than buccal swabs. There are, however, technical challenges in handling discs punched from FTA cards that intending users should be aware of.

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.

Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics.

Science.gov (United States)

Hosokawa-Muto, Junji; Fujinami, Yoshihito; Mizuno, Natsuko

2015-08-01

Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

An optimized work-flow to reduce time-to-detection of carbapenemase-producing Enterobacteriaceae (CPE) using direct testing from rectal swabs.

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O'Connor, C; Kiernan, M G; Finnegan, C; O'Hara, M; Power, L; O'Connell, N H; Dunne, C P

2017-05-04

Rapid detection of patients with carbapenemase-producing Enterobacteriaceae (CPE) is essential for the prevention of nosocomial cross-transmission, allocation of isolation facilities and to protect patient safety. Here, we aimed to design a new laboratory work-flow, utilizing existing laboratory resources, in order to reduce time-to-diagnosis of CPE. A review of the current CPE testing processes and of the literature was performed to identify a real-time commercial polymerase chain reaction (PCR) assay that could facilitate batch testing of CPE clinical specimens, with adequate CPE gene coverage. Stool specimens (210) were collected; CPE-positive inpatients (n = 10) and anonymized community stool specimens (n = 200). Rectal swabs (eSwab™) were inoculated from collected stool specimens and a manual DNA extraction method (QIAamp® DNA Stool Mini Kit) was employed. Extracted DNA was then processed on the Check-Direct CPE® assay. The three step process of making the eSwab™, extracting DNA manually and running the Check-Direct CPE® assay, took method of CPE screening; average time-to-diagnosis of 48/72 h. Utilizing this CPE work-flow would allow a 'same-day' result. Antimicrobial susceptibility testing results, as is current practice, would remain a 'next-day' result. In conclusion, the Check-Direct CPE® assay was easily integrated into a local laboratory work-flow and could facilitate a large volume of CPE screening specimens in a single batch, making it cost-effective and convenient for daily CPE testing.

Use of the VS-sense swab in diagnosing vulvovaginitis.

Science.gov (United States)

Sobel, Jack D; Nyirjesy, Paul; Kessary, Hadar; Ferris, Daron G

2009-09-01

Although pH assessment of vaginal secretions is beneficial for diagnosing vaginitis, it is not commonly done. The purpose of this study was to determine the performance characteristics of the VS-Sense (pH test) swab (Common Sense, Ltd., Caesarea, Israel) in augmenting the diagnosis of vaginitis. We prospectively studied 193 women with acute vulvovaginal symptoms and 74 asymptomatic controls at three medical centers. The VS-Sense swab was administered intravaginally, and results were interpreted by a nurse. These results were compared with final clinical and laboratory diagnoses. In women with an elevated pH caused by bacterial vaginosis (BV), trichomonas, and other types of vaginitis, the VS-Sense test sensitivity and specificity were 82.3% (102 of 124) (95% CI 74.4%-88.5%) and 94.2% (129 of 137) (95% CI 88.8%-97.4%), respectively. There was an 86.2% (95% CI 81.3%-90.1%) overall agreement between pH paper and VS-Sense swab results. The VS-Sense test offers an alternative approach to measuring vaginal pH with nitrazine paper. Use of this simple, more rapid test may facilitate the diagnosis of vulvovaginitis.

Self-collected mid-turbinate swabs for the detection of respiratory viruses in adults with acute respiratory illnesses.

Directory of Open Access Journals (Sweden)

Oscar E Larios

Full Text Available BACKGROUND: The gold standard for respiratory virus testing is a nasopharyngeal (NP swab, which is collected by a healthcare worker. Midturbinate (MT swabs are an alternative due to their ease of collection and possible self-collection by patients. The objective of this study was to compare the respiratory virus isolation of flocked MT swabs compared to flocked NP swabs. METHODS: Beginning in October 2008, healthy adults aged 18 to 69 years were recruited into a cohort and followed up for symptoms of influenza. They were asked to have NP and MT swabs taken as soon as possible after the onset of a fever or two or more respiratory symptoms with an acute onset. The swabs were tested for viral respiratory infections using Seeplex® RV12 multiplex PCR detection kit. Seventy six pairs of simultaneous NP and MT swabs were collected from 38 symptomatic subjects. Twenty nine (38% of these pairs were positive by either NP or MT swabs or both. Sixty nine (91% of the pair results were concordant. Two samples (3% for hCV OC43/HKU1 and 1 sample (1% for rhinovirus A/B were positive by NP but negative by MT. One sample each for hCV 229E/NL63, hCV OC43/HKU1, respiratory syncytial virus A, and influenza B were positive by MT but negative by NP. CONCLUSIONS: Flocked MT swabs are sensitive for the diagnosis of multiple respiratory viruses. Given the ease of MT collection and similar results between the two swabs, it is likely that MT swabs should be the preferred method of respiratory cell collection for outpatient studies. In light of this data, larger studies should be performed to ensure that this still holds true and data should also be collected on the patient preference of collection methods.

Elution of Artificial Sputum from Swab by Rotating Magnetic Field-Induced Mechanical Impingement

Directory of Open Access Journals (Sweden)

Shubham Banik

2017-12-01

Full Text Available Cotton-tipped applicator swabs are used as a collection device for many biological samples and its complete elution is a desired step for clinical and forensic diagnostics. Swabs are used to collect infectious body fluids, where the concentration of pathogens can range from 1 × 104 CFU/mL (colony forming units/mL in respiratory-tract infections and 1 × 105 in urinary-tract infections, to up to 1 × 109 CFU/mL in salivary samples. These samples are then eluted and lysed, prior to DNA (De-oxy Ribonucleic Acid analysis. The recovery of micro-organisms from a matrix of swab fibres depends on the nature of the body fluid, the type of the swab fibres, and the process of elution. Various methods to elute samples from swab include chemical digestion of fibres (~20% recovery, centrifugation (~58% recovery, piezoelectric vibration, or pressurized fluid-flow (~60% recovery. This study reports a magnetically-actuated physical impingement method for elution and recovery of artificial sputum samples from cotton fibres. A device has been fabricated to induce a rotating magnetic field on smaller magnetic particles in a vial that strikes the swab within a confined gap. Elution from the swab in this device was characterized using 2% Methyl cellulose in deionised water, loaded with fluorescent-tagged polystyrene beads and E. coli at various concentrations. The recovery efficiency was found to increase with both rotational speed and elution time, but plateaus after 400 RPM (Revolutions per minute and 120 s, respectively. At a higher concentration of polystyrene beads (5 × 108 particles/mL, a maximum recovery of ~85% was achieved. With lower concentration, (1 × 105 particles/mL the maximum efficiency (~92.8% was found to be almost twice of passive elution (46.7%. In the case of E. coli, the corresponding recovery efficiency at 3.35 × 105 CFU/mL is 90.4% at 500 RPM and 120 s. This elution method is expected to have a wide applicability in clinical diagnostics.

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.

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.

Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

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Adamowicz, Michael S; Stasulli, Dominique M; Sobestanovich, Emily M; Bille, Todd W

2014-01-01

Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C) as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

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...

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

A Non-Invasive Strategy for Neonatal Alloimmune Thrombocytopenia Diagnosis: Newborn Platelet Genotyping with Buccal Swabs

Directory of Open Access Journals (Sweden)

Gérald Bertrand

2016-07-01

Full Text Available Neonatal alloimmune thrombocytopenia results from the maternal immune response against fetal-specific antigens inherited from the father. The diagnosis is ascertained only when the maternal alloantibody and the offending antigen present in the newborn are identified. Up until now most laboratories perform DNA extraction for neonatal genotyping from newborn blood samplings. In order to avoid such an invasive procedure, two protocols of DNA extraction from buccal swabs were developed: a manual protocol using the QIAamp mini blood kit (Qiagen, and an automated procedure with the MagNA Pure Compact instrument (Roche. Both EDTA-blood and buccal swabs from thrombocytopenic newborns were genotyped manually (14 samples, automatically (15 samples or both manually and automatically (two samples. Human Platelet Antigen (HPA genotyping was performed using the BeadChip assay (BioArray, Immucor. Concordant genotypings were obtained for all samples except for one swab with the manual method. The automated DNA extraction from newborn buccal swabs with the MagNA Pure Compact instrument was chosen as the first-line strategy, with a significant gain of time in processing buccal swabs.

Evaluation of chromogenic medium and direct latex agglutination test for detection of group B streptococcus in vaginal specimens from pregnant women in Lebanon and Kuwait.

Science.gov (United States)

Ghaddar, Nahed; Alfouzan, Wadha; Anastasiadis, Elie; Al Jiser, Tamima; Itani, Saad Eddine; Dernaika, Racha; Eid, Toufic; Ghaddar, Ali; Charafeddine, Adib; Dhar, Rita; El Hajj, Hiba

2014-10-01

This study was undertaken to evaluate chromogenic medium and a direct latex agglutination test (DLA) for detection of Group B Streptococcus (GBS) in the vaginal specimens of pregnant women, and to ascertain the prevalence of GBS in this population in Kuwait and Lebanon. Vaginal swabs, collected from women at 35-37 weeks of gestation, were cultured on 5 % sheep blood agar (SBA), colistin nalidixic acid agar (CNA), Strept B Select chromogenic agar (SBS) as well as Lim enrichment broth in 168 cases in Lebanon while only SBA was used for 1391 samples in Kuwait. In addition, vaginal samples from 102 GBS-positive and 20 GBS-negative women near the time of delivery were collected in Kuwait for evaluation of the DLA test. During the study period, the prevalence of GBS colonization was determined to be 20.7 % (288/1391) in Kuwait while 18.4 % (31) of 168 pregnant women in Lebanon had vaginal cultures positive for GBS. By direct plating of vaginal swabs on the three media used, the isolation rates of GBS were 51.6, 64.5 and 77.4 % on SBA, CNA and SBS, respectively, which increased to 90.35, 93.1 and 96.8 %, respectively, following subculture in Lim broth after 18 h of incubation. The sensitivity of the DLA test was found to be dependent on the density of GBS colonization, resulting in 100 % sensitivity and 100 % specificity for heavy (>10(2) c.f.u. per swab) and moderately heavy (50-100 c.f.u. per swab) growth of GBS. However, for vaginal specimens yielding women. The DLA test, in particular, could prove to be a useful tool for immediate detection of GBS in women near delivery so that intrapartum antibiotic prophylaxis can be initiated. © 2014 The Authors.

Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

Directory of Open Access Journals (Sweden)

Michael S Adamowicz

Full Text Available Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents.

Science.gov (United States)

Johnston, Christine; Magaret, Amalia; Roychoudhury, Pavitra; Greninger, Alexander L; Cheng, Anqi; Diem, Kurt; Fitzgibbon, Matthew P; Huang, Meei-Li; Selke, Stacy; Lingappa, Jairam R; Celum, Connie; Jerome, Keith R; Wald, Anna; Koelle, David M

2017-10-01

Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. Genital lesion swabs containing ≥ 10 7 log 10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (U L _U S ) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction. Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated U L_ U S segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids. Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens. Copyright © 2017 Elsevier Inc. All rights reserved.

Gossypiboma – the retained surgical swab: An enduring clinical ...

African Journals Online (AJOL)

Retained abdominal swabs remain a difficult problem. This review ... and continues to date, despite advances .... difficult problem to eradicate even though .... to complete multiple emergency surgeries with no rest is great, ... The position.

Dual quantification of dapivirine and maraviroc in cervicovaginal secretions from ophthalmic tear strips and polyester-based swabs via liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis.

Science.gov (United States)

Parsons, Teresa L; Emory, Joshua F; Seserko, Lauren A; Aung, Wutyi S; Marzinke, Mark A

2014-09-01

Topical microbicidal agents are being actively pursued as a modality to prevent HIV viral transmission during sexual intercourse. Quantification of antiretroviral agents in specimen sources where antiviral activity is elicited is critical, and drug measurements in cervicovaginal fluid can provide key information on local drug concentrations. Two antiretroviral drugs, dapivirine and maraviroc, have gained interest as vaginal microbicidal agents, and rugged methods are required for their quantification in cervicovaginal secretions. Cervicovaginal fluid spiked with dapivirine and maraviroc were applied to ophthalmic tear strips or polyester-based swabs to mimic collection procedures used in clinical studies. Following sample extraction and the addition of isotopically labeled internal standards, samples were subjected to liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis using a Waters BEH C8, 50mm×2.1mm, 1.7μm particle size column, on an API 4000 mass analyzer operated in selective reaction monitoring mode. The method was validated according to FDA Bioanalytical Method Validation guidelines. Due to the disparate saturation capacity of the tested collection devices, the analytical measuring ranges for dapivirine and maravirocin cervicovaginal fluid on the ophthalmic tear strip were 0.05-25ng/tear strip, and 0.025-25ng/tear strip, respectively. As for the polyester-based swab, the analytical measuring ranges were 0.25-125ng/swab for dapivirine and 0.125-125ng/swab for maraviroc. Dilutional studies were performed for both analytes to extended ranges of 25,000ng/tear strip and 11,250ng/swab. Standard curves were generated via weighted (1/x(2)) linear or quadratic regression of calibrators. Precision, accuracy, stability and matrix effects studies were all performed and deemed acceptable according to the recommendations of the FDA Bioanalytical Method Validation guidelines. A rugged LC-MS/MS method for the dual quantification of dapivirine and

Quantification of loosely associated and tightly associated bacteria on broiler carcass skin using swabbing, stomaching, and grinding methods.

Science.gov (United States)

Singh, P; Lee, H C; Chin, K B; Ha, S D; Kang, I

2015-12-01

This research was conducted to quantify bacterial populations after swabbing or stomaching, followed by grinding the swabbed or stomached broiler skins. For each of 3 replications, 3 eviscerated broilers were randomly taken from a processing line in a local broiler processing plant. Ten swabs and 10 stomachs per bird were conducted on the left- and the right-side skins (10×7 cm), respectively, which were then finally ground. Results indicated that mesophilic aerobic bacteria (MAB) in the first swabbed sample were significantly lower than those in the first stomached sample (P0.05). During 10 swabbings followed by final grinding, 8, 9, and 83% of MAB were detected after the first swabbing, after the second through 10th swabbings, and after final grinding of the skin, respectively. During 10 stomachings followed by the final grinding, 17, 18, and 65% of MAB were detected after the first stomaching, after the second through 10th stomachings, and after final grinding of the skin, respectively. Escherichia coli (E. coli) and coliforms were significantly higher in the first stomaching than those in the first swabbing (P0.05). Populations of E. coli and coliforms decreased step-wisely from the highest after grinding to the intermediate after first and second sampling, and to the least after 10th sampling (Pgrinding. In this study, less than 35% of MAB seemed loosely associated in the skin of eviscerated broiler, whereas more than 65% of MAB looked tightly associated, which were not recovered by stomaching or swabbing even 10 times but were recovered by grinding the skin. © 2015 Poultry Science Association Inc.

Cervical Cancer Screening Preferences Among Trans-Masculine Individuals: Patient-Collected Human Papillomavirus Vaginal Swabs Versus Provider-Administered Pap Tests.

Science.gov (United States)

McDowell, Michal; Pardee, Dana J; Peitzmeier, Sarah; Reisner, Sari L; Agénor, Madina; Alizaga, Natalie; Bernstein, Ida; Potter, Jennifer

2017-08-01

Trans-masculine (TM, i.e., persons who have a masculine spectrum gender identity, but were assigned female sex at birth) individuals face disparities in cervical cancer screening rates compared to cisgender women. Some unique barriers to screening in this population are specific to Pap tests. Introduction of self-collected frontal (i.e., vaginal) swabs for human papillomavirus (HPV) testing as a screening strategy may obviate these barriers. This study elucidates cervical cancer screening preferences among TM individuals. TM individuals participated in in-depth interviews (n = 31) and online surveys (n = 32) to explore perceptions and experiences regarding cervical cancer screening, including the acceptability of self-collected frontal HPV swabs for cervical cancer screening compared to provider-administered Pap tests. Provider-collected frontal HPV swab acceptability was also explored. Most TM individuals (94% in-person and 91% online participants) preferred either the self- or provider-collected frontal HPV swab to the Pap test. Participants perceived self- and provider-collected frontal HPV swabs to be less invasive, provoke less gender discordance, and promote a greater sense of agency compared to Pap tests. However, some participants expressed concern about HPV swab accuracy and, regarding the self-collected swab, discomfort about the need to engage with genitals they may not want to acknowledge. Individuals who reported positive provider relationships found Pap tests and provider-collected frontal swabs more acceptable than those who did not. Frontal HPV swabs have the potential to promote regular cervical cancer screening among TM individuals and to narrow screening disparities. Work is ongoing to establish swab accuracy and develop shared decision-making tools.

Self-sampling for human papillomavirus testing among rural young women of KwaZulu-Natal, South Africa.

Science.gov (United States)

Mbatha, J N; Galappaththi-Arachchige, H N; Mtshali, A; Taylor, M; Ndhlovu, P D; Kjetland, E F; Baay, M F D; Mkhize-Kwitshana, Z L

2017-12-06

Cervical cancer is a major problem in women and it is important to find a suitable and acceptable screening method, especially among young in low-resource areas for future human papillomavirus (HPV) vaccine follow-up investigations. The study sought to test the acceptability of self-sampling as well as the suitability of the specimen collecting devices. Ninety-eight young women from rural KwaZulu-Natal were enrolled between March and July 2014. Collected genital specimens were transferred to colour indicator cards for HPV detection. Participants answered a questionnaire where they described their experiences with self-sampling. Samples were tested for high-risk HPV using GP5/6+ PCR. Of the enrolled participants, 91 answered questionnaires and indicated that self-sampling was preferred by 51/91 (56%) women while 40/91 (44%) indicated preference for sampling by a doctor (p = 0.023). The majority, 64% were comfortable using a swab, 22% preferred a brush while 11% were comfortable with both devices. Of the 98 self-sampled specimens 61 were negative for HPV in both specimens while 37 were HPV-positive in either brush or swab. Of the 37, 26 (70%) were HPV-positive in both brush and swab (kappa = 0.743) and 11 (30%) were discordant. Self-sampling was acceptable to the majority of participants in this rural area. The Dacron swab was the preferred device, and can be used in combination with colour indicator cards for comfortable self-sampling, easy storage and transport of specimens plus detection.

Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population

Directory of Open Access Journals (Sweden)

Vargas CY

2016-01-01

Full Text Available Celibell Y Vargas,1 Liqun Wang,1 Yaritza Castellanos de Belliard,1 Maria Morban,1 Hilbania Diaz,1 Elaine L Larson,2,3 Philip LaRussa,1 Lisa Saiman,1,4 Melissa S Stockwell1,5,6 1Department of Pediatrics, 2School of Nursing, 3Department of Epidemiology, Mailman School of Public Health, Columbia University, 4Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, 5Department of Population and Family Health, Mailman School of Public Health, Columbia University, 6NewYork-Presbyterian Hospital, New York, NY, USA Objective: To assess the feasibility and validity of unsupervised participant-collected nasal swabs to detect respiratory pathogens in a low-income, urban minority population. Methods: This project was conducted as part of an ongoing community-based surveillance study in New York City to identify viral etiologies of acute respiratory infection. In January 2014, following sample collection by trained research assistants, participants with acute respiratory infection from 30 households subsequently collected and returned a self-collected/parent-collected nasal swab via mail. Self/parental swabs corresponding with positive reverse transcription polymerase chain reaction primary research samples were analyzed. Results: Nearly all (96.8%, n=30/31 households agreed to participate; 100% reported returning the sample and 29 were received (median time: 8 days. Most (18; 62.1% of the primary research samples were positive. For eight influenza-positive research samples, seven (87.5% self-swabs were also positive. For ten other respiratory pathogen-positive research samples, eight (80.0% self-swabs were positive. Sensitivity of self-swabs for any respiratory pathogen was 83.3% and 87.5% for influenza, and specificity for both was 100%. There was no relationship between level of education and concordance of results between positive research samples and their matching participant swab. Conclusion: In this pilot study, self-swabbing

Technical basis for using nose swab bioassay data for early internal dose assessment

International Nuclear Information System (INIS)

Guilmette, Raymond A.; Bertelli, Luiz; Miller, Guthrie; Little, Tom T.

2007-01-01

One of the challenges to the dose assessment team in response to an inhalation incident in the workplace is to provide the occupational physicians, operational radiation protection personnel and line managers with early estimates of radionuclide intakes so that appropriate consequence management and mitigation can be done. For radionuclides such as Pu, where in vivo counting is not adequately sensitive, other techniques such as the measurement of removable radionuclide from the nasal airway passages can be used. At Los Alamos National Laboratory (LANL), nose swabs of the ET 1 region have been used routinely as a first response to airborne Pu releases in the workplace, as well as for other radionuclides. This paper presents the results of analysing over 15 years of nose swab data, comparing these with dose assessments performed using the Bayesian methods developed at LANL. The results provide empirical support for using nose swab data for early dose assessments. For Pu, a rule of thumb is a dose factor of 0.8 mSv Bq -1 , assuming a linear relationship between nasal swab activity and committed effective dose equivalent. However, this value is specific to the methods and models used at LANL, and should not be applied directly without considering possible differences in measurement and calculation methods. (authors)

Nose swabs and urinalysis as indicators of exposure to I-131

Energy Technology Data Exchange (ETDEWEB)

Barrall, R. C.

1963-06-15

During a maintenance operation on the Aromour Research Reactor, a heat lamp, which was drying a valve, caused a small quantity of I/sup 131/ become airborne. A continuous air monitor sampling in the area gave the alarm and the area ntified by the use of a 256 channel analyzer. Nose swabs of the personnel involved were taken and 24 hour urine samples were obtained. A single channel analyzer was set up, calibrated for I/sup 131/ and thyroid counts were started several hours after the incident. The thyroid count rose during the first 24 hour period and then declined closely following the 8 day half life of I/sup 131/. The urine Samples were analyzed by two different gamma counting techniques. Portions of the 24 hour urine sample were also sent to a commercial urinalysis service and analysis for I/sup 131/specifically requested. The results of the commercial service in this instance appeared to be poor. Nose swabs taken immediately after the incident were analyzed using a NaI well crystal. The average value of the ratio mu c on nose swabs to mu c in thyroid was found to be 2.6 x 1-/sup -1/ with all values within a factor of 6. The average value of the ratio mu c in 24 hour urine sample to mu c in thyroid was 5.7 with all values within a factor of 2. It would appear that at short times after a suspected exposure to I/sup 131/ nose swabs and urine samples are both useful in making a rapid assessment of exposure. The data presented are based on 10 subjects. (auth)

SWAB guidelines for antimicrobial therapy of acute infectious diarrhoea

NARCIS (Netherlands)

Bos, J. C.; Schultsz, C.; Vandenbroucke-Graulsz, C. M. J.; Speelman, P.; Prins, J. M.

2006-01-01

The Dutch Working Party on Antibiotic Policy (SWAB: Stichting Werkgroep Antibioticabeleid) develops evidence-based guidelines for the use of antibiotics in hospitalised adults. In this article we discuss the guideline on antibiotic treatment of acute infectious diarrhoea (AID). AID can be subdivided

Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis.

Science.gov (United States)

Byrne, Allison Q; Rothstein, Andrew P; Poorten, Thomas J; Erens, Jesse; Settles, Matthew L; Rosenblum, Erica Bree

2017-11-01

One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures have advanced our understanding of Bd phylogenetics, genomic architecture and mechanisms of virulence. However, pure cultures are laborious to obtain and whole-genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus, we still know little about the genetic diversity of Bd in natural systems. The most common noninvasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole-genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, noninvasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations. © 2017 John Wiley & Sons Ltd.

Evaluation of a Chlamydia trachomatis-specific, commercial, real-time PCR for use with ocular swabs.

Science.gov (United States)

Pickering, Harry; Holland, Martin J; Last, Anna R; Burton, Matthew J; Burr, Sarah E

2018-02-20

Trachoma, the leading infectious cause of blindness worldwide, is caused by conjunctival Chlamydia trachomatis infection. Trachoma is diagnosed clinically by observation of conjunctival inflammation and/or scarring; however, there is evidence that monitoring C. trachomatis infection may be required for elimination programmes. There are many commercial and 'in-house' nucleic acid amplification tests for the detection of C. trachomatis DNA, but the majority have not been validated for use with ocular swabs. This study evaluated a commercial assay, the Fast-Track Vaginal swab kit, using conjunctival samples from trachoma-endemic areas. An objective, biostatistical-based method for binary classification of continuous PCR data was developed, to limit potential user-bias in diagnostic settings. The Fast-Track Vaginal swab assay was run on 210 ocular swab samples from Guinea-Bissau and Tanzania. Fit of individual amplification curves to exponential or sigmoid models, derivative and second derivative of the curves and final fluorescence value were examined for utility in thresholding for determining positivity. The results from the Fast-Track Vaginal swab assay were evaluated against a commercial test (Amplicor CT/NG) and a non-commercial test (in-house droplet digital PCR), both of whose performance has previously been evaluated. Significant evidence of exponential amplification (R 2  > 0.99) and final fluorescence > 0.15 were combined for thresholding. This objective approach identified a population of positive samples, however there were a subset of samples that amplified towards the end of the cycling protocol (at or later than 35 cycles), which were less clearly defined. The Fast-Track Vaginal swab assay showed good sensitivity against the commercial (95.71) and non-commercial (97.18) tests. Specificity was lower against both (90.00 and 96.55, respectively). This study defined a simple, automated protocol for binary classification of continuous, real-time q

Does Fine Needle Aspiration Microbiology Offer Any Benefit Over Wound Swab in Detecting the Causative Organisms in Surgical Site Infections?

Science.gov (United States)

Sudharsanan, Sundaramurthi; Gs, Sreenath; Sureshkumar, Sathasivam; Vijayakumar, Chellappa; Sujatha, Sistla; Kate, Vikram

2017-09-01

The objective of this study is to determine the role of ne needle aspiration microbiology (FNAM) in detecting the causative organisms of postoperative surgical site infections (SSIs) in comparison with the standard technique of surface swabbing. Ma- terials and Methods. In this study, 150 patients with SSIs following elective and emergency operations were included. In all patients, FNAM was performed along with conventional surface swabbing to identify the causative microorganism. Sensitivity of surface swab and FNAM was calculated as the number of samples collected from the diagnosed case of SSI. A total of 115 positive cultures were obtained from the 150 patients with SSIs; surface swab was positive in 110 cases and FNAM was positive in 94 cases. The mean number of organisms isolated by surface swab, and FNAM was 0.95 and 0.8, respectively. The sensitivity of surface swab was 94.3% in elective cases and 96.25% in emergency cases. The sensitivity of FNAM was 82.8% in elective cases and 82.5% in emergency cases. The sensitivity and negative predictive value of FNAM and surface swab did not signi cantly differ in clean elective cases. The overall sensitivity of surface swab and FNAM was 95.65% and 81.7%, respectively. Comparing the antibiotic suscep- tibility pattern, no difference was observed when the same organ- ism was isolated by both methods, indicating that FNAM does not offer bene t over the conventional wound surface swab in detecting microorganisms in SSI in both elective and emergency surgeries. In certain cases with unexplained wound infections, FNAM can be used as an investigation to identify speci c pathogens not detected by conventional surface swab.

Investigation of internal radionuclide contamination from the analysis of nasal swabs and facial swipes

International Nuclear Information System (INIS)

Raymond Ko; Baki Sadi; Chunsheng Li; Chad Shew; Sharman Perera; Ed Waller; Kristine Mattson; Kathy Nielsen; David Kelly

2014-01-01

Nasal swabs and facial swipes have been used to screen potential internal radioactive contamination for decades. However, the ratio between the lung intake and the activity on a swab or a swipe varies according to the nature of the contaminant involved and the exposure conditions such as particle sizes of the contaminant and the humidity in the air. This paper reports the experimental results using stable La 2 O 3 as an analog for actinide oxides, focusing on the most important parameters such as humidity, plume velocity, and facial condition at a fixed room temperature of 23 ± 2 deg C. The results showed that the effects of humidity, plume velocity, and facial condition vary more on orofacial swipe/lung deposition ratios compared to nasal swab/lung deposition ratios. The amounts on nasal swabs tended to show smaller change with respect to parameters such as plume velocity, humidity, and skin moisture. The amounts on orofacial swipes varied by a factor of 10-15 among the samples collected across all parameters. Such variability would be expected to be even greater in a real-world scenario with a larger range of physiological and environmental conditions. (author)

Skin swabs with FTA® cards as a dry storage source for amphibian DNA

OpenAIRE

Ward, A; Hide, G; Jehle, R

2018-01-01

Amphibians are the most endangered group of vertebrates, and conservation measures increasingly rely on information drawn from genetic markers. The present study explores skin swabs with Whatman FTA® cards as a method to retrieve PCR-amplifiable amphibian DNA. Swabs from ten adult great crested newts (Triturus cristatus) were used to compare FTA® card-based protocols with tissue sampling based on toe clips. PCR success rates were measured for seven microsatellite markers and one mtDNA marker ...

Evaluating the use of dedicated swab for rapid antigen detection ...

African Journals Online (AJOL)

Evaluating the use of dedicated swab for rapid antigen detection testing in group a ... African Journal of Clinical and Experimental Microbiology ... Several generations of rapid antigen detection tests (RADTs) have been developed to facilitate ...

Simplifying sampling for African swine fever surveillance: Assessment of antibody and pathogen detection from blood swabs.

Science.gov (United States)

Carlson, J; Zani, L; Schwaiger, T; Nurmoja, I; Viltrop, A; Vilem, A; Beer, M; Blome, S

2018-02-01

African swine fever (ASF) is a notifiable disease with serious socio-economic consequences that has been present in wild boar in the Baltic States and Poland since 2014. An introduction of ASF is usually accompanied by increased mortality, making fallen wild boar and hunted animals with signs of disease the main target for early warning and passive surveillance. It is difficult, however, to encourage hunters and foresters to report and take samples from these cases. A pragmatic and easy sampling approach with quick-drying swabs could facilitate this. In this study, we further evaluated the use of dry blood swabs for the detection of ASFV antibody and genome with samples from animal trials and diagnostic submissions (blood, bone and organs) from Estonia. Compared to serum samples, dried blood swabs yielded 93.1% (95% confidence interval: [83.3, 98.1]) sensitivity and 100% [95.9, 100.0] specificity in a commercial ASFV antibody ELISA. Similarly, the swabs gave a sensitivity of 98.9% [93.4, 100.0] and a specificity of 98.1% [90.1, 100.0] for genome detection by a standard ASFV p72 qPCR when compared to EDTA blood. The same swabs were tested in a VP72-antibody lateral flow device, with a sensitivity of 94.7% [85.4, 98.9] and specificity of 96.1% [89.0, 99.2] compared to the serum ELISA. When GenoTube samples tested in ELISA and LFD were compared, the sensitivity was 96.3% [87.3, 99.5] and the specificity was 93.8% [86.0, 97.9]. This study demonstrates reliable detection of ASFV antibody and genome from swabs. A field test of the swabs with decomposed wild boar carcasses in an endemic area in Estonia also gave promising results. Thus, this technique is a practical approach for surveillance of ASF in both free and endemic areas. © 2017 Blackwell Verlag GmbH.

Can Unmanned Aerial Systems (Drones Be Used for the Routine Transport of Chemistry, Hematology, and Coagulation Laboratory Specimens?

Directory of Open Access Journals (Sweden)

Timothy K Amukele

Full Text Available Unmanned Aerial Systems (UAS or drones could potentially be used for the routine transport of small goods such as diagnostic clinical laboratory specimens. To the best of our knowledge, there is no published study of the impact of UAS transportation on laboratory tests.Three paired samples were obtained from each one of 56 adult volunteers in a single phlebotomy event (336 samples total: two tubes each for chemistry, hematology, and coagulation testing respectively. 168 samples were driven to the flight field and held stationary. The other 168 samples were flown in the UAS for a range of times, from 6 to 38 minutes. After the flight, 33 of the most common chemistry, hematology, and coagulation tests were performed. Statistical methods as well as performance criteria from four distinct clinical, academic, and regulatory bodies were used to evaluate the results.Results from flown and stationary sample pairs were similar for all 33 analytes. Bias and intercepts were <10% and <13% respectively for all analytes. Bland-Altman comparisons showed a mean difference of 3.2% for Glucose and <1% for other analytes. Only bicarbonate did not meet the strictest (Royal College of Pathologists of Australasia Quality Assurance Program performance criteria. This was due to poor precision rather than bias. There were no systematic differences between laboratory-derived (analytic CV's and the CV's of our flown versus terrestrial sample pairs however CV's from the sample pairs tended to be slightly higher than analytic CV's. The overall concordance, based on clinical stratification (normal versus abnormal, was 97%. Length of flight had no impact on the results.Transportation of laboratory specimens via small UASs does not affect the accuracy of routine chemistry, hematology, and coagulation tests results from selfsame samples. However it results in slightly poorer precision for some analytes.

Can Unmanned Aerial Systems (Drones) Be Used for the Routine Transport of Chemistry, Hematology, and Coagulation Laboratory Specimens?

Science.gov (United States)

Amukele, Timothy K; Sokoll, Lori J; Pepper, Daniel; Howard, Dana P; Street, Jeff

2015-01-01

Unmanned Aerial Systems (UAS or drones) could potentially be used for the routine transport of small goods such as diagnostic clinical laboratory specimens. To the best of our knowledge, there is no published study of the impact of UAS transportation on laboratory tests. Three paired samples were obtained from each one of 56 adult volunteers in a single phlebotomy event (336 samples total): two tubes each for chemistry, hematology, and coagulation testing respectively. 168 samples were driven to the flight field and held stationary. The other 168 samples were flown in the UAS for a range of times, from 6 to 38 minutes. After the flight, 33 of the most common chemistry, hematology, and coagulation tests were performed. Statistical methods as well as performance criteria from four distinct clinical, academic, and regulatory bodies were used to evaluate the results. Results from flown and stationary sample pairs were similar for all 33 analytes. Bias and intercepts were <10% and <13% respectively for all analytes. Bland-Altman comparisons showed a mean difference of 3.2% for Glucose and <1% for other analytes. Only bicarbonate did not meet the strictest (Royal College of Pathologists of Australasia Quality Assurance Program) performance criteria. This was due to poor precision rather than bias. There were no systematic differences between laboratory-derived (analytic) CV's and the CV's of our flown versus terrestrial sample pairs however CV's from the sample pairs tended to be slightly higher than analytic CV's. The overall concordance, based on clinical stratification (normal versus abnormal), was 97%. Length of flight had no impact on the results. Transportation of laboratory specimens via small UASs does not affect the accuracy of routine chemistry, hematology, and coagulation tests results from selfsame samples. However it results in slightly poorer precision for some analytes.

Performance of swabs, lavage, and diluents to quantify biomarkers of female genital tract soluble mucosal mediators.

Directory of Open Access Journals (Sweden)

Charlene S Dezzutti

Full Text Available BACKGROUND: Measurement of immune mediators and antimicrobial activity in female genital tract secretions may provide biomarkers predictive of risk for HIV-1 acquisition and surrogate markers of microbicide safety. However, optimal methods for sample collection do not exist. This study compared collection methods. METHODS: Secretions were collected from 48 women (24 with bacterial vaginosis [BV] using vaginal and endocervical Dacron and flocked swabs. Cervicovaginal lavage (CVL was collected with 10 mL of Normosol-R (n = 20, saline (n = 14, or water (n = 14. The concentration of gluconate in Normosol-R CVL was determined to estimate the dilution factor. Cytokine and antimicrobial mediators were measured by Luminex or ELISA and corrected for protein content. Endogenous anti-HIV-1 and anti-E. coli activity were measured by TZM-bl assay or E. coli growth. RESULTS: Higher concentrations of protein were recovered by CVL, despite a 10-fold dilution of secretions, as compared to swab eluents. After protein correction, endocervical swabs recovered the highest mediator levels regardless of BV status. Endocervical and vaginal flocked swabs recovered significantly higher levels of anti-HIV-1 and anti-E. coli activity than Dacron swabs (P<0.001. BV had a significant effect on CVL mediator recovery. Normosol-R tended to recover higher levels of most mediators among women with BV, whereas saline or water tended to recover higher levels among women without BV. Saline recovered the highest levels of anti-HIV-1 activity regardless of BV status. CONCLUSIONS: Endocervical swabs and CVL collected with saline provide the best recovery of most mediators and would be the optimal sampling method(s for clinical trials.

Swabbing often fails to detect amphibian Chytridiomycosis under conditions of low infection load.

Directory of Open Access Journals (Sweden)

Jaehyub Shin

Full Text Available The pathogenic chytrid fungus, Batrachochytrium dendrobatidis (denoted Bd, causes large-scale epizootics in naïve amphibian populations. Intervention strategies to rapidly respond to Bd incursions require sensitive and accurate diagnostic methods. Chytridiomycosis usually is assessed by quantitative polymerase chain reaction (qPCR amplification of amphibian skin swabs. Results based on this method, however, sometimes yield inconsistent results on infection status and inaccurate scores of infection intensity. In Asia and other regions where amphibians typically bear low Bd loads, swab results are least reliable. We developed a Bd-sampling method that collects zoospores released by infected subjects into an aquatic medium. Bd DNA is extracted by filters and amplified by nested PCR. Using laboratory colonies and field populations of Bombina orientalis, we compare results with those obtained on the same subjects by qPCR of DNA extracted from swabs. Many subjects, despite being diagnosed as Bd-negative by conventional methods, released Bd zoospores into collection containers and thus must be considered infected. Infection loads determined from filtered water were at least 1000 times higher than those estimated from swabs. Subjects significantly varied in infection load, as they intermittently released zoospores, over a 5-day period. Thus, the method might be used to compare the infectivity of individuals and study the periodicity of zoospore release. Sampling methods based on water filtration can dramatically increase the capacity to accurately diagnose chytridiomycosis and contribute to a better understanding of the interactions between Bd and its hosts.

Migration of a retained surgical swab into the jejunum in a dog.

Science.gov (United States)

Day, J L; Pechman, R D; Bahr, R J

2012-12-01

A two-year-old spayed female shih-tzu was referred with a 10-month history of lethargy, chronic diarrhoea and weight loss. On presentation, a partial response to antibiotics was noted. Physical examination revealed an abdominal mass, and serum biochemistry and haematology revealed a mature neutrophilia, hypoalbuminaemia and a non-regenerative anaemia. Contrast radiography and abdominal ultrasound were suggestive of an intraluminal foreign body. Exploratory laparotomy revealed a surgical swab in the lumen of the jejunum that was associated with severe adhesions. Histopathology showed evidence of transmural migration of the swab from the peritoneal cavity to the lumen of the jejunum. © 2012 British Small Animal Veterinary Association.

Imperfect pathogen detection from non-invasive skin swabs biases disease inference

Science.gov (United States)

DiRenzo, Graziella V.; Grant, Evan H. Campbell; Longo, Ana; Che-Castaldo, Christian; Zamudio, Kelly R.; Lips, Karen

2018-01-01

1. Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low-level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals. 2. Our objectives were two-fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis on non-invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity. 3. We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modeling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.

49 CFR 40.71 - How does the collector prepare the specimens?

Science.gov (United States)

2010-10-01

... this requirement: you may use excess urine to conduct clinical tests (e.g., protein, glucose) if the... 49 Transportation 1 2010-10-01 2010-10-01 false How does the collector prepare the specimens? 40.71 Section 40.71 Transportation Office of the Secretary of Transportation PROCEDURES FOR...

Sperm cell purification from mock forensic swabs using SOMAmer™ affinity reagents.

Science.gov (United States)

Katilius, Evaldas; Carmel, Andrew B; Koss, Heidi; O'Connell, Dan; Smith, Breanna C; Sanders, Glenn M; LaBerge, Greggory S

2018-03-27

We have demonstrated a proof of concept with affinity-based purification of sperm cells from mock forensic samples using SOMAmer™ reagents, DNA-based affinity reagents developed by SomaLogic, Inc. SOMAmer reagents were selected in vitro using whole-cell SELEX to bind specifically with intact, detergent-treated sperm cells. Successful separation of sperm from epithelial cells and their debris was demonstrated using buccal swabs with added semen. Primarily male DNA profiles were generated from sperm cells eluted from the types of cotton swabs typically used for rape kit evidence collection. The quality of sperm DNA isolated from samples purified using SOMAmers is comparable to existing commercially available differential extraction-based methods at higher sperm concentrations. This purification method is simple, offers relatively rapid (forensic casework. Copyright © 2018. Published by Elsevier B.V.

