WorldWideScience

Sample records for swab specimen transported

  1. Bacterial isolates from swab specimens and their susceptibilities to ...

    African Journals Online (AJOL)

    Ciprofloxacin and ofloxacin showed uniform activities against Proteus spp, which showed partial resistance to all agents except sparfloxacin. Multi-drugs resistances are high with all organisms. Many pathogens cause infections in swab sites. The knowledge of causative organisms and their sensitivities are important since ...

  2. A Comparison of Dacron versus Flocked Nylon Swabs for Anal Cytology Specimen Collection

    Science.gov (United States)

    Gage, Julia C.; Ghosh, Arpita; Borgonovo, Sylvia; Follansbee, Stephen; Wentzensen, Nicolas; Gravitt, Patti E.; Grabe, Niels; Lahrmann, Bernd; Castle, Philip E.

    2011-01-01

    Objectives We compared the performance of commonly used Dacron versus flocked nylon swabs for anal cytology. Study Design From 23 HIV-positive men screened at Kaiser Permanente San Francisco (San Francisco, Calif., USA), 2 anal specimens were collected, 1 with each swab in random order, and placed into liquid cytology medium. Specimens were tested for cellularity by quantifying a genomic DNA (erv-3). The number of cells was assessed from prepared slides by automated image analysis. Performance was compared between swabs using 2-sample t tests and standard crossover trial analysis methods accounting for period effect. Results Flocked swabs collected slightly more erv-3 cells than Dacron for the first sample although not significantly (p = 0.18) and a similar number of erv-3 cells for the second sample (p = 0.85). Flocked swabs collected slightly more cells per slide than the Dacron swabs at both time periods although this was only significant in the second time period (p = 0.42 and 0.03 for first and second periods, respectively). In crossover trial analysis, flocked swabs outperformed Dacron for cell count per slide based on slide imaging (p = 0.03), but Dacron and flocked swabs performed similarly based on erv-3 quantification (p = 0.14). Conclusions Further studies should determine whether flocked swabs increase the representation of diagnostically important cells compared to Dacron. PMID:21791907

  3. Mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swab specimens in Brazil

    OpenAIRE

    dos Santos, Danielle Caldeira Martins; da Costa, Thaina Miranda; Rabello, Renata Fernandes; Alves, F?bio Aguiar; de Mondino, Silvia Susana Bona

    2015-01-01

    The isolation of mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swabs is reported. Among the 59 isolates, 9 (15%) isolates were mannitol-negative; all of these isolates were categorized as staphylococcal cassette chromosome mec (SCCmec) type IVa. This report emphasizes that mannitol fermentation on mannitol salt agar should not be used as the sole criterion when screening nasal swab specimens for S. aureus.

  4. Mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swab specimens in Brazil

    Directory of Open Access Journals (Sweden)

    Danielle Caldeira Martins dos Santos

    2015-06-01

    Full Text Available The isolation of mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swabs is reported. Among the 59 isolates, 9 (15% isolates were mannitol-negative; all of these isolates were categorized as staphylococcal cassette chromosome mec (SCCmec type IVa. This report emphasizes that mannitol fermentation on mannitol salt agar should not be used as the sole criterion when screening nasal swab specimens for S. aureus.

  5. Mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swab specimens in Brazil.

    Science.gov (United States)

    dos Santos, Danielle Caldeira Martins; da Costa, Thaina Miranda; Rabello, Renata Fernandes; Alves, Fábio Aguiar; de Mondino, Silvia Susana Bona

    2015-06-01

    The isolation of mannitol-negative methicillin-resistant Staphylococcus aureus from nasal swabs is reported. Among the 59 isolates, 9 (15%) isolates were mannitol-negative; all of these isolates were categorized as staphylococcal cassette chromosome mec (SCCmec) type IVa. This report emphasizes that mannitol fermentation on mannitol salt agar should not be used as the sole criterion when screening nasal swab specimens for S. aureus.

  6. Comparison of DRY and WET vaginal swabs with cervical specimens in Roche Cobas 4800 HPV and Abbott RealTime High Risk HPV tests.

    Science.gov (United States)

    Jun, Jae Kwan; Lim, Myong Cheol; Hwang, Sang-Hyun; Shin, Hye Young; Hwang, Na Rae; Kim, Yeon-Jin; Yoo, Chong Woo; Lee, Dong Ock; Joo, Jungnam; Park, Sang-Yoon; Lee, Do-Hoon

    2016-06-01

    Self-collected vaginal swab samples have been proposed as an alternative specimen collection method for human papillomavirus (HPV) DNA detection. Two vaginal swabs (a cone-shaped flocked swab (DRY) and a L-shape FLOQSwab with 2mL eNAT transport medium (WET)) were compared to standard cervical samples for HPV DNA testing. Additionally, they were also compared by using Roche Cobas 4800 HPV (Roche_HPV) and Abbott Real-time High Risk HPV (Abbott_HPV) tests. Ninety-six women were prospectively enrolled from the National Cancer Center in Korea between June and August 2015. WET and DRY vaginal swabs and cervical specimens were collected. Roche_HPV and Abbott_HPV tests were performed. The Roche_HPV test on cervical specimens was used as reference. The observed agreements (kappa) of Roche_HPV and Abbott_HPV between WET and DRY swabs were 89.6% (0.790, 95% confidence interval (95% CI): 0.667-0.913) and 91.7% (0.833, 95%CI: 0.723-0.943), respectively. No statistical difference was observed between WET and DRY swabs (p>0.05 for all comparisons). For HPV16/18, the sensitivity/specificity of Roche_HPV on the DRY and WET samples presented 93.8%/96.3% and 87.5%/97.5%, respectively. For other High Risk HPV (hrHPV), the sensitivity/specificity of Roche_HPV on the DRY and WET swabs presented 91.9%/91.5% and 97.3%/98.3, respectively. The sensitivity/specificity of the Abbott_HPV on the DRY and WET swabs were 93.8%/98.8%, 87.5%/98.8% for HPV16/18, and 91.9%/93.2%, 100.0%/93.2% for other hrHPV, respectively. HPV tests performed similarly when using vaginal DRY and WET swab samples. Using DRY and WET swabs to collect vaginal specimens could be an alternative to collecting cervical samples for HPV DNA testing. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Diagnostic performance of rectal swab versus bulk stool specimens for the detection of rotavirus and norovirus: Implications for outbreak investigations✩

    Science.gov (United States)

    Arvelo, Wences; Hall, Aron J.; Estevez, Alejandra; Lopez, Beatriz; Gregoricus, Nicole; Vinjé, Jan; Gentsch, Jon R.; Parashar, Umesh; Lindblade, Kim A.

    2015-01-01

    Background In January of 2008, during the peak of the rotavirus season in Guatemala, a gastroenteritis outbreak with high mortality among infants was reported in Guatemala. Despite extensive efforts, the investigation was limited by the lack of bulk stool specimens collected, particularly from the more severely dehydrated or deceased children. Objectives We evaluated the diagnostic performance of rectal swab specimens compared with bulk stool for the detection of rotavirus and norovirus. Study design Patients with diarrhea (≥3 loose stools in 24 h) were enrolled through an ongoing surveillance system in Guatemala. From January through March 2009, we attempted to enroll 100 patients <5years old captured by the diarrhea surveillance, and collected paired bulk stool and rectal swabs specimens from them. Specimens were tested for norovirus using real-time reverse transcription-polymerase chain reaction and for rotavirus via enzyme immunoassay. Results We enrolled 102 patients with paired specimens; 91% of 100 paired specimens tested for rotavirus yielded concordant results positive for rotavirus with a negativity rate of 83%. Among 100 paired specimens tested for norovirus, 86% were concordant norovirus detection and the negativity rate was 85%. The diagnostic performance for rotavirus and norovirus detection did not differ significantly between the two specimen types. Conclusions Testing of properly collected fecal specimens using rectal swabs may be a viable alternative to bulk stool for detection of rotavirus and norovirus, particularly during outbreaks where collection of bulk stool may be difficult. PMID:24139675

  8. Vaginal Self-Swab Specimen Collection in a Home-Based Survey of Older Women: Methods and Applications

    Science.gov (United States)

    Hoffmann, Joscelyn N.; Lundeen, Katie; Jaszczak, Angela; McClintock, Martha K.; Jordan, Jeanne A.

    2009-01-01

    Objectives To describe the methods used for, cooperation with, assays conducted on, and applications of vaginal specimens collected by older women in their homes. Methods Community-residing women (N = 1,550), ages 57–85 years, participated in a nationally representative probability survey. Vaginal self-swab specimen collection and in-home interviews were conducted between 2005 and 2006. Specimens were analyzed for bacterial vaginosis (BV), vaginal candidiasis (VC), high-risk human papillomavirus (HR-HPV), and cytological characteristics. Field methods, consent procedures, the swab protocol, laboratory procedures, and results reporting are described. Results One thousand twenty-eight respondents (67.5% weighted) agreed to provide a vaginal specimen; 99.1% were successful. The specimen adequacy rates were BV and VC, 94.1%; HR-HPV, 99.7%; and cytology, 85.5%. The most common recorded reason for nonparticipation was a physical or health problem (38% of nonresponders). Responders were significantly more likely than nonresponders to be younger and more educated, and were more likely to report a recent pelvic examination, menopausal hormone use, and recent sexual activity. Discussion Collection of vaginal self-swab specimens from older women in a population-based study is feasible and provides novel data on microenvironmental characteristics of the female genital tract relevant to analyses of gynecologic health, sexual activity and problems, and immune and inflammatory function. PMID:19204072

  9. Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR.

    Science.gov (United States)

    Kim, Young-Gon; Yun, Seung Gyu; Kim, Min Young; Park, Kwisung; Cho, Chi Hyun; Yoon, Soo Young; Nam, Myung Hyun; Lee, Chang Kyu; Cho, Yun-Jung; Lim, Chae Seung

    2017-01-01

    Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies. Copyright © 2016 American Society for Microbiology.

  10. UriSwab: an effective transport medium for nucleic acid detection of Chlamydia trachomatis, Mycoplasma genitalium and Neisseria gonorrhoeae.

    Science.gov (United States)

    Costa, Anna-Maria G; Garland, Suzanne M; Guy, Rebecca; Wand, Handan; Tabrizi, Sepehr N

    2017-11-01

    Background Patient self-sampling allows for remote collection and return to clinic or laboratory by post. Urine samples, although convenient, are challenging to post. This study evaluated UriSwab (Copan, Brescia, Italy) as a collection and transport vessel for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Mycoplasma genitalium (MG) detection by polymerase chain reaction, compared with flocked swab and neat urine. Five replicates of each specimen type were prepared from previously characterised urine samples (n=330), stored at room temperature (RT) or 37°C, then extracted on day 1, 3, 7, 10 and 16 (VERSANT kPCR Sample Prep System, Siemens, Munich, Germany). Crossing thresholds (Cq) from CT and NG detection (VERSANT CT/GC DNA 1.0 assay kit, Siemens) and MG detection (real-time polymerase chain reaction assay) were compared using logistic regression, stratified by sample type, temperature and analyte. Mixed-model statistical techniques were used to assess correlation between repeated observations. UriSwab showed an increasing trend in Cq values at RT and 37°C for CT and NG, and RT for MG (all P<0.01). UriSwab was not statistically significantly different to neat urine, except CT at RT (0.83, 95% confidence interval: 0.51-1.15). Flocked swab similarly showed increasing Cq values at 37°C for CT, a significant decreasing trend at RT for MG and increasing trend at 37°C for MG. Flocked swab was not statistically significantly different from neat urine at RT and 37°C for CT and MG. UriSwab allows transport of urine for CT, NG and MG detection regardless of storage time or temperature, suggesting that CT and NG are stable for up to 16 days and MG up to 10 days.

  11. A Study of Isolates from Female Genital Swab Specimens in a ...

    African Journals Online (AJOL)

    To detect some common microbial agents of vaginal discharge in order to improve the current syndromic management of abnormal vaginal discharge. A prospective study of female genital swabs collected from Obstetrics and Gynecology units of Aminu Kano Teaching Hospital, Kano Nigeria and analyzed for microscopy, ...

  12. Improved diagnosis of Trichomonas vaginalis infection by PCR using vaginal swabs and urine specimens compared to diagnosis by wet mount microscopy, culture, and fluorescent staining

    NARCIS (Netherlands)

    C. van der Schee (Cindy); A.F. van Belkum (Alex); L. Zwijgers (Lisette); E. van der Brugge; E.L. O'Neill; A. Luijendijk (Ad); T. van Rijsoort-Vos; W.I. van der Meijden (Willem); J.F. Sluiters (Hans); H.A. Verbrugh (Henri)

    1999-01-01

    textabstractFour vaginal cotton swab specimens were obtained from each of 804 women visiting the outpatient sexually transmitted disease clinic of the Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands, for validation of various forms of Trichomonas

  13. Clinical performance of the Solana® Point-of-Care Trichomonas Assay from clinician-collected vaginal swabs and urine specimens from symptomatic and asymptomatic women.

    Science.gov (United States)

    Gaydos, C A; Schwebke, J; Dombrowski, J; Marrazzo, J; Coleman, J; Silver, B; Barnes, M; Crane, L; Fine, P

    2017-03-01

    Solana® (Quidel) is a new rapid (Trichomonas vaginalis (TV) DNA. The assay has two steps: 1) specimen preparation, and 2) amplification and detection using isothermal Helicase-Dependent Amplification (HDA). The objective was to demonstrate the performance of Solana for vaginal swabs and female urines based on comparison to wet mount and TV culture. Performance was also compared to the Aptima-TV assay. Urine and four clinician-collected vaginal swabs were collected. The first two were used for FDA composite reference (wet mount; InPouch TV Culture). The third swab was used for Solana. Sensitivity/specificity were based on the reference method. A specimen was considered positive if either test was positive. The fourth swab was for Aptima-TV. Vaginal swabs and urines were obtained from 501 asymptomatic and 543 symptomatic women. Prevalence of TV by was 11.5%. For swabs, Solana® demonstrated high sensitivity and specificity from asymptomatic (100%/98.9%) and symptomatic (98.6%/98.5%) women, as well as for urines from asymptomatic (98.0%/98.4%) and symptomatic (92.9%/97.9%) women, compared to the reference method. Compared to Aptima-TV, the sensitivity/specificity was 89.7%/99.0% for swabs and 100%/98.9% for urines. The Solana® assay performed well compared to the reference assays.

  14. Comparison of sputum and nasopharyngeal swab specimens for molecular diagnosis of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila.

    Science.gov (United States)

    Cho, Min-Chul; Kim, Hyewon; An, Dongheui; Lee, Miyoung; Noh, Shin-Ae; Kim, Mi-Na; Chong, Young Pil; Woo, Jun Hee

    2012-03-01

    Differentiation of atypical pathogens is important for community-acquired pneumonia (CAP). In this study, we compared sputum and nasopharyngeal swabs (NPS) for use in detection of Mycoplasma pneumoniae (MP), Chlamydophila pneumoniae (CP), and Legionella pneumophila (LP), using Seeplex PneumoBacter ACE Detection Assay (PneumoBacter; Seegene). Sputum and NPS specimens were collected from patients in 15 hospitals. DNA was extracted from sputum using QIAamp DNA Stool Mini Kit (Qiagen) and from NPS using easyMAG (bioMérieux). Both types of specimens were evaluated by multiplex PCR using PneumoBacter. To determine the diagnostic performance of this assay, sputum samples were also tested using BD ProbeTec ET Atypical Pneumonia Assay (APA; Becton Dickinson). Among 217 sputum and NPS, 20 (9.2%), 2 (0.9%), and 0 sputum were positive for MP, LP, and CP, respectively, whereas 8 (3.7%) NPS were positive for MP. The sputum APA test yielded 186, 206, and 204 interpretable results for MP, LP, and CP, respectively. Of these, 21 (11.3%) were positive for MP, 2 (1.0%) were positive for LP, and 0 samples were positive for CP. Compared to APA, the sensitivity and specificity of the sputum assay for MP were 95.2% and 100.0%, respectively, whereas for the NPS assay, these were 38.1% and 93.9%. Sputum testing was more sensitive than NPS testing (P=0.002). For LP and CP diagnosis, PneumoBacter and APA tests agreed 100%. Specimen type is crucial and sputum is preferred over NPS for simultaneous detection of MP, LP, and CP using multiplex PCR in CAP.

  15. Evaluation of Liquid-Based Swab Transport Systems against the New Approved CLSI M40-A2 Standard.

    Science.gov (United States)

    Gizzie, Nina; Adukwu, Emmanuel

    2016-04-01

    Following revised information pertaining to newer swab types and testing protocols in the new CLSI M40-A2 standard, we evaluated three liquid swab transport systems for the recovery of aerobic, anaerobic, and fastidious organisms at room temperature and at 4°C. All tested liquid swab transport systems were fully compliant with the M40-A2 standard, with acceptable performance at both temperatures after the full specified holding period, using both qualitative (roll-plate) and quantitative (swab elution) methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  16. Microbial investigations in throat swab and tracheal aspirate specimens are beneficial to predict the corresponding endotracheal tube biofilm flora among intubated neonates with ventilator-associated pneumonia.

    Science.gov (United States)

    Pan, Yun; Du, Lizhong; Ai, Qing; Song, Sijie; Tang, Xiaoli; Zhu, Danping; Yu, Jialin

    2017-08-01

    Ventilator-associated pneumonia (VAP) is a common nosocomial infection in neonatal intensive care units with high morbidity and mortality. Bacterial biofilm in the endotracheal tube (ET) provides a notable and persistent source of pathogens that may cause VAP, and thus is important for VAP detection. However, during intubation microbial investigations in ET, samples are unavailable due to the infeasibility of collecting ET samples during intubation of neonates. It is therefore of great importance to find alternative sources of samples that can help identify the ET biofilm flora. In the present study, the microbial signatures of throat swabs and tracheal aspirates were compared with ET biofilm samples from VAP neonates using 16S ribosomal RNA gene polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. Sequences were assigned to phylogenetic species using BLAST. Microbial diversity and richness among the three types of specimens were compared based on their DGGE fingerprints, and taxonomic characteristics based on the BLAST results. The microbial richness and diversity of ET biofilms were similar to tracheal aspirate yet significantly different from throat swab samples (P<0.05). Compared with ET biofilms, the overall constituent ratio of microflora was significantly different in throat swab and tracheal aspirate samples (P<0.05). However tracheal aspirate samples were useful for predicting Staphylococcus sp. in ET biofilms with a sensitivity of 85.7% and a specificity of 83.3%. The sensitivity for the combination of tracheal aspirate and throat swab samples to detect Staphylococcus sp. in ET biofilms was 100%. The detection of Pseudomonas sp. in throat swabs assisted its identification in ET biofilms (sensitivity 33.3% and specificity 100%). The results of the present study suggest that microbial investigations in throat swab and tracheal aspirate samples are beneficial for identifying the ET biofilm flora. There may

  17. Comparison of nasopharyngeal aspirate and nasal swab specimens for detection of respiratory syncytial virus in different settings in a developing country

    DEFF Research Database (Denmark)

    Stensballe, L G; Trautner, S; Kofoed, P-E

    2002-01-01

    OBJECTIVE: To compare detection of respiratory syncytial virus (RSV) for diagnostic purposes using nasopharyngeal aspirate (NPA) and nasal swabs (NS) in different clinical settings in a community study in Guinea-Bissau. METHOD: During 1996-98 paired specimens were obtained from 635 children under 5...... years of age (median: 274 days; interquartile range: 144-453 days) with symptoms of lower respiratory infections (LRI). The specimens were analysed by an enzyme-linked immunosorbent assay for RSV antigen in Guinea-Bissau and re-analysed in Denmark using the same assay. The gold standard for RSV antigen...

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

    Directory of Open Access Journals (Sweden)

    Suzanne L Hennigan

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

  19. Comparison of urine with urethral swabs for the detection of ...

    African Journals Online (AJOL)

    Although cell culture has been regarded as the 'gold standard' for C. ... immunofluorescence as a 'gold standard', because of loss of chlamydial ... Specimens for EIA were collected with. Dacron swabs on aluminium shafts with prescored plastic handles. Swabs were immersed and broken off in 1 ml EIA transport media ...

  20. Comparison of Easy-Flow Copan Liquid Stuart's and Starplex Swab transport systems for recovery of fastidious aerobic bacteria.

    Science.gov (United States)

    Drake, Cheryl; Barenfanger, Joan; Lawhorn, Jerry; Verhulst, Steven

    2005-03-01

    Because samples are frequently submitted on swabs from distant sites, viability of the organism must be maintained. We compared two transport systems, a new Copan Liquid Stuart's swab with an Easy-Flow swab applicator and the Starplex Liquid Stuart's swab. The purpose of the study was to assess the release and/or recovery of organisms from the Copan system compared to that from Starplex. Triplicate swabs were seeded with 3 dilutions of Neisseria gonorrhoeae, Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae. Although the amount of the initial inoculum was the same for both transport systems, recovery by the roll-plate method at time zero was consistently increased with the Copan system (31 to 87% higher). This is the most important finding in this study. With N. gonorrhoeae, subsequent recoveries were similar for Copan and Starplex but poor for both systems. With N. meningitidis and Haemophilus, higher levels of recovery were clearly obtained with Copan (P < 0.05 to P < 0.001). With Streptococcus, subsequent recoveries for Copan and Starplex were mixed. In conclusion, Copan generally demonstrated better recovery of organisms compared to Starplex even (and especially) at time zero.

  1. Evaluation of the efficacy of real-time polymerase chain reaction for the routine early detection of Pseudomonas aeruginosa in cystic fibrosis sputum and throat swab specimens.

    LENUS (Irish Health Repository)

    Logan, Catriona

    2012-02-01

    A longitudinal study of 2099 sputa and throat swabs received from 183 pediatric cystic fibrosis patients over a 29-month period was used to evaluate the efficacy of real-time polymerase chain reaction (PCR) for the early detection of Pseudomonas aeruginosa as compared to microbiologic culture. Real-time PCR resulted in an increased number of specimens identified as P. aeruginosa positive. The sensitivity of culture was 82% (373\\/453) and of PCR was 93% (420\\/453) when considering both positive culture and PCR results as true positives. Of the 80 specimens identified as PCR positive\\/culture negative for P. aeruginosa, the subsequent patient sample in 32.5% (26\\/80) of specimens concerned was identified as P. aeruginosa culture positive, suggesting that PCR has the potential to detect P. aeruginosa earlier than the microbiologic culture. Real-time PCR analysis found no evidence of the Liverpool and Manchester epidemic P. aeruginosa strains in the cohort examined. The findings of this study highlight the importance of specimen collection protocols to ensure that adequate samples are received at the laboratory for testing, thereby minimizing the potential for reporting of false-negative P. aeruginosa culture results.

  2. Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

    Science.gov (United States)

    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.

  3. 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.

    Science.gov (United States)

    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.

  4. Novel real-time PCR assays using TaqMan minor groove binder probes for identification of fecal carriage of Streptococcus bovis/Streptococcus equinus complex from rectal swab specimens.

    Science.gov (United States)

    Lopes, Paulo Guilherme Markus; Cantarelli, Vlademir Vicente; Agnes, Grasiela; Costabeber, Ane Micheli; d'Azevedo, Pedro Alves

    2014-03-01

    Real-time PCR based on the recN and gyrB genes was developed to detect four Streptococcus bovis/Streptococcus equinus complex (SBEC) subspecies from rectal swab specimens. The overall prevalence was 35.2%: Streptococcus gallolyticus subsp. gallolyticus (11.1%), S. gallolyticus subsp. pasteurianus (13%), Streptococcus infantarius subsp. coli (20.4%), and S. infantarius subsp. infantarius (11.1%). To conclude, these real-time PCR assays provide a reliable molecular method to detect SBEC pathogenic subspecies from rectal swab specimens.

  5. 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...

  6. Preservation of tissue specimens during transport to mycobacteriology laboratories.

    Science.gov (United States)

    Richards, W D; Wright, H S

    1983-01-01

    Chloramine-T and sodium borate solutions were evaluated for their effectiveness in preserving Mycobacterium bovis and controlling the growth of non-mycobacterial contaminants on tissue specimens during transport to laboratories. The number of culturable M. bovis cells in suspension was reduced by 5.1 log10 upon exposure to chloramine-T solution and by less than 1 log10 upon exposure to sodium borate solution for 7 days. Reinoculation of laboratory media (because of overgrowth by non-mycobacterial contaminants) was required for 52.6% of 190 routine bovine tissue specimens shipped refrigerated in chloramine-T solution and for 6.1% of 520 specimens shipped unrefrigerated in sodium borate solution. M. bovis was isolated from bovine tissue stored in sodium borate solution at 23 degrees C for 17 weeks and at 4 degrees C for 25 weeks. Unrefrigerated sodium borate solution has been used successfully to ship tissue specimens to our laboratory for the past 11 years. PMID:6341397

  7. Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia.

    Science.gov (United States)

    O'Grady, Kerry-Ann F; Torzillo, Paul J; Rockett, Rebecca J; Whiley, David M; Nissen, Michael D; Sloots, Theo P; Lambert, Stephen B

    2011-06-01

    Surveillance programs and research for acute respiratory infections in remote Aboriginal communities are complicated by difficulties in the storage and transport of frozen samples to urban laboratories for testing. This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. We sampled every individual who presented to a remote Aboriginal community clinic in a non-epidemic respiratory season. Two anterior nasal swabs were collected from each participant. The left nare specimen was mailed to the laboratory via routine postal services. The right nare specimen was transported frozen. Testing for 16 viruses was undertaken using real-time multiplex PCR. A total of 140 participants were enrolled who contributed 150 study visits. Respiratory illnesses accounted for 10% of the reasons for presentation. Sixty-one viruses were identified in 50 (33.3%) presentations for 40 (28.6%) individuals; bocavirus and rhinovirus were the most common viruses identified (14.0% and 12.6% of episodes respectively). The sensitivity for any virus detected in mailed specimens was 67.2% (95%CI 55.4, 78.9) compared to 65.6% (95%CI 53.7, 77.5) for frozen specimens. The mailing of unfrozen nasal specimens from remote communities does not compromise the viability of the specimen for viral studies. © 2011 Blackwell Publishing Ltd.

  8. Probability of detecting influenza A virus subtypes H1N1 and H3N2 in individual pig nasal swabs and pen-based oral fluid specimens over time.

    Science.gov (United States)

    Goodell, Christa K; Prickett, John; Kittawornrat, Apisit; Zhou, Fanghong; Rauh, Rolf; Nelson, William; O'Connell, Cate; Burrell, Angela; Wang, Chong; Yoon, Kyoung-Jin; Zimmerman, Jeffrey J

    2013-10-25

    The probability of detecting influenza A virus (IAV) by virus isolation (VI), point-of-care (POC) antigen detection, and real-time reverse-transcription polymerase chain reaction (rRT-PCR) was estimated for pen-based oral fluid (OF) and individual pig nasal swab (NS) specimens. Piglets (n=82) were isolated for 30 days and confirmed negative for porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and IAV infections. A subset (n=28) was vaccinated on day post inoculation (DPI) -42 and -21 with a commercial multivalent vaccine. On DPI 0, pigs were intratracheally inoculated with contemporary isolates of H1N1 (n=35) or H3N2 (n=35) or served as negative controls (n=12). OF (n=370) was collected DPI 0-16 and NS (n=924) DPI 0-6, 8, 10, 12, 14, 16. The association between IAV detection and variables of interest (specimen, virus subtype, assay, vaccination status, and DPI) was analyzed by mixed-effect repeated measures logistic regression and the results used to calculate the probability (pˆ) of detecting IAV in OF and NS over DPI by assay. Vaccination (p-value<0.0001), DPI (p-value<0.0001), and specimen-assay interaction (p-value<0.0001) were significant to IAV detection, but virus subtype was not (p-value=0.89). Vaccination and/or increasing DPI reduced pˆ for all assays. VI was more successful using NS than OF, but both VI and POC were generally unsuccessful after DPI 6. Overall, rRT-PCR on OF specimens provided the highest pˆ for the most DPIs, yet significantly different results were observed between the two laboratories independently performing rRT-PCR testing. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. [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.

  10. Stability Studies on Dry Swabs and Wet Mailed Swabs for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Aptima Assays.

    Science.gov (United States)

    Moncada, Jeanne; Clark, Carey B; Holden, Jeffrey; Hook, Edward W; Gaydos, Charlotte A; Schachter, Julius

    2017-03-01

    The Aptima Combo 2 (AC2) and Aptima CT (ACT) (Hologic Inc., San Diego, CA) are nucleic acid amplification tests (NAATs) that detect Chlamydia trachomatis AC2 also detects Neisseria gonorrhoeae Storage and temperature conditions may impact the utility of NAATs in some settings and screening programs. We evaluated specimen stability for use beyond the Aptima package insert specifications for temperature and duration of storage (between 2°C and 30°C and 60 days, respectively) in two studies: (i) dry C. trachomatis-seeded swabs were used with ACT after storage at 4°C, 23°C, or 36°C for up to 84 days and (ii) swabs seeded with C. trachomatis and N. gonorrhoeae and then placed in transport medium were tested with AC2, after being mailed via the U.S. Postal Service to three different sites. Prolonged storage of samples had no effect, and samples stored at 4°C, 23°C, and 36°C for up to 84 days yielded comparable ACT positivities, although there was a drop in signal intensity for virtually all specimens under all storage/shipping conditions after day 21. In the mailing study, 80%, 52% and 29% of seeded swabs were exposed to temperatures of >30°C during three rounds in transit, and 2% reached temperatures of >40°C. No evidence of signal degradation in the AC2 assay for detection of C. trachomatis or N. gonorrhoeae was observed, although some mailed swabs took more than 5 weeks to reach the laboratory site. These two studies support the potential use of swabs at temperatures above 36°C and storage beyond 60 days and provide confidence regarding this commercially available NAAT for testing of specimens after mailing. Copyright © 2017 American Society for Microbiology.

  11. Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs.

    Science.gov (United States)

    Hernes, S S; Quarsten, H; Hagen, E; Lyngroth, A L; Pripp, A H; Bjorvatn, B; Bakke, P S

    2011-02-01

    The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Samples were obtained from patients 60 years of age or above who were newly admitted to Sorlandet Hospital Arendal, Norway. The patients were interviewed for current symptoms of a respiratory tract infection. Using rayon swabs and nylon flocked swabs, comparable sets of mucosal samples were harvested from the nasopharynx and the oropharynx. The samples were analysed using real-time polymerase chain reaction (PCR) methods. A total of 223 patients (mean age 74.9 years, standard deviation [SD] 9.0 years) were swabbed and a virus was recovered from 11% of the symptomatic patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3-17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Also, regardless of the type of swab, a calculated 19 times higher viral load was found in the samples from the nasopharynx as compared to the oropharynx (95% CI 5.4-67.4, p Nylon flocked swabs appear to be more efficient than rayon swabs.

  12. 21 CFR 866.2900 - Microbiological specimen collection and transport device.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Comparison of three methods for the recovery of skin pathogens from impetigo swabs collected in a remote community of Northern Territory, Australia.

    Science.gov (United States)

    Bowen, Asha C; Tong, Steven Y C; Chatfield, Mark D; Andrews, Ross M; Carapetis, Jonathan R

    2013-06-01

    Impetigo is a common infection in children living in remote areas. Immediate plating of impetigo swabs is the gold standard for bacterial recovery but is rarely feasible in remote regions. Bacterial culture increases our understanding of antibiotic resistance and strain diversity, which guides treatment protocols and epidemiological monitoring. We investigated three practical alternatives for recovering Streptococcus pyogenes and Staphylococcus aureus from transported swabs: dry swabs transported at 4°C with desiccant and plated within 48 h; swabs inoculated into skim milk tryptone glucose glycerol broth (STGGB), transported at 4°C, stored at -70°C and plated within 61 days; and ESwabs inoculated into Amies broth, transported at 4°C and plated within 48 h. Detection of Strep. pyogenes and Staph. aureus from simultaneously collected swabs was compared for the dry vs STGGB (36 sores) and the STGGB vs Amies (39 sores) methods. Swabs were collected from 43 children (75 sores sampled) in a remote community of Northern Territory, Australia in November 2011. The children had impetigo and were participating in the Skin Sore Trial [Australian Clinical Trials Registry ACTRN12609000858291]. Recovery of Strep. pyogenes for dry vs STGGB was 72% (26/36) and 92% (33/36) and for STGGB vs Amies was 92% (36/39) for both methods. Staphylococcus aureus recovery for dry vs STGGB was 69% (25/36) and 72% 26/36) and for STGGB vs Amies was 74% (29/39) and 85% (33/39). STGGB and Amies media provided higher recovery of Strep. pyogenes than dry swabs. These results and the opportunity to batch and store specimens for molecular studies support the use of STGGB transport media for future impetigo research.

  15. Bacteriological pattern of wound swab isolates in patients with ...

    African Journals Online (AJOL)

    PURPOSE: To determine the pattern of bacterial pathogens and their antibiotic sensitivity profile in patients with infected chronic leg ulceration. METHODS: Sixty swab specimens obtained from chronic leg ulcer (CLU) patients were cultured aerobically and the antibiotic sensitivity pattern of the recovered organisms ...

  16. Swab and aspiration specimen collection methods and antibiogram ...

    African Journals Online (AJOL)

    2) RSS feeds. Really Simple Syndication (RSS) helps you to get alerts on new publication right on your desktop without going to the journal's website. You need a software (e.g. RSSReader, Feed Demon, FeedReader, My Yahoo!, NewsGator and. NewzCrawler) to get advantage of this tool. RSS feeds can also be read ...

  17. A Comparison of Tissue versus Swab Culturing of Infected Diabetic Foot Wounds

    Directory of Open Access Journals (Sweden)

    Ying Huang

    2016-01-01

    Full Text Available Objective. To compare the efficacy of swabbing versus tissue biopsy for microbiological diagnosis of diabetic foot infection. Methods. This was a prospective trial. Fifty-six patients with diabetic foot infection were divided into the following 3 groups according to the PEDIS grading system: grade 2 (n=10, grade 3 (n=29, and grade 4 (n=17. Two specimens were collected from each wound for microbial culturing after debridement, including a superficial swab and a deep tissue punch biopsy specimen. Results. Swab culturing identified all of the microorganisms isolated from the corresponding deep tissue specimens in 9/10 of grade 2 wounds (90.0%, and this proportion decreased to 12/29 (41.4% and 7/17 (41.2% for grades 3 and 4 wounds, respectively (p=0.02. Moreover, the sensitivity for identifying Gram-negative bacteria, such as E. coli and Citrobacter, by swabbing was low (33.3%. In addition, some Gram-negative bacteria, such as Serratia and Ralstonia pickettii, were isolated from deep tissues but not from swabs. Conclusions. Swab culturing may be reliable for identification of pathogens in diabetic foot wounds classified as grade 2. However, it is advisable to culture deep tissue specimens for wounds of grade ≥3 because swab culturing is associated with a high risk of missing pathogens, especially Gram-negative bacteria.

  18. Rectal swabs for analysis of the intestinal microbiota.

    Directory of Open Access Journals (Sweden)

    Andries E Budding

    Full Text Available The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

  19. Rectal swabs for analysis of the intestinal microbiota.

    Science.gov (United States)

    Budding, Andries E; Grasman, Matthijs E; Eck, Anat; Bogaards, Johannes A; Vandenbroucke-Grauls, Christina M J E; van Bodegraven, Adriaan A; Savelkoul, Paul H M

    2014-01-01

    The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

  20. 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.

  1. 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.

  2. Specimen Collection and Submission Manual

    Science.gov (United States)

    2016-06-01

    local, approved medical treatment facility collection procedures. Superficial wounds and abscesses Sterile swab Follow local, approved medical...Tests May Include: West Nile virus (WNV), Eastern equine encephalitis virus, Venezuelan equine encephalitis virus, yellow fever virus, dengue virus... Wound Botulism Acceptable Specimens Required Volume/Comments Toxin Assay (T) or Culture (C) Performed Serum (priority sample type) 5 ml (less

  3. Accuracy of self-collected vaginal dry swabs using the Xpert human papillomavirus assay.

    Directory of Open Access Journals (Sweden)

    Rosa Catarino

    Full Text Available Polymerase chain reaction-based Xpert human papillomavirus (HPV assay is a rapid test that detects high-risk HPV (hrHPV infection. This point-of-care test is usually performed by collecting a cervical specimen in a vial of PreservCyt® transport medium. We compared HPV test positivity and accuracy between self-collected sample with a dry swab (s-DRY versus physician-collected cervical sampling using a broom like brush and immediate immersion in PreservCyt (dr-WET.In this cross-sectional study, we recruited 150 women ≥ 18 years old attending the colposcopy clinic in the University Hospital of Geneva. Each participant first self-collected a vaginal sample using a dry swab and then the physician collected a cervical specimen in PreservCyt. HPV analysis was performed with Xpert. Part of the PreservCyt-collected sample was used for hrHPV detection with the cobas® HPV test. HPV test positivity and performance of the two collection methods was compared.HPV positivity was 49.1% for s-DRY, 41.8% for dr-WET and 46.2% for cobas. Good agreement was found between s-DRY and dr-WET samples (kappa±Standard error (SE = 0.64±0.09,, particularly for low-grade squamous intraepithelial lesions (LSIL+ (kappa±SE = 0.80±0.17. Excellent agreement was found between the two samples for HPV16 detection in general (kappa±SE = 0.91±0.09 and among LSIL+ lesions (kappa±SE = 1.00±0.17. Sensitivities and specificities were, respectively, 84.2% and 47.1%(s-DRY, 73.1% and 58.7%. (dr-WET and 77.8% and 45.7% (cobas for CIN2+ detection. The median delay between sampling and HPV analysis was 7 days for the Xpert HPV assay and 19 days for cobas. There were 36 (24.0% invalid results among s-DRY samples and 4 (2.7% among dr-WET (p = 0.001. Invalid results happened due to the long interval between collection and analysis.Self-collected vaginal dry swabs are a valid alternative to collecting cervical samples in PreservCyt solution for HPV testing with the Xpert HPV assay

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-06-07

    Jun 7, 2010 ... Calcium chloride. 0.1. Magnesium chloride. 0.1. Agar. 4.0. pH 2 ± 0.2 swabs evaluated by maintaining the viabilities of both anaerobic and fastidious aerobic organisms for 24 h for majority of the organisms evaluated. This time period should be sufficient for transport of specimens to the clinical microbiology ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-06-07

    Jun 7, 2010 ... Department of Medical Laboratory Science, Faculty of Basic Medical Sciences, College of Medicine, Ambrose Alli. University ... Statistical analysis using the students t-test at 90% confidence limit showed ... Key words: Modified peptone water, Stuart, Amies, transport medium, comparison, swab specimens.

  6. Ultrasensitive detection of oncogenic human papillomavirus in oropharyngeal tissue swabs.

    Science.gov (United States)

    Isaac, Andre; Kostiuk, Morris; Zhang, Han; Lindsay, Cameron; Makki, Fawaz; O'Connell, Daniel A; Harris, Jeffrey R; Cote, David W J; Seikaly, Hadi; Biron, Vincent L

    2017-01-14

    The incidence of oropharyngeal squamous cell carcinoma (OPSCC) caused by oncogenic human papillomavirus (HPV) is rising worldwide. HPV-OPSCC is commonly diagnosed by RT-qPCR of HPV E6 and E7 oncoproteins or by p16 immunohistochemistry (IHC). Droplet digital PCR (ddPCR) has been recently reported as an ultra-sensitive and highly precise method of nucleic acid quantification for biomarker analysis. To validate the use of a minimally invasive assay for detection of oncogenic HPV based on oropharyngeal swabs using ddPCR. Secondary objectives were to compare the accuracy of ddPCR swabs to fresh tissue p16 IHC and RT-qPCR, and to compare the cost of ddPCR with p16 IHC. We prospectively included patients with p16+ oral cavity/oropharyngeal cancer (OC/OPSCC), and two control groups: p16- OC/OPSCC patients, and healthy controls undergoing tonsillectomy. All underwent an oropharyngeal swab with ddPCR for quantitative detection of E6 and E7 mRNA. Surgical specimens had p16 IHC performed. Agreement between ddPCR and p16 IHC was determined for patients with p16 positive and negative OC/OPSCC as well as for healthy control patients. The sensitivity and specificity of ddPCR of oropharyngeal swabs were calculated against p16 IHC for OPSCC. 122 patients were included: 36 patients with p16+OPSCC, 16 patients with p16-OPSCC, 4 patients with p16+OCSCC, 41 patients with p16-OCSCC, and 25 healthy controls. The sensitivity and specificity of ddPCR of oropharyngeal swabs against p16 IHC were 92 and 98% respectively, using 20-50 times less RNA than that required for conventional RT-qPCR. Overall agreement between ddPCR of tissue swabs and p16 of tumor tissue was high at ĸ = 0.826 [0.662-0.989]. Oropharyngeal swabs analyzed by ddPCR is a quantitative, rapid, and effective method for minimally invasive oncogenic HPV detection. This assay represents the most sensitive and accurate mode of HPV detection in OPSCC without a tissue biopsy in the available literature.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilms on Stainless Steel.

    Science.gov (United States)

    Branck, Tobyn A; Hurley, Matthew J; Prata, Gianna N; Crivello, Christina A; Marek, Patrick J

    2017-06-01

    Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, facilitating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilms on stainless steel served as a model system for surface sampling, to test the performance of a sonicating swab in comparison with a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both types of swabs were examined using scanning electron microscopy, to visualize biofilms and surface structures (i.e., polishing grooves and scratches). Laser scanning confocal microscopy was used to image and to quantitate the biofilms remaining after sampling with each swab type. The total viable counts were significantly higher ( P ≤ 0.05) with the sonicating swab than with the standard swab in each trial. The sonicating swab was more consistent in cell recovery than was the standard swab, with coefficients of variation ranging from 8.9% to 12.3% and from 7.1% to 37.6%, respectively. Scanning electron microscopic imaging showed that biofilms remained in the polished grooves of the coupons sampled with the standard swab but were noticeably absent with the sonicating swab. Percent area measurements of biofilms remaining on the stainless steel coupons showed significantly ( P ≤ 0.05) less biofilm remaining when the sonicating swab was used (median, 1.1%), compared with the standard swab (median, 70.4%). The sonicating swab provided greater recovery of cells, with more consistency, than did the standard swab, and it is employs sonication, suction, and scrubbing. IMPORTANCE Inadequate surface sampling can result in foodborne illness outbreaks from biotransfer, since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of

  9. Isolation of Chlamydia trachomatis from men with urethritis: relative value of one vs. two swabs and influence of concomitant gonococcal infection.

    Science.gov (United States)

    Singal, S S; Reichman, R C; Graman, P S; Greisberger, C; Trupei, M A; Menegus, M A

    1986-01-01

    Two successive urethral swabs were used to obtain specimens for culture of Neisseria gonorrhoeae and Chlamydia trachomatis from 136 heterosexual men with urethritis. The first swab was used to culture N. gonorrhoeae and then C. trachomatis; the second was used to culture C. trachomatis only. C. trachomatis cultures from the second swab were positive more often (30 of 31 pairs) than were cultures from the first swab (22 of 31 pairs) (P less than .05). In addition, cultures from swab 2 had greater numbers of inclusions per coverslip more frequently (23 of 31 pairs) than did cultures from the first swab (six of 31 pairs) (P = .003). Numbers of chlamydial inclusions per coverslip were lower in specimens positive for both C. trachomatis and N. gonorrhoeae than in specimens positive for C. trachomatis only (P less than .02). In addition, the presence of N. gonorrhoeae in a specimen adversely affected the quality of the McCoy cell monolayer. In 17 of 21 instances of monolayer toxicity, cultures for N. gonorrhoeae were positive (P less than .01). These results demonstrate that when specimens from men with urethritis are cultured for N. gonorrhoeae and C. trachomatis, use of a second swab will improve rates of recovery of C. trachomatis. Material present in specimens that contain N. gonorrhoeae may adversely affect rates of isolation of C. trachomatis.

  10. 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.

  11. Diagnosis of Clostridium difficile infection: comparison of four methods on specimens collected in Cary-Blair transport medium and tcdB PCR on fresh versus frozen samples

    Science.gov (United States)

    Brown, Noah A.; LeBar, William D.; Young, Carol L.; Hankerd, Rosemary E.; Newton, Duane W.

    2011-01-01

    Clostridium difficile infection (CDI) caused by toxigenic strains of C. difficile is primarily a nosocomial infection with increasing prevalence. Stool specimens are typically collected in Cary-Blair transport medium to maximize culture-based detection of common stool pathogens. The goal of this study was to establish an analytically accurate and efficient algorithm for the detection of CDI in our patient population using samples collected in Cary-Blair transport medium. In addition, we wished to determine whether the sensitivity and specificity of PCR was affected by freezing samples before testing. Using 357 specimens, we compared four methods: enzyme immunoassay for the antigen glutamate dehydrogenase (Wampole™ C. DIFF CHEK-60 Assay, GDH), toxin A and B enzyme immunoassay (Remel ProSpecT™ C. difficile Toxin A/B Microplate Assay, Toxin EIA), cell culture cytotoxicity neutralization assay (Bartels™ Cytotoxicity Assay, CT), and real-time PCR targeting the toxin B gene (BD GeneOhm™ Cdiff Assay, PCR). The analytic sensitivity and specificity of each as determined using a combined gold standard were as follows: GDH, 100% and 93.2%; Toxin EIA, 82.9% and 82.9%; CT, 100% and 100%; PCR (performed on frozen specimens) 74.3% and 96.6%; respectively. However, the sensitivity and specificity of PCR improved to 100% when performed on 50 fresh stool samples collected in Cary-Blair. While CT remains a sensitive method for the detection of CDI, GDH offers an excellent initial screening method to rule out CDI. While the performance of each assay did not appear to be affected by collection in Cary-Blair medium, PCR performed better using fresh specimens. PMID:24470904

  12. Virtual Specimens

    Science.gov (United States)

    de Paor, D. G.

    2009-12-01

    Virtual Field Trips have been around almost as long as the Worldwide Web itself yet virtual explorers do not generally return to their desktops with folders full of virtual hand specimens. Collection of real specimens on fields trips for later analysis in the lab (or at least in the pub) has been an important part of classical field geoscience education and research for generations but concern for the landscape and for preservation of key outcrops from wanton destruction has lead to many restrictions. One of the author’s favorite outcrops was recently vandalized presumably by a geologist who felt the need to bash some of the world’s most spectacular buckle folds with a rock sledge. It is not surprising, therefore, that geologists sometimes leave fragile localities out of field trip itineraries. Once analyzed, most specimens repose in drawers or bins, never to be seen again. Some end up in teaching collections but recent pedagogical research shows that undergraduate students have difficulty relating specimens both to their collection location and ultimate provenance in the lithosphere. Virtual specimens can be created using 3D modeling software and imported into virtual globes such as Google Earth (GE) where, they may be linked to virtual field trip stops or restored to their source localities on the paleo-globe. Sensitive localities may be protected by placemark approximation. The GE application program interface (API) has a distinct advantage over the stand-alone GE application when it comes to viewing and manipulating virtual specimens. When instances of the virtual globe are embedded in web pages using the GE plug-in, Collada models of specimens can be manipulated with javascript controls residing in the enclosing HTML, permitting specimens to be magnified, rotated in 3D, and sliced. Associated analytical data may be linked into javascript and localities for comparison at various points on the globe referenced by ‘fetching’ KML. Virtual specimens open up

  13. Nosocomial viral infections: IV. Guidelines for cohort isolation, the communicable disease survey, collection, and transport of specimens for virus isolation, and considerations for the future.

    Science.gov (United States)

    Valenti, W M; Menegus, M A

    1981-01-01

    Virus transmission within the hospital is related to transmissibility of the virus and susceptibility of the population at risk. General guidelines for the use of cohort isolation, for the control of virus transmission in the hospital, and for the use of the communicable disease survey for pediatric patients and visitors to the hospital are out-lined. We also present a brief review of how to collect and transport specimens for virus isolation to assist the infection control practitioner and the clinician and conclude with recommendations for further investigations in the areas of virology and infection control.

  14. Effect of specimen collection techniques, transport media, and incubation of cultures on the detection rate of Helicobacter pylori

    NARCIS (Netherlands)

    van der Hulst, R. W.; Verheul, S. B.; Weel, J. F.; Gerrits, Y.; ten Kate, F. J.; Dankert, J.; Tytgat, G. N.

    1996-01-01

    Culture and histologic examination are considered "gold standard" methods for the detection of Helicobacter pylori, but discrepancies may occur with either method. Failure to detect Helicobacter pylori may be due to sampling error, inappropriate transport or culture media, or insufficient duration

  15. Effect of collection, transport, processing and storage of blood specimens on the activity of lysosomal enzymes in plasma and leukocytes

    Directory of Open Access Journals (Sweden)

    M. Burin

    2000-09-01

    Full Text Available This study was designed to evaluate the effect of different conditions of collection, transport and storage on the quality of blood samples from normal individuals in terms of the activity of the enzymes ß-glucuronidase, total hexosaminidase, hexosaminidase A, arylsulfatase A and ß-galactosidase. The enzyme activities were not affected by the different materials used for collection (plastic syringes or vacuum glass tubes. In the evaluation of different heparin concentrations (10% heparin, 5% heparin, and heparinized syringe in the syringes, it was observed that higher doses resulted in an increase of at least 1-fold in the activities of ß-galactosidase, total hexosaminidase and hexosaminidase A in leukocytes, and ß-glucuronidase in plasma. When the effects of time and means of transportation were studied, samples that had been kept at room temperature showed higher deterioration with time (72 and 96 h before processing, and in this case it was impossible to isolate leukocytes from most samples. Comparison of heparin and acid citrate-dextrose (ACD as anticoagulants revealed that ß-glucuronidase and hexosaminidase activities in plasma reached levels near the lower normal limits when ACD was used. In conclusion, we observed that heparin should be used as the preferable anticoagulant when measuring these lysosomal enzyme activities, and we recommend that, when transport time is more than 24 h, samples should be shipped by air in a styrofoam box containing wet ice.

  16. Surface-sampling and analysis of TATP by swabbing and gas chromatography/mass spectrometry.

    Science.gov (United States)

    Romolo, Francesco Saverio; Cassioli, Luigi; Grossi, Silvana; Cinelli, Giuseppe; Russo, Mario Vincenzo

    2013-01-10

    The method of sample recovery for trace detection and identification of explosives plays a critical role in several criminal investigations. After bombing, there can be difficulties in sending big objects to a laboratory for analysis. Traces can also be searched for on large surfaces, on hands of suspects or on surfaces where the explosive was placed during preparatory phases (e.g. places where an IED was assembled, vehicles used for transportation, etc.). In this work, triacetone triperoxide (TATP) was synthesized from commercial precursors following reported methods. Several portions of about 6mg of TATP were then spread on different surfaces (e.g. floors, tables, etc.) or used in handling tests. Three different swabbing systems were used: a commercial swab, pre-wetted with propan-2-ol (isopropanol) and water (7:3), dry paper swabs, and cotton swabs wetted with propan-2-ol. Paper and commercial swabs were also used to sample a metal plate, where a small charge of about 4g of TATP was detonated. Swabs were sealed in small glass jars with screw caps and Parafilm(®) M and sent to the laboratory for analysis. Swabs were extracted and analysed several weeks later by gas chromatography/mass spectrometry. All the three systems gave positive results, but wetted swabs collected higher amounts of TATP. The developed procedure showed its suitability for use in real cases, allowing TATP detection in several simulations, including a situation in which people wash their hands after handling the explosive. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  17. Evaluation of a PCR test for detection of treponema pallidum in swabs and blood.

    Science.gov (United States)

    Grange, P A; Gressier, L; Dion, P L; Farhi, D; Benhaddou, N; Gerhardt, P; Morini, J P; Deleuze, J; Pantoja, C; Bianchi, A; Lassau, F; Avril, M F; Janier, M; Dupin, N

    2012-03-01

    Syphilis diagnosis is based on clinical observation, serological analysis, and dark-field microscopy (DFM) detection of Treponema pallidum subsp. pallidum, the etiological agent of syphilis, in skin ulcers. We performed a nested PCR (nPCR) assay specifically amplifying the tpp47 gene of T. pallidum from swab and blood specimens. We studied a cohort of 294 patients with suspected syphilis and 35 healthy volunteers. Eighty-seven of the 294 patients had primary syphilis, 103 had secondary syphilis, 40 had latent syphilis, and 64 were found not to have syphilis. The T. pallidum nPCR results for swab specimens were highly concordant with syphilis diagnosis, with a sensitivity of 82% and a specificity of 95%. Reasonable agreement was observed between the results obtained with the nPCR and DFM methods (kappa = 0.53). No agreement was found between the nPCR detection of T. pallidum in blood and the diagnosis of syphilis, with sensitivities of 29, 18, 14.7, and 24% and specificities of 96, 92, 93, and 97% for peripheral blood mononuclear cell (PBMC), plasma, serum, and whole-blood fractions, respectively. HIV status did not affect the frequency of T. pallidum detection in any of the specimens tested. Swab specimens from mucosal or skin lesions seemed to be more useful than blood for the efficient detection of the T. pallidum genome and, thus, for the diagnosis of syphilis.

  18. Specimen Preparation

    Science.gov (United States)

    Williams, David B.; Carter, C. Barry

    Specimen preparation is a very broad subject; there are books devoted to this topic alone. The intention here is to summarize the techniques, suggest routes that you might follow, and above all to emphasize that there are many ways to produce a TEM specimen; the one you choose will depend on the information you need, time constraints, availability of equipment, your skill, and the material. So we’ll concentrate on the ‘principles of cooking,’ but won’t try to list all the possible ‘recipes.’ One important point to bear in mind is that your technique must not affect what you see or measure, or if it does, then you must know how. Specimen preparation artifacts may be interesting but they are not usually what you want to study. Incidentally, we’ll make ‘specimens’ from the ‘sample’ we’re investigating so we’ll look at ‘TEM specimens,’ but sometimes we, and everyone else, will interchange the two words.

  19. EVA-Compatible Microbial Swab Tool

    Science.gov (United States)

    Rucker, Michelle A.

