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Sample records for swab samples electronic

  1. 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....

  2. 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.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2016-01-01

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

  6. 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...

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

    Science.gov (United States)

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

    2018-02-01

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  11. 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.

  12. 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.

  13. 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

    known higher relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded p values from 0.0088–0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated. Discussion Strong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for C. trachomatis, although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs.

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

    Directory of Open Access Journals (Sweden)

    Marián Prokeš

    2012-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

    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.

  16. 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.

  17. 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

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

    Science.gov (United States)

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

    2002-01-01

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

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

    Science.gov (United States)

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

    2007-12-01

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

  20. 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.

  1. First evaluation of automated specimen inoculation for wound swab samples by use of the Previ Isola system compared to manual inoculation in a routine laboratory: finding a cost-effective and accurate approach.

    Science.gov (United States)

    Mischnik, Alexander; Mieth, Markus; Busch, Cornelius J; Hofer, Stefan; Zimmermann, Stefan

    2012-08-01

    Automation of plate streaking is ongoing in clinical microbiological laboratories, but evaluation for routine use is mostly open. In the present study, the recovery of microorganisms from the Previ Isola system plated polyurethane (PU) swab samples is compared to manually plated control viscose swab samples from wounds according to the CLSI procedure M40-A (quality control of microbiological transport systems). One hundred twelve paired samples (224 swabs) were analyzed. In 80/112 samples (71%), concordant culture results were obtained with the two methods. In 32/112 samples (29%), CFU recovery of microorganisms from the two methods was discordant. In 24 (75%) of the 32 paired samples with a discordant result, Previ Isola plated PU swabs were superior. In 8 (25%) of the 32 paired samples with a discordant result, control viscose swabs were superior. The quality of colony growth on culture media for further investigations was superior with Previ Isola inoculated plates compared to manual plating techniques. Gram stain results were concordant between the two methods in 62/112 samples (55%). In 50/112 samples (45%), the results of Gram staining were discordant between the two methods. In 34 (68%) of the 50 paired samples with discordant results, Gram staining of PU swabs was superior to that of control viscose swabs. In 16 (32%) of the 50 paired samples, Gram staining of control viscose swabs was superior to that of PU swabs. We report the first clinical evaluation of Previ Isola automated specimen inoculation for wound swab samples. This study suggests that use of an automated specimen inoculation system has good results with regard to CFU recovery, quality of Gram staining, and accuracy of diagnosis.

  2. Well swab collar

    Energy Technology Data Exchange (ETDEWEB)

    1969-04-09

    A well swab collar which can be hoisted to bring well fluids upward through a pipe string is described. An elastic swab is used to swab a pipe having a predetermined diameter. The swab consists of a circular shaped elastomer body having an outer diameter a little smaller than the inner diameter of the pipe. The body is divided into multiple swab elements by ring-shaped grooves in the body. The swab element has truncated conical surfaces directed radially at an outward angle, then downward and consequently at an angle inward and then downward. (19 claims)

  3. 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

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

    Science.gov (United States)

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

    2018-06-25

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

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

    Science.gov (United States)

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

    2018-05-01

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

  6. 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

  7. 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)

    Capik, Sarah F; White, Brad J; Lubbers, Brian V; Apley, Michael D; DeDonder, Keith D; Larson, Robert L; Harhay, Greg P; Chitko-McKown, Carol G; Harhay, Dayna M; Kalbfleisch, Ted S; Schuller, Gennie; Clawson, Michael L

    2017-03-01

    OBJECTIVE To compare predictive values, extent of agreement, and gamithromycin susceptibility between bacterial culture results of nasopharyngeal swab (NPS) and bronchoalveolar lavage fluid (BALF) samples obtained from calves with bovine respiratory disease (BRD). ANIMALS 28 beef calves with clinical BRD. PROCEDURES Pooled bilateral NPS samples and BALF samples were obtained for bacterial culture from calves immediately before and at various times during the 5 days after gamithromycin (6 mg/kg, SC, once) administration. For each culture-positive sample, up to 12 Mannheimia haemolytica, 6 Pasteurella multocida, and 6 Histophilus somni colonies underwent gamithromycin susceptibility testing. Whole-genome sequencing was performed on all M haemolytica isolates. For paired NPS and BALF samples collected 5 days after gamithromycin administration, the positive and negative predictive values for culture results of NPS samples relative to those of BALF samples and the extent of agreement between the sampling methods were determined. RESULTS Positive and negative predictive values of NPS samples were 67% and 100% for M haemolytica, 75% and 100% for P multocida, and 100% and 96% for H somni. Extent of agreement between results for NPS and BALF samples was substantial for M haemolytica (κ, 0.71) and H somni (κ, 0.78) and almost perfect for P multocida (κ, 0.81). Gamithromycin susceptibility varied within the same sample and between paired NPS and BALF samples. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated culture results of NPS and BALF samples from calves with BRD should be interpreted cautiously considering disease prevalence within the population, sample collection relative to antimicrobial administration, and limitations of diagnostic testing methods.

  8. Novel Sample Preparation Method for Safe and Rapid Detection of Bacillus anthracis Spores in Environmental Powders and Nasal Swabs

    OpenAIRE

    Luna, Vicki A.; King, Debra; Davis, Carisa; Rycerz, Tony; Ewert, Matthew; Cannons, Andrew; Amuso, Philip; Cattani, Jacqueline

    2003-01-01

    Bacillus anthracis spores have been used as a biological weapon in the United States. We wanted to develop a safe, rapid method of sample preparation that provided safe DNA for the detection of spores in environmental and clinical specimens. Our method reproducibly detects B. anthracis in samples containing

  9. Bacteriological Profile and Antimicrobial Susceptibility Patterns of Bacteria Isolated from Pus/Wound Swab Samples from Children Attending a Tertiary Care Hospital in Kathmandu, Nepal

    Directory of Open Access Journals (Sweden)

    Salu Rai

    2017-01-01

    Full Text Available In Nepal, little is known about the microbiological profile of wound infections in children and their antimicrobial susceptibility patterns. Total of 450 pus/wound swab samples collected were cultured using standard microbiological techniques and the colonies grown were identified with the help of biochemical tests. The antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion technique. Methicillin-resistant Staphylococcus aureus isolates were detected by using cefoxitin disc and confirmed by determining minimum inhibitory concentrations (MIC of oxacillin. 264 (59% samples were culture positive. The highest incidence of bacterial infections was noted in the age group of less than 1 year (76%. Out of 264 growth positive samples, Gram-positive bacteria were isolated from 162 (61% samples and Gram-negative bacteria were found in 102 (39% samples. Staphylococcus aureus (99% was the predominant Gram-positive bacteria isolated and Pseudomonas aeruginosa (44% was predominant Gram-negative bacteria. About 19% of S. aureus isolates were found to be methicillin-resistant MIC of oxacillin ranging from 4 μg/mL to 128 μg/mL. Among the children of Nepal, those of age less than 1 year were at higher risk of wound infections by bacteria. Staphylococcus aureus followed by Pseudomonas aeruginosa were the most common bacteria causing wound infections in children.

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

    Directory of Open Access Journals (Sweden)

    Paula R. Almeida

    2012-08-01

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

  11. Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples.

    Science.gov (United States)

    Verant, Michelle L; Bohuski, Elizabeth A; Lorch, Jeffery M; Blehert, David S

    2016-03-01

    The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer-based qPCR test for P. destructans to refine quantification capabilities of this assay. © 2016 The Author(s).

  12. Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples

    Science.gov (United States)

    Verant, Michelle; Bohuski, Elizabeth A.; Lorch, Jeffrey M.; Blehert, David

    2016-01-01

    The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid fromP. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer–based qPCR test for P. destructans to refine quantification capabilities of this assay.

  13. Electron holography of biological samples.

    Science.gov (United States)

    Simon, P; Lichte, H; Formanek, P; Lehmann, M; Huhle, R; Carrillo-Cabrera, W; Harscher, A; Ehrlich, H

    2008-01-01

    In this paper, we summarise the development of off-axis electron holography on biological samples starting in 1986 with the first results on ferritin from the group of Tonomura. In the middle of the 1990s strong interest was evoked, but then stagnation took place because the results obtained at that stage did not reach the contrast and the resolution achieved by conventional electron microscopy. To date, there exist only a few ( approximately 12) publications on electron holography of biological objects, thus this topic is quite small and concise. The reason for this could be that holography is mostly established in materials science by physicists. Therefore, applications for off-axis holography were powerfully pushed forward in the area of imaging, e.g. electric or magnetic micro- and nanofields. Unstained biological systems investigated by means of off-axis electron holography up to now are ferritin, tobacco mosaic virus, a bacterial flagellum, T5 bacteriophage virus, hexagonal packed intermediate layer of bacteria and the Semliki Forest virus. New results of the authors on collagen fibres and surface layer of bacteria, the so-called S-layer 2D crystal lattice are presented in this review. For the sake of completeness, we will shortly discuss in-line holography of biological samples and off-axis holography of materials related to biological systems, such as biomaterial composites or magnetotactic bacteria.

  14. GET electronics samples data analysis

    International Nuclear Information System (INIS)

    Giovinazzo, J.; Goigoux, T.; Anvar, S.; Baron, P.; Blank, B.; Delagnes, E.; Grinyer, G.F.; Pancin, J.; Pedroza, J.L.; Pibernat, J.; Pollacco, E.; Rebii, A.

    2016-01-01

    The General Electronics for TPCs (GET) has been developed to equip a generation of time projection chamber detectors for nuclear physics, and may also be used for a wider range of detector types. The goal of this paper is to propose first analysis procedures to be applied on raw data samples from the GET system, in order to correct for systematic effects observed on test measurements. We also present a method to estimate the response function of the GET system channels. The response function is required in analysis where the input signal needs to be reconstructed, in terms of time distribution, from the registered output samples.

  15. Swab2know: An HIV-Testing Strategy Using Oral Fluid Samples and Online Communication of Test Results for Men Who Have Sex With Men in Belgium.

    Science.gov (United States)

    Platteau, Tom; Fransen, Katrien; Apers, Ludwig; Kenyon, Chris; Albers, Laura; Vermoesen, Tine; Loos, Jasna; Florence, Eric

    2015-09-01

    As HIV remains a public health concern, increased testing among those at risk for HIV acquisition is important. Men who have sex with men (MSM) are the most important group for targeted HIV testing in Europe. Several new strategies have been developed and implemented to increase HIV-testing uptake in this group, among them the Swab2know project. In this project, we aim to assess the acceptability and feasibility of outreach and online HIV testing using oral fluid samples as well as Web-based delivery of test results. Sample collection happened between December 2012 and April 2014 via outreach and online sampling among MSM. Test results were communicated through a secured website. HIV tests were executed in the laboratory. Each reactive sample needed to be confirmed using state-of-the-art confirmation procedures on a blood sample. Close follow-up of participants who did not pick up their results, and those with reactive results, was included in the protocol. Participants were asked to provide feedback on the methodology using a short survey. During 17 months, 1071 tests were conducted on samples collected from 898 men. Over half of the samples (553/1071, 51.63%) were collected during 23 outreach sessions. During an 8-month period, 430 samples out of 1071 (40.15%) were collected from online sampling. Additionally, 88 samples out of 1071 (8.22%) were collected by two partner organizations during face-to-face consultations with MSM and male sex workers. Results of 983 out of 1071 tests (91.78%) had been collected from the website. The pickup rate was higher among participants who ordered their kit online (421/430, 97.9%) compared to those participating during outreach activities (559/641, 87.2%; Ponline participants were more likely to have never been tested before (17.3% vs 10.0%; P=.001) and reported more sexual partners in the 6 months prior to participation in the project (mean 7.18 vs 3.23; Ponline counseling tool), and in studying the cost effectiveness of the

  16. False Negative Rates of a Macrofoam-Swab Sampling Method with Low Surface Concentrations of Two Bacillus anthracis Surrogates via Real-Time PCR