Value of bacterial culture of vaginal swabs in diagnosis of vaginal infections.

Science.gov (United States)

Nenadić, Dane; Pavlović, Miloš D

2015-06-01

Vaginal and cervical swab culture is still very common procedure in our country's everyday practice whereas simple and rapid diagnostic methods have been very rarely used. The aim of this study was to show that the employment of simple and rapid diagnostic tools [vaginal fluid wet mount microscopy (VFWMM), vaginal pH and potassium hydroxide (KOH) test] offers better assessment of vaginal environment than standard microbiologic culture commonly used in Serbia. This prospective study included 505 asymptomatic pregnant women undergoing VFWMM, test with 10% KOH, determination of vaginal pH and standard culture of cervicovaginal swabs. Combining findings from the procedures was used to make diagnoses of bacterial vaginosis (BV) and vaginitis. In addition, the number of polymorphonuclear leukocytes (PMN) was determined in each sample and analyzed along with other findings. Infections with Candida albicans and Trichomonas vaginalis were confirmed or excluded by microscopic examination. In 36 (6%) patients cervicovaginal swab cultures retrieved several aerobes and facultative anaerobes, whereas in 52 (11%) women Candida albicans was isolated. Based on VFWMM findings and clinical criteria 96 (19%) women had BV, 19 (4%) vaginitis, and 72 (14%) candidiasis. Of 115 women with BV and vaginitis, pH 4.5 was found in 5, and of 390 with normal findings 83 (21%) had vaginal pH 4.5. Elevated numbers of PMN were found in 154 (30%) women--in 83 (54%) of them VFWMM was normal. Specificity and sensitivity of KOH test and vaginal pH determination in defining pathological vaginal flora were 95% and 81%, and 79% and 91%, respectively. Cervicovaginal swab culture is expensive but almost non-informative test in clinical practice. The use of simpler and rapid methods as vaginal fluid wet mount microscopy, KOH test and vaginal pH offers better results in diagnosis, and probably in the treatment and prevention of sequels of vaginal infections.

Screening of Active Lyssavirus Infection in Wild Bat Populations by Viral RNA Detection on Oropharyngeal Swabs

Science.gov (United States)

Echevarría, Juan E.; Avellón, Ana; Juste, Javier; Vera, Manuel; Ibáñez, Carlos

2001-01-01

Brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. Consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. This work describes a new nested reverse transcription (RT)-PCR technique specifically designed for the detection of the European bat virus 1 on oropharyngeal swabs obtained from bats but also able to amplify RNA from the remaining rabies-related lyssaviruses in brain samples. The technique was successfully used for surveillance of a serotine bat (Eptesicus serotinus) colony involved in a case of human exposure, in which 15 out of 71 oropharyngeal swabs were positive. Lyssavirus infection was detected on 13 oropharyngeal swabs but in only 5 brains out of the 34 animals from which simultaneous brain and oropharyngeal samples had been taken. The lyssavirus involved could be rapidly identified by automatic sequencing of the RT-PCR products obtained from 14 brains and three bat oropharyngeal swabs. In conclusion, RT-PCR using oropharyngeal swabs will permit screening of wild bat populations for active lyssavirus infection, for research or epidemiological purposes, in line not only with conservation policies but also in a more efficient manner than classical detection techniques used on the brain. PMID:11574590

Tension test system for irradiated small specimens operated by remote control

International Nuclear Information System (INIS)

Okada, Akira

1993-01-01

A robot-based tension test system has been developed to aid in the mechanical testing of highly radioactive specimens. This system reduces radiation hazards from specimens and allows for the uniform precision of testing results independent of experimenters' skills. The robot system is designed to accommodate a miniaturized tension specimen with a gage section 5.5 by 1.2 mm, with a total length and width of 12.5 and 2.3 mm, respectively, and thickness of about 0.2 mm. The system is composed of a manipulating robot, a vibrational-type specimen feeder, a rotating-type specimen tray, a specimen observation system, a simulated tension text fixture, and a microcomputer for controlling the system. This system accomplishes specimen arrangement in the specimen tray, specimen transportation and loading to the test fixture and testing, and removal of the broken specimen from the fixture. These procedures are performed quickly, safely, and with uniform testing precision by computer control remotely by an unskilled experimenter

Examining the hemagglutinin subtype diversity among wild duck-origin influenza A viruses using ethanol-fixed cloacal swabs and a novel RT-PCR method.

Science.gov (United States)

Wang, Ruixue; Soll, Lindsey; Dugan, Vivien; Runstadler, Jonathan; Happ, George; Slemons, Richard D; Taubenberger, Jeffery K

2008-05-25

This study presents an interconnected approach for circumventing two inherent limitations associated with studies defining the natural history of influenza A viruses in wild birds. The first limiting factor is the ability to maintain a cold chain from specimen collection to the laboratory when study sites are in more remote locations. The second limiting factor is the ability to identify all influenza A virus HA subtypes present in an original sample. We report a novel method for molecular subtyping of avian influenza A virus hemagglutinin genes using degenerate primers designed to amplify all known hemagglutinin subtypes. It was shown previously that templates larger than 200 bp were not consistently amplifiable from ethanol-fixed cloacal swabs. For this study, new primer sets were designed within these constraints. This method was used to perform subtyping RT-PCR on 191 influenza RNA-positive ethanol-fixed cloacal swabs obtained from 880 wild ducks in central Alaska in 2005. Seven different co-circulating hemagglutinin subtypes were identified in this study set, including H1, H3, H4, H5, H6, H8, and H12. In addition, 16% of original cloacal samples showed evidence of mixed infection, with samples yielding from two-to-five different hemagglutinin subtypes. This study further demonstrates the complex ecobiology of avian influenza A viruses in wild birds.

Swab and aspiration specimen collection methods and antibiogram ...

African Journals Online (AJOL)

Correspondence to: Dr. A S Adoga, Department of Surgery, Ear, Nose and Throat unit, Jos University Teaching. Hospital, Plateau State ... Six (4 males, 2 females) and 74 (26 males, 48 females) patients had bilateral and unilateral ear discharges, respectively. ..... El- Sayed Y. Bone conduction impairment in uncomplicated ...

Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment

Science.gov (United States)

Castro, V. A.; Ott, C. M.; Pierson, D. L.

2012-01-01

The determination of risk from infectious disease during spaceflight missions is composed of several factors including both the concentration and characteristics of the microorganisms to which the crew are exposed. Thus, having a good understanding of the microbial ecology aboard spacecraft provides the necessary information to mitigate health risks to the crew. While preventive measures are taken to minimize the presence of pathogens on spacecraft, medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a specific culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. To address this bias in our understanding of the ISS environment, the Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment was designed to investigate and develop monitoring technology to provide better microbial characterization. For the SWAB flight experiment, we hypothesized that environmental analysis using non-culture-based technologies would reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. Key findings during this experiment included: a) Generally, advanced molecular techniques were able to reveal a few organisms not recovered using culture-based methods; however, there is no indication that current monitoring is "missing" any medically significant bacteria or fungi. b) Molecular techniques have tremendous potential for microbial monitoring, however, sample preparation and data analysis present challenges for spaceflight hardware. c) Analytical results indicate that some molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), can

49 CFR 40.99 - How long does the laboratory retain specimens after testing?

Science.gov (United States)

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false How long does the laboratory retain specimens after testing? 40.99 Section 40.99 Transportation Office of the Secretary of Transportation PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Drug Testing Laboratories § 40.99 How...

Swabs to genomes: a comprehensive workflow

Directory of Open Access Journals (Sweden)

Madison I. Dunitz

2015-05-01

Full Text Available The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Identification of rhabdoviral sequences in oropharyngeal swabs from German and Danish bats.

Science.gov (United States)

Fischer, Melina; Freuling, Conrad M; Müller, Thomas; Schatz, Juliane; Rasmussen, Thomas Bruun; Chriel, Mariann; Balkema-Buschmann, Anne; Beer, Martin; Hoffmann, Bernd

2014-11-25

In the frame of active lyssavirus surveillance in bats, oropharyngeal swabs from German (N = 2297) and Danish (N = 134) insectivorous bats were investigated using a newly developed generic pan-lyssavirus real-time reverse transcriptase PCR (RT-qPCR). In total, 15 RT-qPCR positive swabs were detected. Remarkably, sequencing of positive samples did not confirm the presence of bat associated lyssaviruses but revealed nine distinct novel rhabdovirus-related sequences. Several novel rhabdovirus-related sequences were detected both in German and Danish insectivorous bats. The results also prove that the novel generic pan-lyssavirus RT-qPCR offers a very broad detection range that allows the collection of further valuable data concerning the broad and complex diversity within the family Rhabdoviridae.

[A transportation vehicle for laparoscopically obtained follicular specimens].

Science.gov (United States)

Fliess, F R; Sudik, R

1984-01-01

Structure, function and first results with a vehicle for transportation were described. This apparatus allows to store laparoscopic harvested follicular fluids for a while in constant temperature and in air condition with 5% CO2 in compressed air. Simultaneously the follicular fluids were transported in this vehicle from operating theatre to the laboratory.

Value of bacterial culture of vaginal swabs in diagnosis of vaginal infections

Directory of Open Access Journals (Sweden)

Nenadić Dane

2015-01-01

Full Text Available Bacground/Aim. Vaginal and cervical swab culture is still very common procedure in our country’s everyday practice whereas simple and rapid diagnostic methods have been very rarely used. The aim of this study was to show that the employment of simple and rapid diagnostic tools [vaginal fluid wet mount microscopy (VFWMM, vaginal pH and potassium hydroxide (KOH test] offers better assessment of vaginal environment than standard microbiologic culture commonly used in Serbia. Methods. This prospective study included 505 asymptomatic pregnant women undergoing VFWMM, test with 10% KOH, determination of vaginal pH and standard culture of cervicovaginal swabs. Combining findings from the procedures was used to make diagnoses of bacterial vaginosis (BV and vaginitis. In addition, the number of polymorphonuclear leukocytes (PMN was determined in each sample and analyzed along with other findings. Infections with Candida albicans and Trichomonas vaginalis were confirmed or excluded by microscopic examination. Results. In 36 (6% patients cervicovaginal swab cultures retrieved several aerobes and facultative anaerobes, whereas in 52 (11% women Candida albicans was isolated. Based on VFWMM findings and clinical criteria 96 (19% women had BV, 19 (4% vaginitis, and 72 (14% candidiasis. Of 115 women with BV and vaginitis, pH 4.5 was found in 5, and of 390 with normal findings 83 (21% had vaginal pH 4.5. Elevated numbers of PMN were found in 154 (30% women - in 83 (54% of them VFWMM was normal. Specificity and sensitivity of KOH test and vaginal pH determination in defining pathological vaginal flora were 95% and 81%, and 79% and 91%, respectively. Conclusion. Cervicovaginal swab culture is expensive but almost non-informative test in clinical practice. The use of simpler and rapid methods as vaginal fluid wet mount microscopy, KOH test and vaginal pH offers better results in diagnosis, and probably in the treatment and prevention of sequels of vaginal

Early Results and Spaceflight Implications of the SWAB Flight Experiment

Science.gov (United States)

Ott, C. Mark; Pierson, Duane L.

2007-01-01

Microbial monitoring of spacecraft environments provides key information in the assessment of infectious disease risk to the crew. Monitoring aboard the Mir space station and International Space Station (ISS) has provided a tremendous informational baseline to aid in determining the types and concentrations of microorganisms during a mission. Still, current microbial monitoring hardware utilizes culture-based methodology which may not detect many medically significant organisms, such as Legionella pneumophila. We hypothesize that evaluation of the ISS environment using non-culture-based technologies would reveal microorganisms not previously reported in spacecraft, allowing for a more complete health assessment. To achieve this goal, a spaceflight experiment, operationally designated as SWAB, was designed to evaluate the DNA from environmental samples collected from ISS and vehicles destined for ISS. Results from initial samples indicate that the sample collection and return procedures were successful. Analysis of these samples using denaturing gradient gel electrophoresis and targeted PCR primers for fungal contaminants is underway. The current results of SWAB and their implication for in-flight molecular analysis of environmental samples will be discussed.

Isolation of lymphotropic baboon herpesvirus (HVP) from oral swabs of hamadryas baboons of the Sukhumi monkey colony.

Science.gov (United States)

Agrba, V Z; Lapin, B A; Timanovskaya, V V; Dzhachvliany, M C; Kokosha, L V; Chuvirov, G N; Djatchenko, A G

1980-01-01

Ways of lymphotropic baboon herpesvirus (HVP) secretion and its excretion into the environment were investigated. Oral swabs and feces from the Sukhumi main stock hamadryas baboons characterized by a high risk for malignant lymphoma and the baboon stock living in isolation in the forest were used as materials for the investigations. Macaque groups of the Sukhumi stock were used as controls. It could be shown that the HVP was resistent in the oral cavity of the main stock baboons and was isolated from oral swabs of these animals both from those with malignant lymphoma and clinically healthy individuals. No virus was isolated from feces of these animals. The virus could not be isolated from oral swabs of the isolated baboon stock and macaques.

Effect of particle- and specimen-level transport on product state in compacted-powder combustion synthesis and thermal debinding of polymers from molded powders

Science.gov (United States)

Oliveira, Amir Antonio Martins

The existence of large gradients within particles and fast temporal variations in the temperature and species concentration prevents the use of asymptotic approximations for the closure of the volume-averaged, specimen-level formulations. In this case a solution of the particle-level transport problem is needed to complement the specimen-level volume-averaged equations. Here, the use of combined specimen-level and particle-level models for transport in reactive porous media is demonstrated with two examples. For the gasless compacted-powder combustion synthesis, a three-scale model is developed. The specimen-level model is based on the volume-averaged equations for species and temperature. Local thermal equilibrium is assumed and the macroscopic mass diffusion and convection fluxes are neglected. The particle-level model accounts for the interparticle diffusion (i.e., the liquid migration from liquid-rich to liquid-lean regions) and the intraparticle diffusion (i.e., the species mass diffusion within the product layer formed at the surface of the high melting temperature component). It is found that the interparticle diffusion controls the extent of conversion to the final product, the maximum temperature, and to a smaller degree the propagation velocity. The intraparticle diffusion controls the propagation velocity and to a smaller degree the maximum temperature. The initial stages of thermal degradation of EVA from molded specimens is modeled using volume-averaged equations for the species and empirical models for the kinetics of the thermal degradation, the vapor-liquid equilibrium, and the diffusion coefficient of acetic acid in the molten polymer. It is assumed that a bubble forms when the partial pressure of acetic acid exceeds the external ambient pressure. It is found that the removal of acetic acid is characterized by two regimes, a pre-charge dominated regime and a generation dominated regime. For the development of an optimum debinding schedule, the

Buccal swab, a minimally invasive method for the screening of oral cancer in active smokers

Science.gov (United States)

Suyatmi; Subiyantoro, P.; Indrakila, S.

2018-05-01

Smoking is the main risk factor for developing oral cancer. The previous study showed that there was a strong correlation between the length of smoking with the risk to develop oral cancer. Early detection of epithelial changes of oral mucosa will be a good prevention of the incidence of oral cancer among active smokers. This study evaluated the potential use of buccal swab for the screening of early signs of malignancy in active smokers. This study involved 80 participants including those who were smokers and non smokers. The buccal swab was conducted using sterile cytobrush. An epithelial smear was made from the buccal swab and stained with Papanicolaou’s technique. An cytomorphometric analysis was conducted by comparing the ratio of nuclear cell to cytoplasmic diameter (ND/CD) between the two groups. The mean of ND observed in this study were 8.963µ for active smokers and 7.991µ for non smokers groups. While the mean of CD were 58.249µ and 63.473µ for active smoker and non-smoker respectively. The mean of ND/CD ratio were 0.156 for active smokers and 0.129 for non smokers groups. This study detected a significant difference on the ND/CD ratio among active smokers vs non smokers (p<0.0001 95% CI = -0.040 – -0.014). In conclusion buccal swab could be a routine procedure to obtain sample for identification of changes in cells morphology to screen an early development of oral cancer.

Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ® swabs.

Science.gov (United States)

Ambers, Angie; Wiley, Rachel; Novroski, Nicole; Budowle, Bruce

2018-01-01

Previous studies have shown that nylon flocked swabs outperform traditional fiber swabs in DNA recovery due to their innovative design and lack of internal absorbent core to entrap cellular materials. The microFLOQ ® Direct swab, a miniaturized version of the 4N6 FLOQSwab ® , has a small swab head that is treated with a lysing agent which allows for direct amplification and DNA profiling from sample collection to final result in less than two hours. Additionally, the microFLOQ ® system subsamples only a minute portion of a stain and preserves the vast majority of the sample for subsequent testing or re-analysis, if desired. The efficacy of direct amplification of DNA from dilute bloodstains, saliva stains, and touch samples was evaluated using microFLOQ ® Direct swabs and the GlobalFiler™ Express system. Comparisons were made to traditional methods to assess the robustness of this alternate workflow. Controlled studies with 1:19 and 1:99 dilutions of bloodstains and saliva stains consistently yielded higher STR peak heights than standard methods with 1ng input DNA from the same samples. Touch samples from common items yielded single source and mixed profiles that were consistent with primary users of the objects. With this novel methodology/workflow, no sample loss occurs and therefore more template DNA is available during amplification. This approach may have important implications for analysis of low quantity and/or degraded samples that plague forensic casework. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evaluation of two methods for monitoring surface cleanliness-ATP bioluminescence and traditional hygiene swabbing.

Science.gov (United States)

Davidson, C A; Griffith, C J; Peters, A C; Fielding, L M

1999-01-01

The minimum bacterial detection limits and operator reproducibility of the Biotrace Clean-Tracetrade mark Rapid Cleanliness Test and traditional hygiene swabbing were determined. Areas (100 cm2) of food grade stainless steel were separately inoculated with known levels of Staphylococcus aureus (NCTC 6571) and Escherichia coli (ATCC 25922). Surfaces were sampled either immediately after inoculation while still wet, or after 60 min when completely dry. For both organisms the minimum detection limit of the ATP Clean-Tracetrade mark Rapid Cleanliness Test was 10(4) cfu/100 cm2 (p 10(7) cfu/100 cm2. Hygiene swabbing percentage recovery rates for both organisms were less than 0.1% for dried surfaces but ranged from 0.33% to 8.8% for wet surfaces. When assessed by six technically qualified operators, the Biotrace Clean-Tracetrade mark Rapid Cleanliness Test gave superior reproducibility for both clean and inoculated surfaces, giving mean coefficients of variation of 24% and 32%, respectively. Hygiene swabbing of inoculated surfaces gave a mean CV of 130%. The results are discussed in the context of hygiene monitoring within the food industry. Copyright 1999 John Wiley & Sons, Ltd.

Evaluation of the reliability of Levine method of wound swab for ...

African Journals Online (AJOL)

The aim of this paper is to evaluate the reliability of Levine swab in accurate identification of microorganisms present in a wound and identify the necessity for further studies in this regard. Methods: A semi structured questionnaire was administered and physical examination was performed on patients with chronic wounds ...

Short communication: Distribution of Porphyromonas gulae fimA genotypes in oral specimens from dogs with mitral regurgitation.

Science.gov (United States)

Shirai, Mitsuyuki; Nomura, Ryota; Kato, Yukio; Murakami, Masaru; Kondo, Chihiro; Takahashi, Soraaki; Yamasaki, Yoshie; Matsumoto-Nakano, Michiyo; Arai, Nobuaki; Yasuda, Hidemi; Nakano, Kazuhiko; Asai, Fumitoshi

2015-10-01

Porphyromonas gulae, a suspected pathogen for periodontal disease in dogs, possesses approximately 41-kDa fimbriae (FimA) that are encoded by the fimA gene. In the present study, the association of fimA genotypes with mitral regurgitation (MR) was investigated. Twenty-five dogs diagnosed with MR (age range 6-13 years old, average 10.8 years) and 32 healthy dogs (8-15 years old, average 10.8 years) were selected at the participating clinics in a consecutive manner during the same time period. Oral swab specimens were collected from the dogs and bacterial DNA was extracted, then polymerase chain reaction analysis was performed using primers specific for each fimA genotype, with the dominant genotype determined. The rate for genotype C dominant specimens was 48.0% in the MR group, which was significantly higher than that in the control group (18.8%) (P <0.05). These results suggest that P. gulae fimA genotype C is associated with MR. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions.

Science.gov (United States)

Schellenberg, John J; Oh, Angela Yena; Hill, Janet E

2017-05-01

The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT). Three artificial mixtures imitating commonly observed vaginal microbiome profiles were easily distinguished and proportion of sequence reads correlated with the estimated proportion of the organism added to the artificial mixtures. Our results indicate that cpn60 UT amplicon sequencing quantifies the proportional abundance of member organisms in these artificial communities regardless of swab type or storage conditions, although some significant differences were observed between samples that were stored frozen and thawed prior to DNA extraction, compared to extractions from samples stored at room temperature for up to 7days. Our results indicate that an on-the-market device developed for infectious disease diagnostics may be appropriate for vaginal microbiome profiling, an approach that is increasingly facilitated by rapidly dropping deep sequencing costs. Copyright © 2017 Elsevier B.V. All rights reserved.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

Science.gov (United States)

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

Needle-to-incubator transport time: Logistic factors influencing transport time for blood culture specimens

NARCIS (Netherlands)

J.J. Kerremans (Jos); A.K. van der Bij (Akke); W.H.F. Goessens (Wil); H.A. Verbrugh (Henri); M.C. Vos (Margreet)

2009-01-01

textabstractThe maximum recommended transport time for blood cultures is 4 h [L. S. Garcia (ed.), 2007 Update: Clinical Microbiology Procedures Handbook, 2nd ed., 2007]. In a previous study, we found that the average transport time was 10 h. In this cohort study, we measured transport times for

Diagnosis of Neisseria gonorrhoeae among pregnant women by culture method and PCR on cppB gene

Directory of Open Access Journals (Sweden)

Jalal Mardaneh

2013-11-01

Full Text Available Background: Neisseria gonorrhoeae is a human obligate pathogen and the etiological agent of gonorrhea. Health irreparable complications resulting from gonorrhea disease occur mainly in pregnant women and neonates. Aim of this study was diagnosis of Neisseria gonorrhoeae among pregnant women with using culture and molecular method by amplification of cppB gene with PCR. Material and Methods: In this cross-sectional study, two endocervical swab specimens were obtained from 1100 pregnant women who referred to Shiraz Hospitals. Culture on nonselective and selective media and nucleic acid amplification test (NAAT were performed for detection of Neisseria gonorrhoeae cppB gene. Results: All endocervical swabs cultures on selective and nonselective media were negative for Neisseria gonorrhoeae. Among examined endocervical swabs, 13samples (1.18% were positive by nucleic acid amplification of Neisseria gonorrgoeae cppB gene. Conclusion: Negative results of culture and positive results of PCR in this study indicate that however culture is gold standard method for detection of Neisseria gonorrhoeae but due to bacterial autolysis, poor sampling techniques and improper specimen storage and transport, its value decline as compared with Nucleic acid amplification test (NAAT.

[Influence of distinct criteria for selecting patients for swabbing on estimation of the effectiveness of the influenza vaccine].

Science.gov (United States)

Martínez-Baz, Iván; Guevara, Marcela; Elía, Fernando; Ezpeleta, Carmen; Fernández Alonso, Mirian; Castilla, Jesús

2014-01-01

To estimate the effectiveness of the influenza vaccine under different criteria for selecting patients for swabbing. A case-control study was performed of laboratory-confirmed cases (n=909) and negative controls for influenza (n=732) in the 2010-2011 to 2012-2013 seasons in Navarre (Spain). The adjusted vaccine effectiveness was estimated by including all swabs from patients with influenza-like-illness and selecting only the first two cases per physician and week. The first two patients per physician and week were less frequently vaccinated against influenza (7.9% vs. 12.5%, p=0.021) and less often received confirmation of influenza (53.6% vs. 66.4%, p <0.001) than subsequent patients. These differences decreased after adjustment for covariates. The effectiveness of the influenza vaccine was 49% (95% CI: 23-66%) when all swabs were included and was 55% (95% CI: 27-72%) when we selected the first two swabs per week and physician. The selection of the first two patients per physician and week may bias assessment of the effectiveness of the influenza vaccine, although this bias was small in the seasons analyzed. Copyright © 2013 SESPAS. Published by Elsevier Espana. All rights reserved.

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

OpenAIRE

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

1994-01-01

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

Validation of Performance of the Gen-Probe Human Immunodeficiency Virus Type 1 Viral Load Assay with Genital Swabs and Breast Milk Samples

Science.gov (United States)

DeVange Panteleeff, Dana; Emery, Sandra; Richardson, Barbra A.; Rousseau, Christine; Benki, Sarah; Bodrug, Sharon; Kreiss, Joan K.; Overbaugh, Julie

2002-01-01

Human immunodeficiency type 1 (HIV-1) continues to spread at an alarming rate. The virus may be transmitted through blood, genital secretions, and breast milk, and higher levels of systemic virus in the index case, as measured by plasma RNA viral load, have been shown to correlate with increased risk of transmitting HIV-1 both vertically and sexually. Less is known about the correlation between transmission and HIV-1 levels in breast milk or genital secretions, in part because reliable quantitative assays to detect HIV-1 in these fluids are not available. Here we show that the Gen-Probe HIV-1 viral load assay can be used to accurately quantify viral load in expressed breast milk and in cervical and vaginal samples collected on swabs. Virus could be quantified from breast milk and swab samples spiked with known amounts of virus, including HIV-1 subtypes A, C, and D. As few as 10 copies of HIV-1 RNA could be detected above background threshold levels in ≥77% of assays performed with spiked breast milk supernatants and mock swabs. In genital swab samples from HIV-1-infected women, similar levels of HIV-1 RNA were consistently detected in duplicate swabs taken from the same woman on the same clinic visit, suggesting that the RNA values from a single swab sample can be used to measure genital viral load. PMID:12409354

PENCEMARAN KUMAN DI LINGKUNGAN RUMAH SAKIT KHUSUS PENYAKIT MENULAR, JAKARTA

Directory of Open Access Journals (Sweden)

Janas Janas

2012-09-01

Full Text Available A survey to establish environmental contamination was conducted at the Infectious Diseases Hospital (IDH of Jakarta by taking swabs from 90 hospital personnels who are directly involved in patients care. These swabs were taken from their hands, nails, throat and rectum. Swabs and cultures were also obtained from 167 equipments, solid and liquid material, food from the hospital, and the air in the hospital wards. From total of 437 specimen obtained, 73.7% showed presence contaminated result. There was 100% positive culture result noted in hands and nails swabs, 94.8% culture positive for any microorganism result was obtained from throat swabs while rectal swab indicated only 4.4% rate of contamination. Results of 167 swabs from material/equipments in the hospital, showed that 85.1% of them were not sterile, this included 59.1% of 54 liquid material, 37.3% from 35 liquid material which were supposed to be sterile, 100% positive culture of 17 liquid material specimen that were supposed to be clean. From solid materials 66.7% of 51 specimen were not sterile. This included 76.2% from 21 specimen that were supposed to be sterile, and 100% from 7 specimen that supposed to be clean. Also 100% non sterility was obtained from 23 other material and 62 equipment. Recovered bacterias consisted of both gram positive and negative bacterias and almost all of them represented normal human flora. Some of them potentially could became pathogen including pathogen for nosocomial infection. From the hospital personnels hand swabs, 25.4% were spore-forming bacteria and from the throat swabs 46.7% yielded Streptococcus ~ hemolyticus, and 4.4% were positive for coliform bacteria from rectal swabs. Results of material and equipment showed majority of aerobic rods (31.5%. Some of the bacteria recovered, including Pseudomonas aeruginosa and Enterobacter aerogenes were resistant to commonly used antibiotics in the hospital (Ampicillin, Tetracycline and Chloramphenicol.

Comparison of two non-invasive methods of microbial analysis in surgery practice: incision swabbing and the indirect imprint technique.

Science.gov (United States)

Chovanec, Zdenek; Veverkova, Lenka; Votava, Miroslav; Svoboda, Jiri; Jedlicka, Vaclav; Capov, Ivan

2014-12-01

A variety of methods exist to take samples from surgical site infections for cultivation; however, an unambiguous and suitable method has not yet been defined. The aim of our retrospective non-randomized study was to compare two non-invasive techniques of sampling material for microbiologic analysis in surgical practice. We compared bacteria cultured from samples obtained with the use of the swab technique, defined in our study as the gold standard, with the indirect imprint technique. A cotton-tipped swab (Copan, Brescia, Italy) was used; the imprints were taken using Whatman no. 4 filter paper (Macherey-Nagal, Duren, Germany) cut into 5×5 cm pieces placed on blood agar in a Petri dish. To culture the microorganisms in the microbiology laboratory, we used blood agar, UriSelect 4 medium (Bio-Rad, Marnes-la-Coquette, France), and a medium with sodium chloride (blood agar with salt). After careful debridement, a sample was taken from the incision surface by swab and subsequently the same area of the surface was imprinted onto filter paper. The samples were analyzed in the microbiology laboratory under standard safety precautions. The cultivation results of the two techniques were processed statistically using contingency tables and the McNemar test. Those samples that were simultaneously cultivation-positive by imprint and -negative by swabbing were processed in greater detail. Over the period between October 2008 and March 2013, 177 samples from 70 patients were analyzed. Sampling was carried out from 42 males and 28 females. One hundred forty-six samples were from incisions after operations (21 samples from six patients after operation on the thoracic cavity, 73 samples from 35 patients after operation on the abdominal cavity combined with the gastrointestinal tract, 52 samples from 19 patients with other surgical site infections not included above) and 31 samples from 11 patients with no post-operative infection. One patient had a sample taken both from a post

Transporting radioactive rock

International Nuclear Information System (INIS)

Pearce, G.

1990-01-01

The case is made for exempting geological specimens from the IAEA Regulations for Safer Transport of Radioactive Materials. It is pointed out that many mineral collectors in Devon and Cornwall may be unwittingly infringing these regulations by taking naturally radioactive rocks and specimens containing uranium ores. Even if these collectors are aware that these rocks are radioactive, and many are not, few have the necessary equipment to monitor the activity levels. If the transport regulations were to be enforced alarm could be generated and the regulations devalued in case of an accident. The danger from a spill of rock specimens is negligible compared with an accident involving industrial or medical radioactive substances yet would require similar special treatment. (UK)

Reevaluation of nasal swab method for dose estimation at nuclear emergency accident

International Nuclear Information System (INIS)

Yamada, Yuji; Fukutsu, Kumiko; Kurihara, Osamu; Akashi, Makoto

2008-01-01

ICRP Publication 66 human respiratory tract model has been used extensively over in exposure dose assessment. It is well known that respiratory deposition efficiency of inhaled aerosol and its deposition region strongly depend on the particle size. In most of exposure accidents, however, nobody knows a size of inhaled aerosol. And thus two default aerosol sizes of 5μ in AMAD for the workers and 1μ in AMAD for the public are given as being representative in the ICRP model, but both sizes are not linked directly to the maximum dose. In this study, the most hazardous size to our health effects and how to estimate an intake activity was discussed from a viewpoint of emergency medicine. In exposure accident of alpha emitter such as Pu-239, lung monitor and bioassay measurements are not the best methods for rapid estimation with high sensitivity, so that an applicability of nasal swab method has been investigated. A computer software, LUDEP, was used in the calculation of respiratory deposition. It showed that the effective dose per unit intake activity strongly depended on the inhaled aerosol size. In case of Pu-239 dioxide aerosols, it was confirmed that the maximum of dose conversion factor was observed around 0.01μ. It means that this 0.01μ is the most hazardous size at exposure accident of Pu-239. From analysis of the relationship between AI and ET l deposition, it was found that the dose conversion factor from the activity deposited in ET l region also was affected by the aerosol size. The usage of the ICRP's default size in nasal swab method might cause obvious underestimation of the intake activity. Dose estimation based on nasal swab method is possible from safety side at nuclear emergency, and the availability in quantity should be reevaluated for emergency medicine considering of chelating agent administration. (author)

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

49 CFR 40.105 - What happens if the laboratory reports a result different from that expected for a blind specimen?

Science.gov (United States)

2010-10-01

... different from that expected for a blind specimen? 40.105 Section 40.105 Transportation Office of the... for a blind specimen? (a) If you are an employer, MRO, or C/TPA who submits a blind specimen, and if... expected results (obtained from the supplier of the blind specimen), and direct the laboratory to determine...

The laboratory diagnosis of Chlamydia trachomatis infections

Directory of Open Access Journals (Sweden)

Max A Chernesky

2005-01-01

Full Text Available Lower genital tract infections with Chlamydia trachomatis are predominantly asymptomatic in men and women. Diagnostic technology has provided several approaches to the diagnosis of C trachomatis. Outside of cells, Chlamydia can die or degrade without optimal storage and transportation. Because some of the other assays perform better on certain specimen types, it is important for laboratories to recognize these differences and provide advice to physicians and nurses collecting patient specimens, with the objective of diagnosing lower genital tract infections to prevent transmission and upper tract damage. Most invasive specimens, such as cervical or urethral swabs, may be collected for culture, antigen or nucleic acid detection. Noninvasive samples such as first-void urine and vaginal swabs can be easily collected by the patient; these samples must be tested by more sensitive nucleic acid amplification tests. These newer investigative strategies should enable implementation of screening programs to identify and treat partners. Serology has not been particularly useful for the diagnosis of acute C trachomatis infections in adults. Presently, it appears that antibiotic-resistant C trachomatis is not a clinical problem. Laboratories providing C trachomatis diagnosis require participation in continuous quality improvement programs.

Development of resistance welding process. 4. Preparation of pressuring enclosed creep test specimen of 7A material

International Nuclear Information System (INIS)

Endo, Hideo; Seki, Masayuki; Ishibashi, Fujio; Hirako, Kazuhito; Tsukada, Tatsuya

2001-02-01

Mechanical strength in the position welded by resistance welding system was examined in 1999. The test specimens were destroyed in the welding position in a shorter time than expected in the creep test. Therefore, test specimens were prepared to evaluate the cause of destruction. Inner-pressure enclosed creep test specimens were prepared by resistance welding method. Cladding material with low deviation of thickness and high re-crystallization rate was used. Heat treatment after resistance welding was performed to remove the influence of residual stress and the precipitation of carbides. (1) Before preparation of specimens, the welding condition was fixed. Three test specimens were prepared. Two specimens without heat treatment were transported to MMS in Oarai Engineering Center on Aug. 4, 2000. One specimen with heat treatment was transported to MMS after evaluating the residual stress to get optimum heat treatment condition. (2) Specimens were prepared with welding end plugs to both ends of ferritic ODS cladding. Enclosing sides were welded with highly strong Ferritic/Martensitic steel end plugs. The other sides were welded with ferritic ODS end plugs. (3) Some kinds of electrical wave data were obtained during performing welding. Welding position was evaluated with supersonic detector after performing welding. (4) Mechanical strength of welding position in high temperature 800degC was confirmed to be equal to or larger than that of cladding material. The highly qualified specimens in the present were successfully prepared. (author)

Storage Effects on Sample Integrity of Environmental Surface Sampling Specimens with Bacillus anthracis Spores.

Science.gov (United States)

Perry, K Allison; O'Connell, Heather A; Rose, Laura J; Noble-Wang, Judith A; Arduino, Matthew J

The effect of packaging, shipping temperatures and storage times on recovery of Bacillus anthracis . Sterne spores from swabs was investigated. Macrofoam swabs were pre-moistened, inoculated with Bacillus anthracis spores, and packaged in primary containment or secondary containment before storage at -15°C, 5°C, 21°C, or 35°C for 0-7 days. Swabs were processed according to validated Centers for Disease Control/Laboratory Response Network culture protocols, and the percent recovery relative to a reference sample (T 0 ) was determined for each variable. No differences were observed in recovery between swabs held at -15° and 5°C, (p ≥ 0.23). These two temperatures provided significantly better recovery than swabs held at 21°C or 35°C (all 7 days pooled, p ≤ 0.04). The percent recovery at 5°C was not significantly different if processed on days 1, 2 or 4, but was significantly lower on day 7 (day 2 vs. 7, 5°C, 10 2 , p=0.03). Secondary containment provided significantly better percent recovery than primary containment, regardless of storage time (5°C data, p ≤ 0.008). The integrity of environmental swab samples containing Bacillus anthracis spores shipped in secondary containment was maintained when stored at -15°C or 5°C and processed within 4 days to yield the optimum percent recovery of spores.

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.

Human leukocyte antigen typing using buccal swabs as accurate and non-invasive substitute for venipuncture in children at risk for celiac disease.

Science.gov (United States)

Adriaanse, Marlou P M; Vreugdenhil, Anita C E; Vastmans, Véronique; Groeneveld, Lisette; Molenbroeck, Stefan; Schott, Dina A; Voorter, Christina E M; Tilanus, Marcel G J

2016-10-01

Human leukocyte antigen (HLA) typing is an important step in the diagnostic algorithm for celiac disease (CD) and is also used for screening purposes. Collection of blood is invasive and accompanied with emotional impact especially in children. Genetic technological progress now enables HLA typing from buccal cell samples. This study evaluated the reliability and feasibility of HLA typing for CD-associated HLA polymorphisms using buccal swabs as routine test in high-risk individuals. Blood and buccal swabs of 77 children and adolescents with high risk for CD were prospectively collected in this cohort study. Buccal swab collection was performed either by the investigator at the outpatient clinic or by the patient or its parents at home. To evaluate the possibility of self-administration, three families performed the test at home. DNA was extracted using an adapted QIAamp method. Quantity, quality, and purity of DNA were recorded. HLA-DRB1, HLA-DQA1, and HLA-DQB1 typing was examined on buccal cell-derived and blood-derived DNA at low and, if necessary, high resolution level, using sequence-specific oligonucleotide and sequence-based typing, respectively. DNA isolation using buccal swabs yielded a good quality and sufficient quantity of DNA to perform HLA-DQ typing in all individuals. HLA typing results on buccal cell-derived DNA were identical to typing on blood-derived DNA, also for the self-administered samples. Introduction of the buccal swab test for HLA typing of CD risk in routine diagnostics can omit the current venipuncture and enables self-administration at home. Therefore, the buccal swab test is beneficial for individuals with a clinical suspicion for CD, as well as for screening purposes in high-risk populations. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens

Directory of Open Access Journals (Sweden)

El Batrawy Sherouk

2011-04-01

Full Text Available Abstract Background Nasopharyngeal carriage of potential pathogens is important as it is both the major source of transmission and the prerequisite of invasive disease. New methods for detecting carriage could improve comfort, accuracy and laboratory utility. The aims of this study were to compare the sensitivities of a nasopharyngeal swab (NPS and a nasal wash (NW in detecting potential respiratory pathogens in healthy adults using microbiological culture and PCR. Results Healthy volunteers attended for nasal washing and brushing of the posterior nasopharynx. Conventional and real-time PCR were used to detect pneumococcus and meningococcus. Statistical differences between the two nasal sampling methods were determined using a nonparametric Mann-Whitney U test; differences between culture and PCR methods were determined using the McNemar test. Nasal washing was more comfortable for volunteers than swabbing (n = 24. In detection by culture, the NW was significantly more likely to detect pathogens than the NPS (p Conclusions Nasal washing and PCR may provide effective alternatives to nasopharyngeal swabbing and classical microbiology, respectively.

Bacterial vaginosis diagnosed by analysis of first-void-urine specimens

DEFF Research Database (Denmark)

Datcu, Raluca; Gesink, Dionne; Mulvad, Gert

2014-01-01

Bacterial vaginosis (BV) is traditionally diagnosed using vaginal samples. The aim of this study was to investigate whether BV can be diagnosed from first-void urine (FVU). Self-collected vaginal smears, vaginal swabs, and FVU were obtained from 176 women. BV was diagnosed by Nugent's criteria....... The FVU and vaginal swabs were analyzed by quantitative PCRs (qPCRs) for selected vaginal bacteria (Atopobium vaginae, Prevotella spp., Gardnerella vaginalis, bacterial vaginosis-associated bacterium 2, Eggerthella-like bacterium, "Leptotrichia amnionii," Megasphaera type 1), and all had an area under...