    2016-01-01

    When we send humans to search for life on Mars, we'll need to know what we brought with us versus what may already be there. To ensure our crewed spacecraft meet planetary protection requirements—and to protect our science from human contamination—we'll need to know whether micro-organisms are leaking/venting from our ships and spacesuits. This is easily done by swabbing external vents and suit surfaces for analysis, but requires a specialized tool for the job. Engineers at the National Aeronautics and Space Administration (NASA) recently developed an Extravehicular Activity (EVA)-compatible swab tool that can be used to sample current space suits and life support systems. Data collected now will influence Mars life support and EVA hardware early in the planning process, before design changes become difficult and expensive.NASA’s EVA swab tool pairs a Space Shuttle-era tool handle with a commercially available swab tip mounted into a custom-designed end effector. A glove-compatible release mechanism allows the handle to quickly switch between swab tips, much like a shaving razor handle can snap onto a disposable blade cartridge. Swab tips are stowed inside individual sterile containers, each fitted with a microbial filter that allows the container to equalize atmospheric pressure, but prevents cabin contaminants from rushing into the container when passing from the EVA environment into a pressurized cabin. A bank of containers arrayed inside a tool caddy allows up to six individual samples to be collected during a given spacewalk.NASA plans to use the tool in 2016 to collect samples from various spacesuits during ground testing to determine what (if any) human-borne microbial contamination leaks from the suit under simulated thermal vacuum conditions. Next, the tool will be used on board the International Space Station to assess the types of microbial contaminants found on external environmental control and life support system vents. Data will support

  20. Swab sample transfer for point-of-care diagnostics: characterization of swab types and manual agitation methods.

    Directory of Open Access Journals (Sweden)

    Nuttada Panpradist

    Full Text Available BACKGROUND: The global need for disease detection and control has increased effort to engineer point-of-care (POC tests that are simple, robust, affordable, and non-instrumented. In many POC tests, sample collection involves swabbing the site (e.g., nose, skin, agitating the swab in a fluid to release the sample, and transferring the fluid to a device for analysis. Poor performance in sample transfer can reduce sensitivity and reproducibility. METHODS: In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices. Transfer efficiency was measured using quantitative PCR (qPCR for Staphylococcus aureus under conditions representing a range of sampling scenarios: 1 spiking low-volume samples onto the swab, 2 submerging the swab in excess-volume samples, and 3 swabbing dried sample from a surface. RESULTS: Excess-volume samples gave the expected recovery for most swabs (based on tip fluid capacity; a polyurethane swab showed enhanced recovery, suggesting an ability to accumulate organisms during sampling. Dry samples led to recovery of ∼20-30% for all swabs tested, suggesting that swab structure and volume is less important when organisms are applied to the outer swab surface. Low-volume samples led to the widest range of transfer efficiencies between swab types. Rayon swabs (63 µL capacity performed well for excess-volume samples, but showed poor recovery for low-volume samples. Nylon (100 µL and polyester swabs (27 µL showed intermediate recovery for low-volume and excess-volume samples. Polyurethane swabs (16 µL showed excellent recovery for all sample types. This work demonstrates that swab transfer efficiency can be affected by swab material, structure, and fluid capacity and details of the sample. Results and quantitative analysis methods from this study will assist POC assay developers in selecting appropriate swab types and transfer methods.

  1. Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses.

    Science.gov (United States)

    Jeong, Ji Hun; Kim, Kyung Hee; Jeong, Sung Hwan; Park, Jeong Woong; Lee, Sang Min; Seo, Yiel Hea

    2014-12-01

    Diagnostic tests for respiratory viral infections use traditionally either nasopharyngeal washes or swabs. Sputum is representative of the lower respiratory tract but is used rarely for viral testing. The aim of this study was to compare the detection rates of respiratory viruses from nasopharyngeal swabs and sputum using a multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR). Adults who were admitted or presented to the clinics of Gil Medical Center with acute respiratory symptoms were recruited from 1 November 2012 to 31 March 2013. Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The positive rate was 53% (81/154) for nasopharyngeal swabs and 68% (105/154) for sputum (P < 0.001). One hundred thirty-four viruses were identified for 107 illnesses. Influenza A virus, RSV A, HRV, coronavirus OC43, and adenovirus were detected more frequently in sputum samples than in nasopharyngeal swabs (P < 0.001). Importantly, 12 of 44 (27%) influenza A infections and 11 of 27 (41%) RSV infections were positive in only sputum samples. The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real-time multiplex RT-PCR. These findings suggest that sputum would benefit for the detection of respiratory viruses by nucleic acid amplification tests (NAATs) in patients who produce sputum. Further studies are needed to establish standardized RNA extraction methods from sputum samples. © 2014 Wiley Periodicals, Inc.

  2. Screening femoral heads from living donors: a prospective study comparing swab-agar versus bone fragment-broth culture.

    Science.gov (United States)

    Saegeman, Veroniek; Verhaegen, Jan; Simon, Jean-Pierre

    2011-06-01

    Femoral heads are an important source of allograft bone used in reconstructive orthopaedic surgery. The sterility of donor material is of major importance for the recipient. Femoral heads intraoperatively retrieved during hip arthroplasty from medically screened living donors are routinely checked with a surface swab to exclude microbiological contamination. There is, however, evidence that swab cultures have limited sensitivity. We therefore prospectively compared two ways of screening femoral heads. Bacterial recovery from swabs in Amies transport medium taken intraoperatively, subsequently transported to the microbiology laboratory and inoculated on agar and in broth was compared with the recovery from a bone fragment also taken intraoperatively but immediately inoculated into Wilkins Chalgren broth. Forty femoral heads were tested with both methods. Bacteria were cultured neither from the femoral surface swabs nor from the femoral fragments. Consequently no distinct conclusions regarding the sensitivity of both techniques could be drawn. In addition the bacterial yield of two swabs in Amies transport medium streaked on a variety of culture media other than the conventional agar plates was also studied. Culturing of these swabs resulted in the detection of bacteria that are predominantly considered contaminants.

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

    Science.gov (United States)

    Su, Jiunn-Yih; Andersson, Patiyan; Holt, Deborah C.

    2017-01-01

    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 known higher

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

    Science.gov (United States)

    Giffard, Philip M; Su, Jiunn-Yih; Andersson, Patiyan; Holt, Deborah C

    2017-01-01

    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. 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. 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 known higher relative prevalence of gonorrhoeae

  5. 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.

  6. A quantitative swab is a good non-invasive alternative to a quantitative biopsy for quantifying bacterial load in wounds healing by second intention in horses.

    Science.gov (United States)

    Van Hecke, L L; Hermans, K; Haspeslagh, M; Chiers, K; Pint, E; Boyen, F; Martens, A M

    2017-07-01

    The aim of this study was to evaluate different techniques for diagnosing wound infection in wounds healing by second intention in horses and to assess the effect of a vortex and sonication protocol on quantitative bacteriology in specimens with a histologically confirmed biofilm. In 50 wounds healing by second intention, a clinical assessment, a quantitative swab, a semi-quantitative swab, and a swab for cytology were compared to a quantitative tissue biopsy (reference standard). Part of the biopsy specimen was examined histologically for evidence of a biofilm. There was a significant, high correlation (P<0.001; r=0.747) between the outcome of the quantitative swabs and the quantitative biopsies. The semi-quantitative swabs showed a significant, moderate correlation with the quantitative biopsies (P<0.001; ρ=0.524). Higher white blood cell counts for cytology were significantly associated with lower log 10 colony-forming units (CFU) in the wounds (P=0.02). Wounds with black granulation tissue showed significantly higher log 10 CFU (P=0.003). Specimens with biofilms did not yield higher bacteriological counts after a vortex and sonication protocol was performed to release bacteria from the biofilm. Based on these findings, a quantitative swab is an acceptable non-invasive alternative to a quantitative biopsy for quantifying bacterial load in equine wounds healing by second intention. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. 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.

  8. Comparing non-woven, filmateci and woven gauze swabs.

    Science.gov (United States)

    Thomas, S; Loveless, P; Hay, N P; Toyick, N

    1993-01-02

    The physical characteristics and performance of seven non-woven swabs intended for topical use were compared with those of filmated swabs and woven cotton gauze in a series of laboratory tests. The results of this study suggest that the non-woven swabs have significant advantages over the other type examined. Based upon current pricing structures they represent a highly cost-effective alternative to the more traditional products for routine wound management procedures. As the various non-wovens have very different handling characteristics, it should be possible to select a swab to suit most requirements from the range of products available.

  9. Need for appropriate specimen for microbiology diagnosis of chronic osteomyelitis

    Directory of Open Access Journals (Sweden)

    Lakshmi Vemu

    2018-01-01

    CONCLUSION: As per our data, the culture yield from wound swabs was low or contaminated with normal skin flora, as compared to the biopsy or tissue specimen. Hence, an appropriate sampling of the infected bone using recommended protocols is highly essential for improving microbiological yield and the outcome of COM.

  10. Diagnostic performance of swab PCR as an alternative to tissue culture methods for diagnosing infections associated with fracture fixation devices.

    Science.gov (United States)

    Omar, Mohamed; Suero, Eduardo M; Liodakis, Emmanouil; Reichling, Moritz; Guenther, Daniel; Decker, Sebastian; Stiesch, Meike; Krettek, Christian; Eberhard, Jörg

    2016-07-01

    Molecular procedures could potentially improve diagnoses of orthopaedic implant-related infections, but are not yet clinically implemented. Analysis of sonication fluid shows the highest sensitivity for diagnosing implant infections in cases of revision surgery with implant removal. However, there remains controversy regarding the best method for obtaining specimens in cases of revision surgery with implant retention. Tissue culture is the most common diagnostic method for pathogen identification in such cases. Here we aimed to assess the diagnostic performance of swab PCR analysis compared to tissue culture from patients undergoing revision surgery of fracture fixation devices. We prospectively investigated 62 consecutive subjects who underwent revision surgery of fracture fixation devices during a two-year period. Tissue samples were collected for cultures, and swabs from the implant surface were obtained for 16S rRNA PCR analysis. Subjects were classified as having an implant-related infection if (1) they presented with a sinus tract or open wound in communication with the implant; or (2) purulence was encountered intraoperatively; or (3) two out of three tissue cultures tested positive for the presence of the same pathogen. Tissue culture and swab PCR results from the subjects were used to calculate the sensitivity, specificity, accuracy, positive predictive value (PPV), negative predictive value (NPV), and area under the ROC curve (AUC) for identifying an orthopaedic implant-related infection. Orthopaedic implant-related infections were detected in 51 subjects. Tissue culture identified infections in 47 cases, and swab PCR in 35 cases. Among the 11 aseptic cases, tissue culture was positive in 2 cases and swab PCR in 4 cases. Tissue culture showed a significantly higher area under the ROC curve for diagnosing infection (AUC=0.89; 95% CI, 0.67-0.96) compared to swab PCR (AUC=0.66; 95% CI, 0.46-0.80) (p=0.033). Compared to swab PCR, tissue culture showed better

  11. Noninvasive buccal swab antigen sample and molecular testing provides extended antigen typing for patients with hemoglobinopathies.

    Science.gov (United States)

    Rampersad, Angeli; Hampton, Kisha; Duncan, Natalie; Roberson, Chris; Slayten, Jayanna; Davisson, Suzanne; Aronowitz, Jessica; Shapiro, Amy

    2014-11-01

    To demonstrate the feasibility of performing a noninvasive, molecular-based red blood cell (RBC) antigen test on infants and very young children with sickle cell disease as part of a statewide newborn screening follow-up program. A prospective pilot project was conducted using a noninvasive buccal swab and test kit to perform DNA-based, extended RBC phenotyping in 92 children participating in a newborn hemoglobinopathy screening follow-up program. Reported data include the extended panel of antigens detected by molecular analysis compared with unaffected population estimates. Molecular-based RBC antigen testing was successful, with extended RBC typing generated for all subjects. Molecular testing detected several rare negative or rare positive phenotypes, demonstrating the utility of obtaining an extended antigen panel. This study demonstrates the feasibility of performing antigen testing on buccal swab specimens from children with sickle cell disease as part of a newborn screening follow-up program with the aim of allowing specific unit matching to prevent alloimmunization with RBC transfusions. The general applicability of testing may be limited by a lack of uniform insurance coverage for buccal swab testing, however. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Evaluation and clinical validation of an alcohol-based transport medium for preservation and inactivation of respiratory viruses.

    Science.gov (United States)

    Luinstra, Kathy; Petrich, Astrid; Castriciano, Santina; Ackerman, Mona; Chong, Sylvia; Carruthers, Susan; Ammons, Brenna; Mahony, James B; Smieja, Marek

    2011-06-01

    The clinical and public health importance of influenza and other respiratory viruses has accelerated the development of highly sensitive molecular diagnostics, but data are limited regarding preanalytical stages of diagnostic testing. We evaluated CyMol, an alcohol-based transport medium, for its ability to maintain specimen integrity for up to 21 days of storage at various temperatures; for its ability to inactivate virus; and for its compatibility with antigen- or nucleic acid-based diagnostics for respiratory viruses in clinical samples. In mock-infected samples, both universal transport medium (UTM-RT) and CyMol maintained equivalent viral quantities for at least 14 days at room temperature or colder, whereas a dry swab collection maintained viral quantities only if refrigerated or frozen. CyMol inactivated influenza virus within 5 min of sample immersion. UTM-RT- and CyMol-collected nasal swab specimens from 73 symptomatic students attending a campus health clinic were positive for a respiratory virus in 56.2% of subjects by multiplex PCR testing, including influenza A and B viruses, rhinovirus/enteroviruses, coronaviruses, respiratory syncytial virus, parainfluenza viruses, metapneumovirus, and adenovirus. Detection by PCR was equivalent in UTM-RT- and CyMol-collected specimens and in self- and staff-collected swabs. Direct fluorescent antibody (DFA) testing was substantially less sensitive (23.3%) than multiplex PCR, and DFA testing from UTM-RT-collected swabs was more sensitive than that from CyMol-collected swabs. These data indicate that an alcohol-based transport medium such as CyMol preserves respiratory virus integrity, rapidly inactivates viruses, and is compatible with PCR-based respiratory diagnostics.

  13. Nylon flocked swab severely reduces Hexagon Obti sensibility.

    Science.gov (United States)

    Frippiat, Christophe; De Roy, Gilbert; Fontaine, Louis-Marie; Dognaux, Sophie; Noel, Fabrice; Heudt, Laeticia; Lepot, Laurent

    2015-02-01

    Hexagon Obti immunological blood test and flocked swab are widely used in forensic laboratories. Nevertheless, up to now, no compatibility tests have been published between sampling with the ethylene oxide treated flocked swab and the Hexagon Obti blood detection strip. In this study, we investigated this compatibility. Our work shows that sampling with ethylene oxide treated flocked swab reduces by a factor of at least 100 the detection threshold of blood using the Hexagon Obti immunological test. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  14. APTIMA assay on SurePath liquid-based cervical samples compared to endocervical swab samples facilitated by a real time database

    Directory of Open Access Journals (Sweden)

    Khader Samer

    2010-01-01

    Full Text Available Background: Liquid-based cytology (LBC cervical samples are increasingly being used to test for pathogens, including: HPV, Chlamydia trachomatis (CT and Neisseria gonorrhoeae (GC using nucleic acid amplification tests. Several reports have shown the accuracy of such testing on ThinPrep (TP LBC samples. Fewer studies have evaluated SurePath (SP LBC samples, which utilize a different specimen preservative. This study was undertaken to assess the performance of the Aptima Combo 2 Assay (AC2 for CT and GC on SP versus endocervical swab samples in our laboratory. Materials and Methods: The live pathology database of Montefiore Medical Center was searched for patients with AC2 endocervical swab specimens and SP Paps taken the same day. SP samples from CT- and/or GC-positive endocervical swab patients and randomly selected negative patients were studied. In each case, 1.5 ml of the residual SP vial sample, which was in SP preservative and stored at room temperature, was transferred within seven days of collection to APTIMA specimen transfer tubes without any sample or patient identifiers. Blind testing with the AC2 assay was performed on the Tigris DTS System (Gen-probe, San Diego, CA. Finalized SP results were compared with the previously reported endocervical swab results for the entire group and separately for patients 25 years and younger and patients over 25 years. Results: SP specimens from 300 patients were tested. This included 181 swab CT-positive, 12 swab GC-positive, 7 CT and GC positive and 100 randomly selected swab CT and GC negative patients. Using the endocervical swab results as the patient′s infection status, AC2 assay of the SP samples showed: CT sensitivity 89.3%, CT specificity 100.0%; GC sensitivity and specificity 100.0%. CT sensitivity for patients 25 years or younger was 93.1%, versus 80.7% for patients over 25 years, a statistically significant difference (P = 0.02. Conclusions: Our results show that AC2 assay of 1.5 ml SP

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

    African Journals Online (AJOL)

    that raise clinical suspicion, of a condition that may be elusive in presentation on ... A review of the English literature reporting retained abdominal swabs between 1992 and 2012 revealed 100 cases. .... help to explain the variety of associated.

  16. 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. Engineers 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 attachment. This allowed the tool handle to snap onto a fresh swab attachment 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 attachment 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 repressurize 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

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

    Directory of Open Access Journals (Sweden)

    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

  18. Evaluation of a medium (STGG) for transport and optimal recovery of Streptococcus pneumoniae from nasopharyngeal secretions collected during field studies.

    Science.gov (United States)

    O'Brien, K L; Bronsdon, M A; Dagan, R; Yagupsky, P; Janco, J; Elliott, J; Whitney, C G; Yang, Y H; Robinson, L G; Schwartz, B; Carlone, G M

    2001-03-01

    Field studies of Streptococcus pneumoniae (pneumococci) nasopharyngeal (NP) colonization are hampered by the need to directly plate specimens in order to ensure isolate viability. A medium containing skim milk, tryptone, glucose, and glycerin (STGG) has been used to transport and store NP material, but its ability to preserve pneumococci has not been evaluated. Our objective was to qualitatively and semiquantitatively evaluate the ability of STGG to preserve pneumococci in NP secretions. Entwined duplicate calcium alginate NP swab samples were obtained from children. One swab was plated directly onto a gentamicin blood agar plate; the other was placed in STGG. Growth from the directly plated specimen was compared with growth from an STGG aliquot immediately cultured or stored at -70 degrees C for 9 weeks, -20 degrees C for 9 weeks, or 4 degrees C for 5 days. Of 186 specimens, 96 (52%) were positive for pneumococci from the direct plating; 94 (98%) of these were positive from the fresh STGG specimen. Pneumococci were recovered from all 38 positive specimens frozen at -70 degrees C, all 18 positive specimens frozen at -20 degrees C, and 18 of 20 positive specimens stored at 4 degrees C. Recovery of pneumococci after storage of NP material in STGG medium at -70 degrees C is at least as good as that from direct plating. Storage at -20 degrees C is also acceptable. Storage at 4 degrees C for 5 days is not ideal.

  19. Diagnosis of Trichomonas vaginalis infection by PCR using vaginal swab samples.

    Science.gov (United States)

    Madico, G; Quinn, T C; Rompalo, A; McKee, K T; Gaydos, C A

    1998-11-01

    Trichomonas vaginalis infection is the most prevalent nonviral sexually transmitted disease (STD) in the world. A PCR test using vaginal swab samples for the detection of T. vaginalis was developed to add T. vaginalis infection to the growing list of STDs that can be detected by DNA amplification techniques. A primer set, BTUB 9/2, was designed to target a well-conserved region in the beta-tubulin genes of T. vaginalis. All strains (15 of 15) of T. vaginalis tested were successfully detected by PCR giving a single predicted product of 112 bp in gel electrophoresis. No such targeted product was amplified with DNA from Trichomonas tenax, Trichomonas gallinae, Chlamydia trachomatis, Neisseria gonorrhoeae, Giardia lamblia, Chilomastix sulcatus, Dientamoeba fragilis, and Entamoeba histolytica. An optimal analytical sensitivity of one T. vaginalis organism per PCR was achieved. Culture, performed with the Inpouch TV culture system, was examined daily with a light microscope to identify T. vaginalis. Twenty-three of 350 (6.6%) vaginal swab samples from women attending an army medical clinic were culture positive for T. vaginalis. Of these culture positive specimens, PCR detected 22 of 23 (96%) with primer set BTUB 9/2, and wet preparation detected only 12 of 23 (52%). Seventeen specimens were BTUB 9/2-PCR positive and culture negative. Ten of these discordant specimens were determined to be as true positive by PCR using primer sets TVA 5-1/6 and/or AP65 A/B, which target different regions in the T. vaginalis genome, and seven were determined to be false positive. The sensitivity of BTUB 9/2-PCR was 97% and the specificity was 98%. The sensitivities of culture and wet preparation were 70 and 36%, respectively. The diagnosis of T. vaginalis infection by PCR is a sensitive and specific method that could be incorporated into a joint strategy for the screening of multiple STDs by using molecular amplification methods.

  20. Urine culture - catheterized specimen

    Science.gov (United States)

    Culture - urine - catheterized specimen; Urine culture - catheterization; Catheterized urine specimen culture ... International Clinical Practice Guidelines from the Infectious Diseases Society of America. Clin Infect Dis . 2010;50(5): ...

  1. 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

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

    African Journals Online (AJOL)

    language publications were excluded and abstracts of relevant articles were evaluated for .... [5] The diagnosis of a gossypiboma may be made easily on plain film if the radio-opaque marker is intact; however, ... radio-opaque markers are helpful in identification of retained swabs using plain X-ray. An X-ray is taken on table ...

  3. Agreement between self- and clinician-collected specimen results for detection and typing of high-risk human papillomavirus in specimens from women in Gugulethu, South Africa

    NARCIS (Netherlands)

    Jones, Heidi E.; Allan, Bruce R.; van de Wijgert, Janneke H. H. M.; Altini, Lydia; Taylor, Sylvia M.; de Kock, Alana; Coetzee, Nicol; Williamson, Anna-Lise

    2007-01-01

    We assessed the agreement in detection of high-risk human papillomavirus (HPV), as well as specific HPV types, between self- and clinician-obtained specimens for 450 women over 18 years of age attending a community health center in Gugulethu, South Africa. Both self-collected swabs and tampons had

  4. 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....

  5. 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.

  6. 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.

  7. Use of eschar swabbing for the molecular diagnosis and genotyping of Orientia tsutsugamushi causing scrub typhus in Quang Nam province, Vietnam.

    Directory of Open Access Journals (Sweden)

    Nhiem Le Viet

    2017-02-01

    Full Text Available Scrub typhus is a rickettsiosis which is caused by Orientia tsutsugamushi and occurs throughout the Asia-Pacific region. Molecular diagnosis of rickettsioses using eschar swabs has recently emerged, and may be very useful for the diagnosis of these diseases in tropical settings.Quantitative polymerase chain reaction (qPCR was used to detect O. tsutsugamushi DNA in whole blood and eschar swab specimens of 67 patients who were clinically suspected of scrub typhus in Quang Nam province, Vietnam. Among the 20 patients for whom both eschar and whole blood were obtained, 17 (85% of the eschar specimens and 5 (25% of the whole blood specimens tested positive for O. tsutsugamushi. Genetic analysis of the 56-kDa TSA gene sequences demonstrated that the 14 sequences obtained in this study, including 12 eschar swabs and 2 whole blood specimens, were related to 4 groups: Karp, Kawasaki, Gilliam (JG-v and TG-v and TA716. The majority (9/14; 64.4% of contemporary O. tsutsugamushi genotypes in Quang Nam province were related to the Karp group.These results suggest that polyclonal antigen pools used for serological testing in the future should contain at least Karp, Kawasaki, Gilliam and TA716 antigens for Vietnamese patients, as well as patients who have traveled to Vietnam. qPCR after eschar swabbing should be considered for molecular diagnosis of scrub typhus in endemic patients as well as in travelers, since it is easy to perform and appears very useful for the rapid detection of Orientia tsutsugamushi in the early phase of infection.

  8. Development of a polymerase chain reaction to distinguish monocellate cobra (Naja khouthia) bites from other common Thai snake species, using both venom extracts and bite-site swabs.

    Science.gov (United States)

    Suntrarachun, S; Pakmanee, N; Tirawatnapong, T; Chanhome, L; Sitprija, V

    2001-07-01

    A PCR technique was used in this study to identify and distinguish monocellate cobra snake bites using snake venoms and swab specimens from snake bite-sites in mice from bites by other common Thai snakes. The sequences of nucleotide primers were selected for the cobrotoxin-encoding gene from the Chinese cobra (Naja atra) since the sequences of monocellate cobra (Naja kaouthia) venom are still unknown. However, the 113-bp fragment of cDNA of the cobrotoxin-encoding gene was detected in the monocellate cobra venom using RT-PCR. This gene was not found in the venoms of Ophiophagus hannah (king cobra), Bungarus fasciatus (banded krait), Daboia russelii siamensis (Siamese Russell's Viper, and Calloselasma rhodostoma (Malayan pit viper). Moreover, direct PCR could detect a 665-bp fragment of the cobrotoxin-encoding gene in the monocellate cobra venom but not the other snake venoms. Likewise, this gene was only observed in swab specimens from cobra snake bite-sites in mice. This is the first report demonstrating the ability of PCR to detect the cobrotoxin-encoding gene from snake venoms and swab specimens. Further studies are required for identification of this and other snakes from the bite-sites on human skin.

  9. Experimental comparison of excision and swabbing microbiological sampling methods for carcasses.

    Science.gov (United States)

    Pepperell, Richard; Reid, Carol-Ann; Solano, Silvia Nicolau; Hutchison, Michael L; Walters, Lisa D; Johnston, Alexander M; Buncic, Sava

    2005-10-01

    Bovine sides, ovine carcasses, and porcine carcasses were individually inoculated by dipping in various suspensions of a marker organism (Escherichia coli K-12 or Pseudomonas fluorescens), alone or in combination with two meat-derived bacterial strains, and were sampled by two standard methods: cotton wet-dry swabbing and excision. The samples were examined for bacterial counts on plate count agar (PCA plate counts) and on violet red brilliant green agar (VRBGA plate counts) by standard International Organization for Standardization methods. Average bacterial recoveries by swabbing, expressed as a percentage of the appropriate recoveries achieved by excision, varied widely (2 to 100%). Several factors that potentially contributed to relatively low and highly variable bacterial recoveries obtained by swabbing were investigated in separate experiments. Neither the difference in size of the swabbed area (10, 50, or 100 cm2 on beef carcasses) nor the difference in time of swabbing (20 or 60 min after inoculation of pig carcasses) had a significant effect on the swabbing recoveries of the marker organism used. In an experiment with swabs preinoculated with the marker organism and then used for carcass swabbing, on average, 12% of total bacterial load was transferred inversely (i.e., from the swab to the carcass during the standard swabbing procedure). In another experiment, on average, 14% of total bacterial load was not released from the swab into the diluent during standard swab homogenization. Use of custom-made swabs with abrasive butts, around which metal pieces of pan scourers were wound, markedly increased PCA plate count recoveries from noninoculated lamb carcasses at commercial abattoirs compared with cotton swabs. In spite of the observed inferiority of the cotton wet-dry swabbing method compared with the excision method for bacterial recovery, the former is clearly preferred by the meat industry because it does not damage the carcass. Therefore, further large

  10. Detecting and quantifying influenza virus with self- versus investigator-collected mid-turbinate nasal swabs.

    Science.gov (United States)

    Granados, Andrea; Quach, Susan; McGeer, Allison; Gubbay, Jonathan B; Kwong, Jeffrey C

    2017-07-01

    We compared pairs of self- and investigator-collected mid-turbinate nasal swabs to detect and quantify influenza viral loads. We used RNase P, which reflects presence of human cells to determine adequate sample collection. Sixteen pairs of influenza-positive swabs and 25 pairs of influenza-negative swabs were included in this study. The median influenza A viral loads for self- and investigator-collected swabs were 1.68 and 1.67 log10 copies/mL, respectively (P = 0.96). RNase P loads were also similar between self- and investigator-collected swabs (P = 0.51). Self-collected mid-turbinate nasal swabs yield comparable viral loads to investigator-collected swabs, and therefore might be considered for research and clinical management. © 2017 Wiley Periodicals, Inc.

  11. 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...

  12. Duration of Loxosceles reclusa Venom Detection by ELISA from Swabs

    Science.gov (United States)

    McGLASSON, DAVID L; GREEN, JONATHON A; STOECKER, WILLIAM V; BABCOCK, JAMES L; CALCARA, DAVID A

    2011-01-01

    BACKGROUND Diagnosis of Loxosceles reclusa envenomations is currently based upon clinical presentation. An enzyme-linked immunosorbent assay (ELISA) can detect surface Loxosceles venom at the envenomation site, allowing diagnostic confirmation. The length of time that venom on the skin is recoverable non-invasively is unknown. MATERIALS AND METHODS To investigate duration of recoverable venom antigen, whole venom and fractionated sphingomyelinase D venom aliquots were injected subcutaneously in New Zealand White rabbits. Cotton and Dacron swabs were compared for venom recovery over a 21-day period using a surface swab technique. RESULTS Significant amounts of Loxosceles reclusa antigen were found on the surface of rabbit skin after experimental injection of whole venom and sphingomyelinase D. The duration of recoverable antigen using this experimental model appears to be at least two weeks and as long as 21 days in some cases. CONCLUSIONS Because the duration of the recoverable antigen is seen to be at least two weeks, the ELISA venom test appears capable of detecting venom on most patients presenting with Loxosceles envenomations. This detection system will allow the physician more accurate determination of whether the lesion is from a brown recluse spider or some other agent that can cause this type of necrotic ulcer. PMID:19967916

  13. Duration of Loxosceles reclusa venom detection by ELISA from swabs.

    Science.gov (United States)

    McGlasson, David L; Green, Jonathon A; Stoecker, William V; Babcock, James L; Calcara, David A

    2009-01-01

    Diagnosis of Loxosceles reclusa envenomations is currently based upon clinical presentation. An enzyme-linked immunosorbent assay (ELISA) can detect surface Loxosceles venom at the envenomation site, allowing diagnostic confirmation. The length of time that venom on the skin is recoverable non-invasively is unknown. To investigate duration of recoverable venom antigen, whole venom and fractionated sphingomyelinase D venom aliquots were injected subcutaneously in New Zealand White rabbits. Cotton and Dacron swabs were compared for venom recovery over a 21-day period using a surface swab technique. Significant amounts of Loxosceles reclusa antigen were found on the surface of rabbit skin after experimental injection of whole venom and sphingomyelinase D. The duration of recoverable antigen using this experimental model appears to be at least two weeks and as long as 21 days in some cases. Because the duration of the recoverable antigen is seen to be at least two weeks, the ELISA venom test appears capable of detecting venom on most patients presenting with Loxosceles envenomations. This detection system will allow the physician more accurate determination of whether the lesion is from a brown recluse spider or some other agent that can cause this type of necrotic ulcer.

  14. A comparison of tonsillar surface swabbing, fine-needle aspiration core sampling, and dissected tonsillar core biopsy culture in children with recurrent tonsillitis.

    Science.gov (United States)

    Sarkar, Saurav; Sil, Abheek; Sarkar, Soma; Sikder, Biswajit

    2017-06-01

    In recurrent tonsillitis, the pathogenic bacteria are harbored in the tonsil core, and therefore cultures of superficial swab samples are not particularly accurate in identifying specific types of core bacteria. On the other hand, the results of fine-needle aspiration (FNA) cultures of core samples have been closely correlated with the findings of core cultures in excised tonsils, and both methods are far superior to surface swabbing. We conducted a prospective study to compare the accuracy of culture findings from tonsillar tissue obtained by surface swabbing, FNA sampling of the tonsil core in situ, and core sampling of the excised tonsil in children with recurrent tonsillitis. Our patient population was made up of 54 children-22 boys and 32 girls, aged 4 to 14 years (mean: 10.7)-who were undergoing elective tonsillectomy during a 1-year period. On the day of surgery, a surface swab, core FNA sample, and dissected core sample were obtained from each patient and sent for culture. Culture showed that the three methods were in agreement in 34 cases (63.0%). In 9 cases (16.7%) the surface swab culture grew different pathogens from those of the two core cultures, and in 3 other cases (5.6%) the surface swab culture was negative while the two core cultures were positive for the same pathogens. In all, the results of core FNA culture and dissected core culture were in agreement in 46 cases (85.2%); in only 4 cases (7.4%) did the core FNA culture fail to accurately identify the causative pathogens. Overall, the sensitivity and specificity of core FNA sampling were 100 and 50% respectively, compared with 82.9 and 30.8% for the superficial tonsillar swab. We conclude that routine culture of surface swab specimens in patients with chronic or recurrent tonsillitis is neither reliable nor valid. We recommend that core FNA sampling be considered the diagnostic method of choice since it can be done on an outpatient basis, it would reliably allow for culture-directed antibiotic

  15. Evaluation of the BioFire FilmArray respiratory panel and the GenMark eSensor respiratory viral panel on lower respiratory tract specimens.

    Science.gov (United States)

    Ruggiero, Phyllis; McMillen, Tracy; Tang, Yi-Wei; Babady, N Esther

    2014-01-01

    We evaluated the performance characteristics of the FilmArray respiratory panel and the eSensor respiratory viral panel on clinical and spiked lower respiratory tract specimens (LRTS). The overall agreement between the two methods was 89.5% (51/57). The lower limit of detection of both assays for all targets in LRTS was comparable to that for nasopharyngeal swab specimens.

  16. Genomics and museum specimens.

    Science.gov (United States)

    Nachman, Michael W

    2013-12-01

    Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years. © 2013 John Wiley & Sons Ltd.

  17. Evaluation of a rapid method for the detection of streptococcal group A antigen directly from throat swabs.

    Science.gov (United States)

    Venezia, R A; Ryan, A; Alward, S; Kostun, W A

    1985-01-01

    Throat swabs from 196 pediatric patients were processed by a direct extraction-latex agglutination method (Group A Strep Direct Antigen Identification Test [DAI]) that detects group A streptococci in the specimen. The method requires a 45-min enzymatic extraction period at 37 degrees C and a 4-min reaction period with antibody-linked latex particles. The results were compared with those of the culture and fluorescent antibody methods and the clinical presentation of the patient for pharyngitis. Ninety-three percent of the specimens resulted in agreement by all tests, and 28% were culture positive for group A streptococci. Compared with the culture method, the DAI had a sensitivity and a specificity of 83% and 99%, respectively. The positive predictive values were 98% versus the culture method and 93% versus the fluorescent antibody method, whereas the negative predictive values were 94% versus both other methods. Of the 14 discrepant results when both clinical presentation of an acute pharyngitis and the test results were compared, the culture method provided the best correlation. An additional 64 specimens were processed by the DAI and another direct extraction-latex agglutination method (Culturette Ten-Minute Group A Strep ID Test), and the results were compared with those of the culture method. This group had a 40.6% culture isolation rate for group A streptococci. The sensitivity and specificity of the DAI and Strep ID methods versus the culture method were 81 and 100%, and 77 and 97%, respectively. These results indicate that the DAI is accurate for diagnosing group A streptococcal pharyngitis directly from throat swabs. However, negative results in the presence of a symptomatic patient must be confirmed by standard culture techniques. PMID:3884656

  18. Comparison of illumigene Group A Streptococcus Assay with Culture of Throat Swabs from Children with Sore Throats in the New Zealand School-Based Rheumatic Fever Prevention Program.

    Science.gov (United States)

    Upton, Arlo; Bissessor, Liselle; Farrell, Elizabeth; Shulman, Stanford T; Zheng, Xiaotian; Lennon, Diana

    2016-01-01

    Group A streptococcal (GAS) pharyngitis is a particularly important condition in areas of New Zealand where the incidence of acute rheumatic fever remains unacceptably high. Prompt diagnosis and treatment of GAS pharyngitis are cornerstones of the Rheumatic Fever Prevention Programme, but these are hindered by the turnaround time of culture. Tests with excellent performance and rapid turnaround times are needed. For this study, throat swabs (Copan ESwabs) were collected from schoolchildren self-identifying with a sore throat. Samples were tested by routine culture and the illumigene GAS assay using loop-mediated isothermal amplification. Discrepant results were resolved by retesting of the same specimen by an alternative molecular assay. Seven hundred fifty-seven throat swab specimens were tested by both methods. The performance characteristics of the illumigene assay using culture on blood agar as the "gold standard" and following discrepancy analysis were as follows: sensitivity, 82% and 87%, respectively; specificity, 93% and 98%, respectively; positive predictive value, 61% and 88%, respectively; and negative predictive value, 97% and 97%, respectively. In our unique setting of a school-based throat swabbing program, the illumigene assay did not perform quite as well as described in previous reports. Despite this, its improved sensitivity and rapid turnaround time compared with those of culture are appealing. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  19. 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.

  20. 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

  1. Wildlife specimen collection, preservation, and shipment

    Science.gov (United States)

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

    2015-01-01

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

  2. A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods.

    Science.gov (United States)

    Brownlow, Robert J; Dagnall, Kathryn E; Ames, Carole E

    2012-05-01

    The Metropolitan Police Service currently uses cotton swabs to retrieve DNA for forensic profiling. Recently, a new nylon flocked swab type has become available from Copan (MicroRheologics, Brescia, Italy) that it is claimed, offers increased sample recovery and release yields. If true, the flocked swab may have important applications in DNA evidence retrieval. This study examines the DNA retrieval capability of cotton and nylon flocked swabs when extracted using three common extraction platforms (QIAcube, BioRobot EZ1 and manually processed QIAamp DNA investigator kit). Results indicate that both swab types are capable of recovering high percentages of DNA (>50%); however, the extraction platform selected was shown to have a significant effect upon DNA retrieval. Across all experiments, the cotton swab combined with the spin-column extractions was shown to be most effective, with the nylon swab and BioRobot EZ1 combination being the least effective. These findings illustrate the importance of extraction method selection. © 2011 American Academy of Forensic Sciences.

  3. 37 CFR 2.59 - Filing substitute specimen(s).

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Filing substitute specimen(s). 2.59 Section 2.59 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES Drawing § 2.59 Filing substitute specimen(s). (a...

  4. PE-Swab Direct STR Amplification of Forensic Touch DNA Samples.

    Science.gov (United States)

    Liu, Jason Y

    2015-05-01

    The PE-Swab direct STR amplification workflow was developed to process low-level "touch DNA" samples. In this workflow, a forensic sample is first collected on a 4-mm PE-Swab (a novel sample collection device); two 2-mm punches containing collected samples are then generated from the PE-Swab and directly amplified for STR typing. Compared to the conventional STR workflow, which involves DNA extraction, purification, and elution volume reduction, the PE-Swab direct STR amplification workflow does not require sample preparation and takes DNA loss due to sample preparation, the PE-Swab workflow is more sensitive than the conventional STR workflow. The average peak height per sample obtained by the PE-swab workflow is 3 times higher than that from the conventional workflow with both low-level single source and two-contributor mixture samples tested in this study. © 2015 American Academy of Forensic Sciences.

  5. Actinomyces hominis sp. nov., isolated from a wound swab.

    Science.gov (United States)

    Funke, Guido; Englert, Ralf; Frodl, Reinhard; Bernard, Kathryn A; Stenger, Steffen

    2010-07-01

    A coryneform bacterium (strain 1094(T)) was isolated from a wound swab taken from an 89-year-old female patient. Chemotaxonomic investigations suggested that this bacterium was related to the genera Actinomyces, Arcanobacterium and Actinobaculum. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1094(T) was most closely related to Actinomyces europaeus CCUG 32789 A(T) (94.3 % similarity). Phenotypically, the isolate could be separated from its closest phylogenetic neighbours on the basis of being positive for catalase, CAMP reaction, acid phosphatase, N-acetyl-beta-glucosaminidase and raffinose fermentation. Based on the data presented, it is proposed that strain 1094(T) should be classified in a novel species, Actinomyces hominis sp. nov. The type strain is 1094(T) (=CCUG 57540(T) =DSM 22168(T)).

  6. 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.

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

    Science.gov (United States)

    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 (SpO2) 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 SpO2 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 SpO2 and lower PI values than dogs. The authors propose that increased contact pressure is responsible for significantly higher SpO2 and PI readings with the use of a lingual gauze swab resulting from changes in transmural pressure and arterial compliance. British Veterinary Association.

  8. 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

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

    Science.gov (United States)

    Akmatov, Manas K; Gatzemeier, Anja; Schughart, Klaus; Pessler, Frank

    2012-01-01

    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. 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). Nasal self-swabbing for identification of viral ARI pathogens proved to be equivalent to

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

    Directory of Open Access Journals (Sweden)

    Brenda L. Coleman

    2011-12-01

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

  11. 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.

  12. Transportation

    Science.gov (United States)

    2006-01-01

    container. It now permits free transit of shipping containers from their western ports, if transported by rail directly to the U.S. ( Mireles , 2005, p...Transportation Industry Study Seminar. Mireles , Richard, Castillo. (2005, January). A Cure for West Coast Congestion. Logistics Today, Vol. 46, Issue 1. 1

  13. [Investigation of Chlamydia trachomatis with Cell Culture, DFA and PCR Methods in the Genital Swab Samples of Symptomatic Patients].

    Science.gov (United States)

    Ozüberk, Osman Özüberk; Gökahmetoğlu, Selma; Ozçelik, Bülent; Ekmekçioğlu, Oğuz

    2013-01-01

    Chlamydia trachomatis infection is considered the most prevalent bacterial sexually transmitted disease worldwide. C.trachomatis causes eye infections such as trachoma and newborn inclusion conjunctivitis, newborn pneumonia, genitourinary system infections and suppurative inguinal lymphadenitis namely lymphogranuloma venerum. The aim of this study was to investigate C.trachomatis by direct fluorescent antibody (DFA), polymerase chain reaction (PCR) and cell culture methods in the clinical samples sent to the microbiology laboratory with the prediagnosis of genital infections. A total of 50 swab samples obtained from adult patients (49 female, 1 male) who were admitted to Erciyes University Hospital, Kayseri, Turkey between February-March 2010, were included in the study. C.trachomatis antigens were investigated by a commercial DFA (PathoDx, Remel, USA) method. McCoy cell cultures prepared in microplate wells were used for the isolation of C.trachomatis. The growth of C.trachomatis in cell cultures was confirmed by DFA and iodine staining methods. C.trachomatis DNA was investigated by commercially available PCR (Chlamydia trachomatis 330/740 IC; Sacace, Italy) method. In our study, 4 (8%) of the 50 swab samples were found positive with DFA, 1 (2%) was positive with cell culture, and 1 (2%) was positive with PCR. The only sample that gave positive results with all of the three methods was an urethral swab. Three cervical swab samples that were found positive only with DFA method was evaluated as false positivity. When cell culture was considered as the reference method, the sensitivity and specificity of DFA method were estimated as 100% and 94%, respectively, while those rates for PCR were 100% and 100%, respectively. In conclusion, although cell culture is still the gold standard in the diagnosis of C.trachomatis. infections, since it is time consuming and difficult to apply, more rapid and reliable PCR methods may be applied in diagnosis. DFA method which is

  14. Revised SWAB guidelines for antimicrobial therapy of community-acquired pneumonia

    NARCIS (Netherlands)

    Schouten, JA; Prins, JM; Bonten, MJ; Degener, J; Janknegt, RE; Hollander, JMR; Jonkers, RE; Wijnands, WJ; Verheij, TJ; Sachs, APE; Kullberg, BJ

    The Dutch Working Party on Antibiotic Policy (SWAB) develops evidence-based guidelines, aimed at optimalisation of antibiotic use and limitation of the spread of antimicrobial resistance. A revision of the SWAB guideline for the treatment of community-acquired pneumonia (CAP), published in 1998, was

  15. 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.

  16. Self-collected vaginal swabs for the quantitative real-time polymerase chain reaction assay of Atopobium vaginae and Gardnerella vaginalis and the diagnosis of bacterial vaginosis.

    Science.gov (United States)

    Menard, J-P; Fenollar, F; Raoult, D; Boubli, L; Bretelle, F

    2012-04-01

    The aim of this study was to assess the feasibility of using self-collected vaginal specimens for the quantitative real-time polymerase chain reaction (qPCR) assays of bacterial vaginosis (BV)-associated bacteria versus practitioner-collected swabs. A cross-sectional study included 190 pregnant women enrolled before 20 weeks' gestation from September 2008 to November 2009. Self- and practitioner-collected swabs were taken during the same prenatal visit for each woman, qPCR assays performed for each, and the results compared. The quantification of the human albumin gene was used as an internal control to ensure sampling quality and accurate comparisons. The level of agreement of the qPCR assays for each microorganism was calculated with the Spearman product moment correlation coefficient and the kappa statistic. In all, 370 vaginal samples (185 self- and 185 practitioner-collected swabs) had a narrow range of values for the number of albumin gene copies and a significant correlation coefficient (Spearman's rho = 0.532; p Gardnerella vaginalis; p vaginalis (≥10(9) copies/mL; kappa value = 0.903; p vaginalis, and A. vaginae.

  17. Evaluation of the Recovery Rate of Different Swabs for Microbial Environmental Monitoring.

    Science.gov (United States)

    Goverde, Marcel; Willrodt, Julian; Staerk, Alexandra

    Contact plates, dipslides, and swabs are used for the microbiological monitoring of surfaces in controlled environments such as pharmaceutical clean rooms. In the present study, three different swab types using two different methods (direct streaking on agar versus elution followed by membrane filtration) were evaluated. In a first study, representative surfaces in pharmaceutical clean rooms were artificially inoculated using three different environmental strains (in vitro study). In a second study, a naturally inoculated floor was swabbed with the same three swab types, again using the two different recovery methods (in situ study). With the in vitro study, clear differences were found between the three swab types as well as between the two recovery methods. In addition, recovery rate of the swab type was dependent on the recovery method (interactive effect). One swab type showed a higher recovery rate with direct streaking on agar, while the other swab type showed better results using the elution/membrane filtration method. This difference can be explained by the fact that both swabs were each developed for their specific application. The type of surface also had a highly significant effect on the recovery rates. Recovery on stainless steel was better than for the other surfaces, while lexan had the lowest recovery rate. From the three different strains applied in the in vitro study, Micrococcus luteus had significantly higher recovery results compared to the other two strains (Bacillus thuringiensis, Aspergillus brasiliensis). The differences in recovery between the swab type and recovery method were less pronounced in the in situ study. In particular, the recovery of the swab type depending on the recovery method was not found. In conclusion, if swabs are to be used for environmental monitoring, their suitability should first be evaluated. This can be approached with artificially inoculated surfaces. However, naturally inoculated surfaces might be more

  18. Pseudomonas aeruginosa contamination of mouth swabs during production causing a major outbreak

    Directory of Open Access Journals (Sweden)

    Lassen Jørgen

    2007-03-01

    Full Text Available Abstract Background In 2002 we investigated an outbreak comprising 231 patients in Norway, caused by Pseudomonas aeruginosa and linked to the use of contaminated mouth swabs called Dent-O-Sept. Here we describe the extent of contamination of the swabs, and identify critical points in the production process that made the contamination possible, in order to prevent future outbreaks. Methods Environmental investigation with microbiological examination of production, ingredients and product, molecular typing of bacteria and a system audit of production. Results Of the 1565 swabs examined from 149 different production batches the outbreak strain of P. aeruginosa was detected in 76 swabs from 12 batches produced in 2001 and 2002. In total more than 250 swabs were contaminated with one or more microbial species. P. aeruginosa was detected from different spots along the production line. The audit revealed serious breeches of production regulations. Health care institutions reported non-proper use of the swabs and weaknesses in their purchasing systems. Conclusion Biofilm formation in the wet part of the production is the most plausible explanation for the continuous contamination of the swabs with P. aeruginosa over a period of at least 30 weeks. When not abiding to production regulations fatal consequences for the users may ensue. For the most vulnerable patient groups only documented quality-controlled, high-level disinfected products and items should be used in the oropharynx.

  19. Broth versus solid agar culture of swab samples of cadaveric allograft musculoskeletal tissue.

    Science.gov (United States)

    Varettas, Kerry

    2013-12-01

    As part of the donor assessment protocol, bioburden assessment must be performed on allograft musculoskeletal tissue samples collected at the time of tissue retrieval. Swab samples of musculoskeletal tissue allografts from cadaveric donors are received at the microbiology department of the South Eastern Area Laboratory Services (Australia) to determine the presence of bacteria and fungi. This study will review the isolation rate of organisms from solid agar and broth culture of swab samples of cadaveric allograft musculoskeletal tissue over a 6-year period, 2006-2011. Swabs were inoculated onto horse blood agar (anaerobic, 35 °C) and chocolate agar (CO2, 35 °C) and then placed into a cooked meat broth (aerobic, 35 °C). A total of 1,912 swabs from 389 donors were received during the study period. 557 (29.1 %) swabs were culture positive with the isolation of 713 organisms, 249 (34.9 %) from solid agar culture and an additional 464 (65.1 %) from broth culture only. This study has shown that the broth culture of cadaveric allograft musculoskeletal swab samples recovered a greater amount of organisms than solid agar culture. Isolates such as Clostridium species and Staphylococcus aureus would not have been isolated from solid agar culture alone. Broth culture is an essential part of the bioburden assessment protocol of swab samples of cadaveric allograft musculoskeletal tissue in this laboratory.

  20. The Development of Indicator Cotton Swabs for the Detection of pH in Wounds

    Directory of Open Access Journals (Sweden)

    Cindy Schaude

    2017-06-01

    Full Text Available Indicator cotton swabs have been developed in order to enable faster, less expensive, and simpler information gathering of a wound status. Swabs are normally used for cleaning the wound, but here, they were covalently functionalized with indicator chemistry. Thus, they in principle enable simultaneous wound cleaning and wound pH detection. Using an indicator dye with a color change from yellow to red, combined with an inert dye of blue color, a traffic light color change from green to red is induced when pH increases. The indicator cotton swabs (ICSs show a color change from green (appropriate wound pH to red (elevated wound pH. This color change can be interpreted by the naked eye as well as by an optical color measurement device in order to obtain quantitative data based on the CIE L*a*b* color space. Two types of swabs have been developed—indicator cotton swabs ICS1 with a sensitive range from pH 5 to 7 and swabs ICS2 with a sensitive range from 6.5 to 8.5. The swabs are gamma-sterilized and the effect of sterilization on performance was found to be negligible. Furthermore, cytotoxicity testing shows cell viability and endotoxin levels to be within the allowable range.

  1. The Development of Indicator Cotton Swabs for the Detection of pH in Wounds.

    Science.gov (United States)

    Schaude, Cindy; Fröhlich, Eleonore; Meindl, Claudia; Attard, Jennifer; Binder, Barbara; Mohr, Gerhard J

    2017-06-12

    Indicator cotton swabs have been developed in order to enable faster, less expensive, and simpler information gathering of a wound status. Swabs are normally used for cleaning the wound, but here, they were covalently functionalized with indicator chemistry. Thus, they in principle enable simultaneous wound cleaning and wound pH detection. Using an indicator dye with a color change from yellow to red, combined with an inert dye of blue color, a traffic light color change from green to red is induced when pH increases. The indicator cotton swabs (ICSs) show a color change from green (appropriate wound pH) to red (elevated wound pH). This color change can be interpreted by the naked eye as well as by an optical color measurement device in order to obtain quantitative data based on the CIE L*a*b* color space. Two types of swabs have been developed-indicator cotton swabs ICS1 with a sensitive range from pH 5 to 7 and swabs ICS2 with a sensitive range from 6.5 to 8.5. The swabs are gamma-sterilized and the effect of sterilization on performance was found to be negligible. Furthermore, cytotoxicity testing shows cell viability and endotoxin levels to be within the allowable range.

  2. [Correlation between microbial growth in conjunctival swabs of corneal donors and contamination of organ culture media].

    Science.gov (United States)

    Li, S; Bischoff, M; Schirra, F; Langenbucher, A; Ong, M; Halfmann, A; Herrmann, M; Seitz, B

    2014-06-01

    The aim of the study was to determine the rate of contamination in conjunctival swabs from corneal donors by microbiological investigations and to correlate this with microbial contamination of the culture medium. Contamination of conjunctival swabs and culture media was analyzed retrospectively for the years 2009, 2010 and 2011 at the LIONS corneal bank of Saar-Lor-Lux Trier/Westpfalz at the Saarland University Medical Center. The total annual number of conjunctival swabs was 316 in 2009, 341 in 2010 and 381 in 2011. Conjunctival swabs were taken prior to 1.25% povidone-iodine application. After disinfection donor corneas were harvested by in situ corneoscleral disc excision in all cases. The correlation between positive conjunctival swabs and microbial contamination of the culture medium was analyzed. In every year examined the contamination rate of the culture medium was significantly higher in cases of contaminated conjunctival swabs (p culture medium was contaminated in 16.5%, 11.5% and 7.6% of the donated corneas with positive conjunctival swabs and in 7.2%, 1.9% and 0.6% in donated corneas with negative conjunctival swabs, respectively. A positive correlation was found between contamination of the culture medium and microbial colonization of the conjunctival swabs, Nevertheless, microbial colonization of the conjunctiva was high and contamination of the culture medium was relatively low. For the microbial contamination rate of the donated corneas in the medium, conjunctival disinfection time with iodine solution before explantation of the corneoscleral disc and the addition of antibiotics to the culture medium seem to play a protective role.

  3. Transportes

    Directory of Open Access Journals (Sweden)

    Hidalgo Fernández-Cano, Amalio

    1960-01-01

    Full Text Available El movimiento de materiales dentro de la Factoría está atendido por tres principales medios de transporte, en consonancia con las características del material y de los desplazamientos. Así se han establecido: sistemas de cintas transportadoras, una red ferroviaria de ancho normal y una completa malla de caminos enlazando funcionalmente las instalaciones.

  4. 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...

  5. Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus

    Science.gov (United States)

    Hollenback, Nathan; Scheel, David; Gravley, Meg C.; Sage, George K.; Toussaint, Rebecca K.; Talbot, Sandra

    2017-01-01

    We evaluated the efficacy of using swabs to collect cells from the epidermis of octopus as a non-invasive DNA source for classical genetic studies, and demonstrated value of the technique by incorporating it into an effort to determine, within a day, the lineage of captured, live Enteroctopus (E. dofleini or a cryptic lineage). The cryptic lineage was targeted for captive behavioral and morphological studies, while once genetically identified, the non-target lineage could be more rapidly released back to the wild. We used commercially available sterile foamtipped swabs and a high-salt preservation buffer to collect and store paired swab and muscle (arm tip) tissue sampled from live Enteroctopus collected from Prince William Sound, Alaska. We performed a one-day extraction of DNA from epithelial swab samples and amplification of two diagnostic microsatellite loci to determine the lineage of each of the 21 individuals. Following this rapid lineage assessment, which allowed us to release non-target individuals within a day of laboratory work, we compared paired swab and muscle tissue samples from each individual to assess quantity of DNA yields and consistency of genotyping results, followed by assessment of locus-by-locus reliability of DNA extracts from swabs. Epithelial swabs yielded, on average, lower quantities of DNA (170.32 ± 74.72 (SD) ng/μL) relative to DNA obtained from tissues collected using invasive or destructive techniques (310.95 ± 147.37 (SD) ng/μL. We observed some decrease in yields of DNA from extractions of swab samples conducted 19 and 31 months after initial extractions when samples were stored at room temperature in lysis buffer. All extractions yielded quantities of DNA sufficient to amplify and score all loci, which included fragment data from 10 microsatellite loci (nine polymorphic loci and monomorphic locus EdoμA106), and nucleotide sequence data from a 528 base pair portion of the nuclear octopine dehydrogenase gene. All results

  6. Self-collected vaginal swabs for HPV screening: An exploratory study of rural Black Mississippi women

    Directory of Open Access Journals (Sweden)

    Richard A. Crosby

    2017-09-01

    Conclusions: Black rural women from the deep-south are generally comfortable self-collecting cervico-vaginal swabs for HPV testing. Given that nearly 30% tested positive for oncogenic HPV, and that fatalism as well a lack of trust in doctors predicted prevalence, a reasonable screening alternative to Pap testing may be community-based testing for HPV using self-collected vaginal swabs.