    Energy Technology Data Exchange (ETDEWEB)

    Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Piepel, Gregory F. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sydor, Michael A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kaiser, Brooke L.D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-01

    Surface sampling for Bacillus anthracis spores has traditionally relied on detection via bacterial cultivation methods. Although effective, this approach does not provide the level of organism specificity that can be gained through molecular techniques. False negative rates (FNR) and limits of detection (LOD) were determined for two B. anthracis surrogates with modified rapid viability-polymerase chain reaction (mRV-PCR) following macrofoam-swab sampling. This study was conducted in parallel with a previously reported study that analyzed spores using a plate-culture method. B. anthracis Sterne (BAS) or B. atrophaeus Nakamura (BG) spores were deposited onto four surface materials (glass, stainless steel, vinyl tile, and plastic) at nine target concentrations (2 to 500 spores/coupon; 0.078 to 19.375 colony-forming units [CFU] per cm2). Mean FNR values for mRV-PCR analysis ranged from 0 to 0.917 for BAS and 0 to 0.875 for BG and increased as spore concentration decreased (over the concentrations investigated) for each surface material. FNRs based on mRV-PCR data were not statistically different for BAS and BG, but were significantly lower for glass than for vinyl tile. FNRs also tended to be lower for the mRV-PCR method compared to the culture method. The mRV-PCR LOD95 was lowest for glass (0.429 CFU/cm2 with BAS and 0.341 CFU/cm2 with BG) and highest for vinyl tile (0.919 CFU/cm2 with BAS and 0.917 CFU/cm2 with BG). These mRV-PCR LOD95 values were lower than the culture values (BAS: 0.678 to 1.023 CFU/cm2 and BG: 0.820 to 1.489 CFU/cm2). The FNR and LOD95 values reported in this work provide guidance for environmental sampling of Bacillus spores at low concentrations.

  17. Recovery Efficiency, False Negative Rate, and Limit of Detection Performance of a Validated Macrofoam-Swab Sampling Method with Low Surface Concentrations of Two Bacillus anthracis Surrogates

    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); Deatherage Kaiser, Brooke L [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sydor, Michael A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Barrett, Christopher A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-03-31

    The performance of a macrofoam-swab sampling method was evaluated using Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus Nakamura (BG) spores applied at nine low target amounts (2-500 spores) to positive-control plates and test coupons (2 in. × 2 in.) of four surface materials (glass, stainless steel, vinyl tile, and plastic). Test results from cultured samples were used to evaluate the effects of surrogate, surface concentration, and surface material on recovery efficiency (RE), false negative rate (FNR), and limit of detection. For RE, surrogate and surface material had statistically significant effects, but concentration did not. Mean REs were the lowest for vinyl tile (50.8% with BAS, 40.2% with BG) and the highest for glass (92.8% with BAS, 71.4% with BG). FNR values ranged from 0 to 0.833 for BAS and 0 to 0.806 for BG, with values increasing as concentration decreased in the range tested (0.078 to 19.375 CFU/cm2, where CFU denotes ‘colony forming units’). Surface material also had a statistically significant effect. A FNR-concentration curve was fit for each combination of surrogate and surface material. For both surrogates, the FNR curves tended to be the lowest for glass and highest for vinyl title. The FNR curves for BG tended to be higher than for BAS at lower concentrations, especially for glass. Results using a modified Rapid Viability-Polymerase Chain Reaction (mRV-PCR) analysis method were also obtained. The mRV-PCR results and comparisons to the culture results will be discussed in a subsequent report.

  18. Recovery Efficiency, False Negative Rate, and Limit of Detection Performance of a Validated Macrofoam-Swab Sampling Method with Low Surface Concentrations of Two Bacillus anthracis Surrogates

    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); Kaiser, Brooke L. D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sydor, Michael A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Barrett, Christopher A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-16

    The performance of a macrofoam-swab sampling method was evaluated using Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus Nakamura (BG) spores applied at nine low target amounts (2-500 spores) to positive-control plates and test coupons (2 in × 2 in) of four surface materials (glass, stainless steel, vinyl tile, and plastic). Test results from cultured samples were used to evaluate the effects of surrogate, surface concentration, and surface material on recovery efficiency (RE), false negative rate (FNR), and limit of detection. For RE, surrogate and surface material had statistically significant effects, but concentration did not. Mean REs were the lowest for vinyl tile (50.8% with BAS, 40.2% with BG) and the highest for glass (92.8% with BAS, 71.4% with BG). FNR values ranged from 0 to 0.833 for BAS and 0 to 0.806 for BG, with values increasing as concentration decreased in the range tested (0.078 to 19.375 CFU/cm2, where CFU denotes ‘colony forming units’). Surface material also had a statistically significant effect. A FNR-concentration curve was fit for each combination of surrogate and surface material. For both surrogates, the FNR curves tended to be the lowest for glass and highest for vinyl title. The FNR curves for BG tended to be higher than for BAS at lower concentrations, especially for glass. Results using a modified Rapid Viability-Polymerase Chain Reaction (mRV-PCR) analysis method were also obtained. The mRV-PCR results and comparisons to the culture results are discussed in a separate report.

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

    Directory of Open Access Journals (Sweden)

    Surya Prakash Dwivedi

    2012-10-01

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

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

    Science.gov (United States)

    Nakalembe, Miriam; Mutyaba, Twaha; Mirembe, Florence

    2016-03-16

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

  1. False Negative Rates of a Macrofoam-Swab Sampling Method with Low Surface Concentrations of Two Bacillus anthracis Surrogates via Real-Time PCR

    Energy Technology Data Exchange (ETDEWEB)

    Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Piepel, Gregory F. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sydor, Michael A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Deatherage Kaiser, Brooke L [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-05-01

    Surface sampling for Bacillus anthracis spores has traditionally relied on detection via bacterial cultivation methods. Although effective, this approach does not provide the level of organism specificity that can be gained through molecular techniques. False negative rates (FNR) and limits of detection (LOD) were determined for two B. anthracis surrogates with modified rapid viability-polymerase chain reaction (mRV-PCR) following macrofoam-swab sampling. This study was conducted in parallel with a previously reported study that analyzed spores using a plate-culture method. B. anthracis Sterne (BAS) or B. atrophaeus Nakamura (BG) spores were deposited onto four surface materials (glass, stainless steel, vinyl tile, and plastic) at nine target concentrations (2 to 500 spores/coupon; 0.078 to 19.375 colony-forming units [CFU] per cm²). Mean FNR values for mRV-PCR analysis ranged from 0 to 0.917 for BAS and 0 to 0.875 for BG and increased as spore concentration decreased (over the concentrations investigated) for each surface material. FNRs based on mRV-PCR data were not statistically different for BAS and BG, but were significantly lower for glass than for vinyl tile. FNRs also tended to be lower for the mRV-PCR method compared to the culture method. The mRV-PCR LOD₉₅ was lowest for glass (0.429 CFU/cm² with BAS and 0.341 CFU/cm² with BG) and highest for vinyl tile (0.919 CFU/cm² with BAS and 0.917 CFU/cm² with BG). These mRV-PCR LOD₉₅ values were lower than the culture values (BAS: 0.678 to 1.023 CFU/cm² and BG: 0.820 to 1.489 CFU/cm²). The FNR and LOD₉₅ values reported in this work provide guidance for environmental sampling of Bacillus spores at low concentrations.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hutchison, J. R. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Piepel, G. F. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Amidan, B. G. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Hess, B. M. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Sydor, M. A. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA; Deatherage Kaiser, B. L. [National Security Directorate, Pacific Northwest National Laboratory, Richland WA USA

    2018-03-13

    Aims: 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 (LOD95) for recovering Bacillus spores using a macrofoam-swab sampling procedure. Methods and Results: 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 LOD95 results. Conclusions: 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 LOD95 was lowest for glass and highest for vinyl tile. LOD95 values overall were lower for mRV-PCR than for the culture method. Significance and Impact of Study: This study adds to the limited data on FNR and LOD95 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.

  3. Ballistic electron transport in mesoscopic samples

    International Nuclear Information System (INIS)

    Diaconescu, D.

    2000-01-01

    In the framework of this thesis, the electron transport in the ballistic regime has been studied. Ballistic means that the lateral sample dimensions are smaller than the mean free path of the electrons, i.e. the electrons can travel through the whole device without being scattered. This leads to transport characteristics that differ significantly from the diffusive regime which is realised in most experiments. Making use of samples with high mean free path, features of ballistic transport have been observed on samples with sizes up to 100 μm. The basic device used in ballistic electron transport is the point contact, from which a collimated beam of ballistic electrons can be injected. Such point contacts were realised with focused ion beam (FIB) implantation and the collimating properties were analysed using a two opposite point contact configuration. The typical angular width at half maximum is around 50 , which is comparable with that of point contacts defined by other methods. (orig.)

  4. 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.

  5. Shielded scanning electron microscope for radioactive samples

    International Nuclear Information System (INIS)

    Crouse, R.S.; Parsley, W.B.

    1977-01-01

    A small commercial SEM had been successfully shielded for examining radioactive materials transferred directly from a remote handling facility. Relatively minor mechanical modifications were required to achieve excellent operation. Two inches of steel provide adequate shielding for most samples encountered. However, samples reading 75 rad/hr γ have been examined by adding extra shielding in the form of tungsten sample holders and external lead shadow shields. Some degradation of secondary electron imaging was seen but was adequately compensated for by changing operating conditions

  6. Molecular analysis of partial VP-2 gene amplified from rectal swab samples of diarrheic dogs in Pakistan confirms the circulation of canine parvovirus genetic variant CPV-2a and detects sequences of feline panleukopenia virus (FPV).

    Science.gov (United States)

    Ahmed, Nisar; Riaz, Adeel; Zubair, Zahra; Saqib, Muhammad; Ijaz, Sehrish; Nawaz-Ul-Rehman, Muhammad Shah; Al-Qahtani, Ahmed; Mubin, Muhammad

    2018-03-15

    The infection in dogs due to canine parvovirus (CPV), is a highly contagious one with high mortality rate. The present study was undertaken for a detailed genetic analysis of partial VP2 gene i.e., 630 bp isolated from rectal swab samples of infected domestic and stray dogs from all areas of district Faisalabad. Monitoring of viruses is important, as continuous prevalence of viral infection might be associated with emergence of new virulent strains. In the present study, 40 rectal swab samples were collected from diarrheic dogs from different areas of district Faisalabad, Pakistan, in 2014-15 and screened for the presence of CPV by immunochromatography. Most of these dogs were stray dogs showing symptoms of diarrhea. Viral DNA was isolated and partial VP2 gene was amplified using gene specific primer pair Hfor/Hrev through PCR. Amplified fragments were cloned in pTZ57R/T (Fermentas) and completely sequenced. Sequences were analyzed and assembled by the Lasergene DNA analysis package (v8; DNAStar Inc., Madison, WI, USA). The results with immunochromatography showed that 33/40 (82%) of dogs were positive for CPV. We were able to amplify a fragment of 630 bp from 25 samples. In 25 samples the sequences of CPV-2a were detected showing the amino acid substitution Ser297Ala and presence of amino acid (426-Asn) in partial VP2 protein. Interestingly the BLAST analysis showed the of feline panleukopenia virus (FPV) sequences in 3 samples which were already positive for new CPV-2a, with 99% sequence homology to other FPV sequences present in GenBank. Phylogenetic analysis showed clustering of partial CPV-VP-2 gene with viruses from China, India, Japan and Uruguay identifying a new variant, whereas the 3 FPV sequences showed immediate ancestral relationship with viruses from Portugal, South Africa and USA. Interesting observation was that CPV are clustering away from the commercial vaccine strains. In this work we provide a better understanding of CPV prevailing in Pakistan

  7. Potential concerns with analytical Methods Used for the detection of Batrachochytrium salamandrivorans from archived DNA of amphibian swab samples, Oregon, USA

    Science.gov (United States)

    Iwanowicz, Deborah; Olson, Deanna H.; Adams, Michael J.; Adams, Cynthia; Anderson, Chauncey; Blaustein, Andrew R; Densmore, Christine L.; Figiel, Chester; Schill, William B.; Chestnut, Tara

    2017-01-01

    Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    Foot-and-mouth disease virus (FMDV) RNA was measured using quantitative reverse transcription-PCR (qRT-PCR) assays in oralswab and probangsamples collected from cattle and pigs during experimental infections with serotype O FMDV. During acute infection, FMDV RNA was measurable in oralswabs as well...... as in probangsamples from both species. FMDV RNA could be detected in oralswabs and probangsamples 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 oralswabs 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 oralswabs harvested beyond 10 days post infection (dpi), despite the presence of FMDV RNA in probangsamples that had been collected as late as 35 dpi...