Natural history of polyomaviruses in men: the HPV infection in men (HIM) study.

Science.gov (United States)

Hampras, Shalaka S; Giuliano, Anna R; Lin, Hui-Yi; Fisher, Kate J; Abrahamsen, Martha E; McKay-Chopin, Sandrine; Gheit, Tarik; Tommasino, Massimo; Rollison, Dana E

2015-05-01

Several new polyomaviruses have been discovered in the last decade, including Merkel cell polyomavirus (MCPyV). Little is known about the natural history of the more recently discovered polyomaviruses. We estimated the incidence, prevalence, and persistence of 9 polyomaviruses (MCPyV, BK polyomavirus, KI polyomavirus, JC polyomavirus, WU polyomavirus, Human polyomavirus 6 [HPyV6], HPyV7, HPyV9, and Trichodysplasia spinulosa-associated polyomavirus) and examined factors associated with MCPyV infection in a prospective cohort of 209 men initially enrolled in the HPV Infection in Men (HIM) study. Participants enrolled at the US site of the HIM study were recruited into a substudy of cutaneous viral infections and followed for a median of 12.6 months. Eyebrow hair and normal skin swab specimens were obtained at each study visit, and the viral DNA load was measured using multiplex polymerase chain reaction. MCPyV infection showed the highest prevalence (65.1% of normal skin swab specimens and 30.6% of eyebrow hair specimens), incidence (81.7 cases per 1000 person-months among normal skin swab specimens, and 24.1 cases per 1000 person-months among eyebrow hair specimens), and persistence (85.8% of normal skin swab specimens and 58.9% of eyebrow hair specimens) among all polyomaviruses examined. Age of >44 years (odds ratio [OR], 2.11; 95% confidence interval [CI], 1.03-4.33) and Hispanic race (OR, 2.64; 95% CI, 1.01-6.88) were associated with an increased prevalence of MCPyV infection in eyebrow hair and normal skin swab specimens, respectively. MCPyV infection is highly prevalent in adults, with age and race being predisposing factors. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multicenter Clinical Evaluation of the Alere i Respiratory Syncytial Virus Isothermal Nucleic Acid Amplification Assay.

Science.gov (United States)

Hassan, Ferdaus; Hays, Lindsay M; Bonner, Aleta; Bradford, Bradley J; Franklin, Ruffin; Hendry, Phyllis; Kaminetsky, Jed; Vaughn, Michael; Cieslak, Kristin; Moffatt, Mary E; Selvarangan, Rangaraj

2018-03-01

The Alere i respiratory syncytial virus (RSV) assay is an isothermal nucleic acid amplification test capable of detecting RSV directly from respiratory specimens, with results being available in ≤13 min after test initiation. The objective of this study was to evaluate the performance characteristics of the Alere i RSV assay in a point-of-care setting by using direct nasopharyngeal (NP) swab specimens (direct NP) and nasopharyngeal swab specimens eluted and transported in viral transport medium (VTM NP). The study was a prospective, multicenter, clinical trial conducted at 9 sites across the United States to evaluate the clinical performance of the Alere i RSV assay with respiratory specimens obtained from both children (age, 60 years). The performance of the Alere i RSV assay was compared with that of the reference method, the Prodesse ProFlu+ real-time reverse transcriptase PCR (RT-PCR) assay. All specimens with discrepant test results were tested further by a second FDA-cleared PCR assay (the Verigene respiratory virus plus nucleic acid test; Luminex Inc., TX). A total of 554 subjects with signs and symptoms of respiratory infections were enrolled, and respiratory samples were collected in this study. In comparison with the ProFlu+ real-time RT-PCR, the overall sensitivity and specificity of Alere i RSV assay for the detection of RSV were 98.6% (95% confidence interval [CI], 94.4 to 99.7%) and 98.0% (95% CI, 95.8 to 99.1%), respectively, for direct NP and 98.6% (95% CI, 94.4 to 99.7%) and 97.8% (95% CI, 95.5 to 98.9%), respectively, for VTM NP. The Alere i RSV is a highly sensitive and specific molecular assay ideal for rapid RSV detection in patients in the point-of-care setting due to its minimal hands-on time and rapid result availability. Copyright © 2018 American Society for Microbiology.

A study of female genital swabs in primary health care centres in Jos, Nigeria

Directory of Open Access Journals (Sweden)

Samuel Nwadioha

2011-03-01

Full Text Available Objective: To detect some common microbial agents of female genital discharges in order to improve the current syndromic management of abnormal vaginal discharge. Methods: A prospective study of female genital swabs collected from Primary Health Care Centres, Jos, and analysed for microscopy, culture and sensitivity in Jos University Teaching Hospital, December 2006 to December 2007 was carried out. Results: Microbial agents were detected in 70% (700 of a total 1 000 female genital swabs studied. Candida species peaked with 42.0% (420 out of the 1000 samples, followed by Gardnerella vaginalis, an agent of bacterial vaginosis with 26.0%. The distribution of abnormal vaginal discharge was highest in young adults aged 21 to 30 years. Conclusions: It is concluded that abnormal vaginal discharge is most prevalent in the young sexually active age group with Candida species as the commonest agent. We recommend prevention, early diagnosis and prompt treatment of infective female genital discharge in order to reduce the menace of HIV transmission.

Bacterial recovery using sonication versus swabbing of titanium and stainless steel implants inoculated with Staphylococcus pseudintermedius or Pseudomonas aeruginosa.

Science.gov (United States)

Keeshen, Thomas; Case, J Brad; Wellehan, James F; Dujowich, Mauricio

2017-09-12

To evaluate the use of sonication to improve recovery of bacteria from metal discs infected with bacteria commonly associated with implant infections in veterinary medicine. In vitro study in which sterile titanium (Ti6Al4V) and stainless steel (AIS1316-L) discs were incubated with either Staphylococcus pseudintermedius or Pseudomonas aeruginosa for 24 hours. The following three groups were compared: 1) the sonication group involved immersing the discs in sterile saline and sonicating for five minutes; 2) the sham group was considered a negative control in which the discs were immersed in saline for five minutes without sonication; and 3) the swab group involved systematically swabbing the implant with a sterile culturette. All samples were plated on blood agar and incubated for 24 hours. Colonies were then counted and compared. For both species of bacteria, there was a significant increase in bacterial colonies isolated using sonication compared to the other two study groups (p = 0.0001). No differences in bacterial growth were found between the two types of metal implants. There was a significant increase in bacterial colony counts for S. pseudintermedius when comparing the swab group versus the sham group, but this was not significant for P. aeruginosa. Sonication significantly improves recovery of bacteria commonly associated with veterinary implant-associated surgical site infections compared to swabbing of implants in vitro. A prospective clinical evaluation is indicated to determine the in vivo efficacy of sonication in veterinary patients.

Acceptability of Sexually Transmitted Infection Testing Using Self-Collected Vaginal Swabs among College Women

Science.gov (United States)

Fielder, Robyn L.; Carey, Kate B.; Carey, Michael P.

2013-01-01

Objective: To assess the acceptability of sexually transmitted infection (STI) testing using self-collected vaginal swabs (SCVS) among college women. Participants: First-year female students ("N" = 483). Methods: Participants were offered free testing for 3 STIs using SCVS in April 2010 and later completed a survey regarding their…

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

Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

Science.gov (United States)

2009-01-01

Background One of the major sources of human Salmonella infections is meat. Therefore, efficient and rapid monitoring of Salmonella in the meat production chain is necessary. Validation of alternative methods is needed to prove that the performance is equal to established methods. Very few of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non-commercial real-time PCR method for detection of Salmonella in meat and carcass swabs. Results The comparative trial was performed against a reference method (NMKL-71:5, 1999) using artificially and naturally contaminated samples (60 minced veal and pork meat samples, 60 poultry neck-skins, and 120 pig carcass swabs). The relative accuracy was 99%, relative detection level 100%, relative sensitivity 103% and relative specificity 100%. The collaborative trial included six laboratories testing minced meat, poultry neck-skins, and carcass swabs as un-inoculated samples and samples artificially contaminated with 1–10 CFU/25 g, and 10–100 CFU/25 g. Valid results were obtained from five of the laboratories and used for the statistical analysis. Apart from one of the non-inoculated samples being false positive with PCR for one of the laboratories, no false positive or false negative results were reported. Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. Conclusion The real-time PCR method for detection of Salmonella in meat

Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens.

Science.gov (United States)

Gritzfeld, Jenna F; Roberts, Paul; Roche, Lorna; El Batrawy, Sherouk; Gordon, Stephen B

2011-04-13

Nasopharyngeal carriage of potential pathogens is important as it is both the major source of transmission and the prerequisite of invasive disease. New methods for detecting carriage could improve comfort, accuracy and laboratory utility. The aims of this study were to compare the sensitivities of a nasopharyngeal swab (NPS) and a nasal wash (NW) in detecting potential respiratory pathogens in healthy adults using microbiological culture and PCR. Healthy volunteers attended for nasal washing and brushing of the posterior nasopharynx. Conventional and real-time PCR were used to detect pneumococcus and meningococcus. Statistical differences between the two nasal sampling methods were determined using a nonparametric Mann-Whitney U test; differences between culture and PCR methods were determined using the McNemar test.Nasal washing was more comfortable for volunteers than swabbing (n = 24). In detection by culture, the NW was significantly more likely to detect pathogens than the NPS (p < 0.00001). Overall, there was a low carriage rate of pathogens in this sample; no significant difference was seen in the detection of bacteria between culture and PCR methods. Nasal washing and PCR may provide effective alternatives to nasopharyngeal swabbing and classical microbiology, respectively.

Comparison of foam swabs and toothbrushes as oral hygiene interventions in mechanically ventilated patients: a randomised split mouth study.

Science.gov (United States)

Marino, Paola J; Hannigan, Ailish; Haywood, Sean; Cole, Jade M; Palmer, Nicki; Emanuel, Charlotte; Kinsella, Tracey; Lewis, Michael A O; Wise, Matt P; Williams, David W

2016-01-01

During critical illness, dental plaque may serve as a reservoir of respiratory pathogens. This study compared the effectiveness of toothbrushing with a small-headed toothbrush or a foam-headed swab in mechanically ventilated patients. This was a randomised, assessor-blinded, split-mouth trial, performed at a single critical care unit. Adult, orally intubated patients with >20 teeth, where >24 hours of mechanical ventilation was expected were included. Teeth were cleaned 12-hourly using a foam swab or toothbrush (each randomly assigned to one side of the mouth). Cleaning efficacy was based on plaque scores, gingival index and microbial plaque counts. High initial plaque (mean=2.1 (SD 0.45)) and gingival (mean=2.0 (SD 0.54)) scores were recorded for 21 patients. A significant reduction compared with initial plaque index occurred using both toothbrushes (mean change=-1.26, 95% CI -1.57 to -0.95; poral health, which improved after brushing with a toothbrush or foam swab. Both interventions were equally effective at removing plaque and reducing gingival inflammation. NCT01154257; Pre-results.

Evaluation of a new solid media specimen transport card for high risk HPV detection and cervical cancer prevention.

Science.gov (United States)

Maurer, Kathryn; Luo, Hongxue; Shen, Zhiyong; Wang, Guixiang; Du, Hui; Wang, Chun; Liu, Xiaobo; Wang, Xiamen; Qu, Xinfeng; Wu, Ruifang; Belinson, Jerome

2016-03-01

Solid media transport can be used to design adaptable cervical cancer screening programs but currently is limited by one card with published data. To develop and evaluate a solid media transport card for use in high-risk human papillomavirus detection (HR-HPV). The Preventative Oncology International (POI) card was constructed using PK 226 paper(®) treated with cell-lysing solution and indicating dye. Vaginal samples were applied to the POI card and the indicating FTA (iFTA) elute card. A cervical sample was placed in liquid media. All specimens were tested for HR-HPV. Color change was assessed at sample application and at card processing. Stability of the POI card and iFTA elute card was tested at humidity. 319 women were enrolled. Twelve women had at least one insufficient sample with no difference between media (p=0.36). Compared to liquid samples, there was good agreement for HR-HPV detection with kappa of 0.81 (95% CI 0.74-0.88) and 0.71 (95% CI 0.62-0.79) for the POI and iFTA elute card respectively. Sensitivity for ≥CIN2 was 100% (CI 100-100%), 95.1% (CI 92.7-97.6%), and 93.5% (CI 90.7-96.3%) for the HR-HPV test from the liquid media, POI card, and iFTA elute card respectively. There was no color change of the POI card noted in humidity but the iFTA elute card changed color at 90% humidity. The POI card is suitable for DNA transport and HR-HPV testing. This card has the potential to make cervical cancer screening programs more affordable worldwide. Copyright © 2015 Elsevier B.V. All rights reserved.

Silica desiccant packets for storage and transport of Streptococcus pneumoniae and other clinically relevant species.

Directory of Open Access Journals (Sweden)

Casey L Pell

Full Text Available Bacterial isolates are often transported between laboratories for research and diagnostic purposes. Silica desiccant packets (SDPs, which are inexpensive and do not require freezing, were evaluated for storage and recovery of bacterial isolates. Conditions such as inoculum size, swab type and temperature of storage were investigated using ten Streptococcus pneumoniae isolates. The optimized protocol was then tested using 49 additional S. pneumoniae isolates representing 40 serogroups. Overall, S. pneumoniae growth was considered satisfactory (>100 colony forming units for 98/109 (89.9% and 20/20 (100% swabs after 14 days at room temperature or 28 days at 4° C, respectively. Storage in SDPs did not impact on the ability of S. pneumoniae isolates to be subsequently serotyped. When the survival of nine other clinically relevant bacterial species was tested, seven were viable after 28 days at room temperature, the exceptions being Neisseria gonorrhoeae and Haemophilus influenzae. SDPs are suitable for transport and short-term storage of bacterial species including S. pneumoniae.

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

Complete Genome Sequence of a Porcine Polyomavirus from Nasal Swabs of Pigs with Respiratory Disease.

Science.gov (United States)

Hause, Ben M; Smith, Catherine; Bishop, Brian; Stewart, Chelsea; Simonson, Randy

2018-04-26

Metagenomic sequencing of pooled nasal swabs from pigs with unexplained respiratory disease identified a large number of reads mapping to a previously uncharacterized porcine polyomavirus. Sus scrofa polyomavirus 2 was most closely related to betapolyomaviruses frequently detected in mammalian respiratory samples. Copyright © 2018 Hause et al.

National guidelines for the use of antibiotics in hospitalised adult patients: the SWAB guidelines revisited

NARCIS (Netherlands)

Prins, J. M.; Kullberg, B. J.; Gyssens, I. C.

2005-01-01

Since 1996, the Dutch Working Party on Antibiotic Policy (Stichting Werkgroep AntibioticaBeleid, SWAB) has been developing national guidelines for the use of antibiotics in hospitalised adult patients. As a result of both an inventory of the wishes of the users of these guidelines and the recently

Strength characterization of tubular ceramic materials by flexure of semi-cylindrical specimens

DEFF Research Database (Denmark)

Kwok, Kawai; Kiesel, Lutz; Frandsen, Henrik Lund

2014-01-01

Mechanical strength at elevated temperatures and operating atmospheres needs to be characterized during development of tubular ceramic components for advanced energy technologies. Typical procedures are time-consuming because a large number of tests are required for a reliable statistical strength...... characterization and every specimen has to be subjected to the process conditions individually. This paper presents an efficient strength characterization methodology for tubular ceramics. The methodology employs flexure of semi-cylindrical specimens as the strength test and implements the tests within a facility...... conducted on oxygen transport membrane materials at room temperature and 850°C....

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

DEFF Research Database (Denmark)

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards...

Two, four, six, eight... stop and count before it is too late! An audit on swab, needle and instrument counts in theatre.

LENUS (Irish Health Repository)

Donnelly, T.

2014-07-01

A concurrent audit was conducted over a four week period to determine if the counting of swabs, needles and instruments for surgery adhered to local policy and recommended guidelines. Data were collected on 30 abdominal surgical procedures. This audit highlighted failings in the count process. It identified poor communication within the multidisciplinary team. There needs to be an increased awareness about local policy, national and international guidelines regarding the counting of swabs, needles and instruments for all surgical procedures.

Randomized clinical evaluation of self-screening for anal cancer precursors in men who have sex with men

Directory of Open Access Journals (Sweden)

Lampinen Thomas M

2006-03-01

Full Text Available Abstract Background Self-collection of anorectal swab specimens could greatly facilitate the completion of prerequisite studies and future implementation of anal cancer screening among men who have sex with men (MSM. We therefore compared self- versus clinician- collection procedures with respect to specimen adequacy for cytological evaluation, concordance of paired cytological results, and concordance of cytological with biopsy results. Methods Paired self- and clinician- collected anorectal Dacron® swabs for liquid-based (Thin Prep® cytological evaluation were collected in random sequence from a mostly HIV-1 seronegative cohort of young MSM in Vancouver. Slides were reviewed by one cytopathologist. Presence of any cytological abnormality (atypical squamous cells of uncertain significance, ASCUS, or above prompted referral for high-resolution anoscopy and possible biopsy. Results Among 222 patient-clinician specimen pairs, most were adequate for cytological evaluation, though self-collected specimens were less likely to be so (83% versus 92%, McNemar's test p Conclusion Self-collection of anorectal swab specimens for cytologic screening in research and possibly clinical settings appears feasible, particularly if specimen adequacy can be further improved. The severity of biopsy-confirmed anorectal disease is seriously underestimated by cytological screening, regardless of collector.

Analysis of DNA evidence recovered from epithelial cells in penile swabs.

Science.gov (United States)

Drobnic, Katja

2003-06-01

In the rape case presented here, no semen, hair, or other biological evidence were left by the perpetuator at the crime scene or on the victim. The alleged assailant was arrested soon after the crime. A classical stain recovery technique using cotton swab moistened with sterile water was taken for recovering potential female epithelial cells and leukocytes deposited on the alleged assailant's penis during sexual assault. The organic method used for DNA extraction was quantified according to the slot-blot procedure and amplified at 9 and 15 polymorphic loci. Penile swab revealed a DNA profile of mixed origin. In addition to the suspect's DNA profile, DNA contribution from the victim was identified as a minor component in the mixture. Frequency of the profile resulted in a value of 5 x 10(-14) for the multiplex systems AmpFlSTR Plus and 2.5 x 10(-18) for the multiplex system PowerPlex 16, taking into account only non-overlapping alleles between the suspect and the victim from the minor component in the DNA mixture. Moreover, three additional alleles were observed at D21S11 locus by use of PowerPlex and STR SGM plus primers, which could not belong to the suspect. The victim's DNA profile showed the same three-banded genotype at this locus. The same pattern was detected when the victim's saliva or blood were used as reference samples. Our laboratory finding was consistent with the police report that the victim was a person with Down syndrome, a human genetic disease mainly resulting from trisomy (triplication) of the 21 chromosome.

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 ...

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.

Evaluation of an autoclave resistant anatomic nose model for the testing of nasal swabs.

Science.gov (United States)

Bartolitius, Lennart; Frickmann, Hagen; Warnke, Philipp; Ottl, Peter; Podbielski, Andreas

2014-09-01

A nose model that allows for the comparison of different modes of sample acquisition as well as of nasal swab systems concerning their suitability to detect defined quantities of intranasal microorganisms, and further for training procedures of medical staff, was evaluated. Based on an imprint of a human nose, a model made of a silicone elastomer was formed. Autoclave stability was assessed. Using an inoculation suspension containing Staphylococcus aureus and Staphylococcus epidermidis, the model was compared with standardized glass plate inoculations. Effects of inoculation time, mode of sampling, and sample storage time were assessed. The model was stable to 20 autoclaving cycles. There were no differences regarding the optimum coverage from the nose and from glass plates. Optimum sampling time was 1 h after inoculation. Storage time after sampling was of minor relevance for the recovery. Rotating the swab around its own axis while circling the nasal cavity resulted in best sampling results. The suitability of the assessed nose model for the comparison of sampling strategies and systems was confirmed. Without disadvantages in comparison with sampling from standardized glass plates, the model allows for the assessment of a correct sampling technique due to its anatomically correct shape.

Identification of rhabdoviral sequences in oropharyngeal swabs from German and Danish bats

DEFF Research Database (Denmark)

Fischer, Melina; Freuling, Conrad M.; Müller, Thomas

2014-01-01

Background: In the frame of active lyssavirus surveillance in bats, oropharyngeal swabs from German (N = 2297) and Danish (N = 134) insectivorous bats were investigated using a newly developed generic pan-lyssavirus real-time reverse transcriptase PCR (RT-qPCR).Findings: In total, 15 RT-qPCR posi...... bats. The results also prove that the novel generic pan-lyssavirus RT-qPCR offers a very broad detection range that allows the collection of further valuable data concerning the broad and complex diversity within the family Rhabdoviridae....

Optimaliseren van het antibioticabeleid in Nederland. X. SWAB-richtlijn voor antimicrobiële therapie bij gecompliceerde urineweginfecties

NARCIS (Netherlands)

Geerlings, S. E.; van den Broek, P. J.; van Haarst, E. P.; Vleming, L. J.; van Haaren, K. M. A.; Janknegt, R.; Platenkamp, G. J.; Prins, J. M.

2006-01-01

The 'Stichting Werkgroep Antibioticabeleid' (SWAB; Dutch Working Party on Antibiotic Policy) has developed an evidence-based guideline for the empirical antimicrobial treatment of complicated urinary tract infections (UTIs) in hospitalised adult patients. The choice of treatment is based on recent

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.

Flocked nylon swabs versus RODAC plates for detection of multidrug-resistant organisms on environmental surfaces in intensive care units.

Science.gov (United States)

Okamoto, K; Rhee, Y; Schoeny, M; Lolans, K; Cheng, J; Reddy, S; Weinstein, R A; Hayden, M K; Popovich, K J

2018-01-01

To compare two culture methods [nylon fiber flocked swabs with broth enrichment versus RODAC ('replicate organism detection and counting') plates] for recovery of multidrug-resistant organisms, 780 environmental surfaces in 63 rooms of patients on contact precautions in four intensive care units at one hospital were examined. Among sites that had at least one positive culture, swab culture with broth enrichment detected the target organisms more frequently than RODAC plates (37.5% vs 26.0%, P = 0.06). There was moderate agreement between the two methods (κ = 0.44) with agreement better for small or flat surfaces compared to large or irregular surfaces. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Low Prevalence of Enzootic Equine Influenza Virus among Horses in Mongolia

Directory of Open Access Journals (Sweden)

Alexandra Sack

2017-11-01

Full Text Available Horses are critically important for Mongolian herders’ livelihoods, providing transportation and food products, and playing important cultural roles. Equine influenza virus (EIV epizootics have been frequent among Mongolia’s horses, with five occurring since 1970. We sought to estimate the prevalence for EIV infection among horses and Bactrian camels with influenza-like illness between national epizootics. In 2016–2017, active surveillance for EIV was periodically performed in four aimags (provinces. Nasal swabs were collected from 680 horses and 131 camels. Seven of the horse swabs were “positive” for qRT-PCR evidence of influenza A (Ct value ≤ 38. Two more were “suspect positive” (Ct value > 38 and ≤ 40. These nine specimens were collected from four aimags. None of the camel specimens had molecular evidence of infection. Despite serial blind passage in Madin-Darby Canine Kidney cells (MDCK cells, none of the nine horse specimens yielded an influenza A virus. None of the 131 herder households surveyed had recently vaccinated their horses against EIV. It seems likely that sporadic EIV is enzootic in multiple Mongolian aimags. This finding, the infrequent use of EIV vaccination, periodic prevalence of highly pathogenic avian influenza, and the mixing of domestic and wild equid herds suggest that Mongolia may be a hot spot for novel EIV emergence.

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.

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.

Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens.

Science.gov (United States)

Nelson, Gil; Sweeney, Patrick; Gilbert, Edward

2018-02-01

With the advent of the U.S. National Science Foundation's Advancing Digitization of Biodiversity Collections program and related worldwide digitization initiatives, the rate of herbarium specimen digitization in the United States has expanded exponentially. As the number of electronic herbarium records proliferates, the importance of linking these records to the physical specimens they represent as well as to related records from other sources will intensify. Although a rich and diverse literature has developed over the past decade that addresses the use of specimen identifiers for facilitating linking across the internet, few implementable guidelines or recommended practices for herbaria have been advanced. Here we review this literature with the express purpose of distilling a specific set of recommendations especially tailored to herbarium specimen digitization, curation, and management. We argue that associating globally unique identifiers (GUIDs) with physical herbarium specimens and including these identifiers in all electronic records about those specimens is essential to effective digital data curation. We also address practical applications for ensuring these associations.

Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

DEFF Research Database (Denmark)

Löfström, Charlotta; Krause, Michael; Josefsen, Mathilde Hartmann

2009-01-01

of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non....... Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially...... contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. Conclusion: The real-time PCR method for detection of Salmonella in meat and carcass swabs was validated in comparative and collaborative trials according to NordVal recommendations. The PCR method...

Optimaliseren van het antibioticabeleid in Nederland. IX. SWAB-richtlijn voor antimicrobiële therapie bij acute infectieuze diarree

NARCIS (Netherlands)

Bos, J. C.; Schultsz, C.; Vandenbroucke-Grauls, C. M. J.; Speelman, P.; Prins, J. M.

2006-01-01

The 'Stichting Werkgroep Antibioticabeleid' (SWAB; Dutch Working Party on Antibiotic Policy) develops evidence-based guidelines for the use of antibiotics in hospitalised adults. This guideline on acute infectious diarrhoea (AID) concerns the antibiotic treatment of acute infectious inflammation of

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 ...

INDUÇÃO DE OVULAÇÃO COM SWAB VAGINAL EM GATAS DOMÉSTICAS E SEUS EFEITOS SOBRE A MORFOLOGIA UTERINA

OpenAIRE

Silva, Sandra Cristina Becker; Silva, Maíra Corona da; Silva, Fabiana Lessa; Snoeck, Paola Pereira das Neves

2017-01-01

Resumo A ovulação em gatas é induzida por um reflexo neuroendócrino atribuído à estimulação mecânica dos receptores sensoriais durante o coito. Esta estimulação pode ser simulada com auxílio do swab vaginal, desencadeando a pseudogestação. Objetivou-se verificar a eficiência da indução de ovulação com swab, a fim de estabelecer um tratamento contraceptivo natural para felinos domésticos, bem como os efeitos sobre o útero do uso repetido dessa técnica. Na primeira fase do trabalho, foram avali...

HMSRP Hawaiian Monk Seal Specimen Data (includes physical specimens, collection information, status, storage locations, and laboratory results associated with individual specimens)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This data set includes physical specimens, paper logs and Freezerworks database of all logged information on specimens collected from Hawaiian monk seals since 1975....

Improved Specimen-Referral System and Increased Access to Quality Laboratory Services in Ethiopia: The Role of the Public-Private Partnership.

Science.gov (United States)

Kebede, Yenew; Fonjungo, Peter N; Tibesso, Gudeta; Shrivastava, Ritu; Nkengasong, John N; Kenyon, Thomas; Kebede, Amha; Gadde, Renuka; Ayana, Gonfa

2016-04-15

Nonstandardized specimen-transport logistics, lack of laboratory personnel to transport specimens, lack of standard specimen containers, and long turnaround time (TAT) hindered access to quality laboratory services. The objective of the Becton, Dickinson, and Company (BD)-US President's Emergency Plan for AIDS Relief (PEPFAR) Public-Private Partnership (PPP) was to support country-specific programs to develop integrated laboratory systems, services, and quality improvement strategies, with an emphasis on strengthening the specimen-referral system (SRS). In 2007, through the Centers for Disease Control and Prevention (CDC), the Ethiopian Public Health Institute (EPHI) joined with the BD-PEPFAR PPP to strengthen laboratory systems. A joint planning and assessment committee identified gaps in the SRS for prioritization and intervention and piloted the system in Addis Ababa and Amhara Region. The PPP established standardized, streamlined specimen logistics, using the Ethiopian Postal Service Enterprise to support a laboratory network in which 554 facilities referred specimens to 160 laboratories. The PPP supported procuring 400 standard specimen containers and the training of 586 laboratory personnel and 81 postal workers. The average TAT was reduced from 7 days (range, 2-14 days) to 2 days (range, 1-3 days) in Addis Ababa and from 10 days (range, 6-21 days) to 5 days (range, 2-6 days) in Amhara Region. This study highlights the feasibility and untapped potential of PPPs to strengthen laboratory systems. This planned and structured approach to improving specimen referral enhanced access to quality laboratory services. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Altered perineal microbiome is associated with vulvovaginitis and urinary tract infection in preadolescent girls.

Science.gov (United States)

Gorbachinsky, Ilya; Sherertz, Robert; Russell, Gregory; Krane, L Spencer; Hodges, Steve J

2014-12-01

Vulvovaginitis has a known association with urinary tract infections (UTIs) in girls. We hypothesize that vulvovaginitis is a major contributor to UTIs in prepubertal girls by increasing periurethral colonization with uropathogens. Periurethral swabs and urine specimens were obtained from a total of 101 girls (58 with vulvovaginitis and 43 without vulvovaginitis). Specimens were cultured for bacterial growth. The dominant organism in the periurethral swabs and urine cultures was recorded and antibiotic sensitivity profiles were compared. Periurethral swabs from children with vulvovaginitis were associated with a statistically significant increase in uropathogenic bacteria (79% Enterococcus species or Escherichia coli) as the dominant culture compared with swabs from girls without vaginitis (18%) (p vulvovaginitis, 52% of the urine cultures were positive for UTIs, and the dominant organism in the urine cultures matched the species and antibiotic sensitivity profile of the corresponding periurethral swab. Only 11% of the urine cultures from girls without vulvovaginitis were positive for UTIs. Vulvovaginitis may cause UTIs by altering the perineal biome such that there is increased colonization of uropathogens.

Impact of 6-month frozen storage of cervical specimens in alkaline buffer conditions on human papillomavirus genotyping.

Science.gov (United States)

LaMere, Brandon J; Howell, Renee; Fetterman, Barbara; Shieh, Jen; Castle, Philip E

2008-08-01

The impact of 6-month storage of cervical specimens under alkaline conditions that occurs as the result of Hybrid Capture 2 testing on human papillomavirus (HPV) genotyping is not well documented. To examine this issue, 143 frozen hc2-positive specimens in specimen transport medium were selected at random from each of the following groups: specimens stored for 6 months, 4 months, and 2.5 months under alkaline pH (pH 12-13) and specimens stored 1 month at neutral pH (pH 6-7) as controls. Specimens were tested in a masked fashion for 20 HPV genotypes (HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, and 82) using a prototype, research-use-only GP5+/6+ L1 consensus PCR method and multiplex hybridization using Luminex xMAP for detection of specific HPV genotypes One control specimen had missing test results. There were no statistical differences in the number of HPV genotypes detected, number of carcinogenic HPV genotypes detected, or in the signal strength among HPV-positive results across groups. Six-month frozen storage of cervical specimens at alkaline pH had little impact on testing for HPV genotypes among hc2-positive women using this HPV genotyping method.

Detection of mycoplasmas in urethral swabs from HIV-1 infected patients and control individuals using culture techniques and polymerase chain reaction

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CUNHA Regina Ayr Florio da

1998-01-01

Full Text Available The objective of the present study was to determine the prevalence of certain mycoplasma species, i.e., Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma penetrans, in urethral swabs from HIV-1 infected patients compared to swabs from a control group. Mycoplasmas were detected by routine culture techniques and by the Polymerase Chain Reaction (PCR technique, using 16SrRNA generic primers of conserved region and Mycoplasma penetrans specific primers. The positivity rates obtained with the two methods were comparable. Nevertheless, PCR was more sensitive, while the culture techniques allowed the quantification of the isolates. The results showed no significant difference (p < 0.05 in positivity rates between the methods used for mycoplasma detection.

Effects of canine parvovirus strain variations on diagnostic test results and clinical management of enteritis in dogs.

Science.gov (United States)

Markovich, Jessica E; Stucker, Karla M; Carr, Alaina H; Harbison, Carole E; Scarlett, Janet M; Parrish, Colin R

2012-07-01

To estimate the prevalence of canine parvovirus (CPV) strains among dogs with enteritis admitted to a referral hospital in the southwestern United States during an 11-month period and to compare diagnostic test results, disease severity, and patient outcome among CPV strains. Prospective observational study. 72 dogs with histories and clinical signs of parvoviral enteritis. For each dog, a fecal sample or rectal swab specimen was evaluated for CPV antigen via an ELISA. Subsequently, fecal samples (n = 42 dogs) and pharyngeal swab specimens (16) were obtained and tested for CPV antigen via an ELISA and CPV DNA via a PCR assay. For specimens with CPV-positive results via PCR assay, genetic sequencing was performed to identify the CPV strain. 56 dogs tested positive for CPV via ELISA or PCR assay. For 42 fecal samples tested via both ELISA and PCR assay, 27 had positive results via both assays, whereas 6 had positive PCR assay results only. Ten pharyngeal swab specimens yielded positive PCR assay results. Genetic sequencing was performed on 34 fecal or pharyngeal swab specimens that had CPV-positive PCR assay results; 25 (73.5%) were identified as containing CPV type-2c, and 9 (26.5%) were identified as containing CPV type-2b. No association was found between CPV strain and disease severity or clinical outcome. CPV type-2b and CPV type-2c posed similar health risks for dogs; therefore, genetic sequencing of CPV does not appear necessary for clinical management of infected patients. The diagnostic tests used could detect CPV type-2c.

The Use of Multiplex PCR to Determine the Prevalence of Enterotoxigenic Staphylococcus aureus Isolated from Raw Milk, Feta Cheese, and Hand Swabs.

Science.gov (United States)

Zeinhom, Mohamed M A; Abdel-Latef, Gihan K; Jordan, Kieran

2015-12-01

Staphylococcus aureus (S. aureus) can cause mastitis in cattle and, therefore, can be present in milk. This study was undertaken to determine the prevalence of coagulase positive S. aureus and its enterotoxin genes sea, seb, and sec in isolates recovered from raw milk, feta cheese, and human hand swabs of milk and cheese handlers in Beni-Suef province, Egypt. A total of 100 samples of raw milk and 50 samples of pasteurized-milk feta cheese were collected. In addition, 50 hand swabs from milk handlers and 25 hand swabs from cheese handlers were examined for the presence of coagulase positive S. aureus. The isolates were characterized by multiplex PCR for detection of sea, seb, and sec genes, and for resistance to 5 classes of commonly used antibiotics. Twelve (12/100), 12 (6/50), and 17% (13/75) of milk, cheese, and hand swab samples, respectively, were positive for coagulase positive S. aureus. One isolate was obtained from each positive sample (31 isolates), and none contained genes for SEA or SEC production. Twenty-five percent, 33%, and 31%, respectively, of the isolates contained the genes for SEB, resulting in 3%, 4%, and 5% of samples being positive for toxin producing coagulase positive S. aureus, respectively. At least one isolate was resistant to each of the antibiotics tested. Despite the low potential for SEB production shown, preventative measures, such as maintenance of the cold-chain and good hygienic practices should be implemented to further reduce the potential risk to public health from SEB, and to reduce the spread of antimicrobial resistance. © 2015 Institute of Food Technologists®

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

Detection of Mycoplasma hyopneumoniae by ELISA and nested PCR from blood samples and nasal swabs from pigs in Slovakia

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Marián Prokeš

2012-01-01

Full Text Available The aim of our study was to map the situation of swine mycoplasmoses on four farms in the region of Eastern Slovakia. The primary agent of Enzootic pneumonia of swine is Mycoplasma hyopneumoniae. After reviewing the health status of conventional herds and evaluation of clinical symptoms, paired samples of nasal swabs and venous blood samples were collected from 38 pigs with clinical signs of respiratory disease. Nasal swab samples were tested by nested PCR, while blood samples were used to detect antibodies against M. hyopneumoniae by blocking ELISA. The presence of M. hyopneumoniae was confirmed by nested PCR in four pigs (10.5% and by blocking ELISA in 16 pigs (42.1% of all four farms. This work presents for the first time comparison of different methods to diagnose M. hyopneumoniae infection on pig farms in Eastern Slovakia.

False-positive cryptococcal antigen test associated with use of BBL Port-a-Cul transport vials.

Science.gov (United States)

Wilson, Deborah A; Sholtis, Mary; Parshall, Sharon; Hall, Gerri S; Procop, Gary W

2011-02-01

A total of 52 residual CSF and serum specimens, which were originally negative with the Cryptococcal Antigen Latex Agglutination System (CALAS), were shown to become falsely positive after placement in BBL Port-A-Cul anaerobic transport vials. This transport device, although excellent for specimen transportation for subsequent culture, should not be used if cryptococcal antigen testing is needed.

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.

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.

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

Performance evaluation of the Aptima HSV-1 and 2 assay for the detection of HSV in cutaneous and mucocutaneous lesion specimens.

Science.gov (United States)

Sam, Soya S; Caliendo, Angela M; Ingersoll, Jessica; Abdul-Ali, Deborah; Kraft, Colleen S

Timely and precise laboratory diagnosis of Herpes simplex viruses (HSV) is required to guide clinical management. The study evaluated limit of detection (LOD) and performance characteristics of the Aptima HSV 1 & 2 assay in comparison to four assays. The multi-center study compared qualitative detection of HSV-1 and 2 by the Aptima HSV-1 and 2 assay (Hologic) to ELVIS culture, Lyra Direct (Quidel), AmpliVue (Quidel) and a laboratory developed test (LDT). LOD was performed using VTM and STM diluted viral concentrations and clinical performance was evaluated using 505 swab specimens. The Aptima LOD studies performed showed a lower detection limit for STM specimens as 1450 copies/mL and 430 copies/mL for HSV1 and HSV-2 respectively; the LOD for VTM specimens was 9370 copies/mL and 8045 copies/mL for HSV-1 and HSV-2 respectively. When the assays were analyzed based on the positive consensus result established the Aptima had 95% of percent positive agreement (PPA) and 100% negative percent agreement (NPA) for the HSV-1. For the HSV-2, the PPA and NPA for Aptima were 96% and 100% respectively. AmpliVue had 1.8% invalid rate, while Lyra had no invalid results but an inhibition rate of 0.8%. Aptima and LDT did not have any invalid or inhibited results. The results indicate that the Aptima HSV-1 & 2 assay is sensitive and the performance characteristics of the Aptima assay is comparable to the assays analyzed for the detection and differentiation of HSV-1 and 2 from cutaneous and mucocutaneous lesions. Copyright © 2017 Elsevier B.V. All rights reserved.

False-Positive Cryptococcal Antigen Test Associated with Use of BBL Port-A-Cul Transport Vials▿

Science.gov (United States)

Wilson, Deborah A.; Sholtis, Mary; Parshall, Sharon; Hall, Gerri S.; Procop, Gary W.

2011-01-01

A total of 52 residual CSF and serum specimens, which were originally negative with the Cryptococcal Antigen Latex Agglutination System (CALAS), were shown to become falsely positive after placement in BBL Port-A-Cul anaerobic transport vials. This transport device, although excellent for specimen transportation for subsequent culture, should not be used if cryptococcal antigen testing is needed. PMID:21159939

Hydrogen transport behavior of beryllium

Energy Technology Data Exchange (ETDEWEB)

Anderl, R.A.; Hankins, M.R.; Longhurst, G.R.; Pawelko, R.J. (Idaho National Engineering Lab., EG and G Idaho, Inc., Idaho Falls, ID (United States)); Macaulay-Newcombe, R.G. (Dept. of Engineering Physics, Univ. Hamilton, ON (Canada))

1992-12-01

Beryllium is being evaluated for use as a plasma-facing material in the International Thermonuclear Experimental Reactor (ITER). One concern in the evaluation is the retention and permeation of tritium implanted into the plasma-facing surface. We performed laboratory-scale studies to investigate mechanisms that influence hydrogen transport and retention in beryllium foil specimens of rolled powder metallurgy product and rolled ingot cast beryllium. Specimen characterization was accomplished using scanning electron microscopy. Auger electron spectroscopy, and Rutherford backscattering spectrometry (RBS) techniques. Hydrogen transport was investigated using ion-beam permeation experiments and nuclear reaction analysis (NRA). Results indicate that trapping plays a significant role in permeation, re-emission, and retention, and that surface processes at both upstream and downstream surfaces are also important. (orig.).