  7. Fabrication of SERS swab for direct detection of trace explosives in fingerprints.

    Science.gov (United States)

    Gong, Zhengjun; Du, Hongjie; Cheng, Fansheng; Wang, Cong; Wang, Canchen; Fan, Meikun

    2014-12-24

    Swab sampling is of great importance in surface contamination analysis. A cotton swab (cotton Q-tip) was successfully transformed into surface-enhanced Raman scattering (SERS) substrate (SERS Q-tip) through a bottom-up strategy, where Ag NPs were first self-assembled onto the Q-tip followed by in situ growing. The capability for direct swab detection of Raman probe Nile Blue A (NBA) and a primary explosive marker 2,4-dinitrotoluene (2,4-DNT) using the SERS Q-tip was explored. It was found that at optimum conditions, a femotogram of NBA on glass surface could be swab-detected. The lowest detectable amount for 2,4-DNT is only ∼1.2 ng/cm(2) (total amount of 5 ng) on glass surface, 2 orders of magnitude more sensitive than similar surface analysis achieved with infrared technique, and comparable even with that obtained by ion mobility spectrometry-mass spectrometry. Finally, 2,4-DNT left on fingerprints was also analyzed. It was found that SERS signal of 2,4-DNT from 27th fingerprint after touching 2,4-DNT powder can still be clearly identified by swabbing with the SERS Q-tip. We believe this is the first direct SERS swabbing test of explosives on fingerprint on glass. Considering its relative long shelf life (>30 d), the SERS Q-tip may find great potential in future homeland security applications when combined with portable Raman spectrometers.

  8. New technique to take samples from environmental surfaces using flocked nylon swabs.

    Science.gov (United States)

    Hedin, G; Rynbäck, J; Loré, B

    2010-08-01

    Environmental surfaces near infected and/or colonised patients in hospitals are commonly contaminated with potentially pathogenic micro-organisms. At present, however, there is no standardised method for taking samples from surfaces in order to perform quantitative cultures. Usually contact plates or swabs are used, but these methods may give different results. The recovery rate of traditional swabbing, e.g. cotton or rayon, is poor. With a new type of swab utilising flocked nylon, the recovery may be enhanced up to three times compared with a rayon swab. In this study, we inoculated reference strains of Staphylococcus aureus and Enterococcus hirae onto a bedside table and took samples 1h later when inocula were dry. Sequential samples were taken from the same surface. A new sampling technique using two sequential nylon swabs for each sample was validated. The efficiency of the sampling, percentage recovery of the inoculum and the variation of culture results obtained from repeated experiments are described. Enhanced efficiency and higher recovery of inoculum were demonstrated using two sequential flocked nylon swabs for sampling. Copyright 2010 The Hospital Infection Society. Published by Elsevier Ltd. All rights reserved.

  9. Microbial contamination assessment of cryostored autogenous cranial bone flaps: should bone biopsies or swabs be performed?

    Science.gov (United States)

    Bhaskar, Ivan P; Inglis, Timothy J J; Bowman, Jacintha; Lee, Gabriel Y F

    2013-02-01

    Autogenous cranioplasty infection requiring bone flap removal is under-recognised as a major complication causing significant morbidity. Microbial contamination of stored bone flaps may be a significant contributing factor. Current infection control practices and storage procedures vary. It is not known whether 'superficial' swabs or bone cultures provide a more accurate assessment. Twenty-five skull flaps that were cryo-stored for more than 6 months were studied. Two swab samples (superficial and deep) and a bone biopsy sample were taken from each skull flap sample and cultured. Half blood agar and half chocolate agar plates were inoculated with the swabs for anaerobic and aerobic cultures respectively. The bone biopsy samples were cultured in brain-heart broth and subcultured similar to the swabs for 5 days. Incidence of microbial contamination was 20 % in the bone flaps studied. One swab culture and five bone biopsy cultures were positive for bacterial growth, all of which contained Propionibacterium acnes (p = 0.014). Positive cultures were from bone flaps stored less than 18 months, whereas no growth was obtained from bone flaps that were stored longer (p = 0.014). Bone biopsy culture is a more sensitive technique of assessing microbial contamination of cryo-stored autogenous bone flaps than swab cultures. The clinical implications of in vitro demonstration of microbial contamination require further study.

  10. Histopathologic Analysis of Pancreaticoduodenectomy Specimen

    Directory of Open Access Journals (Sweden)

    Ramesh Dhakhwa

    2016-12-01

    Conclusions: Pancreaticoduodenectomy specimen requires thorough histopathological evaluation. Pathologists should also be aware of possibility of a benign diagnosis in PD specimens which have been resected presuming malignancy based on clinical judgement and radiological data. Keywords: histopathologic evaluation, pancreaticoduodenectomy, periampullary carcinoma. | PubMed

  11. Detection of high-risk human papillomavirus infection in tonsillar specimens using 2 commercially available assays.

    Science.gov (United States)

    Cockerill, Cara C; Orvidas, Laura J; Moore, Eric J; Binnicker, Matthew J; Duresko, Brian J; Espy, Mark J; Cockerill, Franklin R; Tombers, Nicole M; Pritt, Bobbi S

    2016-12-01

    THE OBJECTIVE OF THE STUDY IS TO DETERMINE THE PREVALENCE OF HIGH-RISK HUMAN PAPILLOMAVIRUS (HRHPV) INFECTION IN TONSILLAR SWABS AND TISSUE: Patients undergoing tonsillectomy for nonmalignant causes were enrolled. A flocked swab and fresh tissue were collected from the left and right tonsil of each patient. Specimens were tested for hrHPV DNA using the Roche cobas test and for the presence of E6/E7 messenger RNA using the Hologic Aptima hrHPV test. Of the 193 patients enrolled, 129 were in the pediatric group (ages 1-12years; median, 5years), and 64 were in the adult group (ages 13-55; median, 22years). All swab and tissue specimens were negative for hrHPV by both methods. Positive, negative, and internal controls performed as expected. We found a 0% rate of infection indicating that detectable hrHPV infection in tonsillar tissue appears to be uncommon in the children and adults in the population sampled. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Comparison of manual and automated nucleic acid extraction methods from clinical specimens for microbial diagnosis purposes.

    Science.gov (United States)

    Wozniak, Aniela; Geoffroy, Enrique; Miranda, Carolina; Castillo, Claudia; Sanhueza, Francia; García, Patricia

    2016-11-01

    The choice of nucleic acids (NAs) extraction method for molecular diagnosis in microbiology is of major importance because of the low microbial load, different nature of microorganisms, and clinical specimens. The NA yield of different extraction methods has been mostly studied using spiked samples. However, information from real human clinical specimens is scarce. The purpose of this study was to compare the performance of a manual low-cost extraction method (Qiagen kit or salting-out extraction method) with the automated high-cost MagNAPure Compact method. According to cycle threshold values for different pathogens, MagNAPure is as efficient as Qiagen for NA extraction from noncomplex clinical specimens (nasopharyngeal swab, skin swab, plasma, respiratory specimens). In contrast, according to cycle threshold values for RNAseP, MagNAPure method may not be an appropriate method for NA extraction from blood. We believe that MagNAPure versatility reduced risk of cross-contamination and reduced hands-on time compensates its high cost. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. 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.

  14. 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.

  15. Post-coital vaginal sampling with nylon flocked swabs improves DNA typing.

    Science.gov (United States)

    Benschop, Corina C G; Wiebosch, Danielle C; Kloosterman, Ate D; Sijen, Titia

    2010-02-01

    In the examination of sexual assault cases, DNA typing of vaginal samples mostly occurs after differential DNA extraction. Notwithstanding the differential extraction method, the DNA profiles from the seminal fraction often show the male alleles at low-level in combination with female alleles. This unfavorable ratio male to female DNA is due to a limited amount of sperm cells and an overwhelming quantity of female cells. In this study, we compared standard cotton and nylon flocked swabs for post-coital vaginal sampling. Twelve couples donated 88 vaginal swabs - 44 cotton, 44 nylon flocked - which were taken with a time since intercourse (TSI) up to 84 h. These vaginal swabs were sorted into categories on the basis of the TSI and submitted to (1) microscopic examination for the presence of male cells, (2) presumptive tests for the detection of seminal fluid and (3) DNA typing. Cellular elution was found to be 6-fold more efficient from the nylon flocked swabs. This makes microscopic analysis less time consuming as the higher cell yield and better cell morphology simplify detection of male cells. Both swab types reveal similar results regarding presumptive tests and male DNA typing. Positive presumptive tests (RSID-semen and PSA) were obtained up to 60 h TSI and male autosomal profiles up to 72 h TSI. Interestingly, over 50% of the samples negative for both presumptive tests resulted in informative male STR profiles. After differential extraction, less DNA was left on the nylon flocked swabs and more male DNA was isolated. Our results imply that the use of nylon flocked swabs for vaginal sampling will improve microscopic analysis and DNA typing in the medical forensic investigation of sexual assault cases.

  16. Microbiological burden of public transport vehicles

    OpenAIRE

    Birteksöz Tan, Ayşe Seher; Erdoğdu, Gamze

    2017-01-01

    The goal of this study was to determine therole of public transport in the transmission of microorganisms. A total of 60swab samples were collected in the morning and evening from handles in publictransport trams, metrobuses, and buses. Swab samples were examined usingmicrobiological methods, and the number and types of microorganisms weredetermined. Total aerobic bacterial and fungal counts in samples collected inthe evening were higher than those in samples collected in the morning fromtram...

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Campylobacter sp in eggs from cloacal swab positive breeder hens Campylobacter sp em ovos provenientes de matrizes pesadas com swab cloacal positivo

    Directory of Open Access Journals (Sweden)

    Belchiolina Beatriz Fonseca

    2006-12-01

    Full Text Available Campylobacter sp is a microaerophilic, thermotolerating Gram negative bacterium, known to be one of the main causes of food-borne human infections. Among the foods that carry these microorganisms, the chicken is outstanding. In Brazil, a large chicken exporting country, few researches are conducted about their prevalence in breeder hens and the transmission through eggs. The aim of this research was to verify the presence of Campylobacter sp in the shells and within the eggs from positive cloacal swab breeder hens. Microbiological analyses were made on cloacal swabs of 140 weighed breeder hens. The positive breeder hens were set aside and in a total of 244 of their eggs, Campylobacter sp was present in macerated shells and yolk contents during 7 weeks. Out of the 140 researched breeder hens, 25 (17.8% were positive from cloacal swabs, however the eggs were not positive. The physiological characteristics of the birds, their eggs and Campylobacter sp favor the bacterium entering and surviving in the eggs, but in this study, no positive result was found in macerated shells or in the yolks, indicating that vertical transmission is probably an unusual event.Campylobacter sp é reconhecida como uma das principais causas de gastrenterite humana de origem alimentar. Dentre os alimentos veiculadores desses microrganismos, a carne de frango tem sido a mais implicada. Os estudos existentes sobre a transmissão vertical da Campylobacter são escassos e não conclusivos. O objetivo desse estudo foi verificar a presença de Campylobacter sp na casca e interior de ovos de matrizes positivas em swabs cloacais e a possibilidade de transmissão vertical. Foram analisados swabs cloacais de 140 matrizes pesadas e seus ovos colhidos para análise durante 7 semanas consecutivas. Dos 244 ovos colhidos, 129 foram fumigados e 115 analisados sem tratamento. Foram analisados o macerado da casca e a gema. Das 140 matrizes pesquisadas, 25 (17,8% foram positivas em swabs

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

    Science.gov (United States)

    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.

  20. 2003 Dead Bald Eagle Specimen

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The specimen report states the Bald Eagle was found along the side of the I-95 by a motorist who contacted Santee National Wildlife Refuge. The Bald Eagle was taken...

  1. 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).

  2. Novel, rapid optical immunoassay technique for detection of group A streptococci from pharyngeal specimens: comparison with standard culture methods.

    OpenAIRE

    Harbeck, R. J.; Teague, J; Crossen, G R; Maul, D M; Childers, P L

    1993-01-01

    A novel immunoassay system based on the changes in the reflection of light, termed an optical immunoassay (OIA), was utilized to directly detect group A streptococcal (GAS) carbohydrate antigen from clinical specimens. In two studies, a total of 1,275 throat swabs were tested for the presence of this antigen with the Strep A OIA rapid detection system and the results were compared with those of standard culture methods. In both studies, the Strep A OIA yielded more positive results than plati...

  3. Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs.

    Directory of Open Access Journals (Sweden)

    Md Abu Choudhury

    Full Text Available Skin bacteria at peripheral intravenous catheter (PIVC insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs. Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, p<0.001. Methylobacterium spp. was the dominant genus in all PIVC tip samples, but not so for skin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%, Pseudomonas spp., (10% and Acinetobacter spp. (10% were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.

  4. 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...... 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....

  5. Evaluation of the Swabbing of Disposable Absorbent Incontinence Products for Assessing the Carriage of Multiresistant Enterobacteriaceae in Nursing Home Residents

    Directory of Open Access Journals (Sweden)

    Alexis Naf

    2017-09-01

    Full Text Available We compared the performance of incontinence product (IP and rectal swabbing for the detection of multidrug-resistant Enterobacteriaceae (MDRE carriage in a large multicenter study conducted in February 2017 among the residents of 23 French nursing homes. The study included 547 residents who habitually wore IP, 88 of whom were MDRE carriers (16.1%. Positive results were obtained for both rectal and IP swabs for 64 of these residents, for rectal swabs only for 22 and for IP swabs only for two of these patients. The estimated prevalence of MDRE carriage depended on the type of sample: 15.7% for rectal swabs and 12.1% for IP swabs (p < 0.001. The positive percent agreement was 84.2% and the negative percent agreement was 97.4%. Rectal swabbing remains the best method for detecting MDRE carriage in elderly residents, but our findings provide support for the use of swabs from IP used overnight to increase response rates in MDRE surveys in elderly residents that habitually wear IP, when rectal swabbing is not feasible.

  6. Comparison of feces versus rectal swabs for the molecular detection of Lawsonia intracellularis in foals with equine proliferative enteropathy.

    Science.gov (United States)

    Pusterla, Nicola; Mapes, Samantha; Johnson, Cara; Slovis, Nathan; Page, Allen; Gebhart, Connie

    2010-09-01

    The purpose of the current study was to compare the molecular detection rate of Lawsonia intracellularis between feces and rectal swabs collected from 42 foals with suspected equine proliferative enteropathy (EPE). Fecal samples and rectal swabs were processed for DNA purification by using an automated extraction system. The purified DNA was then analyzed by real-time polymerase chain reaction (PCR) for the presence of the aspartate ammonia lyase (aspA) gene of L. intracellularis. Absolute quantitation was calculated by using a standard curve for L. intracellularis and expressed as copy numbers of the aspA gene of L. intracellularis per microliter of purified DNA. The combined PCR detection rate for L. intracellularis was 90%, with 38 foals testing PCR positive in feces (33 samples), rectal swabs (32), or both (27). Six foals tested PCR positive only in feces, whereas 5 tested positive only in rectal swabs. Feces yielded a significantly higher aspA gene copy number of L. intracellularis than rectal swabs. Feces and rectal swabs tested PCR negative from 4 foals. In conclusion, the results showed that feces yielded similar numbers of PCR-positive results, with a higher L. intracellularis aspA gene load than rectal swabs. By analyzing dual samples, the PCR detection rate for L. intracellularis increased from 76% and 79% for rectal swabs and feces, respectively, to 90%. Rectal swabs should be considered as an alternative sample type for EPE-suspected patients with decreased or no fecal output.

  7. Evaluation of BacLite Rapid MRSA, a rapid culture based screening test for the detection of ciprofloxacin and methicillin resistant S. aureus (MRSA from screening swabs

    Directory of Open Access Journals (Sweden)

    Skyrme Margaret

    2006-09-01

    Full Text Available Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA is a major nosocomial pathogen worldwide. The need for accurate and rapid screening methods to detect MRSA carriers has been clearly established. The performance of a novel assay, BacLite Rapid MRSA (Acolyte Biomedica, UK for the rapid detection (5 h and identification of hospital associated ciprofloxacin resistant strains of MRSA directly from nasal swab specimens was compared to that obtained by culture on Mannitol salt agar containing Oxacillin (MSAO after 48 h incubation. Results A total of 1382 nasal screening swabs were tested by multiple operators. The BacLite Rapid MRSA test detected 142 out of the 157 confirmed MRSA that were detected on MSAO giving a diagnostic sensitivity of 90.4, diagnostic specificity of 95.7% and a negative predictive value of 98.7%. Of the 15 false negatives obtained by the BacLite Rapid MRSA test, seven grew small amounts ( Conclusion The Baclite MRSA test is easy to use and provides a similar level of sensitivity to conventional culture for the detection of nasal carriage of MRSA with the advantage that the results are obtained much more rapidly.

  8. 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.

  9. 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.

  10. 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.

  11. Sensitive diagnosis of cutaneous leishmaniasis by lesion swab sampling coupled to qPCR

    NARCIS (Netherlands)

    Adams, Emily R.; Gomez, Maria Adelaida; Scheske, Laura; Rios, Ruby; Marquez, Ricardo; Cossio, Alexandra; Albertini, Audrey; Schallig, Henk; Saravia, Nancy Gore

    2014-01-01

    Variation in clinical accuracy of molecular diagnostic methods for cutaneous leishmaniasis (CL) is commonly observed depending on the sample source, the method of DNA recovery and the molecular test. Few attempts have been made to compare these variables. Two swab and aspirate samples from lesions

  12. 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 ...

  13. 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…

  14. DNA from buccal swabs suitable for high-throughput SNP multiplex analysis.

    Science.gov (United States)

    McMichael, Gai L; Gibson, Catherine S; O'Callaghan, Michael E; Goldwater, Paul N; Dekker, Gustaaf A; Haan, Eric A; MacLennan, Alastair H

    2009-12-01

    We sought a convenient and reliable method for collection of genetic material that is inexpensive and noninvasive and suitable for self-collection and mailing and a compatible, commercial DNA extraction protocol to meet quantitative and qualitative requirements for high-throughput single nucleotide polymorphism (SNP) multiplex analysis on an automated platform. Buccal swabs were collected from 34 individuals as part of a pilot study to test commercially available buccal swabs and DNA extraction kits. DNA was quantified on a spectrofluorometer with Picogreen dsDNA prior to testing the DNA integrity with predesigned SNP multiplex assays. Based on the pilot study results, the Catch-All swabs and Isohelix buccal DNA isolation kit were selected for our high-throughput application and extended to a further 1140 samples as part of a large cohort study. The average DNA yield in the pilot study (n=34) was 1.94 microg +/- 0.54 with a 94% genotyping pass rate. For the high-throughput application (n=1140), the average DNA yield was 2.44 microg +/- 1.74 with a >or=93% genotyping pass rate. The Catch-All buccal swabs are a convenient and cost-effective alternative to blood sampling. Combined with the Isohelix buccal DNA isolation kit, they provided DNA of sufficient quantity and quality for high-throughput SNP multiplex analysis.

  15. Occurrence of Tropheryma whipplei during diarrhea in Hajj pilgrims: a PCR analysis of paired rectal swabs.

    Science.gov (United States)

    Gautret, Philippe; Benkouiten, Samir; Parola, Philippe; Brouqui, Philippe; Memish, Ziad; Raoult, Didier

    2014-01-01

    Tropheryma whipplei was recently associated with gastroenteritis in children. We hypothesize that T. whipplei may be a contributing microbe in traveller's diarrhea. The presence of T. whipplei was investigated by PCR on rectal swab samples of Hajj pilgrims before and after travelling to the Kingdom of Saudi Arabia (KSA). Additionally a rectal swab was performed at the time of diarrhea for some pilgrims. A total of 129 pilgrims underwent rectal swab samples before departure and on return. All pilgrims were negative for T. whipplei before travel. One pilgrim (0.8%) was positive on return but did not reported diarrhea. A total of 30 pilgrims (23.3%) experienced diarrhea during the stay in the KSA. Nine pilgrims with diarrhea underwent the additional rectal swab during their diarrhea episode, two of them were positive for T. whipplei. This work suggests that T. whipplei may be associated with adult traveller's diarrhea, by finding T. whipplei DNA individuals negative before and after the episode of diarrhea. Further study addressing this issue in larger cohorts of Hajj pilgrims with systematic sampling at the time of diarrheal episode may help to understand the potential role of T. whipplei in traveller's diarrhea. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Performance of self-collected penile-meatal swabs compared to clinician-collected urethral swabs for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium by nucleic acid amplification assays.

    Science.gov (United States)

    Dize, Laura; Barnes, Perry; Barnes, Mathilda; Hsieh, Yu-Hsiang; Marsiglia, Vincent; Duncan, Della; Hardick, Justin; Gaydos, Charlotte A

    2016-10-01

    Men were enrolled in a study to assess the performance and acceptability of self-collected penile meatal swabs as compared to clinician-collected urethral swabs for sexually transmitted infections (STIs). We expected penile-meatal swabs to perform favorably to urethral swabs for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) detection by nucleic acid amplification assays (NAATs). Of 203 swab pairs tested; for CT, penile-meatal swab sensitivity was 96.8% and specificity was 98.8%. NG sensitivity and specificity were 100% and 98.9%, respectively. For TV, sensitivity was 85.0% and specificity was 96.7%. For MG sensitivity and specificity were 79.3% and 99.4%, respectively. No significant statistical differences between sample type accuracy (CT: P=0.625; NG: P=0.248; TV: P=0.344; and MG: P=0.070) existed. Most men, 90.1%, reported self-collection of penile-meatal swabs as "Very Easy" or "Easy". Self-collected penile-meatal swabs appeared acceptable for NAAT STI detection and an acceptable collection method by men. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. [Antibiotic sensitivity of beta-hemolytic streptococci isolated from throat swabs and purulent material].

    Science.gov (United States)

    Jachna-Sawicka, Katarzyna; Pietrzak, Anna; Bogiel, Tomasz; Gospodarek, Eugenia

    2010-01-01

    The aim of this study was to evaluate the prevalence and susceptibility of beta-hemolytic streptococci isolated from throat swabs (142--29.9%) and purulent material (333--70.1%) taken from patients treated at University Hospital dr. A. Jurasz in Bydgoszcz Collegium Medicum. L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Torun in 2005-2009. Of the 475 tested strains, 156 (32.8%) were identified as S. pyogenes. This species accounted for 38.8% of strains isolated from purulent material and 19.0% of swabs from the throat. Among the strains isolated from throat swabs of 62 (43.7%) were identified as Streptococcus group C. Only 5.1% strains were identified as Streptococcus group F. All strains of beta-hemolytic streptococci were susceptible to ampicillin or penicillin, fluoroquinolones, vancomycin and linezolid. Erythromycin-susceptible strains was 83.8%, and 89.1% for clindamycin. A total of 51.3% of erythromycin resistance strains had the cMLS(B) phenotype (63.3% for strains from throat swabs and 46.3% of the purulent materials). Sensitivity to tetracycline was characterized by 51.2% of strains of beta-hemolytic streptococci. The percentage of strains susceptible to this antibiotic among isolates from throat swabs was 63.1%, and purulent material--48.0%. The lowest percentage of strains susceptible to tetracycline (14.1%) were found among S. agalactiae and Streptococcus group G (33.6%) strains. During the study time, saw an increase in the percentage of strains susceptible to tetracycline and erythromycin.

  18. Assessing the ability of swab data to determine the true burden of infection for the amphibian pathogen Batrachochytrium dendrobatidis.

    Science.gov (United States)

    Clare, Frances; Daniel, Olivia; Garner, Trent; Fisher, Matthew

    2016-06-01

    Batrachochytrium dendrobatidis (Bd) is a pathogenic fungus which causes the disease chytridiomycosis in amphibians by infecting the animals' epidermis. The most commonly applied method for the detection of Bd is the use of a sterile swab, rubbed over the keratinized areas of an amphibian and then processed to yield DNA for detection by qPCR. This method has been used to infer a threshold of lethal infection in some species; however, how reliable and reproducible the swabbing method is at detecting the true burden of infection suffered by individuals is not known. European midwife toads, Alytes obstetricans, are susceptible to chytridiomycosis and are highly parasitised by Bd across Europe. By quantifying Bd-load throughout the entire skin and comparing this to swab results taken from the same individual, we determined whether epidermal swabs provide a quantifiable and accurate indication of the true fungal burden suffered. Further, we examined whether we could infer a threshold for lethal infection based on comparison of swab data taken from infected A. obstetricans exhibiting different clinical states. From swab data, we detected significantly higher fungal burdens from moribund metamorphs compared to visually healthy individuals; however, the ability of these swab data to provide an accurate indication of the true fungal burden was not reliable. These data suggest that fungal load dynamics play an important role in disease-induced mortality in A. obstetricans at these sites, but that using swab data to infer an exact threshold for Bd-associated mortality might be inappropriate and misleading.

  19. Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients.

    Directory of Open Access Journals (Sweden)

    Darius Seidler

    Full Text Available Due to frequent infections in cystic fibrosis (CF patients, repeated respiratory cultures are obtained to inform treatment. When patients are unable to expectorate sputum, clinicians obtain throat swabs as a surrogate for lower respiratory cultures. There is no clear data in adult subjects demonstrating the adequacy of throat swabs as a surrogate for sputum or BAL. Our study was designed to determine the utility of throat swabs in identifying lung colonization with common organisms in adults with CF.Adult CF subjects (n = 20 underwent bronchoscopy with BAL. Prior to bronchoscopy, a throat swab was obtained. A sputum sample was obtained from subjects who were able to spontaneously expectorate. All samples were sent for standard microbiology culture.Using BAL as the gold standard, we found the positive predictive value for Pseudomonas aeruginosa to be 100% in both sputum and throat swab compared to BAL. However, the negative predictive value for P. aeruginosa was 60% and 50% in sputum and throat swab, respectively. Conversely, the positive predictive value for Staphylococcus aureus was 57% in sputum and only 41% in throat swab and the negative predictive value of S. aureus was 100% in sputum and throat swab compared to BAL.Our data show that positive sputum and throat culture findings of P. aeruginosa reflect results found on BAL fluid analysis, suggesting these are reasonable surrogates to determine lung colonization with P. aeruginosa. However, sputum and throat culture findings of S. aureus do not appear to reflect S. aureus colonization of the lung.

  20. Detection of Pneumocystis in the nasal swabs of immune-suppressed rats by use of PCR and microscopy.

    Science.gov (United States)

    Can, Hüseyin; Caner, Ayşe; Döşkaya, Mert; Değirmenci, Aysu; Karaçalı, Sabire; Polat, Ceylan; Gürüz, Yüksel; Uner, Ahmet

    2013-02-13

    Detection of Pneumocystis jiroveci colonization in lungs or oral samples due to high sensitivity of PCR methods results in undue treatment of patients without any symptoms of Pneumocystis pneumonia. The aim of the present study is to demonstrate Pneumocystis carinii in rats, immune suppressed by oral and subcutaneous administration of dexamethasone. Blood, oral, nasal and eye swabs were collected prior to immune suppression and 2, 6, 12 weeks after administration of dexamethasone. Also, samples were collected from lung, heart, liver, kidney, diaphragm, brain, spleen, tongue, muscle, eye, intestine, and feces. Cysts and trophozoites were investigated in stained slides and MSG gene was detected by PCR. The results showed that weight loss is significantly higher in rats administered oral dexamethasone (Pdexamethasone. PCR was positive in lungs and oral swabs of rats prior to the administration of dexamethasone. After the administration of dexamethasone, the MSG gene was detected in oral swabs, lungs, spleen, kidney and (for the first time) in nasal swabs. PCR was positive in nasal swabs during the second and sixth weeks of oral and subcutaneous administration of dexamethasone, respectively. Presence of P. jiroveci in nasopharyngeal aspirate, oropharyngeal wash, oral swab, induced sputum or BAL, and absence in nasal swab in a patient without symptoms of PCP may support clinician's decision regarding colonization. Overall, detection of P. carinii in nasal swabs of rats by PCR demonstrated that nasal sampling can be used for the diagnosis of Pneumocystis pneumonia.

  1. Replicate PCR Testing and Probit Analysis for Detection and Quantitation of Chlamydia pneumoniae in Clinical Specimens

    Science.gov (United States)

    Smieja, M.; Mahony, J. B.; Goldsmith, C. H.; Chong, S.; Petrich, A.; Chernesky, M.

    2001-01-01

    Nucleic acid amplification of clinical specimens with low target concentration has variable sensitivity. We examined whether testing multiple aliquots of extracted DNA increased the sensitivity and reproducibility of Chlamydia pneumoniae detection by PCR. Nested and non-nested C. pneumoniae PCR assays were compared using 10 replicates of 16 serial dilutions of C. pneumoniae ATCC VR-1310. The proportion positive versus the C. pneumoniae concentration was modeled by probit regression analysis. To validate the model, 10 replicates of 26 previously positive patient specimens of peripheral blood mononuclear cells (PBMC), sputum, or nasopharyngeal swabs (NPS) were tested. The proportion of replicates that were positive varied with the concentration of C. pneumoniae in the sample. At concentrations above 5 infection-forming units (IFU)/ml, both nested and non-nested PCR assay sensitivities were 90% or greater. The nested PCR was more sensitive (median detection, 0.35 versus 0.61 IFU/ml; relative median detection, 0.58; 95% confidence interval, 0.31 to 0.99; P = 0.04). In clinical specimens, replicate PCR detected 15 of 26 (nested) versus 1 of 26 (non-nested, P < 0.001). For PBMC specimens, testing 1, 3, or 5 replicates detected 3, 5, or 9 of 10 positive specimens, respectively. Median C. pneumoniae concentrations were estimated at 0.07 IFU/ml for PBMC and at <0.03 IFU/ml for NPS specimens. We conclude that performing 5 or 10 replicates considerably increased the sensitivity and reproducibility of C. pneumoniae PCR and enabled quantitation for clinical specimens. Due to sampling variability, PCR tests done without replication may miss a large proportion of positive specimens, particularly for specimens with small amounts of target C. pneumoniae DNA present. PMID:11325993

  2. 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.

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

    Science.gov (United States)

    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.

  4. 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 (P<0.05), regardless of swabbing or grinding. 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.

  5. Evaluation of Methods to Improve the Extraction and Recovery of DNA from Cotton Swabs for Forensic Analysis

    Science.gov (United States)

    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. PMID:25549111

  6. Surge and swab pressures in wells with cross-section changes; Pressoes de surge and swab em pocos com variacao de secao

    Energy Technology Data Exchange (ETDEWEB)

    Fedevjcyk, Joao Victor; Junqueira, Silvio Luiz de Mello; Negrao, Cezar Otaviano Ribeiro [Universidade Tecnologica Federal do Parana (UTFPR). Laboratorio de Ciencias Termicas (Lacit) (Brazil)], e-mails: silvio@utfpr.edu.br, negrao@utfpr.edu.br

    2009-12-15

    Well drilling is performed by rotating and applying a weighted drill bit to the geological formation. Well diameter variations and the use of drill pipe accessories might cause changes to the annular cross section space between the drill pipe and the borehole. It should be noted cross section changes influence pressure losses within the well. This study proposes a mathematical/ numerical model to simulate the surge and swab problem in wells with variable cross section areas. The fluid flow yielded by the drill pipe motion is considered to be one-dimensional, isothermal, compressible and transient. The proposed model features the mass and momentum conservation equations, along with a state equation and a constitutive equation for Bingham or Power Law fluids. The governing equations were discretized by the Finite Volume Method. The well is assumed to be impermeable and the drill pipe end to be closed. The results were compared to measured data obtained at the Taquipe experimental well with good agreement. Predictions can now be made as to how changes in cross section areas may significantly affect the transient surge and swab pressures. (author)

  7. Heavy-section fracture toughness screening specimen

    Science.gov (United States)

    Shannon, J. L., Jr.; Brown, W. F., Jr.; Donald, J. K.

    1977-01-01

    The reported study has the objective to fix the proportions and limits of application of a double-edge-notch specimen with one of the notches tipped with a fatigue crack (DENC). Details regarding the DENC specimen are discussed, taking into account specimen length, notch length, specimen width and thickness, and the loading pins. The influence of specimen width and thickness on the crack strenght and apparent plane-strain fracture toughness of the specimen has been determined for eight alloys. It is concluded that the DENC specimen shows promise for screening alloys with reference to their plane-strain fracture toughness in sections up to 1 in.

  8. Validation of Single and Pooled Manure Drag Swabs for the Detection of Salmonella Serovar Enteritidis in Commercial Poultry Houses.

    Science.gov (United States)

    Kinde, Hailu; Goodluck, Helen A; Pitesky, Maurice; Friend, Tom D; Campbell, James A; Hill, Ashley E

    2015-12-01

    Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n  =  525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯  = 2.5 CFU (range 2.5-2.7), or medium, x¯  = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P 0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA

  9. Safety analysis report for Hot-Cell irradiated specimen cask

    Energy Technology Data Exchange (ETDEWEB)

    Ku, J. H.; Lee, J. C.; Seo, K. S.; Lee, D. W. [Korea Atomic Energy Research Institute, Taejon (Korea)

    1999-03-01

    For the examination of spent fuels and radioactive materials by using scanning electron microscope, a irradiated specimen cask is needed to transport the specimen from the hot-cell to the shielded glove box in which the scanning electron microscope is installed. This cask should be easy to handle and transport, has safe to maintain the shielding safety of operators as well as the thermal and structural integrities under prescribed load conditions by the regulations as requirements. Also the cask should be assured that docked perfectly maintaining shielding integrity with the interfaces of hot-cell and shield glove box. Accordingly, the main features of cask were analyzed with functional capabilities, and the integrities of cask under required load conditions were evaluated. Therefore, it was verified that the cask is suitable to use at the outside transport as well as Post Irradiated Examination Facility in KAERI. 9 refs., 50 figs., 14 tabs. (Author)

  10. 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 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. Conclusions: 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....

  11. Standards for the management of swabs, needles and instruments in the operating theatre

    Directory of Open Access Journals (Sweden)

    A. Astrop

    1996-05-01

    Full Text Available The management of swabs, needles and instruments in the operating theatre is a high-risk and problem-prone area for the operating theatre nurse. The purpose of this research is to formulate specific standards on the management of swabs, needles and instruments in the operating theatre to ensure the safety of the patient. An exploratory and descriptive research design was used and executed in 3 hospitals of a private hospital group in Gauteng. A structured two phase process was followed, ie the development phase and the validation phase. This last phase was done by means of deliberate debate. It is recommended that these standards be implemented, tested and validated on a national basis and a monitoring and evaluation system should be developed to ensure nursing compliance with these standards.

  12. Absence of Neisseria meningitidis from throat swabs of Kuwaiti pilgrims after returning from the Hajj.

    Science.gov (United States)

    Husain, Entesar H; Dashti, Ali A; Electricwala, Qudsiya Y; Abdulsamad, Abdulsamad M; Al-Sayegh, Safeya

    2010-01-01

    To investigate whether or not Neisseria meningitidis was present in the throat of Kuwaiti pilgrims after returning from the Hajj. Throat swabs were taken from 177 participants 1 week after returning from the Hajj. The participants were asked about: associated medical conditions, meningococcal vaccination status and the intake of ciprofloxacin before leaving Mecca for Kuwait. There was no throat colonization with N. meningitidis on any of the throat swabs. Of the 177 pilgrims, 163 (92%) were vaccinated with meningococcal quadrivalent vaccine before leaving to Saudi Arabia. Ninety-seven of the pilgrims (83%) had received one dose of ciprofloxacin before leaving Mecca. The result showed that vaccination before leaving Kuwait and ciprofloxacin prophylaxis were effective in preventing throat colonization with Neisseria meningitidis. Copyright 2010 S. Karger AG, Basel.

  13. Optimizing specimen processing for ancient soft tissue specimens.

    Science.gov (United States)

    Prats-Muñoz, G; Malgosa, A; Isidro, A; Galtés, I

    2015-05-01

    Despite many reports concerning processing of ancient soft tissues, scant attention has been paid to optimizing procedures for processing soft tissues that have been altered by taphonomic processes. To determine the best procedures, we investigated the rehydration solution, time of exposure to the solutions, fixative solution and exposure to heat. Processes were evaluated based on the minimum section thickness, degree of tissue fragmentation, definition of tissue architecture and penetration of stains. We found that in desiccated samples, tissue architecture was optimized by using Ruffer's solution for rehydration and Schaffer's solution as fixative, because these tissues require water restoration within the tissues due to their compacted character. Heating enhanced penetration of dyes in these specimens, which improved diagnosis. Saponified tissues that had suffered extensive decomposition were more labile and required slow water uptake. The best histological sections were obtained using Sandison's solution followed by fixation with formaldehyde and avoiding heat. To obtain the best results with paleohistological specimens, the procedure must be determined by the condition of the sample and by accounting for the nature of its damage.

  14. 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 caused by skin swabs in persisting host communities with low-level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions. 4. Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this 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

  15. 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

  16. Nasal swab real-time PCR is not suitable for in vivo diagnosis of bovine tuberculosis

    Directory of Open Access Journals (Sweden)

    Fabiana Q. Mayer

    Full Text Available ABSTRACT: Bovine tuberculosis (bTB is a zoonosis causing economic losses and public health risks in many countries. The disease diagnosis in live animals is performed by intradermal tuberculin test, which is based on delayed hypersensitivity reactions. As tuberculosis has complex immune response, this test has limitations in sensitivity and specificity. This study sought to test an alternative approach for in vivo diagnosis of bovine tuberculosis, based on real-time polymerase chain reaction (PCR. DNA samples, extracted from nasal swabs of live cows, were used for SYBR® Green real-time PCR, which is able to differentiate between Mycobacterium tuberculosis and Mycobacterium avium complexes. Statistical analysis was performed to compare the results of tuberculin test, the in vivo gold standard bTB diagnosis method, with real-time PCR, thereby determining the specificity and sensitivity of molecular method. Cervical comparative test (CCT was performed in 238 animals, of which 193 had suitable DNA from nasal swabs for molecular analysis, as indicated by amplification of glyceraldehyde-3-phosphate dehydrogenase (GAPDH gene, and were included in the study. In total, 25 (10.5% of the animals were CCT reactive, of which none was positive in the molecular test. Of the 168 CCT negative animals, four were positive for M. tuberculosis complex at real time PCR from nasal swabs. The comparison of these results generated values of sensitivity and specificity of 0% and 97.6%, respectively; moreover, low coefficients of agreement and correlation (-0.029 and -0.049, respectively between the results obtained with both tests were also observed. This study showed that real-time PCR from nasal swabs is not suitable for in vivo diagnosis of bovine tuberculosis; thus tuberculin skin test is still the best option for this purpose.

  17. Detection of strep throat causing bacterium directly from medical swabs by touch spray - mass spectrometry

    OpenAIRE

    Jarmusch, Alan K.; Pirro, Valentina; Kerian, Kevin S.; Cooks, Graham

    2014-01-01

    Strep throat causing Streptococcus pyogenes was detected in vitro and in simulated clinical samples by performing touch spray ionization - mass spectrometry. MS analysis took only seconds to reveal characteristic bacterial and human lipids. Medical swabs were used as the substrate for ambient ionization. This work constitutes the initial step in developing a noninvasive MS-based test for clinical diagnosis of strep throat. It is limited to the single species, S. pyogenes, which is responsible...

  18. Detection of Brucella spp. in bottlenose dolphins Tursiops truncatus by a real-time PCR using blowhole swabs.

    Science.gov (United States)

    Wu, Qingzhong; Conway, Jessica; Phillips, Kristen M; Stolen, Megan; Durden, Wendy N; Fauquier, Deborah; McFee, Wayne E; Schwacke, Lori

    2016-08-09

    Blowhole swabs are a simple and non-invasive method for collecting samples from cetaceans and can be used for screening large numbers of animals in the field. This study reports a real-time PCR assay for the detection of Brucella spp. using blowhole swab samples from bottlenose dolphins Tursiops truncatus stranded in the coastal region of Virginia, South Carolina and northern Florida, USA, between 2013 and 2015. We used real-time PCR results on lung samples from the same dolphins in order to estimate the relative sensitivity and specificity of real-time PCR of blowhole swabs. Brucella DNA was detected in lung tissue of 22% (18/81) and in blowhole swabs of 21% (17/81) of the sampled dolphins. The relative sensitivity and specificity of real-time PCR on blowhole swabs as compared to the real-time PCR on lung samples was 94% (17/18) and 100% (63/63), respectively. These results indicate that real-time PCR on blowhole swabs may be used as a non-invasive test for rapid detection of Brucella spp. in the respiratory tract of dolphins. To our knowledge, this is the first report on the use of blowhole swabs for detection of bacterial pathogens by real-time PCR in bottlenose dolphins.

  19. Validation of a Nylon-Flocked-Swab Protocol for Efficient Recovery of Bacterial Spores from Smooth and Rough Surfaces▿

    Science.gov (United States)

    Probst, Alexander; Facius, Rainer; Wirth, Reinhard; Moissl-Eichinger, Christine

    2010-01-01

    In order to meet planetary-protection requirements, culturable bacterial spore loads are measured representatively for the total microbial contamination of spacecraft. However, the National Aeronautics and Space Administration's (NASA's) cotton swab protocols for spore load determination have not changed for decades. To determine whether a more efficient alternative was available, a novel swab was evaluated for recovery of different Bacillus atrophaeus spore concentrations on stainless steel and other surfaces. Two protocols for the nylon-flocked swab (NFS) were validated and compared to the present NASA standard protocol. The results indicate that the novel swab protocols recover 3- to 4-fold more (45.4% and 49.0% recovery efficiency) B. atrophaeus spores than the NASA standard method (13.2%). Moreover, the nylon-flocked-swab protocols were superior in recovery efficiency for spores of seven different Bacillus species, including Bacillus anthracis Sterne (recovery efficiency, 20%). The recovery efficiencies for B. atrophaeus spores from different surfaces showed a variation from 5.9 to 62.0%, depending on the roughness of the surface analyzed. Direct inoculation of the swab resulted in a recovery rate of about 80%, consistent with the results of scanning electron micrographs that allowed detailed comparisons of the two swab types. The results of this investigation will significantly contribute to the cleanliness control of future life detection missions and will provide significant improvement in detection of B. anthracis contamination for law enforcement and security efforts. PMID:20543054

  20. Rapid Diagnosis of Trichomonas vaginalis by Testing Vaginal Swabs in an Isothermal Helicase-Dependent AmpliVue Assay.

    Science.gov (United States)

    Gaydos, Charlotte A; Hobbs, Marcia; Marrazzo, Jeanne; Schwebke, Jane; Coleman, Jenell S; Masek, Billie; Dize, Laura; Jang, Dan; Li, Jenny; Chernesky, Max

    2016-06-01

    The AmpliVue Trichomonas Assay (Quidel) is a new Federal Drug Administration-cleared rapid test for qualitative detection of Trichomonas vaginalis (TV) DNA in female vaginal specimens. The assay is based on BioHelix's helicase-dependent amplification isothermal technology in conjunction with a disposable lateral-flow detection device, with a total turnaround time of approximately 45 minutes. The objective of this study was to compare the performance of this new assay to wet preparation and culture as well as to another Federal Drug Administration-cleared nucleic acid amplification assay. Four clinician collected vaginal swabs were obtained from women attending sexually transmitted disease, family planning, and OB/GYN clinics and tested by AmpliVue Trichomonas Assay and comparator tests: saline microscopy, TV culture (InPouch), and Aptima TV. AmpliVue Trichomonas Assay results were compared with a composite positive comparator (CPC) as determined by the results from culture and/or wet mount microscopic examination. At least one of either the wet preparation or culture reference test results was required to be positive to establish CPC. A total of 992 patients, 342 symptomatic and 650 asymptomatic patients, were included in the study. Results for AmpliVue for all women combined compared with saline microscopy and culture as a CPC yielded a sensitivity of 100%. Specificity for all women was 98.2%. Overall percent agreement versus Aptima TV was 97.8%. Sensitivity for AmpliVue compared with Aptima was 90.7% %, whereas specificity was 98.9%. The rapid AmpliVue Trichomonas Assay performed as well as microscopy and culture, and had comparable sensitivity and specificity to another nucleic acid amplification test for the detection of TV. This study provided evidence of new diagnostic options and indicated very good performance of amplified testing for detection of TV in symptomatic and asymptomatic women.

  1. Rapid Diagnosis of Trichomonas vaginalis by Testing Vaginal Swabs in an Isothermal Helicase-Dependent AmpliVue™ Assay

    Science.gov (United States)

    Gaydos, Charlotte A.; Hobbs, Marcia; Marrazzo, Jeanne; Schwebke, Jane; Coleman, Jenell S.; Masek, Billie; Dize, Laura; Jang, Dan; Li, Jenny; Chernesky, Max

    2016-01-01

    Background The AmpliVue™ Trichomonas Assay (Quidel) is a new FDA cleared rapid test for qualitative detection of Trichomonas vaginalis (TV) DNA in female vaginal specimens. The assay is based on BioHelix’s Helicase-Dependent Amplification (HDA) isothermal technology in conjunction with a disposable lateral-flow detection device, with a total turn-around time of approximately 45 minutes. Objective The objective of this study was to compare the performance of this new assay to wet preparation and culture, as well as to another FDA cleared nucleic acid amplification assay. Methods Four clinician collected vaginal swabs were obtained from women attending STD, family planning, and OB/GYN clinics and tested by AmpliVue™ Trichomonas Assay and comparator tests: saline microscopy, TV culture (InPouch™), and Aptima® TV (ATV). AmpliVue™ Trichomonas Assay results were compared to a composite positive comparator (CPC) as determined by the results from culture and/or wet mount microscopic examination. At least one of either the wet preparation or culture reference test results was required to be positive to establish CPC. Results A total of 992 patients, 342 symptomatic and 650 asymptomatic patients, were included in the study. Results for AmpliVue for all women combined compared to saline microscopy and culture as a composite positive comparator yielded a sensitivity of 100%. Specificity for all women was 98.2%. Overall percent agreement versus Aptima® TV was 97.8%. Sensitivity for AmpliVue compared to Aptima® was 90.7% %, while specificity was 98.9%. Conclusions The rapid AmpliVue™ Trichomonas Assay performed as well as microscopy and culture, and had comparable sensitivity and specificity to another NAAT for the detection of TV. This study provided evidence of new diagnostic options and indicated very good performance of amplified testing for detection of TV in symptomatic and asymptomatic women. PMID:27196258

  2. Abdominal fibrosarcoma associated with a retained surgical swab in a dog.

    Science.gov (United States)

    Rayner, E L; Scudamore, C L; Francis, I; Schöniger, S

    2010-07-01

    An abdominal fibrosarcoma surrounding a retained surgical swab was identified in a 3-year-old neutered female rottweiler dog presented with chronic inappetence and lethargy. Laparotomy revealed a mass within the omentum, multiple hepatic masses and enlarged mesenteric lymph nodes. The dog was humanely destroyed and submitted for necropsy examination. Microscopically, the omental mass was consistent with a sarcoma surrounding centrally located fibres of foreign material and was infiltrated by epithelioid macrophages containing intracytoplasmic fibre fragments. Sarcoma tissue was also present in mesenteric lymph nodes, liver, spleen and lungs, and some affected lymph nodes contained intralesional epithelioid macrophages with fibre fragments. Immunohistochemical and electron microscopical examinations were consistent with a diagnosis of fibrosarcoma. By fibre analysis and electron microscopy, the intratumoural fibres were identified as cotton fibres with features identical to those obtained from a surgical swab. To our knowledge this is the first description of an abdominal fibrosarcoma associated with a retained surgical swab in a dog. Other examples of foreign body-associated sarcomas in the veterinary literature are vaccine- and implant-induced sarcomas. (c) 2010 Elsevier Ltd. All rights reserved.

  3. Detection of Streptococcus agalactiae colonization in pregnant women by using combined swab cultures: cross-sectional prevalence study

    Directory of Open Access Journals (Sweden)

    Camila Marconi

    Full Text Available CONTEXT AND OBJECTIVE: Maternal Streptococcus agalactiae colonization and early-onset neonatal sepsis have aroused interest in the worldwide literature. Streptococcal neonatal disease is associated with significant morbidity and mortality in the perinatal period, especially among premature neonates. The aim of this study was to assess the prevalence of maternal streptococcal colonization by using combined swab cultures, compared with swab collection from a single site. DESIGN AND SETTING: Cross-sectional study at Faculdade de Medicina de Botucatu, Universidade Estadual Paulista. METHODS: Samples were obtained from 405 patients at gestational ages of 35 to 37 weeks. Swabs from the perianal (rectal region, vaginal introitus and upper lateral vaginal vault were cultured in Todd-Hewitt selective broth. Colonies suggestive of Streptococcus agalactiae were subjected to the catalase and CAMP (Christie, Atkins, Munch-Petersen tests. To evaluate the positivity of combined swab cultures, Tukey's test was used for comparison of proportions. RESULTS: The prevalence of streptococcal colonization was 25.4%. Among the patients with positive cultures, 28.1% had this at only one collection site, 24.2% simultaneously at two sites and 47.5% at all three sites. Associating the swabs from two collection sites significantly increased streptococcal isolation, compared with a single swab (P < 0.05, except for perianal (rectal collection. Use of combined swabs from three collection sites showed statistically higher isolation rates. CONCLUSION: In combined swab cultures collected from three collection sites, the prevalence of maternal Streptococcus agalactiae colonization was higher than in swabs collected from a single site.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Field Validation of SYBR Green- and TaqMan-Based Real-Time PCR Using Biopsy and Swab Samples To Diagnose American Tegumentary Leishmaniasis in an Area Where Leishmania (Viannia) braziliensis Is Endemic.

    Science.gov (United States)

    Gomes, Ciro Martins; Cesetti, Mariana Vicente; de Paula, Natália Aparecida; Vernal, Sebastián; Gupta, Gaurav; Sampaio, Raimunda Nonata Ribeiro; Roselino, Ana Maria

    2017-02-01

    The precise diagnosis of American tegumentary leishmaniasis (ATL) is an essential task due to the disease's associated morbidity. A noninvasive, extremely sensitive, and highly specific exam is critical, particularly for mucosal leishmaniasis (ML), in which a low parasite quantity is expected. We aimed to compare the diagnostic accuracy of swab and biopsy sample analysis using SYBR Green- and TaqMan-based real-time PCR (qPCR) assays with that of a composite reference standard consisting of the Montenegro skin test, serology, histopathology, smears, culture, and conventional PCR. In total, 55 patients with ATL (ML, 18 patients; cutaneous leishmaniasis [CL], 37 patients) and 36 patients without ATL were studied. qPCR analysis of swabs was more accurate when using SYBR Green (87.88%; 95% confidence interval [CI], 77.86 to 93.73 patients) than when using TaqMan (78.79%; 95% CI, 67.49 to 86.92%) (P = 0.031). SYBR Green (84.72%; 95% CI, 74.68 to 91.25%) was also more accurate than TaqMan (73.61%; 95% CI, 62.42 to 82.41%) for biopsy samples (P = 0.008). All qPCR methods were 100% specific. Swabs and biopsy specimens had similar sensitivity when using the same chemistry (P = 0.125 for SYBR Green and P = 0.625 for TaqMan). Moreover, qPCR achieved better performance than most existing techniques used for the diagnosis of ATL and also detected the Leishmania parasite in a greater proportion of patients than the associated histopathology, smear, culture, and conventional PCR techniques did. Swabs therefore represent a useful diagnostic tool because they not only are noninvasive but also can achieve an accuracy similar to that of biopsy samples. The high accuracy of SYBR Green-based qPCR may also reduce the requirement for associated parasitological tests for ATL diagnosis. Copyright © 2017 American Society for Microbiology.

  6. Culture-independent qunatification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Schelin, Jenny; Norling, Börje

    2010-01-01

    To facilitate quantitative risk assessment in the meat production chain, there is a need for culture-independent quantification methods. The aim of this study was to evaluate the use of flotation, a non-destructive sample preparation method based on traditional buoyant density centrifugation......, for culture-independent quantification of intact Salmonella in pig carcass gauze swabs (100 cm2) prior to quantitative PCR (qPCR). A novel approach was investigated, excluding the homogenization step prior to flotation, to improve the detection limit and speed up the quantification procedure. The buoyant...... concentrations of ≥ 6.1×108 CFU/swab sample, but not by concentrations ≤ 6.1×106 CFU/swab sample. By using the gauze swabs directly in the flotation procedure, the homogenization step normally used for preparation of food-related samples could be excluded, which simplified the culture independent quantification...

  7. 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...

  8. Comparison of urine samples and penile swabs for detection of human papillomavirus in HIV-negative Dutch men.

    Science.gov (United States)

    Koene, Fleur; Wolffs, Petra; Brink, Antoinette; Dukers-Muijrers, Nicole; Quint, Wim; Bruggeman, Cathrien; Hoebe, Christian

    2016-09-01

    Penile swab sampling is the method of choice when testing for human papillomavirus (HPV) in men. Urine sampling is already used in routine sexually transmitted infections (STI) diagnostics and could provide a less invasive sampling method in men to detect HPV. Therefore we compared detection of HPV types in urine samples and penile swabs by the highly sensitive SPF10-LiPA25 system. First void urine and self-obtained penile swab samples were collected from 120 men, with a mean age of 29.4 years, visiting a STI clinic in South Limburg, the Netherlands. In total 111 of 120 men were included in the analysis. Broad-spectrum HPV DNA amplification and mucosal HPV genotyping were performed using the SPF10 DEIA-LiPA25 system (SPF10 HPV LiPA, V.1). In total 75 (68%) men were positive for HPV in the combined analysis. Sixty-six (59%) paired samples were concordant in being positive or negative. In 39% of the men HPV DNA was detected only in the penile swab. In 2% of the men HPV DNA was detected only in the urine sample. Considering penile swabs as the gold standard, a sensitivity of 41% (95% CI 30% to 53%) and a specificity of 95% (95% CI 81% to 99%) was found. In 6 (5%) urines high risk types were repeatedly found that were not detected in the matching swab. Urine samples are not comparable to penile swabs in the detection of HPV in men. However, the addition of urine samples to penile swabs could be of use in epidemiological or clearance studies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  9. Detection of influenza A virus from live-bird market poultry swab samples in China by a pan-IAV, one-step reverse-transcription FRET-PCR.