  9. 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.

  10. Forensic analysis of explosive residues from hand swabs

    International Nuclear Information System (INIS)

    Umi Khairul Ahmad; Sumathy Rajendran; Syahidah Abu Hassan

    2008-01-01

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

  11. EVA Swab Tool to Support Planetary Protection and Astrobiology Evaluations

    Science.gov (United States)

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

    2018-01-01

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

  12. Detection of Methicillin Resistant Staphylococcus aureus and Determination of Minimum Inhibitory Concentration of Vancomycin for Staphylococcus aureus Isolated from Pus/Wound Swab Samples of the Patients Attending a Tertiary Care Hospital in Kathmandu, Nepal

    Directory of Open Access Journals (Sweden)

    Raghabendra Adhikari

    2017-01-01

    Full Text Available The present study was conducted to evaluate the performance of cefoxitin disc diffusion method and oxacillin broth microdilution method for detection of methicillin resistant S. aureus (MRSA, taking presence of mecA gene as reference. In addition, inducible clindamycin resistance and beta-lactamase production were studied and minimum inhibitory concentration (MIC of vancomycin for S. aureus isolates was determined. A total of 711 nonrepeated pus/wound swab samples from different anatomic locations were included in the study. The Staphylococcus aureus was identified on the basis of colony morphology, Gram’s stain, and biochemical tests. A total of 110 (15.47% S. aureus isolates were recovered, of which 39 (35.50% isolates were identified as MRSA by cefoxitin disc diffusion method. By oxacillin broth microdilution method, 31.82% of the Staphylococcus aureus isolates were found to be MRSA. However, mecA gene was present in only 29.1% of the isolates. Further, beta-lactamase production was observed in 71.82% of the isolates, while inducible clindamycin resistance was found in 10% of S. aureus isolates. The MIC value of vancomycin for S. aureus ranged from 0.016 μg/mL to 1 μg/mL. On the basis of the absolute sensitivity (100%, both phenotypic methods could be employed for routine diagnosis of MRSA in clinical microbiology laboratory; however cefoxitin disc diffusion could be preferred over MIC method considering time and labour factor.

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

    Science.gov (United States)

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

    2009-01-01

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

  14. Isolation and identification of female DNA on postcoital penile swabs.

    Science.gov (United States)

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

    2000-06-01

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

  15. Meatal Swabs Contain Less Cellular Material and Are Associated with a Decrease in Gram Stain Smear Quality Compared to Urethral Swabs in Men.

    Science.gov (United States)

    Jordan, Stephen J; Schwebke, Jane R; Aaron, Kristal J; Van Der Pol, Barbara; Hook, Edward W

    2017-07-01

    Urethral swabs are the samples of choice for point-of-care Gram stain testing to diagnose Neisseria gonorrhoeae infection and nongonococcal urethritis (NGU) in men. As an alternative to urethral swabs, meatal swabs have been recommended for the collection of urethral discharge to diagnose N. gonorrhoeae and Chlamydia trachomatis infection in certain populations by nucleic acid amplification testing (NAAT), as they involve a less invasive collection method. However, as meatal swabs could be sampling a reduced surface area and result in fewer collected epithelial cells compared to urethral swabs, the adequacy of meatal swab specimens to collect sufficient cellular material for Gram stain testing remains unknown. We enrolled 66 men who underwent either urethral or meatal swabbing and compared the cellular content and Gram stain failure rate. We measured the difference in swab cellular content using the Cepheid Xpert CT/NG sample adequacy control crossing threshold (SAC CT ) and determined the failure rate of Gram stain smears (GSS) due to insufficient cellular material. In the absence of discharge, meatal smears were associated with a significant reduction in cellular content ( P = 0.0118), which corresponded with a GSS failure rate significantly higher than that for urethral swabs (45% versus 3%, respectively; P < 0.0001). When discharge was present, there was no difference among results from urethral and meatal swabs. Therefore, if GSS testing is being considered for point-of-care diagnosis of N. gonorrhoeae infection or NGU in men, meatal swabs should be avoided in the absence of a visible discharge. Copyright © 2017 American Society for Microbiology.

  16. Composition quantification of electron-transparent samples by backscattered electron imaging in scanning electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Müller, E., E-mail: erich.mueller@kit.edu; Gerthsen, D.

    2017-02-15

    The contrast of backscattered electron (BSE) images in scanning electron microscopy (SEM) depends on material parameters which can be exploited for composition quantification if some information on the material system is available. As an example, the In-concentration in thin In{sub x}Ga{sub 1−x}As layers embedded in a GaAs matrix is analyzed in this work. The spatial resolution of the technique is improved by using thin electron-transparent specimens instead of bulk samples. Although the BSEs are detected in a comparably small angular range by an annular semiconductor detector, the image intensity can be evaluated to determine the composition and local thickness of the specimen. The measured intensities are calibrated within one single image to eliminate the influence of the detection and amplification system. Quantification is performed by comparison of experimental and calculated data. Instead of using time-consuming Monte-Carlo simulations, an analytical model is applied for BSE-intensity calculations which considers single electron scattering and electron diffusion. - Highlights: • Sample thickness and composition are quantified by backscattered electron imaging. • A thin sample is used to achieve spatial resolution of few nanometers. • Calculations are carried out with a time-saving electron diffusion model. • Small differences in atomic number and density detected at low electron energies.

  17. 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.

  18. 'Swab racks are an old fashioned idea'.

    Science.gov (United States)

    Mumford, M

    1991-12-01

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

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

    Science.gov (United States)

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

    2006-04-01

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

  20. Transmission electron microscope sample holder with optical features

    Science.gov (United States)

    Milas, Mirko [Port Jefferson, NY; Zhu, Yimei [Stony Brook, NY; Rameau, Jonathan David [Coram, NY

    2012-03-27

    A sample holder for holding a sample to be observed for research purposes, particularly in a transmission electron microscope (TEM), generally includes an external alignment part for directing a light beam in a predetermined beam direction, a sample holder body in optical communication with the external alignment part and a sample support member disposed at a distal end of the sample holder body opposite the external alignment part for holding a sample to be analyzed. The sample holder body defines an internal conduit for the light beam and the sample support member includes a light beam positioner for directing the light beam between the sample holder body and the sample held by the sample support member.

  1. Quantitation of tetrabromobisphenol-A from dust sampled on consumer electronics by dispersed liquid-liquid microextraction

    International Nuclear Information System (INIS)

    Di Napoli-Davis, Gina; Owens, Janel E.

    2013-01-01

    Tetrabromobisphenol-A (TBBPA) is a brominated flame retardant used worldwide. Despite its widespread use, there are few data concerning environmental concentrations of TBBPA. Thus, the objective of this work was to optimize an ultrasound-assisted dispersed liquid-liquid microextraction (DLLME) method to analyze swabbed surfaces of consumer electronics to determine TBBPA concentrations. Upon sample preparation with DLLME, TBBPA was derivatized with acetic anhydride and then analyzed by gas chromatography–mass spectrometry (GC/MS). Using a 13 C 12 -TBBPA internal standard to improve precision and quantitation, a recovery study was performed. At concentrations of 250–1000 ng/mL, recoveries were 104–106%. Sample preparation with solid phase extraction had comparable recoveries, although overall, improved analyte recovery and precision were achieved with DLLME. In a small survey study, TBBPA concentrations in dust collected from 100 cm 2 areas on electronic surfaces (monitor, microwave, refrigerator, and TV) were determined to range from less than the LOQ to 523 ng/mL. -- Highlights: •Tetrabromobisphenol-A (TBBPA) concentrations in dust samples were determined. •Dust samples were collected from surfaces of consumer electronics. •Dispersed liquid-liquid microextraction was used to prepare samples for GC/MS. •A 13 C 12 -labeled internal standard was used to improve precision and quantitation. •TBBPA was found in dust samples at levels below LOQ to 523 ng/mL. -- This work describes the analysis of the brominated flame retardant, tetrabromobisphenol-A (TBBPA), from dust sampled on surfaces of consumer electronics

  2. Sample Development on Java Smart-Card Electronic Wallet Application

    OpenAIRE

    Toma Cristian

    2009-01-01

    In this paper, are highlighted concepts as: complete Java card application, life cycle of an applet, and a practical electronic wallet sample implemented in Java card technology. As a practical approach it would be interesting building applets for ID, Driving License, Health-Insurance smart cards, for encrypt and digitally sign documents, for E-Commerce and for accessing critical resources in government and military field. The end of this article it is presented a java card electronic wallet ...

  3. Processing scarce biological samples for light and transmission electron microscopy

    Directory of Open Access Journals (Sweden)

    P Taupin

    2008-06-01

    Full Text Available Light microscopy (LM and transmission electron microscopy (TEM aim at understanding the relationship structure-function. With advances in biology, isolation and purification of scarce populations of cells or subcellular structures may not lead to enough biological material, for processing for LM and TEM. A protocol for preparation of scarce biological samples is presented. It is based on pre-embedding the biological samples, suspensions or pellets, in bovine serum albumin (BSA and bis-acrylamide (BA, cross-linked and polymerized. This preparation provides a simple and reproducible technique to process biological materials, present in limited quantities that can not be amplified, for light and transmission electron microscopy.

  4. Sample Preparation for Electron Probe Microanalysis—Pushing the Limits

    Science.gov (United States)

    Geller, Joseph D.; Engle, Paul D.

    2002-01-01

    There are two fundamental considerations in preparing samples for electron probe microanalysis (EPMA). The first one may seem obvious, but we often find it is overlooked. That is, the sample analyzed should be representative of the population from which it comes. The second is a direct result of the assumptions in the calculations used to convert x-ray intensity ratios, between the sample and standard, to concentrations. Samples originate from a wide range of sources. During their journey to being excited under the electron beam for the production of x rays there are many possibilities for sample alteration. Handling can contaminate samples by adding extraneous matter. In preparation, the various abrasives used in sizing the sample by sawing, grinding and polishing can embed themselves. The most accurate composition of a contaminated sample is, at best, not representative of the original sample; it is misleading. Our laboratory performs EPMA analysis on customer submitted samples and prepares over 250 different calibration standards including pure elements, compounds, alloys, glasses and minerals. This large variety of samples does not lend itself to mass production techniques, including automatic polishing. Our manual preparation techniques are designed individually for each sample. The use of automated preparation equipment does not lend itself to this environment, and is not included in this manuscript. The final step in quantitative electron probe microanalysis is the conversion of x-ray intensities ratios, known as the “k-ratios,” to composition (in mass fraction or atomic percent) and/or film thickness. Of the many assumptions made in the ZAF (where these letters stand for atomic number, absorption and fluorescence) corrections the localized geometry between the sample and electron beam, or takeoff angle, must be accurately known. Small angular errors can lead to significant errors in the final results. The sample preparation technique then becomes very

  5. Sample Preparation for Electron Probe Microanalysis-Pushing the Limits.

    Science.gov (United States)

    Geller, Joseph D; Engle, Paul D

    2002-01-01

    There are two fundamental considerations in preparing samples for electron probe microanalysis (EPMA). The first one may seem obvious, but we often find it is overlooked. That is, the sample analyzed should be representative of the population from which it comes. The second is a direct result of the assumptions in the calculations used to convert x-ray intensity ratios, between the sample and standard, to concentrations. Samples originate from a wide range of sources. During their journey to being excited under the electron beam for the production of x rays there are many possibilities for sample alteration. Handling can contaminate samples by adding extraneous matter. In preparation, the various abrasives used in sizing the sample by sawing, grinding and polishing can embed themselves. The most accurate composition of a contaminated sample is, at best, not representative of the original sample; it is misleading. Our laboratory performs EPMA analysis on customer submitted samples and prepares over 250 different calibration standards including pure elements, compounds, alloys, glasses and minerals. This large variety of samples does not lend itself to mass production techniques, including automatic polishing. Our manual preparation techniques are designed individually for each sample. The use of automated preparation equipment does not lend itself to this environment, and is not included in this manuscript. The final step in quantitative electron probe microanalysis is the conversion of x-ray intensities ratios, known as the "k-ratios," to composition (in mass fraction or atomic percent) and/or film thickness. Of the many assumptions made in the ZAF (where these letters stand for atomic number, absorption and fluorescence) corrections the localized geometry between the sample and electron beam, or takeoff angle, must be accurately known. Small angular errors can lead to significant errors in the final results. The sample preparation technique then becomes very

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

    OpenAIRE

    Ward, A; Hide, G; Jehle, R

    2018-01-01

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

  7. Radioactive and electron microscope analysis of effluent monitor sample lines

    International Nuclear Information System (INIS)

    Kowalski, J.F.