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...

Direct PCR amplification of the HVSI region in mitochondrial DNA from buccal cell swabs

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Kovačević-Grujičić Nataša

2012-01-01

Full Text Available Amplification of human mitochondrial DNA (mtDNA has been widely used in population genetics, human evolutionary and molecular anthropology studies. mtDNA hypervariable segments I and II (HVSI and HVSII were shown to be a suitable tool in genetic analyses due to the unique properties of mtDNA, such as the lack of recombination, maternal mode of inheritance, rapid evolutionary rate and high population-specific polymorphisms. Here we present a rapid and low-cost method for direct PCR amplification of a 330 bp fragment of HVSI from buccal cell samples. Avoiding the DNA isolation step makes this method appropriate for the analysis of a large number of samples in a short period of time. Since the transportation of samples and fieldwork conditions can affect the quality of samples and subsequent DNA analysis, we tested the effects of long-term storage of buccal cell swabs on the suitability of such samples for direct PCR amplification. We efficiently amplified a 330 bp fragment of HVSI even after the long-term storage of buccal cells at room temperature, +4°C or at -20°C, for up to eight months. All examined PCR products were successfully sequenced, regardless of sample storage time and conditions. Our results suggest that the direct PCR amplification of the HVSI region from buccal cells is a method well suited for large-scale mtDNA population studies.[Acknowledgments. This work was supported by the Ministry of Education and Science of the Republic of Serbia (Grant no. III 47025.

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

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

Pilot-Reported Beta-Blockers Identified by Forensic Toxicology Analysis of Postmortem Specimens.

Science.gov (United States)

Canfield, Dennis V; Dubowski, Kurt M; Whinnery, James M; Forster, Estrella M

2018-01-01

This study compared beta-blockers reported by pilots with the medications found by postmortem toxicology analysis of specimens received from fatal aviation accidents between 1999 and 2015. Several studies have compared drugs using the standard approach: Compare the drug found by toxicology analysis with the drug reported by the pilot. This study uniquely examined first the pilot-reported medication and then compared it to that detected by toxicology analysis. This study will serve two purposes: (i) to determine the capability of a toxicology laboratory to detect reported medications, and (ii) to identify pilots with medications below detectable limits. All information required for this study was extracted from the Toxicology Data Base system and was searched using ToxFlo or SQL Server Management Studio. The following information was collected and analyzed: pilot-reported trade and/or generic drug, date specimens received, time of accident, type of aviation operations (CFR), state, pilot level, age, class of medical, specimen type, specimen concentration, dose reported, frequency reported associated with the accident, quantity reported, National Transportation Safety Board (NTSB) accident event number, and all NTSB reports. There were 319 pilots that either reported taking a beta-blocker or were found to be taking a beta-blocker by postmortem toxicology analysis. Time of death, therapeutic concentration and specimen type were found to be factors in the ability of the laboratory to detect beta-blockers. Beta-blockers taken by pilots will, in most cases, be found by a competent postmortem forensic toxicology laboratory at therapeutic concentrations. The dose taken by the pilot was not found to be a factor in the ability of the laboratory to identify beta-blockers. Time of dose, route of administration, specimen tested and therapeutic concentration of the drug were found to be factors in the ability of the laboratory to identify beta-blockers in postmortem specimens

An Evaluation of the Cobas4800 HPV Test on Cervico-Vaginal Specimens in Liquid versus Solid Transport Media.

Directory of Open Access Journals (Sweden)

Hongxue Luo

Full Text Available Determine the ability of the Cobas 4800 assay to detect high-risk human papillomavirus (HrHPV and high-grade cervical lesions when using cervico-vaginal samples applied to liquid medium and solid media cards compared to a direct cervical sample.Two cervico-vaginal specimens (pseudo self-collected were obtained from 319 women. One was applied to an iFTA Card (FTA then the brush placed in liquid-based medium (LSELF; the other was applied to a new solid media: POI card (POI. The clinical performance of Cobas4800 assay using the three aforementioned specimens was compared to direct collected endocervical specimens in liquid media (LDOC.The overall agreements of HrHPV detection were 84.2% (LSELF vs. LDOC, 81.0% (FTA vs. LDOC, and 82.3% (POI vs. LDOC. LSELF, FTA and POI identified 98.0%, 79.6%, and 97.5% positive cases of LDOC. Sensitivity to identify CIN2+ were 98.4% (LSELF, 73.8% (FTA, 95.1% (POI, and 93.4% (LDOC respectively. FTA had 78.1% and 90.4% agreement with the LSELF samples for all HrHPV and HPV16/18 detection respectively, while POI had 91.6% for both.Cobas4800 HPV test combined with cervico-vaginal specimens applied to both liquid media and POI solid card are accurate to detect HrHPV infection and high-grade cervical lesions as compared with direct endocervical samples in liquid media.

An Evaluation of the Cobas4800 HPV Test on Cervico-Vaginal Specimens in Liquid versus Solid Transport Media.

Science.gov (United States)

Luo, Hongxue; Du, Hui; Maurer, Kathryn; Belinson, Jerome L; Wang, Guixiang; Liu, Zhihong; Zhang, Lijie; Zhou, Yanqiu; Wang, Chun; Tang, Jinlong; Qu, Xinfeng; Wu, Ruifang

2016-01-01

Determine the ability of the Cobas 4800 assay to detect high-risk human papillomavirus (HrHPV) and high-grade cervical lesions when using cervico-vaginal samples applied to liquid medium and solid media cards compared to a direct cervical sample. Two cervico-vaginal specimens (pseudo self-collected) were obtained from 319 women. One was applied to an iFTA Card (FTA) then the brush placed in liquid-based medium (LSELF); the other was applied to a new solid media: POI card (POI). The clinical performance of Cobas4800 assay using the three aforementioned specimens was compared to direct collected endocervical specimens in liquid media (LDOC). The overall agreements of HrHPV detection were 84.2% (LSELF vs. LDOC), 81.0% (FTA vs. LDOC), and 82.3% (POI vs. LDOC). LSELF, FTA and POI identified 98.0%, 79.6%, and 97.5% positive cases of LDOC. Sensitivity to identify CIN2+ were 98.4% (LSELF), 73.8% (FTA), 95.1% (POI), and 93.4% (LDOC) respectively. FTA had 78.1% and 90.4% agreement with the LSELF samples for all HrHPV and HPV16/18 detection respectively, while POI had 91.6% for both. Cobas4800 HPV test combined with cervico-vaginal specimens applied to both liquid media and POI solid card are accurate to detect HrHPV infection and high-grade cervical lesions as compared with direct endocervical samples in liquid media.

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).

Multiple antimicrobial resistance in bacterial isolates from clinical ...

African Journals Online (AJOL)

A total of 545 clinical specimens (pus, blood, urine, and stool) and environmental specimens (air sample, saline solution, nasal swabs etc) were cultured for isolation and identification of aerobic bacteria and antimicrobial susceptibility testing. Out of these, 356(65%) specimens yielded one or more bacterial strains. Frequent ...

Bacteriology of post–operative wound infections in the surgical ...

African Journals Online (AJOL)

A total of 248 swab specimens from post-operative wounds suspected to be infected were bacteriologically evaluated. Of these, bacterial growth was recorded in 204 specimens (82.3%) while 44 specimens (17.7%) yielded no growth. The bacteria isolated from the samples in decreasing order of prevalence were: ...

Anatomical characteristics of teats and premilking bacterial counts of teat skin swabs of primiparous cows exposed to different types of bedding.

Science.gov (United States)

Guarín, J F; Baumberger, C; Ruegg, P L

2017-02-01

Bacterial populations of teat skin are associated with risk of intramammary infection and may be influenced by anatomical characteristics of teats. The objective of this study was to evaluate associations of selected anatomical characteristics of teats with bacterial counts of teat skin of cows exposed to different types of bedding. Primarily primiparous Holstein cows (n = 128) were randomly allocated to 4 pens within a single barn. Each pen contained 1 type of bedding [new sand (NES), recycled sand (RS), deep-bedded manure solids (DBMS), and shallow-bedded manure solids over foam core mattresses (SBMS)]. During a single farm visit udders (n = 112) were scored for hygiene and 1 front (n = 112) and 1 rear teat (n = 111) of each enrolled cow were scored for hyperkeratosis (HK). Teat length, teat barrel diameter, and teat apex diameter were measured and teat skin swabs were systematically collected for microbiological analysis. Linear type evaluation data for udders of each cow were retrieved for each cow. Teat position (front or rear) was associated with occurrence of clinical mastitis during the 12 mo before the farm visit and more cases occurred in front quarters. The proportion of udders that were classified as clean (score 1 or 2) was 68, 82, 54, and 95% for cows housed in pens containing NES, RS, SBMS, and DBMS, respectively. No association was found between HK score and teat position and no association was found between HK score and teat skin bacterial count. Bacterial counts of teat skin swabs from front teats of cows in pens containing RS and SBMS were significantly less than those of rear teats of cows in pens containing DBMS or NES. Teat skin bacterial counts were significantly greater for swabs obtained from teats of cows with udder hygiene scores of 3 and 4 as compared with swabs obtained from cows with cleaner udders. Of all udder conformation traits evaluated, only narrower rear teat placement was positively associated with bacterial counts on teat skin

Public transport as a reservoir of methicillin-resistant staphylococci.

Science.gov (United States)

Stepanović, S; Cirković, I; Djukić, S; Vuković, D; Svabić-Vlahović, M

2008-10-01

The aim of this study was to explore the occurrence of methicillin-resistant staphylococci in a large urban public transport system. Samples were taken from hand rails, which passengers hold onto when they are standing. In total, 1400 swabs taken from 55 vehicles (trolleybuses, trams and buses) were examined. As many as 30.1% samples were positive for the presence of methicillin-resistant coagulase-negative staphylococci (MRCoNS), but none for methicillin-resistant Staphylococcus aureus (MRSA). MRCoNS were isolated from all 55 vehicles. Nearly 50% of MRCoNS isolates displayed resistance not only to beta-lactams, but at least to two or more other classes of antimicrobials as well. This study demonstrated widespread occurrence of MRCoNS on hand rails in public transport vehicles. MRSA was not detected. The recovery of methicillin-resistant staphylococci from public transport system implies a potential risk for transmission of these bacteria in an out-hospital environment.

Experimental Behavior of Fatigued Single Stiffener PRSEUS Specimens

Science.gov (United States)

Jegley, Dawn C.

2009-01-01

NASA, the Air Force Research Laboratory and The Boeing Company have worked to develop new low-cost, light-weight composite structures for aircraft. A Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept has been developed which offers advantages over traditional metallic structure. In this concept a stitched carbon-epoxy material system has been developed with the potential for reducing the weight and cost of transport aircraft structure by eliminating fasteners, thereby reducing part count and labor. By adding unidirectional carbon rods to the top of stiffeners, the panel becomes more structurally efficient. This combination produces a more damage tolerant design. This document describes the results of experimentation on PRSEUS specimens loaded in unidirectional compression in fatigue and to failure.

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

Prevalence of mycoplasmas in the semen and vaginal swabs of Danish stallions and mares

DEFF Research Database (Denmark)

Baczynska, Agata; Fedder, J.; Schougaard, H.

2006-01-01

may occur. Mycoplasmas have been implicated in genital disorders and infertility of many species including humans and horses. However, their role as commensals or pathogens of the genital tract of horses is still not determined. Bacteriological examinations made on the fossa glandis, urethra, penis...... and semen of stallions, showed the presence of different Mycoplasma species. Therefore our study aimed to find the prevalence of Mycoplasma species and a possible association with fertility problems in Danish riding horses. Eighty semen samples from stallions and 19 vaginal swab samples from mares were...

Prevalence of mycoplasmas in the semen and vaginal swabs of Danish stallions and mares

DEFF Research Database (Denmark)

Baczynska, Agata; Fedder, J; Schougaard, H

2007-01-01

may occur. Mycoplasmas have been implicated in genital disorders and infertility of many species including humans and horses. However, their role as commensals or pathogens of the genital tract of horses is still not determined. Bacteriological examinations made on the fossa glandis, urethra, penis...... and semen of stallions, showed the presence of different Mycoplasma species. Therefore our study aimed to find the prevalence of Mycoplasma species and a possible association with fertility problems in Danish riding horses. Eighty semen samples from stallions and 19 vaginal swab samples from mares were...

Acceptability of study procedures (self-collected introital swabs, blood draws and stool sample collection) by students 10-16 years for an HPV vaccine effectiveness study: a pilot study.

Science.gov (United States)

Nakalembe, Miriam; Mutyaba, Twaha; Mirembe, Florence

2016-03-16

A cohort study was planned to evaluate vaccine immunogenicity and effect of malaria and helminth co-infections on the bivalent Human papilloma virus (HPV) vaccine. The study would involve self collected introital swabs, blood draws and stool sample collection. We therefore conducted a pilot study to assess the acceptability of these procedures among the students and their parents. A cross-sectional study among forty four students from two purposively selected primary schools of Western Uganda. Exit interviews and two focus group discussions (FGD) (for parents) were conducted. Acceptability was measured by willingness to undergo the procedures again, recommending the procedures to others as well as proportion of introital swabs positive for β globulin. FGD determined acceptability of the parents and explored opinions and perceptions that would influence their decisions. HPV-16/18 and β globulin deoxyribonucleic acid (DNA) were analysed using a polymerase chain reaction (PCR) kit. All the students (100%) in the study were willing to provide a self- collected introital swab and a stool sample as well as recommending their friends while (86.3%) were willing for blood draws. There were 40/44 (90.1%) self collected introital swabs that had positive result for human β globulin though none of them was positive for HPV-16/18. In the FGD, it emerged that parents concerns were on the blood draws and introital swab collection which were addressed. The study procedures were highly acceptable among this study population of students and their parents. Follow-up to assess HPV vaccine effectiveness and factors that may influence the vaccine in this age group is feasible.

[Optimizing antibiotics policy in the Netherlands. VI. SWAB advice: no selective decontamination of intensive care patients on mechanical ventilation

NARCIS (Netherlands)

Bonten, M.J.; Kullberg, B.J.; Filius, P.M.

2001-01-01

The Working Party on Antibiotic Policy (Dutch acronym is SWAB) has issued a guideline in which the pro and cons of the routine use of selective decontamination (SD) in patients in intensive care (IC) on mechanical ventilation are compared in order to decide whether SD is indicated. The effectiveness

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)

Current Microbial Isolates from Wound Swab and Their Susceptibility Pattern in a Private Medical College Hospital in Dhaka city

Directory of Open Access Journals (Sweden)

Shahin Sultana

2015-03-01

Full Text Available Background: Wound infection is one of the major health problems that are caused and aggravated by the invasion of pathogenic organisms where empiric treatment is routine. Objective: To isolate and identify the bacteria causing wound infection and to determine the antimicrobial susceptibility pattern. Materials and method: A total of 263 wound swab and pus samples were collected during the period of January to December 2012 from Delta Medical College and Hospital, Dhaka, Bangladesh. Swabs from the wound were inoculated on appropriate media and cultured and the isolates were identified by standard procedures as needed. Antimicrobial susceptibility testing was performed by disk diffusion method according to ‘The Clinical Laboratory Standard Institute’ guidelines. Results: In this study 220 bacterial isolates were recovered from 263 samples showing an isolation rate of 83.65%. The predominant bacteria isolated from infected wounds were Staphylococcus aureus 89 (40.45% followed by Escherichia coli 62 (28.18%, Pseudomonas aeruginosa 34 (15.45%, Enterococci 18 (8.18%, Acinetobacter 5 (2.27%, Klebsiella 9 (4.09% and Proteus 3 (3.36%. Staphylococcus aureus was sensitive to linezolid (94.38%, fusidic acid (91.01%, vancomycin (87.64%, amikacin (74.15% and gentamicin (73.03%. Among the Gram negative isolates Escherichia coli was predominant and showed sensitivity to imipenem (93.54% amikacin (83.87% colistin (53.22% and piperacillin and tazobactum (53.22% and pseudomonas showed sensitivity to amikacin (73.52%, imipenem (70.58% and colistin (70.58%. Conclusion: Staphylococcus aureus was the most frequently isolated pathogen from wound swab and the antibiotic sensitivity pattern of various isolates help to assist the clinician in appropriate selection of empirical antibiotics against wound infection.

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

Magnetic type transportation system

International Nuclear Information System (INIS)

Kobama, Masao.

1981-01-01

Purpose: To enable automatic transportation of nuclear substances with optional setting for the transportation distance, even for a long distance, facilitating the automation of the transportation and decreasing the space for the installation of a direction converging section of the transporting path. Constitution: A transporting vehicle having a pair of permanent magnets or ferromagnetic bodies mounted with a predetermined gap to each other along the transporting direction is provided in the transporting path including a bent direction change section for transporting specimens such as nuclear materials, and a plurality of driving vehicles having permanent magnets or ferromagnetic bodies for magnetically attracting the transporting vehicle from outside of the transporting path are arranged to the outside of the transporting path. At least one of the driving vehicles is made to run along the transporting direction of the transporting path by a driving mechanism incorporating running section such as an endless chain to drive the transportation vehicle, and the transporting vehicle is successively driven by each of the driving mechanisms. (Kawakami, Y.)

Evaluation of penicillin G residues by kidney inhibition swab tests in sow body fluids and tissues following intramuscular injection

Science.gov (United States)

In 2011, the USDA-Food Safety and Inspection Service (FSIS) changed the method used for screening swine tissues for antimicrobial residues from the Fast Antimicrobial Screen Test to the Kidney Inhibition Swab (KIS(TM)). Here, we describe the use of KIS(TM) test for the detection of penicillin G res...

The high vaginal swab in general practice: clinical correlates of possible pathogens.

Science.gov (United States)

Dykhuizen, R S; Harvey, G; Gould, I M

1995-06-01

Clinical features, diagnosis and treatment of 286 women whose high vaginal swabs (HVS) submitted by their general practitioners showed pure, heavy growth of Staphylococcus aureus, beta haemolytic streptococci groups A, C or G, Streptococcus milleri, Streptococcus pneumoniae or Haemophilus influenzae were analysed. Women with group A, C and G streptococci frequently had clinical vulvovaginitis and although the numbers were too small for statistical confirmation, S. pneumoniae and H. influenzae appeared to cause clinical disease as well. The association of S. aureus or S. milleri with clinical vulvovaginitis was much less convincing. It seems relevant for laboratories to report sensitivities for group A, C and G streptococci. Further research is needed to determine the pathogenicity of S. pneumoniae and H. influenzae.

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...

Influência do conteúdo vaginal de gestantes sobre a recuperação do estreptococo do grupo B nos meios de transporte Stuart e Amies Influence of vaginal environment of pregnant women on the recovery of group B streptococcus in Stuart and Amies transport media

Directory of Open Access Journals (Sweden)

José Antonio Simões

2005-11-01

Full Text Available OBJETIVO: avaliar a influência do meio vaginal de gestantes na sobrevivência do estreptococo do grupo B (EGB mantido por 8, 24 e 48 horas nos meios de transporte Amies e Stuart. MÉTODOS: foram coletados três swabs vaginais de 30 gestantes atendidas no Ambulatório de Pré-Natal do Centro de Atenção Integral à Saúde da Mulher (CAISM, Universidade Estadual de Campinas (UNICAMP. O primeiro swab foi mergulhado diretamente no meio seletivo de Todd-Hewitt; o segundo foi utilizado para a realização da bacterioscopia corada pelo Gram e o terceiro foi mergulhado em 2 mL de solução salina à qual foram acrescentados 200 µL de uma suspensão contendo EGB na concentração de 1-2 x 10(8 unidades formadoras de colônia. Desta última suspensão de EGB, foram colhidos três swabs do meio Amies e três do meio Stuart, os quais foram mantidos em temperatura ambiente por 8, 24 e 48 horas, para posterior semeadura em ágar sangue. A leitura do crescimento das placas foi realizada após 24 horas de incubação e classificada semiquantitativamente (0-3 cruzes de acordo com o número de colônias observadas. A análise estatística foi efetuada com o teste exato de Fisher. RESULTADOS: a recuperação do EGB nos meios de transporte Amies e Stuart após 48 horas de estocagem foi de 97 e 87%, respectivamente. Em um dos quatro casos em que não houve a recuperação do EGB após 48 horas de armazenamento, o pH vaginal foi superior a 4,5 e em dois casos havia a presença de vaginose citolítica. CONCLUSÕES: ambos os meios de transporte mostraram-se adequados para a recuperação do EGB em gestantes até 48 horas após a coleta. As características do meio vaginal não influenciaram a recuperação do EGB no presente estudo.PURPOSE: to evaluate the influence of vaginal environment of pregnant women on group B streptococcus (GBS survival after 8, 24 e 48 h in Amies and Stuart transport media. METHODS: Three vaginal samples were collected from 30 pregnant

Canine Skin and Conjunctival Swab Samples for the Detection and Quantification of Leishmania infantum DNA in an Endemic Urban Area in Brazil

Science.gov (United States)

de Almeida Ferreira, Sidney; Leite, Rodrigo Souza; Ituassu, Leonardo Trindade; Almeida, Gregório Guilherme; Souza, Daniel Menezes; Fujiwara, Ricardo Toshio; de Andrade, Antero Silva Ribeiro; Melo, Maria Norma

2012-01-01

Background We evaluated kDNA PCR/hybridization and quantitative real-time PCR (qPCR) targeting the gene of DNA polymerase of Leishmania infantum for CVL diagnosis and assessment of parasite load in clinical samples obtained invasively and non-invasively. Methodology/Principal Findings Eighty naturally infected dogs from an endemic urban area in Brazil were used. Animals were divided into two groups based on the presence or absence of CVL clinical sings. Skin biopsies, bone marrow, blood and conjunctival swabs samples were collected and submitted to L. infantum DNA detection. In addition, anti-Leishmania antibody titers were measured by Immunofluorescence antibody test. The symptomatic dogs had increased titers compared to asymptomatic dogs (P = 0.025). The frequencies of positive results obtained by kDNA PCR/hybridization for asymptomatic and symptomatic dogs, respectively, were as follows: right conjunctiva, 77.5% and 95.0%; left conjunctiva, 75.0% and 87.5%; skin, 45.0% and 75.0%; bone marrow, 50.0% and 77.5%; and blood, 27.5% and 22.5%. In both groups, the parasite load in the skin samples was the highest (P<0.0001). The parasite loads in the conjunctival swab and bone marrow samples were statistically equivalent within each group. The parasite burden in conjunctival swabs was higher in the dogs with clinical signs than in asymptomatic dogs (P = 0.028). This same relationship was also observed in the bone marrow samples (P = 0.002). No differences in amastigotes load in the skin were detected between the groups. Conclusions The conjunctival swab is a suitable clinical sample for qualitative molecular diagnosis of CVL. The highest parasite burdens were detected in skin regardless of the presence of VL-associated clinical signs. The qPCR results emphasized the role of dogs, particularly asymptomatic dogs, as reservoirs for CVL because of the high cutaneous parasite loads. These results may help to explain the maintenance of high transmission rates and

Study on flow and mass transport through fractured soft sedimentary rocks (Contact research)

International Nuclear Information System (INIS)

Shimo, Michito; Kumamoto, Sou; Maekawa, Keisuke

2007-03-01

It is important for safety assessment of HLW geological disposal to evaluate groundwater flow and mass transport in deep underground accurately. Though it is considered that the mass transport in sedimentary rock occurs in pores between grains mainly, fractures of sedimentary rock can be main paths. The objective of this study is to establish a conceptual model for flow and mass transport in fractured soft sedimentary rock. In previous study, a series of laboratory hydraulic and tracer tests and numerical analyses were carried out using sedimentary rock specimens obtained from Koetoi and Wakkanai formation. Single natural fractured cores and rock block specimen were used for the tests and analyses. The results indicated that the matrix diffusion played an important role for mass transport in the fractured soft sedimentary rocks. In this study, the following two tasks were carried out: (1) laboratory hydraulic and tracer experiments of rock cores of Koetoi and Wakkanai formation obtained at HDB-9, HDB-10 and HDB-11 boreholes and a rock block specimen, Wakkanai formation, obtained at an outcrop in the Horonobe area, (2) a numerical study on the conceptual model of flow and mass transport through fractured soft sedimentary rocks. Non-sorbing tracer experiments using naturally fractured cores and rock block specimens were carried out. Pottasium iodide was used as a tracer. The obtained breakthrough curves were interpreted and fitted by using a numerical simulator, and mass transport parameters, such as longitudinal dispersivity, matrix diffusion coefficient, transport aperture, were obtained. Mass transport simulations using a fracture network model, a continuum model and a double porosity model were performed to study the applicability of continuum model and double porosity model for transport in fractured sedimentary rock. (author)

Safe transport of radioactive materials

Energy Technology Data Exchange (ETDEWEB)

NONE

1977-12-31

The film shows the widespread use of radioactive materials in industry, medicine and research and explains the need for transporting nuclear material from producer to user. It shows the way in which packages containing radioactive materials are handled during transport and explains the most important provisions of the IAEA transport regulations, safety series no. 6, such as packaging design criteria and testing requirements, illustrated by various tests carried out, specimen packages and package and freight container labelling. Also illustrated are practical measures to be taken in case of an accident

Application of kidney inhibition swab tests to evaluate penicillin-G residues in sow tissues and body fluids following intramuscular injection

Science.gov (United States)

Kidney inhibition swab (KIS) tests, recently adapted by the US FSIS for antibiotics on-site screening, were employed to evaluate the depletion of penicillin-G residues from kidney, liver, muscle, serum, and urine of sows after intramuscular (IM) penicillin-G procaine administration. Sows (n=130; 22...

49 CFR 40.173 - Who is responsible for paying for the test of a split specimen?

Science.gov (United States)

2010-10-01

... is responsible for paying for the test of a split specimen? (a) As the employer, you are responsible... 49 Transportation 1 2010-10-01 2010-10-01 false Who is responsible for paying for the test of a.... (b) As the employer, you must not condition your compliance with these requirements on the employee's...

Numerical model for surge and swab pressures on wells with cross-section variation

Energy Technology Data Exchange (ETDEWEB)

Fedevjcyk, Joao Victor; Junqueira, Silvio Luiz de Mello; Negrao, Cezar Otaviano Ribeiro [UTFPR - Federal University of Technology - Parana - Curitiba, PR (Brazil)], e-mails: silvio@utfpr.edu.br, negrao@utfpr.edu.br

2010-07-01

Drilling is one of the most complex steps in petroleum exploration. The process is accomplished by rotating a drill bit to compress the rock formation. During drilling, a fluid is pumped into the well to lubricate and cool down the drill bit, to clean up the well, to avoid the formation fluid influx to the well and also to stabilize the borehole walls. Fluid circulation, however, can be interrupted for maintenance reasons and the drill pipe can be moved to remove the drill bit. The downward or upward movement of the drill pipe displaces the fluid within the well causing either under pressure (swab) or over pressure (surge), respectively. If the pressure at the well bore overcomes the formation fracture pressure, a loss of circulation can take place. On the other way round, the upward movement may reduce the pressure below the pore pressure and an inflow of fluid to the well (kick) can occur. An uncontrolled kick may cause a blowout with serious damages. The transient flow induced by the axial movement of the drill pipe is responsible for the pressure changes at the well bore. Nevertheless, the well bore cross section variation may modify the pressure change within the pipe. In this paper, the effects of diameter variation of the drilling well on the surge and swab pressures are investigated. The equations that represent the phenomenon (mass and momentum conservation) are discretized by the finite volume method. Despite its non-Newtonian properties, the fluid is considered Newtonian in this first work. The drill pipe is considered closed and the flow is assumed as single-phased, one-dimensional, isothermal, laminar, compressible and transient. A sensitivity analysis of the flow parameters is carried out. The cross-section changes cause the reflection of the pressure wave, and consequently pressure oscillations. (author)

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

The rate-limiting process of hydrogen transport in Mo

Energy Technology Data Exchange (ETDEWEB)

Ohkoshi, Keishiro; Chikazawa, Yoshitaka; Bandourko, V; Yamaguchi, Kenji; Yamawaki, Michio [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab.

1996-10-01

Hydrogen isotope transport characteristics of Mo, whose refractory properties are considered to be suitable as plasma facing material, was investigated by applying 3 keV D{sub 2}{sup +} beam to the membrane specimen. The Arrhenius plot of deuterium permeation probability showed linear increase against the reciprocal temperature and its apparent activation energy was determined as 41.5 kJ/mol. The simultaneous irradiation of 3 keV Ar{sup +} onto backside surface of specimen had little effect on the deuterium permeation rate. According to these results, the rate-limiting process of deuterium transport in Mo was determined. (author)

Rapid detection of Van genes in rectal swabs by real time PCR in Southern Brazil

Directory of Open Access Journals (Sweden)

Vlademir Cantarelli

2011-10-01

Full Text Available INTRODUCTION: Laboratory-based surveillance is an important component in the control of vancomycin resistant enterococci (VRE. METHODS: The study aimed to evaluate real-time polymerase chain reaction (RT-PCR (genes vanA-vanB for VRE detection on 115 swabs from patients included in a surveillance program. RESULTS: Sensitivity of RT-PCR was similar to primary culture (75% and 79.5%, respectively when compared to broth enriched culture, whereas specificity was 83.1%. CONCLUSIONS: RT-PCR provides same day results, however it showed low sensitivity for VRE detection.

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

A general mixed mode fracture mechanics test specimen: The DCB-specimen loaded with uneven bending moments

Energy Technology Data Exchange (ETDEWEB)

Soerensen, B.F.; Joergensen, K.; Oestergaard, R.C. [Risoe National Lab., Materials Dept., Roskilde (Denmark); Jacobsen, T.K. [LM Glasfiber A/S, Lunderskov (Denmark)

2004-03-01

A mixed mode specimen is proposed for fracture mechanics characterisation of adhesive joints, laminates and multilayers. The specimen is a double cantilever beam specimen loaded with uneven bending moments at the two free beams. By varying the ratio between the two applied moments, the full mode mixity range from pure mode I to pure mode II can be generated for the same specimen geometry. The specimen allows stable crack growth. In case of large scale crack bridging, mixed mode cohesive laws can be obtained by a J integral based approach. As a preliminary example, fracture of adhesive joints between two glass-fibre laminates was studied. The mixed mode fracture resistance increased with increasing crack length due to fibre cross over bridging, eventually reaching a steady-state level (R-curve behaviour). The steady-state fracture toughness level increased with increasing tangential crack opening displacement. Cohesive stresses were determined by a J integral approach. The deducted shear stress was found to be relative high ({approx} = 20 MPa) in comparison with the normal stress ({approx} = 1 MPa). (au)

Molecular detection and confirmation of Neisseria gonorrhoeae in urogenital and extragenital specimens using the Abbott CT/NG RealTime assay and an in-house assay targeting the porA pseudogene.

LENUS (Irish Health Repository)

Walsh, A

2011-04-01

Culture for detection of Neisseria gonorrhoeae (NG) is being replaced by molecular assays, but difficulties are observed with false positive and negatives results, especially for extragenital samples. This study evaluates the Abbott CT\\/NG Real-Time assay and a real-time porA pseudogene assay. Samples (n = 600) from a mixed prevalence Irish population include 164 male urines with corresponding urethral swabs, 58 endocervical swabs, 173 male pharyngeal swabs, 205 male rectal swabs, 36 NG clinical isolates and 26 commensal Neisseria species isolates. There was a 100% concordance between the Abbott CT\\/NG Real-Time and the porA assay. The positivity rate was 1.2%, 1.7%, 8.1% and 5.8% for FVU\\/urethral swabs, endocervical, pharyngeal and rectal swabs, respectively. These results were compared to culture and discrepancies were found with nine pharyngeal and three rectal swabs. Seven of the 12 discrepant positive samples were sequenced and were confirmed "true positives". The sensitivity and specificity of the molecular assays was 100%. The sensitivity of the culture-based testing was 100% for urogenital samples but 36% and 75% for pharyngeal and rectal swabs, respectively. The combined Abbott CT\\/NG and porA assays provide a valuable alternative to culture and also generate a significant increase in the diagnosis of pharyngeal and rectal NG infection.

Identification and genotyping of molluscum contagiosum virus from genital swab samples by real-time PCR and Pyrosequencing.

Science.gov (United States)

Trama, Jason P; Adelson, Martin E; Mordechai, Eli

2007-12-01

Laboratory diagnosis of molluscum contagiosum virus (MCV) is important as lesions can be confused with those caused by Cryptococcus neoformans, herpes simplex virus, human papillomavirus, and varicella-zoster virus. To develop a rapid method for identifying patients infected with MCV via swab sampling. Two dual-labeled probe real-time PCR assays, one homologous to the p43K gene and one to the MC080R gene, were designed. The p43K PCR was designed to be used in conjunction with Pyrosequencing for confirmation of PCR products and discrimination between MCV1 and MCV2. Both PCR assays were optimized with respect to reaction components, thermocycling parameters, and primer and probe concentrations. The specificities of both PCR assays were confirmed by non-amplification of 38 known human pathogens. Sensitivity assays demonstrated detection of as few as 10 copies per reaction. Testing 703 swabs, concordance between the two real-time PCR assays was 99.9%. Under the developed conditions, Pyrosequencing of the p43K PCR product was capable of providing enough nucleotide sequence to definitively differentiate MCV1 and MCV2. These real-time PCR assays can be used for the rapid, sensitive, and specific detection of MCV and, when combined with Pyrosequencing, can further discriminate between MCV1 and MCV2.

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.

An X-ray diffractometer specimen holder for use with reactive and toxic materials

International Nuclear Information System (INIS)

Huyton, A.; Munden, A.B.

1979-04-01

An X-ray diffractometer specimen holder has been designed for analysis of reactive sodium compounds which will satisfactorily seal the sample from the atmosphere. The holder can be readily filled in a glove-box and is easily transported for mounting on a vertical Philips PW 1051 X-ray diffractometer. It is considered that this holder could also be applied to a wide range of other reactive and toxic materials, e.g. plutonium or its compounds. (author)

A general mixed mode fracture mechanics test specimen: The DCB-specimen loaded with uneven bending moments

DEFF Research Database (Denmark)

Sørensen, Bent F.; Jørgensen, K.; Jacobsen, T.K.

2004-01-01

A mixed mode specimen is proposed for fracture mechanics characterisation of adhesive joints, laminates and multilayers. The specimen is a double cantilever beam specimen loaded with uneven bending moments at the two free beams. By varying the ratiobetween the two applied moments, the full mode...... glass-fibre laminates was studied. The mixed mode fracture resistance increased with increasing crack length due to fibre bridging, eventually reaching asteady-state level (R-curve behaviour). The steady-state fracture toughness level increased with increasing tangential crack opening displacement....

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.

Recent advances in FIB-TEM specimen preparation techniques

International Nuclear Information System (INIS)

Li Jian; Malis, T.; Dionne, S.

2006-01-01

Preparing high-quality transmission electron microscopy (TEM) specimens is of paramount importance in TEM studies. The development of the focused ion beam (FIB) microscope has greatly enhanced TEM specimen preparation capabilities. In recent years, various FIB-TEM foil preparation techniques have been developed. However, the currently available techniques fail to produce TEM specimens from fragile and ultra-fine specimens such as fine fibers. In this paper, the conventional FIB-TEM specimen preparation techniques are reviewed, and their advantages and shortcomings are compared. In addition, a new technique suitable to prepare TEM samples from ultra-fine specimens is demonstrated

Reliability of 46,XX results on miscarriage specimens: a review of 1,222 first-trimester miscarriage specimens.

Science.gov (United States)

Lathi, Ruth B; Gustin, Stephanie L F; Keller, Jennifer; Maisenbacher, Melissa K; Sigurjonsson, Styrmir; Tao, Rosina; Demko, Zach

2014-01-01

To examine the rate of maternal contamination in miscarriage specimens. Retrospective review of 1,222 miscarriage specimens submitted for chromosome testing with detection of maternal cell contamination (MCC). Referral centers requesting genetic testing of miscarriage specimens at a single reference laboratory. Women with pregnancy loss who desire complete chromosome analysis of the pregnancy tissue. Analysis of miscarriage specimens using single-nucleotide polymorphism (SNP) microarray technology with bioinformatics program to detect maternal cell contamination. Chromosome content of miscarriages and incidence of 46,XX results due to MCC. Of the 1,222 samples analyzed, 592 had numeric chromosomal abnormalities, and 630 were normal 46,XX or 46,XY (456 and 187, respectively). In 269 of the 46,XX specimens, MCC with no embryonic component was found. With the exclusion of maternal 46,XX results, the chromosomal abnormality rate increased from 48% to 62%, and the ratio for XX to XY results dropped from 2.6 to 1.0. Over half of the normal 46,XX results in miscarriage specimens were due to MCC. The use of SNPs in MCC testing allows for precise identification of chromosomal abnormalities in miscarriage as well as MCC, improving the accuracy of products of conception testing. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Development of fatigue life evaluation technique using miniature specimen

International Nuclear Information System (INIS)

Nogami, Shuhei; Nishimura, Arata; Fujiwara, Masaharu; Hisaka, Tomoaki

2012-01-01

To develop the fatigue life evaluation technique using miniature specimen, the investigation of the effect of specimen size and specimen shape on the fatigue life and the development of the fatigue testing machine, especially the extensometer, were carried out. The effect of specimen size on the fatigue life was almost negligible for the round-bar specimens. The shorter fatigue life at relatively low strain range conditions for the hourglass specimen that the standard specimen were observed. Therefore the miniature round-bar specimen was considered to be adequate for the fatigue life evaluation using small specimen. Several types of the extensometer system using a strain gauge and a laser has been developed for realizing the fatigue test of the miniature round-bar specimen at high temperature in vacuum. (author)

Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding Center Known to Cause Multistate Meningitis Outbreak in United States Using ITS Sequencing

Directory of Open Access Journals (Sweden)

Irshad M. Sulaiman

2014-08-01

Full Text Available A multistate fungal meningitis outbreak started in September of 2012 which spread in 20 states of the United States. The outbreak has been fatal so far, and has affected 751 individuals with 64 deaths among those who received contaminated spinal injections manufactured by a Compounding Center located in Massachusetts. In a preliminary study, Food and Drug Administration (FDA investigated the outbreak in collaboration with Centers for Disease Control and Prevention (CDC, state and local health departments, and identified four fungal and several bacterial contaminations in the recalled unopened injection vials. This follow-up study was carried out to assess DNA sequencing of the ITS1 region of rRNA gene for rapid identification of fungal pathogens during public health outbreak investigations. A total of 26 environmental swabs were collected from several locations at the manufacturing premises of the Compounding Center known to have caused the outbreak. The swab samples were initially examined by conventional microbiologic protocols and a wide range of fungal species were recovered. Species-identification of these microorganisms was accomplished by nucleotide sequencing of ITS1 region of rRNA gene. Analysis of data confirmed 14 additional fungal species in the swabs analyzed.

Diagnostic Procedures to Detect Chlamydia trachomatis Infections

Directory of Open Access Journals (Sweden)

Thomas Meyer

2016-08-01

Full Text Available The intracellular life style of chlamydia and the ability to cause persistent infections with low-grade replication requires tests with high analytical sensitivity to directly detect C. trachomatis (CT in medical samples. Nucleic acid amplification tests (NAATs are the most sensitive assays with a specificity similar to cell culture and are considered the method of choice for CT detection. In addition, NAATs can be performed on various clinical specimens that do not depend on specific transport and storage conditions, since NAATs do not require infectious bacteria. In the case of lower genital tract infections, first void urine and vaginal swabs are the recommended specimens for testing males and females, respectively. Infections of anorectal, oropharyngeal and ocular epithelia should also be tested by NAAT analysis of corresponding mucosal swabs. In particular, anorectal infections of men who have sex with men (MSM should include evaluation of lymphogranuloma venereum (LGV by identification of genotypes L1, L2 or L3. Detection of CT antigens by enzyme immunoassay (EIAs or rapid diagnostic tests (RDTs are unsuitable due to insufficient sensitivity and specificity. Recent PCR-based RDTs, however, are non-inferior to standard NAATs, and might be used at the point-of-care. Serology finds application in the diagnostic work-up of suspected chronic CT infection but is inappropriate to diagnose acute infections.