    Science.gov (United States)

    Luan, Lu; Sun, Zhihao; Kaltenboeck, Bernhard; Huang, Ke; Li, Min; Peng, Daxin; Xu, Xiulong; Ye, Jianqiang; Li, Jing; Guo, Weina; Wang, Chengming

    2016-07-22

    The persistent public health threat of animal to human transmission of influenza A virus (IAV) has stimulated interest in rapid and accurate detection of all IAV subtypes in clinical specimens of animal origin. In this study, a new set of primers and probes was designed for one-step pan-IAV reverse-transcription fluorescence resonance energy transfer (FRET)-PCR. The detection limit of one-step pan-IAV RT FRET-PCR was 10 copies of the matrix gene per reaction, and proved to be equivalent or superior to virus isolation in detecting nine IAV subtypes. Application of the pan-IAV RT FRET-PCR to oral-pharyngeal and cloacal swab specimens collected from healthy poultry in 34 live bird markets in 24 provinces of China revealed that 9.2% of the animals (169/1,839) or 6.3% of their oral-pharyngeal or cloacal swabs (233/3,678) were positive for IAV, and 56.8% of IAV-positive samples were of the H9N2 subtype. Paralleling detection of IAV in H9N2-infected SPF chickens and chickens from LBM showed that pan-IAV FRET-PCR had a higher detection limit than virus isolation in eggs while the results by FRET-PCR and virus isolation overall matched. It is expected that this strategy can be useful for facile surveillance for IAV in clinical samples from a variety of sources.

  10. Observational study of Streptococcus pyogenes isolated from vaginal swabs of adult women in a hospital and community laboratory.

    Science.gov (United States)

    Upton, Arlo; Taylor, Susan

    2013-12-01

    Streptococcus pyogenes or group A streptococcus (GAS) is a common cause of vulvo-vaginitis in pre-pubertal females but is uncommonly isolated from the vaginal swabs of adult females. We aimed to describe the clinical and laboratory findings of adult females with GAS isolated from vaginal swabs in a community and hospital laboratory. Over a 19 week period the two laboratories identified females ≥ 15 years of age with GAS isolated from vaginal swabs. At least 2 weeks after reporting, the referring doctor or midwife was telephoned by the authors for clinical information or the clinical notes were reviewed. Laboratory data were also collected. One hundred adult females with GAS isolated from vaginal swabs were identified from approximately 4500-5000 community laboratory, and 20 from approximately 2000 hospital laboratory swabs. Community patients were more likely to have presented with vaginal symptoms such as discharge, while hospital patients were more likely to have ascending infection related to pregnancy/recent delivery. Of the community patients, 15% were asymptomatic compared with 5% of the hospital patients. Review of Gram stain and culture quantification was not found to be particularly useful for discriminating between clinical infection and asymptomatic colonisation. Isolation of GAS from the vaginal swabs of adult females is uncommon. In the community setting it may represent infection with vulvo-vaginitis or asymptomatic colonisation. In the hospital setting, its isolation is frequently associated with pregnancy-related infectious complications.

  11. 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.

  12. Detection of strep throat causing bacterium directly from medical swabs by touch spray-mass spectrometry.

    Science.gov (United States)

    Jarmusch, Alan K; Pirro, Valentina; Kerian, Kevin S; Cooks, R Graham

    2014-10-07

    Strep throat causing Streptococcus pyogenes was detected in vitro and in simulated clinical samples by performing touch spray ionization-mass spectrometry. MS analysis took only seconds to reveal characteristic bacterial and human lipids. Medical swabs were used as the substrate for ambient ionization. This work constitutes the initial step in developing a non-invasive MS-based test for clinical diagnosis of strep throat. It is limited to the single species, S. pyogenes, which is responsible for the vast majority of cases. The method is complementary to and, with further testing, a potential alternative to current methods of point-of-care detection of S. pyogenes.

  13. 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.

  14. 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.

  15. 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.

  16. Polymerase chain reaction for detection of Chlamydia trachomatis in conjunctival swabs

    Science.gov (United States)

    Elnifro, E.; Storey, C.; Morris, D.; Tullo, A.

    1997-01-01

    AIMS/BACKGROUND—Ocular Chlamydia trachomatis infection in the west occurs as ophthalmia neonatorum, acquired from the mother, or adult paratrachoma which is also associated with current genital tract infection. Accurate rapid laboratory diagnosis facilitates management, but the relative merits of antigen detection or DNA amplification tests are unresolved.
METHODS—A polymerase chain reaction (PCR) test was developed which amplified part of the plasmid shared by all the serovars of C trachomatis. Conjunctival swabs were tested using an in house immune dot-blot test (IDBT) for chlamydial lipopolysaccharide antigen, a commercial direct fluorescent antibody (DFA) test for chlamydial elementary bodies, and the PCR (DNA extracted using guanidinium lysis buffer).
RESULTS—The PCR achieved a detection limit of 100 plasmid copies (10 elementary bodies). In a combined retrospective and prospective clinical evaluation, the PCR and IDBT gave identical results with 21 positive and 57 negative eye swabs. However, interpretation of the DFA test required meticulous examination of the stained smear, sometimes by two microscopists.
CONCLUSIONS—The PCR is likely to play an increasing role in the diagnosis of ocular C trachomatis infection because of its excellent sensitivity and specificity.

 PMID:9274416

  17. [The German Environmental Specimen Bank].

    Science.gov (United States)

    Schröter-Kermani, Christa; Gies, Andreas; Kolossa-Gehring, Marike

    2016-03-01

    The main objective of the German Environmental Specimen Bank (ESB) is the long-term storage of environmental and human samples under stable deep-freeze conditions for future research. The ESB is unique in providing a continuous historical record of environmental and human exposure to chemicals in Germany. ESB was started parallel to the development of the first German Chemicals Legislation in the late 1970s. In 1979, the ESB test operation began. After the Chemicals Law came into force in 1982, the ESB was established as a permanent facility in 1985. With the new European Chemicals Legislation, REACH, in 2007 responsibility for the safety of commercial chemicals and risk assessment was assigned to the industry. Since then, the ESB has become even more important in verifying the self-assessment of the industry, in evaluating the effectiveness of regulations, thus ensuring the protection of humans and the environment against adverse effects caused by exposure to chemicals. These objectives are pursued by the regular monitoring of contaminations and the assessment of temporal trends. Demonstrating the necessity of deriving exposure reduction measures, ESB results serve as key information for policy-makers. Information on preventing exposure to chemicals is available to the general public and to the public health services. The ESB is thus an important monitoring instrument of the Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety. The Federal Environment Agency operates the ESB based on its own concepts, heads the scientific data evaluation and transfers results into the environmental policy arena and to the general public.

  18. 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

  19. Evaluation of Three Swabbing Devices for Detection of Listeria monocytogenes on Different Types of Food Contact Surfaces

    Directory of Open Access Journals (Sweden)

    Evy Lahou

    2014-01-01

    Full Text Available Listeria monocytogenes can adhere to different types of food contact surfaces within a food processing environment. Therefore, environmental sampling devices should be capable of detecting unacceptable contamination. In this study, a sponge-stick, foam spatula and an environmental swab were evaluated on their ability to detect low concentrations of L. monocytogenes on different types of food contact surfaces. A cocktail of four L. monocytogenes serotypes was inoculated with a concentration of 100 CFU/250 cm2 onto stainless steel (SS, high density polyethylene (HDPE and rubber surfaces in a 250 cm2 area. Immediately after inoculation and after 1 h exposure, the surfaces were swabbed with the different swabbing devices. The results of the study show only minor differences in the ability of the swabbing devices to detect L. monocytogenes. All devices were capable to detect the contamination immediately after inoculation. However, when the surfaces were allowed to air-dry for 1 h, L. monocytogenes was undetected in 11.1% of the samples (n = 27 with the sponge stick, in 7.4% of the samples (n = 27 with the foam spatula and in 3.7% of the samples (n = 27 with the environmental swab, especially on SS surfaces. The detection ability of the different devices for L. monocytogenes can be concluded to be rather high on different types of food contact surfaces.

  20. 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

    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....... 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......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...

  1. 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.

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

    DEFF Research Database (Denmark)

    Baczynska, Agata; Fedder, Jens; Schougaard, Hans

    2007-01-01

    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......The reproduction rate of horses is one of the lowest within domestic livestock despite advances the veterinary medicine. Infertility in horses may be due mainly to the lack of suitable selection criteria in the breeding of horses. However, acquired infertility due to genital, bacterial infections...... 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...

  3. 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

    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......The reproduction rate of horses is one of the lowest within domestic livestock despite advances the veterinary medicine. Infertility in horses may be due mainly to the lack of suitable selection criteria in the breeding of horses. However, acquired infertility due to genital, bacterial infections...... 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...

  4. Detection of Leishmania infantum DNA in conjunctival swabs of cats by quantitative real-time PCR.

    Science.gov (United States)

    Benassi, Julia Cristina; Benvenga, Graziella U; Ferreira, Helena Lage; Pereira, Vanessa F; Keid, Lara B; Soares, Rodrigo; Oliveira, Tricia Maria Ferreira de Sousa

    2017-06-01

    Although some studies have investigated the potential role of cats as a reservoir for Leishmania, their role in the epidemiology of visceral leishmaniasis (VL) is still poorly understood. Molecular diagnostic techniques are an important tool in VL diagnosis, and PCR shows high sensitivity and specificity for Leishmania spp. detection. Quantitative real-time PCR (qPCR) is a method that permits quantitative analysis of a large number of samples, resulting in more sensitive, accurate, and reproducible measurements of specific DNA present in the sample. This study compared real-time PCR (qPCR) and conventional PCR (cPCR) for detection of Leishmania spp. in blood and conjunctival swab (CS) samples of healthy cats from a non-endemic area in the state of São Paulo, Brazil. Of all CS samples, 1.85% (2/108) were positive for Leishmania spp. by both cPCR as qPCR (kappa index = 1), indicating excellent agreement between the two methods. The DNA from the two CS-cPCR- and CS-qPCR-positive samples was further tested with a PCR test amplifying the Leishmania spp. discriminative rRNA internal transcribed spacer 1 (ITS 1), of which one sample generated a 300-350-bp DNA fragment whose size varies according to the Leishmania species. Following sequencing, the fragment showed 100% similarity to a GenBank L. infantum sequence obtained from a cat in Italy. In conclusion, the association of qPCR and CS proved to be effective for detection of Leishmania in cats. Conjunctival swab samples were shown to be a practical and better alternative to blood samples and may be useful in the diagnosis and studies of feline leishmaniasis. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. 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)

  6. 36 CFR 2.5 - Research specimens.

    Science.gov (United States)

    2010-07-01

    ... Federal agency for the purpose of research, baseline inventories, monitoring, impact analysis, group study... if removal of the specimen would result in damage to other natural or cultural resources, affect... available to the public and reports and publications resulting from a research specimen collection permit...

  7. 36 CFR 1002.5 - Research specimens.

    Science.gov (United States)

    2010-07-01

    ... of research, baseline inventories, monitoring, impact analysis, group study, or museum display when... of the specimen would result in damage to other natural or cultural resources, affect adversely... specimens will be made available to the public and reports and publications resulting from a research...

  8. Fatigue Specimens for Sheet and Plate Material

    NARCIS (Netherlands)

    Schijve, J.

    1998-01-01

    The usefulness of simple sheet and plate specimens is discussed for various experimental research purposes. Specimens should be representative as much as possible for the conditions of fatigue problems in practice, which is more difficult to achieve for the fatigue crack initiation phase than for

  9. 37 CFR 2.56 - Specimens.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Specimens. 2.56 Section 2.56 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES Drawing § 2.56 Specimens. (a) An application under section 1(a) of...

  10. Machining technique prevents undercutting in tensile specimens

    Science.gov (United States)

    Moscater, R. E.; Royster, D. M.

    1968-01-01

    Machining technique prevents undercutting at the test section in tensile specimens when machining the four corners of the reduced section. Made with a gradual taper in the test section, the width of the center of the tensile specimen is less than the width at the four corners of the reduced section.

  11. 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

  12. Comparison of the BD MAX MRSA XT to the Cepheid™ Xpert® MRSA assay for the molecular detection of methicillin-resistant Staphylococcus aureus from nasal swabs.

    Science.gov (United States)

    Mehta, Sanjay R; Estrada, Jasmine; Ybarra, Juan; Fierer, Joshua

    2017-04-01

    Variation in MRSA genotypes may affect the sensitivity of molecular assays to detect this organism. We compared 2 commonly used screening assays, the Cepheid™ Xpert® MRSA and the BD MAX™ MRSA XT on consecutively obtained nasal swabs from 479 subjects. Specimens giving discordant results were subjected to additional microbiologic and molecular testing. Six hundred forty-two (97.6%) of the 658 test results were concordant. Of the 16 discordant results from 12 subjects, additional results suggested that 9 (60%) of the 15 MRSA XT assays were likely correct, and 6 (40%) of the 15 Xpert® assays were likely correct. One discordant result could not be resolved. A mecA dropout and novel mec right-extremity junction (MREJ) sites led to false-positive and negative results by Xpert®. While both assays performed well, continued vigilance is needed to monitor for Staphylococcus aureus with novel MREJ sites, mecA dropouts, and mecC, leading to inaccurate results in screening assays. Published by Elsevier Inc.

  13. 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)

  14. The Effect of Antibiotic Exposure and Specimen Volume on the Detection of Bacterial Pathogens in Children With Pneumonia.

    Science.gov (United States)

    Driscoll, Amanda J; Deloria Knoll, Maria; Hammitt, Laura L; Baggett, Henry C; Brooks, W Abdullah; Feikin, Daniel R; Kotloff, Karen L; Levine, Orin S; Madhi, Shabir A; O'Brien, Katherine L; Scott, J Anthony G; Thea, Donald M; Howie, Stephen R C; Adrian, Peter V; Ahmed, Dilruba; DeLuca, Andrea N; Ebruke, Bernard E; Gitahi, Caroline; Higdon, Melissa M; Kaewpan, Anek; Karani, Angela; Karron, Ruth A; Mazumder, Razib; McLellan, Jessica; Moore, David P; Mwananyanda, Lawrence; Park, Daniel E; Prosperi, Christine; Rhodes, Julia; Saifullah, Md; Seidenberg, Phil; Sow, Samba O; Tamboura, Boubou; Zeger, Scott L; Murdoch, David R

    2017-06-15

    Antibiotic exposure and specimen volume are known to affect pathogen detection by culture. Here we assess their effects on bacterial pathogen detection by both culture and polymerase chain reaction (PCR) in children. PERCH (Pneumonia Etiology Research for Child Health) is a case-control study of pneumonia in children aged 1-59 months investigating pathogens in blood, nasopharyngeal/oropharyngeal (NP/OP) swabs, and induced sputum by culture and PCR. Antibiotic exposure was ascertained by serum bioassay, and for cases, by a record of antibiotic treatment prior to specimen collection. Inoculated blood culture bottles were weighed to estimate volume. Antibiotic exposure ranged by specimen type from 43.5% to 81.7% in 4223 cases and was detected in 2.3% of 4863 controls. Antibiotics were associated with a 45% reduction in blood culture yield and approximately 20% reduction in yield from induced sputum culture. Reduction in yield of Streptococcus pneumoniae from NP culture was approximately 30% in cases and approximately 32% in controls. Several bacteria had significant but marginal reductions (by 5%-7%) in detection by PCR in NP/OP swabs from both cases and controls, with the exception of S. pneumoniae in exposed controls, which was detected 25% less frequently compared to nonexposed controls. Bacterial detection in induced sputum by PCR decreased 7% for exposed compared to nonexposed cases. For every additional 1 mL of blood culture specimen collected, microbial yield increased 0.51% (95% confidence interval, 0.47%-0.54%), from 2% when volume was ≤1 mL to approximately 6% for ≥3 mL. Antibiotic exposure and blood culture volume affect detection of bacterial pathogens in children with pneumonia and should be accounted for in studies of etiology and in clinical management.

  15. The Effect of Antibiotic Exposure and Specimen Volume on the Detection of Bacterial Pathogens in Children With Pneumonia

    Science.gov (United States)

    Deloria Knoll, Maria; Hammitt, Laura L.; Baggett, Henry C.; Brooks, W. Abdullah; Feikin, Daniel R.; Kotloff, Karen L.; Levine, Orin S.; Madhi, Shabir A.; O’Brien, Katherine L.; Scott, J. Anthony G.; Thea, Donald M.; Howie, Stephen R. C.; Adrian, Peter V.; Ahmed, Dilruba; DeLuca, Andrea N.; Ebruke, Bernard E.; Gitahi, Caroline; Higdon, Melissa M.; Kaewpan, Anek; Karani, Angela; Karron, Ruth A.; Mazumder, Razib; McLellan, Jessica; Moore, David P.; Mwananyanda, Lawrence; Park, Daniel E.; Prosperi, Christine; Rhodes, Julia; Saifullah, Md.; Seidenberg, Phil; Sow, Samba O.; Tamboura, Boubou; Zeger, Scott L.; Murdoch, David R.; O’Brien, Katherine L.; Levine, Orin S.; Knoll, Maria Deloria; Feikin, Daniel R.; DeLuca, Andrea N.; Driscoll, Amanda J.; Fancourt, Nicholas; Fu, Wei; Hammitt, Laura L.; Higdon, Melissa M.; Kagucia, E. Wangeci; Karron, Ruth A.; Li, Mengying; Park, Daniel E.; Prosperi, Christine; Wu, Zhenke; Zeger, Scott L.; Watson, Nora L.; Crawley, Jane; Murdoch, David R.; Brooks, W. Abdullah; Endtz, Hubert P.; Zaman, Khalequ; Goswami, Doli; Hossain, Lokman; Jahan, Yasmin; Ashraf, Hasan; Howie, Stephen R. C.; Ebruke, Bernard E.; Antonio, Martin; McLellan, Jessica; Machuka, Eunice; Shamsul, Arifin; Zaman, Syed M. A.; Mackenzie, Grant; Scott, J. Anthony G.; Awori, Juliet O.; Morpeth, Susan C.; Kamau, Alice; Kazungu, Sidi; Ominde, Micah Silaba; Kotloff, Karen L.; Tapia, Milagritos D.; Sow, Samba O.; Sylla, Mamadou; Tamboura, Boubou; Onwuchekwa, Uma; Kourouma, Nana; Toure, Aliou; Madhi, Shabir A.; Moore, David P.; Adrian, Peter V.; Baillie, Vicky L.; Kuwanda, Locadiah; Mudau, Azwifarwi; Groome, Michelle J.; Mahomed, Nasreen; Baggett, Henry C.; Thamthitiwat, Somsak; Maloney, Susan A.; Bunthi, Charatdao; Rhodes, Julia; Sawatwong, Pongpun; Akarasewi, Pasakorn; Thea, Donald M.; Mwananyanda, Lawrence; Chipeta, James; Seidenberg, Phil; Mwansa, James; wa Somwe, Somwe; Kwenda, Geoffrey; Anderson, Trevor P.; Mitchell, Joanne

    2017-01-01

    Abstract Background. Antibiotic exposure and specimen volume are known to affect pathogen detection by culture. Here we assess their effects on bacterial pathogen detection by both culture and polymerase chain reaction (PCR) in children. Methods. PERCH (Pneumonia Etiology Research for Child Health) is a case-control study of pneumonia in children aged 1–59 months investigating pathogens in blood, nasopharyngeal/oropharyngeal (NP/OP) swabs, and induced sputum by culture and PCR. Antibiotic exposure was ascertained by serum bioassay, and for cases, by a record of antibiotic treatment prior to specimen collection. Inoculated blood culture bottles were weighed to estimate volume. Results. Antibiotic exposure ranged by specimen type from 43.5% to 81.7% in 4223 cases and was detected in 2.3% of 4863 controls. Antibiotics were associated with a 45% reduction in blood culture yield and approximately 20% reduction in yield from induced sputum culture. Reduction in yield of Streptococcus pneumoniae from NP culture was approximately 30% in cases and approximately 32% in controls. Several bacteria had significant but marginal reductions (by 5%–7%) in detection by PCR in NP/OP swabs from both cases and controls, with the exception of S. pneumoniae in exposed controls, which was detected 25% less frequently compared to nonexposed controls. Bacterial detection in induced sputum by PCR decreased 7% for exposed compared to nonexposed cases. For every additional 1 mL of blood culture specimen collected, microbial yield increased 0.51% (95% confidence interval, 0.47%–0.54%), from 2% when volume was ≤1 mL to approximately 6% for ≥3 mL. Conclusions. Antibiotic exposure and blood culture volume affect detection of bacterial pathogens in children with pneumonia and should be accounted for in studies of etiology and in clinical management. PMID:28575366

  16. Evaluation of irradiated coating material specimens

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yong Jin; Nam, Seok Woo; Cho, Lee Moon [RCS Korea Co., Ltd., Seoul (Korea, Republic of)

    2007-12-15

    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{sup 4} Gy/hr, and radiated TID 2.0 X 10{sup 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{sup 6} Gy)

  17. A Biaxial Fatigue Specimen for Uniaxial Loading

    OpenAIRE

    Bellett, Daniel; Morel, Franck; Morel, Anne; Lebrun, Jean-Lou

    2011-01-01

    International audience; The aim of this paper is to present a novel un-notched fatigue test specimen in which a biaxial stress state is achieved using a uniaxial loading condition. This allows the problem of multi-axial fatigue to be studied using relatively common one-axis servo-hydraulic testing machines. In addition the specimen presented here is very compact and can be made using a small volume of material (100x40x4.5mm). For this specimen, the degree of biaxiality, defined by the paramet...

  18. PCR-based assay to detect sheeppox virus in ocular, nasal, and rectal swabs from infected Moroccan sheep.

    Science.gov (United States)

    Zro, K; Azelmat, S; Bendouro, Y; Kuhn, J H; El Fahime, E; Ennaji, M M

    2014-08-01

    Sheeppox is now enzootic in Morocco. The development of a reliable method for rapid diagnosis of the disease is a central part of any control strategy. The aim of this study is to determine the diagnostic value of a variety of clinical samples such as ovine nasal, ocular or rectal swabs for the detection of sheeppox virus (SPPV) by qualitative conventional polymerase chain reaction (PCR), using a single pair of primers targeting the inverted terminal repeats of the SPPV InS-1 strain, a virulent field isolate. Swab and blood samples were collected from forty animals naturally infected with SPPV who had clinical signs of sheeppox. All animals tested PCR-positive for SPPV. Positive results were obtained infrequently with blood samples, whereas swab samples from at least two sites (nasal, ocular, rectal) were positive per evaluated animal. These results indicate that swab samples are suitable for quantitative molecular SPPV diagnosis. PCR product sequences obtained from all types of sheep samples proved to be identical to the corresponding regions of sheeppox virus strain Romania 65. Copyright © 2014. Published by Elsevier B.V.

  19. [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.

  20. 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...

  1. Ninhydrin treatment as a screening method for the suitability of swabs taken from contact stains for DNA analysis.

    Science.gov (United States)

    Anslinger, K; Selbertinger, U; Bayer, B; Rolf, B; Eisenmenger, W

    2004-04-01

    More and more swabs containing unknown traces of biological material are submitted for forensic DNA analysis. Most of the samples are swabs taken from handled items such as tools, weapons and handles etc. Therefore, we tried to develop a screening method in order to focus the investigation on samples containing biomolecules, such as amino acids which might be associated with nucleic acids. A total of 285 swabs taken from various items collected during crime scene investigations were treated with ninhydrin which leads to a purple colour for samples containing amino acids. Of the swabs 158 were classified as ninhydrin positive and 76% of these samples yielded DNA profiles that fulfil the criteria for inclusion in the German national DNA database (profile frequency greater than 1 in 100,000) or in DNA mixtures which could at least be compared with suspects. In comparison only 9% of the 127 samples shown to be ninhydrin negative, revealed a usable DNA profile. Consequently, ninhydrin treatment was found to be an effective screening method which resulted in an increase in the rate of successfully typed samples and subsequently in a reduction of the costs due to the lower number of samples that needed to be typed.

  2. Optimisation of the antibiotic guidelines in The Netherlands. VII. SWAB guidelines for antimicrobial therapy in adult patients with infectious endocarditis

    NARCIS (Netherlands)

    Verhagen, D. W. M.; van der Feltz, M.; Plokker, H. W. M.; Buiting, A. G. M.; Tjoeng, M. M.; van der Meer, J. T. M.

    2003-01-01

    The Working Party on Antibiotic Policy (Dutch acronym is SWAB) is a Dutch organisation that develops guidelines for in-hospital antimicrobial therapy of bacterial infectious diseases. This present guideline describes the antimicrobial treatment for adult patients with infective endocarditis. The

  3. [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

  4. CPS Trawl Life History Specimen Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Individual specimens measured (weight in grams and length in mm) and sexed from mainly targeted species caught during SWFSC-FRD fishery independent trawl surveys of...

  5. Gardnerella vaginalis and Mollicute detection in rectal swabs from men who have sex with men.

    Science.gov (United States)

    Cox, Ciara; Watt, Alison P; McKenna, James P; Coyle, Peter V

    2017-06-01

    The numbers of rectal sexually transmitted infections are on the rise especially among men who have sex with men. Males from men who have sex with men population are encouraged to send a rectal swab to the laboratory for sexually transmitted infection screening at their visit to the Genitourinary Medicine Clinic. In healthy asymptomatic males, the range of pathogens tested is limited therefore other pathogens may be left untreated allowing infections to persist among sexual partners. Molecular techniques have revolutionarised sexually transmitted infection testing enabling the detection of previously difficult-to-culture pathogens in extra-genital sites and have increased the evidence base for their clinical significance. The present study tests 107 rectal swabs from men who have sex with men negative for Chlamydia trachomatis and Neisseria gonorrhoeae against quantitative polymerase chain reaction (qPCR) assays targeting five common sexually transmitted bacteria which include Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Gardnerella vaginalis. The pathogenic role of these five bacteria in men who have sex with men is currently unknown. Amongst the 107 patients, a positive qPCR was obtained respectively for G. vaginalis 89 (83.2%); U. urealyticum 26 (24.3%); M. hominis 26 (24.3%); M. genitalium 10 (9.3%) and U. parvum 5 (4.7%). Bacterial loads in single and co-infections were compared for each organism. G. vaginalis and M. hominis loads were significantly ( p = 0.007 and p = 0.005, respectively) higher when co-infecting with at least one other organism. Amongst co-infections, the loads of each organism were assessed to determine possible synergies. G. vaginalis and M. hominis displayed a synergistic pattern ( r = 0.51; p = 0.02) which is in keeping with a similar synergy detected previously in the vagina of women with bacterial vaginosis. This study outlines that potential significant infections are being

  6. 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.

  7. Comparison of culture and a multiplex probe PCR for identifying Mycoplasma species in bovine milk, semen and swab samples.

    Directory of Open Access Journals (Sweden)

    Alysia M Parker

    Full Text Available Mycoplasma spp. are a major cause of mastitis, arthritis and pneumonia in cattle, and have been associated with reproductive disorders in cows. While culture is the traditional method of identification the use of PCR has become more common. Several investigators have developed PCR protocols to detect M. bovis in milk, yet few studies have evaluated other sample types or other important Mycoplasma species. Therefore the objective of this study was to develop a multiplex PCR assay to detect M. bovis, M. californicum and M. bovigenitalium, and evaluate its analytical performance against traditional culture of bovine milk, semen and swab samples. The PCR specificity was determined and the limit of detection evaluated in spiked milk, semen and swabs. The PCR was then compared to culture on 474 field samples from individual milk, bulk tank milk (BTM, semen and swab (vaginal, preputial, nose and eye samples. Specificity analysis produced appropriate amplification for all M. bovis, M. californicum and M. bovigenitalium isolates. Amplification was not seen for any of the other Mollicutes or eubacterial isolates. The limit of detection of the PCR was best in milk, followed by semen and swabs. When all three Mycoplasma species were present in a sample, the limit of detection increased. When comparing culture and PCR, overall there was no significant difference in the proportion of culture and PCR positive samples. Culture could detect significantly more positive swab samples. No significant differences were identified for semen, individual milk or BTM samples. PCR identified five samples with two species present. Culture followed by 16S-23S rRNA sequencing did not enable identification of more than one species. Therefore, the superior method for identification of M. bovis, M. californicum and M. bovigenitalium may be dependent on the sample type being analysed, and whether the identification of multiple target species is required.

  8. Multicenter Evaluation of Meridian Bioscience HSV 1&2 Molecular Assay for Detection of Herpes Simplex Virus 1 and 2 from Clinical Cutaneous and Mucocutaneous Specimens.

    Science.gov (United States)

    Faron, Matthew L; Ledeboer, Nathan A; Patel, Anami; Beqa, Safedin H; Yen-Lieberman, Belinda; Kohn, Debra; Leber, Amy L; Mayne, Donna; Northern, William I; Buchan, Blake W

    2016-08-01

    Herpes simplex virus (HSV) causes acute and relapsing symptoms characterized by ulcerative lesions. Laboratory diagnosis of HSV in cutaneous or mucocutaneous lesions has historically been performed with the use of viral cell culture systems; however, these tests are laborious and suffer decreased sensitivity for advanced-stage lesions. The recent availability of FDA-cleared moderately complex assays has resulted in the increased use of molecular diagnostics for the routine detection of HSV in superficial swab specimens. We performed a clinical evaluation of the recently FDA-cleared illumigene HSV 1&2 loop-mediated isothermal amplification (LAMP) assay (Meridian Bioscience, Cincinnati OH) for the detection and differentiation of HSV-1 and HSV-2 in cutaneous and mucocutaneous swab specimens. A total of 1,153 clinical swab specimens were collected and tested at 7 different clinical centers. Each specimen was tested for the presence of HSV-1 and HSV-2 using the illumigene assay, and results were compared to those of the enzyme-linked virus-inducible system (ELVIS) as the reference method. Overall, the illumigene assay demonstrated a sensitivity and specificity of 94.8% and 95.5%, respectively, for the detection of HSV-1. Detection of HSV-2 was similar, with a sensitivity of 98.9% and a specificity of 95.5%. Discrepant analysis was performed using an alternative molecular test (AmpliVue HSV1+2 assay; Quidel Molecular, San Diego, CA) on 91/99 specimens that were recorded as false positive (FP) or false negative (FN) compared to the reference method. In total, 57/78 (73%) FP and 9/13 (69%) FN illumigene results were supported by the AmpliVue result. The illumigene HSV 1&2 assay demonstrated high sensitivity and specificity to detect and differentiate HSV in clinical specimens and identified 57 additional specimens that were positive for HSV compared to culture. The use of LAMP eliminates the need for the cycling of temperatures and provides results in less than 60 min

  9. Morphometric analysis of one anatomic scoliotic specimen.

    Science.gov (United States)

    Parent, Stefan; Labelle, Hubert; Mitulescu, Anca; Latimer, Bruce; Skalli, Wafa; Lavaste, François; de Guise, Jacques

    2002-01-01

    Idiopathic scoliosis is a 3-D deformation affecting the position of the spine in space. The regional deformity has been studied extensively but the local changes have not been widely investigated and this being mainly due to the rarity of anatomical specimens. The objective of this study was to identify a deformation pattern for idiopathic scoliosis. We thus studied one complete scoliotic specimen using a digitizing protocol developed by our research group. The anatomical specimen was selected from the Hamann-Todd Osteology Collection at the Cleveland Natural History Museum, which contains over 1,300 skeletons. We were also able to match this scoliotic specimen with one normal specimen for age, sex, race, height and weight. Each vertebra was measured by taking approximately 200 points on each surface. Parameters for each vertebra were then calculated from these sets of points. Each scoliotic vertebra was then compared with a corresponding normal vertebra of the matched specimen. We present the first findings of these measurements, which show pedicle and posterior elements changes that are thought to be secondary to the scoliotic deformation.

  10. Morphometric analysis of anatomic scoliotic specimens.

    Science.gov (United States)

    Parent, Stefan; Labelle, Hubert; Skalli, Wafa; Latimer, Bruce; de Guise, Jacques

    2002-11-01

    Morphometric analysis of anatomic scoliotic specimens. The objective of this study was to identify a typical deformation pattern for thoracic and lumbar vertebrae in idiopathic scoliosis. Idiopathic scoliosis is a three-dimensional deformity affecting the orientation and position of the spine in space. The regional deformity has been studied extensively, but most of the knowledge we currently have regarding the local deformity is the result of isolated observations made on rare scoliotic specimens with severe deformities. Thirty scoliotic specimens from two major osteologic sources were studied using a three-dimensional digitizing protocol developed by our research group creating a precise three-dimensional reconstruction of the vertebrae. Parameters were then calculated for each vertebra from these reconstructions. Every scoliotic specimen was then matched with a normal specimen to provide for a representative control group. A total of 984 vertebrae (472 scoliotic and 512 normal vertebrae) were measured, creating the largest database of normal and scoliotic vertebral specimens. A characteristic deformity pattern was identified consisting of progressive vertebral wedging, decreased pedicle width on the concave side of the curve, and articular facet surface varying greatly with all findings increasingly more important toward the apex of the curve and as curve severity increased. All findings were statistically significant with P< 0.05. These results are of critical importance for the understanding of the local and regional deformity and in understanding curve progression. Our results also advocate caution in the use of pedicle screws in the thoracic spine, especially on the concave side of the curve.

  11. Evaluation of a Self-Administered Intravaginal Swab for PCR Detection of Genitourinary Tract Infections Including Chlamydia, Gonorrhea, Trichomonas and Human Papillomavirus in Active Duty Military Women

    Science.gov (United States)

    1998-10-01

    Trichomonas bmcei subsp. rhodesiense, K02836; Trypanosoma cmzi, M97956; Toxop/asma gon- gallinae ATCC 30002, Giardia lamblia ATCC SF-741 30888, Chilomastix...Administered Intravaginal Swab for PCR Detection of Genitourinary Tract Infections Including Chlamydia, Gonorrhea, Trichomonas and Human...FUNDING NUMBERS Intravaginal Swab for PCR Detection of Genitourinary DAMD17-96-1-6309 Tract Infections Including Chlamydia, Gonorrhea, Trichomonas

  12. A simple and rapid DNA extraction method for Chlamydia trachomatis detection from urogenital swabs.

    Science.gov (United States)

    Butzler, Matthew A; Reed, Jennifer L; McFall, Sally M

    2017-11-01

    A highly sensitive and specific Chlamydia trachomatis (CT) diagnostic test was developed by combining filtration isolation of nucleic acid (FINA) extraction with quantitative polymerase chain reaction including an internal control to identify test inhibition. A pilot study of 40 clinical specimens yielded 100% sensitivity and specificity. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Detection of Campylobacter jejuni in rectal swab samples from Rousettus amplexicaudatus in the Philippines.

    Science.gov (United States)

    Hatta, Yuki; Omatsu, Tsutomu; Tsuchiaka, Shinobu; Katayama, Yukie; Taniguchi, Satoshi; Masangkay, Joseph S; Puentespina, Roberto; Eres, Eduardo; Cosico, Edison; Une, Yumi; Yoshikawa, Yasuhiro; Maeda, Ken; Kyuwa, Shigeru; Mizutani, Tetsuya

    2016-09-01

    Bats are the second diversity species of mammals and widely distributed in the world. They are thought to be reservoir and vectors of zoonotic pathogens. However, there is scarce report of the evidence of pathogenic bacteria kept in bats. The precise knowledge of the pathogenic bacteria in bat microbiota is important for zoonosis control. Thus, metagenomic analysis targeting the V3-V4 region of the 16S rRNA of the rectal microbiota in Rousettus amplexicaudatus was performed using high throughput sequencing. The results revealed that 103 genera of bacteria including Camplyobacter were detected. Campylobacter was second predominant genus, and Campylobacter coli and Campylobacter jejuni were identified in microbiome of R. amplexicaudatus. Campylobacteriosis is one of the serious bacterial diarrhea in human, and the most often implicated species as the causative agent of campylobacteriosis is C. jejuni. Therefore, we investigated the prevalence of C. jejuni in 91 wild bats with PCR. As a result of PCR assay targeted on 16S-23S intergenic spacer, partial genome of C. jejuni was detected only in five R. amplexicaudatus. This is the first report that C. jejuni was detected in bat rectal swab samples. C. jejuni is the most common cause of campylobacteriosis in humans, transmitted through water and contact with livestock animals. This result indicated that R. amplexicaudatus may be a carrier of C. jejuni.

  14. Isolation of thermotolerant campylobacters and C. hyointestinalis from rectal swabs of healthy pigs

    Directory of Open Access Journals (Sweden)

    Mrenoski Slavco

    2007-11-01

    Full Text Available Thermotolerant campylobacters are the most common bacterial etiological agents of human infectious gastroenteritis worldwide. The most frequent isolated species among them are Campylobacter jejuni and C. coli, and less frequent C. upsaliensis and C. lari. Also C. hyointestinalis, that not belong to the group of thermotolerant campylobacters, has been indicate as an agent of human infectious gastroenteritis. Natural reservoir of all named campylobacters is the intestinal tract of many mammals and birds, including domestic animals. In these animals, campylobacters are commonly present as commensals and their feces is considered as a prime source for environmental contamination. Unlike the human feces which is usually examined in the cases of diarrhea, thermotolerant campylobacters and C. hyointestinalis in the animal feces are generally present in a much lesser amount and the isolation very often could be unsuccessful. The aim of this study was to estimate the validity of applied procedure for isolation (and identification of thermotolerant campylobacters and C. hyointestinalis from pig rectal swabs, as a procedure for detection of healthy animal carriers.

  15. Impact of Rectal Swabs on Infectious Complications after Transrectal Prostate Biopsy.

    Science.gov (United States)

    Trujillo, Carlos Gustavo; Plata, Mauricio; Caicedo, Juan Ignacio; Cataño Cataño, Juan Guillermo; Mariño Alvarez, Angela Marcela; Castelblanco, Diana; Robledo, Daniela

    2016-01-01

    To determine the impact of rectal swabs (RSs) on infectious complications (IC) following prostate biopsy (PB). A retrospective cohort study was conducted including all patients subjected to PB between 2009 and 2013. Group B consisted of patients with a RS and group A of patients without. RS reported the presence of gram-positive or negative germs, sensitive or resistant to ciprofloxacin. Antimicrobial prophylaxis was adjusted to the result. Frequency of IC in each group was determined. Group B had 548 (47.20%) patients and group A 613 (52.80%). From group B, 250 (45.62%) of the RSs showed fluoroquinolone (FQ)-resistant germs. Forty nine (16.44%) patients with sensitive germs vs. 147 (59.51%) with resistant germs had a history of previous FQ treatment (p < 0.0001). IC were observed in 33 (5.49%) patients from group A and in 7 (1.28%) patients from group B (p < 0.0001), requiring hospitalization in 4.99 vs. 1.28%, respectively. IC and hospital admissions were reduced in 76.68 and 74.34%, respectively, following the implementation of RS. RS and targeted antibiotic prophylaxis prior to PB was associated with a significant reduction in IC and hospital admissions. Ceftriaxone could be an alternative in cases of known resistance. Past history of FQ treatment is associated with increased resistance. © 2016 S. Karger AG, Basel.

  16. Genotyping of potentially pathogenic Acanthamoeba strains isolated from nasal swabs of healthy individuals in Peru.

    Science.gov (United States)

    Cabello-Vílchez, Alfonso Martín; Martín-Navarro, Carmen María; López-Arencibia, Atteneri; Reyes-Batlle, María; González, Ana C; Guerra, Humberto; Gotuzzo, Eduardo; Valladares, Basilio; Piñero, José E; Lorenzo-Morales, Jacob

    2014-02-01

    Free Living Amoebae (FLA) of Acanthamoeba genus are widely distributed in the environment and can be found in the air, soil and water; and have also been isolated from air-conditioning units. In humans, they are causative agents of a sight-threating infection of the cornea, Acanthamoeba keratitis (AK) and a fatal infection of the central nervous system known as Granulomatous Amoebic Encephalitis (GAE). In this study, a survey was conducted in order to determine the presence and pathogenic potential of free-living amoebae of Acanthamoeba genus in nasal swabs from individuals in two regions of Peru. Identification of isolates was based on cyst morphology and PCR-sequencing of the Diagnostic Fragment 3 to identify strains at the genotype level. The pathogenic potential of the isolates was also assayed using temperature and osmotolerance assays and extracellular proteases zymograms. The obtained results revealed that all isolated strains exhibited pathogenic potential. After sequencing the highly variable DF3 (Diagnostic Fragment 3) region in the 18S rRNA gene as previously described, genotype T4 was found to be the most common one in the samples included in this study but also genotype T15 was identified. To the best of our knowledge, this is the first study on the characterization of Acanthamoeba strains at the genotype level and the first report of genotype T4 and T15 in Peru. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. 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.

  18. Closeout of JOYO-1 Specimen Fabrication Efforts

    Energy Technology Data Exchange (ETDEWEB)

    ME Petrichek; JL Bump; RF Luther

    2005-10-31

    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.

  19. 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.

  20. The importance of positive bacterial cultures of specimens obtained during clean orthopaedic operations.

    Science.gov (United States)

    Dietz, F R; Koontz, F P; Found, E M; Marsh, J L

    1991-09-01

    Microbiological cultures of specimens of tissue and of fluids from the wound in forty patients who had had consecutive clean, elective orthopaedic operations (excluding total joint replacements) and had not received antibiotics preoperatively were analyzed. Of the forty patients, twenty-three (58 per cent) had a positive culture on at least one of the media that were used and seventeen (43 per cent) had negative cultures. Of the forty specimens that were obtained from swabbing of the wound, eight (20 per cent) were positive on culture, compared with twenty (50 per cent) that were obtained from biopsy of tissue. Of these twenty-eight positive cultures, thirteen (46 per cent) were on routine blood-agar plates and fifteen (54 per cent), in broth only. Of the thirty-three bacterial organisms that were identified in the twenty-eight positive cultures of the wound, nineteen (58 per cent) were coagulase-negative Staphylococcus; eight (24 per cent), Propionibacterium acnes; two (6 per cent), Peptostreptococcus; and four (12 per cent), miscellaneous organisms. In all of the positive cultures on the blood-agar plates, except in those showing Propionibacterium acnes, there were five colonies or fewer. One patient had a clinical infection with Staphylococcus aureus that developed later, but the initial cultures of the wound had been positive for Staphylococcus epidermidis only. None of the bacteria that grew on culture were Staphylococcus aureus or the less common pathogenic gram-negative bacteria, such as Escherichia coli, Pseudomonas, or Klebsiella.(ABSTRACT TRUNCATED AT 250 WORDS)

  1. Comparative evaluation of the Abbott RealTime High Risk HPV test and INNO-LiPA HPV Genotyping Extra test for detecting and identifying human papillomaviruses in archival tissue specimens of head and neck cancers:

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Gale, Nina; Zidar, Nina; Maver Vodičar, Polona; Hošnjak, Lea; Odar, Katarina

    2012-01-01

    Introduction: The Abbott RealTime is a novel real-time PCR assay designed for concurrent individual genotyping of HPV16 and HPV18 and pooled detection of 12 HPV genotypes: HPV31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68 in cervical swab specimens. In this study, the performance of RealTime for detecting HPV in formalin-fixed, paraffin-embedded tissue specimens of head and neck cancers was compared to the Innogenetics INNO-LiPA assay, which allows identification of 28 HPVs, including all...

  2. FilmArray Respiratory Panel Assay: Comparison of Nasopharyngeal Swabs and Bronchoalveolar Lavage Samples.

    Science.gov (United States)

    Azadeh, Natalya; Sakata, Kenneth K; Brighton, Anjuli M; Vikram, Holenarasipur R; Grys, Thomas E

    2015-12-01

    The FilmArray respiratory panel (FARP) reliably and rapidly identifies 17 viruses and 3 bacterial pathogens. A nasopharyngeal swab FARP (NP FARP) is performed for many patients with respiratory symptoms. For patients who are acutely ill or immunocompromised or fail to improve, a bronchoalveolar lavage sample FARP (BAL FARP) is performed in addition to the NP FARP. To date, no studies have compared the yield of a BAL FARP with that of an NP FARP. We retrospectively studied all patients who had a BAL FARP within 7 days after an NP FARP between June 2013 and May 2014. Demographic information, comorbidities, FARP results, and all microbiologic data from BAL fluid were collected. Eighty-six patients had a BAL FARP performed within 7 days (mean, 1.6; median, 1) after an NP FARP. Of these, 66 (77%) had concordant BAL and NP FARP results: 15 (23%) had the same pathogen identified from the NP and BAL FARPs, and 51 (77%) had concordant negative FARP results. In 18 of the 86 patients (21%), a pathogen was detected from the NP FARP; of these, 15 (83%) had a concordant match on a subsequent BAL FARP, and the remaining 3 had negative BAL FARPs. In 17 of the 86 patients (20%), pathogens were identified from the BAL FARPs that were not detected by the NP FARPs; of these, 16 (94%) had initial negative NP FARPs. The data suggest that once a pathogen is identified by an NP FARP, a subsequent BAL FARP is unlikely to add new microbiologic information. However, a BAL FARP may provide new, useful microbiologic information when performed within 7 days after a negative NP FARP. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  3. Evaluation of Rectoanal Mucosal Swab Sampling for Molecular Detection of Enterohemorrhagic Escherichia coli in Beef Cattle.

    Science.gov (United States)

    Agga, Getahun E; Arthur, Terrance M; Hinkley, Susanne; Bosilevac, Joseph M

    2017-04-01

    Cattle are a primary reservoir of enterohemorrhagic Escherichia coli (EHEC), and contaminated beef products are a source of human infections. The U.S. Department of Agriculture Food Safety and Inspection Service declared seven EHEC serogroups (O26, O45, O103, O111, O121, O145, and O157) as adulterants in raw ground beef. Sampling a large number of animals for EHEC surveillance or evaluations of EHEC-focused preharvest interventions requires a convenient and robust sampling method. We evaluated the diagnostic performance of rectoanal mucosal swab (RAMS) for the detection of the top seven EHEC serogroups. Paired fecal grab (FG) and RAMS samples were collected from 176 beef cattle and tested using the NeoSEEK Shiga toxin-producing E. coli (STEC) confirmation method. The prevalence of virulence-associated genes (stx 1 , stx 2 , stx 2c , eae, and nleB) was higher in RAMS than in FG samples. The results of the two methods had poor agreement, as indicated by kappa statistics, for the detection of the seven serogroups. When FG and RAMS results were combined for comparison, RAMS was more sensitive than FG for the detection of serogroups O103 (82% versus 39%), O157 (75% versus 67%), and O45 (79% versus 73%) with similar sensitivity for the detection of serogroup O145 (67%). Serogroups O111 and O121 were detected from one and two samples, respectively, by FG and were not detected by RAMS. Serogroup O26 was not detected with either method. RAMS appears to be equivalent or superior to FG sampling for detection of the top seven EHEC serogroups in the feces of beef cattle with the NeoSEEK STEC confirmation test.

  4. The Value of Agricultural Voucher Specimens

    OpenAIRE

    Barkworth, Mary; Wolf, Paul; Kinosian,Sylvia; Dyreson,Curtis; Pearse,Will; Brandt, Benjamin; Cobb, Neil

    2017-01-01

    Voucher specimens are the ultimate raw data of biodiversity studies because they document the interpretation of the names used in papers and reports resulting from such studies. The value of voucher specimens is increased by making their records web-accessible but they can be further enhanced by linking them to other online resources, particularly if the links are birectional.  In this presentation, we discuss the potential benefits of such links for a group of agricultural significance, the ...

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

    DEFF Research Database (Denmark)

    Hansen, Mie Johanne; Bertelsen, Mads Frost; 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...

  6. Utility of nasal swab and age in detecting methicillin-resistant Staphylococcus aureus in pediatric head and neck abscesses.

    Science.gov (United States)

    Bradford, Benjamin D; Macias, David; Liu, Yuan F; Inman, Jared C; Dyleski, Robin A

    2017-10-01

    To identify risk factors associated with the presence of methicillin-resistant Staphylococcus aureus (MRSA) in surgical cultures taken from incision and drainage (I&D) of head and neck abscesses in the pediatric population. Retrospective case series. All patients under 18 years of age with a head and neck abscess requiring I&D from 2009 to 2015 were reviewed. MRSA nasal swab cultures were taken from all patients upon hospitalization. Surgical cultures were obtained from all patients and correlated with MRSA nasal swab results. Univariate and multivariate logistic regression was performed, and odds ratios (ORs) along with descriptive statistics were analyzed. Of a total of 272 patients, there were 68 (25%) MRSA-positive abscesses. The majority (86.8%) of these abscesses were in children under 2 years of age. Overall, 12 (4.4%) presented with positive admission MRSA nasal swabs. Of these, 91.7% had MRSA-positive abscess cultures. Decreasing age in years showed an OR of 1.650 (P MRSA-positive abscess, with children less than 1 year old having the highest OR of 10.74 (P MRSA nasal colonization were two statistically significant risk factors for developing an MRSA abscess of the head and neck. This study demonstrates a high positive predictive value for MRSA-positive neck abscesses when nasal swab screenings were MRSA-positive (91.7%). Children under 2 years of age-especially those under 1 year of age-or those with MRSA nasal colonization can be considered a high-risk population that may benefit from empiric antibiotics against MRSA for head and neck abscesses. 4. Laryngoscope, 127:2407-2412, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  7. Detection of Pneumocystis in the nasal swabs of immune-suppressed rats by use of PCR and microscopy

    OpenAIRE

    Can, H?seyin; Caner, Ay?e; D??kaya, Mert; De?irmenci, Aysu; Kara?al?, Sabire; Polat, Ceylan; G?r?z, Y?ksel; ?ner, Ahmet

    2013-01-01

    Background Detection of Pneumocystis jiroveci colonization in lungs or oral samples due to high sensitivity of PCR methods results in undue treatment of patients without any symptoms of Pneumocystis pneumonia. The aim of the present study is to demonstrate Pneumocystis carinii in rats, immune suppressed by oral and subcutaneous administration of dexamethasone. Material/Methods Blood, oral, nasal and eye swabs were collected prior to immune suppression and 2, 6, 12 weeks after administration o...

  8. Efficiency of noninvasive sampling methods (swab together with Polymerase Chain Reaction (PCR for diagnosing American Tegumentary Leishmaniasis

    Directory of Open Access Journals (Sweden)

    Sara Macente Boni

    Full Text Available ABSTRACT Traditional diagnostic methods used to detect American Tegumentary Leishmaniasis, such as histopathology using biopsy samples, culture techniques, and direct search for parasites, have low sensitivity and require invasive collection procedures. This study evaluates the efficiency of noninvasive sampling methods (swab along with Polymerase Chain Reaction (PCR for diagnosing American Tegumentary Leishmaniasis using skin and mucous samples from 25 patients who had tested positive for leishmaniasis. The outcome of the tests performance on swab samples was compatible with PCR results on biopsy samples. The findings have also shown that PCR-kDNA test is more efficient than PCR-HSP70 and qPCR tests (sensitivity of 92.3%, 40.7%, and 41%, respectively. Given the high sensitivity of the tests and the fact that the sampling method using swabs affords greater patient comfort and safety, it could be said that this method is a promising alternative to conventional biopsy-based methods for the molecular diagnosis of leishmaniasis.

  9. Contribution of the Ogawa-Kudoh swab culture method to the diagnosis of pulmonary tuberculosis in Brazil.

    Science.gov (United States)

    Palaci, M; Peres, R L; Maia, R; Cunha, E A T; Ribeiro, M O; Lecco, R; de Souza Ribeiro, C; Ferro E Silva, R R; Vinhas, S A; Dietze, R; Vianna, S; de Morais, C G V

    2013-06-01

    To analyse the contribution of the Ogawa-Kudoh (O-K) swab culture method to the diagnosis of pulmonary tuberculosis (PTB) in four different regions of Brazil. This study was carried out in two phases. Phase 1 was designed to compare the direct swab culture method (O-K) with the culture concentrated method (N-acetyl-L-cysteine-sodium hydroxide [NALC-NaOH]); for this purpose, 569 sputum samples were cultured by both methods. Phase 2 was carried out to assess the contribution of the O-K method to the diagnosis of PTB in four different regions in Brazil, based on the evaluation of 19,163 sputum samples. In the first phase of the study, O-K culture had a sensitivity of 94.8% and specificity of 99.8% in cases confirmed by NALC-NaOH/Löwenstein-Jensen (LJ) culture. In the second phase of the study, the overall contribution of O-K culture compared to acid-fast bacilli (AFB) examination (AFB-/culture+) to the diagnosis of PTB was 29.8%. O-K culture contributes significantly to the diagnosis of smear-negative PTB. Importantly, this method allows the recovery of clinical isolates in areas where use of the standard culture centrifuge is impossible, indicating that the O-K swab culture method should become a standard method for TB diagnosis in these regions.

  10. A novel quantitative real-time polymerase chain reaction method for detecting toxigenic Pasteurella multocida in nasal swabs from swine.

    Science.gov (United States)

    Scherrer, Simone; Frei, Daniel; Wittenbrink, Max Michael

    2016-12-01

    Progressive atrophic rhinitis (PAR) in pigs is caused by toxigenic Pasteurella multocida. In Switzerland, PAR is monitored by selective culture of nasal swabs and subsequent polymerase chain reaction (PCR) screening of bacterial colonies for the P. multocida toxA gene. A panel of 203 nasal swabs from a recent PAR outbreak were used to evaluate a novel quantitative real-time PCR for toxigenic P. multocida in porcine nasal swabs. In comparison to the conventional PCR with a limit of detection of 100 genome equivalents per PCR reaction, the real-time PCR had a limit of detection of 10 genome equivalents. The real-time PCR detected toxA-positive P. multocida in 101 samples (49.8%), whereas the conventional PCR was less sensitive with 90 toxA-positive samples (44.3%). In comparison to the real-time PCR, 5.4% of the toxA-positive samples revealed unevaluable results by conventional PCR. The approach of culture-coupled toxA PCR for the monitoring of PAR in pigs is substantially improved by a novel quantitative real-time PCR.