    1986-01-01

    Effluent air sampling at nuclear power plant often leads to the question ''How representative is the sample of the effluent stream?'' Samples from radiation monitors are typically obtained at great distances from the sample nozzle because of high background concerns under postulated accidents. Sample line plateout during normal effluent sampling becomes the major concern. A US Nuclear Regulatory Commission inspection raised a concern that monitors were not collecting representative samples per ANSI standard N13.1. A comprehensive 2-yr study at Beaver Valley was performed during normal effluent releases in two phases: 1) weekly charcoal and glass fiber filter samples were analyzed for radioactivity for 6 months, and 2) nuclepore membrane filter samples were analyzed by electron microscope for 4- and 6-h periods. A specially designed test nozzle was directly inserted into an effluent stream for comparison with the radiation monitor samples. Particle behavior characteristics can be determined during effluent releases using a simple test probe. While particle plateout was the major purpose of the study, other particle behavior characteristics were evident and equally as important. Particle travel through long sample lines can also lead to (a) agglomeration or the coagulation of smaller particles to form larger ones, (b) particle splitting or fracturing upon impact with the sample line interior walls, and (c) resuspension of large particles in sample lines

  8. 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.

  9. Early Results and Spaceflight Implications of the SWAB Flight Experiment

    Science.gov (United States)

    Ott, C. Mark; Pierson, Duane L.

    2007-01-01

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

  10. 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.

  11. Electron Spin Resonance (ESR) studies of returned comet nucleus samples

    International Nuclear Information System (INIS)

    Tsay, Fundow; Kim, S.S.; Liang, R.H.

    1989-01-01

    The most important objective of the Comet Nucleus Sample Returm Mission is to return samples which could reflect formation conditions and evolutionary processes in the early solar nebula. It is expected that the returned samples will consist of fine-grained silicate materials mixed with ices composed of simple molecules such as H 2 O, NH 3 , CH 4 as well as organics and/or more complex compounds. Because of the exposure to ionizing radiation from cosmic-ray, gamma-ray, and solar wind protons at low temperature, free radicals are expected to be formed and trapped in the solid ice matrices. The kind of trapped radical species together with their concentration and thermal stability can be used as a dosimeter as well as a geothermometer to determine thermal and radiation histories as well as outgassing and other possible alternation effects since the nucleus material was formed. Since free radicals that are known to contain unpaired electrons are all paramagnetic in nature, they can be readily detected and characterized in their native form by the Electron Spin Resonance (ESR) method. In fact, ESR has been shown to be a non-destructive, highly sensitive tool for the detection and characterization of paramagnetic, ferromagnetic, and radiation damage centers in terrestrial and extraterrestrial geological samples. The potential use of ESR as an effective method in the study of returned comet nucleus samples, in particular, in the analysis of fine-grained solid state icy samples is discussed

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Gérald Bertrand

    2016-07-01

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

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Michael S Adamowicz

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

  16. Quantification of multielement-multilayer-samples in electron probe analysis

    International Nuclear Information System (INIS)

    Pfeiffer, A.

    1995-03-01

    The following dissertation presents the theoretical basis of analytical correction models and Monte Carlo simulations in the field of electron probe microanalysis to describe the excitation conditions of x-rays in a multilayer-multielement-sample. In this connection analyzing programs have been developed to make a quantitative investigation of heterogeneous samples possible. In the work the mathematical methods and formulas, which are mainly based on empirical and semiempirical findings, are described and their validity is discussed in detail. Especially the improvements of the 'multiple reflections'-model by August are compared with the Φ(ρz)-models by Pouchou, Merlet and Bastin. The calculations of depth distribution functions for characteristics and continuous fluorescence excitation result in a consistent and completeΦ(ρz)-model. This allows to analyze layered structures in great detail. Because of the increasing importance in electron probe microanalysis and as a reference method a Monte Carlo model is described. With this model electron trajectories and excitation conditions in arbitrary two dimensional geometries can be calculated. The validity of the analytical model is proven with a comprehensive comparison of results of new calculations to published data. To show an application of the programs and models in routine use in the industrial research and development, a quantitative analysis of a Co/Si system is made. In the conclusion of this dissertation some reflections upon investigations, which are based on this work and which should be made in future are outlined. (author)

  17. 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.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2001-01-01

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

  20. Sample acceptance time criteria, electronic issue and alloimmunisation in thalassaemia.

    Science.gov (United States)

    Trompeter, S; Baxter, L; McBrearty, M; Zatkya, E; Porter, J

    2015-12-01

    To determine the safety of a 1-week acceptance criteria of sample receipt in laboratory to transfusion commencement in transfusion dependent thalassaemia with respect to alloimmunisation. To determine the safety of electronic issue of blood components in such a setting. Retrospective audit of alloimmunisation (1999-2012) and blood exposure in registered thalassaemia patients at a central London thalassaemia centre where the acceptance criteria for the group and save sample from arrival in the laboratory to the time of issue of blood for transfusion for someone who has been transfused in the last 28 days was 1 week, and there was electronic issue protocol for patients who have always had a negative antibody screen (other than temporary positivity in pregnant women receiving prophylactic anti-D or anti Le-a, Anti Le-b and Anti P1 that are no longer detectable). There were 133 patients with thalassemia variants regularly attending UCLH for review. A total of 105 patients had transfusion dependent thalassaemia (TDT) (7 E-beta thalassaemia, 98 beta thalassaemia major). Ten of the 84 patients who received their transfusions at UCLH were alloimmunised. Seven of them had been alloimmunised prior to arrival at UCLH. Only two patients developed antibodies at UCLH during this period. The prevalence of alloantibody formation of 2% in UCLH transfused patients, with presumptive incidence of 0.01 alloantibodies per 100 units or 0·001 immunisations per person per year compares favourably with other reported series and suggests that 1 week interval with appropriate electronic issue is acceptable practice. © 2015 British Blood Transfusion Society.

  1. 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.

  2. 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

  3. Scanning electron microscope autoradiography of critical point dried biological samples

    International Nuclear Information System (INIS)

    Weiss, R.L.

    1980-01-01

    A technique has been developed for the localization of isotopes in the scanning electron microscope. Autoradiographic studies have been performed using a model system and a unicellular biflagellate alga. One requirement of this technique is that all manipulations be carried out on samples that are maintained in a liquid state. Observations of a source of radiation ( 125 I-ferritin) show that the nuclear emulsion used to detect radiation is active under these conditions. Efficiency measurement performed using 125 I-ferritin indicate that 125 I-SEM autoradiography is an efficient process that exhibits a 'dose dependent' response. Two types of labeling methods were used with cells, surface labeling with 125 I and internal labeling with 3 H. Silver grains appeared on labeled cells after autoradiography, removal of residual gelatin and critical point drying. The location of grains was examined on a flagellated green alga (Chlamydomonas reinhardi) capable of undergoing cell fusion. Fusion experiments using labeled and unlabeled cells indicate that 1. Labeling is specific for incorporated radioactivity; 2. Cell surface structure is preserved in SEM autoradiographs and 3. The technique appears to produce reliable autoradiographs. Thus scanning electron microscope autoradiography should provide a new and useful experimental approach

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

    Directory of Open Access Journals (Sweden)

    Charlene S Dezzutti

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

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

    Science.gov (United States)

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

    2018-04-26

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

  6. Self-Collected Nasal Swabs for Respiratory Virus Surveillance

    Science.gov (United States)

    Jackson, Michael L.; Nguyen, Matthew; Kirlin, Beth; Madziwa, Lawrence

    2015-01-01

    We tested whether 135 patients reporting acute respiratory illness (ARI) could self-collect nasal swab specimens and ship them for laboratory testing. Most subjects (78.2%) collected and shipped their specimens without errors; 10.5% excluded ≥1 packing components; 12.9% made ≥1 packing errors. Self-swabbing at home is feasible for confirming ARI etiology. PMID:26613095

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

    Directory of Open Access Journals (Sweden)

    Shubham Banik

    2017-12-01

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

  8. Scanning Electron Microscopy with Samples in an Electric Field

    Czech Academy of Sciences Publication Activity Database

    Frank, Luděk; Hovorka, Miloš; Mikmeková, Šárka; Mikmeková, Eliška; Müllerová, Ilona; Pokorná, Zuzana

    2012-01-01

    Roč. 5, č. 12 (2012), s. 2731-2756 ISSN 1996-1944 R&D Projects: GA ČR GAP108/11/2270; GA TA ČR TE01020118; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : scanning electron microscopy * slow electrons * low energy SEM * low energy STEM * cathode lens Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 2.247, year: 2012

  9. 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.

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Science.gov (United States)

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

    2011-07-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  13. Seeking responsibility for the lost swab? Search elsewhere.

    Science.gov (United States)

    Wheeler, R; Blackburn, S; Biggs, H

    2014-04-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  15. Sparse sampling and reconstruction for electron and scanning probe microscope imaging

    Science.gov (United States)

    Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

    2015-07-28

    Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

  16. 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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Barrall, R. C.

    1963-06-15

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

  1. Detecting Rickettsia parkeri Infection from Eschar Swab Specimens

    Science.gov (United States)

    2013-05-01

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

  2. Detectors, sampling, shielding, and electronics for positron emission tomography

    International Nuclear Information System (INIS)

    Derenzo, S.E.

    1981-08-01

    A brief discussion of the important design elements for positron emission tomographs is presented. The conclusions are that the instrumentation can be improved by the use of larger numbers of small, efficient detectors closely packed in many rings, the development of new detector materials, and novel electronic designs to reduce the deadtime and increase maximum event rates

  3. Sample Preparation and Imaging of Exosomes by Transmission Electron Microscopy.

    Science.gov (United States)

    Jung, Min Kyo; Mun, Ji Young

    2018-01-04

    Exosomes are nano-sized extracellular vesicles secreted by body fluids and are known to represent the characteristics of cells that secrete them. The contents and morphology of the secreted vesicles reflect cell behavior or physiological status, for example cell growth, migration, cleavage, and death. The exosomes' role may depend highly on size, and the size of exosomes varies from 30 to 300 nm. The most widely used method for exosome imaging is negative staining, while other results are based on Cryo-Transmission Electron Microscopy, Scanning Electron Microscopy, and Atomic Force Microscopy. The typical exosome's morphology assessed through negative staining is a cup-shape, but further details are not yet clear. An exosome well-characterized through structural study is necessary particular in medical and pharmaceutical fields. Therefore, function-dependent morphology should be verified by electron microscopy techniques such as labeling a specific protein in the detailed structure of exosome. To observe detailed structure, ultrathin sectioned images and negative stained images of exosomes were compared. In this protocol, we suggest transmission electron microscopy for the imaging of exosomes including negative staining, whole mount immuno-staining, block preparation, thin section, and immuno-gold labelling.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2018-03-27

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

  6. Transmission electron microscope cells for use with liquid samples

    Science.gov (United States)

    Khalid, Waqas; Alivisatos, Paul A.; Zettl, Alexander K.