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

TEM specimen preparation of semiconductor-PMMA-metal interfaces

International Nuclear Information System (INIS)

Thangadurai, P.; Lumelsky, Yulia; Silverstein, Michael S.; Kaplan, Wayne D.

2008-01-01

Transmission electron microscopy (TEM) cross-section specimens of PMMA in contact with gold and Si were prepared by focused ion beam (FIB) and compared with plan-view PMMA specimens prepared by a dip-coating technique. The specimens were characterized by TEM and electron energy loss spectroscopy (EELS). In the cross-section specimens, the thin films of PMMA were located in a Si-PMMA-Au multilayer. Different thicknesses of PMMA films were spin-coated on the Si substrates. The thickness of the TEM specimens prepared by FIB was estimated using EELS to be 0.65 of the plasmon mean-free-path. Along the PMMA-Au interface, Au particle diffusion into the PMMA was observed, and the size of the Au particles was in the range of 2-4 nm. Dip-coating of PMMA directly on Cu TEM grids resulted in thin specimens with a granular morphology, with a thickness of 0.58 of the plasmon mean-free-path. The dip-coated specimens were free from ion milling induced artifacts, and thus serve as control specimens for comparison with the cross-sectioned specimens prepared by FIB

Comparison of gross anatomy test scores using traditional specimens vs. QuickTime Virtual Reality animated specimens

Science.gov (United States)

Maza, Paul Sadiri

In recent years, technological advances such as computers have been employed in teaching gross anatomy at all levels of education, even in professional schools such as medical and veterinary medical colleges. Benefits of computer based instructional tools for gross anatomy include the convenience of not having to physically view or dissect a cadaver. Anatomy educators debate over the advantages versus the disadvantages of computer based resources for gross anatomy instruction. Many studies, case reports, and editorials argue for the increased use of computer based anatomy educational tools, while others discuss the necessity of dissection for various reasons important in learning anatomy, such as a three-dimensional physical view of the specimen, physical handling of tissues, interactions with fellow students during dissection, and differences between specific specimens. While many articles deal with gross anatomy education using computers, there seems to be a lack of studies investigating the use of computer based resources as an assessment tool for gross anatomy, specifically using the Apple application QuickTime Virtual Reality (QTVR). This study investigated the use of QTVR movie modules to assess if using computer based QTVR movie module assessments were equal in quality to actual physical specimen examinations. A gross anatomy course in the College of Veterinary Medicine at Cornell University was used as a source of anatomy students and gross anatomy examinations. Two groups were compared, one group taking gross anatomy examinations in a traditional manner, by viewing actual physical specimens and answering questions based on those specimens. The other group took the same examinations using the same specimens, but the specimens were viewed as simulated three-dimensional objects in a QTVR movie module. Sample group means for the assessments were compared. A survey was also administered asking students' perceptions of quality and user-friendliness of the QTVR

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)

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...

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

Modelling anisotropic water transport in polymer composite ...

Indian Academy of Sciences (India)

Parameters for Fickian diffusion and polymer relaxation models were determined by .... Water transport process of resin and polymer composite specimens at ..... simulation. ... Kwon Y W and Bang H 1997 Finite element method using matlab.

Loop-mediated isothermal amplification assay for rapid detection of Streptococcus agalactiae (group B streptococcus) in vaginal swabs - a proof of concept study.

Science.gov (United States)

McKenna, James Patrick; Cox, Ciara; Fairley, Derek John; Burke, Rachael; Shields, Michael D; Watt, Alison; Coyle, Peter Valentine

2017-03-01

Neonatal sepsis caused by Streptococcus agalactiae [group B streptococcus (GBS)] is a life-threatening condition, which is preventable if colonized mothers are identified and given antibiotic prophylaxis during labour. Conventional culture is time consuming and unreliable, and many available non-culture diagnostics are too complex to implement routinely at point of care. Loop-mediated isothermal amplification (LAMP) is a method that, enables the rapid and specific detection of target nucleic acid sequences in clinical materials without the requirement for extensive sample preparation. A prototype LAMP assay targeting GBS sip gene is described. The assay was 100 % specific for GBS, with a limit of detection of 14 genome copies per reaction. The clinical utility of the LAMP assay for rapid direct molecular detection of GBS was determined by testing a total of 157 vaginal swabs with minimal sample processing using a rapid lysis solution. Compared to a reference quantitative real-time PCR assay, the direct LAMP protocol had a sensitivity and specificity of 95.4 and 100 %, respectively, with positive and negative predictive values of 100 and 98.3 %, respectively. Positive and negative likelihood ratios were infinity and 0.05, respectively. The direct LAMP method required a mean time of 45 min from the receipt of a swab to generation of a confirmed result, compared to 2 h 30 min for the reference quantitative real-time PCR test. The direct LAMP protocol described is easy to perform, facilitating rapid and accurate detection of GBS in vaginal swabs. This test has a potential for use at point of care.

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

Molecular Characterization of Syphilis in Patients in Canada: Azithromycin Resistance and Detection of Treponema pallidum DNA in Whole-Blood Samples versus Ulcerative Swabs▿

Science.gov (United States)

Martin, Irene E.; Tsang, Raymond S. W.; Sutherland, Karen; Tilley, Peter; Read, Ron; Anderson, Barbara; Roy, Colleen; Singh, Ameeta E.

2009-01-01

Although detection of Treponema pallidum DNA in whole-blood specimens of syphilis patients has been reported, it is uncertain at what stage of the disease such specimens are most suitable for the molecular diagnosis of syphilis. Also, few studies have directly compared the different gene targets for routine laboratory diagnostic usage in PCR assays. We examined 87 specimens from 68 patients attending two urban sexually transmitted disease clinics in Alberta, Canada. PCR was used to amplify the T. pallidum tpp47, bmp, and polA genes as well as a specific region of the 23S rRNA gene linked to macrolide antibiotic susceptibility. In primary syphilis cases, PCR was positive exclusively (75% sensitivity rate) in ulcerative swabs but not in blood specimens, while in secondary syphilis cases, 50% of the blood specimens were positive by PCR. Four out of 14 (28.6%) of our PCR-positive syphilis cases were found to be caused by an azithromycin-resistant strain(s). Our results confirmed that swabs from primary ulcers are the specimens of choice for laboratory diagnostic purposes. However, further research is required to determine what specimen(s) would be most appropriate for molecular investigation of syphilis in secondary and latent syphilis. PMID:19339468

Specimen loading list for the varying temperature experiment

International Nuclear Information System (INIS)

Qualls, A.L.; Sitterson, R.G.

1998-01-01

The varying temperature experiment HFIR-RB-13J has been assembled and inserted in the reactor. Approximately 5300 specimens were cleaned, inspected, matched, and loaded into four specimen holders. A listing of each specimen loaded into the steady temperature holder, its position in the capsule, and the identification of the corresponding specimen loaded into the varying temperature holder is presented in this report

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)

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)

Does Pneumatic Tube System Transport Contribute to Hemolysis in ED Blood Samples?

Science.gov (United States)

Phelan, Michael P; Reineks, Edmunds Z; Hustey, Fredric M; Berriochoa, Jacob P; Podolsky, Seth R; Meldon, Stephen; Schold, Jesse D; Chamberlin, Janelle; Procop, Gary W

2016-09-01

Our goal was to determine if the hemolysis among blood samples obtained in an emergency department and then sent to the laboratory in a pneumatic tube system was different from those in samples that were hand-carried. The hemolysis index is measured on all samples submitted for potassium analysis. We queried our hospital laboratory database system (SunQuest(®)) for potassium results for specimens obtained between January 2014 and July 2014. From facility maintenance records, we identified periods of system downtime, during which specimens were hand-carried to the laboratory. During the study period, 15,851 blood specimens were transported via our pneumatic tube system and 92 samples were hand delivered. The proportions of hemolyzed specimens in the two groups were not significantly different (13.6% vs. 13.1% [p=0.90]). Results were consistent when the criterion was limited to gross (3.3% vs 3.3% [p=0.99]) or mild (10.3% vs 9.8% [p=0.88]) hemolysis. The hemolysis rate showed minimal variation during the study period (12.6%-14.6%). We found no statistical difference in the percentages of hemolyzed specimens transported by a pneumatic tube system or hand delivered to the laboratory. Certain features of pneumatic tube systems might contribute to hemolysis (e.g., speed, distance, packing material). Since each system is unique in design, we encourage medical facilities to consider whether their method of transport might contribute to hemolysis in samples obtained in the emergency department.

Detection of newly produced T and B lymphocytes by digital PCR in blood stored dry on nylon flocked swabs.

Science.gov (United States)

Tessitore, Marion Vaglio; Sottini, Alessandra; Roccaro, Aldo M; Ghidini, Claudia; Bernardi, Simona; Martellosio, Giovanni; Serana, Federico; Imberti, Luisa

2017-04-05

A normal number of T-cell receptor excision circles (TRECs) and K-deleting recombination excision circles (KRECs) is considered a biomarker for adequate new T- and B-cell production. In newborns, detection of TRECs and KRECs by real time PCR from dried blood spotted on filter paper is used for the screening of severe immunodeficiency. In adults, elderly and during diseases, where the number of TRECs is lower than in newborns and children, a large amount of DNA and a sensitive method of amplification are necessary to identify newly produced lymphocytes. DNA was prepared from blood of 203 healthy adults (range: 18-91 years old) absorbed for 10 s on flocked swabs and let to dry, or from peripheral blood mononuclear cells. DNA was subjected to digital PCR and to well established conventional real time PCR-based method using TREC- and KREC-specific primers and probes. The number of TRECs and KRECs was expressed per mL of blood. Statistical analysis was performed by nested ANOVA, Pearson coefficient of determination, and by linear regression tests. The novel method for the storage of dried blood on nylon flocked swabs and the use of digital PCR allow quantification of TRECs and KRECs with high degree of sensitivity, specificity, accuracy, and precision. TRECs and KRECs were amplified by digital PCR in all tested blood samples, including those obtained from elderly individuals (>70 years old) and that were negative by real time PCR. Furthermore, values of TRECs and KRECs obtained by digital PCR were in the range of those acquired by real time PCR. Our findings demonstrate that DNA isolation from dried blood on flocked swabs followed by digital PCR-based analysis represents a useful tool for studying new lymphocyte production in adults and elderly individuals. This suggests the potential use of the methodology when monitoring of clinical variables is limited by the number of molecules that can be amplified and detected, such as in patients with immunodeficiency or under

Evaluation of the HB&L carbapenemase and extended spectrum beta lactamase-AmpC automated screening kits for the rapid detection of resistant Enterobacteriaceae in rectal swabs

Directory of Open Access Journals (Sweden)

Sara Marani

2017-03-01

Full Text Available Background. In the past two decades, a rapid increase of infections due to multidrug-resistant Enterobacteriaceae was reported worldwide, including in Italy. These bacteria express genes encoding for extended-spectrum β-lactamases (ESBL or bear a plasmid-mediated AmpC that induce phenotypically a resistance to the last-generation cephalosporins; even more worrying is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (CPE. Materials and methods. The gut may serve as reservoir for these antibiotic drug-resistant bacteria: as a consequence, the rapid detection of drug resistant Enterobacteriaceae from rectal swabs is an important tool to identify rectal carriage of resistant bacteria. This procedure is the basic tool to successfully implement the infection control measures in the hospital wards. The study evaluated the capability of the HB&L ESBL/AmpC and CARBAPENEMASE screening kit (Alifax, Padua, Italy to rapidly identify the drug resistant enterobacteriaceae from rectal swabs: the performance was compared with the conventional method. Results and conclusions. The overall agreement was very good (91% for the detection of ESBL-AmpC, and 96.2% for the identification of CPE; this method is thus an efficient tool to quickly report positive multidrug resistant bacteria in rectal swabs.

Preflight and postflight microbiological results from 25 space shuttle crews

Science.gov (United States)

Pierson, Duane L.; Bassinger, Virginia J.; Molina, Thomas C.; Gunter, Emelie G.; Groves, Theron O.; Cioletti, Louis J.; Mishra, S. K.

1993-01-01

Clinical-microbiological investigations are an important aspect of the crew health stabilization program. To ensure that space crews have neither active nor latent infections, clinical specimens, including throat and nasal swabs and urine samples, are collected at 10 days (L-10) and 2days (L-2) before launch, and immediately after landing (L+0). All samples are examined for the presence of bacteria and fungi. In addition, fecal samples are collected at L-10 and examined for bacteria, fungi and parasites. This paper describes clinical-microbiological findings from 144 astronauts participating in 25 Space Shuttle missions spanning Space Transportation System (STS)-26 to STS-50. The spectrum of microbiological findings from the specimens included 25 bacterial and 11 fungal species. Among the bacteria isolated most frequently were Staphylococcus aureus, Enterobacter aerogenes, Enterococcus faecalis, Escherichia coli, Proteus mirabilis and Streptococcus agalactiae. Candida albicans was the most frequently isolated fungal pathogen.

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

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

Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

Directory of Open Access Journals (Sweden)

Paula R. Almeida

2012-08-01

Full Text Available The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC and polymerase chain reaction (PCR or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs or frozen (tissue pieces. M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

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...

Laboratory investigation and phylogenetic analysis of an imported Middle East respiratory syndrome coronavirus case in Greece.

Directory of Open Access Journals (Sweden)

Athanasios Kossyvakis

Full Text Available Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1st and 2nd day of patient hospitalization and tested using two real-time RT-PCR (rRT-PCR assays targeting the UpE and Orf-1a regions of the MERS-CoV genome and RT-PCR and partial sequencing of RNA-dependent RNA polymerase and nucleocapsid genes. Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient's history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.

HER2 testing on core needle biopsy specimens from primary breast cancers: interobserver reproducibility and concordance with surgically resected specimens

International Nuclear Information System (INIS)

Tsuda, Hitoshi; Kurosumi, Masafumi; Umemura, Shinobu; Yamamoto, Sohei; Kobayashi, Takayuki; Osamura, Robert Yoshiyuki

2010-01-01

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. 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. 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 2+ differed among specimens processed at

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

Molecular Auditing: An Evaluation of Unsuspected Tissue Specimen Misidentification.

Science.gov (United States)

Demetrick, Douglas J

2018-06-18

Context Specimen misidentification is the most significant error in laboratory medicine, potentially accounting for hundreds of millions of dollars in extra health care expenses and significant morbidity in patient populations in the United States alone. New technology allows the unequivocal documentation of specimen misidentification or contamination; however, the value of this technology currently depends on suspicion of the specimen integrity by a pathologist or other health care worker. Objective To test the hypothesis that there is a detectable incidence of unsuspected tissue specimen misidentification among cases submitted for routine surgical pathology examination. Design To test this hypothesis, we selected specimen pairs that were obtained at different times and/or different hospitals from the same patient, and compared their genotypes using standardized microsatellite markers used commonly for forensic human DNA comparison in order to identify unsuspected mismatches between the specimen pairs as a trial of "molecular auditing." We preferentially selected gastrointestinal, prostate, and skin biopsies because we estimated that these types of specimens had the greatest potential for misidentification. Results Of 972 specimen pairs, 1 showed an unexpected discordant genotype profile, indicating that 1 of the 2 specimens was misidentified. To date, we are unable to identify the etiology of the discordance. Conclusions These results demonstrate that, indeed, there is a low level of unsuspected tissue specimen misidentification, even in an environment with careful adherence to stringent quality assurance practices. This study demonstrates that molecular auditing of random, routine biopsy specimens can identify occult misidentified specimens, and may function as a useful quality indicator.

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.)

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.

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...

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

Experimental Design for a Macrofoam-Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

Energy Technology Data Exchange (ETDEWEB)

Piepel, Gregory F. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-12-05

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam-swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (culture and polymerase chain reaction) will be used. Only one previous study has investigated how the false negative rate depends on test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam-swab sampling at low concentrations.

Experimental Design for a Macrofoam Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

Energy Technology Data Exchange (ETDEWEB)

Piepel, Gregory F.; Hutchison, Janine R.

2014-04-16

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (plating/counting and polymerase chain reaction) will be used. Only one previous study has investigated false negative as a function of affecting test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam swab sampling at low concentrations.

Does Pneumatic Tube System Transport Contribute to Hemolysis in ED Blood Samples?

Directory of Open Access Journals (Sweden)

Fredric M. Hustey

2016-09-01

Full Text Available Introduction: Our goal was to determine if the hemolysis among blood samples obtained in an emergency department and then sent to the laboratory in a pneumatic tube system was different from those in samples that were hand-carried. Methods: The hemolysis index is measured on all samples submitted for potassium analysis. We queried our hospital laboratory database system (SunQuest® for potassium results for specimens obtained between January 2014 and July 2014. From facility maintenance records, we identified periods of system downtime, during which specimens were hand-carried to the laboratory. Results: During the study period, 15,851 blood specimens were transported via our pneumatic tube system and 92 samples were hand delivered. The proportions of hemolyzed specimens in the two groups were not significantly different (13.6% vs. 13.1% [p=0.90]. Results were consistent when the criterion was limited to gross (3.3% vs 3.3% [p=0.99] or mild (10.3% vs 9.8% [p=0.88] hemolysis. The hemolysis rate showed minimal variation during the study period (12.6%–14.6%. Conclusion: We found no statistical difference in the percentages of hemolyzed specimens transported by a pneumatic tube system or hand delivered to the laboratory. Certain features of pneumatic tube systems might contribute to hemolysis (e.g., speed, distance, packing material. Since each system is unique in design, we encourage medical facilities to consider whether their method of transport might contribute to hemolysis in samples obtained in the emergency department.

Prevalência de bactérias potencialmente patogênicas em espécimes respiratórios de fibrocísticos do Recife Prevalence of potentially pathogenic bacteria in respiratory specimens of cystic fibrosis patients from Recife

Directory of Open Access Journals (Sweden)

Marcelo Magalhães

2004-08-01

Full Text Available Entre 147 espécimes respiratórios (114 escarros e 33 swabs faríngeos coletados de 36 portadores de fibrose cística durante consultas de rotina ou na exacerbação de seus sintomas respiratórios, no período de dezembro de 2000 a dezembro de 2002, isolaram-se: Pseudomonas aeruginosa (65,3%, Staphylococcus aureus (29,9%, Burkholderia cepacia (29,2% e Haemophilus influenzae (20,4%. Entre os isolados de S. aureus e H. influenzae, 6,8% foram resistentes à oxacilina e 6,7% foram produtores de beta-lactamase, respectivamente. Das 96 linhagens de P. aeruginosa encontradas, 59,4% foram do fenótipo mucóide. Em 12 espécimes, ambos os biótipos, mucóide e não-mucóide, estiveram presentes. Bactérias gram-negativas emergentes, tais como Stenotrophomonas maltophilia e Achromobacter xylosoxidans, foram isoladas em pequeno número. Com exceção do H. influenzae, mais freqüente nas crianças entre seis e 12 anos, não se encontrou diferença entre espécie bacteriana isolada e grupo etário.Of 147 respiratory specimens (114 sputum and 33 pharyngeal swabs collected from 36 cystic fibrosis patients during routine visits or exacerbation of their respiratory symptoms, from December 2000 to December 2002, the following bacterial species were recovered: Pseudomonas aeruginosa (65.3%, Staphylococcus aureus (29.9%, Burkholderia cepacia (29.2%, and Haemophilus influenzae (20.4%. Among the S. aureus and H. influenzae isolates, 6.8% were oxacillin resistant and 6.7% were beta-lactamase producers, respectively. Of 96 isolates of P. aeruginosa, 59.4% belonged to the mucoid phenotype. Both mucoid and non-mucoid morphotypes were simultaneously found in 12 specimens. Emerging gram-negative bacteria, such as Stenotrophomonas maltophilia and Achromobacter xylosoxidans, were present at a low number. H. influenzae was more prevalent in the cystic fibrosis children between six and 12 years old. Concerning the other bacterial species there was not preference for age

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.

Original Article. Evaluation of Rapid Detection of Nasopharyngeal Colonization with MRSA by Real-Time PCR

Directory of Open Access Journals (Sweden)

Kang Feng-feng

2012-03-01

Full Text Available Objective To investigate the clinical application of Real-Time PCR for rapid detection of methicillin-resistant Staphylococcus aureus (MRSA directly from nasopharyngeal swab specimens.

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

Prevalence and Molecular Detection of Quinolone-Resistant E. coli in Rectal Swab of Apparently Healthy Cattle in Bangladesh

OpenAIRE

Md. Montasir Mamun; Jayedul Hassan; K. H. M. Nazmul Hussain Nazir; Md. Alimul Islam; Khalada Zesmin; Md. Bahanur Rahman; Md. Tanvir Rahman

2017-01-01

Emergence of antibiotic resistance is a serious health problem both in human and animal all over the world. In this study, we investigated the prevalence of quinolone-resistant E. coli isolated from apparently healthy cattle in Mymensingh district, Bangladesh. A total of 137 rectal swabs was screened among which 95 was found positive for E. coli. Confirmation of isolation of E. coli was done by PCR targeting 16S rRNA gene of E. coli (prevalence 69.3%). Resistance against quinolone is primaril...

Replacement/Refurbishment of JSC/NASA POD Specimens

Science.gov (United States)

Castner, Willard L.

2010-01-01

The NASA Special NDE certification process requires demonstration of NDE capability by test per NASA-STD-5009. This test is performed with fatigue cracked specimens containing very small cracks. The certification test results are usually based on binomial statistics and must meet a 90/95 Probability of Detection (POD). The assumption is that fatigue cracks are tightly closed, difficult to detect, and inspectors and processes passing such a test are well qualified for inspecting NASA fracture critical hardware. The JSC NDE laboratory has what may be the largest inventory that exists of such fatigue cracked NDE demonstration specimens. These specimens were produced by the hundreds in the late 1980s and early 1990s. None have been produced since that time and the condition and usability of the specimens are questionable.

The influence of specimen size on creep crack growth rate in cross-weld CT specimens cut out from a welded component

International Nuclear Information System (INIS)

Andersson, Peder; Segle, Peter; Samuelson, Lars Aa.

1999-04-01

A 3D finite element study of creep crack growth in cross-weld CT specimens with material properties of 2.25Cr1Mo at 550 deg C is carried out, where large strain and displacement theory is used. The creep crack growth rate is calculated using a creep ductility based damage model, in which the creep strain rate perpendicular to the crack plane ahead of the crack tip is integrated, considering the multiaxial stress state. The influence of specimen size on creep crack growth rate under constant load is given special attention, but the possibility to transfer results from cross-weld CT specimens to welded high temperature components is also investigated. The creep crack growth rate of a crack in a circumferentially welded pipe is compared with the creep crack growth rate of cross-weld CT specimens of three different sizes, cut out from the pipe. Although the constraint ahead of the crack tip is higher for a larger CT specimen, the creep crack growth rate is higher for a smaller specimen than for a larger one if they are loaded to attain the same stress intensity factor. If the specimens are loaded to the same C* value, however, a more complicated pattern occurs; depending on the material properties of the weldment constituents, the CT specimen with the intermediate size will either yield the highest or the lowest creep crack growth rate

Microbiologia de swabs retais e otológicos em carnívoros silvestres do zoológico do Parque Estadual de Dois Irmãos, Pernambuco

Directory of Open Access Journals (Sweden)

Débora Costa Viegas de Lima

2012-02-01

Full Text Available O estudo epidemiológico de patógenos em populações selvagens no ambiente in situ e ex situ é fundamental para implementação de programas de prevenção, controle e monitoramento de enfermidades e para elaboração de políticas públicas de saúde pública e animal. O estudo foi realizado no zoológico do Parque Estadual de Dois Irmãos no período de janeiro a julho de 2011 onde foram coletados swabs anais e otológicos referentes a 29 carnívoros silvestres cativos do zoológico. Dos swabs otológicos analisados, 1/29 (3,4% foi positivo para Malassezia pachy dermatis no exame direto. No exame microbiológico dos swabs otológicos, observou-se maior freqüência para bactérias do gênero Bacillus 16/29 (55,2%, seguida de Sta phylococcus 15/29 (51,7%, Escherichia coli 7/29 (24,1%, Streptobacillus 1/29 (3,4%, Micrococcus 1/29 (3,4% e Klebsiella 1/29 (3,4%. Com relação ao exame presuntivo para o gênero Salmonella a partir das amostras de swab retal, observou-se positividade para seis raposas (Cerdocyon thous e um guaxinim (Procyon cancrivorus. O isolamento de Salmonella spp. em C. thous e em P. cancrivorus indica um risco à saúde pública, principalmente para os profissionais do zoológico que trabalham diretamente com esses animais. Essa pesquisa reforça a importância da criação de estratégias de vigilância epidemiológica voltadas para a prevenção, controle e monitoramento de potenciais reservatórios de agentes etiológicos de doenças infecciosas e parasitárias no ambiente dos zoológicos.

Evaluation of a new T2 Magnetic Resonance assay for rapid detection of emergent fungal pathogen Candida auris on clinical skin swab samples.

Science.gov (United States)

Sexton, D Joseph; Bentz, Meghan L; Welsh, Rory M; Litvintseva, Anastasia P

2018-06-25

Candida auris is a multidrug-resistant pathogenic yeast whose recent emergence is of increasing public-health concern. C. auris can colonize multiple body sites, including patients' skin, and survive for weeks in the healthcare environment, facilitating patient-to-patient transmission and fueling healthcare-associated outbreaks. Rapid and accurate detection of C. auris colonization is essential for timely implementation of infection control measures and prevent transmission. Currently, axilla/groin composite swabs, used to assess colonization status, are processed using a culture-based method that is sensitive and specific but requires 14 days. This delay limits the opportunity to respond and highlights the need for a faster alternative. The culture-independent T2 Magnetic Resonance (T2MR) system is a rapid diagnostic platform shown to detect target pathogens of interest from unprocessed blood samples in T2 assay was evaluated for screening of the skin surveillance samples. Inclusivity and limit of detection of the T2 C. auris assay were assessed with spiked samples in a representative skin flora background. The T2 C. auris assay recognized isolates from each of the 4 known clades of C. auris and consistently detected cells at 5 CFU/mL. Finally, 89 clinical axilla/groin swab samples were processed with the T2 C. auris assay. The culture-based diagnostic assay was used as a gold standard to determine performance statistics including sensitivity (0.89) and specificity (0.98). Overall, the T2 C. auris assay performed well as a rapid diagnostic and could help expedite the detection of C. auris in patient skin swabs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

On impact testing of subsize Charpy V-notch type specimens

International Nuclear Information System (INIS)

Mikhail, A.S.; Nanstad, R.K.

1994-01-01

The potential for using subsize specimens to determine the actual properties of reactor pressure vessel steels is receiving increasing attention for improved vessel condition monitoring that could be beneficial for light-water reactor plant-life extension. This potential is made conditional upon, on the one hand, by the possibility of cutting samples of small volume from the internal surface of the pressure vessel for determination of actual properties of the operating pressure vessel. The plant-life extension will require supplemental surveillance data that cannot be provided by the existing surveillance programs. Testing of subsize specimens manufactured from broken halves of previously tested surveillance Charpy V-notch (CVN) specimens offers an attractive means of extending existing surveillance programs. Using subsize CVN type specimens requires the establishment of a specimen geometry that is adequate to obtain a ductile-to-brittle transition curve similar to that obtained from full-size specimens. This requires the development of a correlation of transition temperature and upper-shelf toughness between subsize and full-size specimens. The present study was conducted under the Heavy-Section Steel Irradiation Program. Different published approaches to the use of subsize specimens were analyzed and five different geometries of subsize specimens were selected for testing and evaluation. The specimens were made from several types of pressure vessel steels with a wide range of yield strengths, transition temperatures, and upper-shelf energies (USEs). Effects of specimen dimensions, including depth, angle, and radius of notch have been studied. The correlation of transition temperature determined from different types of subsize specimens and the full-size specimen is presented. A new procedure for transforming data from subsize specimens was developed and is presented

Application of subsize specimens in nuclear plant life extension

International Nuclear Information System (INIS)

Rosinski, S.T.; Kumar, A.S.; Cannon, N.S.; Hamilton, M.L.

1993-01-01

The US Department of Energy is sponsoring a research effort through Sandia National Laboratories and the University of Missouri-Rolla to test a correlation for the upper shelf energy (USE) values obtained from the impact testing of subsize Charpy V-notch specimens to those obtained from the testing of full-size samples. The program involves the impact testing of unirradiated and irradiated full-, half-, and third-size Charpy V-notch specimens. To verify the applicability of the correlation on LWR materials, unirradiated and irradiated full-, half-, and third-size Charpy V-notch specimens of a commercial pressure vessel steel (ASTM A533 Grade B) will be tested. The correlation methodology is based on the partitioning of the USE into crack initiation and crack propagation energies. To accomplish this partition, both precracked and notched-only specimens will be used. Whereas the USE of notched-only specimens is the sum of both crack initiation and crack propagation energies, the USE of precracked specimens reflects only the crack propagation component. The difference in the USE of the two types of specimens represents a measure of the crack initiation energy. Normalizing the values of the crack initiation energy to the fracture volume of the sample produces similar values for the full-, half-, and third-size specimens. In addition, the ratios of the USE and the crack propagation energy are also in agreement for full-, half-, and third-size specimens. These two observations will be used to predict the USE of full-size specimens based on subsize USE data. This paper provides details of the program and presents results obtained from the application of the developed correlation methodology to the impact testing of the unirradiated full-, half-, and third-size A533 Grade B Charpy V-notch specimens

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.

Miniature tensile test specimens for fusion reactor irradiation studies

International Nuclear Information System (INIS)

Klueh, R.L.

1985-01-01

Three miniature sheet-type tensile specimens and a miniature rod-type specimen are being used to determine irradiated tensile properties for alloy development for fusion reactors. The tensile properties of type 316 stainless steel were determined with these different specimens, and the results were compared. Reasonably good agreement was observed. However, there were differences that led to recommendations on which specimens are preferred. 4 references, 9 figures, 6 tables

Automated, simple, and efficient influenza RNA extraction from clinical respiratory swabs using TruTip and epMotion.

Science.gov (United States)

Griesemer, Sara B; Holmberg, Rebecca; Cooney, Christopher G; Thakore, Nitu; Gindlesperger, Alissa; Knickerbocker, Christopher; Chandler, Darrell P; St George, Kirsten

2013-09-01

Rapid, simple and efficient influenza RNA purification from clinical samples is essential for sensitive molecular detection of influenza infection. Automation of the TruTip extraction method can increase sample throughput while maintaining performance. To automate TruTip influenza RNA extraction using an Eppendorf epMotion robotic liquid handler, and to compare its performance to the bioMerieux easyMAG and Qiagen QIAcube instruments. Extraction efficacy and reproducibility of the automated TruTip/epMotion protocol was assessed from influenza-negative respiratory samples spiked with influenza A and B viruses. Clinical extraction performance from 170 influenza A and B-positive respiratory swabs was also evaluated and compared using influenza A and B real-time RT-PCR assays. TruTip/epMotion extraction efficacy was 100% in influenza virus-spiked samples with at least 745 influenza A and 370 influenza B input gene copies per extraction, and exhibited high reproducibility over four log10 concentrations of virus (extraction were also positive following TruTip extraction. Overall Ct value differences obtained between TruTip/epMotion and easyMAG/QIAcube clinical extracts ranged from 1.24 to 1.91. Pairwise comparisons of Ct values showed a high correlation of the TruTip/epMotion protocol to the other methods (R2>0.90). The automated TruTip/epMotion protocol is a simple and rapid extraction method that reproducibly purifies influenza RNA from respiratory swabs, with comparable efficacy and efficiency to both the easyMAG and QIAcube instruments. Copyright © 2013 Elsevier B.V. All rights reserved.

10 CFR 26.165 - Testing split specimens and retesting single specimens.

Science.gov (United States)

2010-01-01

... (c), as applicable. If the specimen in Bottle A is free of any evidence of drugs or drug metabolites... suitable inquiry conducted under the provisions of § 26.63 or to any other inquiry or investigation... records must be provided to personnel conducting reviews, inquiries into allegations, or audits under the...

Evaluation of Presto(plus) assay and LightMix kit Trichomonas vaginalis assay for detection of Trichomonas vaginalis in dry vaginal swabs.

Science.gov (United States)

de Waaij, Dewi J; Ouburg, Sander; Dubbink, Jan Henk; Peters, Remco P H; Morré, Servaas A

2016-08-01

This is an evaluation study of the Presto(plus) Assay for T. vaginalis by comparing to the TIB MOLBIOL LightMix Kit Trichomonas vaginalis Assay using 615 dry collected vaginal and rectal swabs. Discordant samples were analyzed by the Qiagen® Microbial DNA qPCR for TV Assay. Both assays showed comparable performances (McNemar p>0.05). Copyright © 2016 Elsevier B.V. All rights reserved.

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

Chemical polishing of partially oxidized T-111 alloy

International Nuclear Information System (INIS)

Teaney, P.E.

1974-01-01

The specimens were pressure-mounted in Bakelite and ground through 600 grit on silicon carbide papers. The specimens were rough-polished on a vibratory polisher for 4 to 6 h, using a water slurry of one micron alumina on Texmet, followed by 0.3-μ alumina on Texmet overnight. Final polishing was accomplished by continuous swabbing with a chemical polish. A chemical polish consisting of ten parts lactic acid, four parts nitric acid, and four parts hydrofluoric acid worked well for the T-111 parent material specimens; however, in the partially oxidized specimens, considerable pitting and staining occurred in the oxygen-affected zone and in the transition zone between the oxygen-affected zone and the parent material. A chemical polish was developed for the partially oxidized specimens by adjusting the ratio of the acids to ten parts lactic acid, two parts nitric acid, and two parts hydrofluoric acid. This slowed the chemical attack on the oxygen-affected zone considerably and, with continuous swabbing, the pitting and stain could be avoided. The specimens were rinsed and checked occasionally on the metallograph to determine when the proper polish had been obtained. Some specimens required intermittent polishing times up to 1 / 2 hour. No relationship could be established between the oxygen content of the specimen and the time required for chemical polishing in the partially oxidized specimens. However, the microstructure of the transition zone was the most difficult to obtain, and specimens with uniform reaction zones across the width of the specimen polished quicker than those with the transition zone

Elastic-plastic analysis of the SS-3 tensile specimen

International Nuclear Information System (INIS)

Majumdar, S.

1998-01-01

Tensile tests of most irradiated specimens of vanadium alloys are conducted using the miniature SS-3 specimen which is not ASTM approved. Detailed elastic-plastic finite element analysis of the specimen was conducted to show that, as long as the ultimate to yield strength ratio is less than or equal to 1.25 (which is satisfied by many irradiated materials), the stress-plastic strain curve obtained by using such a specimen is representative of the true material behavior

Progress Report on Alloy 617 Notched Specimen Testing

Energy Technology Data Exchange (ETDEWEB)

McMurtrey, Michael David [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wright, Richard Neil [Idaho National Lab. (INL), Idaho Falls, ID (United States); Lillo, Thomas Martin [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-08-01

Creep behavior of Alloy 617 has been extensively characterized to support the development of a draft Code Case to qualify Alloy 617 in Section III division 5 of the ASME Boiler and Pressure Vessel Code. This will allow use of Alloy 617 in construction of nuclear reactor components at elevated temperatures and longer periods of time (up to 950°C and 100,000 hours). Prior to actual use, additional concerns not considered in the ASME code need to be addressed. Code Cases are based largely on uniaxial testing of smooth gage specimens. In service conditions, components will generally be under multi axial loading. There is also the concern of the behavior at discontinuities, such as threaded components. To address the concerns of multi axial creep behavior and at geometric discontinuities, notched specimens have been designed to create conditions representative of the states that service components experience. Two general notch geometries have been used for these series of tests: U notch and V notch specimens. The notches produce a tri axial stress state, though not uniform across the specimen. Characterization of the creep behavior of the U notch specimens and the creep rupture behavior of the V notch specimens provides a good approximation of the behavior expected of actual components. Preliminary testing and analysis have been completed and are reported in this document. This includes results from V notch specimens tested at 900°C and 800°C. Failure occurred in the smooth gage section of the specimen rather than at the root of the notch, though some damage was present at the root of the notch, where initial stress was highest. This indicates notch strengthening behavior in this material at these temperatures.

Scanning transmission ion micro-tomography (STIM-T) of biological specimens

International Nuclear Information System (INIS)

Schwertner, Michael; Sakellariou, Arthur; Reinert, Tilo; Butz, Tilman

2006-01-01

Computed tomography (CT) was applied to sets of Scanning Transmission Ion Microscopy (STIM) projections recorded at the LIPSION ion beam laboratory (Leipzig) in order to visualize the 3D-mass distribution in several specimens. Examples for a test structure (copper grid) and for biological specimens (cartilage cells, cygospore) are shown. Scanning Transmission Micro-Tomography (STIM-T) at a resolution of 260 nm was demonstrated for the first time. Sub-micron features of the Cu-grid specimen were verified by scanning electron microscopy. The ion energy loss measured during a STIM-T experiment is related to the mass density of the specimen. Typically, biological specimens can be analysed without staining. Only shock freezing and freeze-drying is required to preserve the ultra-structure of the specimen. The radiation damage to the specimen during the experiment can be neglected. This is an advantage compared to other techniques like X-ray micro-tomography. At present, the spatial resolution is limited by beam position fluctuations and specimen vibrations

Final Report: Posttest Analysis of Omega II Optical Specimens

International Nuclear Information System (INIS)

Newlander, C D; Fisher, J H

2007-01-01

Preliminary posttest analyses have been completed on optical specimens exposed during the Omega II test series conducted on 14 July 2006. The Omega Facility, located at the Laboratory for Laser Energetics (LLE) at the University of Rochester was used to produce X-ray environments through the interaction of intense pulsed laser radiation upon germanium-loaded silica aerogels. The optical specimen testing was supported by GH Systems through experiment design, pre- and post-test analyses, specimen acquisition, and overall technical experience. The test specimens were fabricated and characterized by Surface Optics Corporation (SOC), San Diego, CA and were simple protected gold coatings on silica substrates. Six test specimens were exposed, five filtered with thin beryllium foil filters, and one unfiltered which was exposed directly to the raw environment. The experimental objectives were: (1) demonstrate that tests of optical specimens could be performed at the Omega facility; (2) evaluate the use and survivability of beryllium foil filters as a function of thickness; (3) obtain damage data on optical specimens which ranged from no damage to damage; (4) correlate existing thermal response models with the damage data; (5) evaluate the use of the direct raw environment upon the specimen response and the ability/desirability to conduct sensitive optical specimen tests using the raw environment; and (6) initiate the development of a protocol for performing optical coatings/mirror tests. This report documents the activities performed by GH Systems in evaluating and using the environments provided by LLNL, the PUFFTFT analyses performed using those environments, and the calculated results compared to the observed and measured posttest data

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

Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1 isolated from a vaginal swab of a woman with spontaneous abortion

Directory of Open Access Journals (Sweden)

Gartemann Karl-Heinz

2010-02-01

Full Text Available Abstract Background Corynebacterium aurimucosum is a slightly yellowish, non-lipophilic, facultative anaerobic member of the genus Corynebacterium and predominantly isolated from human clinical specimens. Unusual black-pigmented variants of C. aurimucosum (originally named as C. nigricans continue to be recovered from the female urogenital tract and they are associated with complications during pregnancy. C. aurimucosum ATCC 700975 (C. nigricans CN-1 was originally isolated from a vaginal swab of a 34-year-old woman who experienced a spontaneous abortion during month six of pregnancy. For a better understanding of the physiology and lifestyle of this potential urogenital pathogen, the complete genome sequence of C. aurimucosum ATCC 700975 was determined. Results Sequencing and assembly of the C. aurimucosum ATCC 700975 genome yielded a circular chromosome of 2,790,189 bp in size and the 29,037-bp plasmid pET44827. Specific gene sets associated with the central metabolism of C. aurimucosum apparently provide enhanced metabolic flexibility and adaptability in aerobic, anaerobic and low-pH environments, including gene clusters for the uptake and degradation of aromatic amines, L-histidine and L-tartrate as well as a gene region for the formation of selenocysteine and its incorporation into formate dehydrogenase. Plasmid pET44827 codes for a non-ribosomal peptide synthetase that plays the pivotal role in the synthesis of the characteristic black pigment of C. aurimucosum ATCC 700975. Conclusions The data obtained by the genome project suggest that C. aurimucosum could be both a resident of the human gut and possibly a pathogen in the female genital tract causing complications during pregnancy. Since hitherto all black-pigmented C. aurimucosum strains have been recovered from female genital source, biosynthesis of the pigment is apparently required for colonization by protecting the bacterial cells against the high hydrogen peroxide concentration in

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.