  11. Sterilization monitoring by biological indicators and conventional swab test of different sterilization processes used in orthodontics: A comparative study

    Directory of Open Access Journals (Sweden)

    Shantanu Khattri

    2015-01-01

    Full Text Available Introduction: The need of effective sterilization method and their monitoring is necessary. Biological indicators are specific microorganisms with high resistance toward particular sterilization methods. Their processes include steam autoclave, dry heat sterilizer, ethylene oxide sterilizer. This article has considered various methods to monitor the effectiveness of different sterilization methods used in orthodontics. Materials and Methods: The parameters for comparison were the control and experimental instruments utilized in orthodontic treatment. The efficacy of sterilization was evaluated by comparison of bacterial growth obtained in monitoring by biological indicators and swab test method. Results: No spore growth was found when sterilization process was evaluated by biological indicators in comparison to swab test where spore growth was present. Instruments dipped in Bioclenz-G solution for 10 min showed spore growth, but no spore growth was seen in 10 h cycle. Discussion: The result of the study verifies the established effectiveness of biological indicators over conventional swab test method in monitoring various sterilization processes used in orthodontics. Bioclenz-G solution can be used as an effective cold sterilization method for sterilization. Conclusion: For evaluating the effectiveness of sterilization, biological indicators preclude the drawbacks of incomplete verification of destruction of all vegetation and inordinate delay in procurement of results as is the case with chemical indicators and lab culture, respectively.

  12. Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay.

    Science.gov (United States)

    Nilyanimit, Pornjarim; Chansaenroj, Jira; Karalak, Anant; Laowahutanont, Piyawat; Junyangdikul, Pairoj; Poovorawan, Yong

    2017-01-01

    Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0.05). Urine samples processed with the GenoArray assay is an alternative for women who decline to undergo Pap smear even though it is not ideal as the first-line screening option.

  13. 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.

  14. Clinical Evaluation of the Cepheid Xpert® TV Assay for detection of Trichomonas vaginalis with Prospectively Collected Female and Male Specimens.

    Science.gov (United States)

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

    2017-11-22

    Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and acquisition/transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA-cleared in the United States for detection of Trichomonas vaginalis (TV) in specimens from both women and men. This current study reports the results of a multicenter study recently conducted using the Xpert TV Assay to test specimens from both men and women. On-demand results were available in as little as 40 minutes for positive specimens. A total of 1867 women and 4791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV Assay was compared to a patient infected status (PIS) derived from results of InPouch TV broth culture and Aptima NAAT for TV. Diagnostic sensitivity and specificity of the Xpert TV Assay for the combined female specimens (urines, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 - 100% and 99.4 - 99.9%, respectively. For male urines, diagnostic sensitivity and specificity was 97.2% and 99.9% respectively, compared to a PIS derived from results of broth culture for TV and bi-directional gene sequencing of the 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 TV in both men and women and hopefully improved control of this infection. Copyright © 2017 Schwebke et al.

  15. Combined Testing for Chlamydia, Gonorrhea, and Trichomonas by Use of the BD Max CT/GC/TV Assay with Genitourinary Specimen Types.

    Science.gov (United States)

    Van Der Pol, Barbara; Williams, James A; Fuller, DeAnna; Taylor, Stephanie N; Hook, Edward W

    2017-01-01

    The BD Max CT/GC/TV (MAX) assay is a true multiplex assay for simultaneous detection of chlamydia (CT), gonorrhea (GC), and trichomonas (TV). We evaluated assay performance for women using endocervical and vaginal swabs as well as urine specimens. A total of 1,143 women were tested for CT, GC, and TV and, subsequently, another 847 (1,990 total women) for CT and GC only, with positivity rates for CT, GC, and TV of 7.1%, 2.3%, and 13.5%, respectively. In men, the performance for CT and GC was determined using only urine specimens. TV performance was not assessed in male urine samples. Among men, 181/830 (21.8%) and 108/840 (12.9%) chlamydia and gonorrhea infections, respectively, were identified. Comparator assays included BD ProbeTec Chlamydia trachomatis Qx (CTQ)/Neisseria gonorrhoeae Qx (GCQ), Hologic Aptima Combo 2 (AC2) and Aptima TV (ATV), trichomonas microscopy, and culture. MAX CT sensitivity was 99.3% (95% confidence interval [CI], 96.1% to 99.9%), 95.7% (90.8% to 98.0%), 91.5% (85.8% to 95.1%), and 96.1% (92.2% to 98.1%) for vaginal swabs, endocervical swabs, female urine samples, and male urine samples, respectively. MAX GC sensitivity was 95.5% (84.9% to 98.7%), 95.5% (84.9% to 98.7%), 95.7% (85.5% to 99.8%), and 99.1% (94.9% to 99.8%) in the same order. MAX TV sensitivity was 96.1% (91.7% to 98.2%) for vaginal swabs, 93.4% (88.3% to 96.4%) for endocervical swabs, and 92.9% (87.8% to 96.0%) for female urine samples. Specificity for all organisms across all sample types was ≥98.6%. Performance estimates for the MAX assays were consistent with estimates calculated for the comparator assays (all P values were >0.1). The availability of a CT/GC/TV multiplexed assay on a benchtop instrument with a broad menu has the potential to facilitate local sexually transmitted infection (STI) testing at smaller laboratories and may encourage expanded screening for these highly prevalent infections. Copyright © 2016 American Society for Microbiology.

  16. Diagnosis of Trichomonas vaginalis from vaginal specimens by wet mount microscopy, in pouch TV culture system, and PCR

    Directory of Open Access Journals (Sweden)

    Madhumati J Patil

    2012-01-01

    Full Text Available Background: In recent years, trichomoniasis has emerged as the most common sexually transmitted disease and limited data are available on the effective screening technique for the diagnosis of Trichomonas vaginalis. Aim : The aim was to compare and evaluate different diagnostic methods like wet mount microscopy, In Pouch TV culture, and Polymerase chain reaction (PCR to establish which method or combination of methods was most effective for detection of Trichomonas vaginalis in vaginal swab specimens. Settings and Design : This is a cross-sectional study. Materials and Methods : A total of 200 patients complaining of vaginal discharge were included in the study. Three vaginal swabs were screened for trichomoniasis by wet mount microscopy, In Pouch TV culture system and PCR, using TVK3 and TVK7 specific primers. Results : Of the 200 cases studied, 36 (18% were positive by wet mount microscopy, 44 (22% by In Pouch TV culture system and 60(30% by PCR. Sensitivity and specificity of wet mount were 60% and 100%, respectively, whereas sensitivity and specificity of the In Pouch TV culture system were 73.33% and 100%, respectively when compared to PCR. Conclusion : Comparison of different methods showed that at least two techniques, such as wet mount microscopy and culture have a better chance of detection of T. vaginalis infection. Diagnosis of trichomoniasis by PCR was found to be highly specific and sensitive, but its availability and cost effectiveness limit its use in routine diagnostic laboratories.

  17. The Comparison of Chlorhexidine Solution and Swab With Toothbrush and Toothpaste Effect on Preventing Oral Lesions in Hospitalized Patients in Intensive Care Unit

    National Research Council Canada - National Science Library

    Estaji, Zahra; Alinejad, Mohammad; Hassan Rakhshani, Mohammad; Rad, Mojtaba

    2016-01-01

    .... In this study, 30 patients were selected with target-based approach and equally divided into two groups through the permutation blocking method for oral care toothbrush and toothpaste and using chlorhexidine and swab...

  18. Comparison of the diagnostic performance of bacterial culture of nasopharyngeal swab and bronchoalveolar lavage fluid samples obtained from calves with bovine respiratory disease

    Science.gov (United States)

    Objective: Examine the culture results, gamithromycin susceptibility, predictive values, and agreement of pooled bilateral nasopharyngeal swabs (NPS) and bronchoalveolar lavages (BAL) for identification of Mannheimia haemolytica genotypes, Pasteurella multocida, and Histophilus somni in calves treat...

  19. Breast specimen shrinkage following formalin fixation

    Directory of Open Access Journals (Sweden)

    Horn CL

    2014-02-01

    Full Text Available Christopher L Horn, Christopher Naugler Department of Pathology and Laboratory Medicine, University of Calgary, and Calgary Laboratory Services, Calgary, AB, Canada Abstract: Accurate measurement of primary breast tumors and subsequent surgical margin assessment is critical for pathology reporting and resulting patient therapy. Anecdotal observations from pathology laboratory staff indicate possible shrinkage of breast cancer specimens due to the formalin fixation process. As a result, we conducted a prospective study to investigate the possible shrinkage effects of formalin fixation on breast cancer specimens. The results revealed no significant changes in tumor size, but there were significant changes in the distance to all surgical resection margins from the unfixed to fixed state. This shrinkage effect could interfere with the accuracy of determining distance to margin assessment and tumor-free margin assessment. Thus, changes in these measurements due to the formalin fixation process have the potential to alter treatment options for the patient. Keywords: breast margins, formalin, shrinkage, cancer

  20. Standard guide for preparation of metallographic specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2011-01-01

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

  1. Damage modeling in Small Punch Test specimens

    DEFF Research Database (Denmark)

    Martínez Pañeda, Emilio; Cuesta, I.I.; Peñuelas, I.

    2016-01-01

    Ductile damage modeling within the Small Punch Test (SPT) is extensively investigated. The capabilities ofthe SPT to reliably estimate fracture and damage properties are thoroughly discussed and emphasis isplaced on the use of notched specimens. First, different notch profiles are analyzed....... Furthermore,Gurson-Tvergaard-Needleman model predictions from a top-down approach are employed to gain insightinto the mechanisms governing crack initiation and subsequent propagation in small punch experiments.An accurate assessment of micromechanical toughness parameters from the SPT...

  2. Causes and impact of specimen rejection in a clinical chemistry laboratory.

    Science.gov (United States)

    Cao, Liyun; Chen, Meng; Phipps, Ron A; Del Guidice, Robert E; Handy, Beverly C; Wagar, Elizabeth A; Meng, Qing H

    2016-07-01

    Pre-analytical errors necessitate specimen rejection and negatively affect patient safety. Our purpose was to investigate the factors leading to specimen rejection and its impact. Specimen rejections in a clinical chemistry laboratory during a 1-year period were reviewed retrospectively and analyzed for frequency, cause, circumstances, and impact. Of the 837,862 specimens received, 2178 (0.26%) were rejected. The most common reasons for specimen rejection were contamination (n=764, 35.1%), inappropriate collection container/tube (n=330, 15.2%), quantity not sufficient (QNS) (n=329, 15.1%), labeling errors (n=321, 14.7%), hemolyzed specimen (n=205, 9.4%), and clotted specimen (n=203, 9.3%). The analytes most often affected were glucose (n=192, 8.8%); calcium (n=152, 7.0%), magnesium (n=148, 6.8%), potassium (n=137, 6.3%), creatinine (n=100, 4.6%), and blood urea nitrogen (n=97, 4.4%). Outpatient service and blood draw by phlebotomists were associated with low rejection rates (536/493,501 or 0.11% and 368/586,503 or 0.06%, respectively). Recollection due to specimen rejection increased the turnaround time by an average of 108min. The total cost for the recollection was around $43,210 USD with an average cost around $21.9 USD. The factors associated with rejection are remediable by improved training and quality assurance measures. Policies and procedures specific to specimen collection, transportation, and preparation should be strictly followed. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. 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.

  4. A Review of Sleeve Gastrectomy Specimen Histopathology.

    Science.gov (United States)

    Kinsinger, Luke A; Garber, James C; Whipple, Oliver

    2016-11-01

    With the increasing popularity of sleeve gastrectomy, many stomach specimens are being evaluated. Understanding the significance and treatment for unexpected pathology is important. This study examines the incidence of relevant histopathology of sleeve gastrectomy specimens. It evaluates previous data for each histopathology and provides recommendations for treatment. In this study, a retrospective review was performed for 241 patients who underwent sleeve gastrectomy from 2009 to 2014 at a single institution. Of the specimens, 122 had no significant histopathology, 91 had gastritis, 13 had lymphoid aggregates, 5 had hyperplasia, 3 had intestinal metaplasia, 3 had gastrointestinal stromal tumors (GISTs), and 3 had gastric polyps. Of the GISTs all had a low mitotic rate and the size of the tumor ranged from 1.5 to 4.5 cm. The findings of metaplasia may be a marker for increased risk of malignancy and may require additional surveillance. The findings of GIST may warrant interval imaging to survey for recurrence, though the likelihood of recurrence for the tumors in this study is less than 2 per cent based on previous studies.

  5. 10 CFR 26.113 - Splitting the urine specimen.

    Science.gov (United States)

    2010-01-01

    ... splitting of the urine specimen and to maintain visual contact with both specimen bottles until the custody... 10 Energy 1 2010-01-01 2010-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy... Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

  6. Specimen loading list for the varying temperature experiment

    Energy Technology Data Exchange (ETDEWEB)

    Qualls, A.L.; Sitterson, R.G. [Oak Ridge National Lab., TN (United States)

    1998-09-01

    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.

  7. 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....

  8. Evaluation of the Essen Rotary as a new technique for bacterial swabs: results of a prospective controlled clinical investigation in 50 patients with chronic leg ulcers.

    Science.gov (United States)

    Al Ghazal, Philipp; Körber, Andreas; Klode, Joachim; Schmid, Ernst N; Buer, Jan; Dissemond, Joachim

    2014-02-01

    Most chronic wounds are colonised with different microorganisms, especially problematic bacteria like methicillin-resistant Staphylococcus aureus (MRSA), which represent an increasing therapeutic challenge in the modern wound therapy regimen. Therefore, it is essential to specify the bacteria in wounds for an individual-specific treatment. In most patients, an exemplary bacterial swab is taken from the centre of the wound surface. This so-called Levine technique is propagated currently as the gold standard. The aim of our clinical investigation was to compare the results of different swab techniques to the new established Essen Rotary. In this monocentric prospective investigation, 50 patients with chronic leg ulcers were examined consecutively. The results of our clinical study show that bacteria are heterogeneously spread on wound surfaces. The analysis of the semiquantitative measured results showed that the Essen Rotary could detect significant more bacteria with a total amount of 111 bacteria (P = 0·049) compared to usual swab techniques. Considerably, only the Essen Rotary identified five compared to three MRSA-patients detected by other techniques. The Essen Rotary is an efficient, economic and uncomplicated modification of bacteriological swab techniques which detects significant more bacteria compared to other conventional swab techniques. Therefore, the Essen Rotary may become the new gold standard in routinely taken bacteriological swabs especially for MRSA screenings in patients with chronic leg ulcers. © 2012 The Authors. International Wound Journal © 2012 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

  9. Comparison of molecular diagnostic methods for the detection of Acanthamoeba spp. from clinical specimens submitted for keratitis.

    Science.gov (United States)

    Khairnar, Krishna; Tamber, Gurdip S; Ralevski, Filip; Pillai, Dylan R

    2011-08-01

    Acanthamoeba spp. are responsible for a significant annual number of keratitis (AK) cases leading to vision-threatening disease worldwide. Current methods rely on direct examination of specimens by microscopy and/or culture. The former lacks sensitivity and the latter suffers from a poor turnaround time. We undertook a comparison of all published molecular methods, evaluating performance characteristics such as analytical sensitivity, specificity, limit of detection (LOD), reproducibility, accuracy, and cost of test. The study population comprised 128 patients. Eligible specimens were tested prospectively between April 2007 and May 2010 by microscopy and/or culture. Eleven different specimen types were used including corneal scrapings (51.5%), corneal swab (17.9%), and contact lens material (10.9%). Results of 2 published gel-based polymerase chain reaction (PCR) and 2 published real-time quantitative (Q) PCR methods were compared in a blinded manner to direct microscopic examination and/or culture for the detection of Acanthamoeba in clinical specimens. QPCR (Riviere method) had the highest sensitivity at 89.3%, excellent accuracy using ROC analysis (AUC ∼0.90), lowest LOD down to 0.1 organism per microliter, and superior linear correlation with parasite density (R(2) = 0.9965) when compared with microscopy, culture, and other molecular methods. Phylogenetic analysis using a sequence-based typing method revealed that clinical isolates in this population with AK were genetically distinct from granulomatous amebic encephalitis or environmental isolates. The QPCR method was more expensive ($14.80) than traditional methods such as culture ($2.50) or microscopy ($2.50). However, 13 culture- and microscopy-negative specimens were positive by QPCR during the study period, suggesting that detection using QPCR may result in reduced complications and health care costs associated with misdiagnosed AK. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. 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.

  11. Detection of group A streptococcal antigen directly from throat swabs with a ten-minute latex agglutination test.

    OpenAIRE

    Miceika, B G; Vitous, A S; Thompson, K D

    1985-01-01

    Results obtained with the Culturette brand 10-Minute Group A Strep ID system were compared with culture results to measure the ability of this system to detect group A streptococci directly from more than 800 throat swabs. Our study showed a sensitivity of 92.4% and a specificity of 92.8% for this acid extraction, latex agglutination method when compared with anaerobic culturing for group A streptococci. The results suggest that the 10-Minute Group A Strep ID method may prove to be a useful, ...

  12. Evaluation of Three Automated Nucleic Acid Extraction Systems for Identification of Respiratory Viruses in Clinical Specimens by Multiplex Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Yoonjung Kim

    2014-01-01

    Full Text Available 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.

  13. 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.

  14. 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.

  15. Muscle degeneration in inguinal hernia specimens.

    Science.gov (United States)

    Amato, G; Agrusa, A; Romano, G; Salamone, G; Gulotta, G; Silvestri, F; Bussani, R

    2012-06-01

    There are few articles in the literature reporting the histological changes of groin structures affected by inguinal hernia. A deeper knowledge of this matter could represent an important step forward in the identification of the causes of hernia protrusion. This study aimed to recognise the pathological modifications of muscular structures in autopsy specimens excised from tissues surrounding the hernia orifice. Inguinal hernia was identified in 30 autopsied cadavers, which presented different varieties of hernia, including indirect, direct and mixed. Tissue specimens were resected for histological study from structures of the inguinal area surrounding the hernia opening, following a standardised procedure. The histological examination was focussed on the detection of structural changes in the muscle tissues. The results were compared with biopsy specimens resected from corresponding sites of the inguinal region in a control group of 15 fresh cadavers without hernia. Significant modification of the muscular arrangement of the inguinal area was recognized. Pathological alterations such as atrophy, hyaline and fibrotic degeneration, as well as fatty dystrophy of the myocytes were detected. These findings were observed consistently in the context of multistructural damage also involving vessels and nerves. In cadavers with hernia these alterations were always present independent of hernia type. No comparable damage was found in control cadavers without hernia. The high degree of degenerative changes in the muscle fibres in the inguinal area involved in hernia protrusion described in this report seems to be consistent with chronic compressive damage. These alterations could embody one important factor among the multifactorial sources of hernia genesis. Conjectures concerning its impact on the physiology and biodynamics of the inguinal region are made. The relationship between the depicted degenerative injuries and the genesis of inguinal hernia is also a focus of

  16. 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....

  17. Fabrication and testing of composite ring specimens

    Science.gov (United States)

    Liber, T.; Daniel, I. M.; Labedz, R.; Niiro, T.

    1979-01-01

    The tooling and techniques used in the fabrication of composite laminate tubes of any desired ply orientation and stacking sequence are described along with techniques for cutting ring specimens under internal pressure. The method consists of laying up the tube on a central circular mandrel, and by means of internal pressure, expanding the prepreg tube against the cavity wall of an external mold tool, which forms the geometric curing envelope for the tube. Tube quality is assessed by laminate wall thickness measurement, by hoop strength measurement on rings cut from the ends of the tube, and by ultrasonic inspection.

  18. 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)

    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.; O., K. L.; L., O. S.; K., M. D.; F., D. R.; D., A. N.; D., A. J.; Fancourt, Nicholas; F., W.; H., L. L.; H., M. M.; Wangeci Kagucia, E.; K., R. A.; L., M.; P., D. E.; P., C.; Wu, Zhenke; Z., S. L.; Watson, Nora L.; Crawley, Jane; M., D. R.; W. A., B.; Endtz, Hubert P.; Khalequ, Zaman; Goswami, Doli; H., L.; J., Y.; Ashraf, Hasan; H., S. R. C.; Ebruke, Bernard E.; A., M.; McLellan, Jessica; Machuka, Eunice; Shamsul, Arifin; Zaman, Syed M. A.; Mackenzie, Grant; S., J. A. G.; A., J. O.; M., S. C.; Kamau, Alice; K., S.; Ominde, Micah Silaba; K., K. L.; T., M. D.; Sow, Samba O.; S., M.; Tamboura, Boubou; Onwuchekwa, Uma; Kourouma, Nana; Toure, Aliou; M., S. A.; M., D. P.; Adrian, Peter V.; B., V. L.; Kuwanda, Locadiah; Mudau, Azwifarwi; Groome, Michelle J.; Mahomed, Nasreen; B., H. C.; Thamthitiwat, Somsak; Maloney, Susan A.; Bunthi, Charatdao; Rhodes, Julia; S., P.; Akarasewi, Pasakorn; T., D. M.; M., L.; Chipeta, James; S., P.; Mwansa, James; wa Somwe, Somwe; Kwenda, Geoffrey; Anderson, Trevor P.; Mitchell, Joanne

    2017-01-01

    Abstract Background. 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. Methods. 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). Results. 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). Conclusions. Using advanced molecular methods with IS specimens provided little additional diagnostic information beyond that obtained with NP/OP swab specimens. PMID

  19. 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.

  20. Development of fatigue life evaluation method using small specimen

    Science.gov (United States)

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

    2013-10-01

    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.

  1. Flexor tendon specimens in organ cultures.

    Science.gov (United States)

    Rank, F; Eiken, O; Bergenholtz, A; Lundborg, G; Erkel, L J

    1980-01-01

    The healing process of sectioned and subsequently sutured rabbit tendon segments was studied over a period of 3 weeks, using an organ culture technique. In one series, the tendon specimens were exposed to a chemically defined culture medium for nutrition. In two control series, the specimens were kept in the synovial cavity of the knee joint for varying periods of time, before being transferred to the culture medium. The tendons remained viable in the medium. The superficial tendon cells demonstrated the morphological characteristics of fibroblasts, but cellular fibroplasia could not be detected. The two control series subjected to synovia prior to transfer into the culture medium showed superficial repair similar to the findings in previous studies on healing capacity of tendon nourished by synovia. The investigation supports the hypothesis that superficial tendon cells are fibroblasts with a potential for repair and that synovia is an efficient nutrient medium. Thus, the beneficial effects on repair exercised by the tendon sheath function should be utilized in flexor tendon surgery.

  2. Automated clinical annotation of tissue bank specimens.

    Science.gov (United States)

    Gilbertson, John R; Gupta, Rajnish; Nie, Yimin; Patel, Ashokkumar A; Becich, Michael J

    2004-01-01

    Modern, molecular bio-medicine is driving a growing demand for extensively annotated tissue bank specimens. With careful clinical, pathologic and outcomes annotation, samples can be better matched to the research question at hand and experimental results better understood and verified. However, the difficulty and expense of detailed specimen annotation is well beyond the capability of most banks and has made access to well documented tissue a major limitation in medical re-search. In this context, we have implemented automated annotation of banked tissue by integrating data from three clinical systems--the cancer registry, the pathology LIS and the tissue bank inventory system--through a classical data warehouse environment. The project required modification of clinical systems, development of methods to identify patients between and map data elements across systems and the creation of de-identified data in data marts for use by researchers. The result has been much more extensive and accurate initial tissue annotation with less effort in the tissue bank, as well as dynamic ongoing annotation as the cancer registry follows patients over time.

  3. Detection of Bordetella avium by TaqMan real-time PCR in tracheal swabs from wildlife birds.

    Science.gov (United States)

    Stenzel, T; Pestka, D; Tykałowski, B; Śmiałek, M; Koncicki, A; Bancerz-Kisiel, A

    2017-03-28

    Bordetella avium, the causing agent of bordetellosis, a highly contagious infection of the respiratory tract in young poultry, causes significant losses in poultry farming throughout the world. Wildlife birds can be a reservoir of various pathogens that infect farm animals. For this reason the studies were conducted to estimate the prevalence of Bordetella avium in wildlife birds in Poland. Tracheal swab samples were collected from 650 birds representing 27 species. The bacterial DNA was isolated directly from the swabs and screened for Bordetella avium by TaqMan real-time PCR. The assay specificity was evaluated by testing DNA isolated from 8 other bacteria that can be present in avian respiratory tract, and there was no amplification from non-Bordetella avium agents. Test sensitivity was determined by preparing standard tenfold serial dilutions of DNA isolated from positive control. The assay revealed to be sensitive, with detection limit of approximately 4.07x10^2 copies of Bordetella avium DNA. The genetic material of Bordetella avium was found in 54.54% of common pheasants, in 9.09% of Eurasian coots, in 3.22% of black-headed gulls and in 2.77% of mallard ducks. The results of this study point to low prevalence of Bordetella avium infections in wildlife birds. The results also show that described molecular assay proved to be suitable for the rapid diagnosis of bordetellosis in the routine diagnostic laboratory.

  4. "DETECTION OF BACTERIAL, METHICILLIN RESISTANCE, AND β-LACTAMASE GENES FOUND IN WOUND SWABS BY MULTIPLEX POLYMERASE CHAIN REACTION"

    Directory of Open Access Journals (Sweden)

    S. Sadeghian

    2004-05-01

    Full Text Available Coagulase-positive and coagulase negative, methicillin-resistant staphylococci are major causes of serious nosocomial infections and it is very important to have a reliable test to detect these bacteria. A multiplex polymerase chain reaction (mPCR was used on 100 clinical samples for simultaneous amplification of the universal bacterial, mec-A encoding the penicillin binding protein 2a, which is associated with staphylococcal methicillin resistance and TEM-1 encoding the β-lactamase, which accounts for the majority of all cases of the plasmid β-lactamase resistance worldwide. Out of 100 wound swabs tested, 99% with universal primers, 26% with TEM-1 primers and 6% with mec-A primers were positive. Dot blot Digoxigenin hybridization on the 30 samples was carried out to confirm identified bacteria with specific bacterial probes. Out of 100 wound swabs, 38% were positive with Staphylococcus aureus probe, 23% were positive with enteric bacteria probe, 7% were positive with Streptococcus agalactia probe and 1% were positive with Haemophilus influenza probe. The mPCR method used in this study, was designed to be incorporated into the workflow of the clinical microbiology laboratory and allows for the identification of intrinsic resistance in a timely and reliable manner.

  5. 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.

  6. Culture-Independent Detection and Genotyping of Mycoplasma pneumoniae in Clinical Specimens from Beijing, China.

    Directory of Open Access Journals (Sweden)

    Fei Zhao

    Full Text Available A duplex real-time PCR assay was designed for simultaneous detection and genotyping of Mycoplasma pneumoniae (M. pneumoniae. The detection/typing performance of this duplex PCR method, targeting specific genes for M. pneumoniae type 1 (mpn 459 and type 2 (mpna 5864, was compared to that of the previously published MpP1 real-time PCR assay and the genotyping method for the adhesin P1 gene (mpn 141. A total of 1,344 throat swab specimens collected from patients in Beijing, China were tested for M. pneumoniae by bacterial culture, MpP1 real-time PCR assay, and our duplex PCR assay, and positive detection rates of 26.9%, 34.4%, and 33.7%, respectively, were obtained. The duplex PCR method demonstrated high sensitivity and accuracy for detecting and genotyping M. pneumoniae, and significant differences in genotyping ability were observed when compared to the conventional P1 gene-based method. M. pneumoniae type 1 was the predominate genotype from 2008 to 2012 in Beijing, and a shift from type 1 to type 2 began to occur in 2013. To our knowledge, this is the first reported incidence of a type shift phenomenon of M. pneumoniae clinical isolates in China. These genotyping results provide important information for understanding recent changes in epidemiological characteristics of M. pneumoniae in Beijing.

  7. Mannheimiose pulmonar experimental em bezerros: swab nasal e nasofaringeano como auxílio diagnóstico Experimental pneumonic mannheimiosis in calves: nasal and nasopharingeal swabs for diagnostic

    Directory of Open Access Journals (Sweden)

    Adriana de Souza Coutinho

    2009-01-01

    Full Text Available Um modelo experimental de mannheimiosepneumônica bovina (MPB foi utilizado com o objetivo de avaliar as espécies bacterianas das cavidades nasais e nasofaringeanas em diferentes momentos do curso da doença, bem como verificar a eficiência diagnóstica do exame microbiológico dos swabs nasais (SN e nasofaringeanos (SNF. Um total de 28 bezerros foi distribuído aleatoriamente em quatro grupos experimentais (G1 a G4. SN e SNF foram colhidos sete dias antes e 12 (G1, 24 (G2, 48 (G3 e 72 (G4 horas após a inoculação intrabronquial de Mannheimia haemolytica. Após a indução da MPB, a bactéria M. haemolytica biotipo A foi predominante nos SN e SNF, sendo isolada em todos os momentos avaliados, com exceção de um SN colhido 24 horas após a indução da infecção. Não houve diferença significativa nas taxas de isolamento de Pasteurella multocida nos SN ou SNF, colhidos antes e após a indução da MPB. Contudo, esta bactéria passou a ser isolada mais freqüentemente após a indução da MPB, principalmente no SNF. Portanto, pode-se concluir que o exame microbiológico de SN e SNF é um teste auxiliar no diagnóstico da MPB.An experimental model of bovine pneumonic mannheimiosis (BPM was used to evaluate the nasal and nasopharynx bacterial species of calves during the course of the disease and for checking the diagnostic efficiency of nasal swab (NS and nasopharingeal swab (NPS microbiological exams. A total of 28 calves were randomized into four experimental groups (G1-G4. NS and NPS were obtained 7 days before and 12 (G1, 24 (G2, 48 (G3 e 72 (G4 hours after intrabronchial inoculation of Mannheimia haemolytica. After the induction of BPM, M. haemolytica biotype A was the predominant isolated bacterium in NS and NPS in all evaluated sampling times, except for one NS (harvested 24 hours. There were no significant statistical differences for the rates of Pasteurella multocida isolation in NS and NPS, harvested before and after the induction

  8. Detection of Leishmania infantum DNA by real-time PCR in canine oral and conjunctival swabs and comparison with other diagnostic techniques.

    Science.gov (United States)

    Lombardo, Gabriella; Pennisi, Maria Grazia; Lupo, Tiziana; Migliazzo, Antonella; Caprì, Alessandra; Solano-Gallego, Laia

    2012-02-28

    The use of non invasive sampling, such as collection of conjunctival swabs, as a diagnostic tool for the detection of Leishmania DNA is of interest. The purpose of this study was to evaluate the diagnostic utility of detecting Leishmania infection with the use of conjunctival swab samples in dogs living in a highly endemic area for leishmaniosis and to investigate, for the first time, the presence of Leishmania DNA in oral swabs in the same population. One hundred sixty-three dogs living outdoor and recruited in various provinces of Sicily were studied. Leishmania infantum indirect fluorescent antibody test (IFAT), delayed-type hypersensitivity reaction to leishmanin (DTH) and real-time PCR of blood (BL), lymph node (LN), conjunctival (CS) and oral swab (OS) samples were performed. The positive PCR percentages in LN, CS, OS and BL samples were: 24.5%, 22.1%, 8.7% and 5.5%, respectively. Serological and DTH positive percentages were 27.0% and 73.8%, respectively. Seropositive and LN-PCR positive dogs had a high likelihood to be positive by CS-PCR. The similar positive PCR percentages found in CS and LN samples suggest the use of CS-PCR as non-invasive alternative technique to LN-PCR for the detection of Leishmania infection in dogs. In addition, this study demonstrated, for the first time, the presence of Leishmania DNA in oral swabs in dogs. © 2011. Published by Elsevier B.V.

  9. 46 CFR 4.06-40 - Specimen handling and shipping.

    Science.gov (United States)

    2010-10-01

    ... qualified to conduct tests on such specimens. A proper chain of custody must be maintained for each specimen... collection procedures of § 16.113 of this chapter and the chain of custody requirements of 49 CFR part 40...

  10. High Temperature Fatigue Life Evaluation Using Small Specimen

    National Research Council Canada - National Science Library

    NOGAMI, Shuhei; HISAKA, Chiaki; FUJIWARA, Masaharu; WAKAI, Eichi; HASEGAWA, Akira

    2017-01-01

    For developing the high temperature fatigue life evaluation method using small specimen, the effect of specimen size and test environment on the high temperature fatigue life of the reduced activation...

  11. The use of conjunctival swab samples for PCR screening for visceral leishmaniasis in vaccinated dogs O uso de amostras de swab conjuntival para triagem por PCR da leishmaniose visceral em cães vacinados

    Directory of Open Access Journals (Sweden)

    Rodrigo Souza Leite

    2011-03-01

    Full Text Available The polymerase chain reaction (PCR has been shown to provide a rapid and sensitive technique for Leishmania detection. The aim of this study was to evaluate the technique of noninvasive conjunctival swabs (CS as a sampling method for molecular screening for visceral leishmaniasis (VL in a group of 42 police dogs, all of them vaccinated against VL, and to compare the results with those obtained by serological tests. The serological assays were performed independently by three laboratories. Laboratories 1 and 2 were private laboratories and laboratory 3 was the National Reference Laboratory. The first serological screening performed by laboratory 1 showed 15 reactive dogs and 4 indeterminate. Laboratory 2 confirmed only 3 reactive dogs and 2 indeterminate. Laboratory 3 confirmed 7 reactive dogs and 3 indeterminate. The PCR diagnosis using the CS procedure was performed on all 42 animals and was able to detect Leishmania DNA in 17 dogs. The PCR assay confirmed all the cases that were simultaneously reactive in the serological tests by two laboratories. The results showed that the CS technique was a sensitive and practical method for sample collection, thus allowing reliable diagnostic tests through PCR.A PCR (do inglês Polymerase Chain Reaction tem demonstrado ser uma técnica rápida e sensível para detecção de Leishmania. O objetivo deste estudo foi avaliar a técnica não invasiva do swab conjuntival na identificação por PCR de animais infectados em um grupo de 42 cães policiais, todos vacinados contra a Leishmaniose Visceral (VL, e comparar os resultados com aqueles obtidos pelos testes sorológicos. Os ensaios sorológicos foram realizados independentemente por três laboratórios. Os laboratórios 1 e 2 eram privados. O laboratório 3 era o Laboratório de Referência Nacional. A primeira triagem sorológica realizada pelo laboratório 1 apresentou 15 cães reativos e 4 indeterminados. O laboratório 2 confirmou apenas 3 cães reativos

  12. The use of saliva specimens for detection of influenza A and B viruses by rapid influenza diagnostic tests.

    Science.gov (United States)

    Yoon, Jung; Yun, Seung Gyu; Nam, Jeonghun; Choi, Sung-Hyuk; Lim, Chae Seung

    2017-05-01

    Diagnostic tests for influenza infection commonly use nasopharyngeal swabs (NPS) even though these are invasive to obtain. As an alternative specimen, we evaluated the diagnostic usefulness of saliva samples with rapid influenza diagnostic tests (RIDTs). Both NPS and saliva samples were collected from 385 influenza suspected patients and analyzed using Sofia Influenza A+B Fluorescence Immunoassay (Quidel Corporation, San Diego, CA, USA), ichroma TRIAS Influenza A+B (Boditech, Chuncheon, Korea), SD Bioline Influenza Ag (Standard Diagnostic, Yonggin, Korea), BinaxNOW Influenza A/B antigen kit (Alere Inc., Waltham, MA, USA), and real-time reverse transcriptase PCR (RT-PCR). Of the 385 patients, 31.2% (120/385) were positive for influenza A, and 7.5% (29/385) were positive for influenza B virus with saliva or NPS by RT-PCR. The diagnostic sensitivity was slightly higher in NPS than in saliva samples for both influenza A and B by all of the four RIDTs. The diagnostic sensitivities of Sofia and ichroma TRIAS were significantly superior to those of the other conventional influenza RIDTs with both types of sample. The sensitivities of Sofia and ichroma TRIAS with saliva specimens were comparable to the sensitivities of the other two conventional RIDTs with NPS specimens. The simultaneous use of saliva and NPS samples exhibited improved sensitivity from 10.0% to 13.3% for influenza A and from 10.3% to 17.2% for influenza B compared to using NPS alone. This study demonstrates that saliva is a useful specimen for influenza detection, and that the combination of saliva and NPS could improve the sensitivities of influenza RIDTs. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Elastic-plastic analysis of the SS-3 tensile specimen

    Energy Technology Data Exchange (ETDEWEB)

    Majumdar, S. [Argonne National Lab., IL (United States)

    1998-09-01

    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.

  14. 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

  15. ORIGINAL ARTICLES Validity of oral mucosal transudate specimens ...

    African Journals Online (AJOL)

    samples, with DBS as the gold-standard specimen. Results. Paired DBS and OMT specimens were .... within 24 hours signified complete elution. Positive and negative control specimens provided by the ... Using the DBS as the gold standard test, HIV prevalence was 3.2% overall. Prevalence was highest in the 6 - 8-year ...

  16. The role of a commercial enzyme immuno assay antigen detection system for diagnosis of C. trachomatis in genital swab samples

    Directory of Open Access Journals (Sweden)

    A Mukherjee

    2011-01-01

    Full Text Available In the present pilot study, endocervical and urethral swabs collected from 100 patients attending sexually transmitted disease (STD clinics and regional centre for STD in two referral hospitals in New Delhi were analyzed by enzyme immune assay (EIA, polymerase chain reaction (PCR and direct fluorescent antibody (DFA for detection of C. trachomatis. It was found that EIA could detect a very low number of cases (3/100 as against DFA (11/100 and PCR (9/100. Thus, in spite of the widespread availability, lower cost and ease of performance of the enzyme-linked-immunosorbent serologic assay, the present study highlights the need to employ sophisticated diagnostic tools like DFA and PCR for detection of Chlamydia trachomatis in STD patients.

  17. The utility of polyester and cotton as swabbing substrates for the removal of cellular material from surfaces.

    Science.gov (United States)

    Mulligan, Christina M; Kaufman, Stacie R; Quarino, Lawrence

    2011-03-01

    Various types of cotton and polyester fabrics were tested to ascertain the optimal physical and chemical characteristics of fabrics needed for the removal of cellular material from surfaces. DNA quantitation values obtained on dried saliva stains showed no difference between cotton and polyester across all constructions and solvent conditions. Fabrics used dry and with water yielded higher quantitation values than those used with isopropanol. Quantitation values were also higher for wovens and nonwovens than knits across all solvent conditions. Low thread count fabrics used with water yielded higher quantitation values, but no correlation between thread count and quantitation values was observed with dry fabrics. A low thread count woven fabric, however, outperformed other tested fabrics when swabbing object surfaces in a highly used room. Full DNA profiles from fingerprints on glass surfaces were obtained with low thread count woven and nonwoven fabrics but not with the knit fabric tested. © 2011 American Academy of Forensic Sciences.

  18. The application of alkaline lysis and pressure cycling technology in the differential extraction of DNA from sperm and epithelial cells recovered from cotton swabs.

    Science.gov (United States)

    Nori, Deepthi V; McCord, Bruce R

    2015-09-01

    This study reports the development of a two-step protocol using pressure cycling technology (PCT) and alkaline lysis for differential extraction of DNA from mixtures of sperm and vaginal epithelial cells recovered from cotton swabs. In controlled experiments, in which equal quantities of sperm and female epithelial cells were added to cotton swabs, 5 min of pressure pulsing in the presence of 0.4 M NaOH resulted in 104 ± 6% recovery of female epithelial DNA present on the swab. Following the pressure treatment, exposing the swabs to a second 5-min alkaline treatment at 95 °C without pressure resulted in the selective recovery of 69 ± 6% of the sperm DNA. The recovery of the vaginal epithelia and sperm DNA was optimized by examining the effect of sodium hydroxide concentration, incubation temperature, and time. Following the alkaline lysis steps, the samples were neutralized with 2 M Tris (pH 7.5) and purified with phenol-chloroform-isoamyl alcohol to permit downstream analysis. The total processing time to remove both fractions from the swab was less than 20 min. Short tandem repeat (STR) analysis of these fractions obtained from PCT treatment and alkaline lysis generated clean profiles of female epithelial DNA and male sperm DNA for 1:1 mixtures of female and male cells and predominant male profiles for mixtures up to 5:1 female to male cells. By reducing the time and increasing the recovery of DNA from cotton swabs, this new method presents a novel and potentially useful procedure for forensic differential extractions.

  19. The comparative utility of oral swabs and probang samples for detection of foot-and-mouth disease virus infection in cattle and pigs.

    Science.gov (United States)

    Stenfeldt, Carolina; Lohse, Louise; Belsham, Graham J

    2013-03-23

    Foot-and-mouth disease virus (FMDV) RNA was measured using quantitative reverse transcription-PCR (qRT-PCR) assays in oral swab and probang samples collected from cattle and pigs during experimental infections with serotype O FMDV. During acute infection, FMDV RNA was measurable in oral swabs as well as in probang samples from both species. FMDV RNA could be detected in oral swabs and probang samples from a time point corresponding to the onset of viremia in directly inoculated animals, whereas animals which were infected through contact exposure had low levels of FMDV RNA in oral swabs before viral RNA could be measured in serum. Analysis of samples collected from cattle persistently infected with FMDV showed that it was not possible to detect FMDV RNA in oral swabs harvested beyond 10 days post infection (dpi), despite the presence of FMDV RNA in probang samples that had been collected as late as 35 dpi. An interesting feature of the persistent infection in the cattle was the apparent decline in the level of FMDV RNA in probang samples after the acute phase of infection, which was followed by a marked rise again (in all the carrier animals) by 28 dpi. Results from this study indicate that qRT-PCR analysis of oral swabs is a useful approach in order to achieve a time efficient and reliable initial diagnosis of acute FMD in cattle and pigs, whereas probang sampling is essential for the detection of cattle that are persistently infected "carriers" of FMDV. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Methicillin-resistant Staphylococcus Aureus Nasal Swab and Suction Drain Tip Cultures in 4573 Spinal Surgeries: Efficacy in Management of Surgical Site Infections.

    Science.gov (United States)

    Kawabata, Atsuyuki; Sakai, Kenichiro; Sato, Hirokazu; Sasaki, Shinichi; Torigoe, Ichiro; Tomori, Masaki; Yuasa, Masato; Matsukura, Yu; Arai, Yoshiyasu

    2017-08-01

    A retrospective single-center study. To assess the diagnostic value of methicillin-resistant Staphylococcus aureus (MRSA) nasal swab and suction drain tip cultures. The prognostic value of MRSA nasal swab and suction drain tip cultures has not been firmly established in spinal surgery. This study retrospectively included 4573 consecutive patients who underwent spinal surgery between January 2008 and December 2014. Patients diagnosed with infectious disease were excluded. Prophylactic antibiotics were administered intraoperatively and postoperatively for 48 h. MRSA nasal swab cultures were taken from all patients before surgery. Drains were removed when the volume of postoperative fluid drainage was less than 50 mL in the preceding 24 h and cultures were made. Surgical site infection (SSI) was defined according to Centers for Disease Control and Prevention criteria. SSI was identified in 94 cases (2.1%) and bacteria were isolated in 87 cases (92.6%). Positive MRSA nasal swab cultures were identified in 49 cases (1.1%). There was no significant difference in the SSI positivity rate between the MRSA nasal swab culture (+) and (-) groups. Positive drain tip cultures were found in 382 cases (8.4%), 28 of which developed SSI. There was a significant difference in the SSI positivity rate between the drain tip culture (+) and (-) groups. The sensitivity of drain tip culture was 29.8% and the specificity was 92.1%. In 16 of the 28 patients in the SSI (+) group with positive drain cultures, the same bacteria were isolated from the surgical site, giving a bacteria matching rate of 57.1%. MRSA nasal swab and drain tip cultures were not useful for predicting SSI. However, drain tip culture had a high positivity rate in the SSI group and the coincidence rate for the causative pathogen was relatively high. 4.

  1. Apparatus and method for magnetically processing a specimen

    Science.gov (United States)

    Ludtka, Gerard M; Ludtka, Gail M; Wilgen, John B; Kisner, Roger A; Jaramillo, Roger A

    2013-09-03

    An apparatus for magnetically processing a specimen that couples high field strength magnetic fields with the magnetocaloric effect includes a high field strength magnet capable of generating a magnetic field of at least 1 Tesla and a magnetocaloric insert disposed within a bore of the high field strength magnet. A method for magnetically processing a specimen includes positioning a specimen adjacent to a magnetocaloric insert within a bore of a magnet and applying a high field strength magnetic field of at least 1 Tesla to the specimen and to the magnetocaloric insert. The temperature of the specimen changes during the application of the high field strength magnetic field due to the magnetocaloric effect.

  2. Urine specimen collection following consensual intercourse - A forensic evidence collection method for Y-DNA and spermatozoa.

    Science.gov (United States)

    Joki-Erkkilä, Minna; Tuomisto, Sari; Seppänen, Mervi; Huhtala, Heini; Ahola, Arja; Karhunen, Pekka J

    2016-01-01

    The purpose of the prospective research was to evaluate the benefit of urine specimen as a collection technique for biological forensic evidence in adult volunteers following consensual intercourse. For detecting Y-chromosomal material Buccal Swab Spin Protocol(®) was used in DNA extraction and purification and samples were analysed with Quantifiler Y Human Male DNA Quantification Kit(®). The time frame for positive Y-DNA was evaluated. Immediate microscopy for detection of spermatozoa was performed. Y-DNA was detected in 173/205 (84.4%) urine samples. Of the 86 first post-coital void urine samples available, Y-DNA was detected in 83 (96.5%) specimens. Of the 119 urine samples from volunteers with post-coital activities Y-DNA was still measurable in 70 (58.8%) urine specimens. The male DNA amount was below 0.023 ng/μl in 28/153 (18.3%) urine samples. Of the 22 urine samples obtained after 24 post-coital hours, 9 (40.9%) were still Y-DNA positive. No associations were found between coital durance, coital frequency during the past two weeks prior to the study intercourse, post-coital activities, and the urine sample Y-DNA positivity. Of the 111 urine samples where the immediate microscopy was performed, in 66 (59.5%) samples spermatozoa were verified and one sample even contained motile spermatozoa. Microscopy detected 66 (67.3%) and failed to detect spermatozoa in 32 (32.7%) of Y-DNA positive samples. In addition to conventional invasive swab techniques, urine samples seem to be an effective biological trace collection method for Y-DNA and spermatozoa within 24 h following penile-vaginal penetration. Furthermore, it may be considered as a non-invasive collection method in suspected acute child sexual abuse cases to diminish time delay in forensic evidence collection and to improve patients' positive attitudes towards evidence collection. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  3. PCR for detection of Chlamydia trachomatis in endocervical, urethral, rectal, and pharyngeal swab samples obtained from patients attending an STD clinic.

    Science.gov (United States)

    Ostergaard, L; Agner, T; Krarup, E; Johansen, U B; Weismann, K; Gutschik, E

    1997-01-01

    OBJECTIVE: To investigate, by use of the Amplicor PCR in a routine setting, the recovery rate of Chlamydia trachomatis in ano-rectal and pharyngeal swab samples obtained from males and females attending an STD clinic in relation to sexual practices, symptoms, and signs. DESIGN: Data regarding sexual practices, and symptoms and signs related to the rectum and pharynx, were obtained from 196 females and 208 males, including 31 homosexuals and eight bisexuals. Swab samples were obtained from the urethra, rectum, and pharynx from all the patients. An additional endocervical swab sample was obtained from the females. METHODS: All samples were analysed by the Amplicor PCR (Roche). SETTING: Rudolph Bergh's Hospital, a clinic for sexually transmitted diseases situated in the centre of Copenhagen, Denmark. RESULTS: The overall prevalence of urogenital C trachomatis infection was 9.2% (37/404). The specificity of the Amplicor PCR was 100% for both ano-rectal and pharyngeal swab samples. In females three (13%) of the 23 infections were detected only by testing an ano-rectal or throat swab sample. In homosexual males two (67%) of three infections were detected only by the anorectal swab sample. Ano-rectal intercourse without use of condom was reported by 44% of females and by 52% of homosexual males. Fellatio without condom use was reported by 91% of females, and 80% of heterosexual males practised cunnilingus. Pharyngeal infection, however, occurred only in females, and the presence of pharyngeal symptoms or signs seemed predictive for pharyngeal C trachomatis infection, for which the time of incubation or colonisation exceeded 3 months. The presence of ano-rectal signs or symptoms was not predictive for an ano-rectal C trachomatis infection. CONCLUSION: The Amplicor PCR can be used on ano-rectal and pharyngeal swab samples. Ano-rectal swab samples should be obtained in females and homosexual males at high risk of being infected. Pharyngeal samples should be taken in females

  4. Pressurised irrigation versus swabbing method in cleansing wounds healed by secondary intention: a randomised controlled trial with cost-effectiveness analysis.

    Science.gov (United States)

    Mak, Suzanne So-Shan; Lee, Man-Ying; Cheung, Jeanny Sui-Sum; Choi, Kai-Chow; Chung, Tak-Ki; Wong, Tze-Wing; Lam, Kit-Yee; Lee, Diana Tze-fan

    2015-01-01

    Wound cleansing should create an optimal healing environment by removing excess debris, exudates, foreign and necrotic material which are commonly present in the wounds that heal by secondary intention. At present, there is no research evidence for whether pressurised irrigation has better wound healing outcomes compared with conventional swabbing practice in cleansing wound. This study investigated the differences between pressurised irrigation and swabbing method in cleansing wounds that healed by secondary intention in relation to wound healing outcomes and cost-effectiveness. Multicentre, prospective, randomised controlled trial. The study took place in four General Outpatient Clinics in Hong Kong. Two hundred and fifty six patients with wounds healing by secondary intention were randomly assigned by having a staff independent of the study opening a serially numbered, opaque and sealed envelope to either pressurised irrigation (n=122) or swabbing (n=134). Staff undertaking study-related assessments was blinded to treatment assignment. Patients' wounds were followed up for 6 weeks or earlier if wounds had healed to determine wound healing, infection, symptoms, satisfaction, and cost effectiveness. The primary outcome was time-to-wound healing. Patients were analysed according to their treatment allocation. This trial is registered with ClinicalTrials.gov, number NCT01885273. Intention-to-treat analysis showed that pressurised irrigation group was associated with a shorter median time-to-wound healing than swabbing group [9.0 days (95% CI: 7.4-13.8) vs. 12.0 (95% CI: 10.2-13.8); p=0.007]. Pressurised irrigation group has significantly more patients experiencing lower grade of pain during wound cleansing (93.4% vs. 84.2%; p=0.02), and significantly higher median satisfaction with either comfort or cleansing method (MD 1 [95% CI: 5-6]; p=0.002; MD 1 [95% CI: 5-6]; pirrigation group and in 7 (5.2%) patients in swabbing group (p=0.44). Cost-effectiveness analysis

  5. Evaluation of 3 analyte-specific reagents for detection of Bordetella pertussis and Bordetella parapertussis in clinical specimens.

    Science.gov (United States)

    Hassan, Ferdaus; Hays, Lindsay; Bell, Jeremiah; Selvarangan, Rangaraj

    2014-11-01

    The performance of 3 analyte-specific reagents (ASRs), Elitech Biosciences, EraGen Biosciences, and Focus Diagnostic, was evaluated for detection of Bordetella pertussis (BP) and Bordetella parapertussis (BPP) in nasopharyngeal swab specimens. A total of 104 frozen, leftover clinical specimens obtained from pediatric patients during 2011-2012 were included in this study. Performance was compared to the Bordetella real-time polymerase chain reaction (PCR) laboratory-developed test (LDT). The positive percent agreement for detection of BP by Elitech was 96% (95% confidence interval [CI]: 85.14-99.30); EraGen and Focus was 98% (95% CI: 87.99-99.89) in comparison to LDT PCR assay. The negative percent agreement of Elitech, EraGen, and Focus in comparison to LDT was 96% (95% CI: 85.14-99.30), 92% (95% CI: 79.89-97.41), and 96% (95% CI: 85.14-99.30), respectively. Limit of detection (LOD) for BP was 0.1 CFU/reaction by both Focus and EraGen and 1.0 CFU/reaction by Elitech. However, LOD for BPP was lower by EraGen (0.1 CFU/reaction) compared to Focus (1.0 CFU/reaction) and Elitech (1.0 CFU/reaction). These results demonstrate that all 3 ASRs tested are comparable and reliable for routine clinical diagnosis of pertussis and parapertussis. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Evaluation of hybrid composite materials in cylindrical specimen geometries

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1976-01-01

    Static and fatigue properties of three composite materials and hybrids were examined. The materials investigated were graphite/epoxy, S-glass/epoxy, PRD-49 (Kevlar 49)/epoxy, and hybrids in angle-ply configurations. A new type of edgeless cylindrical specimen was developed. It is a flattened tube with two flat sides connected by curved sections and it is handled much like the standard flat coupon. Special specimen fabrication, tabbing, and tab region reinforcing techniques were developed. Axial modulus, Poisson's ratio, strength, and ultimate strain were obtained under static loading from flattened tube specimens of nine laminate configurations. In the case of graphite/epoxy the tubular specimens appeared to yield somewhat higher strength and ultimate strain values than flat specimens. Tensile fatigue tests were conducted with all nine types of specimens and S-N curves obtained. Specimens surviving 10 million cycles of tensile loading were subsequently tested statically to failure to determine residual properties.

  7. Gradient field microscopy of unstained specimens

    Science.gov (United States)

    Kim, Taewoo; Sridharan, Shamira; Popescu, Gabriel

    2012-01-01

    We present a phase derivative microscopy technique referred to as gradient field microscopy (GFM), which provides the first-order derivatives of the phase associated with an optical field passing through a transparent specimen. GFM utilizes spatial light modulation at the Fourier plane of a bright field microscope to optically obtain the derivatives of the phase and increase the contrast of the final image. The controllable spatial modulation pattern allows us to obtain both one component of the field gradient (derivative along one direction) and the gradient intensity, which offers some advantages over the regular differential interference contrast (DIC) microscopy. Most importantly, unlike DIC, GFM does not use polarizing optics and, thus, it is applicable to birefringent samples. We demonstrate these features of GFM with studies of static and dynamic biological cells (HeLa cells and red blood cells). We show that GFM is capable of qualitatively providing information about cell membrane fluctuations. Specifically, we captured the disappearance of the bending mode of fluctuations in osmotically swollen red blood cells. PMID:22418558

  8. Nerve degeneration in inguinal hernia specimens.

    Science.gov (United States)

    Amato, G; Ober, E; Romano, G; Salamone, G; Agrusa, A; Gulotta, G; Bussani, R

    2011-02-01

    The histological study of the herniated inguinal area is rare in the literature. This report is focused on the detection of structural changes of the nerves within tissues bordering the inguinal hernia of cadavers. Their physiopathological consequences are hypothesized. Primary inguinal hernia was diagnosed in 30 fresh cadavers. Tissue specimens from the inguinal region close to and around the hernia opening were excised for histological examination. A control of the data was achieved through tissue samples excised from equivalent sites of the inguinal region in 15 cadavers without hernia. The detected nerves in the inguinal area demonstrated pathological changes such as fibrotic degeneration, atrophy, and fatty dystrophy of the axons. The thickening of the perineural sheath was constantly seen. These findings were consistently present, independent of the hernia type. The detected nerve alterations lead us to imagine a worsening, or even the cessation, of the nervous impulse to the muscles, leading to atrophy and weakening of the abdominal wall. This could represent one of the multifactorial causes of hernia genesis.