    2016-08-09

    This disclosure provides systems, methods, and devices related to transmission electron microscopy cells for use with liquids. In one aspect a device includes a substrate, a first graphene layer, and a second graphene layer. The substrate has a first surface and a second surface. The first surface defines a first channel, a second channel, and an outlet channel. The first channel and the second channel are joined to the outlet channel. The outlet channel defines a viewport region forming a though hole in the substrate. The first graphene layer overlays the first surface of the substrate, including an interior area of the first channel, the second channel, and the outlet channel. The second graphene layer overlays the first surface of the substrate, including open regions defined by the first channel, the second channel, and the outlet channel.

  7. An electron-hadron separator for digital sampling calorimeters

    International Nuclear Information System (INIS)

    Winter, K. de; Geiregat, D.; Vilain, P.; Wilquet, G.; Bergsma, F.; Binder, U.; Burkard, H.; Capone, A.; Ereditato, A.; Flegel, W.; Grote, H.; Nieuwenhuis, C.; Oeveras, H.; Palladino, V.; Panman, J.; Piredda, G.; Winter, K.; Zacek, G.; Zacek, V.; Bauche, T.; Beyer, R.; Blobel, V.; Buesser, F.W.; Foos, C.; Gerland, L.; Niebergall, F.; Staehelin, P.; Tadsen, A.; Gorbunov, P.; Grigoriev, E.; Khovansky, V.; Maslennikov, A.; Rosanov, A.; Lippich, W.; Nathaniel, A.; Staude, A.; De Pedis, D.; Di Capua, E.; Dore, U.; Loverre, P.F.; Rambaldi-Frenkel, A.; Santacesaria, R.; Zanello, D.

    1989-01-01

    A fast and effective algorithm for electromagnetic and hadronic shower separation has been developed for the digital sampling calorimeter of the CHARM II experiment. It is based on a generalization of the minimal spanning tree concept and can be easily applied to other existing calorimeters. In this particular application, which requires the highest efficiency for retaining electromagnetic showers, one gets, for 99% efficiency, a rejection factor of the order of 100 for hadronic showers. (orig.)

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Science.gov (United States)

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

    2018-02-20

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

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

    Science.gov (United States)

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

    2014-11-25

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

  11. 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.

  12. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy.

    Science.gov (United States)

    Zhang, Ying; Huang, Tao; Jorgens, Danielle M; Nickerson, Andrew; Lin, Li-Jung; Pelz, Joshua; Gray, Joe W; López, Claudia S; Nan, Xiaolin

    2017-01-01

    Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.

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

    Science.gov (United States)

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

    1999-01-01

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

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

    Science.gov (United States)

    Suyatmi; Subiyantoro, P.; Indrakila, S.

    2018-05-01

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

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

    Science.gov (United States)

    Nenadić, Dane; Pavlović, Miloš D

    2015-06-01

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

  17. SWAB guidelines for antimicrobial therapy of acute infectious diarrhoea

    NARCIS (Netherlands)

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

    2006-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    DEFF Research Database (Denmark)

    Baczynska, Agata; Fedder, J; Schougaard, H

    2007-01-01

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

  20. Electronic-nose technology using sputum samples in diagnosis of patients with tuberculosis

    NARCIS (Netherlands)

    Kolk, A.; Hoelscher, M.; Maboko, L.; Jung, J.; Kuijper, S.; Cauchi, M.; Bessant, C.; van Beers, S.; Dutta, R.; Gibson, T.; Reither, K.

    2010-01-01

    We investigated the potential of two different electronic noses (EN; code named "Rob" and "Walter") to differentiate between sputum headspace samples from tuberculosis (TB) patients and non-TB patients. Only samples from Ziehl-Neelsen stain (ZN)- and Mycobacterium tuberculosis culture-positive

  1. Influence of Plastic Deformation of Steel Samples on the Fast electron Backscattering

    International Nuclear Information System (INIS)

    Sierra Trujillo, J. X.; Herrera Palma, V.; Desdin Garcia, L. F.; Codorniu Pujals, D.

    2013-01-01

    A considerable fraction of a fast electron beam incident on a target is scattered in backward direction. It is a very complex process involving electron - nucleus and electron - electron collisions. The fraction of backscattered electrons is described by a parameterization as a function of the atomic number and energy of the incident electrons. In such approaches the possible influence of the material structure is not taken into account. In this paper, the behavior of the 90 Sr/ 90 Y backscattered electrons from 08JuA and 15GJuT steel strained samples is investigated. A clear dependence between the degree of plastic deformation and the fraction of backscattered electrons was observed. This relationship is explained by the interaction of electrons with the dislocations in the material, whose density depends on the magnitude of the strain in the plastic region. On the basis of a simple model for describing this interaction, a mathematical expression is obtained for the relationship between the fraction of backscattered electrons and the degree of deformation. (Author)

  2. Use of the VS-sense swab in diagnosing vulvovaginitis.

    Science.gov (United States)

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

    2009-09-01

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

  3. Diagnostic herd sensitivity using environmental samples

    DEFF Research Database (Denmark)

    Vigre, Håkan; Josefsen, Mathilde Hartmann; Seyfarth, Anne Mette

    either at farm or slaughter. Three sample matrices were collected; dust samples (5 environmental swabs), nasal swabs (10 pools with 5 animals per pool) and air samples (1 filter). Based on the assumption that MRSA occurred in all 48 herds the overall herd sensitivity was 58% for nasal swabs, 33% for dust....... In our example, the prevalence of infected pigs in each herd was estimated from the pooled samples of nasal swabs. Logistic regression was used to estimate the effect of animal prevalence on the probability to detect MRSA in the dust and air samples at herd level. The results show a significant increase...

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

    Science.gov (United States)

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

    2017-09-12

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

  5. Dynamical "in situ" observation of biological samples using variable pressure scanning electron microscope

    Czech Academy of Sciences Publication Activity Database

    Neděla, Vilém

    2008-01-01

    Roč. 126, - (2008), 012046:1-4 ISSN 1742-6588. [Electron Microscopy and Analysis Group Conference 2007 (EMAG 2007). Glasgow, 03.09.2007-07.09.2007] R&D Projects: GA ČR(CZ) GA102/05/0886; GA AV ČR KJB200650602 Institutional research plan: CEZ:AV0Z20650511 Keywords : biological sample * VP-SEM * dynamical experiments Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  6. The electron transport problem sampling by Monte Carlo individual collision technique

    International Nuclear Information System (INIS)

    Androsenko, P.A.; Belousov, V.I.

    2005-01-01

    The problem of electron transport is of most interest in all fields of the modern science. To solve this problem the Monte Carlo sampling has to be used. The electron transport is characterized by a large number of individual interactions. To simulate electron transport the 'condensed history' technique may be used where a large number of collisions are grouped into a single step to be sampled randomly. Another kind of Monte Carlo sampling is the individual collision technique. In comparison with condensed history technique researcher has the incontestable advantages. For example one does not need to give parameters altered by condensed history technique like upper limit for electron energy, resolution, number of sub-steps etc. Also the condensed history technique may lose some very important tracks of electrons because of its limited nature by step parameters of particle movement and due to weakness of algorithms for example energy indexing algorithm. There are no these disadvantages in the individual collision technique. This report presents some sampling algorithms of new version BRAND code where above mentioned technique is used. All information on electrons was taken from Endf-6 files. They are the important part of BRAND. These files have not been processed but directly taken from electron information source. Four kinds of interaction like the elastic interaction, the Bremsstrahlung, the atomic excitation and the atomic electro-ionization were considered. In this report some results of sampling are presented after comparison with analogs. For example the endovascular radiotherapy problem (P2) of QUADOS2002 was presented in comparison with another techniques that are usually used. (authors)

  7. The electron transport problem sampling by Monte Carlo individual collision technique

    Energy Technology Data Exchange (ETDEWEB)

    Androsenko, P.A.; Belousov, V.I. [Obninsk State Technical Univ. of Nuclear Power Engineering, Kaluga region (Russian Federation)

    2005-07-01

    The problem of electron transport is of most interest in all fields of the modern science. To solve this problem the Monte Carlo sampling has to be used. The electron transport is characterized by a large number of individual interactions. To simulate electron transport the 'condensed history' technique may be used where a large number of collisions are grouped into a single step to be sampled randomly. Another kind of Monte Carlo sampling is the individual collision technique. In comparison with condensed history technique researcher has the incontestable advantages. For example one does not need to give parameters altered by condensed history technique like upper limit for electron energy, resolution, number of sub-steps etc. Also the condensed history technique may lose some very important tracks of electrons because of its limited nature by step parameters of particle movement and due to weakness of algorithms for example energy indexing algorithm. There are no these disadvantages in the individual collision technique. This report presents some sampling algorithms of new version BRAND code where above mentioned technique is used. All information on electrons was taken from Endf-6 files. They are the important part of BRAND. These files have not been processed but directly taken from electron information source. Four kinds of interaction like the elastic interaction, the Bremsstrahlung, the atomic excitation and the atomic electro-ionization were considered. In this report some results of sampling are presented after comparison with analogs. For example the endovascular radiotherapy problem (P2) of QUADOS2002 was presented in comparison with another techniques that are usually used. (authors)

  8. A new Langmuir probe concept for rapid sampling of space plasma electron density

    International Nuclear Information System (INIS)

    Jacobsen, K S; Pedersen, A; Moen, J I; Bekkeng, T A

    2010-01-01

    In this paper we describe a new Langmuir probe concept that was invented for the in situ investigation of HF radar backscatter irregularities, with the capability to measure absolute electron density at a resolution sufficient to resolve the finest conceivable structure in an ionospheric plasma. The instrument consists of two or more fixed-bias cylindrical Langmuir probes whose radius is small compared to the Debye length. With this configuration, it is possible to acquire absolute electron density measurements independent of electron temperature and rocket/satellite potential. The system was flown on the ICI-2 sounding rocket to investigate the plasma irregularities which cause HF backscatter. It had a sampling rate of more than 5 kHz and successfully measured structures down to the scale of one electron gyro radius. The system can easily be adapted for any ionospheric rocket or satellite, and provides high-quality measurements of electron density at any desired resolution

  9. A Transmission Electron Microscope Investigation of Space Weathering Effects in Hayabusa Samples

    Science.gov (United States)

    Keller, Lindsay P.; Berger, Eve L.