Tensile-Creep Test Specimen Preparation Practices of Surface Support Liners

Science.gov (United States)

Guner, Dogukan; Ozturk, Hasan

2017-12-01

Ground support has always been considered as a challenging issue in all underground operations. Many forms of support systems and supporting techniques are available in the mining/tunnelling industry. In the last two decades, a new polymer based material, Thin Spray-on Liner (TSL), has attained a place in the market as an alternative to the current areal ground support systems. Although TSL provides numerous merits and has different application purposes, the knowledge on mechanical properties and performance of this material is still limited. In laboratory studies, since tensile rupture is the most commonly observed failure mechanism in field applications, researchers have generally studied the tensile testing of TSLs with modification of American Society for Testing and Materials (ASTM) D-638 standards. For tensile creep testing, specimen preparation process also follows the ASTM standards. Two different specimen dimension types (Type I, Type IV) are widely preferred in TSL tensile testing that conform to the related standards. Moreover, molding and die cutting are commonly used specimen preparation techniques. In literature, there is a great variability of test results due to the difference in specimen preparation techniques and practices. In this study, a ductile TSL product was tested in order to investigate the effect of both specimen preparation techniques and specimen dimensions under 7-day curing time. As a result, ultimate tensile strength, tensile yield strength, tensile modulus, and elongation at break values were obtained for 4 different test series. It is concluded that Type IV specimens have higher strength values compared to Type I specimens and moulded specimens have lower results than that of prepared by using die cutter. Moreover, specimens prepared by molding techniques have scattered test results. Type IV specimens prepared by die cutter technique are suggested for preparation of tensile test and Type I specimens prepared by die cutter technique

AGC-2 Specimen Post Irradiation Data Package Report

Energy Technology Data Exchange (ETDEWEB)

Windes, William Enoch [Idaho National Lab. (INL), Idaho Falls, ID (United States); Swank, W. David [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rohrbaugh, David T. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cottle, David L. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-08-01

This report documents results of the post-irradiation examination material property testing of the creep, control, and piggyback specimens from the irradiation creep capsule Advanced Graphite Creep (AGC)-2 are reported. This is the second of a series of six irradiation test trains planned as part of the AGC experiment to fully characterize the neutron irradiation effects and radiation creep behavior of current nuclear graphite grades. The AGC-2 capsule was irradiated in the Idaho National Laboratory Advanced Test Reactor at a nominal temperature of 600°C and to a peak dose of 5 dpa (displacements per atom). One-half of the creep specimens were subjected to mechanical stresses (an applied stress of either 13.8, 17.2, or 20.7 MPa) to induce irradiation creep. All post-irradiation testing and measurement results are reported with the exception of the irradiation mechanical strength testing, which is the last destructive testing stage of the irradiation testing program. Material property tests were conducted on specimens from 15 nuclear graphite grades using a similar loading configuration as the first AGC capsule (AGC-1) to provide easy comparison between the two capsules. However, AGC-2 contained an increased number of specimens (i.e., 487 total specimens irradiated) and replaced specimens of the minor grade 2020 with the newer grade 2114. The data reported include specimen dimensions for both stressed and unstressed specimens to establish the irradiation creep rates, mass and volume data necessary to derive density, elastic constants (Young’s modulus, shear modulus, and Poisson’s ratio) from ultrasonic time-of-flight velocity measurements, Young’s modulus from the fundamental frequency of vibration, electrical resistivity, and thermal diffusivity and thermal expansion data from 100–500°C. No data outliers were determined after all measurements were completed. A brief statistical analysis was performed on the irradiated data and a limited comparison between

Simulation of surge and swab pressures in well drilling operations; Simulacao do problema de 'surge' e 'swab' em atividades de perfuracao de pocos de petroleo

Energy Technology Data Exchange (ETDEWEB)

Almeida, Fernando T.G.M.C. de; Kimura, Hudson Faglioni; Ramalho, Vanessa; Negrao, Cezar O. Ribeiro; Junqueira, Silvio L.M. [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil); Martins, Andre Leibsohn [PETROBRAS, Rio de Janeiro, RJ (Brazil)

2008-07-01

The movements of the well drilling pipe, known as trips, cause variations in the well inner pressure. When the pipe is moving downwards, in an operation called 'running', the pressure increases and is known as surge pressure and, when it is moving upwards, in an operation called 'pulling', the pressure decreases and it is so called a swab pressure. The study of this phenomenon is of great importance not only due to financial reasons but also for the determination of speeds and accelerations which should be used in running and pulling operations. Among the researchers have studied this problem, Fontenot and Clark are two of the most important. They formulated the problem solution through considerations about the friction factor. The present work's target is to develop a computational program which allows the calculus of those pressures, according to previous investigations and models found in the literature and for different types of fluids as well, such as Bingham fluid and Power Law fluid. (author)

Optimization of Quantitative PCR Methods for Enteropathogen Detection

Science.gov (United States)

Liu, Jie; Gratz, Jean; Amour, Caroline; Nshama, Rosemary; Walongo, Thomas; Maro, Athanasia; Mduma, Esto; Platts-Mills, James; Boisen, Nadia; Nataro, James; Haverstick, Doris M.; Kabir, Furqan; Lertsethtakarn, Paphavee; Silapong, Sasikorn; Jeamwattanalert, Pimmada; Bodhidatta, Ladaporn; Mason, Carl; Begum, Sharmin; Haque, Rashidul; Praharaj, Ira; Kang, Gagandeep; Houpt, Eric R.

2016-01-01

Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen’s extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease. PMID:27336160

A Debonded Sandwich Specimen Under Mixed Mode Bending (MMB)

DEFF Research Database (Denmark)

Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

2008-01-01

Face/core interface crack propagation in sandwich specimens is analyzed. A thorough analysis of the typical failure modes in sandwich composites was performed in order to design the MMB specimen to promote face/core debond fracture. Displacement, compliance and energy release rate expressions...... for the MMB specimen were derived from a superposition analysis. An experimental verification of the methodology proposed was performed using MMB sandwich specimens with H100 PVC foam core and E-glass/polyester non-crimp quadro-axial [0/45/90/-45]s DBLT-850 faces. Different mixed mode loadings were applied...

Quantitative estimation of hydrogen concentration on the Ni3Al specimens surface in the process of hydrogen release

International Nuclear Information System (INIS)

Katano, Gen; Sano, Shogo; Saito, Hideo; Mori, Minoru

2000-01-01

The method to calculate the hydrogen concentration in metal specimens is given by tritium counts with the liquid scintillation counter. As segments to measure, Ni 3 Al intermetallic compound crystals were used. Tritium was charged to crystals with the method of cathode charging. The charged tritium was transported by diffusion and released from specimen surface. The tritium releasing rate was calculated from the increasing rate of tritium activity. Then the concentration of hydrogen at the surface was calculated from tritium counts. The outcome showed that the hydrogen concentration decreases at specimens surface by elapsed time. Then, the behavior of tritium diffusion was affected by doped boron (up to 0.235 atom% B and 0.470 atom% B) in Ni 3 Al crystals. As the amount of boron increased, the tritium diffusion coefficient decreased. And the hydrogen concentration varied with the amount of boron. After passing enough time, the hydrogen concentration in crystals with boron was much larger than the one without boron. Since it is very likely that the hydrogen concentration is affected by the number of hydrogen sites in the crystal, it is obvious judging by these phenomena, that by doping boron, numbers of hydrogen trapping sites were created. As the hydrogen distribution becomes homogenous after passing enough time, it is possible to measure the hydrogen concentration in all the crystals from β-ray counts at specimens surface. (author)

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.

Design and use of nonstandard tensile specimens for irradiated materials testing

International Nuclear Information System (INIS)

Panayotou, N.F.

1984-10-01

Miniature, nonstandard, tensile-type specimens have been developed for use in radiation effects experiments at high energy neutron sources where the useful radiation volume is as small as a few cubic centimeters. The end result of our development is a sheet-type specimen, 12.7 mm long with a 5.1 mm long, 1.0 mm wide gage section, which is typically fabricated from 0.25 mm thick sheet stock by a punching technique. Despite this miniature geometry, it has been determined that the data obtained using these miniature specimens are in good agreement with data obtained using much larger specimens. This finding indicates that miniature tensile specimen data may by used for engineering design purposes. Furthermore, it is clear that miniature tensile specimen technology is applicable to fields other than the study of radiation effects. This paper describes the miniature specimen technology which was developed and compares the data obtained from these miniature specimens to data obtained from much larger specimens. 9 figures

Viral, Serological, and Antioxidant Investigations of Equine Rhinitis A Virus in Serum and Nasal Swabs of Commercially Used Horses in Poland

Directory of Open Access Journals (Sweden)

Barbara Bażanów

2018-01-01

Full Text Available Background. Equine rhinitis A virus (ERAV is considered to be an important pathogen in horses, but relatively few studies are available. Aims. The purpose of this study was to verify ERAV seroprevalence in selected horses in Poland, in addition to correlation between ERAV and age and sex of analysed animals and the antioxidant status. Methods. The material collected from clinically healthy horses was tested using the VNT (353 serum samples and virus isolation method (44 nasal swabs. 27 serum samples with antibody titers between 0 and ≥1 : 2048 were chosen for further analysis. The study was conducted in group 1 (ERAV titer ≤ 64 and group 2 (ERAV titer > 64. Results. Seroneutralisation tests showed positive results in 72% of serum samples. No significant correlation between ERAV seropositive results and selected biochemical indicators was observed. Group 2 had statistically higher concentrations of SOD and CuZnSOD than the analysed group 1. Conclusions. ERAV was not detected in the nasal swab samples. Antioxidant parameters did not significantly vary between horses of different breed, sex, or age. The ERAV virus had an impact on plasma total SOD and Cu/Zn SOD activity in horses in early stages of convalescence.

Phonon Transport through Nanoscale Contact in Tip-Based Thermal Analysis of Nanomaterials.

Science.gov (United States)

Dulhani, Jay; Lee, Bong Jae

2017-07-28

Nanomaterials have been actively employed in various applications for energy and sustainability, such as biosensing, gas sensing, solar thermal energy conversion, passive radiative cooling, etc. Understanding thermal transports inside such nanomaterials is crucial for optimizing their performance for different applications. In order to probe the thermal transport inside nanomaterials or nanostructures, tip-based nanoscale thermometry has often been employed. It has been well known that phonon transport in nanometer scale is fundamentally different from that occurred in macroscale. Therefore, Fourier's law that relies on the diffusion approximation is not ideally suitable for describing the phonon transport occurred in nanostructures and/or through nanoscale contact. In the present study, the gray Boltzmann transport equation (BTE) is numerically solved using finite volume method. Based on the gray BTE, phonon transport through the constriction formed by a probe itself as well as the nanoscale contact between the probe tip and the specimen is investigated. The interaction of a probe and a specimen (i.e., treated as a substrate) is explored qualitatively by analyzing the temperature variation in the tip-substrate configuration. Besides, each contribution of a probe tip, tip-substrate interface, and a substrate to the thermal resistance are analyzed for wide ranges of the constriction ratio of the probe.

Evaluation of the Behavior of Technova Corporation Rod-Stiffened Stitched Compression Specimens

Science.gov (United States)

Jegley, Dawn C.

2013-01-01

Under Space Act Agreement 1347 between NASA and Technova Corporation, Technova designed and fabricated two carbon-epoxy crippling specimens and NASA loaded them to failure in axial compression. Each specimen contained a pultruded rod stiffener which was held to the specimen skin with through-the-thickness stitches. One of these specimens was designed to be nominally the same as pultruded rod stitched specimens fabricated by Boeing under previous programs. In the other specimen, the rod was prestressed in a Technova manufacturing process to increase its ability to carrying compressive loading. Experimental results demonstrated that the specimen without prestressing carried approximately the same load as the similar Boeing specimens and that the specimen with prestressing carried significantly more load than the specimen without prestressing.

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

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

Mumps vaccine virus genome is present in throat swabs obtained from uncomplicated healthy recipients.

Science.gov (United States)

Nagai, T; Nakayama, T

2001-01-08

Seven children were followed for up to 42 days post-vaccination with live mumps vaccine and 37 throat swabs were obtained serially. Viral genomic RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) in the phosphoprotein (P) and hemagglutinin-neuraminidase (HN) regions. Virus isolation was also attempted. Genomic differentiation of detected mumps virus genome was performed by sequence analysis and/or restriction fragment length polymorphism (RFLP). No adverse reaction was observed in these children. Although mumps virus was not isolated from any of the samples, viral RNA was detected in four samples from three vaccine recipients, 18, 18 and 26, and 7 days after vaccination, respectively. Detected viral RNA was identified as the vaccine strain. Our data suggests that vaccine virus inoculated replicates in the parotid glands but the incidence of virus transmission from recipients to other susceptible subjects should be low.

Measurement of tissue azithromycin levels in self-collected vaginal swabs post treatment using liquid chromatography and tandem mass spectrometry (LC-MS/MS.

Directory of Open Access Journals (Sweden)

Lenka A Vodstrcil

Full Text Available Azithromycin is recommended for the treatment of uncomplicated urogenital chlamydia infection although the standard 1gram dose sometimes fails to eradicate the infection (treatment failure. One hypothesis proposed for treatment failure has been insufficient levels of the antibiotic at the site of infection. We developed an assay using liquid chromatography and tandem mass spectrometry (LC-MS/MS to measure azithromycin concentration in high-vaginal swabs and monitor how concentration changes over time following routine azithromycin treatment.Azithromycin concentrations were measured in two groups of women either within the first 24h of taking a 1g dose (N = 11 or over 9 days (N = 10. Azithromycin concentrations were normalised to an internal standard (leucine enkephalin, and the bulk lipid species phosphatidylcholine [PC(34:1], using an Agilent 6490 triple quadrupole instrument in positive ionisation mode. The abundances of azithromycin, PC(34:1, and leu-enkephalin were determined by multiple reaction monitoring and absolute levels of azithromycin estimated using standard curves prepared on vaginal specimens.Vaginal azithromycin concentrations of women were rapidly obtained after 5h post-treatment (mean concentration = 1031mcg/mg of lipid, range = 173-2693mcg/mg. In women followed for 9 days, peak concentrations were highest after day 2 (mean concentration = 2206mcg/mg, range = 721-5791mcg/mg, and remained high for at least 9 days with a mean concentration of 384mcg/mg (range = 139-1024mcg/mg on day 9.Our study confirmed that a single 1g dose of azithromycin is rapidly absorbed and remains in the vagina at relatively high levels for at least a week, suggesting that poor antibiotic absorption is unlikely to be an explanation for treatment failure.

Thermal expansion of epoxy-fiberglass composite specimens

International Nuclear Information System (INIS)

McElroy, D.L.; Weaver, F.J.; Bridgman, C.

1986-01-01

The thermal expansion behavior of three epoxy-fiberglass composite specimens was measured from 20 to 120 0 C (70 to 250 0 F) using a fused quartz push-rod dilatometer. Billets produced by vacuum impregnating layers of two types of fiberglass cloth with an epoxy resin were core-drilled to produce cylindrical specimens. These were used to study expansion perpendicular and parallel to the fiberglass layers. The dilatometer is held at a preselected temperature until steady-state is indicated by stable length and temperature data. Before testing the composite specimens, a reliability check of the dilatometer was performed using a copper secondary standard. This indicated thermal expansion coefficient (α) values within +-2% of expected values from 20 to 200 0 C

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.

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

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.

Comparison of three media for transport and storage of the samples collected for detection of avian influenza virus.

Science.gov (United States)

Zhang, Xiao-Chun; Liu, Shuo; Hou, Guang-Yu; Zhuang, Qing-Ye; Wang, Kai-Cheng; Jiang, Wen-Ming; Wang, Su-Chun; Li, Jin-Ping; Yu, Jian-Min; Du, Xiang; Huang, Bao-Xu; Chen, Ji-Ming

2015-09-15

Detection of avian influenza viruses (AIVs) is important for diagnosis, surveillance and control of avian influenza which is of great economic and public health significance. Proper transport and storage of samples is critical for the detection when the samples cannot be detected immediately. As recommended by some international or national authoritative entities and some publications, phosphate buffered saline (PBS), PBS-glycerol and brain heart infusion broth (BHIB) are frequently used for transport and storage of the samples collected for detection of AIVs worldwide. In this study, we compared these three media for transport and storage of simulated and authentic swab and feces samples collected for detection of AIVs using virus isolation and reverse transcription-PCR. The results suggest that PBS-glycerol is superior to PBS and BHIB as the sample transport and storage media. The results also suggest that the samples collected for detection of AIVs should be detected as soon as possible because the virus concentration of the samples may decline rapidly during storage within days at 4 or -20°C. Copyright © 2015 Elsevier B.V. All rights reserved.

Demonstration of Laser Cutting System for Tube Specimen

Energy Technology Data Exchange (ETDEWEB)

Jin, Y. G.; Kim, G. S.; Heo, G. S.; Baik, S. J.; Kim, H. M.; Ahn, S. B. [KAERI, Daejeon (Korea, Republic of)

2016-05-15

The oxide layer removal system was also developed because the oxide layer on the surface of the irradiated fuel cladding and components interrupted the applying the electric current during the processing. However, it was found that the mechanical testing data of the irradiated specimens with removal of oxide layer was less reliable than the specimens with oxide layer . The laser cutting system using Nd:YAG with fiber optic beam delivery has great potential in material processing applications of the irradiated fuel cladding and components due to non-contact process. Thus, the oxide layer doesn't interrupt the fabrication process during the laser cutting system. In the present study, the laser cutting system was designed to fabricate the mechanical testing specimens from the unirradiated fuel cladding with and without oxide. The feasibility of the laser cutting system was demonstrated for the fabrication of various types of unirradiated specimens. The effect of surface oxide layer was also investigated for machining process of the zirlo fuel cladding and it was found that laser beam machining could be a useful tool to fabricate the specimens with surface oxide layer. Based on the feasibility studies and demonstration, the design of the laser cutting machine for fully or partially automatic and remotely operable system will be proposed and made.

DISTRIBUTION OF COAGULASE-NEGATIVE STAPHYLOCOCCI SPECIES ON TEAT SKIN AND IN MILK SAMPLES FROM DAIRY COWS IN AUTOMATIC MILKING SYSTEMS

DEFF Research Database (Denmark)

Mahmmod, Yasser Saadeldien Ibrahim; Svennesen, Line; Pedersen, Karl

) to identify the predisposing cow level risk factors for specific CNS IMI and teat colonization.In each herd, 30- 40 cows with somatic cell counts > 200,000 cells/ml in the previous milk recording are randomly selected and teat skin swabs and aseptic quarter foremilk samples are taken. Teat skin swabs...... are collected using a modified wet-dry method. First a wet swab immersed in ¼ Ringer’s solution followed by a dry swab are rotated 360° around the teat canal orifice and both swab tips transferred into one tube with 2 ml of ¼ Ringer’s solution. Samples are transported on ice for culturing in the laboratory...

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.

Laboratory specimens and genetic privacy: evolution of legal theory.

Science.gov (United States)

Lewis, Michelle Huckaby

2013-03-01

Although laboratory specimens are an important resource for biomedical research, controversy has arisen when research has been conducted without the knowledge or consent of the individuals who were the source of the specimens. This paper summarizes the most important litigation regarding the research use of laboratory specimens and traces the evolution of legal theory from property claims to claims related to genetic privacy interests. © 2013 American Society of Law, Medicine & Ethics, Inc.

50 CFR 31.11 - Donation and loan of wildlife specimens.

Science.gov (United States)

2010-10-01

... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Donation and loan of wildlife specimens... of Wildlife Reduction and Disposal § 31.11 Donation and loan of wildlife specimens. Wildlife specimens may be donated or loaned to public institutions for specific purposes. Donation or loans of...

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)

Real-Time Polymerase Chain Reaction Detection of Trichomonas vaginalis from vaginal swabs: Validation of a Diagnostic Method and Preliminary Epidemiological Application

Directory of Open Access Journals (Sweden)

Carlo Mengoli

2009-06-01

Full Text Available Background Trichomonas vaginalis is the most common nonviral sexually trasmitted diseases (STDs agent. For females, the diagnostic gold standard is the culture of vaginal swab, which is labour-exacting.The direct microscopic examination of vaginal secretions is the most used approach, but its sensitivity depends on the skill of the observer. Objectives We evaluated an original real-time TaqMan-based Polymerase Chain Reaction (PCR technique.The scope of the study was to confirm the effectiveness of the molecular approach in a clinical context and to explore its relevance to an epidemiological investigation. Study Design a ß-tubulin gene was chosen as target sequence.The assay was designed to exploit the quantitative potential of the TaqMan procedure.The population sample was 583 adult females presenting at the Service from January 2005 to December 2005.Three vaginal swabs were collected from each patient, one for wet mount microscopy, one for broth culture, and one for the molecular assay. Results The prevalence was 3.3% (culture, 3.1% (microscopy, 3.8% (PCR.An excess risk was detected in the immigrant population (risk ratio by PCR = 28. Conclusions The molecular approach was the most accurate way to detect the protozoon.The real-time PCR is convenient in a busy laboratory, provided the necessary equipment is available, and it is suitable for epidemiological investigation.

Feasibility Study of Laser Cutting for Fabrication of Tensile Specimen

International Nuclear Information System (INIS)

Jin, Y. G.; Baik, S. J.; Kim, G. S.; Heo, G. S.; Yoo, B. O.; Ahn, S. B.; Chun, Y. B.

2015-01-01

The specimen fabrication technique was established to machine the specimen from the irradiated materials. The wire cut EDM(electric discharge machine) was modified to fabricate the mechanical testing specimens from irradiated components and fuel claddings. The oxide layer removal system was also developed because the oxide layer on the surface of the irradiated components and claddings interrupted the applying the electric current during the processing. However, zirconium oxide is protective against further corrosion as well as beneficial to mechanical strength for the tensile deformation of the cladding. Thus, it is important to fabricate the irradiated specimens without removal of oxide layer on the surface of the irradiated structural components and claddings. In the present study, laser cutting system was introduced to fabricate the various mechanical testing specimens from the unirradiated fuel cladding and the feasibility of the laser cutting system was studied for the fabrication of various types of irradiated specimens in a hot cell at IMEF (Irradiated Materials Examination Facility) of KAERI. Laser beam machining system was introduced to fabricate the various mechanical testing specimens from the unirradiated fuel cladding and the dimensions were compared for the feasibility of the laser cutting system. The effect of surface oxide layer was also investigated for machining process of the zircaloy-4 fuel cladding and it was found that laser beam machining could be a useful tool to fabricate the specimens with surface oxide layer

Feasibility Study of Laser Cutting for Fabrication of Tensile Specimen

Energy Technology Data Exchange (ETDEWEB)

Jin, Y. G.; Baik, S. J.; Kim, G. S.; Heo, G. S.; Yoo, B. O.; Ahn, S. B.; Chun, Y. B. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2015-05-15

The specimen fabrication technique was established to machine the specimen from the irradiated materials. The wire cut EDM(electric discharge machine) was modified to fabricate the mechanical testing specimens from irradiated components and fuel claddings. The oxide layer removal system was also developed because the oxide layer on the surface of the irradiated components and claddings interrupted the applying the electric current during the processing. However, zirconium oxide is protective against further corrosion as well as beneficial to mechanical strength for the tensile deformation of the cladding. Thus, it is important to fabricate the irradiated specimens without removal of oxide layer on the surface of the irradiated structural components and claddings. In the present study, laser cutting system was introduced to fabricate the various mechanical testing specimens from the unirradiated fuel cladding and the feasibility of the laser cutting system was studied for the fabrication of various types of irradiated specimens in a hot cell at IMEF (Irradiated Materials Examination Facility) of KAERI. Laser beam machining system was introduced to fabricate the various mechanical testing specimens from the unirradiated fuel cladding and the dimensions were compared for the feasibility of the laser cutting system. The effect of surface oxide layer was also investigated for machining process of the zircaloy-4 fuel cladding and it was found that laser beam machining could be a useful tool to fabricate the specimens with surface oxide layer.

Validity of fracture toughness determined with small bend specimens

International Nuclear Information System (INIS)

Wallin, K.; Rintamaa, R.; Valo, M.

1994-02-01

This report considers the validity of fracture toughness estimates obtained with small bend specimens in relation to fracture toughness estimates obtained with large specimens. The study is based upon the analysis and comparison of actual test results. The results prove the validity of the fracture toughness determined based upon small bend specimens, especially when the results are only used to determine the fracture toughness transition temperature T o . In this case the possible error is typically less than 5 deg C and at most 10 deg C. It can be concluded that small bend specimens are very suitable for the estimation of fracture toughness in the case of brittle fracture, provided the results are corrected for statistical size effects. (orig.). (20 refs., 17 figs.)

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

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.

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

Assessment of plastic flow and fracture properties with small specimens test techniques for IFMIF-designed specimens

International Nuclear Information System (INIS)

Spaetig, P.; Campitelli, E.N.; Bonade, R.; Baluc, N.

2005-01-01

The primary mission of the International Fusion Material Irradiation Facility (IFMIF) is to generate a material database to be used for the design of various components, for the licensing and for the assessment of the safe operation of a demonstration fusion reactor. IFMIF is an accelerator-based high-energy neutron source whose irradiation volume is quite limited (0.5 l for the high fluence volume). This requires the use of small specimens to measure the irradiation-induced changes on the physical and mechanical properties of materials. In this paper, we developed finite element models to better analyze the results obtained with two different small specimen test techniques applied to the tempered martensitic steel F82H-mod. First, one model was used to reconstruct the load-deflection curves of small ball punch tests, which are usually used to extract standard tensile parameters. It was shown that a reasonable assessment of the overall plastic flow can be done with small ball punch tests. Second, we investigated the stress field sensitivity at a crack tip to the constitutive behavior, for a crack modeled in plane strain, small-scale yielding and fracture mode I conditions. Based upon a local criterion for cleavage, that appears to be the basis to account for the size and geometry effects on fracture toughness, we showed that the details of the constitutive properties play a key role in modeling the irradiation-induced fracture toughness changes. Consequently, we suggest that much more attention and efforts have to be paid in investigating the post-yield behavior of the irradiated specimens and, in order to reach this goal, we recommend the use of not only tensile specimens but also that of compression ones in the IFMIF irradiation matrices. (author)

Specimen's plane misaligned installation solution based on charge fluctuation inside SEM

Science.gov (United States)

Lu, Haojian; Liu, Yanting; Yang, Yuanyuan; Wang, Panbing; Shen, Yajing

2018-04-01

Precise specimen's installation is a sticking point to ensure the characterization accuracy of the in-situ material property test. Although it is common knowledge that specimen's plane misaligned installation (PMI) would cause extra force loading during mechanical testing, there are few effective solutions available to deal with it at the current stage, especially during the in-situ scanning electron microscopy (SEM) test. Taking into consideration the charge fluctuation phenomenon under SEM, this paper proposes a highlight area variation (HAV) method for specimen deformation judgment, i.e., the specimen deformation is defined when the highlight area changes greater than 20% of the initial value of the specimen surface. Three types of specimens with different resistivities, i.e., human hair (electrical resistivity ˜3 × 1012 Ω cm), optical fiber (electrical resistivity ˜1017 Ω cm), and magnetic wire (electrical resistivity ˜2 × 10-5 Ω cm), are chosen to verify the effectiveness of the HAV method. Furthermore, combined with the developed robot-aided alignment system, the specimen's PMI problem can also be solved. In the demonstration, the human hair specimen is installed across two specimen stages and its in-situ twisting (in 360°) test is implemented. The results clearly indicate that the HAV method and the robot-aided alignment system are practical and reliable, and the specimen can be aligned on the same plane and installed precisely with accuracy up to 3 μm. This method will benefit the in-situ SEM material mechanical property test and has a significant impact in fundamental material research.

Fracture mechanics characterisation of medium-size adhesive joint specimens

DEFF Research Database (Denmark)

Sørensen, Bent F.; Jacobsen, T.K.

2004-01-01

Medium-size specimens (glass-fibre beams bonded together by an adhesive layer were tested in four point bending to determine their load carrying capacity. Specimens having different thickness were tested. Except for onespecimen, the cracking occurred as cracking...... along the adhesive layer; initially cracking occurred along the adhesive/laminate interface, but after some crack extension the cracking took place inside the laminate (for one specimen the later part of thecracking occurred unstably along the adhesive/ laminate interface). Crack bridging by fibres...

Recovery and Stability of Δ9-Tetrahydrocannabinol Using the Oral-Eze® Oral Fluid Collection System and Intercept® Oral Specimen Collection Device.

Science.gov (United States)

Samano, Kimberly L; Anne, Lakshmi; Johnson, Ted; Tang, Kenneth; Sample, R H Barry

2015-10-01

Oral fluid (OF) is increasingly used for clinical, forensic and workplace drug testing as an alternative to urine. Uncertainties surrounding OF collection device performance, drug stability and testing reproducibility may be partially responsible for delays in the implementation of OF testing in regulated drug testing programs. Stability of Δ(9)-tetrahydrocannabinol (THC) fortified and authentic specimens was examined after routine collection, transport and laboratory testing. Acceptable recovery and stability were observed when THC-fortified OF (1.5 and 4.5 ng/mL) was applied to Oral-Eze devices. Neat OF samples collected with Oral-Eze, processed per the package insert, and fortified with THC (3 and 6 ng/mL) were stable (±20%) at room temperature (21-25°C), refrigerated (2-8°C) and frozen (-25 to -15°C) conditions up to 1 month, while samples collected with Intercept devices showed decreases at refrigerated and room temperatures. After long-term refrigerated or frozen storage, maximum reductions in THC concentrations were 42% for Oral-Eze and 69% for Intercept. After ≥1 year frozen storage, 80.7% of laboratory specimens positive for THC (3 ng/mL cut-off) by GC-MS were reconfirmed positive (within 25%), with an average THC decrease of 4.2%. Specimens (n = 47) processed with Oral-Eze (diluted) and tested via enzyme immunoassay were concordant with LC-MS-MS results and showed 100% sensitivity and 95% specificity. Paired specimens collected with Oral-Eze and Intercept exhibited 98% overall agreement between the immunoassay test systems. Collectively, these data demonstrate consistent and reproducible recovery and stability of THC in OF after collection, transport and laboratory testing using the Oral-Eze OF Collection System. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A proposed standard round compact specimen for plane strain fracture toughness testing

Science.gov (United States)

Underwood, J. H.; Newman, J. C., Jr.; Seeley, R. R.

1980-01-01

A round, disk-shaped specimen is proposed as a standard test specimen for addition to ASTM Test for Plane-Strain Fracture Toughness of Metallic Materials (E 399-78A). The specimen is diametrically cracked, and loaded in the same way as the existing standard compact specimen. Tests and analyses were performed to verify that the proposed round compact specimen and associated stress intensity factor K solution are appropriate for a standard plane strain fracture toughness test. The use of the round compact specimen for other fracture tests is described.

Test methodology and technology of fracture toughness for small size specimens

Energy Technology Data Exchange (ETDEWEB)

Wakai, E.; Takada, F.; Ishii, T.; Ando, M. [Japan Atomic Energy Agency, Naga-gun, Ibaraki-ken (Japan); Matsukawa, S. [JNE Techno-Research Co., Kanagawa-ken (Japan)

2007-07-01

Full text of publication follows: Small specimen test technology (SSTT) is required to investigate mechanical properties in the limited availability of effective irradiation volumes in test reactors and accelerator-based neutron and charged particle sources. The test methodology guideline and the manufacture processes for very small size specimens have not been established, and we would have to formulate it. The technology to control exactly the load and displacement is also required in the test technology under the environment of high dose radiation produced from the specimens. The objective of this study is to examine the test technology and methodology of fracture toughness for very small size specimens. A new bend test machine installed in hot cell has been manufactured to obtain fracture toughness and DBTT (ductile - brittle transition temperature) of reduced-activation ferritic/martensitic steels for small bend specimens of t/2-1/3PCCVN (pre-cracked 1/3 size Charpy V-notch) with 20 mm length and DFMB (deformation and fracture mini bend specimen) with 9 mm length. The new machine can be performed at temperatures from -196 deg. C to 400 deg. C under unloading compliance method. Neutron irradiation was also performed at about 250 deg. C to about 2 dpa in JMTR. After the irradiation, fracture toughness and DBTT were examined by using the machine. Checking of displacement measurement between linear gauge of cross head's displacement and DVRT of the specimen displacement was performed exactly. Conditions of pre-crack due to fatigue in the specimen preparation were also examined and it depended on the shape and size of the specimens. Fracture toughness and DBTT of F82H steel for t/2-1/3PCCVN, DFMB and 0.18DCT specimens before irradiation were examined as a function of temperature. DBTT of smaller size specimens of DFMB was lower than that of larger size specimen of t/2-1/3PCCVN and 0.18DCT. The changes of fracture toughness and DBTT due to irradiation were also

Old Plants, New Tricks: Phenological Research Using Herbarium Specimens.

Science.gov (United States)

Willis, Charles G; Ellwood, Elizabeth R; Primack, Richard B; Davis, Charles C; Pearson, Katelin D; Gallinat, Amanda S; Yost, Jenn M; Nelson, Gil; Mazer, Susan J; Rossington, Natalie L; Sparks, Tim H; Soltis, Pamela S

2017-07-01

The timing of phenological events, such as leaf-out and flowering, strongly influence plant success and their study is vital to understanding how plants will respond to climate change. Phenological research, however, is often limited by the temporal, geographic, or phylogenetic scope of available data. Hundreds of millions of plant specimens in herbaria worldwide offer a potential solution to this problem, especially as digitization efforts drastically improve access to collections. Herbarium specimens represent snapshots of phenological events and have been reliably used to characterize phenological responses to climate. We review the current state of herbarium-based phenological research, identify potential biases and limitations in the collection, digitization, and interpretation of specimen data, and discuss future opportunities for phenological investigations using herbarium specimens. Copyright © 2017 Elsevier Ltd. All rights reserved.

Design of four-point SENB specimens with stable crack growth

DEFF Research Database (Denmark)

Jørgensen, Jeppe Bjørn; Kildegaard, Casper; Sørensen, Bent F.

2018-01-01

A four-point single-edge-notch-beam (SENB) test specimen loaded in displacement control (fixed grip) is proposed for studying crack deflection at bi-material interfaces. In order to ensure stable crack growth, a novel analytical model of the four-point SENB specimen in fixed grip is derived...... and compared with numerical models. Model results show that the specimen should be short and thick, and the start-crack length should be deep for the crack to propagate stable towards the bi-material interface. Observations from experimental tests of four-point SENB specimens with different start-crack lengths...

Molecular detection of candida species from hospitalized patient’s specimens.

Science.gov (United States)

Camacho-Cardoso, José Luis; Martínez-Rivera, María Ángeles; Manzano-Gayosso, Patricia; Méndez-Tovar, Luis Javier; López-Martínez, Rubén; Hernández-Hernández, Francisca

To identify the most frequent Candida species in specimens from patients hospitalized in different medical centers of Mexico City, with suspected fungal infection. Specimens were grown on Sabouraud dextrose agar at 28°C for 72 h. In addition, DNA was extracted. Isolates were grown on CHROMagar Candida™, at 37°C for 48 h. The molecular identification was performed by polymerase chain reaction (PCR) using primers specific for four species. Eighty one specimens were processed and included: bronchial lavage, pleural, cerebrospinal, peritoneal, ascites and bile fluids; blood, sputum, bone marrow, oro-tracheal cannula and ganglion. By culture, 30 samples (37%) were positive, and by PCR, 41 (50.6%). By PCR, the frequency of species was: Candida albicans 82.9%, Candida tropicalis 31.7%, Candida glabrata 24.4%, and Candida parapsilosis 4.9%. In 34.1% of specimens a species mixture was detected suggesting a co-infection: Two species in five specimens (C. albicans-C tropicalis and C. albicans-C glabrata), and three species in three specimens (C. albicans-C. glabrata-C. tropicalis). The PCR is an useful tool for detection the most common Candida species causing infection in hospitalized patients, it avoids the requirement of culture weather we start from clinical specimen and it favors the early diagnosis of invasive candidiasis. Copyright: © 2017 SecretarÍa de Salud

Comparison between culture and a multiplex quantitative real-time polymerase chain reaction assay detecting Ureaplasma urealyticum and U. parvum.

Science.gov (United States)

Frølund, Maria; Björnelius, Eva; Lidbrink, Peter; Ahrens, Peter; Jensen, Jørgen Skov

2014-01-01

A novel multiplex quantitative real-time polymerase chain reaction (qPCR) for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard's 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.

Comparison between culture and a multiplex quantitative real-time polymerase chain reaction assay detecting Ureaplasma urealyticum and U. parvum.

Directory of Open Access Journals (Sweden)

Maria Frølund

Full Text Available A novel multiplex quantitative real-time polymerase chain reaction (qPCR for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard's 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.

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.

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)

Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis

Science.gov (United States)

Lunny, Carole; Taylor, Darlene; Hoang, Linda; Wong, Tom; Gilbert, Mark; Lester, Richard; Krajden, Mel; Ogilvie, Gina

2015-01-01

Background The increases in STI rates since the late 1990s in Canada have occurred despite widespread primary care and targeted public health programs and in the setting of universal health care. More innovative interventions are required that would eliminate barriers to STI testing such as internet-based or mail-in home and community service testing for patients that are hard to reach, who refuse to go for clinician-based testing, or who decline an examination. Jurisdictions such as New Zealand and some American states currently use self-collected sampling, but without the required evidence to determine whether self-collected specimens are as accurate as clinician-collected specimens in terms of chlamydia and gonorrhea diagnostic accuracy. The objective of the review is to compare self-collected vaginal, urine, pharyngeal and rectal samples to our reference standard - clinician-collected cervical, urethral, pharyngeal and rectal sampling techniques to identify a positive specimen using nucleic acid amplification test assays. Methods The hierarchical summary receiver operating characteristic and the fixed effect models were used to assess the accuracy of comparable specimens that were collected by patients compared to clinicians. Sensitivity and specificity estimates with 95% confidence intervals (CI) were reported as our main outcome measures. Findings We included 21 studies based on over 6100 paired samples. Fourteen included studies examined chlamydia only, 6 compared both gonorrhea and chlamydia separately in the same study, and one examined gonorrhea. The six chlamydia studies comparing self-collection by vaginal swab to a clinician-collected cervical swab had the highest sensitivity (92%, 95% CI 87-95) and specificity (98%, 95% CI 97-99), compared to other specimen-types (urine/urethra or urine/cervix). Six studies compared urine self-samples to urethra clinician-collected samples in males and produced a sensitivity of 88% (95% CI 83-93) and a specificity of

Post-deformation examination of specimens subjected to SCC testing

Energy Technology Data Exchange (ETDEWEB)

Gussev, Maxim N. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Field, Kevin G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Busby, Jeremy T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Leonard, Keith J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-09-01

This report details the results of post-radiation and post-deformation characterizations performed during FY 2015–FY 2016 on a subset of specimens that had previously been irradiated at high displacement per atom (dpa) damage doses. The specimens, made of commercial austenitic stainless steels and alloys, were subjected to stress-corrosion cracking tests (constant extension rate testing and crack growth testing) at the University of Michigan under conditions typical of nuclear power plants. After testing, the specimens were returned to Oak Ridge National Laboratory (ORNL) for further analysis and evaluation.

An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

Science.gov (United States)

Eminaga, O; Semjonow, A; Oezguer, E; Herden, J; Akbarov, I; Tok, A; Engelmann, U; Wille, S

2014-01-01

The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

A test specimen for characterizing the fracture energy of interfaces in composites

International Nuclear Information System (INIS)

Shaw, L.; Abbaschian, R.