  9. Principles of laser microdissection and catapulting of histologic specimens and live cells.

    Science.gov (United States)

    Vogel, Alfred; Horneffer, Verena; Lorenz, Kathrin; Linz, Norbert; Hüttmann, Gereon; Gebert, Andreas

    2007-01-01

    Rapid contact- and contamination-free procurement of specific samples of histologic material for proteomic and genomic analysis as well as separation and transport of living cells can be achieved by laser microdissection (LMD) of the sample of interest followed by a laser-induced forward transport process [laser pressure "catapulting," (LPC)] of the dissected material. We investigated the dynamics of LMD and LPC with focused and defocused laser pulses by means of time-resolved photography. The working mechanism of microdissection was found to be plasma-mediated ablation. Catapulting is driven by plasma formation, when tightly focused pulses are used, and by ablation at the bottom of the sample for moderate and strong defocusing. Driving pressures of several hundred megapascals accelerate the specimen to initial velocities of 100-300 m/s before it is rapidly slowed down by air friction. With strong defocusing, driving pressure and initial flight velocity decrease considerably. On the basis of a characterization of the thermal and optical properties of the histologic specimens and supporting materials used, we calculated the temporal evolution of the heat distribution in the sample. After laser microdissection and laser pressure catapulting (LMPC), the samples were inspected by scanning electron microscopy. Catapulting with tightly focused or strongly defocused pulses results in very little collateral damage, while slight defocusing involves significant heat and UV exposure of up to about 10% of the specimen volume, especially if samples are catapulted directly from a glass slide. Time-resolved photography of live-cell catapulting revealed that in defocused catapulting strong shear forces originate from the flow of the thin layer of culture medium covering the cells. By contrast, pulses focused at the periphery of the specimen cause a fast rotational movement that makes the specimen wind its way out of the culture medium, thereby undergoing much less shear stresses

  10. Relative quantification and detection of different types of infectious bursal disease virus in bursa of Fabricius and cloacal swabs using real time RT-PCR SYBR green technology

    DEFF Research Database (Denmark)

    Li, Yiping; Handberg, K.J.; Kabell, Susanne

    2007-01-01

    In present study, different types of infectious bursal disease virus (IBDV), virulent strain DK01, classic strain F52/70 and vaccine strain D78 were quantified and detected in infected bursa of Fabricius (BF) and cloacal swabs using quantitative real time RT-PCR with SYBR green dye. For selection...

  11. 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...

  12. Development of a real time PCR for the detection of Taylorella equigenitalis directly from genital swabs and discrimination from Taylorella asinigenitalis

    NARCIS (Netherlands)

    Wakeley, P.R.; Errington, J.; Hannon, S.; Roest, H.I.J.; Carson, T.; Hunt, B.; Sawyer, J.; Heath, P.

    2006-01-01

    discriminatory real time PCR for the detection of Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), and the related species T. asinigenitalis was developed for the direct examination of genital swabs. The 112 bp amplicons produced from the two species were

  13. Clinical utility of a nasal swab methicillin-resistant Staphylococcus aureus polymerase chain reaction test in intensive and intermediate care unit patients with pneumonia.

    Science.gov (United States)

    Giancola, Stephanie E; Nguyen, Ai Thi; Le, Binh; Ahmed, Omar; Higgins, Catherine; Sizemore, James A; Orwig, Kara W

    2016-11-01

    This retrospective study aimed to validate the concordance between nasal swab methicillin-resistant Staphylococcus aureus (MRSA) polymerase chain reaction (PCR) test and respiratory culture and to determine the number of potentially preventable days of anti-MRSA therapy in patients with pneumonia. Two hundred adult inpatients in the intensive and intermediate care units were included. The nasal swab MRSA PCR test was positive in 55 (27.5%) patients. MRSA was isolated from respiratory culture in 21 (10.5%) patients. The nasal swab MRSA PCR test demonstrated 90.5% sensitivity, 79.9% specificity, 34.5% positive predictive value, and 98.6% negative predictive value. Anti-MRSA therapy was initiated in 168 (84%) patients. Patients in the study received a combined 782days of anti-MRSA therapy; 300days were considered potentially preventable. This study suggests that the nasal swab MRSA PCR test may be used to guide discontinuation of anti-MRSA antibiotics in patients with clinically confirmed pneumonia in the intensive or intermediate care units. Published by Elsevier Inc.

  14. Evaluation of composite flattened tubular specimen. [fatigue tests

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1978-01-01

    Flattened tubular specimens of graphite/epoxy, S-glass/epoxy, Kevlar-49/epoxy, and graphite/S-glass/epoxy hybrid materials were evaluated under static and cyclic uniaxial tensile loading and compared directly with flat coupon data of the same materials generated under corresponding loading conditions. Additional development for the refinement of the flattened specimen configuration and fabrication was required. Statically tested graphite/epoxy, S-glass/epoxy, and Kevlar 49/epoxy flattened tube specimens exhibit somewhat higher average strengths than their corresponding flat coupons. Flattened tube specimens of the graphite/S-glass/epoxy hybrid and the graphite/epoxy flattened tube specimens failed in parasitic modes with consequential lower strength than the corresponding flat coupons. Fatigue tested flattened tube specimens failed in parasitic modes resulting in lower fatigue strengths than the corresponding flat coupons.

  15. Multicenter Clinical Evaluation of the Luminex Aries Flu A/B & RSV Assay for Pediatric and Adult Respiratory Tract Specimens

    Science.gov (United States)

    Mahony, James; Buller, Richard S.; Manji, Ryhana; Dunbar, Sherry; Walker, Kimberly; Rao, Arundhati

    2017-01-01

    ABSTRACT Influenza A and B viruses and respiratory syncytial virus (RSV) are three common viruses implicated in seasonal respiratory tract infections and are a major cause of morbidity and mortality in adults and children worldwide. In recent years, an increasing number of commercial molecular tests have become available to diagnose respiratory viral infections. The Luminex Aries Flu A/B & RSV assay is a fully automated sample-to-answer molecular diagnostic assay for the detection of influenza A, influenza B, and RSV. The clinical performance of the Aries Flu A/B & RSV assay was prospectively evaluated in comparison to that of the Luminex xTAG respiratory viral panel (RVP) at four North American clinical institutions over a 2-year period. Of the 2,479 eligible nasopharyngeal swab specimens included in the prospective study, 2,371 gave concordant results between the assays. One hundred eight specimens generated results that were discordant with those from the xTAG RVP and were further analyzed by bidirectional sequencing. Final clinical sensitivity values of the Aries Flu A/B & RSV assay were 98.1% for influenza A virus, 98.0% for influenza B virus, and 97.7% for RSV. Final clinical specificities for all three pathogens ranged from 98.6% to 99.8%. Due to the low prevalence of influenza B, an additional 40 banked influenza B-positive specimens were tested at the participating clinical laboratories and were all accurately detected by the Aries Flu A/B & RSV assay. This study demonstrates that the Aries Flu A/B & RSV assay is a suitable method for rapid and accurate identification of these causative pathogens in respiratory infections. PMID:28539342

  16. Prestress losses evaluation in prestressed concrete prismatic specimens

    OpenAIRE

    CARO FORERO, LIBARDO ANDRÉS; Martí Vargas, José Rocío; Serna Ros, Pedro

    2013-01-01

    This paper presents an experimental research work to evaluate prestress losses in pretensioned prestressed concrete. An experimental program including variables such as concrete mix design, specimen cross-section size and concrete age at the prestress transfer was carried out. Several pretensioned prestressed concrete prismatic specimens were made and tested using the ECADA+ test method, based on measuring prestressing reinforcement force. In addition, specimens were instrumented to obtain th...

  17. 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 (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...

  18. Specimen Provenance Testing Identifies Contamination That Affects Molecular Prognostic Assay Results in Prostate Cancer Biopsy Specimens.

    Science.gov (United States)

    Wojno, Lathem; Minutella, Caitlyn; Moylan, Donald; Bush, Arla; Wojno, Kirk

    2018-02-21

    To determine if tissue contamination in histologic specimens can significantly affect the results of prognostic molecular markers that are routinely used as confirmatory tests to safely assign appropriate candidates to prostate cancer active surveillance protocols. This study evaluates 2,134 cases from a single, large urology practice that were successfully tested for DNA specimen provenance verification using short tandem repeat analysis for the presence of a significant level of contaminating DNA. After removal of the contamination, five of the samples were retested, and the results of the molecular diagnostic test were compared. 49 of the 2,134 cases (2.3%) sent for DNA provenance analysis were found to possess significant levels of contamination. Of these 49 cases, seven of them were resent for a repeat molecular diagnostic test after being decontaminated. Five of these prostate cancer specimens had sufficient tissue and RNA to give a more accurate cell cycle progression (CCP) score. The average absolute change in these patient's CCP scores was 0.48, with a low of a 0.1-unit and a high of a 1.0-unit difference. These changes in CCP scores are significant enough to cause meaningful alterations in a patient's calculated 10-year mortality rate, as defined by their combined risk score (CRS). DNA contamination in unstained tissue sections sent for prognostic prostate cancer molecular diagnostic testing occurs on 2.3% of cases, and can be of a magnitude that affects the results and subsequent clinical decision of appropriateness for active surveillance. Copyright © 2018. Published by Elsevier Inc.

  19. 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)

  20. A freeze-fracture replication apparatus for biological specimens.

    Science.gov (United States)

    Stolinski, C

    1975-08-01

    A freeze-fracture apparatus of original design has been constructed which can be fitted onto a standard vacuum evaporator unit. In it, cell suspensions and organized tissue may be processed by inserting a sample into a cylindrical holder. By leaving a small part of the tissue protruding from the holder, pre-selected and aligned portions of the specimen can subsequently be revealed by fracture under vacuum. After rapid freezing, the specimen remains firmly attached to the inner wall of the sample holder, preventing its possible loss during fracturing. A mechanism, in the form of a double-sided converging wedge, which is operated from outside the vacuum chamber, is used to produce a fracture in the specimen. The device gently induces a fracture in the desired part of the tissue and lifts the protruding part of the specimen out of the way. In this way, reasonably flat fracture faces are produced for subsequent replication. As the fracturing mechanism comes into contact only with the outer edges of the specimen, damage and contamination liable to occur when the entire specimen is traversed by a blade, is avoided. In addition the specimen stage is surrounded by a cold metal shroud which acts as an efficient trap for contaminants. In this way, favourable vacuum conditions are produced in the vicinity of the specimen. Such effective enclosing of the specimen also facilitates controlled sublimation of the sample.

  1. Immunodetection of rasP21 and c-myc oncogenes in oral mucosal swab preparation from clove cigarette smokers

    Directory of Open Access Journals (Sweden)

    Silvi Kintawati

    2008-12-01

    Full Text Available Background: Smoking is the biggest factor for oral cavity malignancy. Some carcinogens found in cigar will stimulate epithel cell in oral cavity and cause mechanism disturbance on tissue resistance and produce abnormal genes (oncogenes. Oncogenes ras and myc are found on malignant tumor in oral cavity which are associated with smoking. Purpose: This research is to find the expression of oncogenes rasP21 and c-myc in oral mucosa epithelial of smoker with immunocytochemistry reaction. Methods: An oral mucosal swab was performed to 30 smokers categorized as light, moderate, and chain, and 10 non smokers which was followed by immunocytochemistry reaction using antibody towards oncogene rasP21 and c-myc is reacted to identify the influence of smoking towards malignant tumor in oral cavity. The result is statistically analyzed using Kruskal-Wallis test. Result: Based on the observation result of oncogene rasP21reaction, it shows that there is significant difference between non smoker group and light smoker, compared to moderate and chain smoker group (p < 0.01. On the other side, the observation result of oncogene c-myc indicates that there is no significant difference between the group of non smokers and the group of light, moderate, and chain smokers (p > 0.05. Conclusion: The higher the possibility of oral cavity malignancy and that the antibody for rasP21 oncogene can be used as a marker for early detection of oral cavity malignancy caused by smoking.

  2. Some virulence genes of Escherichia coli isolated from cloacal swabs of healthy Alagoas Curassows (Pauxi mitu in Brazil

    Directory of Open Access Journals (Sweden)

    André A.B. Saidenberg

    2013-04-01

    Full Text Available Birds of the Cracidae family (curassows, guans, and chachalacas are endemic of the Neotropics and 50 species are currently classified. Brazil has 22 species, seven of which are considered threatened. The Alagoas Curassow (Pauxi mitu species is considered extinct in the wild; but about 120 birds are alive in captivity. Conservation of this species depends entirely on correct management. Health reports of both wildlife and captive curassows are rare. In this study the presence of Escherichia coli was evaluated in 23 healthy Alagoas Curassows from two private breeding centres. E. coli was isolated from cloacal swabs, and the presence of genes encoding cytotoxic necrotising factor 1 (cnf1, alpha-haemolysin (hly, aerobactin (iuc, serum resistance (iss and the following adhesions: S fimbriae (sfa, pili associated with pyelonephritis (pap and temperature-sensitive haemagglutinin (tsh were investigated. E. coli was isolated from 78.3% (18/23 of the birds, and the percentage of curassows colonized by E. coli was similar between the two facilities. From the 22 E. coli isolates, 15 (68.2% were positive for at least one virulence factor by PCR, and the most frequently found gene was iss (50%. No curassows had clinical signs of disease. Nevertheless, the presence of some E. coli strains may be a concern to the wildlife in captivity. Additional health surveillance studies are essential to guarantee successful conservation programmes for threatened cracids in Brazil.

  3. Healthy Farms in Slovakia: Antibiotic Sensitivity of Escherichia coli Isolated from Rectal Swabs of Chicken and Ram

    Directory of Open Access Journals (Sweden)

    Jaroslav Pochop

    2012-10-01

    Full Text Available The aim of this experiment was determine of antibiotic resistance profile of Escherichia coli isolated from rectal swabs of chicken and ram from two different conventional breeding from Slovakia. For the antibiotic susceptibility testing disk diffusion method was used. A tested bacterium, Escherichia coli was exposed against four antibiotics: amikacin, gentamycin, tetracycline and chloramphenicol. For the identification of this strain, we used Chromogenic coliform agar, Triple sugar iron agar and biochemical test (ENTEROtest 24. For genetic identification of Escherichia coli Step One Real Time PCR with using special primer was used. Was determined that antibiotic resistance in Escherichia coli was not found. Was found susceptibility in all cases of Escherichia coli isolates. Antibiotic resistance is a biological danger. Bacteria, which we study, are considered to reservoirs of resistant genes and they are facultative and obligate pathogens. If these pathogen bacteria cause diseases those these diseases are difficult to treat. In this study, we determined that we have healthy farms in Slovakia too. In this farm antibiotic was not use and we do not determined any resistance to antibiotics, which we used in experiment.

  4. Comparison of eight methods for the extraction of Bacillus atrophaeus spore DNA from eleven common interferents and a common swab.

    Directory of Open Access Journals (Sweden)

    Helen L Rose

    Full Text Available Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum and one solid (Underarm deodorant, the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar, and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method.

  5. Performance of transport and selective media for swine Bordetella bronchiseptica recovery and it comparison to polymerase chain reaction detection Desempenho de meios de transporte e seletivo na recuperação de Bordetella bronchiseptica de suínos e sua comparação à detecção pela reação em cadeia pela polimerase

    Directory of Open Access Journals (Sweden)

    Tania Alen Coutinho

    2009-09-01

    Full Text Available Three comparative assays were performed seeking to improve the sensitivity of the diagnosis of Bordetella bronchiseptica infection analyzing swine nasal swabs. An initial assay compared the recovery of B. bronchiseptica from swabs simultaneously inoculated with B. bronchiseptica and some interfering bacteria, immersed into three transport formulations (Amies with charcoal, trypticase soy broth and phosphate buffer according to Soerensen supplemented with 5% of bovine fetal serum and submitted to different temperatures (10ºC and 27ºC and periods of incubation (24, 72 and 120 hours. A subsequent assay compared three selective media (MacConkey agar, modified selective medium G20G and a ceftiofur medium for their recovery capabilities from clinical specimens. One last assay compared the polymerase chain reaction to the three selective media. In the first assay, the recovery of B. bronchiseptica from transport systems was better at 27ºC and the three formulations had good performances at this temperature, but the collection of qualitative and quantitative analysis indicated the advantage of Amies medium for nasal swabs transportation. The second assay indicated that MacConkey agar and modified G20G had similar results and were superior to the ceftiofur medium. In the final assay, polymerase chain reaction presented superior capability of B. bronchiseptica detection to culture procedures.Três ensaios comparativos foram feitos com o objetivo de aperfeiçoar a sensibilidade do diagnóstico da infecção pela Bordetella bronchiseptica a partir de suabes nasais de leitões. O experimento inicial comparou a recuperação de B. bronchiseptica a partir de suabes, simultaneamente inoculados com B. bronchiseptica e algumas bactérias interferentes, imersos em três formulações para transporte (meio Amies com carvão, caldo tripticaseína de soja e tampão de fosfatos segundo Soerensen suplementado com 5% de soro fetal bovino e submetidos a diferentes

  6. Analysis of off-axis tension test of wood specimens

    Science.gov (United States)

    Jen Y. Liu

    2002-01-01

    This paper presents a stress analysis of the off-axis tension test of clear wood specimens based on orthotropic elasticity theory. The effects of Poisson's ratio and shear coupling coefficient on stress distribution are analyzed in detail. The analysis also provides a theoretical foundation for the selection of a 10° grain angle in wood specimens for the...

  7. stomach contents of a specimen of proteles cristatus from angola

    African Journals Online (AJOL)

    north of Sa da Bandeira, Angola (at about 140. SO' Sjl3° 35' E). The skin and skull were deposited in the Alexander McGregor Memorial Museum. Kimberley, Cape (Collectors No. 276a). The stomach contents of this specimen are detailed in. Table I. The habitat where the specimen was obtained was degraded ...

  8. Design Analysis of the Mixed Mode Bending Sandwich Specimen

    DEFF Research Database (Denmark)

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

    2010-01-01

    . The analysis facilitates selection of the appropriate geometry for the MMB sandwich specimen to promote debond failure. An experimental study is performed using MMB sandwich specimens with a H100 PVC foam core and E-glass–polyester faces. The results reveal that debond propagation is successfully achieved...

  9. A Debonded Sandwich Specimen Under Mixed Mode Bending (MMB)

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  10. Validity of oral mucosal transudate specimens for HIV testing using ...

    African Journals Online (AJOL)

    The overall sensitivity of OMT specimens for HIV testing in children using ELISA was low. Stratifying the analysis by sector showed that OMT samples are good specimens for HIV testing. It is important to note that factors such as the low HIV prevalence in our study population, quality of the OMT, diet and oral hygiene could ...

  11. 16 CFR Figures 3 and 4 to Subpart... - Test Specimens

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test Specimens 3 Figures 3 and 4 to Subpart... REGULATIONS SAFETY STANDARD FOR ARCHITECTURAL GLAZING MATERIALS The Standard Pt. 1201, Subpt. A, Figs. 3, 4 Figures 3 and 4 to Subpart A of Part 1201—Test Specimens EC03OC91.006 ...

  12. Progress towards an optimal specimen support for electron cryomicroscopy.

    Science.gov (United States)

    Russo, Christopher J; Passmore, Lori A

    2016-04-01

    The physical principles of electron-specimen interaction govern the design of specimen supports for electron cryomicroscopy (cryo-EM). Supports are constructed to suspend biological samples within the vacuum of the electron microscope in a way that maximises image contrast. Although the problem of specimen motion during imaging has been known since cryo-EM was first developed, the role of the support in this movement has only been recently identified. Here we review the key technological advances in specimen supports for cryo-EM. This includes the use of graphene as a surface for the adsorption of proteins and the design of an ultrastable, all-gold substrate that reduces the motion of molecules during electron irradiation. We discuss the implications of these and other recent improvements in specimen supports on resolution, and place them in the context of important developments in structure determination by cryo-EM. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Tensile strength of various nylon PA6 specimen modes

    Science.gov (United States)

    Raz, Karel; Zahalka, Martin

    2017-05-01

    This article explores the influence of production technique on the strength of nylon parts. Identical specimens were manufactured by various techniques. The material of specimens was nylon PA6. 3D printing and injection molding were used, with various orientations of printed layers, and various orientations of specimens in the working space of the 3D printer. The variants are described in detail. A special mold was used for the injection molding process in order to make specimens with and without a weld line. The effect of this weld line was evaluated. All specimens were tested using the standard tensile test configuration. The strength was compared. It was found that the same plastic material has very different mechanical properties depending on the production process.

  14. Resistance to Antibiotics in Strains of Staphylococcus spp., Enterococcus spp. and Escherichia coli Isolated from Rectal Swabs of Pigs

    Directory of Open Access Journals (Sweden)

    M. Kolář

    2008-01-01

    Full Text Available The study aimed at determining the level of resistance of selected bacterial species (Staphylococcus spp., Enterococcus spp., Escherichia coli isolated from rectal swabs of pigs to antimicrobial agents. The tested strains were isolated from piglets aged 7 to 30 days. Bacterial species were identified by standard microbiological techniques and susceptibility to antibiotics was determined quantitatively by the standard microdilution method. Resistance of the Staphylococcus aureus strain to oxacillin was confirmed by detection of the mecA gene and PBP2a. A total of 115 Staphylococcus spp. isolates were collected. In the case of Staphylococcus aureus, the methicillin-resistant strain (MRSA was identified. Moreover, higher frequency of coagulase-negative staphylococci with minimum inhibitory concentration of oxacillin ≥ 0.5 mg/l was noticed. Inducible resistance to clindamycin in the Staphylococcus hominis strain was also detected. The strains of Enterococcus spp. (61 isolates exhibited high resistance to tetracycline (98.5%, erythromycin (86.8% and chloramphenicol (54.4%. Vancomycin-resistant enterococci were not isolated. In the case of Escherichia coli strains (111 isolates, higher frequency of resistant strains to tetracycline (81.1% and ampicillin (62.2% was documented. Resistance to fluoroquinolones and production of broad-spectrum β-lactamases was not noticed. The presented study may be considered as a pilot project assessing the prevalence of resistant bacteria in piglets kept on a single farm. It demonstrated the presence of resistant strains of Staphylococcus spp., including one MRSA strain, Enterococcus spp. and Escherichia coli. These strains may be present as a result of postnatal colonization with both bacterial microflora of dams and environmental microflora.

  15. Shape optimization of shear fracture specimen considering plastic anisotropy

    Science.gov (United States)

    Zhang, S.; Yoon, J. W.; Lee, S.; Lou, Y.

    2017-10-01

    It is important to fabricate fracture specimens with minimum variation of triaxiality in order to characterize the failure behaviors experimentally. Fracture in ductile materials is usually calibrated by uniaxial tensile, shear and plane strain tests. However, it is often observed that triaxiality for shear specimen changes severely during shear fracture test. The nonlinearity of triaxiality is most critical for shear test. In this study, a simple in-plane shear specimen is optimized by minimizing the variation of stress triaxiality in the shear zone. In the optimization, the Hill48 and Yld2000-2d criteria are employed to model the anisotropic plastic deformation of an aluminum alloy of 6k21. The evolution of the stress triaxiality of the optimized shear specimen is compared with that of the initial design of the shear specimen. The comparison reveals that the stress triaxiality changes much less for the optimized shear specimen than the evolution of the stress triaxiality with the original design of the shear specimen.

  16. 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.

  17. 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.

  18. Effect of specimen size on work-of-fracture measurements.

    Science.gov (United States)

    Rogers, L L; Moyle, D D

    1988-01-01

    It has been suggested that work-of-fracture, which quantifies the ability of a material to resist fracture, is dependent on specimen size. This experiment compared work-of-fracture, calculated as energy per unit area, for different specimen sizes of Plexiglas, bovine tibial bone and aluminum. Three different geometrically similar cross sections were tested for each material for a total of 54 specimens. Work-of-fracture was measured by loading a notched beam (triangular cross section) in three-point bending at a constant deformation rate. The energy necessary to cause fracture was measured from a load-deformation curve. Specimen fracture area was determined using macrophotography. Atomic absorption spectrophotometry was used to determine weight percent calcium of bone specimens and quantitative light microscopy was used to determine fractional void area. Analysis of variance showed no effect of specimen size on work-of-fracture for aluminum or Plexiglas specimens (p greater than 0.05). A significant difference was found, however, between the large (area = 11.7 +/- 1.9 mm2) and small (area = 3.48 +/- 0.68 mm2) bone specimens and between the medium (area = 5.89 +/- 0.69 mm2) and small (area = 3.48 +/- 0.68 mm2) bone specimens. No correlation was found between work-of-fracture and either calcium content (r2 = 0.128) or fractional void area (r2 = 0.0713). The mean work-of-fracture values found are as follows: aluminum, 59.8 +/- 13.7 kJ m-2; Plexiglas, 0.620 +/- 0.074 kJ m-2; bone (area 5.89 +/- 0.69 mm2-11.7 +/- 1.9 mm2), 9.72 +/- 1.93 kJ m-2 and bone (area 3.48 +/- 0.68 mm2), 5.48 +/- 1.79 kJ m-2.

  19. Final Report: Posttest Analysis of Omega II Optical Specimens

    Energy Technology Data Exchange (ETDEWEB)

    Newlander, C D; Fisher, J H

    2007-01-30

    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.

  20. 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.

  1. 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®

  2. Etiologic predictive value of a rapid immunoassay for the detection of group A Streptococcus antigen from throat swabs in patients presenting with a sore throat.

    Science.gov (United States)

    Orda, Ulrich; Gunnarsson, Ronny; Orda, Sabine; Fitzgerald, Mark; Rofe, Geoff; Dargan, Anna

    2016-04-01

    Clinical reasoning utilizing certain symptoms and scores has not proven to be a reliable decision-making tool to determine whether or not to suspect a group A Streptococcus (GAS) infection in the patient presenting with a sore throat. Culture as the so-called 'gold standard' is impracticable because it takes 1 to 2 days (and even longer in remote locations) for a result, and thus treatment decisions will be made without the result available. Rapid diagnostic antigen tests have demonstrated sufficient sensitivities and specificities in detecting GAS antigens to identify GAS throat infections. Throat swab samples were collected from patients attending the Mount Isa Hospital emergency department for a sore throat; these samples were compared to swab samples collected from healthy controls who did not have a sore throat. Both groups were aged 3-15 years. All swab samples were analyzed with a point-of-care test (Alere Test Pack +Plus with OBC Strep A). The etiologic predictive value (EPV) of the throat swab was calculated. The 95% confidence interval for positive EPV was 88-100% and for negative EPV was 97-99%, depending on assumptions made. This study demonstrates that the point-of-care test Alere Test Pack +Plus Strep A has a high positive predictive value and is able to rule in GAS infection as long as the proportion of carriers is low. Also the negative predictive value for ruling out GAS as the etiologic agent is very high irrespective of the carrier rate. Hence, this test is always useful to rule out GAS infection. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Fabrication and testing of prestressed composite rotor blade spar specimens

    Science.gov (United States)

    Gleich, D.

    1974-01-01

    Prestressed composite spar specimens were fabricated and evaluated by crack propagation and ballistic penetration tests. The crack propagation tests on flawed specimens showed that the prestressed composite spar construction significantly suppresses crack growth. Damage from three high velocity 30 caliber projectile hits was confined to three small holes in the ballistic test specimen. No fragmentation or crack propagation was observed indicating good ballistic damage resistance. Rotor attachment approaches and improved structural performance configurations were identified. Design theory was verified by tests. The prestressed composite spar configuration consisted of a compressively prestressed high strength ARDEFORM 301 stainless steel liner overwrapped with pretensioned S-994 fiberglass.

  4. Small Specimen Data from a High Temperature HFIR Irradiation Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Burchell, Timothy D [ORNL; McDuffee, Joel Lee [ORNL; Thoms, Kenneth R [ORNL

    2014-01-01

    The HTV capsule is a High Flux Isotope Reactor (HFIR) target-rod capsule designed to operate at very high temperatures. The graphite containing section of the capsule (in core) is approximately 18 inches (457.2 mm) long and is separated into eight temperature zones. The specimen diameters within each zone are set to achieve the desired gas gap and hence design temperature (900 C, 1200 C or 1500 C). The capsule has five zones containing 0.400 inch (10.16 mm) diameter specimens, two zones containing 0.350 inch (8.89 mm) diameter specimens and one zone containing 0.300 inch (7.62 mm) diameter specimens. The zones have been distributed within the experiment to optimize the gamma heating from the HFIR core as well as minimize the axial heat flow in the capsule. Consequently, there are two 900 C zones, three 1200 C zones, and three 1500 C zones within the HTV capsule. Each zone contains nine specimens 0.210 0.002 inches (5.334 mm) in length. The capsule will be irradiated to a peak dose of 3.17 displacements per atom. The HTV specimens include samples of the following graphite grades: SGL Carbon s NBG-17 and NBG-18, GrafTech s PCEA, Toyo Tanso s IG-110, Mersen s 2114 and the reference grade H-451 (SGL Carbon). As part of the pre-irradiation program the specimens were characterized using ASTM Standards C559 for bulk density, and ASTM C769 for approximate Young s modulus from the sonic velocity. The probe frequency used for the determination of time of flight of the ultrasonic signal was 2.25 MHz. Marked volume (specimen diameter) effects were noted for both bulk density (increased with increasing specimen volume or diameter) and Dynamic Young s modulus (decreased with increasing specimen volume or diameter). These trends are extended by adding the property vs. diameter data for unirradiated AGC-1 creep specimens (nominally 12.5 mm-diameter x 25.4 mm-length). The relatively large reduction in Dynamic Young s Modulus was surprising given the trend for increasing density

  5. 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.

  6. 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.

  7. Eradication of methicillin-resistant Staphylococcus aureus in pressure ulcers comparing a polyhexanide-containing cellulose dressing with polyhexanide swabs in a prospective randomized study.

    Science.gov (United States)

    Wild, Thomas; Bruckner, Maria; Payrich, Martina; Schwarz, Christoph; Eberlein, Thomas; Andriessen, Anneke

    2012-01-01

    The study evaluated eradication of methicillin-resistant Staphylococcus aureus (MRSA) from pressure ulcers comparing swabs containing polyhexanide with a cellulose dressing + polyhexanide. After receiving approval from the ethics committee and informed consent, patients from the centers were recruited. Prospective randomized study. Thirty patients (n = 15/n = 15), not responding to wound disinfection after a washout period of 2 weeks, were included in the intention-to-treat analysis. This study was performed on hospital patients. Patients had pressure ulcers containing MRSA. For the control group, cleansing was performed with polyhexanide swabs (20 minutes), after which a foam dressing was applied. The study group received a polyhexanide-containing cellulose dressing. For bacterial analysis, semiquantitative swab cultures (Robert Koch Institute recommendations) were taken on days 0, 7, and 14 and during 3 consecutive days. The groups were comparable at baseline. At day 7, in the control group, 6 of 15 (40%) MRSA eradication. For the study group, there were 13 of 15 (86.67%) who showed MRSA eradication. At day 14, in the control group, there were 10 of 15 (66.67%) who had MRSA eradication, compared with the study group, where 15 of 15 (100%; P polyhexanide was shown to be successful in both groups, showing superior results for the study group.

  8. Streptococcus pneumoniae carriage prevalence in Nepal: evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation.

    Directory of Open Access Journals (Sweden)

    Sarah Hanieh

    Full Text Available Pneumococcal disease is a significant cause of morbidity and mortality in young children in Nepal, and currently available pneumococcal conjugate vaccines offer moderate coverage of invasive disease isolates.A prevalence study of children aged 1.5 to 24 months in urban and rural Nepal was conducted. In the urban group, nasopharyngeal swabs (NPS were transported using silica desiccant packages (SDP with delayed processing (2 weeks, or skim-milk-tryptone-glucose-glycerin (STGG with immediate processing (within 8 hours. Pneumococcal nasopharyngeal carriage prevalence, serogroup/type distribution and isolate genotypes (as defined by multilocus sequence typing were determined.1101 children were enrolled into the study: 574 in the urban group and 527 in the rural group. Overall carriage prevalence based on culture from specimens transported and stored in STGG was 58.7% (337/574, compared to 40.9% (235/574 in SDP. There was concordance of detection of pneumococcus in 67% of samples. Using the SDP method, pneumococcal carriage prevalence was higher in the rural population (69.2%; 364/526 compared to the urban population (40.9%; 235/574. Serogroup/type distribution varied with geographical location. Over half of the genotypes identified in both the urban and rural pneumococcal populations were novel.The combination of delayed culture and transport using SDP underestimates the prevalence of pneumococcal carriage; however, in remote areas, this method could still provide a useful estimate of carriage prevalence and serogroup/type distribution. Vaccine impact is unpredictable in a setting with novel genotypes and limited serotype coverage as described here. Consequently, continued surveillance of pneumococcal isolates from carriage and disease in Nepali children following the planned introduction of pneumococcal conjugate vaccines introduction will be essential.

  9. Edgeless composite laminate specimen for static and fatigue testing

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1978-01-01

    The influence of edge effects on the tensile properties of angle-ply laminate composites can be eliminated by using edgeless (round tubular) specimens. However, uniaxial tests with such specimens, static and fatigue, have been generally unsuccessful because of the differential Poisson effect between the test section and the grips. An edgeless cylindrical specimen, developed to circumvent these difficulties, is examined in the present paper. It is a flattened tube consisting of two flat sides connected by curved sections. It can be handled much like the standard flat coupon. The flat ends of the specimen are provided with crossplied fiberglass gripping tabs, the same as used for flat test coupons. As part of the tabbing, the hollow ends must be plugged with inserts to prevent crushing of the ends. A special insert design was developed to minimize detrimental Poisson effects ordinarily introduced by inserts.

  10. 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.

  11. Description of Specimens in the Marine Mammal Osteology Reference Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NMFS Alaska Fisheries Science Center National Marine Mammal Laboratory (NMML) Marine Mammal Osteology Collection consists of approximately 2500 specimens (skulls...

  12. North Mississippi Refuges Complex Dragonfly Vouchered Specimens 2005

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report contains a list of dragonflies and photographs of them collected in 2005 from the refuge complex. These were verified by Steve Krotzer and specimens retained...

  13. Control of Contamination in Psittacosis Specimens by Antibiotics

    Science.gov (United States)

    Lewis, Vester J.; Engelman, Helen M.

    1971-01-01

    Diluent containing a combination of vancomycin, kanamycin, and streptomycin is shown to be more effective than diluent previously used for isolating Chlamydia psittaci from bird tissue specimens. PMID:4940879

  14. Specimen thickness effect on elastic-plastic constraint parameter A

    National Research Council Canada - National Science Library

    GP Nikishkov; YuG Matvienko

    2015-01-01

    .... Distributions of the J-integral and constraint parameter A along the crack front for varying specimen thickness and crack depth are determined for edge cracked plate, center cracked plate, three...

  15. Radiation Transport

    Energy Technology Data Exchange (ETDEWEB)

    Urbatsch, Todd James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-06-15

    We present an overview of radiation transport, covering terminology, blackbody raditation, opacities, Boltzmann transport theory, approximations to the transport equation. Next we introduce several transport methods. We present a section on Caseology, observing transport boundary layers. We briefly broach topics of software development, including verification and validation, and we close with a section on high energy-density experiments that highlight and support radiation transport.

  16. 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

    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.......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...

  17. 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....

  18. Section planes of snow specimens visualized with sudan black B

    OpenAIRE

    ハチクボ, アキヒロ; アラカワ, ハヤト; ニシダ; フクザワ, タクヤ; アキタヤ, エイジ; Akihiro, HACHIKUBO; Hayato, Arakawa; Kenlo, Nishida; Takuya, Fukuzawa; Eizi, AKITAYA

    2000-01-01

    A technique for preparing section planes of snow specimens dyed with sudan black B was introduced. After the pour space of a snow specimen is filled with aniline and frozen solid, a section plane is microtomed and rubbed with sudan black B powder for contrast enhancement. Compared with previous methods, this technique was simple and provided high-contrast images and reduction of noise on a section plane.

  19. Fe-based magnetic shape memory alloy-sheet specimen

    Science.gov (United States)

    Kanada, Tsugunori; Enokizono, Masato

    1999-05-01

    We contrived a new composite functional alloy which is compatible for both magnetization and the shape memory effect (SME). A FeMnSiCr alloy, one of the shape memory alloys (SMA) has strong magnetization in addition to SME after heating in air. It is because the specimen is composed of a ferromagnetic iron oxide Fe 3O 4 (magnetite) surface layer, the inside being SMA. The measurements were carried out on a sheet specimen.

  20. 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.

  1. Stress Analysis of a Secondary-Bending Specimen

    Science.gov (United States)

    1993-11-01

    Control Office Ansett Airlines of Australia, Library 0 Qantas Airways Limited Hawker de Havilland Aust Pty Ltd, Victoria, Library Hawker de Havilland...elements are also used to restrict the movement 0 of linked nodes, however, in a limited way. They enable the adjacent components to separate and slide but...sketch of the specimen for clarity. The presence of the SPATE signal outside the boundary of the specimen is due to limitations in the depth of field of

  2. Biaxial Testing of 2195 Aluminum Lithium Alloy Using Cruciform Specimens

    Science.gov (United States)

    Johnston, W. M.; Pollock, W. D.; Dawicke, D. S.; Wagner, John A. (Technical Monitor)

    2002-01-01

    A cruciform biaxial test specimen was used to test the effect of biaxial load on the yield of aluminum-lithium alloy 2195. Fifteen cruciform specimens were tested from 2 thicknesses of 2195-T8 plate, 0.45 in. and 1.75 in. These results were compared to the results from uniaxial tensile tests of the same alloy, and cruciform biaxial tests of aluminum alloy 2219-T87.

  3. Innovation for reducing blood culture contamination: initial specimen diversion technique.

    Science.gov (United States)

    Patton, Richard G; Schmitt, Timothy

    2010-12-01

    We hypothesized that diversion of the first milliliter of venipuncture blood-the initial specimen diversion technique (ISDT)-would eliminate incompletely sterilized fragments of skin from the culture specimen and significantly reduce our blood culture contamination rate (R). We studied our hypothesis prospectively beginning with our control culture (C) definition: one venipuncture with two sequentially obtained specimens, 10 ml each, the first specimen (M1) for aerobic and the second (M2) for anaerobic media. The test ISDT culture (D) was identical, with the exception that each was preceded by diverting a 1-ml sample (DS) from the same venipuncture. During the first of two sequential 9-month periods, we captured D versus C data (n=3,733), where DMXR and CMXR are R for D and C specimens. Our hypothesis predicted DS would divert soiled skin fragments from DM1, and therefore, CM1R would be significantly greater than DM1R. This was confirmed by CM1R (30/1,061 [2.8%]) less DM1R (37/2,672 [1.4%]; P=0.005), which equals 1.4%. For the second 9-month follow-up period, data were compiled for all cultures (n=4,143), where ADMXR is R for all (A) diversion specimens, enabling comparison to test ISDT. Our hypothesis predicted no significant differences for test ISDT versus all ISDT. This was confirmed by DM1R (37/2,672 [1.4%]) versus ADM1R (42/4,143 [1.0%]; P=0.17) and DM2R (21/2,672 [0.80%]) versus ADM2R (39/4,143 [0.94%]; P=0.50). We conclude that our hypothesis is valid: venipuncture needles soil blood culture specimens with unsterilized skin fragments and increase R, and ISDT significantly reduces R from venipuncture-obtained blood culture specimens.

  4. 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.)

  5. Specimen Sample Preservation for Cell and Tissue Cultures

    Science.gov (United States)

    Meeker, Gabrielle; Ronzana, Karolyn; Schibner, Karen; Evans, Robert

    1996-01-01

    The era of the International Space Station with its longer duration missions will pose unique challenges to microgravity life sciences research. The Space Station Biological Research Project (SSBRP) is responsible for addressing these challenges and defining the science requirements necessary to conduct life science research on-board the International Space Station. Space Station will support a wide range of cell and tissue culture experiments for durations of 1 to 30 days. Space Shuttle flights to bring experimental samples back to Earth for analyses will only occur every 90 days. Therefore, samples may have to be retained for periods up to 60 days. This presents a new challenge in fresh specimen sample storage for cell biology. Fresh specimen samples are defined as samples that are preserved by means other than fixation and cryopreservation. The challenge of long-term storage of fresh specimen samples includes the need to suspend or inhibit proliferation and metabolism pending return to Earth-based laboratories. With this challenge being unique to space research, there have not been any ground based studies performed to address this issue. It was decided hy SSBRP that experiment support studies to address the following issues were needed: Fixative Solution Management; Media Storage Conditions; Fresh Specimen Sample Storage of Mammalian Cell/Tissue Cultures; Fresh Specimen Sample Storage of Plant Cell/Tissue Cultures; Fresh Specimen Sample Storage of Aquatic Cell/Tissue Cultures; and Fresh Specimen Sample Storage of Microbial Cell/Tissue Cultures. The objective of these studies was to derive a set of conditions and recommendations that can be used in a long duration microgravity environment such as Space Station that will permit extended storage of cell and tissue culture specimens in a state consistent with zero or minimal growth, while at the same time maintaining their stability and viability.

  6. 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.

  7. 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

  8. Specimen aspect ratio and light transmission in photoactive dental resins.

    Science.gov (United States)

    Hadis, Mohammed A; Shortall, Adrian C; Palin, William M

    2012-11-01

    To test the influence of specimen dimensions on light transmission and shrinkage strain properties of curing dental resins. Photocurable resin specimens (Bis-GMA/TEGDMA) with aspect ratios (AR) of 2 (4mm×2mm); 4 (4mm×1mm and 8mm×2mm); 8 (8mm×1mm); 12 (AR: 12mm×1mm); and 24 (12mm×0.5mm) were light cured. Light transmission and shrinkage-strain data were recorded throughout, and upper and lower surface hardness measurements were performed following cure. Light transmission was significantly affected by the specimen aspect ratio even at similar thicknesses (presin without photoinitiator, the lowest AR specimens showed a relative increase in transmission above 100% throughout curing, which was caused by specimen constraint. The extent of lower surface cure (as assessed by increasing hardness) was principally affected by cavity height and decreased for thicker specimens (presin-based restorations through depth. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  9. [Methods for collection, transport and culture media].

    Science.gov (United States)

    Ercolani, F; Morera, E; Panichi, G; Occhionero, M; Luzzi, I; Gianfrilli Mastrantonio, P

    1979-01-01

    A crucial factor affecting the ultimate success of anaerobic cultures is a proper specimen collection, with care to avoid inclusion of normal flora often present on human mucosa. In general, material for anaerobic cultures is best obtained using a needle and syringe, from which the air must be expelled. Then the specimens should be placed immediately into an anaerobic transport broth and then in suitable culture pre-reduced media.

  10. Test results for composite specimens and elements containing joints and cutouts

    Science.gov (United States)

    Sumida, P. T.; Madan, R. C.; Hawley, A. V.

    1988-01-01

    A program was conducted to develop the technology for joints and cutouts in a composite fuselage that meets all design requirements of a large transport aircraft for the 1990s. An advanced trijet derivative of the DC-10 was selected as the baseline aircraft. Design and analysis of a 30-foot-long composite fuselage barrel provided a realistic basis for the test effort. The primary composite material was Hexcel F584 resin on 12 K IM6 fiber, in tape and broadgoods form. Fiberglass broadgoods were used in E-glass and S-glass fiber form in the cutout region of some panels. Additionally, injection-molded chopped graphite fiber/PEEK was used for longeron-to-frame shear clips. The test effort included four groups of test specimens, beginning with coupon specimens of mono-layer and cross-piled laminates, progressing through increasingly larger and more complex specimens, and ending with two 4- by 5-foot curved fuselage side panels. One of the side panels incorporated a transverse skin splice, while the second included two cabin window cutouts.

  11. GLUT3 protein and mRNA in autopsy muscle specimens

    Science.gov (United States)

    Stuart, C. A.; Wen, G.; Jiang, J.

    1999-01-01

    GLUT3 is expressed in rat muscle, but this glucose transporter protein has not been identified previously in adult human skeletal muscle. We quantified the rapidity of disappearance of mRNA and protein from human skeletal muscle at room temperature and at 4 degrees C. Fifty percent of the immunologically detectable GLUT3 protein disappeared by 1 hour at 20 degrees C and by 2 hours at 4 degrees C. mRNA for GLUT3 was decreased 50% by 2.2 hours at 20 degrees C and by 24 hours at 4 degrees C. Half of the measurable mRNAs for GLUT4, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), alpha-actin, and beta-myosin disappeared by 0.8 to 2.1 hours at 20 degrees C and by 5.0 to 16.6 hours at 4 degrees C. Previous conclusions that GLUT3 is not expressed in human muscle were likely drawn because of artifacts related to degradation of GLUT3 protein in the specimens prior to study. Because of the rapid degradation of protein and mRNA, autopsy specimens of muscle must be obtained within 6 hours of death, and even then, protein and mRNA data will likely dramatically underestimate their expression in fresh muscle. Some previously published conclusions and recommendations regarding autopsy specimens are not stringent enough to consistently yield useful protein and mRNA.

  12. 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

  13. Induced Polarization Responses of the Specimen with Sulfide Ore Minerals

    Science.gov (United States)

    Park, S.; Sung, N. H.

    2012-04-01

    Basic data of the physical properties of the rocks is required to effectively interpret geologic structures and mineralized zones in study areas from the geophysical data in the field of subsurface investigations and mineral resources explorations. In this study, the spectral induced polarization (SIP) measurement system in the laboratory was constructed to obtain the IP characteristics of the specimen with sulfide ore minerals. The SIP measurement system consists of lab transmitter for electrical current transmission, and GDP-32 for current receiver. The SIP system employs 14 steps of frequencies from 0.123 to 1,024 Hz, and uses copper sulfate solution as an electrolyte. The SIP data for system verification was acquired using a measurement system of parallel circuit with fixed resistance and condenser. This measured data was in good agreement with Cole-Cole model data. First of all, the experiment on the SIP response was conducted in the laboratory with the mixture of glass beads and pyrite powders for ore grade assessment using characteristics of IP response of the rocks. The results show that the phase difference of IP response to the frequency is nearly proportional to the weight content of pyrite, and that the dominant frequency of the IP response varies with the size of the pyrite powder. Subsequently, the specimens used for SIP measurement are slate and limestone which were taken from drilling cores and outcrops of skarn ore deposits. All specimens are cylindrical in shape, with a diameter of 5 cm and a length of 10 cm. When measuring SIP of water-saturated specimens, the specimen surface is kept dry, tap water is put into the bottom of sample holder and a lid is closed. It is drawn that the SIP characteristics of the rocks show the phase difference depends on the amount of the sulfide minerals. The phase difference did not occur with frequencies applied in the absence of sulfide minerals in the rock specimens. On the contrary, the rock specimens containing

  14. Microwave applications to rock specimen drying in laboratory

    Science.gov (United States)

    Park, Jihwan; Park, Hyeong-Dong

    2014-05-01

    Microwave heating is the process in which electromagnetic wave with 300 MHz - 300 GHz heats dielectric material. Although in the beginning microwave was mainly used in food industry to cook or heat the food, it soon became clear that microwave had a large potential for other applications. It was thus introduced in geological fields of investigation like mineral processing, oil sand and oil shale extraction, soil remediation, waste treatment. However, the drying techniques using microwave was rarely treated in geology field. According to the ISRM suggested methods, experimental rock specimens in laboratory test were dried in 105°C oven for a period of at least 24 hours. In this method, hot air transmits heats to material by means of thermal conduction, and the heat was transferred from the surface to the inside of the rock specimens. The thermal gradient and moisture gradient can deteriorate the specimens, and energy can be wasted in bulk heating the specimens. The aim of our study was to compare physical property, microstructural property, and energy efficiency between microwave drying method and conventional oven drying method, and to suggest new method for rock drying. Granite, basalt, and sandstone were selected as specimens and were made in cylinder shape with 54 mm diameter. To compare two different methods, one set of saturated specimens were dried in 105°C conventional oven and the other set of saturated specimens were dried in microwave oven. After dried, the specimens were cooled and saturated in 20°C water 48 hours. The saturation-drying were repeated 50 cycles, and the physical property and microstructural property were measured every 10 cycles. Absorption and elastic wave velocity were measured to investigate the change of physical property, and microscope image and X-ray computed tomography image were obtained to investigate the change of microstructural property of rock specimens. The electricity consumption of conventional oven and microwave oven

  15. Culture of Urine Specimens by Use of chromID CPS Elite Medium Can Expedite Escherichia coli Identification and Reduce Hands-On Time in the Clinical Laboratory.

    Science.gov (United States)

    Yarbrough, Melanie L; Wallace, Meghan A; Marshall, Cynthia; Mathias, Erin; Burnham, C A

    2016-11-01

    Urine is one of the most common specimen types submitted to the clinical microbiology laboratory; the use of chromogenic agar is one method by which the laboratory might expedite culture results and reduce hands-on time and materials required for urine culture analysis. The objective of our study was to compare chromID CPS Elite (bioMérieux), a chromogenic medium, to conventional primary culture medium for evaluation of urine specimens. Remnant urine specimens (n = 200) were inoculated into conventional media and into chromID CPS Elite agar (chromID). The time to identification and consumables used were documented for both methods. Clinically significant pathogen(s) were recovered from 51 cultures using conventional media, with Escherichia coli being the most frequently recovered organism (n = 22). The rate of exact uropathogen agreement between conventional and chromogenic media was 82%, while overall categorical agreement was 83.5% The time interval between plating and final organism identification was decreased with chromID agar versus conventional media for E. coli (mean of 24.4 h versus 27.1 h, P cultures required less hands-on time per culture (mean of 1 min and 2 s [1:02 min]) compared to conventional media (mean of 1:31 min). In addition, fewer consumables (2.4 versus 3.3 sticks and swabs) and rapid biochemical tests (1.0 versus 1.9) were necessary using chromID versus conventional media. Notably, antimicrobial susceptibility testing demonstrated good overall agreement (97.4%) between the chromID and conventional media for all antibiotics tested. chromID CPS Elite is accurate for uropathogen identification, reduces consumable usage, and may expedite the identification of E. coli in clinical specimens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  16. Sustainable Transportation

    DEFF Research Database (Denmark)

    Hall, Ralph P.; Gudmundsson, Henrik; Marsden, Greg

    2014-01-01

    that relate to the construction and maintenance of transportation infrastructure and the operation or use of the different transportation modes. The concept of sustainable transportation emerged in response to these concerns as part of the broader notion of sustainable development. Given the transportation...

  17. Design optimization of cruciform specimens for biaxial fatigue loading

    Directory of Open Access Journals (Sweden)

    R. Baptista

    2014-10-01

    Full Text Available In order to correctly assess the biaxial fatigue material properties one must experimentally test different load conditions and stress levels. With the rise of new in-plane biaxial fatigue testing machines, using smaller and more efficient electrical motors, instead of the conventional hydraulic machines, it is necessary to reduce the specimen size and to ensure that the specimen geometry is appropriated for the load capacity installed. At the present time there are no standard specimen’s geometries and the indications on literature how to design an efficient test specimen are insufficient. The main goal of this paper is to present the methodology on how to obtain an optimal cruciform specimen geometry, with thickness reduction in the gauge area, appropriated for fatigue crack initiation, as a function of the base material sheet thickness used to build the specimen. The geometry is optimized for maximum stress using several parameters, ensuring that in the gauge area the stress is uniform and maximum with two limit phase shift loading conditions. Therefore the fatigue damage will always initiate on the center of the specimen, avoiding failure outside this region. Using the Renard Series of preferred numbers for the base material sheet thickness as a reference, the reaming geometry parameters are optimized using a derivative-free methodology, called direct multi search (DMS method. The final optimal geometry as a function of the base material sheet thickness is proposed, as a guide line for cruciform specimens design, and as a possible contribution for a future standard on in-plane biaxial fatigue tests.

  18. Primary cultivation: factors affecting contamination and Mycobacterium ulcerans growth after long turnover time of clinical specimens.

    Science.gov (United States)

    Bratschi, Martin W; Bolz, Miriam; Grize, Leticia; Kerber, Sarah; Minyem, Jacques C; Um Boock, Alphonse; Yeboah-Manu, Dorothy; Ruf, Marie-Thérèse; Pluschke, Gerd

    2014-11-30

    While cultivation of pathogens represents a foundational diagnostic approach in the study of infectious diseases, its value for the confirmation of clinical diagnosis of Buruli ulcer is limited by the fact that colonies of Mycobacterium ulcerans appear only after about eight weeks of incubation at 30°C. However, for molecular epidemiological and drug sensitivity studies, primary isolation of M. ulcerans remains an essential tool. Since for most of the remote Buruli ulcer endemic regions of Africa cultivation laboratories are not easily accessible, samples from lesions often have to be stored for extended periods of time prior to processing. The objective of the current study therefore was to determine which transport medium, decontamination method or other factors decrease the contamination rate and increase the chance of primary isolation of M. ulcerans bacilli after long turnover time. Swab and fine needle aspirate (FNA) samples for the primary cultivation were collected from clinically confirmed Buruli ulcer patients in the Mapé Basin of Cameroon. The samples were either stored in the semi-solid transport media 7H9 or Amies or dry for extended period of time prior to processing. In the laboratory, four decontamination methods and two inoculation media were evaluated and statistical methods applied to identify factors that decrease culture contamination and factors that increase the probability of M. ulcerans recovery. The analysis showed: i) that the use of moist transport media significantly increased the recovery rate of M. ulcerans compared to samples kept dry; ii) that the choice of the decontamination method had no significant effect on the chance of M. ulcerans isolation; and iii) that Löwenstein-Jensen supplemented with antibiotics as inoculation medium yielded the best results. We further found that, ten extra days between sampling and inoculation lead to a relative decrease in the isolation rate of M. ulcerans by nearly 20%. Finally, collection and

  19. Comparison of the Cepheid GeneXpert CT/NG assay to the Hologic Aptima Combo2 assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in self-collected rectal swabs.

    Science.gov (United States)

    Dize, Laura; Silver, Barbara; Gaydos, Charlotte

    2018-02-01

    Self-collected rectal-swabs were tested for CT and NG on GeneXpert CT/NG as compared to APTIMA Combo2. Of 448 rectal-swabs, 22 were positive for CT; 7 for NG on both assays; two were discordant. Sensitivity and specificity of GeneXpert was 95.5% and 99.7% for chlamydia, respectively; for gonorrhea both were 100%. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. 3D volume reconstruction from serial breast specimen radiographs for mapping between histology and 3D whole specimen imaging.