    2014-01-01

    The Hayabusa mission to asteroid 25143 Itokawa successfully returned the first direct samples of the regolith from the surface of an asteroid. The Hayabusa samples thus present a special opportunity to directly investigate the evolution of asteroidal surfaces, from the development of the regolith to the study of the more complex effects of space weathering. Here we describe the mineralogy, microstructure and composition of three Hayabusa mission particles using transmission electron microscope (TEM) techniques

  10. The Atmospheric Scanning Electron Microscope with open sample space observes dynamic phenomena in liquid or gas.

    Science.gov (United States)

    Suga, Mitsuo; Nishiyama, Hidetoshi; Konyuba, Yuji; Iwamatsu, Shinnosuke; Watanabe, Yoshiyuki; Yoshiura, Chie; Ueda, Takumi; Sato, Chikara

    2011-12-01

    Although conventional electron microscopy (EM) requires samples to be in vacuum, most chemical and physical reactions occur in liquid or gas. The Atmospheric Scanning Electron Microscope (ASEM) can observe dynamic phenomena in liquid or gas under atmospheric pressure in real time. An electron-permeable window made of pressure-resistant 100 nm-thick silicon nitride (SiN) film, set into the bottom of the open ASEM sample dish, allows an electron beam to be projected from underneath the sample. A detector positioned below captures backscattered electrons. Using the ASEM, we observed the radiation-induced self-organization process of particles, as well as phenomena accompanying volume change, including evaporation-induced crystallization. Using the electrochemical ASEM dish, we observed tree-like electrochemical depositions on the cathode. In silver nitrate solution, we observed silver depositions near the cathode forming incidental internal voids. The heated ASEM dish allowed observation of patterns of contrast in melting and solidifying solder. Finally, to demonstrate its applicability for monitoring and control of industrial processes, silver paste and solder paste were examined at high throughput. High resolution, imaging speed, flexibility, adaptability, and ease of use facilitate the observation of previously difficult-to-image phenomena, and make the ASEM applicable to various fields. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Minimum detection limit and spatial resolution of thin-sample field-emission electron probe microanalysis

    International Nuclear Information System (INIS)

    Kubo, Yugo; Hamada, Kotaro; Urano, Akira

    2013-01-01

    The minimum detection limit and spatial resolution for a thinned semiconductor sample were determined by electron probe microanalysis (EPMA) using a Schottky field emission (FE) electron gun and wavelength dispersive X-ray spectrometry. Comparison of the FE-EPMA results with those obtained using energy dispersive X-ray spectrometry in conjunction with scanning transmission electron microscopy, confirmed that FE-EPMA is largely superior in terms of detection sensitivity. Thin-sample FE-EPMA is demonstrated as a very effective method for high resolution, high sensitivity analysis in a laboratory environment because a high probe current and high signal-to-noise ratio can be achieved. - Highlights: • Minimum detection limit and spatial resolution determined for FE-EPMA. • Detection sensitivity of FE-EPMA greatly superior to that of STEM-EDX. • Minimum detection limit and spatial resolution controllable by probe current

  12. Process and device of elementary and chemical analysis of a sample through a spectral analysis of the secondary electron energies

    International Nuclear Information System (INIS)

    Le Gressus, Claude; Massignon, Daniel; Sopizet, Rene.

    1975-01-01

    The present invention relates to a method of chemical and elementary analysis of samples through a spectral analysis of secondary electrons (Auger electrons) emitted from said sample under a primary monokinetic electron beam concentrated on its surface. Said method is characterized in that the intensity of the primary monokinetic electron beam emitted from an electron gun is modulated at a frequency ω; and in that the secondary electrons of energy E emitted from the sample are then collected. A reference voltage corresponding to the modulation in intensity of the primary electron beam is applied at the input of a phase sensitive detector together with a voltage proportional to the intensity of the flux of said collected secondary electrons to obtain at the output of said detector a voltage proportional to the number of the secondary electrons of energy E. The secondary emission energy spectrum of the sample is then plotted [fr

  13. Secondary electron emission and self-consistent charge transport in semi-insulating samples

    Energy Technology Data Exchange (ETDEWEB)

    Fitting, H.-J. [Institute of Physics, University of Rostock, Universitaetsplatz 3, D-18051 Rostock (Germany); Touzin, M. [Unite Materiaux et Transformations, UMR CNRS 8207, Universite de Lille 1, F-59655 Villeneuve d' Ascq (France)

    2011-08-15

    Electron beam induced self-consistent charge transport and secondary electron emission (SEE) in insulators are described by means of an electron-hole flight-drift model (FDM) now extended by a certain intrinsic conductivity (c) and are implemented by an iterative computer simulation. Ballistic secondary electrons (SE) and holes, their attenuation to drifting charge carriers, and their recombination, trapping, and field- and temperature-dependent detrapping are included. As a main result the time dependent ''true'' secondary electron emission rate {delta}(t) released from the target material and based on ballistic electrons and the spatial distributions of currents j(x,t), charges {rho}(x,t), field F(x,t), and potential V(x,t) are obtained where V{sub 0} = V(0,t) presents the surface potential. The intrinsic electronic conductivity limits the charging process and leads to a conduction sample current to the support. In that case the steady-state total SE yield will be fixed below the unit: i.e., {sigma} {eta} + {delta} < 1.

  14. Acetic Acid Detection Threshold in Synthetic Wine Samples of a Portable Electronic Nose

    Directory of Open Access Journals (Sweden)

    Miguel Macías Macías

    2012-12-01

    Full Text Available Wine quality is related to its intrinsic visual, taste, or aroma characteristics and is reflected in the price paid for that wine. One of the most important wine faults is the excessive concentration of acetic acid which can cause a wine to take on vinegar aromas and reduce its varietal character. Thereby it is very important for the wine industry to have methods, like electronic noses, for real-time monitoring the excessive concentration of acetic acid in wines. However, aroma characterization of alcoholic beverages with sensor array electronic noses is a difficult challenge due to the masking effect of ethanol. In this work, in order to detect the presence of acetic acid in synthetic wine samples (aqueous ethanol solution at 10% v/v we use a detection unit which consists of a commercial electronic nose and a HSS32 auto sampler, in combination with a neural network classifier (MLP. To find the characteristic vector representative of the sample that we want to classify, first we select the sensors, and the section of the sensors response curves, where the probability of detecting the presence of acetic acid will be higher, and then we apply Principal Component Analysis (PCA such that each sensor response curve is represented by the coefficients of its first principal components. Results show that the PEN3 electronic nose is able to detect and discriminate wine samples doped with acetic acid in concentrations equal or greater than 2 g/L.

  15. 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.

  16. 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.

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

    Science.gov (United States)

    2009-01-01

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

  18. Interpretation of nasal swab measurements following suspected releases of actinide aerosols

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  19. 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.

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

    Science.gov (United States)

    Nagai, T; Nakayama, T

    2001-01-08

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

  1. Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm.

    Science.gov (United States)

    Famulari, Gabriel; Pater, Piotr; Enger, Shirin A

    2017-07-07

    The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(>E)/f(>0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.

  2. Electro-optic sampling for time resolving relativistic ultrafast electron diffraction

    International Nuclear Information System (INIS)

    Scoby, C. M.; Musumeci, P.; Moody, J.; Gutierrez, M.; Tran, T.

    2009-01-01

    The Pegasus laboratory at UCLA features a state-of-the-art electron photoinjector capable of producing ultrashort (<100 fs) high-brightness electron bunches at energies of 3.75 MeV. These beams recently have been used to produce static diffraction patterns from scattering off thin metal foils, and it is foreseen to take advantage of the ultrashort nature of these bunches in future pump-probe time-resolved diffraction studies. In this paper, single shot 2-d electro-optic sampling is presented as a potential technique for time of arrival stamping of electron bunches used for diffraction. Effects of relatively low bunch charge (a few 10's of pC) and modestly relativistic beams are discussed and background compensation techniques to obtain high signal-to-noise ratio are explored. From these preliminary tests, electro-optic sampling is suitable to be a reliable nondestructive time stamping method for relativistic ultrafast electron diffraction at the Pegasus lab.

  3. The problem of large samples. An activation analysis study of electronic waste material

    International Nuclear Information System (INIS)

    Segebade, C.; Goerner, W.; Bode, P.

    2007-01-01

    Large-volume instrumental photon activation analysis (IPAA) was used for the investigation of shredded electronic waste material. Sample masses from 1 to 150 grams were analyzed to obtain an estimate of the minimum sample size to be taken to achieve a representativeness of the results which is satisfactory for a defined investigation task. Furthermore, the influence of irradiation and measurement parameters upon the quality of the analytical results were studied. Finally, the analytical data obtained from IPAA and instrumental neutron activation analysis (INAA), both carried out in a large-volume mode, were compared. Only parts of the values were found in satisfactory agreement. (author)

  4. On the preparation of electron sensor using LiRbSO4 samples

    Science.gov (United States)

    El-Muraikhi, M.; Kassem, M. E.; Gaafar, M.; Abdel Gawad, M. M. H.; Ragab, I. M.

    2005-01-01

    The dielectric spectroscopy of metal-metal sulfate LiRbSO4 samples are described with particular emphasis on sensor performance to be used in the field of radiation. The obtained results as the effect of different electron energy beams at fixed dose, 0.5 Gy, showed abrupt change of the electrical properties (electrical conductivity, capacitance, and loss tangent). The results can be explained on the basis of radiation-induced defects followed by radiation quenching. The prepared samples can be used in the field of radiation dosimeter.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  6. Note: A scanning electron microscope sample holder for bidirectional characterization of atomic force microscope probe tips

    Energy Technology Data Exchange (ETDEWEB)

    Eisenstein, Alon; Goh, M. Cynthia [Department of Chemistry and Institute for Optical Sciences, University of Toronto, 80 St. George Street, Toronto M5S 3H6 (Canada)

    2012-03-15

    A novel sample holder that enables atomic force microscopy (AFM) tips to be mounted inside a scanning electron microscopy (SEM) for the purpose of characterizing the AFM tips is described. The holder provides quick and easy handling of tips by using a spring clip to hold them in place. The holder can accommodate two tips simultaneously in two perpendicular orientations, allowing both top and side view imaging of the tips by the SEM.

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

    Science.gov (United States)

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

    2011-04-13

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

  8. Electron spin resonance of particulate soot samples from automobiles to help environmental studies

    International Nuclear Information System (INIS)

    Yamanaka, C.; Matsuda, T.; Ikeya, M.

    2005-01-01

    The application of electron spin resonance (ESR) was studied for diesel soot samples and suspended particulate matter (SPM) from automobile engines. Soot samples or diesel exhaust particles (DEP) were recovered at various points: in the exhaust pipe of a diesel engine, at the dust sampler of a highway tunnel (standard DEP), on the soundproofing wall alongside a heavy traffic road, and on the filters of a dust sampler for SPM. The diesel soot samples apparently showed two ESR spectra: one was a broad spectrum at g=2.1 with a line width of ca. 80-120mT and the other was a sharp signal of a carbon radical at g=2.003 with a line width of 0.4mT. Annealing experiments with a DEP sample at 250 deg. C revealed drastic enhancement of the sharp ESR signal, which suggested a thermal process of carbonization of remnant organics. An oximetric study by ESR showed an enhancement of the broad signal in the diesel soot sample as well as in the sharp ESR signal. Therefore, the main part of the broad ESR signal would be attributed to carbon radicals, which form a different configuration, probably closely interacting aggregates. Enhancement of the sharp ESR signal was not observed in the standard DEP sample under vacuum condition, which suggested less adsorption sites on the surface of DEP samples

  9. Evaluation of swabs, transport media, and specimen transport conditions for optimal detection of viruses by PCR.

    Science.gov (United States)

    Druce, Julian; Garcia, Katherine; Tran, Thomas; Papadakis, Georgina; Birch, Chris

    2012-03-01

    Depletion of swabs and viral transport medium during epidemics may prompt the use of unvalidated alternatives. Swabs collected and transported dry or in saline were compared to commercially available swab/medium combinations for PCR detection of influenza, enterovirus, herpes simplex virus, and adenovirus. Each was detected at an ambient temperature (22°C) and 4°C for 7 days. Detection of influenza on dry or saline swabs is important because of its capacity to cause outbreaks involving large numbers of cases.

  10. 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 (SpO 2 ) and peripheral perfusion index (PI) were recorded. Placement of a gauze swab between the pulse oximeter probe and the tongue in anaesthetised dogs and cats resulted in significantly higher SpO 2 values compared with the control group. In dogs, PI values were significantly higher than the control in all groups except the quarter thickness swab group. In cats, PI was significantly higher in the double thickness swab and white paper groups compared with the control. Cats had significantly higher SpO 2 and lower PI values than dogs. The authors propose that increased contact pressure is responsible for significantly higher SpO 2 and PI readings with the use of a lingual gauze swab resulting from changes in transmural pressure and arterial compliance. British Veterinary Association.

  11. 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

  12. Relativistic electron influence on sanitary-model microorganisms and antibiotics in model samples

    International Nuclear Information System (INIS)

    Antipov, V.S.; Berezhna, I.V.; Kovpik, O.F.; Babych, E.M.; Voliansky, Yu.L.; Sklar, N.I.