1993-01-01

A sandwich-type chevron-notched specimen, which has a phase angle of loading near zero, is proposed to measure interfacial fracture energy arising mainly from chemical bonding. With the specimen configuration of this kind, the advantages from both sandwich test specimens and chevron-notched specimens can be combined to provide an easy and accurate test for the measurement of interfacial fracture energy. The validity of the specimen has been analyzed in terms of the mechanics of sandwich-type specimens and chevron-notched specimens, and demonstrated using the Al 2 O 3 /Nb bimaterial system. The results show that for a phase angle of loading around -7 degrees the Al 2 O 3 /Nb interface has a fracture energy of 9.3 ± 0.2 J/m 2 . 39 refs

Catalog of insect type specimens preserved at the Kunming Institute of Zoology, Chinese Academy of Science with corrections of some specimens.

Science.gov (United States)

Li, Kai-Qin; Wang, Yun-Zhen; Dong, Da-Zhi; Zhang, Li-Kun

2015-09-18

This article presents a list of insect types preserved in Kunming Natural History Museum of Zoology (KNHMZ). As of March, 2015, 3 412 type specimens belonging to 266 species/subspecies of 37 families in 9 orders (Odonata, Isoptera, Mantodea, Orthoptera, Hemiptera, Coleoptera, Diptera, Hymenoptera and Lepidoptera) are included. Information corrections of some specimens are provided in this article.

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

Uniaxial compression tests on diesel contaminated frozen silty soil specimens

International Nuclear Information System (INIS)

Chenaf, D.; Stampli, N.; Bathurst, R.; Chapuis, R.P.

1999-01-01

Results of a uniaxial, unconfined compression test on artificial diesel-contaminated and uncontaminated frozen silty soils are discussed. The testing program involved 59 specimens. The results show that for the same fluid content, diesel contamination reduced the strength of the frozen specimens by increasing the unfrozen water content. For example, in specimens containing 50 per cent diesel oil of the fluid content by weight the maximum strength was reduced by 95 per cent compared to the strength of an uncontaminated specimen. Diesel contamination was also shown to contribute to the slippage between soil particles by acting as a lubricant, thus accelerating the loss of compressive strength.13 refs., 18 figs

Comparison of PCR method with the culture method for identification of gonococci from endocervical swabs

Directory of Open Access Journals (Sweden)

Alam A

2002-01-01

Full Text Available Gonococcal infection remains still a major cause of morbidity among sexually active individuals. Diagnosis of the infection in a female case is more difficult than that in a male. This was a prospective study among 269 female commercial sex workers (CSWs to screen them for gonococcal infection, comparing the rapid method of identification of gonococci by polymerase chain reaction (PCR with the selective culture method. A total of 92 (34.2% CSWs were identified positive for Neisseria gonorrhoeae by combination of the two methods. The PCR method identified 87 of the specimens to harbour cppB gene of N. gonorrhoeae, whereas culture method identified 83 specimens showing colonies of gonococci. Taking into consideration of the total positive cases (92, the PCR method showed a sensitivity of 94.57%, whereas sensitivity of culture method was 90.22%. The selective culture method appears to be the most applicable in the identification of gonococci from clinical specimens, particularly in the less resourceful countries like Bangladesh.

Effects of Specimen Diameters on the Distribution of Corrosion Fatigue Cracks

OpenAIRE

石原, 外美; 塩澤, 和章; 宮尾, 嘉寿

1988-01-01

The distribution of corrosion fatigue cracks observed on the un-notched round specimen surface differs with specimen diameter, especially in the low stress amplitude region. At a constant fatigue life ratio, many long cracks are initiated on the larger specimen, 12 mm (diameter), in comparison with the smaller specimen, 6 mm (diameter). On the other hand, in the high stress amplitude region of corrosion fatigue and fatigue in laboratory air, the distribution of cracks during the fatigue proce...

Comparison of a modified peptone water transport medium with two ...

African Journals Online (AJOL)

A laboratory modified peptone water medium was evaluated alongside Stuart and Amies media for their relative suitability as transport media for aerobic bacteria isolated from wound specimens obtained from Central Hospital, Benin City, Nigeria. The survival rates of isolates from the three media were assessed ...

Mesh-morphing algorithms for specimen-specific finite element modeling.

Science.gov (United States)

Sigal, Ian A; Hardisty, Michael R; Whyne, Cari M

2008-01-01

Despite recent advances in software for meshing specimen-specific geometries, considerable effort is still often required to produce and analyze specimen-specific models suitable for biomechanical analysis through finite element modeling. We hypothesize that it is possible to obtain accurate models by adapting a pre-existing geometry to represent a target specimen using morphing techniques. Here we present two algorithms for morphing, automated wrapping (AW) and manual landmarks (ML), and demonstrate their use to prepare specimen-specific models of caudal rat vertebrae. We evaluate the algorithms by measuring the distance between target and morphed geometries and by comparing response to axial loading simulated with finite element (FE) methods. First a traditional reconstruction process based on microCT was used to obtain two natural specimen-specific FE models. Next, the two morphing algorithms were used to compute mappings from the surface of one model, the source, to the other, the target, and to use this mapping to morph the source mesh to produce a target mesh. The microCT images were then used to assign element-specific material properties. In AW the mappings were obtained by wrapping the source and target surfaces with an auxiliary triangulated surface. In ML, landmarks were manually placed on corresponding locations on the surfaces of both source and target. Both morphing algorithms were successful in reproducing the shape of the target vertebra with a median distance between natural and morphed models of 18.8 and 32.2 microm, respectively, for AW and ML. Whereas AW-morphing produced a surface more closely resembling that of the target, ML guaranteed correspondence of the landmark locations between source and target. Morphing preserved the quality of the mesh producing models suitable for FE simulation. Moreover, there were only minor differences between natural and morphed models in predictions of deformation, strain and stress. We therefore conclude that

A Multiplex Microsphere-Based Immunoassay Increases the Sensitivity of SIV-Specific Antibody Detection in Serum Samples and Mucosal Specimens Collected from Rhesus Macaques Infected with SIVmac239.

Science.gov (United States)

Powell, Rebecca L R; Ouellette, Ian; Lindsay, Ross W; Parks, Christopher L; King, C Richter; McDermott, Adrian B; Morrow, Gavin

2013-06-01

Results from recent HIV-1 vaccine studies have indicated that high serum antibody (Ab) titers may not be necessary for Ab-mediated protection, and that Abs localized to mucosal sites might be critical for preventing infection. Enzyme-linked immunosorbent assay (ELISA) has been used for decades as the gold standard for Ab measurement, though recently, highly sensitive microsphere-based assays have become available, with potential utility for improved detection of Abs. In this study, we assessed the Bio-Plex(®) Suspension Array System for the detection of simian immunodeficiency virus (SIV)-specific Abs in rhesus macaques (RMs) chronically infected with SIV, whose serum or mucosal SIV-specific Ab titers were negative by ELISA. We developed a SIVmac239-specific 4-plex bead array for the simultaneous detection of Abs binding to Env, Gag, Pol, and Nef. The 4-plex assay was used to quantify SIV-specific serum IgG and rectal swab IgA titers from control (SIV-naive) and SIVmac239-infected RMs. The Bio-Plex assay specifically detected anti-SIV Abs in specimens from SIV-infected animals for all four analytes when compared to SIV-naive control samples (p≤0.04). Furthermore, in 70% of Env and 79% of Gag ELISA-negative serum samples, specific Ab was detected using the Bio-Plex assay. Similarly, 71% of Env and 48% of Gag ELISA-negative rectal swab samples were identified as positive using the Bio-Plex assay. Importantly, assay specificity (i.e., probability of true positives) was comparable to ELISA (94%-100%). The results reported here indicate that microsphere-based methods provide a substantial improvement over ELISA for the detection of Ab responses, aid in detecting specific Abs when analyzing samples containing low levels of Abs, such as during the early stages of a vaccine trial, and may be valuable in attempts to link protective efficacy of vaccines with induced Ab responses.

Standard practice for fracture testing with surface-crack tension specimens

CERN Document Server

American Society for Testing and Materials. Philadelphia

2003-01-01

1.1 This practice covers the design, preparation, and testing of surface-crack tension (SCT) specimens. It relates specifically to testing under continuously increasing force and excludes cyclic and sustained loadings. The quantity determined is the residual strength of a specimen having a semielliptical or circular-segment fatigue crack in one surface. This value depends on the crack dimensions and the specimen thickness as well as the characteristics of the material. 1.2 Metallic materials that can be tested are not limited by strength, thickness, or toughness. However, tests of thick specimens of tough materials may require a tension test machine of extremely high capacity. The applicability of this practice to nonmetallic materials has not been determined. 1.3 This practice is limited to specimens having a uniform rectangular cross section in the test section. The test section width and length must be large with respect to the crack length. Crack depth and length should be chosen to suit the ultimate pu...

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.)

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

Intraoperative specimen radiography in patients with nonpalpable malignant breast lesions.

Science.gov (United States)

Schmachtenberg, C; Engelken, F; Fischer, T; Bick, U; Poellinger, A; Fallenberg, E M

2012-07-01

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. 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). 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. 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. © Georg Thieme Verlag KG Stuttgart · New York.

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.)

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

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

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.

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....

Failed PCR of Ganoderma type specimens affects nomenclature.

Science.gov (United States)

Paterson, R R M; Lima, N

2015-06-01

The nomenclature of Ganoderma used as a Chinese medicine is debated. A group of researchers could not amplify the DNA of type specimens and concluded the DNA was degraded irreparably. New topotypes were used as the type specimens which was premature. The use of internal amplification controls is recommended to determine if other factors were involved as alternative explanations. Copyright © 2014 Elsevier Ltd. All rights reserved.

The use of coroner's autopsy reports to validate the use of targeted swabbing rather than tissue collection for rapid confirmation of virological causes of sudden death in the community.

Science.gov (United States)

Moore, Catherine; Jones, Rachel

2015-02-01

In this study, coroner's autopsy reports were used to validate results obtained from respiratory virus screening of swabs rather than tissue collected during autopsy in cases of adult death of unknown cause. Coroner's autopsy samples collected for respiratory virus screening between October 2010 and February 2011, were identified. Autopsy reports were requested from cases positive for a virus. Each report was reviewed to correlate findings at autopsy with the virology result and to determine whether the virus found was listed as a contributing factor in the death. Sixty-four coroner's autopsy cases were identified and a respiratory virus was found in 25 cases. Influenza A(H1N1)pdm09 virus was found most frequently, then RSV and influenza B with a dual influenza A and B infection and a parainfluenza type 1. Where multiple sites were swabbed, the virus was detected in all sites. Autopsy reports for 12 cases were obtained each reporting findings consistent with respiratory infection. Influenza A was always listed as a contributing factor in the death whereas RSV was listed once and influenza B was omitted in one case. The quality of the reports was variable and full histology was less likely to be performed in the elderly. While coroner's reports supported the use of swabbing rather than tissue collection, the lack of consistency and omission of the virology findings as contributing factors to death means that the burden of viruses on mortality statistics will remain under-estimated particularly in the elderly. Copyright © 2014 Elsevier B.V. All rights reserved.

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)

Increasing the efficiency of digitization workflows for herbarium specimens.

Science.gov (United States)

Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers, Barbara M

2012-01-01

The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation's new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

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.

Chicken parvovirus viral loads in cloacal swabs from malabsorption syndrome-affected and healthy broilers.

Science.gov (United States)

Finkler, Fabrine; de Lima, Diane Alves; Cerva, Cristine; Cibulski, Samuel Paulo; Teixeira, Thais Fumaco; Dos Santos, Helton Fernandes; de Almeida, Laura Lopes; Roehe, Paulo Michel; Franco, Ana Cláudia

2016-12-01

Chicken parvovirus (ChPV) has been associated with malabsorption syndrome (MAS) in broilers. However, the participation of this virus in such syndrome is unclear, since it may be detected in diseased and healthy chickens. In the course of these studies, it was argued whether ChPV genome loads might be correlated to the occurrence of MAS. To check such a hypothesis, a SYBR green-based quantitative polymerase chain reaction was developed to detect and quantify ChPV genomes. Cloacal swabs from 68 broilers with MAS and 59 from healthy animals were collected from different poultry farms. Genomes of ChPV were detected in all samples, regardless of their health status. However, viral genome loads in MAS-affected broilers were significantly higher (1 × 10 5 genome copies per 100 ng DNA) than in healthy animals (1.3 × 10 3 GC/100 ng DNA). These findings indicate that there is an association between high ChPV genome loads and the occurrence of MAS in broilers.

Tonsillar Surface Micro Flora: Does it Truly Represent Pathological Tonsillar Flora?

Science.gov (United States)

Haq, Syed Nadeem Ul; Ayub, Zeeshan; Ahmed, Azeema

2017-01-01

To determine the best method of identifying core tonsillar flora. Quasi-experimental study. ENT Department, Combined Military Hospital, Lahore, from September 2013 to October 2015. Eighty-seven patients of recurrent tonsillitis undergoing tonsillectomy were included. All the patients, after being anaesthetised, had surface swabs taken from the tonsillar surface followed by tonsillar aspiration with a 5cc syringe. Following tonsillectomy, the tonsils were sent for culture of core flora. All three specimens from each patient were cultured according to established criteria. The patient population had 33 (37%) female and 54 (62%) male patients. Flora of 12 (13.8%) surface swabs and 68 (78.2%) tonsillar aspirates matched the flora cultured from core of the tonsils. Chi-square test showed this difference to be significant (p-value flora as compared to surface swabs.

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

Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification.

Science.gov (United States)

Unger, Jakob; Merhof, Dorit; Renner, Susanne

2016-11-16

Global Plants, a collaborative between JSTOR and some 300 herbaria, now contains about 2.48 million high-resolution images of plant specimens, a number that continues to grow, and collections that are digitizing their specimens at high resolution are allocating considerable recourses to the maintenance of computer hardware (e.g., servers) and to acquiring digital storage space. We here apply machine learning, specifically the training of a Support-Vector-Machine, to classify specimen images into categories, ideally at the species level, using the 26 most common tree species in Germany as a test case. We designed an analysis pipeline and classification system consisting of segmentation, normalization, feature extraction, and classification steps and evaluated the system in two test sets, one with 26 species, the other with 17, in each case using 10 images per species of plants collected between 1820 and 1995, which simulates the empirical situation that most named species are represented in herbaria and databases, such as JSTOR, by few specimens. We achieved 73.21% accuracy of species assignments in the larger test set, and 84.88% in the smaller test set. The results of this first application of a computer vision algorithm trained on images of herbarium specimens shows that despite the problem of overlapping leaves, leaf-architectural features can be used to categorize specimens to species with good accuracy. Computer vision is poised to play a significant role in future rapid identification at least for frequently collected genera or species in the European flora.

Maintaining respect and fairness in the usage of stored shared specimens.

Science.gov (United States)

Mduluza, Takafira; Midzi, Nicholas; Duruza, Donold; Ndebele, Paul

2013-01-01

Every year, research specimens are shipped from one institution to another as well as across national boundaries. A significant proportion of specimens move from poor to rich countries. Concerns are always raised on the future usage of the stored specimens shipped to research institutions from developing countries. Creating awareness of the processes is required in all sectors involved in biomedical research. To maintain fairness and respect in sharing biomedical specimens and research products requires safeguarding by Ethics Review Committees in both provider and recipient institutions. Training in basic ethical principles in research is required to all sectors involved in biomedical research so as to level up the research playing field. By agreeing to provide specimens, individuals and communities from whom samples are collected would have placed their trust and all ensuing up-keep of the specimens to the researchers. In most collaborative set-up, laid down material transfer agreements are negotiated and signed before the shipment of specimens. Researchers, research ethics committees (RECs) and institutions in the countries of origin are supposed to serve as overseers of the specimens. There is need to advocate for honesty in sample handling and sharing, and also need to oversee any written commitments by researchers, RECs and institutions at source as well as in recipient institution. Commitments from source RECs and Institutional Review Boards (IRBs) and in the receiving institution on overseeing the future usage of stored specimens are required; including the ultimate confirmation abiding by the agreement. Training in ethical issues pertaining to sample handling and biomedical research in general is essential at all levels of academic pursuit. While sharing of biological specimens and research data demands honesty and oversight by ethical regulatory agents from both institutions in developing country and recipient institutions in developed countries. Archiving

Evaluation of the Cepheid Xpert Flu Assay for rapid identification and differentiation of influenza A, influenza A 2009 H1N1, and influenza B viruses.

Science.gov (United States)

Novak-Weekley, S M; Marlowe, E M; Poulter, M; Dwyer, D; Speers, D; Rawlinson, W; Baleriola, C; Robinson, C C

2012-05-01

The Xpert Flu Assay cartridge is a next-generation nucleic acid amplification system that provides multiplexed PCR detection of the influenza A, influenza A 2009 H1N1, and influenza B viruses in approximately 70 min with minimal hands-on time. Six laboratories participated in a clinical trial comparing the results of the new Cepheid Xpert Flu Assay to those of culture or real-time PCR with archived and prospectively collected nasal aspirate-wash (NA-W) specimens and nasopharyngeal (NP) swabs from children and adults. Discrepant results were resolved by DNA sequence analysis. After discrepant-result analysis, the sensitivities of the Xpert Flu Assay for prospective NA-W specimens containing the influenza A, influenza A 2009 H1N1, and influenza B viruses compared to those of culture were 90.0%, 100%, and 100%, respectively, while the sensitivities of the assay for prospective NP swabs compared to those of culture were 100%, 100%, and 100%, respectively. The sensitivities of the Xpert Flu Assay for archived NA-W specimens compared to those of Gen-Probe ProFlu+ PCR for the influenza A, influenza A 2009 H1N1, and influenza B viruses were 99.4%, 98.4%, and 100%, respectively, while the sensitivities of the Xpert Flu Assay for archived NP swabs compared to those of ProFlu+ were 98.1%, 100%, and 93.8%, respectively. The sensitivities of the Xpert Flu Assay with archived NP specimens compared to those of culture for the three targets were 97.5%, 100%, and 93.8%, respectively. We conclude that the Cepheid Xpert Flu Assay is an accurate and rapid method that is suitable for on-demand testing for influenza viral infection.

Evaluation of A-1 reactor heavy-water calandria specimens

International Nuclear Information System (INIS)

Brumovsky, M.

1976-01-01

Container chains with surveillance specimens were placed in two special channels of the core peripheral part to test changes in mechanical properties due to reactor operation of caisson tube material. The specimens were made from the caisson tube material and placed by eight pieces on the outer surface of the containers. The first removed specimens were tested for corrosion losses, tensile strength, and fractured surfaces were then assessed. The changes in strength properties were found to be similar in both base material and welded joints. The corrosion film on surveillance specimens did not practically affect strength properties nor ductility. It was found that the Al-Mg-Si alloy used for the heavy water vessel caisson tubes following stabilization annealing was fully stable at operating temperatures of up to 100 degC. Slio.ht changes in properties can be attributed to the effect of a high neutron dose. Thus, the high radiation and temperature stability of the alloy was confirmed. (O.K.)

Review of forensically important entomological specimens collected from human cadavers in Malaysia (2005-2010).

Science.gov (United States)

Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Azirun, Mohd Sofian

2013-07-01

Forensic entomological specimens collected from human decedents during crime scene investigations in Malaysia in the past 6 years (2005-2010) are reviewed. A total of 80 cases were recorded and 93 specimens were collected. From these specimens, 10 species of cyclorrphagic flies were identified, consisting of Chrysomya rufifacies (Macquart) -38 specimens (40.86%), Chrysomya megacephala (Fabricius) -36 specimens (38.70%), Chrysomya villeneuvi (Patton) -2 specimens (2.15%), Chrysomya nigripes (Aubertin) -2 specimens (2.15%), Chrysomya pinguis (Walker) -1 specimen (1.08%), Hermetia illucens (Linnaeus) -1 specimen (1.08%), Hemipyrellia liguriens (Wiedemann) -5 specimens (5.37%), Synthesiomyia nudiseta (Wulp) -1 specimen (1.08%), Megaselia scalaris (Loew)-1 specimen (1.08%) and Sarcophaga ruficornis (Fabricius) -4 specimens (4.30%). In two specimens (2.15%), the maggots were not identifiable. Ch. megacephala and Ch. rufifacies were the commonest species found in human decedents from three different ecological habitats. S. nudiseta is an uncommon species found only on human cadavers from indoors. A total of 75 cases (93.75%) had a single fly infestation and 5 cases (6.25%) had double fly infestation. In conclusion, although large numbers of fly species were found on human decedents, the predominant species are still those of Chrysomya. Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

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)

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.

Influence of specimen size on the creep of rock salt

International Nuclear Information System (INIS)

Senseny, P.E.

1982-01-01

Triaxial compression creep data for Avery Island dome salt are analyzed to determine the influence of specimen size on creep deformation. Laboratory experiments were performed on 50- and 100-mm-diameter specimens in the temperature range from 25 to 200 0 C and the axial stress difference range from 2.5 to 31.0 MPa. The strain-vs-time data from each test are divided into transient and steady-state components. Results of statistical analysis of these data show that transient creep of the small specimens is a stronger function of stress, temperature, and time than is transient creep of the larger specimens. Analysis of the steady-state data show no size effect, however. 14 references, 7 figures, 3 tables

Laparoscopic right-sided colonic resection with transluminal colonoscopic specimen extraction

Science.gov (United States)

Kayaalp, Cuneyt; Kutluturk, Koray; Yagci, Mehmet Ali; Ates, Mustafa

2015-01-01

AIM: To study the transcolonic extraction of the proximally resected colonic specimens by colonoscopic assistance at laparoscopic colonic surgery. METHODS: The diagnoses of our patients were Crohn’s disease, carcinoid of appendix and adenocarcinoma of cecum. We preferred laparoscopic total mesocolic resections. Colon and terminal ileum were divided with endoscopic staplers. A colonoscope was placed per anal and moved proximally in the colon till to reach the colonic closed end under the laparoscopic guidance. The stump of the colon was opened with laparoscopic scissors. A snare of colonoscope was released and the intraperitoneal complete free colonic specimen was grasped. Specimen was moved in to the colon with the help of the laparoscopic graspers and pulled gently through the large bowel and extracted through the anus. The open end of the colon was closed again and the ileal limb and the colon were anastomosed intracorporeally with a 60-mm laparoscopic stapler. The common enterotomy orifice was closed in two layers with a running intracorporeal suture. RESULTS: There were three patients with laparoscopic right-sided colonic resections and their specimens were intended to remove through the remnant colon by colonoscopy but the procedure failed in one patient (adenocarcinoma) due to a bulky mass and the specimen extraction was converted to transvaginal route. All the patients had prior abdominal surgeries and had related adhesions. The operating times were 210, 300 and 500 min. The lengths of the specimens were 13, 17 and 27 cm. In our cases, there were no superficial or deep surgical site infections or any other complications. The patients were discharged uneventfully within 4-5 d and they were asymptomatic after a mean 7.6 mo follow-up (ranged 4-12). As far as we know, there were only 12 cases reported yet on transcolonic extraction of the proximal colonic specimens by colonoscopic assistance after laparoscopic resections. With our cases, success rate of the

Methicillin-resistant Staphylococcus aureus in the environment of public transport: data from the metropolitan network in Lyon, France.

Science.gov (United States)

Gaymard, Alexandre; Pichon, Maxime; Degaud, Michaël; Tasse, Jason; Dupieux, Céline; Laurent, Frédéric

2016-10-01

Methicillin-resistant Staphylococcus aureus (MRSA) is involved in community-acquired and nosocomial diseases. The means of MRSA transmission and dissemination in the community remain uncertain. Studies have shown that public transport systems could be a source of MRSA and may serve as a potential source for community-acquired MRSA infections. This study aimed to investigate MRSA contamination on Lyon's metropolitan network (Métro) in France. Hand-touched surfaces were sampled with sterile swabs (Transystem(®)) during a 1-day transversal study by collecting 50 samples in seven hub stations and two trains for each of the four Métro lines. Then, during a longitudinal study, one sample was collected twice daily for 30 consecutive days in the busiest and most congested hub station. All swabs were incubated in enrichment medium for 24 h and then each suspension was plated onto a chromogenic selective medium for MRSA. After 24 h at 36 °C, all presumptive MRSA colonies were tested using VITEK(®) MS to confirm identification as S. aureus as well as by Alere™ PBP2a Culture Colony Test and mecA/mecC PCR to check methicillin resistance. Of the 110 swabs tested, 24 presumptive MRSA colonies were isolated, of which 2 were confirmed as S. aureus by VITEK(®) MS. These two isolates were tested negative using the PBP2a Culture Colony Test and PCR. Unlike other foreign cities such as Lisbon, the current data suggest a low level of MRSA contamination of hand-touched surfaces on Lyon's Métro. This should be put in perspective with the low level of MRSA colonisation in the French community. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Laser weld reconstitution of conventional Charpy and Miniaturized Notch Test (MNT) specimens

International Nuclear Information System (INIS)

Manahan, M.P.; Williams, J.; Martukanitz, R.P.

1993-01-01

As nuclear power plants approach end-of-license (EOL) and consideration is given to license renewal, there is an ever increasing need to expand the amount of data obtainable from the original surveillance specimens. A laser welding technique to reconstitute broken Charpy specimens is being developed to produce both conventional and miniaturized Charpy specimens. This paper reports on early laser welding development efforts and summarizes previous proof-of-principle experiments on a 1/16 scale miniaturized Charpy test. In order to benchmark the laser welding procedure, the laser-reconstituted specimen data have been compared with the original specimen data. In addition, the microstructure after welding has been examined to ensure that the material in the vicinity of the notch is essentially unchanged after the welding process. Data which characterize the thermal transient during welding are obtained by attaching thermocouples to the specimens. Other important considerations include perturbation of the stress field near the notch, dynamic stress waves, and contact of the weld region with the tup. Precise control of welding parameters has been demonstrated, heat-affected zones as small as 0.25 mm can be achieved, and sufficient penetration depth can be obtained to enable welding thick sections (1T or greater) to yield conventional Charpy specimens or fracture toughness specimens and thin sections (∼5 mm) to yield Miniaturized Notch Test (MNT) specimens

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)

Altered biomarkers of mucosal immunity and reduced vaginal Lactobacillus concentrations in sexually active female adolescents.

Directory of Open Access Journals (Sweden)

Rebecca Pellett Madan

Full Text Available Genital secretions collected from adult women exhibit in vitro activity against herpes simplex virus (HSV and Escherichia coli (E. coli, but prior studies have not investigated this endogenous antimicrobial activity or its mediators in adolescent females.Anti-HSV and anti-E.coli activity were quantified from cervicovaginal lavage (CVL specimens collected from 20 sexually active adolescent females (15-18 years. Soluble immune mediators that may influence this activity were measured in CVL, and concentrations of Lactobacillus jensenii and crispatus were quantified by PCR from vaginal swabs. Results for adolescents were compared to those obtained from 54 healthy, premenopausal adult women. Relative to specimens collected from adults, CVL collected from adolescent subjects had significantly reduced activity against E. coli and diminished concentrations of protein, IgG, and IgA but significantly increased anti-HSV activity and concentrations of interleukin (IL-1α, IL-6 and IL-1 receptor antagonist. Vaginal swabs collected from adolescent subjects had comparable concentrations of L. crispatus but significantly reduced concentrations of L. jensenii, relative to adult swabs.Biomarkers of genital mucosal innate immunity may differ substantially between sexually active adolescents and adult women. These findings warrant further study and may have significant implications for prevention of sexually transmitted infections in adolescent females.

Increasing the efficiency of digitization workflows for herbarium specimens

Directory of Open Access Journals (Sweden)

Melissa Tulig

2012-07-01

Full Text Available The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR of specimen images. With the launch of the National Science Foundation’s new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

Genital Herpes Simplex Virus Type 2 Shedding Among Adults With and Without HIV Infection in Uganda.

Science.gov (United States)

Phipps, Warren; Nakku-Joloba, Edith; Krantz, Elizabeth M; Selke, Stacy; Huang, Meei-Li; Kambugu, Fred; Orem, Jackson; Casper, Corey; Corey, Lawrence; Wald, Anna

2016-02-01

Despite the high prevalence of herpes simplex virus type 2 (HSV-2) in sub-Saharan Africa, the natural history of infection among Africans is not well characterized. We evaluated the frequency of genital HSV shedding in HIV-seropositive and HIV-seronegative men and women in Uganda. Ninety-three HSV-2-seropositive Ugandan adults collected anogenital swab specimens for HSV DNA quantification by polymerase chain reaction 3 times daily for 6 weeks. HSV-2 was detected from 2484 of 11 283 swab specimens collected (22%), with a median quantity of 4.3 log10 HSV copies/mL (range, 2.2-8.9 log10 HSV copies/mL). Genital lesions were reported on 749 of 3875 days (19%), and subclinical HSV shedding was detected from 1480 of 9113 swab specimens (16%) collected on days without lesions. Men had higher rates of total HSV shedding (relative risk [RR], 2.0 [95% confidence interval {CI}, 1.3-2.9]; P genital lesions (RR, 2.1 [95% CI, 1.2-3.4]; P = .005), compared with women. No differences in shedding rates or lesion frequency were observed based on HIV serostatus. HSV-2 shedding frequency and quantity are high among HSV-2-seropositive adults in sub-Saharan Africa, including persons with and those without HIV infection. Shedding rates were particularly high among men, which may contribute to the high prevalence of HSV-2 and early acquisition among African women. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

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

Guidebook for the fabrication of non-destructive testing (NDT) test specimens

International Nuclear Information System (INIS)

2001-01-01

Non-destructive testing (NDT) test specimens constitute a very important part of training and certification of NDT personnel and are important for carrying out actual inspection and testing, and for achieving international harmonization of NDT practices. The IAEA organized an advisory group of experts to develop a Guidebook for Fabrication of NDT Test Specimens. The experts consulted the ISO/FDIS 9712-1999 requirements for training and certification of personnel and the suitability of various types of NDT test specimens that are needed to meet such requirements This guidebook presents a set of NDT test specimens, and the methodology and procedures for their fabrication

Tensile and Creep Testing of Sanicro 25 Using Miniature Specimens

Science.gov (United States)

Dymáček, Petr; Jarý, Milan; Dobeš, Ferdinand; Kloc, Luboš

2018-01-01

Tensile and creep properties of new austenitic steel Sanicro 25 at room temperature and operating temperature 700 °C were investigated by testing on miniature specimens. The results were correlated with testing on conventional specimens. Very good agreement of results was obtained, namely in yield and ultimate strength, as well as short-term creep properties. Although the creep rupture time was found to be systematically shorter and creep ductility lower in the miniature test, the minimum creep rates were comparable. The analysis of the fracture surfaces revealed similar ductile fracture morphology for both specimen geometries. One exception was found in a small area near the miniature specimen edge that was cut by electro discharge machining, where an influence of the steel fracture behavior at elevated temperature was identified. PMID:29337867

Tensile and Creep Testing of Sanicro 25 Using Miniature Specimens.

Science.gov (United States)

Dymáček, Petr; Jarý, Milan; Dobeš, Ferdinand; Kloc, Luboš

2018-01-16

Tensile and creep properties of new austenitic steel Sanicro 25 at room temperature and operating temperature 700 °C were investigated by testing on miniature specimens. The results were correlated with testing on conventional specimens. Very good agreement of results was obtained, namely in yield and ultimate strength, as well as short-term creep properties. Although the creep rupture time was found to be systematically shorter and creep ductility lower in the miniature test, the minimum creep rates were comparable. The analysis of the fracture surfaces revealed similar ductile fracture morphology for both specimen geometries. One exception was found in a small area near the miniature specimen edge that was cut by electro discharge machining, where an influence of the steel fracture behavior at elevated temperature was identified.

Alfredo Dugès' type specimens of amphibians and reptiles revisited.

Science.gov (United States)

Flores-Villela, Oscar; Ríos-Muñoz, César A; Magaña-Cota, Gloria E; Quezadas-Tapia, Néstor L

2016-03-14

The type specimens of amphibians and reptiles of the Museo de Historia Natural Alfredo Dugès, at the University of Guanajuato (MADUG) were reviewed following Smith & Necker's (1943) summary. Owing to this collection's eventful history and its historical importance as the oldest herpetological collection in Mexico, a review of its conservation status was needed. After many years, the collection has received proper recognition at the University of Guanajuato with a portion of the herpetological types considered "Precious Assets" of the university. We found 34 type specimens pertaining to 18 taxa; six are additional specimens to those previously reported; six herpetological types are missing, including the body of the type of Adelophis copei. All specimens are in good to reasonable condition except for the type of Rhinocheilus antonii, which has dried out completely. All specimens are illustrated to show their condition.

Investigation of smooth specimen scc test procedures; variations in environment, specimen size, stressing frame, and stress state. [for high strength aluminum alloys

Science.gov (United States)

Lifka, B. W.; Sprowls, D. O.; Kelsey, R. A.

1975-01-01

The variables studied in the stress-corrosion cracking performance of high strength aluminum alloys were: (1) corrosiveness of the environment, (2) specimen size and stiffness of the stressing system, (3) interpretation of transgranular cracking, and (4) interaction of the state of stress and specimen orientation in a product with an anisotropic grain structure. It was shown that the probability of failure and time to fracture for a specimen loaded in direct tension are influenced by corrosion pattern, the stressing assembly stiffness, and the notch tensile strength of the alloy. Results demonstrate that the combination of a normal tension stress and a shear stress acting on the plane of maximum susceptibility in a product with a highly directional grain cause the greatest tendency for stress-corrosion cracking.

Antibiotic resistance properties of uropathogenic Escherichia coli ...

African Journals Online (AJOL)

Purpose: To investigate the antibiotic resistance pattern of uropathogenic Escherichia coli (UPEC) strains isolated from pregnant women with history of recurrent urinary tract infections (RUTIs) and healthy pregnant women. Methods: A total of 485 high vaginal swab specimens were collected from pregnant women with ...

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

DEFF Research Database (Denmark)

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

2003-01-01

A one-tube reverse transcriptase/polymerase chain reaction coupled with an enzyme-linked immunosorbent assay (RT-PCR-ELISA) was developed for the rapid detection of avian influenza virus (AIV) in clinical specimens. A total of 419 swab pools were analyzed from chickens experimentally infected...

Aetiology of male urethritis in patients recruited from a population with a high HIV prevalence.

NARCIS (Netherlands)

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

2004-01-01

The aetiology of urethritis, the significance of potential pathogens and the relation of urethritis to HIV infection were determined in 335 men (cases) with and 100 men (controls) without urethral symptoms. Urethral swab specimens were tested for different organisms by PCR or by culture for

Physiological response of invasive mussel Limnoperna fortunei (Dunker, 1857 (Bivalvia: Mytilidae submitted to transport and experimental conditions

Directory of Open Access Journals (Sweden)

N. I. S. Cordeiro

Full Text Available Abstract Successful animal rearing under laboratory conditions for commercial processes or laboratory experiments is a complex chain that includes several stressors (e.g., sampling and transport and incurs, as a consequence, the reduction of natural animal conditions, economic losses and inconsistent and unreliable biological results. Since the invasion of the bivalve Limnoperna fortunei (Dunker, 1857 in South America, several studies have been performed to help control and manage this fouling pest in industrial plants that use raw water. Relatively little attention has been given to the laboratory rearing procedure of L. fortunei, its condition when exposed to a stressor or its acclimation into laboratory conditions. Considering this issue, the aims of this study are to (i investigate L. fortunei physiological responses when submitted to the depuration process and subsequent air transport (without water/dry condition at two temperatures, based on glycogen concentrations, and (ii monitor the glycogen concentrations in different groups when maintained for 28 days under laboratory conditions. Based on the obtained results, depuration did not affect either of the groups when they were submitted to approximately eight hours of transport. The variation in glycogen concentration among the specimens that were obtained from the field under depurated and non-depurated conditions was significant only in the first week of laboratory growth for the non-depurated group and in the second week for the depurated group. In addition, the tested temperature did not affect either of the groups that were submitted to transport. The glycogen concentrations were similar to those of the specimens that were obtained from the field in third week, which suggests that the specimens acclimated to laboratory conditions during this period of time. Thus, the results indicate that the air transport and acclimation time can be successfully incorporated into experimental studies

Anterolateral Ligament of the Knee Shows Variable Anatomy in Pediatric Specimens.

Science.gov (United States)

Shea, Kevin G; Milewski, Matthew D; Cannamela, Peter C; Ganley, Theodore J; Fabricant, Peter D; Terhune, Elizabeth B; Styhl, Alexandra C; Anderson, Allen F; Polousky, John D

2017-06-01

Anterior cruciate ligament (ACL) reconstruction failure rates are highest in youth athletes. The role of the anterolateral ligament in rotational knee stability is of increasing interest, and several centers are exploring combined ACL and anterolateral ligament reconstruction for these young patients. Literature on the anterolateral ligament of the knee is sparse in regard to the pediatric population. A single study on specimens younger than age 5 years demonstrated the presence of the anterolateral ligament in only one of eight specimens; therefore, much about the prevalence and anatomy of the anterolateral ligament in pediatric specimens remains unknown. We sought to (1) investigate the presence or absence of the anterolateral ligament in prepubescent anatomic specimens; (2) describe the anatomic relationship of the anterolateral ligament to the lateral collateral ligament; and (3) describe the anatomic relationship between the anterolateral ligament and the physis. Fourteen skeletally immature knee specimens (median age, 8 years; range, 7-11 years) were dissected (12 male, two female specimens). The posterolateral structures were identified in all specimens, including the lateral collateral ligament and popliteus tendon. The presence or absence of the anterolateral ligament was documented in each specimen, along with origin, insertion, and dimensions, when applicable. The relationship of the anterolateral ligament origin to the lateral collateral ligament origin was recorded. The anterolateral ligament was identified in nine of 14 specimens. The tibial attachment point was consistently located in the same region on the proximal tibia, between the fibular head and Gerdy's tubercle; however, the femoral origin of the anterolateral ligament showed considerable variation with respect to the lateral collateral ligament origin. The median femoral origin of the anterolateral ligament was 10 mm (first interquartile 6 mm, third interquartile 13) distal to the distal

46 CFR 57.06-4 - Production testing specimen requirements.

Science.gov (United States)

2010-10-01

... WELDING AND BRAZING Production Tests § 57.06-4 Production testing specimen requirements. (a) For test... 46 Shipping 2 2010-10-01 2010-10-01 false Production testing specimen requirements. 57.06-4... to welding shall not throw the finished test plate out of line by an angle of over 5°. (c) Where the...

Thermal Cycling of Uranium Dioxide - Tungsten Cermet Fuel Specimens

Energy Technology Data Exchange (ETDEWEB)

Gripshover, P.J.; Peterson, J.H.

1969-12-08

In phase I tungsten clad cermet fuel specimens were thermal cycled, to study the effects of fuel loading, fuel particle size, stablized fuel, duplex coatings, and fabrication techniques on dimensional stability during thermal cycling. In phase II the best combination of the factors studies in phase I were combined in one specimen for evaluation.

Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting.

Science.gov (United States)

Maneg, Daniela; Sponsel, Janina; Müller, Iris; Lohr, Benedikt; Penders, John; Madlener, Katharina; Hunfeld, Klaus-Peter

2016-01-01

Infective endocarditis (IE) is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5%) with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke's diagnostic classification scheme.

Transmission electron microscopy of bulk specimens over 10 µm in thickness

Energy Technology Data Exchange (ETDEWEB)

Sadamatsu, Sunao, E-mail: sadamatsu@mech.kagoshima-u.ac.jp [Department of Mechanical Engineering, Kagoshima University, Korimoto, Kagoshima 890-0065 (Japan); Tanaka, Masaki; Higashida, Kenji [Department of Materials Science and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395 (Japan); Matsumura, Syo [Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395 (Japan); Ultramicroscopy Research Center, Kyushu University, Nishi-ku, Fukuoka 819-0395 (Japan)

2016-03-15

We succeeded the observation of microstructures in bulk-sized specimens of over 10 µm in thickness by employing a technique that combines transmission electron microscopy (TEM) with energy-filtered imaging based on electron energy-loss spectroscopy (EELS). This method is unique in that it incorporates the inelastically scattered electrons into the imaging process. Using this technique, bright and sharp images of dislocations in crystalline silicon specimens as thick as 10 µm were obtained. A calibration curve to determine foil thickness of such a thick specimen was also derived. This method simply extends the observable thickness range in TEM. If combined with tilt series of observation over a significant range of angle, it will disclose three dimensional nanostructures in a µm-order block of a specimen, promoting our understanding of the controlling mechanisms behind various bulky material properties. - Highlights: • We developed a method which enables thick specimens to be observed using EF-TEM. • The effects of energy filter width and position on images were determined. • We suggested a method to determine the thickness of a thick film sample. • We achieved observation of microstructures in specimens with a thickness of 10 µm.