    Science.gov (United States)

    Mertzanidou, Thomy; Hipwell, John H; Reis, Sara; Hawkes, David J; Ehteshami Bejnordi, Babak; Dalmis, Mehmet; Vreemann, Suzan; Platel, Bram; van der Laak, Jeroen; Karssemeijer, Nico; Hermsen, Meyke; Bult, Peter; Mann, Ritse

    2017-03-01

    In breast imaging, radiological in vivo images, such as x-ray mammography and magnetic resonance imaging (MRI), are used for tumor detection, diagnosis, and size determination. After excision, the specimen is typically sliced into slabs and a small subset is sampled. Histopathological imaging of the stained samples is used as the gold standard for characterization of the tumor microenvironment. A 3D volume reconstruction of the whole specimen from the 2D slabs could facilitate bridging the gap between histology and in vivo radiological imaging. This task is challenging, however, due to the large deformation that the breast tissue undergoes after surgery and the significant undersampling of the specimen obtained in histology. In this work, we present a method to reconstruct a coherent 3D volume from 2D digital radiographs of the specimen slabs. To reconstruct a 3D breast specimen volume, we propose the use of multiple target neighboring slices, when deforming each 2D slab radiograph in the volume, rather than performing pairwise registrations. The algorithm combines neighborhood slice information with free-form deformations, which enables a flexible, nonlinear deformation to be computed subject to the constraint that a coherent 3D volume is obtained. The neighborhood information provides adequate constraints, without the need for any additional regularization terms. The volume reconstruction algorithm is validated on clinical mastectomy samples using a quantitative assessment of the volume reconstruction smoothness and a comparison with a whole specimen 3D image acquired for validation before slicing. Additionally, a target registration error of 5 mm (comparable to the specimen slab thickness of 4 mm) was obtained for five cases. The error was computed using manual annotations from four observers as gold standard, with interobserver variability of 3.4 mm. Finally, we illustrate how the reconstructed volumes can be used to map histology images to a 3D specimen

  1. 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

  2. Standard Guide for Reconstitution of Irradiated Charpy-Sized Specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2007-01-01

    1.1 This guide covers procedures for the reconstitution of ferritic pressure boundary steels used in nuclear power plant applications, Type A Charpy (Test Methods E 23) specimens and specimens suitable for testing in three point bending in accordance with Test Methods E 1921 or E 1820. Materials from irradiation programs (principally broken specimens) are reconstituted by welding end tabs of similar material onto remachined specimen sections that were unaffected by the initial test. Guidelines are given for the selection of suitable specimen halves and end tab materials, for dimensional control, and for avoidance of overheating the notch area. A comprehensive overview of the reconstitution methodologies can be found in Ref (1). 1.2 The values stated in SI units are to be regarded as the standard. The values given in parentheses are for information only. This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard...

  3. Small specimen technique for assessing mechanical properties of metallic components

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, Raquel M.; Andrade, Arnaldo H.P.; Morcelli, Aparecido E., E-mail: rmlobo@ipen.br, E-mail: morcelliae@gmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-11-01

    Small Punch Test (SPT) is one of the most promising techniques of small specimen test, which was originally applied in testing of irradiated materials in nuclear engineering. Then it was introduced to other fields as an almost nondestructive method to measure the local mechanical properties that are difficult to be obtained using conventional mechanical tests. Most studies to date are focused on metallic materials, although SPT applications are recently spreading to other materials. The small punch test (SPT) employs small-sized specimens (for example, samples measuring 8 mm in diameter and 0.5 mm thick). The specimen is firmly clamped between two circular dies and is bi-axially strained until failure into a circular hole using a hemispherical punch. The 'load-punch displacement' record can be used to estimate the yield strength, the ultimate tensile strength, the tensile elongation, and the temperature of the ductile-to-brittle transition. Recently, some researchers are working on the use of miniature notched or pre-cracked specimens (denoted as p-SPT) to validate its geometry and dimensions for obtaining the fracture properties of metallic materials. In a first approach, the technique makes it possible to convert primary experimental data into conventional mechanical properties of a massive specimen. In this paper a comprehensive review of the different STP applications is presented with the aim of clarifying its usefulness. (author)

  4. Digital staining of pathological tissue specimens using spectral transmittance

    Science.gov (United States)

    Bautista, Pinky A.; Abe, Tokiya; Yamaguchi, Masahiro; Yagi, Yukako; Ohyama, Nagaaki

    2005-04-01

    Staining of tissue specimens is a classical procedure in pathological diagnosis to enhance the contrast between tissue components such that identification and classification of these components can be easily performed. In this paper, a framework for digital staining of pathological specimens using the information derived from the L-band spectral transmittance of various pathological tissue components is introduced, particularly the transformation of a Hematoxylin and Eosin (HE) stained specimen to its Masson-Trichrome (MT) stained counterpart. The digital staining framework involves the classification of tissue components, which are highlighted when the specimen is actually stained with MT stain, e.g. fibrosis, from the HE-stained image; and the linear mapping between specific sets of HE and MT stained transmittance spectra through pseudo-inverse procedure to produce the LxL transformation matrices that will be used to transform the HE stained transmittance to its equivalent MT stained transmittance configuration. To generate the digitally stained image, the decisions of multiple quadratic classifiers are pooled to form the weighting factors for the transformation matrices. Initial results of our experiments on liver specimens show the viability of multispectral imaging (MSI) for the implementation of digital staining in the pathological context.

  5. Factors affecting the risk of blood bank specimen hemolysis.

    Science.gov (United States)

    Tanabe, Paula; Kyriacou, Demetrios N; Garland, Franklyn; Kyriacou, Demetrious

    2003-08-01

    To evaluate simultaneously several possible risk factors for blood bank specimen hemolysis. This was a prospective cohort study of emergency department and labor and delivery patients to estimate the effect of various factors on the risk of blood bank specimen hemolysis. Study variables included patient demographics, type and gauge of needle or catheter, anatomic location of venipuncture, and patient care area. Hemolysis was determined by blood bank laboratory technicians. Cox proportional hazards multivariate regression modeling was performed to estimate the adjusted relative risks for hemolysis. Of the 605 subjects with complete data, 194 (32.1%) subjects had blood specimens drawn directly with a steel needle, and 411 (69.1%) had specimens drawn through a Vialon (BD Medical Systems, Inc., Sandy, UT) intravenous (IV) angiocatheter. The overall risk of hemolysis for all was 7%, 10% for Vialon IV angiocatheters and 1.5% for steel needles. In the multivariate analysis, the factors most closely associated with hemolysis were the use of Vialon IV catheters and sampling from an anatomic site other than the antecubital area. Blood bank specimens drawn from Vialon IV catheters (particularly smaller gauge catheters) and from veins outside the antecubital area are at significantly increased risk to hemolyze.

  6. Xanthogranulomatous appendicitis in interval appendectomy specimens of children

    Directory of Open Access Journals (Sweden)

    Yusuf Hakan Çavuşoğlu

    2016-05-01

    Full Text Available Xanthogranulomatous inflammation is common in interval appendectomy specimens in adults, but it is unusual in children. Histopathologic specimens of interval appendectomy, within an 8-year period, were reevaluated to assess the true incidence. A computer search of the hospital database of all appendectomies was performed between January 2008 and June 2015 to identify all interval appendectomy cases. A total of 2694 patients underwent appendectomies. Of these, 13 were interval appendectomies. After pathologic evaluation, 2 (15.4% of the specimens were reported as xanthogranulomatous appendicitis (XA. Histopathologic examination of these interval appendectomy specimens, granulomas (59%, xanthogranulomatous inflammation (36% and Crohn-like changes (50% were common in adults. However, XA is a particularly rare clinical entity among children. Two cases of XA were reported in children in the English literature. One was a 12-year old boy that underwent interval appendectomy 6 weeks after an episode of acute appendicitis. The other was an 11-year old boy with acute (non-interval appendicitis, but the complete blood count was suggestive of an acute suppurative inflammation. These two cases are the 3rd and 4th cases of XA reported in children in the English literature, and both were managed by interval appendectomy. Thus, XA may be encountered in interval appendectomy specimens and association with IBD has to be ruled out.

  7. Comparative evaluation of the Abbott RealTime High Risk HPV test and INNO-LiPA HPV Genotyping Extra test for detecting and identifying human papillomaviruses in archival tissue specimens of head and neck cancers.

    Science.gov (United States)

    Kocjan, Bostjan J; Maver, Polona J; Hosnjak, Lea; Zidar, Nina; Odar, Katarina; Gale, Nina; Poljak, Mario

    2012-12-01

    The Abbott RealTime is a novel real-time PCR assay designed for concurrent individual genotyping of HPV16 and HPV18 and pooled detection of 12 HPV genotypes: HPV31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68 in cervical swab specimens. In this study, the performance of RealTime for detecting HPV in formalin-fixed, paraffin-embedded tissue specimens of head and neck cancers was compared to the Innogenetics INNO-LiPA assay, which allows identification of 28 HPVs, including all 14 covered by RealTime. A total of 60 FFPE tissue specimens obtained from the same number of patients with histologically confirmed cancer of the oral cavity or oropharynx were included in the study. Following DNA extraction using a Qiagen DNA Mini Kit, RealTime and INNO-LiPA were performed on all samples, as instructed by the manufacturers. A 136-bp fragment of human beta-globin serving as an internal control in RealTime was successfully amplified from all 60 tissue samples included in the study. RealTime and INNO-LiPA showed 100% agreement and detected HPV DNA in 5/60 (8.3%) of the cancer samples, which all contained genotype HPV16. RealTime assay is a reliable, sensitive, and specific diagnostic tool for the detection and partial genotyping of targeted HPV genotypes in FFPE tissue specimens of oral and oropharyngeal cancer.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nevalainen, M.J. [VTT Manufacturing Technology, Espoo (Finland)

    1997-06-01

    The effect of the specimen size and geometry on fracture toughness has been investigated both by experimental tests and computational analyses. The methods for constraint description, namely T-stress, Q-parameter and Small-Scale Yielding Correction (SSYC) have been compared and applied for various geometries. A statistical treatment for the specimen thickness effect on cleavage fracture toughness has been investigated. Elliptical surface cracks were compared with straight-thickness cracks and a method for crack shape correction was presented. Based on the results, the differences in apparent fracture toughness values obtained from various specimen configurations can be better understood and taken into account. 64 refs. The thesis includes also four previous publications by author.

  9. Positivity of Demodex spp. in biopsy specimens of nevi.

    Science.gov (United States)

    Serpil, S; Ulku, K; Cemil, C; Nasuhi Engin, A; Sezai, S; Meryem, I

    2009-04-01

    Melanocytic skin tumors are caused by nevus cells, epidermal melanocytes and dermal melanocytes. The aim of the study was to detect the positivity of Demodex spp. in biopsy specimens of skin diagnosed as nevus. In this retrospective study, the specimens obtained from 110 patients diagnosed with nevus and stained by hematoxylin & eosin (H&E) method were assessed for Demodex. Statistical analysis was done using independent sample t test, Pearson Chi-square and Yates' adjusted Chi-square test. For statistics, p < 0.05 was considered significant. Consequently, 43 (39.1%) out of 110 specimens were detected to have Demodex spp. Demodex colonization augmented in nevi can be explained by the possible affinity of the parasite to the melanin pigment.

  10. Determining mechanical behavior of solid materials using miniature specimens

    Science.gov (United States)

    Manahan, M.P.; Argon, A.S.; Harling, O.K.

    1986-02-04

    A Miniaturized Bend Test (MBT) capable of extracting and determining mechanical behavior information from specimens only so large as to have at least a volume or smallest dimension sufficient to satisfy continuum behavior in all directions is disclosed. The mechanical behavior of the material is determined from the measurements taken during the bending of the specimen and is processed according to the principles of linear or nonlinear material mechanics or both. In a preferred embodiment the determination is carried out by a code which is constructed according to the finite element method, and the specimen used for the determinations is a miniature disk simply supported for central loading at the axis on the center of the disk. 51 figs.

  11. 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

    . 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......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...... 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...

  12. T*{sub {epsilon}} integral analysis of fracture specimens

    Energy Technology Data Exchange (ETDEWEB)

    Omori, Y.; Ma, L.; Kobayashi, A.S. [Univ. of Washington, Seattle, WA (United States)] [and others

    1996-12-31

    T*{sub {epsilon}} integral values associated with stable crack growth in thin 2024-T3 aluminum compact (CT) specimens and A606 HSLA steel single edge notched (SEN) specimens were determined directly from the crack tip displacement field obtained by moire interferometry. Stable crack growth in the SEN specimen was also simulated by an elastic-plastic finite element (FE) model which was driven by the experimentally determined boundary conditions. T*{sub {epsilon}} obtained experimentally and by FE were in reasonable agreements with each other. Unlike the vanishing J integrals with crack extension, T*{sub {epsilon}} reached steady state values with stable crack growth. Thus, for a given integration contour, {Gamma}{sub {epsilon}}, near the crack tip, T*{sub {epsilon}} can be used as a stable crack growth as well as a ductile fracture criteria.

  13. Specimen edge effects on bending fatigue of carburized steel

    Science.gov (United States)

    Cohen, R. E.; Matlock, D. K.; Krauss, G.

    1992-10-01

    The effects of specimen geometry on the fatigue behavior of SAE 4320 steel carburized at 927 °C were evaluated with two sets of cantilever bend specimens, one set machined with square edges and one set machined with round edges. The specimens with square edges exhibited a 13% lower fatigue limit. In comparison to the rounded samples, the lower fatigue limit in the square-edged samples was attributed to the presence of a higher volume fraction of retained austenite in the sample corners and a lower surface residual compressive stress. As a result of the differences in residual stress, preferential crack initiation sites existed in the square-edged samples at a location approximately 200 to 900 ώm from the square edge. The implications of this study on laboratory analyses of the bending fatigue performance of carburized gear steels are discussed.

  14. 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.

  15. Strip specimen tests for pipeline materials and girth welds

    Energy Technology Data Exchange (ETDEWEB)

    Mohr, William C. [Edison Welding Institute (EWI), Columbus, Ohio (United States)

    2009-07-01

    Strip specimen testing of pipeline materials has been widely applied as a method of getting data relevant to the performance of pipelines under axial direction loading. Comparisons of strip specimen against smaller standard tests (round tensile bar, fracture toughness specimens, polished round bars) and against full-scale or large-scale testing will be explored. Data from early-generation pipe welds from the 1920's to the 1940's to the most recent materials for offshore reeled pipe will be used for examples. Strip samples can provide full thickness information to take account of varying material properties or imperfection distribution through the thickness. Strip samples can also accommodate measurement of effects of the original surface finish or weld surface shape. Strip samples have more design flexibility than standard tests, but must be designed to limit stress concentrations and effects of local bending. (author)

  16. Simplicimonas-like DNA in vaginal swabs of cows and heifers cross-reacting in the real-time PCR for T. foetus.

    Science.gov (United States)

    Frey, Caroline F; Müller, Norbert; Stäuber, Norbert; Marreros, Nelson; Hofmann, Larissa; Hentrich, Brigitte; Hirsbrunner, Gaby

    2017-04-15

    Cows on an alpine pasture were presented with severe signs of vaginitis. To rule out infection with Tritrichomonas foetus, vaginal swabs were taken and real-time PCR based on detection via fluorescence resonance energy transfer (FRET) probes and targeting the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA (rDNA) was performed. PCR was positive in 25 of totally 34 assessed cows. However, the melting profiles of the probes targeting the diagnostic PCR products differed from the T. foetus positive control. Subsequent sequencing of the amplicons revealed 91% identity to Simplicimonas sp. sequences deposited in GenBank™. Furthermore, there was no clear association between positive PCR result and presence of vaginitis. To investigate the distribution of this Simplicimonas-like organism in cows, more herds grazing on the same alpine pastures as well as unrelated cows were tested. In total, 133 cows and 16 heifers were sampled, 53 cows and 6 heifers even twice. Vaginitis was evident in 43 cows and 4 heifers. All-over-positivity of PCR was 44%, including nine tests performed on heifers. Melting peak analysis indicated Simplicimonas-like organisms in all positive samples. Culture attempts in bovine InPouch ™ TF failed. No association between a positive PCR result and the presence of vaginitis was found. This is, to the best of our knowledge, the first report on Simplicimonas-like DNA in vaginal swabs of female cattle. Our data suggest that when testing vaginal swabs of cattle by means of T. foetus PCR, false positive reactions due to Simplicimonas-like organisms may occur. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Comparison of plasmid and chromosomal omp1 gene-based PCR and two DNA extraction methods for diagnosing Chlamydia trachomatis in endocervical swab samples

    Directory of Open Access Journals (Sweden)

    Behrouz Taheri Beni

    2012-10-01

    Full Text Available Objective: To evaluate the effectiveness of boiling and proteolytic DNA extraction methods and also to compare the sensitivity of plasmid polymerase chain reaction (PCR and chromosomal omp1 gene PCR for genital Chlamydia trachomatis swab samples in women. Methods: 710 cervical swab samples were obtained from women with symptomatic genital infection at 11 gynecology and obstetric clinics located in Ahvaz, Iran. DNA extraction was performed using proteolysis and boiling manners for all samples. Plasmid PCR and chromosomal omp1 gene primary- and seminested-PCR were then performed separately on extracted DNA in boiling and proteolytic methods. Results: The prevalence of this infection was 17.6% as determined by plasmid-PCR, 13.2% by omp1-primary PCR and 15.8% by omp1-nested PCR. Sensitivities of boiling and proteolytic extraction-directed PCR were 93.6%, and 68.8%, respectively, which are significantly different (P=0.02. The sign of swab-induced bleeding was significantly found to be the most frequent among women infected with this bacterium (P=0.001 and had a sensitivity of 33.6% and a specificity of 80.5%. Conclusions: In order to obtain confident statistical results about sensitivity of each manner, in present study these evaluations were carried out for high numbers of samples (710 samples; high number of samples is statistical advantage of this study in comparing with other studies which were performed with low numbers of samples. Using boilingDNA extraction manner and targeting plasmid sequence for PCR can increase the sensitivity of C. trachomatis diagnosis.

  18. Occurrence of biflavones in leaves of Caesalpinia pyramidalis specimens

    Directory of Open Access Journals (Sweden)

    Marcus V. Bahia

    2010-01-01

    Full Text Available The chloroform partition of methanol extract of leaves of Caesalpinia pyramidalis was submitted to different chromatographic procedures which afforded besides agathisflavone and taxifolin, the minor biflavones loniflavone, amentoflavone, 5'- hydroxyamentoflavone and podocarpusflavone A. The structures of the compounds were established on the basis of NMR and MS data analysis. Besides, the content of biflavones of different specimens of C. pyramidalis, which are collected in different habitats of the Brazilian semi-arid region, was determinated by LC-APCI-MS analysis. These analysis demonstrated that only the specimens harvested in Bahia state showed collectively the presence of agathisflavone, amentoflavone, sequoiaflavone and podocarpusflavone A.

  19. Dataset of herbarium specimens of threatened vascular plants in Catalonia.

    Science.gov (United States)

    Nualart, Neus; Ibáñez, Neus; Luque, Pere; Pedrol, Joan; Vilar, Lluís; Guàrdia, Roser

    2017-01-01

    This data paper describes a specimens' dataset of the Catalonian threatened vascular plants conserved in five public Catalonian herbaria (BC, BCN, HGI, HBIL and MTTE). Catalonia is an administrative region of Spain that includes large autochthon plants diversity and 199 taxa with IUCN threatened categories (EX, EW, RE, CR, EN and VU). This dataset includes 1,618 records collected from 17(th) century to nowadays. For each specimen, the species name, locality indication, collection date, collector, ecology and revision label are recorded. More than 94% of the taxa are represented in the herbaria, which evidence the paper of the botanical collections as an essential source of occurrence data.

  20. Study of cavities in a creep crack growth test specimen

    OpenAIRE

    Jazaeri, H; Bouchard, P. J.; Hutchings, M. T.; Mamun, A. A.; Heenan, R K

    2016-01-01

    Small Angle Neutron Scattering (SANS) and Scanning Electron Microscopy (SEM) have been used to determine the degree of cavitation damage, of length scale 5-300 nm, associated with a creep crack grown in a compact tension specimen cut from a Type 316H stainless steel weldment. The specimen was supplied by EDF Energy as part of an extensive study of creep crack growth in the heat affected zone of reactor components. The creep crack propagates along a line 1.5 mm away from, and parallel to, the ...

  1. 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

  2. Antibacterial activity of marine culturable bacteria collected from a global sampling of ocean surface waters and surface swabs of marine organisms

    DEFF Research Database (Denmark)

    Gram, Lone; Melchiorsen, Jette; Bruhn, Jesper Bartholin

    2010-01-01

    The purpose of the present study was to isolate marine culturable bacteria with antibacterial activity and hence a potential biotechnological use. Seawater samples (244) and 309 swab samples from biotic or abiotic surfaces were collected on a global Danish marine research expedition (Galathea 3......). Total cell counts at the seawater surface were 5 × 105 to 106 cells/ml, of which 0.1–0.2% were culturable on dilute marine agar (20°C). Three percent of the colonies cultured from seawater inhibited Vibrio anguillarum, whereas a significantly higher proportion (13%) of colonies from inert or biotic...

  3. 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

  4. Apparatus for Testing Flat Specimens of Thermal Insulation

    Science.gov (United States)

    Fesmire, James E.; Augustynowicz, Stanislaw D.

    2005-01-01

    An apparatus has been developed to implement an improved method of testing flat-plate specimens of thermal-insulation materials for cryogenic application. The method includes testing under realistic use conditions that could include vacuum and mechanical loading at a pressure up to 70 psi (=0.48 MPa). The apparatus can accommodate a rigid or flexible specimen having thickness up to 1.25 in. (=3.2 cm) and diameters between 6 and 10 in. (about 15.2 and 25.4 cm, respectively). Typical test conditions include boundary temperatures between 77 K and 373 K and vacuum/interstitial gas filling at a pressure between 10(exp -6) torr (=1.3 x 10(exp -4) Pa) and 760 torr (atmospheric pressure =0.1 MPa). The interstitial gas could be N2, He, CO2, or any other suitable gas to which the insulation is expected to be exposed in use. Relative to prior apparatuses and testing methods, this apparatus and the testing method that it implements offer advantages of relative simplicity and ease of use. The basic principle of operation of the apparatus is that of boil-off calorimetry, using liquid nitrogen or any other suitable liquid that boils at a desired temperature below ambient temperature. Comparative rates of flow of heat through the thicknesses of the specimens (heat-leak rates) and apparent-thermal-conductivity values are obtained from tests of specimens. Absolute values of heat-leak rates and apparent thermal conductivities are computed from a combination of (1) the aforementioned comparative values and (2) calibration factors obtained by testing reference specimens of materials that have known thermal-insulation properties. The apparatus includes a full complement of temperature sensors, a vacuum pump and chamber, a monitoring and control system, and tools and fixtures that enable rapid and reliable installation and removal of specimens. A specimen is installed at the bottom of the vacuum chamber, and a cold-mass assembly that includes a tank is lowered into position above and

  5. Neurotransmitter transporters

    DEFF Research Database (Denmark)

    Gether, Ulrik; Andersen, Peter H; Larsson, Orla M

    2006-01-01

    The concentration of neurotransmitters in the extracellular space is tightly controlled by distinct classes of membrane transport proteins. This review focuses on the molecular function of two major classes of neurotransmitter transporter that are present in the cell membrane of neurons and....../or glial cells: the solute carrier (SLC)1 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of glutamate, and the SLC6 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of dopamine, 5-HT, norepinephrine, glycine and GABA....... Recent research has provided substantial insight into the structure and function of these transporters. In particular, the recent crystallizations of bacterial homologs are of the utmost importance, enabling the first reliable structural models of the mammalian neurotransmitter transporters...

  6. 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

  7. Characterization of Two Historic Smallpox Specimens from a Czech Museum

    Czech Academy of Sciences Publication Activity Database

    Pajer, P.; Dresler, J.; Kabickova, H.; Píša, L.; Aganov, P.; Fucik, K.; Elleder, Daniel; Hron, Tomáš; Kuželka, V.; Velemínský, P.; Klimentová, J.; Fučíková, A.; Pejchal, J.; Hrabáková, Rita; Beneš, V.; Rausch, T.; Dundr, P.; Pilin, A.; Čabala, R.; Hubálek, Martin; Stříbrný, J.; Antwerpen, M.H.; Meyer, H.

    2017-01-01

    Roč. 9, č. 8 (2017), č. článku 200. ISSN 1999-4915 Institutional support: RVO:68378050 ; RVO:67985904 ; RVO:61388963 Keywords : smallpox * variola virus * evolution * next generation suquencing * historic specimen * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.465, year: 2016

  8. Rate of occult specimen provenance complications in routine clinical practice.

    Science.gov (United States)

    Pfeifer, John D; Liu, Jingxia

    2013-01-01

    Occult specimen provenance complications (SPCs), which occur when there is an absence of any direct or indirect indication that a specimen switch or contamination may have occurred, constitute a significant patient safety and medical-legal problem because they can lead to misdiagnosis. However, the rate at which occult SPCs occur is unknown because, by definition, this category of errors is not identified by standard laboratory practices. In this study, we evaluated a data set comprising almost 13,000 prostate biopsies that were prospectively tested for specimen provenance errors as part of routine clinical practice. The frequency of occult type 1 errors (a complete transposition between patients) and type 2 errors (contamination of the patient's tissue with 1 or more unrelated patients) was 0.26% and 0.67%, respectively; every urology practice setting and surgical pathology laboratory type with a representative sample size experienced at least 1 type 1 and 1 type 2 error during the study period. Overall, the mean frequency of SPCs across practice settings was 0.22% for type 1 errors and 1.69% for type 2 errors. The type 1 rate showed no correlation with a surgical pathology laboratory setting or urologic practice group setting; the type 2 rate correlated solely with a surgical pathology laboratory setting. The occult SPC rate in this limited data set provides an estimate of the scope of the problem of potential misdiagnosis as a result of occult specimen provenance errors in routine clinical practice.

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

    African Journals Online (AJOL)

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

  10. Effect of erodent particles on the erosion of metal specimens

    Energy Technology Data Exchange (ETDEWEB)

    Razzaque, M. Mahbubur, E-mail: mmrazzaque@me.buet.ac.bd; Alam, M. Khorshed; Khan, M. Ishak, E-mail: ishak.buet@gmail.com [Department of Mechanical Engineering Bangladesh University of Engineering and Technology (BUET), Dhaka (Bangladesh)

    2016-07-12

    This paper presents the experimental results of the measurement of erosion rate of carbon steel specimens in sand water slurry system in a slurry pot tester. Sylhet sand has been sieved to get three sizes of erodent particles; namely, less than 250 micron, 250 to 590 micron and 590 to 1190 micron. Experiments are done with three sand concentrations (10%, 15% and 20%). The rate of erosion of the carbon steel specimens is measured as the loss of weight per unit surface area per unit time under the dynamic action of solid particles. The eroded surfaces of the specimens are examined using Scanning Electron Microscopy (SEM) to visualize the impact of the slurry of various conditions. It is seen that irrespective of the particle size the rate of erosion increases with the increase of slurry concentration. This increment of erosion rate at high concentration is high for large particles. High erosion rate is observed in case of large sand particles. In case of small and fine particles erosion rate is small because of low impact energy as well as the wastage of energy to overcome the hindrance of the finer particles before striking on the specimen surface.

  11. Comparison of three methods of collecting nasal specimens for ...

    African Journals Online (AJOL)

    Background: Nasopharyngeal aspiration (NPA) is used widely in the collection of nasal specimens for respiratory virus diagnosis. The method has limitations in relation to technical expertise, patient anxiety, and apparatus dependence. Nasal washing (NW) offers an alternative approach. Objective: To identify the merits of ...

  12. Isolation of Proteus mirabilis from Clinical Urogenital Specimens: A ...

    African Journals Online (AJOL)

    This retrospective study was designed to ascertain the epidemiological sources and antibiotic susceptibility patterns of Proteus mirabilis strains recovered from urogenital specimens in Jos University Teaching Hospital; (JUTH) over a five year period (Janurary 2000 – December 2004). Information on epidemiological and ...

  13. 50 CFR 31.12 - Sale of wildlife specimens.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Sale of wildlife specimens. 31.12 Section 31.12 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM WILDLIFE SPECIES MANAGEMENT Terms and Conditions of Wildlife...

  14. Natural Selection: Finding Specimens in a Natural History Collection

    NARCIS (Netherlands)

    Erp, M. van; Bosch, A.P.J. van den; Hunt, S.; Meij, M. van der; Dekker, R.; Lendvai, P.

    2011-01-01

    The natural history domain is rich in information. For hundreds of years, biodiversity researchers have collected specimens and samples, and meticulously recorded the how, what, and where of these objects of research. To retrace this information, however, deep knowledge of the collection and

  15. Is routine histopathology of tonsil specimen necessary? | Adoga ...

    African Journals Online (AJOL)

    Background: Tonsillar diseases are common in paediatric and adult otolaryngological practice. These diseases require tonsillectomy. Specimens are subjected to histopathology routinely in my institution for fear of infections and tumour without consideration for risk factors. The financial burden is on the patients and waste ...

  16. Cell-based quantification of molecular biomarkers in histopathology specimens.

    Science.gov (United States)

    Al-Kofahi, Yousef; Lassoued, Wiem; Grama, Kedar; Nath, Sumit K; Zhu, Jianliang; Oueslati, Ridha; Feldman, Michael; Lee, William M F; Roysam, Badrinath

    2011-07-01

    To investigate the use of a computer-assisted technology for objective, cell-based quantification of molecular biomarkers in specified cell types in histopathology specimens, with the aim of advancing current visual estimation and pixel-level (rather than cell-based) quantification methods. Tissue specimens were multiplex-immunostained to reveal cell structures, cell type markers, and analytes, and imaged with multispectral microscopy. The image data were processed with novel software that automatically delineates and types each cell in the field, measures morphological features, and quantifies analytes in different subcellular compartments of specified cells.The methodology was validated with the use of cell blocks composed of differentially labelled cultured cells mixed in known proportions, and evaluated on human breast carcinoma specimens for quantifying human epidermal growth factor receptor 2, estrogen receptor, progesterone receptor, Ki67, phospho-extracellular signal-related kinase, and phospho-S6. Automated cell-level analyses closely matched human assessments, but, predictably, differed from pixel-level analyses of the same images. Our method reveals the type, distribution, morphology and biomarker state of each cell in the field, and allows multiple biomarkers to be quantified over specified cell types, regardless of their abundance. It is ideal for studying specimens from patients in clinical trials of targeted therapeutic agents, for investigating minority stromal cell subpopulations, and for phenotypic characterization to personalize therapy and prognosis. © 2011 Blackwell Publishing Limited.

  17. 21 CFR 58.51 - Specimen and data storage facilities.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Specimen and data storage facilities. 58.51 Section 58.51 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL... storage facilities. Space shall be provided for archives, limited to access by authorized personnel only...

  18. Biochemical modulation in male specimens of Channa punctatus ...

    African Journals Online (AJOL)

    admin

    Biochemical modulation in male specimens of Channa punctatus (Bloch) under different habitats and seasons. C. P. Singh1, R. N. Ram2, Mohd. Danish2* and .... were analyzed using titrimetric method. (APHA, 1992) and temperature, pH, total dissolved solids and conductivity were measured using electronic digital meter.

  19. Automatic grinding apparatus to control uniform specimen thicknesses

    Science.gov (United States)

    Bryner, J.S.

    1981-01-07

    This invention is directed to a new and improved grinding apparatus comprisng: (1) a movable grinding surface; (2) a specimen holder; (3) a dislacing means for moving the holder and/or grinding surface toward one another; and (4) at least three means for limiting displacement of the holder to the grinding surface.

  20. Letter to the editor The number of urine specimens for ...

    African Journals Online (AJOL)

    contents/approach-to-the-adult-with-asymptomatic- bacteriuria. Letter to the editor. The number of urine specimens for bacteriological examination in women. Ertugrul Guclu, Tuba Damar, Oguz Karabay. 1. Department of Infectious Diseases and Clinical Microbiology, Sakarya University Faculty of Medicine, Sakarya, Turkey.

  1. Observation of Intralaminar Cracking in the Edge Crack Torsion Specimen

    Science.gov (United States)

    Czabaj, Michael W.; Ratcliffe, James G.; Davidson, Barry D.

    2013-01-01

    The edge crack torsion (ECT) test is evaluated to determine its suitability for measuring fracture toughness associated with mode III delamination growth onset. A series of ECT specimens with preimplanted inserts with different lengths is tested and examined using nondestructive and destructive techniques. Ultrasonic inspection of all tested specimens reveals that delamination growth occurs at one interface ply beneath the intended midplane interface. Sectioning and optical microscopy suggest that the observed delamination growth results from coalescence of angled intralaminar matrix cracks that form and extend across the midplane plies. The relative orientation of these cracks is approximately 45 deg with respect to the midplane, suggesting their formation is caused by resolved principal tensile stresses arising due to the global mode-III shear loading. Examination of ECT specimens tested to loads below the level corresponding to delamination growth onset reveals that initiation of intralaminar cracking approximately coincides with the onset of nonlinearity in the specimen's force-displacement response. The existence of intralaminar cracking prior to delamination growth onset and the resulting delamination extension at an unintended interface render the ECT test, in its current form, unsuitable for characterization of mode III delamination growth onset. The broader implications of the mechanisms observed in this study are also discussed with respect to the current understanding of shear-driven delamination in tape-laminate composites.

  2. Pathological findings in reduction mammoplasty specimens: A South ...

    African Journals Online (AJOL)

    The increased prevalence of carcinoma of the breast in these women suggests that they may ultimately develop ... Pathological findings in reduction mammoplasty specimens: A South African perspective .... Indeed, 'The primary intent of mammoplasty is cosmetic, but it is a medical procedure, taking place in a medical ...

  3. Fracture Mechanics Analysis of a Modified TSD Specimen

    DEFF Research Database (Denmark)

    Berggreen, Christian; Carlsson, Leif A.

    2008-01-01

    The Tilted Sandwich Debond (TSD) specimen has been recognized as a viable candidate for characterization of the face/core fracture resistance. Analysis, however, shows that the range of phase angles that can be realized by altering the tilt angle is quite limited. A parametric study however shows...

  4. Resistance to freezing and thawing of mortar specimens made from ...

    Indian Academy of Sciences (India)

    Resistance to freezing and thawing of mortar specimens made from sulphoaluminate–belite cement (M–SAB) is compared with that of mortars made from portland cement (M–PC). The results suggest that larger median radius of the pores and total porosity of M–SAB compared to those of M–PC are primarily caused by the ...

  5. Dimensioning of dog bone specimens and numerical analysis of the ...

    African Journals Online (AJOL)

    The effects of different fillet radii, clamp area dimensions, and pinhole loading through a hole located in the clamp area of a dog bone specimen were investigated using the Finite Element Analysis (FEA) software Abaqus. Changes in the fillet radius were shown to have little effect on the distribution and magnitude of the von ...

  6. Pathological findings in reduction mammoplasty specimens: A South ...

    African Journals Online (AJOL)

    Background: Preoperative, intraoperative and follow-up guidelines for managing occult carcinoma in reduction mammoplasty specimens are scant. Methods: We retrospectively analysed the records and pathology reports of 200 patients who had undergone reduction mammoplasty at two major public hospitals in ...

  7. specimens of patients with bloody diarrhoea in Mwanza, Tanzania

    African Journals Online (AJOL)

    Bacteriological cultures were done at the National Institute for Medical Research laboratory. .... Mwanza for culture. For optimal isolation ofS/rigc/lo and Salmonella species three different media and an enrichment medium were used. Stool specimens were inoculated .... antibiotics, the establishment of hygienic measures.

  8. Experiments on Methane Displacement by Carbon Dioxide in Large Coal Specimens

    Science.gov (United States)

    Liang, Weiguo; Zhao, Yangsheng; Wu, Di; Dusseault, Maurice B.

    2011-09-01

    changes in the microstructure of the coal itself. Artificial stimulation (e.g. hydraulic fracturing) to improve coalbed transport properties for either CO2 sequestration or enhanced coal bed methane recovery will be necessary. The interactions of large-scale induced fractures with the fabric at the scale of observable fissures and fractures in the laboratory specimens, as well as to the pore scale processes associated with adsorption and desorption, remain of profound interest and a great challenge.

  9. 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.

  10. The use of buccal swabs as a minimal-invasive method for detecting effects of pesticide exposure on enzymatic activity in common wall lizards.

    Science.gov (United States)

    Mingo, Valentin; Lötters, Stefan; Wagner, Norman

    2017-01-01

    Habitat loss and environmental pollution are among the main causes responsible for worldwide biodiversity loss. The resulting species and population declines affect all vertebrates including reptiles. Especially in industrialized countries, pollution by agrochemicals is of remarkable importance. Here, habitat loss has historically been associated with expansion of agriculture. Species persisting in such environments do not only need to cope with habitat loss, but more recently, also with chemical intensification, namely pesticide exposure. In this study, we examined effects of different fungicide and herbicide applications on the common wall lizard (Podarcis muralis) in grape-growing areas. We used three enzymatic biomarkers (GST, GR, AChE) and for the first time saliva from buccal swabs as a minimal-invasive sampling method for detection. Our results demonstrate absorption of substances by lizards and effects of pesticide exposure on enzymatic activities. Our findings are in accordance with those of previous laboratory studies, although samples were retrieved from natural habitats. We conclude that buccal swabs could become a useful tool for the detection of pesticide exposure in reptiles and have the potential to replace more invasive methods, such as organ extraction or cardiac puncture. This is an important finding, as reptiles are non-target organisms of pesticide applications, and there is a strong need to integrate them into pesticide risk assessments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. 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, Janine R; Piepel, Greg F; Amidan, Brett G; Hess, Becky M; Sydor, Michael A; Deatherage Kaiser, Brooke L

    2018-01-21

    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 coupon -1 ) 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. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  12. 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

    2017-12-13

    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.

  13. 49 CFR 40.153 - How does the MRO notify employees of their right to a test of the split specimen?

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false How does the MRO notify employees of their right... and the Verification Process § 40.153 How does the MRO notify employees of their right to a test of... his or her right to have the split specimen tested. You must also notify the employee of the...

  14. 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.

  15. Gene expression in intestinal mucosal biopsy specimens obtained from dogs with chronic enteropathy.

    Science.gov (United States)

    Wilke, Vicki L; Nettleton, Dan; Wymore, Meghan J; Gallup, Jack M; Demirkale, Cumhur Yusuf; Ackermann, Mark R; Tuggle, Chris K; Ramer-Tait, Amanda E; Wannemuehler, Michael J; Jergens, Albert E

    2012-08-01

    To characterize mucosal gene expression in dogs with chronic enteropathy (CE). 18 dogs with CE and 6 healthy control dogs. Small intestinal mucosal biopsy specimens were endoscopically obtained from dogs. Disease severity in dogs with CE was determined via inflammatory bowel index scores and histologic grading of biopsy specimens. Total RNA was extracted from biopsy specimens and microchip array analysis (approx 43,000 probe sets) and quantitative reverse transcriptase PCR assays were performed. 1,875 genes were differentially expressed between dogs with CE and healthy control dogs; 1,582 (85%) genes were downregulated in dogs with CE, including neurotensin, fatty acid-binding protein 6, fatty acid synthase, aldehyde dehydrogenase 1 family member B1, metallothionein, and claudin 8, whereas few genes were upregulated in dogs with CE, including genes encoding products involved in extracellular matrix degradation (matrix metallopeptidases 1, 3, and 13), inflammation (tumor necrosis factor, interleukin-8, peroxisome proliferator-activated receptor γ, and S100 calcium-binding protein G), iron transport (solute carrier family 40 member 1), and immunity (CD96 and carcinoembryonic antigen-related cell adhesion molecule [CEACAM] 18). Dogs with CE and protein-losing enteropathy had the greatest number of differentially expressed genes. Results of quantitative reverse transcriptase PCR assay for select genes were similar to those for microchip array analysis. Expression of genes encoding products regulating mucosal inflammation was altered in dogs with CE and varied with disease severity. Impact for Human Medicine-Molecular pathogenesis of CE in dogs may be similar to that in humans with inflammatory bowel disease.

  16. Comparison of dacron and nylon-flocked self-collected vaginal swabs and urine for the detection of Trichomonas vaginalis using analyte-specific reagents in a transcription-mediated amplification assay.

    Science.gov (United States)

    Jang, Dan; Gilchrist, Jodi; Portillo, Eder; Smieja, Marek; Toor, Ramandeep; Chernesky, Max

    2012-04-01

    To compare self-collected vaginal swab (SCVS) types and first-catch urine (FCU) to diagnose Trichomonas vaginalis using analyte-specific reagents designed to be used in a transcription-mediated amplification assay. A total of 241 women (group A) collected a FCU and a SCVS using a dacron swab (APTIMA collection kit). A second group of 289 women (group B) collected two SCVS using one dacron swab and one nylon-flocked swab. Of 75 young women (street youth) determined to be infected with T vaginalis only seven reported symptoms of vaginal discharge or irritation. Using a cutoff of 50,000 relative light units, the sensitivity and specificity was 97.2% and 97.6%, respectively for dacron SCVS compared with 41.7% and 100% for FCU in group A; 92.3% and 98.8% for dacron SCVS and 92.3% and 99.2% for flocked-nylon SCVS in group B. The assay tested 96 samples in 6 h. Dacron and nylon-flocked SCVS performed equally well and significantly better than FCU using analyte-specific reagents in the APTIMA transcription-mediated amplification assay. Either swab type could be used for self-collection.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Recently, vacuum-based preservation of surgical specimens has been proposed as a safe alternative to formalin fixation at the surgical theater. The method seems feasible from a practical point of view, but no systematic study has examined the effect of vacuum sealing alone with respect to tissue...... preservation. In this study, we therefore subjected tissue samples from 5 different organs to treatments with and without vacuum sealing and cooling at 4°C to study the effect of vacuum sealing of surgical specimens with respect to tissue preservation and compare it with the effect of cooling. No preserving...... effect of vacuum sealing was observed with respect to cellular morphology, detection of immunohistochemical epitopes, or RNA integrity. In contrast, storage at 4°C was shown to preserve tissue to a higher degree than storage at room temperature for all included endpoints, independently of whether...

  18. Study of Biological Pigments by Single Specimen Derivative Spectrophotometry

    Science.gov (United States)

    Goldstein, Jack M.

    1970-01-01

    The single specimen derivative (SSD) method provides an absolute absorption spectrum of a substance in the absence of a suitable reference. Both a reference and a measuring monochromatic beam pass through a single sample, and the specimen itself acts as its own reference. The two monochromatic beams maintain a fixed wavelength difference upon scanning, and the difference in absorbance of the two beams is determined. Thus, the resulting spectrum represents the first derivative of the conventional type absorption spectrum. Tissues and cell fractions have been examined at room and liquid N2 temperature and chromophoric molecules such as the mitochondrial cytochromes and blood pigments have been detectable in low concentrations. In the case of isolated cellular components, the observed effects of substrates and inhibitors confirm similar studies by conventional spectrophotometry. The extension of the SSD concept to the microscopic level has permitted the study of the tissue compartmentalization and function of cytochromes and other pigments within layered tissue. PMID:4392452

  19. Photorealistic Modeling of the Growth of Filamentous Specimens

    Science.gov (United States)

    Sedlář, Jiří; Flusser, Jan; Sedlářová, Michaela

    2007-12-01

    We present a new method for modeling the development of settled specimens with filamentous growth patterns, such as fungi and oomycetes. In phytopathology, the growth parameters of such microorganisms are frequently examined. Their development is documented repeatedly, in a defined time sequence, leaving the growth pattern incomplete. This restriction can be overcome by reconstructing the missing images from the images acquired at consecutive observation sessions. Image warping is a convenient tool for such purposes. In the proposed method, the parameters of the geometric transformation are estimated by means of the growth tracking based on the morphological skeleton. The result is a sequence of photorealistic artificial images that show the development of the specimen within the interval between observations.

  20. Photorealistic Modeling of the Growth of Filamentous Specimens

    Directory of Open Access Journals (Sweden)

    Michaela Sedlářová

    2008-02-01

    Full Text Available We present a new method for modeling the development of settled specimens with filamentous growth patterns, such as fungi and oomycetes. In phytopathology, the growth parameters of such microorganisms are frequently examined. Their development is documented repeatedly, in a defined time sequence, leaving the growth pattern incomplete. This restriction can be overcome by reconstructing the missing images from the images acquired at consecutive observation sessions. Image warping is a convenient tool for such purposes. In the proposed method, the parameters of the geometric transformation are estimated by means of the growth tracking based on the morphological skeleton. The result is a sequence of photorealistic artificial images that show the development of the specimen within the interval between observations.

  1. Preparation And Analysis Of Specimens Of Ablative Materials

    Science.gov (United States)

    Solomon, William C.

    1994-01-01

    Procedure for chemical analysis of specimens of silicone-based ablative thermal-insulation materials SLA-561 and MA25 involves acid digestion of specimens to prepare them for analysis by inductively-coupled-plasma/atomic-emission spectroscopy (ICP/AES). In comparison with atomic-absorption spectroscopy (AAS), ICP/AES is faster and more accurate than AAS. Results of analyses stored in data base, used to trace variations in concentrations of chemical elements in materials during long-term storage, and used in timely manner in investigations of failures. Acid-digestion portion of procedure applied to other thermal-insulation materials containing room-temperature-vulcanizing silicones and enables instrumental analysis of these materials.

  2. Design and Realization of Geographic Information System for Plant Specimens

    Directory of Open Access Journals (Sweden)

    Zhenran Gao

    2016-03-01

    Full Text Available The thesis research work is based on adopting the combination of theory and technology research. For the unique characteristics of bambusoideae in yunnan province, analyses the characteristics, value and the present situation of resources of bambusoideae plant resources in yunnan province. According to the system requirements of the specimen of bambusoideae in Yunnan province, by Microsoft. Net framework platform, a collection of Web services and ASP.NET technology, based on the data of Microsoft SQL Server2008 and ADO.NET technology support, selecting desktop GIS Arc GIS platform (Arc GIS Desktop and server (Arc GIS Server as a system of GIS secondary development of GIS, and using developed tools of Microsoft Visual Studio 2010 Visual, Finally, the information system of plant specimen which based on GIS integration development of bambusoideae is finished .

  3. A COMPLETE SPECIMEN OF MYSTRIOSUCHUS (REPTILIA, PHYTOSAURIA FROM THE NORIAN (LATE TRIASSIC OF LOMBARDY (NORTHERN ITALY

    Directory of Open Access Journals (Sweden)

    EMANUELE GOZZI

    2003-11-01

    Full Text Available A complete and nearly articulated new phytosaur specimen is described in detail. The skeleton, about 4 metres long, has been collected from the uppermost level of the Calcare di Zorzino (Norian, Upper Triassic in the small quarry of Endenna (Bergamo, Northern Italy. Available characters of the skull allow assignment of this long snouted, uncrested phytosaur to Mystriosuchus planirostris Von Meyer 1863. The postcranial anatomy, detailed here for the first time for this species, suggests a stronger adaptation to aquatic life in Mystriosuchus than in other phytosaurs, and may increase available data to improve our knowledge of the systematic relationships among phytosaurs. The discovery of this nearly complete skeleton in a marine intraplatform basin suggests that a short post-mortem transport of the carcass occurred and thus this phytosaur may have lived whether in a fresh water environment or in a shallow marine habitat, close to emerged lands. 

  4. Dataset of herbarium specimens of threatened vascular plants in Catalonia

    OpenAIRE

    Neus Nualart; Neus Ibáñez; Pere Luque; Joan Pedrol; Lluís Vilar; Roser Guàrdia

    2017-01-01

    This data paper describes a specimens’ dataset of the Catalonian threatened vascular plants conserved in five public Catalonian herbaria (BC, BCN, HGI, HBIL and MTTE). Catalonia is an administrative region of Spain that includes large autochthon plants diversity and 199 taxa with IUCN threatened categories (EX, EW, RE, CR, EN and VU). This dataset includes 1,618 records collected from 17th century to nowadays. For each specimen, the species name, locality indication, collection date, collecto...

  5. Innovations in macroscopic evaluation of pancreatic specimens and radiologic correlation

    Directory of Open Access Journals (Sweden)

    Charikleia Triantopoulou

    2016-01-01

    Full Text Available The purpose of this study was to evaluate the feasibility of a novel dissection technique of surgical specimens in different cases of pancreatic tumors and provide a radiologic pathologic correlation. In our hospital, that is a referral center for pancreatic diseases, the macroscopic evaluation of the pancreatectomy specimens is performed by the pathologists using the axial slicing technique (instead of the traditional procedure with longitudinal opening of the main pancreatic and/or common bile duct and slicing along the plane defined by both ducts. The specimen is sliced in an axial plane that is perpendicular to the longitudinal axis of the descending duodenum. The procedure results in a large number of thin slices (3–4 mm. This plane is identical to that of CT or MRI and correlation between pathology and imaging is straightforward. We studied 70 cases of suspected different solid and cystic pancreatic tumors and we correlated the tumor size and location, the structure—consistency (areas of necrosis—hemorrhage—fibrosis—inflammation, the degree of vessels’ infiltration, the size of pancreatic and common bile duct and the distance from resection margins. Missed findings by imaging or pitfalls were recorded and we tried to explain all discrepancies between radiology evaluation and the histopathological findings. Radiologic-pathologic correlation is extremely important, adding crucial information on imaging limitations and enabling quality assessment of surgical specimens. The deep knowledge of different pancreatic tumors’ consistency and way of extension helps to improve radiologists’ diagnostic accuracy and minimize the radiological-surgical mismatching, preventing patients from unnecessary surgery.

  6. Solution Preserves Nucleic Acids in Body-Fluid Specimens

    Science.gov (United States)

    Pierson, Duane L.; Stowe, Raymond P.

    2004-01-01

    A solution has been formulated to preserve deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in specimens of blood, saliva, and other bodily fluids. Specimens of this type are collected for diagnostic molecular pathology, which is becoming the method of choice for diagnosis of many diseases. The solution makes it possible to store such specimens at room temperature, without risk of decomposition, for subsequent analysis in a laboratory that could be remote from the sampling location. Thus, the solution could be a means to bring the benefits of diagnostic molecular pathology to geographic regions where refrigeration equipment and diagnostic laboratories are not available. The table lists the ingredients of the solution. The functions of the ingredients are the following: EDTA chelates divalent cations that are necessary cofactors for nuclease activity. In so doing, it functionally removes these cations and thereby retards the action of nucleases. EDTA also stabilizes the DNA helix. Tris serves as a buffering agent, which is needed because minor contaminants in an unbuffered solution can exert pronounced effects on pH and thereby cause spontaneous degradation of DNA. SDS is an ionic detergent that inhibits ribonuclease activity. SDS has been used in some lysis buffers and as a storage buffer for RNA after purification. The use of the solution is straightforward. For example, a sample of saliva is collected by placing a cotton roll around in the subject's mouth until it becomes saturated, then the cotton is placed in a collection tube. Next, 1.5 mL of the solution are injected directly into the cotton and the tube is capped for storage at room temperature. The effectiveness of the solution has been demonstrated in tests on specimens of saliva containing herpes simplex virus. In the tests, the viral DNA, as amplified by polymerase chain reaction, was detected even after storage for 120 days.

  7. Evaluation of miniature tensile specimen fabrication techniques and performance

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, M.L. [Pacific Northwest Lab., Richland, WA (United States); Blotter, M.A.; Edwards, D.J. [Missouri Univ., Rolla, MO (United States)

    1992-01-01

    The confident application of miniature tensile specimens requires adequate control over their fabrication and is facilitated by automated test and analysis techniques. Three fabrication processes -- punching, chemical, milling, and electrical discharge machining (EDM) -- were recently evaluated, leading to the replacement of the previously used punching technique with a wire EDM technique. The automated data acquisition system was upgraded, and an interactive data analysis program was developed.

  8. Enteropathogenic bacteria isolated from specimens of patients with diarrhea

    OpenAIRE

    Salary M

    1997-01-01

    Acute infectious gastroenteritis is one of the most common infectious diseases of humans in the world. Diarrheal disease still ranks very high as a major cause of illness and death especially in developing nations. This study has been carried out to investigate enteropathogenic bacteria isolated from 2517 specimens of patients with diarrhea. The results obtained are as follow: Salmonella typhimurium: 6 cases 3.1 percent, Salmonella havana: 5 cases 2.6 percent, Shigella dysenteriae: 12 cases 6...

  9. Museum specimen data predict crop damage by tropical rodents

    OpenAIRE

    Sánchez-Cordero, Víctor; Martínez-Meyer, Enrique

    2000-01-01

    Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rod...

  10. The management of incidental findings of reduction mammoplasty specimens

    OpenAIRE

    Goodwin, Jessica T.; DeCroff, Chantelle; Dauway, Emilia; Sybenga, Amelia; Mahabir, Raman C

    2013-01-01

    Reduction mammoplasty is one of the most commonly performed procedures in plastic surgery. Occasionally, there are findings reported by pathologists that are unfamiliar to the treating surgeon. The aim of the present study was to determine the types of pathologies encountered in reduction mammoplasty specimens. From this list of diagnoses, a best practice guideline for management will be organized to better assist plastic surgeons in the management of patients with incidental findings on path...

  11. NEW TRIASSIC ASTEROIDEA (ECHINODERMATA SPECIMENS AND THEIR EVOLUTIONARY SIGNIFICANCE

    Directory of Open Access Journals (Sweden)

    DANIEL B. BLAKE

    2017-04-01

    Full Text Available The Paleozoic-Mesozoic transition saw the disappearance of asteroid stem groups and the ascent of the crown group, but late Paleozoic and Triassic asteroids are rare and transition events are poorly documented. Three new Middle and Late Triassic specimens augment existing data; included are a specimen of Trichasteropsis weissmanni from Germany, a specimen of Trichasteropsis? sp. indet. from Italy, and a possible member of the extant Poraniidae from Slovenia. Presence of a small ossicle at the interbrachial midline and adjacent to the marginal series of the new T. weissmanni specimen is consistent with similar expressions not only of other trichasteropsids but also occurrence of two interbrachial ossicles in Paleozoic, stem-group asterozoans; presence is in turn consistent with a hypothesis of derivation of the axillary/odontophore coupling from two ossicles rather than direct derivation of the crown-group odontophore from a single stem-group axillary. Morphology of Trichasteropsis? sp. indet., including, for example, the evenly-tapering arms are reminiscent of those of diverse crown-group asteroids whereas the enlarged distal arms of T. weissmanni are unique, the morphology of T? sp. indet. thereby potentially indicative of a plesiomorphic, stemward positioning within the Trichasteropsiidae. The range of the Poraniidae is tentatively extended to the Carnian. Similarities shared by the Poraniidae and the Trichasteropsiidae suggest stemward positioning within crown-group diversification; however, known Triassic fossils do not appear closely related to extant taxa identified in recent molecular studies as basal within the crown-group. A temperate climate is suggested as preferred by the Triassic asteroids rather than a tropical, warmer one.