    2004-01-01

    A series of the investigations of the electron beam influence on sanitary-model test cultures and antibiotics in model solutions has been carried out. For each of the test objects, the authors have found the boundary doses of the absorbed radiation. The higher doses cause the sharp increase in the bactericidal influence, which becomes complete. The sanitary-bactericidal indices of the water samples remain sable during 6 days. The samples of antibiotics in various concentrations (from 100 UA) have been irradiated. It is proved that the substratum processing by the beam (in the regimes 30 kGy) causes diminution and complete neutralization of the antibacterial activity in all probes of the samples

  13. On the role of the gas environment, electron-dose-rate, and sample on the image resolution in transmission electron microscopy

    DEFF Research Database (Denmark)

    Ek, Martin; Jespersen, Sebastian Pirel Fredsgaard; Damsgaard, Christian Danvad

    2016-01-01

    on the electron-dose-rate. In this article, we demonstrate that both the total and areal electron-dose-rates work as descriptors for the dose-rate-dependent resolution and are related through the illumination area. Furthermore, the resolution degradation was observed to occur gradually over time after......The introduction of gaseous atmospheres in transmission electron microscopy offers the possibility of studying materials in situ under chemically relevant environments. The presence of a gas environment can degrade the resolution. Surprisingly, this phenomenon has been shown to depend...... initializing the illumination of the sample and gas by the electron beam. The resolution was also observed to be sensitive to the electrical conductivity of the sample. These observations can be explained by a charge buildup over the electron-illuminated sample area, caused by the beam–gas–sample interaction...

  14. Atmospheric scanning electron microscope system with an open sample chamber: Configuration and applications

    International Nuclear Information System (INIS)

    Nishiyama, Hidetoshi; Koizumi, Mitsuru; Ogawa, Koji; Kitamura, Shinich; Konyuba, Yuji; Watanabe, Yoshiyuki; Ohbayashi, Norihiko; Fukuda, Mitsunori; Suga, Mitsuo; Sato, Chikara

    2014-01-01

    An atmospheric scanning electron microscope (ASEM) with an open sample chamber and optical microscope (OM) is described and recent developments are reported. In this ClairScope system, the base of the open sample dish is sealed to the top of the inverted SEM column, allowing the liquid-immersed sample to be observed by OM from above and by SEM from below. The optical axes of the two microscopes are aligned, ensuring that the same sample areas are imaged to realize quasi-simultaneous correlative microscopy in solution. For example, the cathodoluminescence of ZnO particles was directly demonstrated. The improved system has (i) a fully motorized sample stage, (ii) a column protection system in the case of accidental window breakage, and (iii) an OM/SEM operation system controlled by a graphical user interface. The open sample chamber allows the external administration of reagents during sample observation. We monitored the influence of added NaCl on the random motion of silica particles in liquid. Further, using fluorescence as a transfection marker, the effect of small interfering RNA-mediated knockdown of endogenous Varp on Tyrp1 trafficking in melanocytes was examined. A temperature-regulated titanium ASEM dish allowed the dynamic observation of colloidal silver nanoparticles as they were heated to 240 °C and sintered. - Highlights: • Atmospheric SEM (ASEM) allows observation of samples in liquid or gas. • Open sample chamber allows in situ monitoring of evaporation and sintering processes. • in situ monitoring of processes during reagent administration is also accomplished. • Protection system for film breakage is developed for ASEM. • Usability of ASEM has been improved significantly including GUI control

  15. Atmospheric scanning electron microscope system with an open sample chamber: Configuration and applications

    Energy Technology Data Exchange (ETDEWEB)

    Nishiyama, Hidetoshi, E-mail: hinishiy@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Koizumi, Mitsuru, E-mail: koizumi@jeol.co.jp [JEOL Technics Ltd., 2-6-38 Musashino, Akishima, Tokyo 196-0021 (Japan); Ogawa, Koji, E-mail: kogawa@jeol.co.jp [JEOL Technics Ltd., 2-6-38 Musashino, Akishima, Tokyo 196-0021 (Japan); Kitamura, Shinich, E-mail: kitamura@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Konyuba, Yuji, E-mail: ykonyuub@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Watanabe, Yoshiyuki, E-mail: watanabeyoshiy@pref.yamagata.jp [Yamagata Research Institute of Technology, 2-2-1, Matsuei, Yamagata 990-2473 (Japan); Ohbayashi, Norihiko, E-mail: n.ohbayashi@m.tohoku.ac.jp [Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Fukuda, Mitsunori, E-mail: nori@m.tohoku.ac.jp [Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Suga, Mitsuo, E-mail: msuga@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Sato, Chikara, E-mail: ti-sato@aist.go.jp [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-4, Umezono, Tsukuba 305-8568 (Japan)

    2014-12-15

    An atmospheric scanning electron microscope (ASEM) with an open sample chamber and optical microscope (OM) is described and recent developments are reported. In this ClairScope system, the base of the open sample dish is sealed to the top of the inverted SEM column, allowing the liquid-immersed sample to be observed by OM from above and by SEM from below. The optical axes of the two microscopes are aligned, ensuring that the same sample areas are imaged to realize quasi-simultaneous correlative microscopy in solution. For example, the cathodoluminescence of ZnO particles was directly demonstrated. The improved system has (i) a fully motorized sample stage, (ii) a column protection system in the case of accidental window breakage, and (iii) an OM/SEM operation system controlled by a graphical user interface. The open sample chamber allows the external administration of reagents during sample observation. We monitored the influence of added NaCl on the random motion of silica particles in liquid. Further, using fluorescence as a transfection marker, the effect of small interfering RNA-mediated knockdown of endogenous Varp on Tyrp1 trafficking in melanocytes was examined. A temperature-regulated titanium ASEM dish allowed the dynamic observation of colloidal silver nanoparticles as they were heated to 240 °C and sintered. - Highlights: • Atmospheric SEM (ASEM) allows observation of samples in liquid or gas. • Open sample chamber allows in situ monitoring of evaporation and sintering processes. • in situ monitoring of processes during reagent administration is also accomplished. • Protection system for film breakage is developed for ASEM. • Usability of ASEM has been improved significantly including GUI control.

  16. Sample preparation technique for transmission electron microscopy anodized Al-Li-SiC metal matrix composite

    International Nuclear Information System (INIS)

    Shahid, M.; Thomson, G.E.

    1997-01-01

    Along with improved mechanical properties, metal matrix composites (MMC) have a disadvantage of enhanced corrosion susceptibility in aggressive environments. Recent studies on corrosion behaviour of an Al-alloy 8090/SiC MMC, revealed considerably high corrosion rates of the MMC in near neutral solutions containing chloride ions. Anodizing is one of the potential surface treatment for the MMC to provide protective coating against corrosion. The surface and cross section of the anodized MMC can easily be observed using scanning electron microscope. The anodizing behaviour of the MMC can be understood further if the anodized cross section in examined under transmission electron microscope (TEM). However, it is relatively difficult to prepare small (3 mm diameter) electron transparent specimens of the MMC supporting an anodic film. In the present study a technique has been developed for preparing thin electron transparent specimens of the anodized MMC. This technique employed conventional ion beam thinning process but the preparation of small discs was a problem. A MMMC consisting of Al-alloy 8090 with 20 % (by weight) SiC particulate with an average size of 5 Mu m, was anodized and observed in TEM after preparing the samples using the above mentioned techniques. (author)

  17. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy.

    Science.gov (United States)

    Faas, F G A; Bárcena, M; Agronskaia, A V; Gerritsen, H C; Moscicka, K B; Diebolder, C A; van Driel, L F; Limpens, R W A L; Bos, E; Ravelli, R B G; Koning, R I; Koster, A J

    2013-03-01

    Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and structural information from a selected field of view at nm-scale resolution. Previously, an integrated approach to room temperature correlative microscopy was described. Combined use of light and electron microscopy within one instrument greatly simplifies sample handling, avoids cumbersome experimental overheads, simplifies navigation between the two modalities, and improves the success rate of image correlation. Here, an integrated approach for correlative microscopy under cryogenic conditions is presented. Its advantages over the room temperature approach include safeguarding the native hydrated state of the biological specimen, preservation of the fluorescence signal without risk of quenching due to heavy atom stains, and reduced photo bleaching. The potential of cryo integrated light and electron microscopy is demonstrated for the detection of viable bacteria, the study of in vitro polymerized microtubules, the localization of mitochondria in mouse embryonic fibroblasts, and for a search into virus-induced intracellular membrane modifications within mammalian cells. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Directory of Open Access Journals (Sweden)

    El Batrawy Sherouk

    2011-04-01

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

  20. 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.

  1. Measurement of Sub-Picosecond Electron Bunches via Electro-Optic Sampling of Coherent Transition Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, Timothy John [Northern Illinois U.

    2012-01-01

    Future collider applications as well as present high-gradient laser plasma wakefield accelerators and free-electron lasers operating with picosecond bunch durations place a higher demand on the time resolution of bunch distribution diagnostics. This demand has led to significant advancements in the field of electro-optic sampling over the past ten years. These methods allow the probing of diagnostic light such as coherent transition radiation or the bunch wakefields with sub-picosecond time resolution. We present results on the single-shot electro-optic spectral decoding of coherent transition radiation from bunches generated at the Fermilab A0 photoinjector laboratory. A longitudinal double-pulse modulation of the electron beam is also realized by transverse beam masking followed by a transverse-to-longitudinal phase-space exchange beamline. Live profile tuning is demonstrated by upstream beam focusing in conjunction with downstream monitoring of single-shot electro-optic spectral decoding of the coherent transition radiation.

  2. The SAMPLE experiment: Parity-violating electron scattering from the proton and deuteron

    International Nuclear Information System (INIS)

    Pitt, M.; Arrington, J.; Beck, D.; Beise, E.; Candell, E.; Cardman, L.; Carr, R.; Dodson, G.; Dow, K.; Duncan, F.; Farkhondeh, M.; Filippone, B.; Forest, T.; Gao, H.; Korsch, W.; Kowalski, S.; Lung, A.; McKeown, R.; Mohring, R.; Mueller, B.; Napolitano, J.; Simicevic, N.; Terburg, B.; Witkowski, M.

    1995-01-01

    Recent experimental evidence on nucleon structure has provided indications that some strange quark matrix elements can be comparable to those involving up and down quarks. The SAMPLE experiment will determine the strange magnetic form factor G s M at Q 2 =0.1 (GeV/c) 2 from a measurement of the asymmetry in the scattering of polarized electrons from the proton. The error on the extraction of G s M is ultimately limited by a theoretical uncertainty---the uncertain electroweak hadronic radiative correction to the axial form factor, R T=1 A . To address this issue, the collaboration is also approved to measure the asymmetry in parity-violating quasielastic electron scattering from the deuteron. The combination of the proton and deuteron measurements will yield a value of G s M that is almost completely free of the uncertainty in R T=1 A

  3. Focussed ion beam thin sample microanalysis using a field emission gun electron probe microanalyser

    Science.gov (United States)

    Kubo, Y.

    2018-01-01

    Field emission gun electron probe microanalysis (FEG-EPMA) in conjunction with wavelength-dispersive X-ray spectrometry using a low acceleration voltage (V acc) allows elemental analysis with sub-micrometre lateral spatial resolution (SR). However, this degree of SR does not necessarily meet the requirements associated with increasingly miniaturised devices. Another challenge related to performing FEG-EPMA with a low V acc is that the accuracy of quantitative analyses is adversely affected, primarily because low energy X-ray lines such as the L- and M-lines must be employed and due to the potential of line interference. One promising means of obtaining high SR with FEG-EPMA is to use thin samples together with high V acc values. This mini-review covers the basic principles of thin-sample FEG-EPMA and describes an application of this technique to the analysis of optical fibres. Outstanding issues related to this technique that must be addressed are also discussed, which include the potential for electron beam damage during analysis of insulating materials and the development of methods to use thin samples for quantitative analysis.