Design Analysis of the Mixed Mode Bending Sandwich Specimen

DEFF Research Database (Denmark)

Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

2010-01-01

A design analysis of the mixed mode bending (MMB) sandwich specimen for face–core interface fracture characterization is presented. An analysis of the competing failure modes in the foam cored sandwich specimens is performed in order to achieve face–core debond fracture prior to other failure modes...... for the chosen geometries and mixed mode loading conditions....

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.)

FLOQSwabTM: optimisation of procedures for the recovery of microbiological samples from surfaces

Directory of Open Access Journals (Sweden)

Guido Finazzi

2016-08-01

Full Text Available The FLOQSwabTM is a specimen collection device worldwide recognised for its superior performance in the clinical diagnostics. The aim of this work was to evaluate FLOQSwabTM for the recovery of microbiological samples from surfaces compared to the traditional swab (rayon tipped swab as per ISO 18593:2004 standard. The FLOQSwabTM, thanks to its innovative manufacturing technology, allows improving the efficiency of recovery and release of analyte. The study has been divided into two experiments. In the first experiment the two swabs were evaluated for their capacity to recover and release the analyte (three different bacterial loads of Escherichia coli. In the second experiment, the two swabs were evaluated for their capacity to recover three different bacterial loads of E. coli from two different surface materials (stainless steel and polypropylene. In all experiments the flocked swab demonstrated a higher recovery rate compared to the traditional rayon tipped swab. The data obtained from this preliminary study demonstrated that the FLOQSwabTM could be a good food surfaces collection device, which improves the recovery of the analyte and thus produces accurate results. Based on the outcomes of the study, a larger field study is in progress using the FLOQSwabTM for samples collection to improve both environmental monitoring and the efficacy of the hygiene controls for food safety.

Diagnosis of trichomonas vaginalis infection by PCR

International Nuclear Information System (INIS)

Issa, R.M.; Shalaby, M.A.

2007-01-01

To compare the sensitivity of PCR, wet preparation and culture in detecting Trichomonas vaginalis in urine and vaginal fluid. A PCR targeting the beta-tubulin genes of T. vaginalis was used for the detection of the organism in both vaginal swab and urine specimens from infected patients. Random urine samples were collected from 30 patients (23 females and 7 males), and tested for T. vaginalis by wet preparation and the Inpouch T. vaginalis culture systeme. Two vaginal swabs were collected by each woman. PCR detection. was carried out on samples negative by first methods. The positive result was found in 28.57% in male urine and 39.13% in female urine samples, 65.21% in 1st swab and 78.26 % in 2nd swab by wet preparation. By culture, the male urine samples showed 42.85% positive, female urine 69.56% while 1st swab showed 86.95% positive and 2nd swab 91.30% positive. All negative cases by culture in urine and vaginal samples were tested by PCR, which showed 2 cases to be positive in male urine samples and 5 cases positive in female urine sample. PCR assay was as good as or more sensitive than wet preparation and culture and resulted in practical advantage of providing results in shorter time. However, PCR test is still very expensive. (author)

Characterization of Cement Particles Found in Peri-implantitis-Affected Human Biopsy Specimens.

Science.gov (United States)

Burbano, Maria; Wilson, Thomas G; Valderrama, Pilar; Blansett, Jonathan; Wadhwani, Chandur P K; Choudhary, Pankaj K; Rodriguez, Lucas C; Rodrigues, Danieli C

2015-01-01

Peri-implantitis is a disease characterized by soft tissue inflammation and continued loss of supporting bone, which can result in implant failure. Peri-implantitis is a multifactorial disease, and one of its triggering factors may be the presence of excess cement in the soft tissues surrounding an implant. This descriptive study evaluated the composition of foreign particles from 36 human biopsy specimens with 19 specimens selected for analysis. The biopsy specimens were obtained from soft tissues affected by peri-implantitis around cement-retained implant crowns and compared with the elemental composition of commercial luting cement. Nineteen biopsy specimens were chosen for the comparison, and five test cements (TempBond, Telio, Premier Implant Cement, Intermediate Restorative Material, and Relyx) were analyzed using scanning electron microscopy equipped with energy dispersive x-ray spectroscopy. This enabled the identification of the chemical composition of foreign particles embedded in the tissue specimens and the composition of the five cements. Statistical analysis was conducted using classification trees to pair the particles present in each specimen with the known cements. The particles in each biopsy specimen could be associated with one of the commercial cements with a level of probability ranging between .79 and 1. TempBond particles were found in one biopsy specimen, Telio particles in seven, Premier Implant Cement particles in four, Relyx particles in four, and Intermediate Restorative Material particles in three. Particles found in human soft tissue biopsy specimens around implants affected by peri-implant disease were associated with five commercially available dental cements.

Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs.

LENUS (Irish Health Repository)

Wernecke, Martina

2009-01-01

BACKGROUND: Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS) disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test) for the identification of GBS in vaginal swabs from pregnant women. METHODS: The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm StrepB Assay and culture for the identification of GBS. RESULTS: The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. CONCLUSION: The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the ssrA gene as a suitable and

Placental Infection With Ureaplasma species Is Associated With Histologic Chorioamnionitis and Adverse Outcomes in Moderately Preterm and Late-Preterm Infants.

Science.gov (United States)

Sweeney, Emma L; Kallapur, Suhas G; Gisslen, Tate; Lambers, Donna S; Chougnet, Claire A; Stephenson, Sally-Anne; Jobe, Alan H; Knox, Christine L

2016-04-15

The human Ureaplasma species are the microbes most frequently isolated from placentae of women who deliver preterm. The role of Ureaplasma species has been investigated in pregnancies at <32 weeks of gestation, but currently no studies have determined the prevalence of ureaplasmas in moderately preterm and late-preterm (hereafter, "moderate/late preterm") infants, the largest cohort of preterm infants. Women delivering moderate/late preterm infants (n = 477) and their infants/placentae (n = 535) were recruited, and swab specimens of chorioamnion tissue, chorioamnion tissue specimens, and cord blood specimens were obtained at delivery. Swab and tissue specimens were cultured and analyzed by 16S ribosomal RNA polymerase chain reaction (PCR) for the presence of microorganisms, while cord blood specimens were analyzed for the presence of cytokines, chemokines, and growth factors. We detected microorganisms in 10.6% of 535 placentae (443 were delivered late preterm and 92 were delivered at term). Significantly, Ureaplasma species were the most prevalent microorganisms, and their presence alone was associated with histologically confirmed chorioamnionitis in moderate/late preterm and term placentae (P < .001). The presence of ureaplasmas in the chorioamnion was also associated with elevated levels of granulocyte colony-stimulating factor (P = .02). These findings have important implications for infection and adverse pregnancy outcomes throughout gestation and should be of major consideration for obstetricians and neonatologists. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Corynebacterium species isolated from patients with mastitis.

Science.gov (United States)

Paviour, Sue; Musaad, Sahar; Roberts, Sally; Taylor, Graeme; Taylor, Susan; Shore, Keith; Lang, Selwyn; Holland, David

2002-12-01

Corynebacteria were isolated from breast tissue, pus, or deep wound swabs of 24 women; the most common species isolated was the newly described Corynebacterium kroppenstedtii, followed by Corynebacterium amycolatum and Corynebacterium tuberculostearicum. Gram-positive bacilli were seen in samples sent for culture or in histological specimens for 12 women, and 9 of the 12 women from whom adequate histological specimens were obtained had conditions that met the criteria for granulomatous lobular mastitis, a chronic inflammatory disease of unknown etiology.

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

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.

Tensile tests and metallography of brazed AISI 316L specimens after irradiation

International Nuclear Information System (INIS)

Groot, P.; Franconi, E.

1994-01-01

Stainless steel type 316L tensile specimens were vacuum brazed with three kinds of alloys: BNi-5, BNi-6, and BNi-7. The specimens were irradiated up to 0.7 dpa at 353 K in the High Flux Reactor at JRC Petten, the Netherlands. Tensile tests were performed at a constant displacement rate of 10 -3 s -1 at room temperature in the ECN hot cell facility. BNi-5 brazed specimens showed ductile behaviour. Necking and fractures were localized in the plate material. BNi-6 and BNi-7 brazed specimens failed brittle in the brazed zone. This was preceded by uniform deformation of the plate material. Tensile test results of irradiated specimens showed higher stresses due to radiation hardening and a reduction of the elongation of the plate material compared to the reference. SEM examination of the irradiated BNi-6 and BNi-7 fracture surfaces showed nonmetallic phases. These phases were not found in the reference specimens. ((orig.))

Reducing intraocular-pressure spike after intravitreal-bevacizumab injection with ocular decompression using a sterile cotton swab soaked in proparacaine 0.5%: A quasi-experimental study.

Science.gov (United States)

Qureshi, Naveed A; Mansoor, Hassan; Ahmad, Sabihuddin; Zafar, Sarah; Asif, Muhammad

2016-01-01

The study was conducted to determine the effect of preinjection ocular decompression by a cotton swab soaked in local anesthetic on the immediate postinjection rise in intraocular pressure (IOP) after intravitreal bevacizumab (IVB). A nonrandomized, quasi-experimental interventional study was conducted at Al-Shifa Trust Eye Hospital, Pakistan, from August 1, 2013 to July 31, 2014. One hundred ( n = 100) patients receiving 0.05-mL IVB injection for the first time were assigned to two preinjection anesthetic methods: one with ocular decompression using a sterile cotton swab soaked in proparacaine 0.5%, and the other without ocular decompression using proparacaine 0.5% eyedrops. The IOP was recorded in the eye receiving IVB at three time intervals: Time 1 (preinjection), Time 2 (immediately after injection), and Time 3 (30 minutes after injection). There was a significant difference in the mean IOP change (between Time 1 and Time 2) for the group injected with ocular decompression [ M = 1.00, standard deviation (SD) = 1.47] and the group injected without ocular decompression ( M = 5.00, SD = 2.38; t (68) = 9.761, p 0.5% experience significantly lower postinjection IOP spike, and that too for a considerably shorter duration as compared to those receiving IVB without ocular decompression.

Role of specimen US for predicting resection margin status in breast conserving therapy.

Science.gov (United States)

Moschetta, M; Telegrafo, M; Introna, T; Coi, L; Rella, L; Ranieri, V; Cirili, A; Stabile Ianora, A A; Angelelli, G

2015-01-01

To assess the diagnostic accuracy of specimen ultrasound (US) for predicting resection margin status in women undergoing breast conserving therapy for US-detected cancer, having the histological findings as the reference standard. A total of 132 consecutive patients (age range, 34-87 years; mean, 51 years) underwent breast-conserving surgery for US-detected invasive breast cancer. All surgical specimens underwent US examination. The presence of lesion within the specimen and its distance from the specimen margins were assessed considering a threshold distance between the lesion and specimen margins of 10 mm. US findings were then compared with the pathological ones and specimen US. Sensitivity, specificity, diagnostic accuracy, positive (PPV) and negative predictive values (NPV) for predicting histological margin status were evaluated, having the histological findings as the reference standard. The histological examination detected invasive ductal carcinoma in 96/132 (73%) cases, invasive lobular carcinoma in 32/132 (24%), mucinous carcinoma in 4/132 (3%). The pathological margin analysis revealed 96/132 (73%) negative margins and 36 (27%) close/positive margins. US examination detected all 132 breast lesions within the surgical specimens. 110 (83%) negative margins and 22 (17%) positive margins were found on US. Sensitivity, specificity, diagnostic accuracy, PPV and NPV of 44%, 94%, 80%, 73% and 82%, respectively, were found for specimen US. Specimen US represents a time and cost saving imaging tool for evaluating the presence of US detected-breast lesion within surgical specimen and for predicting the histological margin status.

Strain Measurement System Developed for Biaxially Loaded Cruciform Specimens

Science.gov (United States)

Krause, David L.

2000-01-01

A new extensometer system developed at the NASA Glenn Research Center at Lewis Field measures test area strains along two orthogonal axes in flat cruciform specimens. This system incorporates standard axial contact extensometers to provide a cost-effective high-precision instrument. The device was validated for use by extensive testing of a stainless steel specimen, with specimen temperatures ranging from room temperature to 1100 F. In-plane loading conditions included several static biaxial load ratios, plus cyclic loadings of various waveform shapes, frequencies, magnitudes, and durations. The extensometer system measurements were compared with strain gauge data at room temperature and with calculated strain values for elevated-temperature measurements. All testing was performed in house in Glenn's Benchmark Test Facility in-plane biaxial load frame.

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...

JR-curves of wide plates and CT25 specimens

International Nuclear Information System (INIS)

Aurich, D.; Wobst, K.; Krafka, H.

1987-01-01

In connection with the problem of the applicability of the characteristic specimen date - i.e. the initiation and stable crack propagation under maximal loads, together with the elastic-plastic material behaviour - to that of actual components, spot-check type beside tests were conducted using wide-plate central crack, central notch (CCT, CNT) and double external crack (DECT) samples. The material in question was an StE 460 steel. A comparison between the determined values shows that the assessed pressure vessel behaviour differs extensively to the values derived from the CCT and CNT specimens. The corresponding results obtained from the CT25 and DECT specimens vary only slightly in the region of interest and correspond to real vessel values. (orig./DG) [de

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.

Delayed Microbial Cure of Lymphogranuloma Venereum Proctitis with Doxycycline Treatment

NARCIS (Netherlands)

de Vries, H.J.C.; Smelov, V.; Middelburg, J.G.; Pleijster, J.; Speksnijder, A.G.; Morré, S.A.

2009-01-01

Microbial cure of chlamydia proctitis (lymphogranuloma venereum [LGV] and non-LGV) with doxycycline treatment was evaluated by chlamydia DNA and RNA persistence in anal swab specimens. In LGV proctitis, RNA persisted for up to 16 days. In non-LGV chlamydia proctitis, DNA was undetectable after 7

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).

10 CFR 26.159 - Assuring specimen security, chain of custody, and preservation.

Science.gov (United States)

2010-01-01

... other entity has reason to question the integrity and identity of the specimens, the specimens may not... identification numbers on the custody-and-control form; (iii) A specimen bottle seal is broken or shows evidence... of the shipping containers are inaccessible without breaking a tamper-evident seal. (g) Couriers...

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.

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%.

Discovery of a novel Parvovirinae virus, porcine parvovirus 7, by metagenomic sequencing of porcine rectal swabs.

Science.gov (United States)

Palinski, Rachel M; Mitra, Namita; Hause, Ben M

2016-08-01

Parvoviruses are a diverse group of viruses containing some of the smallest known species that are capable of infecting a wide range of animals. Metagenomic sequencing of pooled rectal swabs from adult pigs identified a 4103-bp contig consisting of two major open reading frames encoding proteins of 672 and 469 amino acids (aa) in length. BLASTP analysis of the 672-aa protein found 42.4 % identity to fruit bat (Eidolon helvum) parvovirus 2 (EhPV2) and 37.9 % to turkey parvovirus (TuPV) TP1-2012/HUN NS1 proteins. The 469-aa protein had no significant similarity to known proteins. Genetic and phylogenetic analyses suggest that PPV7, EhPV2, and TuPV represent a novel genus in the family Parvoviridae. Quantitative PCR screening of 182 porcine diagnostic samples found a total of 16 positives (8.6 %). Together, these data suggest that PPV7 is a highly divergent novel parvovirus prevalent within the US swine.

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)

Lack of Measles Transmission to Susceptible Contacts from a Health Care Worker with Probable Secondary Vaccine Failure - Maricopa County, Arizona, 2015.

Science.gov (United States)

Jones, Jefferson; Klein, Ron; Popescu, Saskia; Rose, Karen; Kretschmer, Melissa; Carrigan, Alice; Trembath, Felicia; Koski, Lia; Zabel, Karen; Ostdiek, Scott; Rowell-Kinnard, Paula; Munoz, Esther; Sunenshine, Rebecca; Sylvester, Tammy

2015-08-07

On January 23, 2015, the Maricopa County Department of Public Health (MCDPH) was notified of a suspected measles case in a nurse, a woman aged 48 years. On January 11, the nurse had contact with a patient with laboratory-confirmed measles associated with the Disneyland theme park-related outbreak in California. On January 21, she developed a fever (103°F [39.4°C]), on January 23 she experienced cough and coryza, and on January 24, she developed a rash. The patient was instructed to isolate herself at home. On January 26, serum, a nasopharyngeal swab, and a urine specimen were collected. The following day, measles infection was diagnosed by real time reverse transcription polymerase chain reaction testing of the nasopharyngeal swab and urine specimen and by detection of measles-specific immunoglobulin (Ig)M and IgG in serum by enzyme-linked immunosorbent assay. Because of her symptoms and laboratory results, the patient was considered to be infectious.

Development of a loop-mediated isothermal amplification assay for detection of Trichomonas vaginalis.

Science.gov (United States)

Reyes, John Carlo B; Solon, Juan Antonio A; Rivera, Windell L

2014-07-01

A loop-mediated isothermal amplification (LAMP) assay targeting the 2-kbp repeated DNA species-specific sequence was developed for detection of Trichomonas vaginalis, the causative agent of trichomoniasis. The analytical sensitivity and specificity of the LAMP assay were evaluated using pooled genital swab and urine specimens, respectively, spiked with T. vaginalis trophozoites. Genital secretion and urine did not inhibit the detection of the parasite. The sensitivity of the LAMP was 10-1000 times higher than the PCR performed. The detection limit of LAMP was 1 trichomonad for both spiked genital swab and urine specimens. Also, LAMP did not exhibit cross-reactivity with closely-related trichomonads, Trichomonas tenax and Pentatrichomonas hominis, and other enteric and urogenital microorganisms, Entamoeba histolytica, Candida albicans, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. This is the first report of a LAMP assay for the detection of T. vaginalis and has prospective application for rapid diagnosis and control of trichomoniasis. Copyright © 2014 Elsevier Inc. All rights reserved.

Bacterial enteropathogens associated with diarrhea in a rural population of Haiti

Directory of Open Access Journals (Sweden)

Jackson JC

2011-09-01

Full Text Available John C Jackson, Anthony L Farone, Mary B Farone Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA Purpose: Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Patients and methods: Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBLTM Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBLTM CrystalTM Enteric/Nonferementing Identification system (Becton, Dickinson and Company. Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR. Results: Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. Conclusion: This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified. Keywords: Escherichia, Cronobacter, diarrheagenic, stool

Use of precracked Charpy and smaller specimens to establish the master curve

International Nuclear Information System (INIS)

Sokolov, M.A.; McCabe, D.E.; Nanstad, R.K.; Davidov, Y.A.

1997-01-01

The current provisions used in the U.S. Code of Federal Regulations for the determination of the fracture toughness of reactor pressure vessel steels employs an assumption that there is a direct correlation between K Ic lower-bound toughness and the Charpy V-notch transition curve. Such correlations are subject to scatter from both approaches which weakens the reliability of fracture mechanics-based analyses. In this study, precracked Charpy and smaller size specimens are used in three-point static bend testing to develop fracture mechanics based K k values. The testing is performed under carefully controlled conditions such that the values can be used to predict the fracture toughness performance of large specimens. The concept of a universal transition curve (master curve) is applied. Data scatter that is characteristic of commercial grade steels and their weldments is handled by Weibull statistical modeling. The master curve is developed to describe the median K Jc fracture toughness for 1T size compact specimens. Size effects are modeled using weakest-link theory and are studied for different specimen geometries. It is shown that precracked Charpy specimens when tested within their confined validity limits follow the weakest-link size-adjustment trend and predict the fracture toughness of larger specimens. Specimens of smaller than Charpy sizes (5 mm thick) exhibit some disparities in results relative to weakest-link size adjustment prediction suggesting that application of such adjustment to very small specimens may have some limitations

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

Thermo-mechanical Fatigue Failure of Thermal Barrier Coated Superalloy Specimen

Science.gov (United States)

Subramanian, Rajivgandhi; Mori, Yuzuru; Yamagishi, Satoshi; Okazaki, Masakazu

2015-09-01

Failure behavior of thermal barrier coated (TBC) Ni-based superalloy specimens were studied from the aspect of the effect of bond coat material behavior on low cycle fatigue (LCF) and thermo-mechanical fatigue (TMF) at various temperatures and under various loading conditions. Initially, monotonic tensile tests were carried out on a MCrAlY alloy bond coat material in the temperature range of 298 K to 1273 K (25 °C to 1000 °C). Special attention was paid to understand the ductile to brittle transition temperature (DBTT). Next, LCF and TMF tests were carried out on the thermal barrier coated Ni-based alloy IN738 specimen. After these tests, the specimens were sectioned to understand their failure mechanisms on the basis of DBTT of the bond coat material. Experimental results demonstrated that the LCF and TMF lives of the TBC specimen were closely related to the DBTT of the bond coat material, and also the TMF lives were different from those of LCF tests. It has also been observed that the crack density in the bond coat in the TBC specimen was significantly dependent on the test conditions. More importantly, not only the number of cracks but also the crack penetration probability into substrate were shown to be sensitive to the DBTT.

[Study on the pathogens correlated to sexually transmitted diseases in 285 pre-pubertal girls with vulvovaginitis in Beijing].

Science.gov (United States)

Liu, Xiao-Yan; Sun, Hong-Mei; Feng, Yan-Ling; Hu, Jin; Zhao, Han-Qing; Zhang, Li-Ya

2007-08-01

To study the relationship between vulvovaginitis in pre-pubertal girls and pathogens as Chlamydia trachomatis (Ct), N. gonorrhoeae (Ng), Mycoplasma, Ureaplasma urealyticum (Uu), Mycoplasma hominis (Mh), M. genitalium (Mg), M. fermentans (Mf) and M. penetrans (Mpe), as well as to find out the proportion of mycoplasma which is correlated to sexually transmitted diseases (STD) and AIDS. METHODS Vulvae swab specimens from 285 pre-pubertal girls with vulvovaginitis (case group) and 128 healthy girls (control group) were collected and detected by nested polymerase chain reaction (nPCR) to identify the existence of pathogens as Ct, Ng, Uu, Mh, Mg, Mf and Mpe. nPCR with both high specificity and sensitivity, would not be influenced by the amount of pathogens in specimens or inactivated during the process of storage or transportation. The rate of detection on pathogens was 59.65% in the 285 specimens from case group including 'one kind of pathogen in one specimen' as 37.54% and 'two kinds' as 16.84% and 'three kinds' as 5.26%. However, in the 128 specimens from control group, the detectable rate of pathogen was 6.25%. Relationships were found between Ng (P vulvovaginitis in pre-pubertal girls. In control group the pathogens were detected from 7 specimens including 5 Uu and 2 Mh. Some of the pathogens were correlated to STD and were important in causing vulvovaginitis in pre-pubertal girls. Vulvovaginitis might have been caused by more than one kind of pathogen in pre-pubertal girls. The locations of Mg, Mf and Ng in outer genital tracts were correlated to seasonal change. Macrolide seemed to be quite effective clinically in treating urogenital tract infection caused by mycoplasma and Ct.

Comparison of false-negative rates and limits of detection following macrofoam-swab sampling of Bacillus anthracis surrogates via Rapid Viability PCR and plate culture.

Science.gov (United States)

Hutchison, J R; Piepel, G F; Amidan, B G; Hess, B M; Sydor, M A; Deatherage Kaiser, B L

2018-05-01

We evaluated the effects of Bacillus anthracis surrogates, low surface concentrations, surface materials and assay methods on false-negative rate (FNR) and limit of detection (LOD 95 ) for recovering Bacillus spores using a macrofoam-swab sampling procedure. Bacillus anthracis Sterne or Bacillus atrophaeus Nakamura spores were deposited over a range of low target concentrations (2-500 per coupon) onto glass, stainless steel, vinyl tile and plastic. Samples were assayed using a modified Rapid Viability-PCR (mRV-PCR) method and the traditional plate culture method to obtain FNR and LOD 95 results. Mean FNRs tended to be lower for mRV-PCR compared to culturing, and increased as spore concentration decreased for all surface materials. Surface material, but not B. anthracis surrogate, influenced FNRs with the mRV-PCR method. The mRV-PCR LOD 95 was lowest for glass and highest for vinyl tile. LOD 95 values overall were lower for mRV-PCR than for the culture method. This study adds to the limited data on FNR and LOD 95 for mRV-PCR and culturing methods with low concentrations of B. anthracis sampled from various surface materials by the CDC macrofoam-swab method. These are key inputs for planning characterization and clearance studies for low contamination levels of B. anthracis. © 2018 The Society for Applied Microbiology.

An automated tensile machine for small specimens heavily neutron irradiated in FFTF/MOTA

International Nuclear Information System (INIS)

Kohyama, Akira; Sato, Shinji; Hamada, Kenichi

1993-01-01

The objective of this work is to develop a fully automated tensile machine for post-irradiation examination (PIE) of Fast Flux Test Facility (FFTF)/Materials Open Test Assembly (MOTA) irradiated miniature tension specimens. The anticipated merit of the automated tensile machine is to reduce damage to specimens during specimen handling for PIE and to reduce exposure to radioactive specimens. This machine is designed for testing at elevated temperatures, up to 873 K, in a vacuum or in an inert gas environment. Twelve specimen assemblies are placed in the vacuum chamber that can be tested successively in a fully automated manner. A unique automated tensile machine for the PIE of FFTF/MOTA irradiated specimens, the Monbusho Automated Tensile Machine (MATRON) consists of a test frame with controlling units and an automated specimen-loading apparatus. The qualification of the test frame has been completed, and the results have satisfied the machine specifications. The capabilities of producing creep and relaxation data have been demonstrated for Cu, Al, 316SS, and ferritic steels. The specimen holders for the three-point bending test and the small bulge test (small punch test; SP test) were also designed and produced

Assessment of two different types of sample for the early detection and isolation of thermophilic Campylobacter in broiler farms.

Science.gov (United States)

Urdaneta, Saulo; Dolz, Roser; Cerdà-Cuéllar, Marta

2015-01-01

In order to assess the optimal method for the early detection and isolation of thermophilic Campylobacter in broilers at farm level, two types of samples were compared: caecal contents obtained by necropsy and cloacal swabs transported in charcoal Amies medium. The study was conducted in five batches of broilers from five different farms, where weekly samples (caecal contents and cloacal swabs) from 30 birds were obtained. Samples were plated onto selective agar (modified charcoal cefoperazone desoxycholate agar, mCCDA) for Campylobacter isolation. Four out of five batches were positive for Campylobacter. No marked differences in sensitivity of both sample types were observed. However, a higher percentage of positive birds were detected when cloacal swabs were used. The results show that cloacal swab samples are adequate, and in some cases even better than caecal samples for the early detection of Campylobacter in broiler flocks at farm level. Also, this sample avoids sacrificing birds to test Campylobacter, which not only allows saving time in sample collection, transportation and processing at the laboratory, but also improves bird welfare and cost of sampling.

Enhanced radiometric detection of Mycobacterium paratuberculosis by using filter-concentrated bovine fecal specimens

International Nuclear Information System (INIS)

Collins, M.T.; Kenefick, K.B.; Sockett, D.C.; Lambrecht, R.S.; McDonald, J.; Jorgensen, J.B.

1990-01-01

A commercial radiometric medium, BACTEC 12B, was modified by addition of mycobactin, egg yolk suspension, and antibiotics (vancomycin, amphotericin B, and nalidixic acid). Decontaminated bovine fecal specimens were filter concentrated by using 3-microns-pore-size, 13-mm-diameter polycarbonate filters, and the entire filter was placed into the radiometric broth. Comparison of the radiometric technique with conventional methods on 603 cattle from 9 Mycobacterium paratuberculosis-infected herds found that of 75 positive specimens, the radiometric technique detected 92% while conventional methods detected 60% (P less than 0.0005). Only 3.9% of radiometric cultures were contaminated. To measure the effect of filter concentration of specimens on the detection rate, 5 cattle with minimal and 5 with moderate ileum histopathology were sampled weekly for 3 weeks. M. paratuberculosis was detected in 33.3% of nonfiltered specimens and 76.7% of filtered specimens (P less than 0.005). Detection rates were directly correlated with the severity of disease, and the advantage of specimen concentration was greatest on fecal specimens from cattle with low-grade infections. Detection times were also correlated with infection severity: 13.4 +/- 5.9 days with smear-positive specimens, 27.9 +/- 8.7 days with feces from cows with typical subclinical infections, and 38.7 +/- 3.8 days with fecal specimens from cows with low-grade infections. Use of a cocktail of vancomycin, amphotericin B, and nalidixic acid for selective suppression of nonmycobacterial contaminants was better than the commercial product PANTA (Becton Dickinson Microbiologic Systems, Towson, Md.) only when specimens contained very low numbers of M. paratuberculosis

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

Nasopharyngeal bacterial carriage and antimicrobial resistance in underfive children with community acquired pneumonia

Directory of Open Access Journals (Sweden)

Cissy B. Kartasasmita

2001-12-01

Full Text Available Lung puncture is the best way to determine the etiology of pneumonia since it yields the highest rate of positive cultures. However, this procedure is difficult, especially for a study in the community. According to WHO, isolates to be tested for antimicrobial resistance in the community should be obtained from nasopharyngeal (NP swabs. Previous studies support the use of NP isolates to determine antimicrobial resistance patterns of isolates from children with pneumonia. The aim of our study was to know the bacterial patterns of the nasopharynx in underfive children with community acquired pneumonia and their antimicrobial resistance. The study was carried out in 4 Primary Health Clinics in Majalaya sub-district, Bandung, Indonesia. All underfives with cough or difficult breathing and classified as having non-severe pneumonia (WHO guidelines, were included in the study. Nasopharyngeal swabs (CDC/WHO Manual were obtained by the doctor, the swabs were placed in Amies transport medium and stored in a sterile jar before taken to the laboratory in the same day. All children were treated with co-trimoxazole. During the nine month study, 698 children with clinical signs of non-severe pneumonia were enrolled. About 25% of the nasopharyngeal specimens yielded bacterial isolates; the two most frequently found were S. pneumoniae and S. epidermidis. The antimicrobial resistance test to co-trimoxazole showed 48.2% S. pneumoniae strain had full resistance and 32.7% showed intermediate resistance to co-trimoxazole. This result is almost similar to other studies from Asian countries. It seems that H. influenzae is not a problem in the study area; however, further studies are needed.

Influence of impacts on static and low-cycle fatigue characteristics of composite specimens (Draft)

NARCIS (Netherlands)

Walters, C.L.

2012-01-01

This paper describes the effect of impacts on the possible reduction of the structural characteristics and damage growth of graphite-epoxy specimens. The considered specimens are undamaged specimens and specimens impacted with two different energy levels. In particular, barely visible impact damage

Bireflectance imaging of coal and carbon specimens

Energy Technology Data Exchange (ETDEWEB)

Crelling, J.C. [Department of Geology, 1259 Lincoln Drive, Southern Illinois University, Carbondale, Illinois 62901 (United States); Glasspool, I.J.; Gibbins, J.R.; Seitz, M. [Department of Mechanical Engineering, Imperial College, Exhibition Road, London, SW7 2BX (United Kingdom)

2005-11-10

Although bireflectance measurements are routine, to date they have been limited to selected single point measurements. This study uses a 360{sup o} rotating polarizer in the incident light path combined with digital imaging to map the optical bireflectance of a polished specimen over the complete field of view, a system herein referred to as 'Bireflectance Imaging of Coal and Carbon Specimens' (BRICCS). True maximum reflectance maps and maps of polarizer angle for maximum reflectance (to identify co-ordered regions) are obtainable from the same data. A variety of coal, coke, char, graphite, and carbon/carbon specimens have been examined with the BRICCS system and the results demonstrate that the system can produce accurate maximum and apparent minimum reflectance, bireflectance, and extinction angle images. For example, flakes of natural graphite show no bireflectance along their long axis except in areas that have been strained. The images are maps showing the value of every pixel that has been calibrated by mineral reflectance standards. The maps are unique in that they show fields of view that cannot be seen by normal viewing through the microscope. For example, the bireflectance maps show the maximum difference between the maximum and apparent minimum reflectance for each of the million pixels at twenty orientations of the polarizer. (author)

Crack Propagation on ESE(T) Specimens Strengthened with CFRP Sheets

DEFF Research Database (Denmark)

Hansen, Christian Skodborg; Jensen, Peter Holmstrøm; Dyrelund, Jens

2009-01-01

In this paper fatigue tests on side notched steel test specimens strengthened with adhesive bonded fibre reinforced polymer (FRP) sheets are presented. The specimens are subject to crack growth both in the steel and bond line. Influence of the load ratio and initial crack length on the overall...

Retrospective biomonitoring of chemical contamination in the marine coastal environment of Terra Nova Bay (Ross Sea, Antarctica) by environmental specimen banking.

Science.gov (United States)

Grotti, Marco; Pizzini, Sarah; Abelmoschi, Maria Luisa; Cozzi, Giulio; Piazza, Rossano; Soggia, Francesco

2016-12-01

Antarctica offers a good opportunity to investigate planetary-scale pollution and climate change, and provides baseline values for contaminants such as Trace Elements (TEs) and Persistent Organic Pollutants (POPs). Literature data on contaminant levels in the Antarctic environment indicate that long-range atmospheric transport is the primary pathway by which pollutants from surrounding continents are carried to this pristine environment. However, local contamination sources represented by the scientific stations are also not negligible. Climate change and global warming are altering the global budget of anthropogenic contaminants and their monitoring in Antarctica ecosystems is very important to protect the global environment. In this work, eighty specimens of Adamussium colbecki (Smith, 1902), a benthic Antarctic scallop, collected from 1996 to 2009 and stored in the Antarctic Environmental Specimen Bank, were analyzed to quantify TEs and POPs, including polychlorinated biphenyls (PCBs), polychlorinated naphthalenes (PCNs) and polycyclic aromatic hydrocarbons (PAHs). Metals concentrations were not affected by anthropogenic contributions, highlighting a natural accumulation with the age of the organism. Similarly, no temporal trend was found for PCNs, PCBs and PAHs. However, specimens collected during the summer 1997-98 showed enhanced concentration levels of PCBs and PAHs that could refer to a local anthropogenic source of contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Residual stress state in pipe cut ring specimens for fracture toughness testing

Energy Technology Data Exchange (ETDEWEB)

Damjanovic, Darko [J.J. Strossmayer Univ. of Osijek, Slavonski Brod (Croatia). Mechanical Engineering Faculty; Kozak, Drazan [Zagreb Univ. (Croatia). Dept. for Mechanical Design; Marsoner, Stefan [Materials Center, Leoben (Austria).; Gubeljak, Nenad [Maribor Univ. (Slovenia). Chair of Mechanics

2017-07-01

Thin-walled pipes are not suitable for measuring fracture toughness parameters of vital importance because longitudinal crack failure is the most common failure mode in pipes. This is due to the impossibility to manufacture standard specimens for measuring fracture toughness, such as SENB or CT specimens, from the thin wall of the pipe. Previous works noticed this problem, but until now, a good and convenient solution has not been found or developed. To overcome this problem, very good alternative solution was proposed, the so-called pipe ring notched bend specimen (PRNB) [1-5]. Until now, only the idealized geometry PRNB specimen is analyzed, i. e., a specimen which is not cut out from an actual pipe but produced from steel plate. Based on that, residual stresses are neglected along with the imperfections in geometry (elliptical and eccentricity). The aim of this research is to estimate the residual stress state(s) in real pipes used in the boiler industry produced by hot rolling technique. These types of pipes are delivered only in normalized condition, but not stress relieved. Therefore, there are residual stresses present due to the manufacturing technique, but also due to uneven cooling after the production process. Within this paper, residual stresses are estimated by three methods: the incremental hole drilling method (IHMD), X-ray diffraction (XRD) and the splitting method (SM). Knowing the residual stress state in the ring specimen, it is possible to assess their impact on fracture toughness measured on the corresponding PRNB specimen(s).

Residual stress state in pipe cut ring specimens for fracture toughness testing

International Nuclear Information System (INIS)

Damjanovic, Darko; Kozak, Drazan; Marsoner, Stefan; Gubeljak, Nenad

2017-01-01

Thin-walled pipes are not suitable for measuring fracture toughness parameters of vital importance because longitudinal crack failure is the most common failure mode in pipes. This is due to the impossibility to manufacture standard specimens for measuring fracture toughness, such as SENB or CT specimens, from the thin wall of the pipe. Previous works noticed this problem, but until now, a good and convenient solution has not been found or developed. To overcome this problem, very good alternative solution was proposed, the so-called pipe ring notched bend specimen (PRNB) [1-5]. Until now, only the idealized geometry PRNB specimen is analyzed, i. e., a specimen which is not cut out from an actual pipe but produced from steel plate. Based on that, residual stresses are neglected along with the imperfections in geometry (elliptical and eccentricity). The aim of this research is to estimate the residual stress state(s) in real pipes used in the boiler industry produced by hot rolling technique. These types of pipes are delivered only in normalized condition, but not stress relieved. Therefore, there are residual stresses present due to the manufacturing technique, but also due to uneven cooling after the production process. Within this paper, residual stresses are estimated by three methods: the incremental hole drilling method (IHMD), X-ray diffraction (XRD) and the splitting method (SM). Knowing the residual stress state in the ring specimen, it is possible to assess their impact on fracture toughness measured on the corresponding PRNB specimen(s).

An Inset CT Specimen for Evaluating Fracture in Small Samples of Material

Science.gov (United States)

Yahyazadehfar, M.; Nazari, A.; Kruzic, J.J.; Quinn, G.D.; Arola, D.

2013-01-01

In evaluations on the fracture behavior of hard tissues and many biomaterials, the volume of material available to study is not always sufficient to apply a standard method of practice. In the present study an inset Compact Tension (inset CT) specimen is described, which uses a small cube of material (approximately 2×2×2 mm3) that is molded within a secondary material to form the compact tension geometry. A generalized equation describing the Mode I stress intensity was developed for the specimen using the solutions from a finite element model that was defined over permissible crack lengths, variations in specimen geometry, and a range in elastic properties of the inset and mold materials. A validation of the generalized equation was performed using estimates for the fracture toughness of a commercial dental composite via the “inset CT” specimen and the standard geometry defined by ASTM E399. Results showed that the average fracture toughness obtained from the new specimen (1.23 ± 0.02 MPa•m0.5) was within 2% of that from the standard. Applications of the inset CT specimen are presented for experimental evaluations on the crack growth resistance of dental enamel and root dentin, including their fracture resistance curves. Potential errors in adopting this specimen are then discussed, including the effects of debonding between the inset and molding material on the estimated stress intensity distribution. Results of the investigation show that the inset CT specimen offers a viable approach for studying the fracture behavior of small volumes of structural materials. PMID:24268892

Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting

Directory of Open Access Journals (Sweden)

Daniela Maneg

2016-01-01

Full Text Available Infective endocarditis (IE is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5% with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke’s diagnostic classification scheme.

Detection of Mycobacterium leprae nasal carriers in populations for which leprosy is endemic

NARCIS (Netherlands)

Klatser, P. R.; van Beers, S.; Madjid, B.; Day, R.; de Wit, M. Y.

1993-01-01

In order to better understand the role of Mycobacterium leprae nasal carriage in the maintenance of infection reservoirs and transmission of leprosy, we applied a polymerase chain reaction (PCR) that detected a 531-bp fragment of the pra gene of M. leprae on nasal swab specimens collected through a

Thinning of specimens for examination under the electron microscope

International Nuclear Information System (INIS)

Franks, J.

1982-01-01

Heretofore specimens have been thinned to penetration for examination by electron microscopy techniques, by ion erosion techniques. A more rapid technique is disclosed employing a beam or beams comprised solely of neutral particles. In tests carried out using this technique the sputtering rate from a sample specimen has been shown to be several percentages greater using a neutral source than from an ion source with the same flux density. (author)