  12. Histopathological Study of Uterine and Cervical Lesions in Hysterectomy Specimens.

    Directory of Open Access Journals (Sweden)

    Dr.Varsha Dhuliya

    2016-12-01

    Full Text Available Background: The adult nulliparous uterus is a hollow, pear shaped organ that weights 40-80 grams. It is divided into the Cervix and Corpus. The uterus being a vital reproductive and hormone-responsive organ, is subjected to a variety of physiological changes and benign and malignant disorders. Hysterectomy is the most common major gynecological procedure in the world. It can be done through either abdominal or vaginal route. Aims and objectives: The present study was aimed at detailed histopathological evaluation of all lesion of hysterectomy specimen Material and methods: This was a retrospective study of the gross and histopathological findings of uterus and cervix in 150 hysterectomy specimens received in the pathology department, B. J. Medical college, Ahmedabad during the period from July to December 2015.The hysterectomy specimens received were fixed in 10% formalin for 24 hours, were examined grossly and necessary sections were obtained. The tissue pieces were then processed in automated tissue processor , well labeled paraffin blocks were made. Sections were cut with the help of microtome and were stained routinely by Hematoxylin & Eosin stain and special stains wherever necessary. Sections were examined with the help of light microscopy. Results: Peak age group of hysterectomy was 41-50 years. Most common pathology found was uterine leiomyomas in 55 cases and next to it was adenomyosis. In cervix most common finding was chronic cervicitis in 116 cases. Conclusion: Most common benign lesion in uterus is leiomyoma followed by adenomyosis and in cervix it is chronic cervicitis in hysterectomy specimens received in our department.

  13. Instrumented Impact Testing: Influence of Machine Variables and Specimen Position

    Energy Technology Data Exchange (ETDEWEB)

    Lucon, E.; McCowan, C. N.; Santoyo, R. A.

    2008-09-15

    An investigation has been conducted on the influence of impact machine variables and specimen positioning on characteristic forces and absorbed energies from instrumented Charpy tests. Brittle and ductile fracture behavior has been investigated by testing NIST reference samples of low, high and super-high energy levels. Test machine variables included tightness of foundation, anvil and striker bolts, and the position of the center of percussion with respect to the center of strike. For specimen positioning, we tested samples which had been moved away or sideways with respect to the anvils. In order to assess the influence of the various factors, we compared mean values in the reference (unaltered) and altered conditions; for machine variables, t-test analyses were also performed in order to evaluate the statistical significance of the observed differences. Our results indicate that the only circumstance which resulted in variations larger than 5 percent for both brittle and ductile specimens is when the sample is not in contact with the anvils. These findings should be taken into account in future revisions of instrumented Charpy test standards.

  14. Banking Brain Tumor Specimens Using a University Core Facility.

    Science.gov (United States)

    Bregy, Amade; Papadimitriou, Kyriakos; Faber, David A; Shah, Ashish H; Gomez, Carmen R; Komotar, Ricardo J; Egea, Sophie C

    2015-08-01

    Within the past three decades, the significance of banking human cancer tissue for the advancement of cancer research has grown exponentially. The purpose of this article is to detail our experience in collecting brain tumor specimens in collaboration with the University of Miami/Sylvester Tissue Bank Core Facility (UM-TBCF), to ensure the availability of high-quality samples of central nervous system tumor tissue for research. Successful tissue collection begins with obtaining informed consent from patients following institutional IRB and federal HIPAA guidelines, and it needs a well-trained professional staff and continued maintenance of high ethical standards and record keeping. Since starting in 2011, we have successfully banked 225 brain tumor specimens for research. Thus far, the most common tumor histology identified among those specimens has been glioblastoma (22.1%), followed by meningioma (18.1%). The majority of patients were White, non-Hispanics accounting for 45.1% of the patient population; Hispanic/Latinos accounted for 23%, and Black/African Americans accounted for 14%, which represent the particular population of the State of Florida according to the 2010 census data. The most common tumors found in each subgroup were as follows: Black/African American, glioblastoma and meningioma; Hispanic, metastasis and glioblastoma; White, glioblastoma and meningioma. The UM-TBCF is a valuable repository, offering high-quality tumor samples from a unique patient population.

  15. Processing and Quality Evaluation of Additive Manufacturing Monolayer Specimens

    Directory of Open Access Journals (Sweden)

    Christiane Wendt

    2016-01-01

    Full Text Available Although its importance has increased significantly, Additive Manufacturing is not yet a fully accepted industrial manufacturing process for load-carrying parts. The future success of the process group depends on its standardization. This work proposes a methodology for the design, manufacturing, and quality evaluation of specimens manufactured by Fused Layer Modeling that are composed of only one layer (so-called monolayers. The processing methodology and properties of monolayers have not been studied systematically yet. A first systematic design of monolayers for mechanical testing is presented. Rectangular and circular monolayers adapted to the loads of tensile and compression testing are manufactured using different trajectory strategies. Frequently occurring macro- and microgeometrical defects are evaluated and categorized in order to optimize the part quality. This work also studies the effect of some manufacturing parameters such as the gap between print head and machine bed, trajectory strategy, bed leveling, and temperatures on part quality. The most suitable specimens are tested mechanically in tensile or compression tests. In the case of study, tensile strength values are only 8.6% lower than the values for reference tests on the unextruded filament. However, the properties deviate more strongly for compression tests which may be due to the selected specimen geometry.

  16. Antarctic environmental specimen bank. A tool for chemical monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Soggia, F.; Dalla Riva, S.; Abelmoschi, M.L.; Frache, R. [Genoa Univ., Genoa (Italy). Dipt. di Chimica e Chimica Industriale

    2000-02-01

    The work illustrates the project on Antarctic Environmental Specimen Bank (BCAA), which is an integral part of the Italian project on the micropollutants chemistry (sector on chemical contamination of the Italian Antarctic Research program, PNRA), begun in 1994 when the BCAA was installed in the department of chemistry and industrial chemistry (Genoa University, Italy). Its objective underlines an emphasis on environmental chemistry and the establishment of baselines similar to the approaches followed by the other environmental specimen banks, begun at the end of Sixties with the aim of long-term storage of representative environmental specimens in order to study the presence and the evolution of dangerous substances, but focus on the chemical characterization of samples. [Italian] Il lavoro illustra le finalita' del Progetto su una Banca Campioni Ambientali Antartici (BCAA), che e' parte integrante del progetto Chmica dei microinquinannti del Settore Contaminazione chimica del Programma Nazionale di ricerche in Antartide (ONRA), nata nel 1994 presso il dipartimento di chimicia e chimica industriale dell'universita' di Genova. A differenza di altri progetti internazionali che enfatizzano gli aspetti biologici, ecologici e medici, il progetto BCAA enfatizza la chimica ambientale.

  17. Frequency of adenomyosis in hysterectomy specimens performed for benign indications

    Directory of Open Access Journals (Sweden)

    bulent cakmak

    2012-09-01

    Results: Adenomyosis frequency was determined as 11.7% (17 of 149 patients received for the elavuation for this study. There was no statistically significance in terms of ages among the cases with or without adenomyosis (49.4+/-8.3 vs 50.5+/-9.7 (p>0.05. Similarly there was no statistically significance between two groups in the number of pregnancy and parous (p>0.05. Adenomyosis was determined as 13.2% in hysterectomy specimens performed for leiomyoma and again it was determined as 17.8% in hysterectomy specimens performed for refracter menorrhagia. There was no statistically significance between two indication groups for the sake of being determined of adenomyosis hystopathologically in hysterectomy specimens (p>0.05. Conclusion: Adenomyosis can be seen in patients with leiomyoma and menorrhagia. So the possibility of adenomyosis detection should not be forgotten when the treatment is planned for the cases with leiomyoma and menorrhagia. [J Contemp Med 2012; 2(3.000: 158-161

  18. Development of a quantitative real time PCR assay to detect and enumerate Escherichia coli O157 and O26 serogroups in bovine recto-anal swabs.

    Science.gov (United States)

    Lawal, Dolapo; Burgess, Catherine; McCabe, Evonne; Whyte, Paul; Duffy, Geraldine

    2015-07-01

    Escherichia coli O157 and O26 shedding patterns in cattle are known to vary widely. To address gaps in the understanding of the underlying factors which impact on shedding dynamics, sensitive and rapid quantitative methods which can be applied in surveillance studies on cattle are required. Current approaches for enumeration of verocytotoxigenic E. coli (VTEC) in cattle faeces are based on direct plating onto selective agars, most probable number (MPN) or real time PCR applied directly to faecal samples, all of which have limitations in terms of the labour involved or their sensitivity. The objective of this study was to develop a sensitive real time quantitative PCR assay, to quantify O157 and O26 in bovine recto-anal junction (RAJ) swabs. The approach was to target serogroup specific genes rfbE and wzx, and to couple a short enrichment, with the use of a standard calibration curve relating real time PCR cycle threshold (Ct) values against the initial concentration of the pathogen in the sample. Following initial experiments in broth culture, a 5h enrichment in modified tryptone soya broth with novobiocin (20 mg/l) (mTSBn) was found to be optimal, and a linear correlation between inocula (Log10 1 to 6 CFU ml(-1)) and the PCR Ct values for both E. coli O157 (R(2)=0.99, rsd=0.58) and E. coli O26 (R(2)=0.99, rsd=0.44) was confirmed. The developed method was then applied to bovine RAJ swab samples (n=153), which were inoculated with E. coli O157 or O26 (Log10 1 to 7 CFU swab(-1)). Calibration curves yielded correlations for E. coli O157 of R(2)=0.86, rsd=0.72 and for O26 (R(2)=0.88, rsd=0.69). In conclusion, a sensitive method for detection and enumeration of two significant VTEC serogroups in bovine RAJ samples has been developed and validated, and will support studies on the bovine shedding dynamics of these pathogens in cattle. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. 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

  20. Sediment Transport

    DEFF Research Database (Denmark)

    Liu, Zhou

    Flow and sediment transport are important in relation to several engineering topics, e.g. erosion around structures, backfilling of dredged channels and nearshore morphological change. The purpose of the present book is to describe both the basic hydrodynamics and the basic sediment transport...... mechanics. Chapter 1 deals with fundamentals in fluid mechanics with emphasis on bed shear stress by currents, while chapter 3 discusses wave boundary layer theory. They are both written with a view to sediment transport. Sediment transport in rivers, cross-shore and longshore are dealt with in chapters 2...

  1. The Venice specimen of Ouranosaurus nigeriensis (Dinosauria, Ornithopoda

    Directory of Open Access Journals (Sweden)

    Filippo Bertozzo

    2017-06-01

    Full Text Available Ouranosaurus nigeriensis is an iconic African dinosaur taxon that has been described on the basis of two nearly complete skeletons from the Lower Cretaceous Gadoufaoua locality of the Ténéré desert in Niger. The entire holotype and a few bones attributed to the paratype formed the basis of the original description by Taquet (1976. A mounted skeleton that appears to correspond to O. nigeriensis has been on public display since 1975, exhibited at the Natural History Museum of Venice. It was never explicitly reported whether the Venice specimen represents a paratype and therefore, the second nearly complete skeleton reported in literature or a third unreported skeleton. The purpose of this paper is to disentangle the complex history of the various skeletal remains that have been attributed to Ouranosaurus nigeriensis (aided by an unpublished field map of the paratype and to describe in detail the osteology of the Venice skeleton. The latter includes the paratype material (found in 1970 and collected in 1972, with the exception of the left femur, the right coracoid and one manus ungual phalanx I, which were replaced with plaster copies, and (possibly other manus phalanges. Some other elements (e.g., the first two chevrons, the right femur, the right tibia, two dorsal vertebrae and some pelvic bones were likely added from other individual/s. The vertebral column of the paratype was articulated and provides a better reference for the vertebral count of this taxon than the holotype. Several anatomical differences are observed between the holotype and the Venice specimen. Most of them can be ascribed to intraspecific variability (individual or ontogenetic, but some are probably caused by mistakes in the preparation or assemblage of the skeletal elements in both specimens. The body length of the Venice skeleton is about 90% the linear size of the holotype. Osteohistological analysis (the first for this taxon of some long bones, a rib and a dorsal

  2. 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.

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

    DEFF Research Database (Denmark)

    Datcu, Raluca; Gesink, Dionne; Mulvad, Gert

    2014-01-01

    . 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...

  4. Influence of gross specimen sampling on the incidence of incidental prostatic carcinoma in cystoprostatectomy specimens of patients with bladder carcinoma

    Directory of Open Access Journals (Sweden)

    Jernej Mlakar

    2016-05-01

    Full Text Available Reported prostate cancer incidence rates vary greatly among cystoprostatectomy samples. We investigated how the thoroughness of prostate sampling influences prostatic carcinoma incidence in bladder cancer patients. In a retrospective study, 313 cystoprostatectomy cases of urinary bladder carcinoma were analysed for the presence of concurrent prostatic carcinoma. Patients were divided into two groups: patients who had undergone the operation before and after 2007, when a policy of preferably complete prostate sampling in cystoprostatectomy specimens was introduced at our institution. Cases processed after the 2007 recommended sampling changes had a significantly higher rate of incidental prostatic carcinoma and clinically significant prostatic carcinoma than the pre-2007 group (p < 0.0001 and p = 0.003, respectively. Complete prostate processing in cystoprostatectomy specimens results in a higher incidence of incidental prostatic carcinoma than with partial processing. More patients with clinically significant prostate cancer are consequently discovered. In conclusion, we believe that complete prostate sampling should be mandatory.

  5. Physical and Hydraulic Properties of Rock Specimens from Grimsel Test Site, Switzerland

    Science.gov (United States)

    Zhang, M.; Takeda, M.

    2007-12-01

    The Grimsel Test Site (GTS) is located at an altitude of 1730 meters in the granite rock of Aar Massif in central Switzerland. It lies at a depth of around 450 meters beneath the surface and was established over 20 years ago by the National Cooperative for the Disposal of Radioactive Waste (Nagra) as a center for underground Research and Development (R&D) supporting a wide range of related research projects. Among many of them, an international cooperative project defined as the Long Term Diffusion (LTD) has been performing to obtain quantitative information on matrix diffusion in rock strata under in-situ conditions. A set of laboratory experiments is also planed to determine the physical, hydraulic and diffusive transport properties of rock specimens taken from the same test site. In this poster, we present the preliminary results of both physical and hydraulic properties of the rock specimens being tested, including the bulk density, porosity, specific surface area and pore distribution, microstructure, P and S wave velocities, electrical resistivity, air and water permeabilities. The results obtained in this study indicate that: 1) The porosity and wave velocities of Grimsel granite are relatively low compared to the average values of igneous rocks indicating that micro-cracks can potentially exist within grain minerals. 2) The air and water permeabilities obtained from the air and water permeability tests are consistent that illustrates the accuracy of both experiments. 3) Permeability is not a simple function of effective confining pressure. It is very sensitive to confining pressure especially at low pressure levels. Besides, the permeability is hysteretic depending on confining pressure, pore pressure and stress history. 4) Similar to the hydraulic properties, diffusive transport properties of rock specimens can also be significantly affected by the confining pressure conditions. Laboratory diffusion tests considering the effects of stress conditions are

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    The presence of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals and the community is a serious problem. Accordingly, a comprehensive plan has been implemented in the County of Vejle, Denmark, to identify colonised and/or infected individuals and to control the spread of MRSA. Since...... 2005, all patients and healthcare personnel have been screened for MRSA colonisation, involving analysis of 300-400 samples daily. To deal with this number of samples, a PCR-based method customised for high-throughput analysis and a system for fast reporting of MRSA carrier status were developed. Swab...... samples were incubated overnight in a selective tryptone soya broth and were analysed by PCR the following day. Using this strategy, non-colonised individuals were identified within 24 h, while MRSA-positive samples were analysed further by traditional microbiological methods to determine the resistance...

  7. Viral load of equine herpesviruses 2 and 5 in nasal swabs of actively racing Standardbred trotters: Temporal relationship of shedding to clinical findings and poor performance.

    Science.gov (United States)

    Back, Helena; Ullman, Karin; Treiberg Berndtsson, Louise; Riihimäki, Miia; Penell, Johanna; Ståhl, Karl; Valarcher, Jean-François; Pringle, John

    2015-09-30

    The equine gamma herpesviruses 2 and 5 (EHV-2 and -5) have frequently been observed in the equine population and until recently presumed low to nonpathogenic. However, recent reports linking presence of equine gamma herpesviruses with clinical signs of mild to severe lung disease, suggest that the role of these viruses in respiratory disease and poor performance syndrome is still unclear. Moreover, baseline data regarding the temporal pattern of shedding of EHV-2 and EHV-5 within stables and within individual actively racing horses have been lacking. In a prospective longitudinal study, we followed elite racing Standardbred trotters at monthly intervals for 13 months, to investigate whether the amount of EHV-2 and EHV-5 shedded in nasal secretions varied over time within and between individual horses. Sixty-six elite horses were investigated by analyzing nasal swabs and serum samples, a health check and evaluation of athletic performance monthly during the study period. Nasal swabs were analyzed with two newly developed qPCR assays for EHV-2 and EHV-5, respectively. Of 663 samples, 197 (30%) were positive for EHV-2 and 492 (74%) positive for EHV-5. Furthermore, 176 (27%) of the samples were positive for both EHV-2 and EHV-5 simultaneously. There was considerable variation in the amount and frequency of shedding of EHV-2 and EHV-5 within and between individual horses. Viral load varied seasonally, but neither EHV-2 nor EHV-5 viral peaks were associated with clinical respiratory disease and/or poor performance in racing Standardbred trotters. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. The detection and antimicrobial susceptibility profile of Shigella isolates from meat and swab samples at butchers' shops in Gondar town, Northwest Ethiopia.

    Science.gov (United States)

    Garedew, Legesse; Hagos, Zenabu; Zegeye, Bidir; Addis, Zelalem

    2016-01-01

    Food borne pathogens are major causes of deaths, illnesses and billions of dollars of expenses. The burden of food borne illness is worsened by the ever increasing rate of antimicrobial resistance microbes. Shigella, a bacterial pathogen associated with food, is reported to account for higher prevalence rates of food borne illness in different settings. A cross-sectional study was conducted from February 10 to June 30, 2013, at the butcher houses of Gondar town in the Northwest of Ethiopia to assess the prevalence and antimicrobial susceptibility pattern of Shigella. Cattle raw meat and swab samples from selected critical control points, including knives, chopping boards, and the hands and noses of butchers, were collected and analyzed. The identification of Shigella was carried out using colony characteristics, the Gram reaction, and biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method. The overall hygienic status of the butcher shops was also assessed using a checklist. An observational analysis revealed that the sanitary condition of the butcher shops and their premises was poor. Of 306 samples screened, 10.5% were positive for Shigella. Approximately 7.4% of meat samples and 10.2% of swab samples were contaminated with Shigella. Out of the total Shigella isolates, 90.6%, 46.9%, 18.8% and 9.4% were resistant to ampicillin, amoxicillin, ceftriaxone and tetracycline, respectively. A multidrug resistance pattern was recorded in 27.8% of the isolates. In conclusion, the safety of meat sold at Gondar butchers houses was poor. The identified Shigella isolates showed high levels of drug resistance and multidrug resistance patterns for commonly used antimicrobials in veterinary and human medicine. Practicing wise use of antimicrobials and strict sanitary interventions at different critical control points is strongly recommended, in addition to further in-depth studies to prevent unprecedented consequences from

  9. Self-taken vaginal swabs versus clinician-taken for detection of candida and bacterial vaginosis: a case-control study in primary care.

    Science.gov (United States)

    Barnes, Pam; Vieira, Rute; Harwood, Jayne; Chauhan, Mayur

    2017-12-01

    Vaginal discharge and vulvitis are common presenting symptoms in general practice. Few studies have specifically looked at the validity of self-taken low vulvovaginal swabs (LVS) for the diagnosis of vulvovaginal candidiasis (VVC) and bacterial vaginosis (BV). To assess if patient self-taken LVS are a valid alternative to clinician-taken high vaginal swabs (HVS) for the detection of VVC and BV. Case-control study with the patient acting as their own control in an urban sexual health centre in Newcastle upon Tyne, UK. Females aged 16-65 years attending with symptomatic vaginal discharge, vulval irritation, genital pain, and an offensive genital smell were recruited into the study. Participants took a self-taken LVS before vaginal examination, during which a clinician took an HVS (reference standard). Main outcome measures were the diagnosis of BV or VVC infection. A total of 104 females were enrolled. Of those, 45 were diagnosed with VVC and 26 with BV. The sensitivities of self-taken LVS for VVC and BV were 95.5% and 88.5% respectively. Cohen's κ coefficient showed 'strong agreement' for the detection of both VVC and BV. Vulval itching was the most common symptom associated with VVC (69%), whereas 50% of females diagnosed with BV presented with an offensive discharge. Both symptoms had poor positive predictive values (0.63 and 0.50, respectively). Self-taken LVS appears to be a valid alternative to clinician-taken HVS for detecting VVC and BV infections. Symptoms were found to be a poor indicator of underlying infection. © British Journal of General Practice 2017.

  10. Evaluation of Simplexa™ Group A Strep Direct Kit compared to Hologic® Group A streptococcal direct assay for detection of Group A Streptococcus (GAS) in throat swabs.

    Science.gov (United States)

    Church, Deirdre L; Lloyd, Tracie; Larios, Oscar; Gregson, Daniel B

    2018-01-05

    Diagnosis of bacterial pharyngitis is confirmed by detection of Group A Streptococcus (GAS) in patient throat samples. Testing of throat samples has historically relied on culture but new molecular methods allow much faster test turnaround time (i.e., same day vs. 48-72h for culture). Our laboratory uses the Hologic® GAS Direct (GASD) assay for screening more than 125,000 throat samples per annum. Simplexa™ GAS Direct is a new real-time PCR (qPCR) assay that does not require initial DNA extraction. Performance of Simplexa qPCR was compared to GASD. 289 throat swabs were collected from patients attending ambulatory clinics in Calgary. A total of 60 (20.8%) of the samples were initially GAS positive by either method; 54 by both methods, 4 by Simplex qPCR alone, and 2 by GASD alone. An in-house PCR using a unique GAS primer set was used to resolve the 6 discrepant results. Overall, GASD compared to Simplexa qPCR had sensitivity, specificity, positive predictive value and negative predictive value of 93.1% vs 100%, 100% vs. 100%, 100% vs. 100% and 98.31% vs. 100% respectively. Implementation of Simplexa qPCR in our laboratory setting would cost more but allow the high sample volume to be reported in half the time and save 0.62 MLT FTE. In comparison to culture, the implementation of Simplexa qPCR would save 2.79 MLA FTE plus 0.94 MLT FTE. Simplexa qPCR has improved performance and diagnostic efficiency in a high-volume laboratory compared to GASD for GAS detection in throat swabs. Copyright © 2018 American Society for Microbiology.

  11. 49 CFR 219.205 - Specimen collection and handling.

    Science.gov (United States)

    2010-10-01

    ... via air express, air freight or equivalent means. The railroad must maintain and document secure chain of custody of the kit from release by the medical facility to delivery for transportation, as...

  12. Generation of voxelized breast phantoms from surgical mastectomy specimens.

    Science.gov (United States)

    O'Connor, J Michael; Das, Mini; Dider, Clay S; Mahd, Mufeed; Glick, Stephen J

    2013-04-01

    In the research and development of dedicated tomographic breast imaging systems, digital breast object models, also known as digital phantoms, are useful tools. While various digital breast phantoms do exist, the purpose of this study was to develop a realistic high-resolution model suitable for simulating three-dimensional (3D) breast imaging modalities. The primary goal was to design a model capable of producing simulations with realistic breast tissue structure. The methodology for generating an ensemble of digital breast phantoms was based on imaging surgical mastectomy specimens using a benchtop, cone-beam computed tomography system. This approach allowed low-noise, high-resolution projection views of the mastectomy specimens at each angular position. Reconstructions of these projection sets were processed using correction techniques and diffusion filtering prior to segmentation into breast tissue types in order to generate phantoms. Eight compressed digital phantoms and 20 uncompressed phantoms from which an additional 96 pseudocompressed digital phantoms with voxel dimensions of 0.2 mm(3) were generated. Two distinct tissue classification models were used in forming breast phantoms. The binary model classified each tissue voxel as either adipose or fibroglandular. A multivalue scaled model classified each tissue voxel as percentage of adipose tissue (range 1%-99%). Power spectral analysis was performed to compare simulated reconstructions using the breast phantoms to the original breast specimen reconstruction, and fits were observed to be similar. The digital breast phantoms developed herein provide a high-resolution anthropomorphic model of the 3D uncompressed and compressed breast that are suitable for use in evaluating and optimizing tomographic breast imaging modalities. The authors believe that other research groups might find the phantoms useful, and therefore they offer to make them available for wider use.

  13. Optimal z-axis scanning parameters for gynecologic cytology specimens.

    Science.gov (United States)

    Donnelly, Amber D; Mukherjee, Maheswari S; Lyden, Elizabeth R; Bridge, Julia A; Lele, Subodh M; Wright, Najia; McGaughey, Mary F; Culberson, Alicia M; Horn, Adam J; Wedel, Whitney R; Radio, Stanley J

    2013-01-01

    The use of virtual microscopy (VM) in clinical cytology has been limited due to the inability to focus through three dimensional (3D) cell clusters with a single focal plane (2D images). Limited information exists regarding the optimal scanning parameters for 3D scanning. The purpose of this study was to determine the optimal number of the focal plane levels and the optimal scanning interval to digitize gynecological (GYN) specimens prepared on SurePath™ glass slides while maintaining a manageable file size. The iScanCoreo Au scanner (Ventana, AZ, USA) was used to digitize 192 SurePath™ glass slides at three focal plane levels at 1 μ interval. The digitized virtual images (VI) were annotated using BioImagene's Image Viewer. Five participants interpreted the VI and recorded the focal plane level at which they felt confident and later interpreted the corresponding glass slide specimens using light microscopy (LM). The participants completed a survey about their experiences. Inter-rater agreement and concordance between the VI and the glass slide specimens were evaluated. This study determined an overall high intra-rater diagnostic concordance between glass and VI (89-97%), however, the inter-rater agreement for all cases was higher for LM (94%) compared with VM (82%). Survey results indicate participants found low grade dysplasia and koilocytes easy to diagnose using three focal plane levels, the image enhancement tool was useful and focusing through the cells helped with interpretation; however, the participants found VI with hyperchromatic crowded groups challenging to interpret. Participants reported they prefer using LM over VM. This study supports using three focal plane levels and 1 μ interval to expand the use of VM in GYN cytology. Future improvements in technology and appropriate training should make this format a more preferable and practical option in clinical cytology.

  14. Optimal z-axis scanning parameters for gynecologic cytology specimens

    Directory of Open Access Journals (Sweden)

    Amber D Donnelly

    2013-01-01

    Full Text Available Background: The use of virtual microscopy (VM in clinical cytology has been limited due to the inability to focus through three dimensional (3D cell clusters with a single focal plane (2D images. Limited information exists regarding the optimal scanning parameters for 3D scanning. Aims: The purpose of this study was to determine the optimal number of the focal plane levels and the optimal scanning interval to digitize gynecological (GYN specimens prepared on SurePath™ glass slides while maintaining a manageable file size. Subjects and Methods: The iScanCoreo Au scanner (Ventana, AZ, USA was used to digitize 192 SurePath™ glass slides at three focal plane levels at 1 μ interval. The digitized virtual images (VI were annotated using BioImagene′s Image Viewer. Five participants interpreted the VI and recorded the focal plane level at which they felt confident and later interpreted the corresponding glass slide specimens using light microscopy (LM. The participants completed a survey about their experiences. Inter-rater agreement and concordance between the VI and the glass slide specimens were evaluated. Results: This study determined an overall high intra-rater diagnostic concordance between glass and VI (89-97%, however, the inter-rater agreement for all cases was higher for LM (94% compared with VM (82%. Survey results indicate participants found low grade dysplasia and koilocytes easy to diagnose using three focal plane levels, the image enhancement tool was useful and focusing through the cells helped with interpretation; however, the participants found VI with hyperchromatic crowded groups challenging to interpret. Participants reported they prefer using LM over VM. This study supports using three focal plane levels and 1 μ interval to expand the use of VM in GYN cytology. Conclusion: Future improvements in technology and appropriate training should make this format a more preferable and practical option in clinical cytology.

  15. A Century of Shope Papillomavirus in Museum Rabbit Specimens.

    Science.gov (United States)

    Escudero Duch, Clara; Williams, Richard A J; Timm, Robert M; Perez-Tris, Javier; Benitez, Laura

    2015-01-01

    Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansas and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco-Mexico's first-and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), pre-dating Shope's first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though

  16. Effective electromagnetic forces in thin sheet metal specimen

    Directory of Open Access Journals (Sweden)

    Langstädtler L.

    2015-01-01

    Full Text Available Electromagnetic forming is mainly investigated for the macro world as the body forces in this high speed process are decreasing with the volume of the specimen. For micro metal sheets different effects are observed which make an analysis of the acting forces more difficult. Hence, the validity of process simulations for electromagnetic forming is still limited. In this research the effective electromagnetic force on thin EN AW-1050A (Al99.5 sheet metals is investigated by varying the loading energy EC, the ration sR between sheet thickness and skin depth, the sheets width b and the distance dC between passive tool and sheet metal.

  17. Experimental Determination of Stress Intensity in a Cracked Cylindrical Specimen,

    Science.gov (United States)

    1980-05-01

    CRACKED CYLINDRICAL SPEC IMEN 7 ABSTRACT The range of stress intensity at the tip of a fatigue crack is the major factor controlling the crack growth...of this report will be similarly clesiied): The range of stress intensity at the tip of a fatigue crack is the major factor controlling the crack...EXPERIMENTAL STRESS INTENSITY CALIBRATION 3 3. EXPERIMENTAL DETAILS 4 3.1 Specimen Geometries 4 3.2 Material 5 3.3 Fatigue Loading 5 3.4 Crack Length

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

    Directory of Open Access Journals (Sweden)

    Nunes Cáris Maroni

    2006-01-01

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

  19. Museum specimen data predict crop damage by tropical rodents.

    Science.gov (United States)

    Sánchez-Cordero, V; Martínez-Meyer, E

    2000-06-20

    Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rodent species for seven of nine crops. Museum collections may thus provide important baseline information for designing land-use and agricultural pest-management programs.

  20. [Candida dubliniensis in clinical specimens and possibilities for identification].

    Science.gov (United States)

    Mahelová, M; Růžička, F

    2014-06-01

    The species Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans, the most common yeast species isolated from clinical specimens. This is a considerable complication for the detection and identification of Candida dubliniensis from clinical specimens. The lack of data on the incidence of C. dubliniensis in the Czech Republic was the motivation behind the efforts to detect this pathogen in specimens analyzed at the Institute for Microbiology, Faculty of Medicine Masaryk University and St. Anne's Faculty Hospital in Brno. Another aim was to test the reliability of the culture methods used. Altogether 2260 yeast isolates initially identified as C. albicans were analysed. To differentiate C. dubliniensis from C. albicans, four phenotypic methods were used: colour-based differentiation on CHROMagar Candida medium, culture on medium with 6.5% of NaCl, growth at 42 °C, and colony characteristics on Staib agar. To verify the results, the Bichro-Dubli Fumouze latex agglutination test and species-specific polymerase chain reactions (PCR) were used. Using phenotypic methods, latex agglutination, and PCR, 50 (2.2%) strains from the study set were assigned to C. dubliniensis. Most (31) C. dubliniensis isolates were recovered from the respiratory tract and the remaining others were three urine isolates, four stool isolates, one central venous catheter isolate, and one blood isolate. With the exception of colour-based differentiation on CHROMagar Candida medium showing a specificity of 85.5%, all the culture methods used have a high sensitivity and a high specificity. Identification of C. dubliniensis as C. albicans was confirmed in various clinical specimens, most often from the upper respiratory tract. The colour-based differentiation of C. dubliniensis from C. albicans on chromogenic CHROMagar Candida medium can only be recommended as a screening test for the differentiation of C. dubliniensis from other species of the genus Candida

  1. Animal Transports

    Directory of Open Access Journals (Sweden)

    Diana Ludrovcová

    2016-08-01

    Full Text Available Purpose and Originality: The research is aimed to the animal transports issue, from two points of view – first is the animal cruelty and second is the policy and economic consideration. The goal is to acquaint the readers with the transports risks and its cruelty and evaluation of the economic, political aspects for he involved countries. The study is oriented on more points of view, what is rare in works with a similar theme. Method: This paper examines many issues and examinations from different authors and subsequently summarized the findings with authors own knowledge to one expanded unit. Results: Results proves, that livestock transports have negative impact on animal´s health, environment. Number of transported animals is rising every year. Society: Research familiarize the society with the animal transports, cruelty against animals during them, and influence of transports on some countries, their economy, policy. People get better informed and can form their own opinion on this topic. They may start acting, undertaking some steps to improve the present situation, what could help a lot to animals and environment. Limitations / further research: Future research could show progress and improvement of transports, quality of food supply and economics.

  2. SUSTAINABLE TRANSPORTATION

    Directory of Open Access Journals (Sweden)

    Linda STEG

    2007-01-01

    Full Text Available This paper discusses possible contributions of psychologists to sustainable transportation. It is argued that in order to reach sustainable transportation, among others, behaviour changes of individual car users are needed. As transport policies will be more effective if they target important antecedents of travel behaviour, first, factors influencing such behaviour are discussed. It is argued that car use is very attractive and sometimes even necessary for many different reasons. This implies that a combination of policies is called for, each targeting different factors that support car use and hinder the use of more sustainable modes of transport. Next, the paper elaborates on policy strategies that may be employed to achieve sustainable transportation by changing car use. Increasing the attractiveness of sustainable transport modes by means of pull measures seems not sufficient to reduce the level of car use. Besides, car use should be made less attractive by means of push measures to force drivers to reconsider their travel behaviour. The acceptability of such policies may be increased by clearly communicating the aim of these policies, and the expected positive consequences (e.g., less congestion, improved environmental quality. Moreover, possible negative effects for individual freedom may be compensated by implementing additional policies aimed at facilitating the use of sustainable transport modes.

  3. 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.

  4. Electron microscopy by specimen design: application to strain measurements.

    Science.gov (United States)

    Cherkashin, Nikolay; Denneulin, Thibaud; Hÿtch, Martin J

    2017-09-29

    A bewildering number of techniques have been developed for transmission electron microscopy (TEM), involving the use of ever more complex combinations of lens configurations, apertures and detector geometries. In parallel, the developments in the field of ion beam instruments have modernized sample preparation and enabled the preparation of various types of materials. However, the desired final specimen geometry is always almost the same: a thin foil of uniform thickness. Here we will show that judicious design of specimen geometry can make all the difference and that experiments can be carried out on the most basic electron microscope and in the usual imaging modes. We propose two sample preparation methods that allow the formation of controlled moiré patterns for general monocrystalline structures in cross-section and at specific sites. We developed moiré image treatment algorithms using an absolute correction of projection lens distortions of a TEM that allows strain measurements and mapping with a nanometer resolution and 10-4 precision. Imaging and diffraction techniques in other fields may in turn benefit from this technique in perspective.

  5. Characterization of some biological specimens using TEM and SEM

    Science.gov (United States)

    Ghosh, Nabarun; Smith, Don W.

    2009-05-01

    The advent of novel techniques using the Transmission and Scanning Electron Microscopes improved observation on various biological specimens to characterize them. We studied some biological specimens using Transmission and Scanning Electron Microscopes. We followed negative staining technique with Phosphotungstic acid using bacterial culture of Bacillus subtilis. Negative staining is very convenient technique to view the structural morphology of different samples including bacteria, phage viruses and filaments in a cell. We could observe the bacterial cell wall and flagellum very well when trapped the negative stained biofilm from bacterial culture on a TEM grid. We cut ultra thin sections from the fixed root tips of Pisum sativum (Garden pea). Root tips were pre fixed with osmium tetroxide and post fixed with uranium acetate and placed in the BEEM capsule for block making. The ultrathin sections on the grid under TEM showed the granular chromatin in the nucleus. The protein bodies and large vacuoles with the storage materials were conspicuous. We followed fixation, critical point drying and sputter coating with gold to view the tissues with SEM after placing on stubs. SEM view of the leaf surface of a dangerous weed Tragia hispida showed the surface trichomes. These trichomes when break on touching releases poisonous content causing skin irritation. The cultured tissue from in vitro culture of Albizia lebbeck, a tree revealed the regenerative structures including leaf buds and stomata on the tissue surface. SEM and TEM allow investigating the minute details characteristic morphological features that can be used for classroom teaching.

  6. Usual interstitial pneumonia: histologic study of biopsy and explant specimens.

    Science.gov (United States)

    Katzenstein, Anna-Luise A; Zisman, David A; Litzky, Leslie A; Nguyen, Binh T; Kotloff, Robert M

    2002-12-01

    The pathologic findings in biopsy and subsequent explant specimens from 20 patients with usual interstitial pneumonia (UIP) were reviewed to refine histologic criteria for diagnosis, to identify factors that may confound diagnosis, and to assess the relationship of UIP and nonspecific interstitial pneumonia (NSIP). One case of NSIP was also identified and included for comparison. Surgical biopsies from 15 of the 20 UIP cases were diagnosed as UIP, whereas 5 showed only nondiagnostic changes. An important new observation is that areas resembling nonspecific interstitial pneumonia (NSIP-like areas) are present in the majority of UIP cases in both biopsy and explant specimens, and they are extensive in some. Ten of the 15 UIP biopsies were considered straightforward, with typical patchy interstitial fibrosis, honeycomb change, and fibroblast foci. Five cases were considered difficult because of prominent NSIP-like areas in two, extensive honeycomb change in one, superimposed diffuse alveolar damage in one, and superimposed bronchiolitis obliterans-organizing pneumonia in one. The most helpful feature for diagnosing UIP in difficult cases was the presence of a distinct patchwork appearance to the characteristic uneven or variegated parenchymal involvement along with evidence of architectural derangement. No explant showing UIP was preceded by biopsy findings of NSIP, and the one NSIP case appeared similar at biopsy and explant. NSIP or NSIP-like areas and UIP may reflect different mechanisms of fibrosis related either to different severity of injury or to different injuries.

  7. Correlations between Standard and Miniaturised Charpy-V Specimens

    Energy Technology Data Exchange (ETDEWEB)

    Lucon, E.; Van Walle, E.; Fabry, A.; Puzzolante, J.-L.; Verstrepen, A.; Vosch, R.; Van de Velde, L

    1998-12-01

    A total of 565 instrumented impact tests (232 performed on full-size and 333 on sub-size Charpy-V specimens) have been analysed in order to derive meaningful assumptions on the correlations existing between test results obtained on specimens of different size. Nine materials (pressure vessel steels) have been considered, in both as-received and irradiated state, for a total of 19 conditions examined. For the analysis of data, conventional as well novel approaches have been investigated; former ones, based on a review of the existing literature, include predictions of USE values by the use of normalization factors (NF), shifts of index temperatures related to energy/lateral expansion/shear fracture levels, and a combination of both approaches (scaling and shifting of energy curves). More original and recent proposals have also been verified, available in the literature but also proposed by SCK-CEN in the frame of enhanced surveillance of nuclear reactor pressure vessels. Conclusions have been drawn regarding the applicability and reliability of these methodologies, and recommendations have been given for future developments of the activities on this topic.

  8. Thermal diffusivity measurement of ring specimens by infrared thermography

    Science.gov (United States)

    Ferrarini, G.; Bison, P.; Bortolin, A.; Cadelano, G.; Rossi, S.

    2017-05-01

    The thermal diffusivity of solid materials is usually measured with the well-known flash method. In the traditional setup, the tested specimens have the shape of a small disc. However, several industrial applications need to test different typologies of samples. This work is focused on ring specimens, that are widely used as joints or sealants in various applications. The goal is investigating the possibilities and limitations of the flash method, applying minimum adjustments to the traditional experimental setup. A preliminary numerical study is conducted with the creation of a finite element model. Firstly, the model is checked with the standard case of a full disk. Then the simulation investigates the case of an aluminum oxide ring, that is taken as the reference case to determine the reliability of the proposed technique. After the simulation, an experimental measurement is performed on the aluminum oxide ring reference case. Several samples are tested and useful information on the practical feasibility of the experimental setup are collected. The obtained thermal diffusivity values fall into the expected range for the material, confirming the validity of the suggested method.

  9. Toxicological Analysis of Exhumed Specimens: A Challenge for Toxicologists

    Directory of Open Access Journals (Sweden)

    Muhammad Taimoor Chaudhary

    2016-06-01

    Full Text Available The objective of this work is to describe the type of biological samples submitted for toxicological analysis after exhumation. Forensic toxicologists receive a variety of biological samples, but exhumed biological specimens with varying degrees of putrefaction pose a greater challenge for analysis. Usually, immunoassay and colorimetric screening are the first line approach for toxicological analysis. Suitable samples can be selected for direct analysis using chromatographic techniques with a mass spectrometer, providing reliable results. The authors report two case studies where exhumed specimens were submitted for the determination of possible intoxication. The deceased were severely injured and remained hospitalized for more than 24 hours before death. Their corpses were exhumed for chemical analysis. For the toxicological analysis, selected samples were analyzed by immunoassay and a gas chromatograph mass spectrometer (GC/MS with electron impact ionization. Although the samples were negative for drugs of abuse (benzodiazepines and opiates, by immunoassay, midazolam (benzodiazepine was detected in putrefied material using GC/MS, thus indicating the hospitalization before death.

  10. Stabilizing specimens for routine ammonia testing in the clinical laboratory.

    Science.gov (United States)

    Gifford, Jessica L; Nguyen, William N T; de Koning, Lawrence; Seiden-Long, Isolde

    2017-12-16

    In vitro deamination generates ammonia in freshly collected blood specimens. To prevent this, samples for ammonia testing are usually collected on ice and run rapidly (e.g., within 1h). We developed a method to stabilize specimens for ammonia analysis. Following plasma separation, 500μmol/l cycloserine or a combination of 2mmol/l sodium borate with 5mmol/l l-serine were added to sample pools with normal or increased concentrations of ALT and/or GGT to inhibit deamination; and/or residual platelets were removed via centrifugation. Sample pools were then incubated at room temperature or 4°C. Untreated sample pools were also incubated at -80°C. Ammonia was measured at 0, 1, 2, 4, 8, 16, and 24h. When incubated at 4°C without treatment, sample pools with enzymes within their reference limit had an increase of 0.5μmol/l/h, whereas sample pools with ALT and/or GGT activity above their upper reference limit had an increase of 3.6μmol/l/h (p12h. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Simplified, Accurate Method for Antibiotic Assay of Clinical Specimens

    Science.gov (United States)

    Bennett, John V.; Brodie, Jean L.; Benner, Ernest J.; Kirby, William M. M.

    1966-01-01

    Large glass plates are used for this modified agar-well diffusion assay method, allowing up to 81 replications on a single plate. With a specially designed agar punch, it is possible to prepare the small agar wells very quickly. The saving in serum resulting from fewer replications of standards with the large plates, and the small volume of the agar wells, makes it economically feasible to use pooled human serum for the standard antibiotic solutions. Methods are described for preparing the standard solutions, and for providing controls for the deterioration of standards and unknowns. Procedures for preparing and maintaining the commonly used assay organisms are presented. Serum specimens are tested directly rather than diluting them to a narrow range of antibiotic concentrations. This is possible because of a procedure for calculations that recognizes the curvilinear relationship between zone sizes and antibiotic concentrations. Adaptation of this method to a number of the commonly used antibiotics is described. With this method, it has been possible to test large numbers of clinical specimens in a minimal time, and with accuracy consistently better than 10%. Images Fig. 1 PMID:4959982

  12. Characterization of Two Historic Smallpox Specimens from a Czech Museum.

    Science.gov (United States)

    Pajer, Petr; Dresler, Jiri; Kabíckova, Hana; Písa, Libor; Aganov, Pavel; Fucik, Karel; Elleder, Daniel; Hron, Tomas; Kuzelka, Vitezslav; Velemínsky, Petr; Klimentova, Jana; Fucikova, Alena; Pejchal, Jaroslav; Hrabakova, Rita; Benes, Vladimir; Rausch, Tobias; Dundr, Pavel; Pilin, Alexander; Cabala, Radomir; Hubalek, Martin; Stríbrny, Jan; Antwerpen, Markus H; Meyer, Hermann

    2017-07-27

    Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees. Here, we determined two complete variola virus genomes from human tissues kept in a museum in Prague dating back 60 and 160 years, respectively. Moreover, mass spectrometry-based proteomic, chemical, and microscopic examinations were performed. The 60-year-old specimen was most likely an importation from India, a country with endemic smallpox at that time. The genome of the 160-year-old specimen is related to clade 2 West African and variola minor strains. This sequence likely represents a new endemic European variant of variola virus circulating in the midst of the 19th century in Europe.

  13. Human tissue thickness measurements from excised sleeve gastrectomy specimens.

    Science.gov (United States)

    Rawlins, Logan; Rawlins, Melissa P; Teel, Donovan

    2014-03-01

    Little basic science data exists regarding the thickness of transected stomach as the limits of smaller gastric sleeves are created closer to the lesser curvature in laparoscopic sleeve gastrectomy (SG). We sought to determine the tissue thickness trends along the staple line and examine what factors might predispose to thicker tissue. This was a single-center, single-surgeon nonrandomized prospective study of patients undergoing SG. Excised SG specimens, with patient consent, underwent tissue measurement at multiple predetermined locations and at the midpoint of each fired staple cartridge. After 9 months, ending in July 2012, we met our goal enrollment of 50 gastric sleeve specimens. Most of the patients were female (80 %) and white (92.5 %). Average age was 42 years (range, 19-60 years), and average body mass index (BMI) was 49 kg/m(2) (range, 34-82 kg/m(2)). Tissue thickness was significantly different (p 50 kg/m(2)) and gender (male) are associated with increased tissue thickness, but only in the antrum. Surgeons should consider using a thicker staple load, such as black, when these factors are present. Also, significant changes in tissue thickness at the fourth and fifth staple fires suggest stepwise alteration in staple cartridge color selection.

  14. Immunohistochemistry of Programmed Cell Death in Archival Human Pathology Specimens

    Directory of Open Access Journals (Sweden)

    Takami Matsuyama

    2012-05-01

    Full Text Available Immunohistochemistry (IHC for detecting key signal molecules involved in programmed cell death (PCD in archival human pathology specimens is fairly well established. Detection of cleaved caspase-3 in lymphocytes in rheumatoid arthritis (RA and gastric surface foveolar glandular epithelia but not in synoviocytes in RA, gastric fundic glandular epithelia, or nasal NK/T-cell lymphoma (NKTCL cells suggests anti-apoptotic mechanisms in cell differentiation and in oncogenesis such as the induction of survivin. Enzymatically pretreated and ultra-super sensitive detection of beclin-1 in synoviocytes in RA and gastric fundic glandular epithelia suggests enhanced autophagy. The deposition of beclin-1 in fibrinoid necrosis in RA and expression of beclin-1 in detached gastric fundic glandular cells suggest that enhanced autophagy undergoes autophagic cell death (ACD. NKTCL exhibited enhanced autophagy through LC3 labeling and showed densely LC3 labeled cell-debris in regions of peculiar necrosis without deposition of beclin-1, indicating massive ACD in NKTCL and the alternative pathway enhancing autophagy following autophagic vesicle nucleation. Autophagy progression was monitored by labeling aggregated mitochondria and cathepsin D. The cell-debris in massive ACD in NKTCL were positive for 8-hydroxydeoxyguanosine, suggesting DNA oxidation occurred in ACD. Immunohistochemical autophagy and PCD analysis in archival human pathology specimens may offer new insights into autophagy in humans.

  15. Constitutive Modeling and Numerical Simulation of Frp Confined Concrete Specimens

    Directory of Open Access Journals (Sweden)

    Smitha Gopinath

    2014-09-01

    Full Text Available Fiber-reinforced polymer (FRP composites are generally used for the seismic retrofit of concrete members to enhance their strength and ductility. In the present work, the confining effect of Carbon Fiber-Reinforced Polymer (CFRP composite layers has been investigated by numerical simulation. The numerical simulation has been carried out using nonlinear finite element analysis (FEA to predict the response behaviour of CFRP-wrapped concrete cylinders. The nonlinear behaviour of concrete in compression and the linear elastic behaviour of CFRP has been modeled using an appropriate constitutive relationship. A cohesive model has been developed for modeling the interface between the concrete and CFRP. The interaction and damage failure criteria between the concrete to the cohesive element and the cohesive element to the CFRP has also been accounted for in the modeling. The response behaviour of the wrapped concrete specimen has been compared with the proposed interface model and with a perfectly bonded condition. The results obtained from the present study showed good agreement with the experimental load-displacement response and the failure pattern in the literature. Further, a sensitivity analysis has been carried out to study the effect of the number of layers of CFRP on the concrete specimens. It has been observed that wrapping with two layers was found to be the optimum, beyond which the response becomes flexible but with a higher load-carrying capacity

  16. Constitutive Modeling and Numerical Simulation of Frp Confined Concrete Specimens

    Science.gov (United States)

    Smitha, Gopinath; Ramachandramurthy, Avadhanam; Nagesh, Ranganatha Iyer; Shahulhameed, Eduvammal Kunhimoideen

    2014-09-01

    Fiber-reinforced polymer (FRP) composites are generally used for the seismic retrofit of concrete members to enhance their strength and ductility. In the present work, the confining effect of Carbon Fiber-Reinforced Polymer (CFRP) composite layers has been investigated by numerical simulation. The numerical simulation has been carried out using nonlinear finite element analysis (FEA) to predict the response behaviour of CFRP-wrapped concrete cylinders. The nonlinear behaviour of concrete in compression and the linear elastic behaviour of CFRP has been modeled using an appropriate constitutive relationship. A cohesive model has been developed for modeling the interface between the concrete and CFRP. The interaction and damage failure criteria between the concrete to the cohesive element and the cohesive element to the CFRP has also been accounted for in the modeling. The response behaviour of the wrapped concrete specimen has been compared with the proposed interface model and with a perfectly bonded condition. The results obtained from the present study showed good agreement with the experimental load-displacement response and the failure pattern in the literature. Further, a sensitivity analysis has been carried out to study the effect of the number of layers of CFRP on the concrete specimens. It has been observed that wrapping with two layers was found to be the optimum, beyond which the response becomes flexible but with a higher load-carrying capacity

  17. Identities of Microbacterium spp. encountered in human clinical specimens.

    Science.gov (United States)

    Gneiding, Kathrina; Frodl, Reinhard; Funke, Guido

    2008-11-01

    In the present study, 50 strains of yellow-pigmented gram-positive rods that had been isolated from human clinical specimens and collected over a 5-year period were further characterized by phenotypic and molecular genetic methods. All 50 strains belonged to the genus Microbacterium, and together they represented 18 different species. Microbacterium oxydans (n = 11), M. paraoxydans (n = 9), and M. foliorum (n = 7) represented more than half of the strains included in the present study. The isolation of strains belonging to M. hydrocarbonoxydans (n = 2), M. esteraromaticum (n = 1), M. oleivorans (n = 1), M. phyllosphaerae (n = 1), and M. thalassium (n = 1) from humans is reported for the first time. Microbacterium sp. strain VKM Ac-1389 (n = 1) and the previously uncultured Microbacterium sp. clone YJQ-29 (n = 1) probably represent new species. Comprehensive antimicrobial susceptibility data are given for the 50 Microbacterium isolates. This study is, so far, the largest on Microbacterium spp. encountered in human clinical specimens and outlines the heterogeneity of clinical Microbacterium strains.

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

    Directory of Open Access Journals (Sweden)

    Vuruskan Hakan

    2011-07-01

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

  19. Where are primary type specimens of new mite species deposited?

    Science.gov (United States)

    Liu, Jian-Feng; Wei, Xiao-Ying; Li, Guang-Yun; Zhang, Zhi-Qiang

    2017-12-08

    A list of type depositories of new mite species published in two journals (Systematic & Applied Acarology and Zootaxa) during the last five years (2012-2016) is presented in this paper. The 1370 new species are deposited unevenly among 134 collections. The top collection is the Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia (145 species), which alone accounts for 10% of the total new species, and the top ten collections accounted for 48% of the total. The average number of new species per collection is 10 and over three quarters of the collections are below the average. Just over half (51%) of the collections are in Europe. However, overall there were still more new species deposited in collections in developing counties (741) than developed countries (629). The top country for type depositories of new mite species for each continent is: Russia (199 species) for Europe, Brazil (134 species) for South America, Iran (133 species) for Asia, Australia (87 species) for Oceania, USA (80 species) for North America and South Africa (36 species) for Africa. The top European collections hold type specimens mostly of foreign origin, whereas those of South America, Asia, Africa and Australasia hold type specimens mostly originating from their own countries.

  20. The management of incidental findings of reduction mammoplasty specimens.

    Science.gov (United States)

    Goodwin, Jessica T; Decroff, Chantelle; Dauway, Emilia; Sybenga, Amelia; Mahabir, Raman C

    2013-01-01

    Reduction mammoplasty is one of the most commonly performed procedures in plastic surgery. Occasionally, there are findings reported by pathologists that are unfamiliar to the treating surgeon. The aim of the present study was to determine the types of pathologies encountered in reduction mammoplasty specimens. From this list of diagnoses, a best practice guideline for management will be organized to better assist plastic surgeons in the management of patients with incidental findings on pathology reports. A total of 441 pathology reports from patients who underwent bilateral or unilateral reduction mammoplasty in the past three years were identified. A list of 21 different pathologies was generated from the pathology reports, along with supplemental data from recent texts and articles. Occult carcinomas were encountered in two cases (0.45%) and high-risk lesions were found in three cases (0.68%) at the authors' institution. An algorithm was then constructed to organize the pathologies according to risk of malignancy and assign them to a management guideline. There are many different lesions encountered incidentally in reduction mammoplasty specimens that may or may not confer some cancer risk. It is important for plastic surgeons to know which lesions need closer follow-up to provide the best care for their patients.