  4. Use of an Electronic Tongue System and Fuzzy Logic to Analyze Water Samples

    Science.gov (United States)

    Braga, Guilherme S.; Paterno, Leonardo G.; Fonseca, Fernando J.

    2009-05-01

    An electronic tongue (ET) system incorporating 8 chemical sensors was used in combination with two pattern recognition tools, namely principal component analysis (PCA) and Fuzzy logic for discriminating/classification of water samples from different sources (tap, distilled and three brands of mineral water). The Fuzzy program exhibited a higher accuracy than the PCA and allowed the ET to classify correctly 4 in 5 types of water. Exception was made for one brand of mineral water which was sometimes misclassified as tap water. On the other hand, the PCA grouped water samples in three clusters, one with the distilled water; a second with tap water and one brand of mineral water, and the third with the other two other brands of mineral water. Samples in the second and third clusters could not be distinguished. Nevertheless, close grouping between repeated tests indicated that the ET system response is reproducible. The potential use of the Fuzzy logic as the data processing tool in combination with an electronic tongue system is discussed.

  5. Differentiating gold nanorod samples using particle size and shape distributions from transmission electron microscope images

    Science.gov (United States)

    Grulke, Eric A.; Wu, Xiaochun; Ji, Yinglu; Buhr, Egbert; Yamamoto, Kazuhiro; Song, Nam Woong; Stefaniak, Aleksandr B.; Schwegler-Berry, Diane; Burchett, Woodrow W.; Lambert, Joshua; Stromberg, Arnold J.

    2018-04-01

    Size and shape distributions of gold nanorod samples are critical to their physico-chemical properties, especially their longitudinal surface plasmon resonance. This interlaboratory comparison study developed methods for measuring and evaluating size and shape distributions for gold nanorod samples using transmission electron microscopy (TEM) images. The objective was to determine whether two different samples, which had different performance attributes in their application, were different with respect to their size and/or shape descriptor distributions. Touching particles in the captured images were identified using a ruggedness shape descriptor. Nanorods could be distinguished from nanocubes using an elongational shape descriptor. A non-parametric statistical test showed that cumulative distributions of an elongational shape descriptor, that is, the aspect ratio, were statistically different between the two samples for all laboratories. While the scale parameters of size and shape distributions were similar for both samples, the width parameters of size and shape distributions were statistically different. This protocol fulfills an important need for a standardized approach to measure gold nanorod size and shape distributions for applications in which quantitative measurements and comparisons are important. Furthermore, the validated protocol workflow can be automated, thus providing consistent and rapid measurements of nanorod size and shape distributions for researchers, regulatory agencies, and industry.

  6. Conversion electron Moessbauer and XPS study on the effect of polishing of a stainless steel sample

    International Nuclear Information System (INIS)

    Vertes, Cs.; Kuzmann, E.; Lakatos-Varsanyi, M.; Vertes, A.; Vass, G.; Romhanyi, K.

    1994-01-01

    Conversion electron Moessbauer spectroscopy (CEMS) and XPS has been used for the surface analysis of an 'X10CrNiTi 18/9 (DIN 1.7440)'-type stainless steel in order to determine the supposed structural and/or chemical changes in the surface layer caused by polishing. Both, CEMS and XPS results can be associated with the appearance of Fe nitride in the outer layer of steel samples after polishing, while no sing of nitrogen was detected in the bulk material. (author) 9 refs.; 3 figs.; 1 tab

  7. Thermal diffusivity and electron transport properties of NTC samples obtained by the photoacoustic method

    International Nuclear Information System (INIS)

    Savic, S.M.; Aleksic, O.S.; Nikolic, M.V.; Lukovic, D.T.; Pejovic, V.Z.; Nikolic, P.M.

    2006-01-01

    Thermal diffusivity and electron transport parameters of sintered NTC samples were determined by the photoacoustic (PA) technique. Powder mixtures composed of MnO, NiO, CoO and Fe 2 O 3 were milled to nanometer particle size. NTC discs were dry powder pressed and sintered at different temperatures in the range from 900 deg. C to 1300 deg. C for 30 min. A second group of NTC discs was sintered at 1200 deg. C with the sintering time varying from 30 min to 360 min. These NTC samples were polished and exposed to a chopped laser beam in order to plot a response in the acoustic range. The thermal diffusivity of sintered NTC layers based on a metal oxide powder mixture was measured at room temperature by the photoacoustic technique. An increase of thermal diffusivity with the sintering temperature and time of sintering was observed

  8. Thermal diffusivity and electron transport properties of NTC samples obtained by the photoacoustic method

    Energy Technology Data Exchange (ETDEWEB)

    Savic, S.M. [Institute of Technical Sciences of SASA, Knez Mihailova 35/IV, 11000 Belgrade (Serbia); Aleksic, O.S. [Center for Multidisciplinary Studies of the University of Belgrade, Kneza Viseslava 1, 11000 Belgrade (Serbia); Nikolic, M.V. [Center for Multidisciplinary Studies of the University of Belgrade, Kneza Viseslava 1, 11000 Belgrade (Serbia); Lukovic, D.T. [Institute of Technical Sciences of SASA, Knez Mihailova 35/IV, 11000 Belgrade (Serbia); Pejovic, V.Z. [Center for Multidisciplinary Studies of the University of Belgrade, Kneza Viseslava 1, 11000 Belgrade (Serbia); Nikolic, P.M. [Institute of Technical Sciences of SASA, Knez Mihailova 35/IV, 11000 Belgrade (Serbia)]. E-mail: nikolic@sanu.ac.yu

    2006-07-15

    Thermal diffusivity and electron transport parameters of sintered NTC samples were determined by the photoacoustic (PA) technique. Powder mixtures composed of MnO, NiO, CoO and Fe{sub 2}O{sub 3} were milled to nanometer particle size. NTC discs were dry powder pressed and sintered at different temperatures in the range from 900 deg. C to 1300 deg. C for 30 min. A second group of NTC discs was sintered at 1200 deg. C with the sintering time varying from 30 min to 360 min. These NTC samples were polished and exposed to a chopped laser beam in order to plot a response in the acoustic range. The thermal diffusivity of sintered NTC layers based on a metal oxide powder mixture was measured at room temperature by the photoacoustic technique. An increase of thermal diffusivity with the sintering temperature and time of sintering was observed.

  9. Impact of ambient environment on the electronic structure of CuPc/Au sample

    Science.gov (United States)

    Sinha, Sumona; Mukherjee, M.

    2018-02-01

    The performances of organic devices are crucially connected with their stability in the ambient environment. The impact of 24 h. Ambient environment exposure to the electronic structures of about 12 nm thick CuPc thin film on clean Au substrate have been studied employing UV photoemission spectroscopy technique. X-ray photoemission spectroscopy (XPS) was used to find out the origin of the change of the electronic structures in the sample with the exposure. The XPS study suggests that the oxidation occurs at the CuPc thin film. Due to the adsorption of oxygen in the CuPc film from the ambient air, charge carriers are formed within the CuPc film. Moreover, the XPS results imply that the CuPc film is sufficiently thinner for diffusing oxygen molecules through it and gets physically absorbed on Au substrate during the ambient exposure. Consequently, the hole injection barrier height of pristine CuPc film, grown on Au substrate, is reduced by about 0.50 eV and work-function of the pristine CuPc sample is enhanced by around 0.25 eV in the exposure. The findings will help to understand the mechanism that governs the degradation of performance of CuPc based devices in ambient environment.

  10. Virtual rough samples to test 3D nanometer-scale scanning electron microscopy stereo photogrammetry.

    Science.gov (United States)

    Villarrubia, J S; Tondare, V N; Vladár, A E

    2016-01-01

    The combination of scanning electron microscopy for high spatial resolution, images from multiple angles to provide 3D information, and commercially available stereo photogrammetry software for 3D reconstruction offers promise for nanometer-scale dimensional metrology in 3D. A method is described to test 3D photogrammetry software by the use of virtual samples-mathematical samples from which simulated images are made for use as inputs to the software under test. The virtual sample is constructed by wrapping a rough skin with any desired power spectral density around a smooth near-trapezoidal line with rounded top corners. Reconstruction is performed with images simulated from different angular viewpoints. The software's reconstructed 3D model is then compared to the known geometry of the virtual sample. Three commercial photogrammetry software packages were tested. Two of them produced results for line height and width that were within close to 1 nm of the correct values. All of the packages exhibited some difficulty in reconstructing details of the surface roughness.

  11. Characterization of electron microscopes with binary pseudo-random multilayer test samples

    Science.gov (United States)

    Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.

    2011-09-01

    Verification of the reliability of metrology data from high quality X-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested [1,2] and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [5]. Here we describe the details of development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanning (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi 2/Si multilayer coating with pseudo-randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize X-ray microscopes. Corresponding work with X-ray microscopes is in progress.

  12. Characterization of electron microscopes with binary pseudo-random multilayer test samples

    International Nuclear Information System (INIS)

    Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.

    2011-01-01

    Verification of the reliability of metrology data from high quality X-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [5]. Here we describe the details of development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanning (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi 2 /Si multilayer coating with pseudo-randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize X-ray microscopes. Corresponding work with X-ray microscopes is in progress.

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

    Science.gov (United States)

    Drobnic, Katja

    2003-06-01

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

  14. Willingness to Provide a Hair Sample for Drug Testing among Electronic Dance Music Party Attendees.

    Science.gov (United States)

    Palamar, Joseph J; Salomone, Alberto; Cleland, Charles M; Sherman, Scott

    2018-04-25

    Non-disclosure of drug use on surveys is common and many drug users unknowingly ingest adulterant or replacement drugs, which leads to underreporting of use of these drugs. Biological testing can complement survey research, and hair-testing is an appealing method as many drugs are detectable for months post-use. We examined willingness to donate a hair sample to be tested among those surveyed in a population at high risk for consuming adulterated drugs-electronic dance music (EDM) party attendees. We surveyed 933 adults entering EDM parties in New York City in 2017. Hair donation response rates and reasons for refusal were examined from this cross-sectional study. A third (n = 312; 33.4%) provided a hair sample. Lack of interest (21.0%), lack of time (19.8%), not wanting a lock of hair cut (17.7%), and disinterest in having hair cut in public (13.8%) were the main reported reasons for refusal. 4.7% refused because they could not receive results. Past-year drug users were more likely to fear identification than non-users (p<.001). Asian participants were at lower odds of providing a hair sample (aOR = 0.53, 95% CI = 0.32-0.87), and those reporting past-year use of LSD (aOR = 1.62, 95% CI = 1.11-2.35), opioids (nonmedical; aOR = 1.93, 95% CI = 1.25-2.99), and/or methamphetamine (aOR = 3.43, 95% CI = 1.36-8.62) were at higher odds of providing a sample than non-users of these drugs. Only a third of participants provided a hair sample and we found individual-level differences regarding willingness to provide a sample. Factors contributing to refusal should be considered to increase response rates and generalizability of results.

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

    Science.gov (United States)

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

    2018-04-01

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

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

    Directory of Open Access Journals (Sweden)

    D. McGolrick

    2016-09-01

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

  17. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  18. In-focus electron microscopy of frozen-hydrated biological samples with a Boersch phase plate

    Energy Technology Data Exchange (ETDEWEB)

    Barton, B.; Rhinow, D.; Walter, A.; Schroeder, R. [Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main (Germany); Benner, G.; Majorovits, E.; Matijevic, M.; Niebel, H. [Carl Zeiss NTS GmbH, D-73447 Oberkochen (Germany); Mueller, H.; Haider, M. [CEOS GmbH, Englerstr. 26, 69126 Heidleberg (Germany); Lacher, M.; Schmitz, S.; Holik, P. [Caesar Research Center, Ludwig-Erhard-Allee 2, D-53175 Bonn (Germany); Kuehlbrandt, W., E-mail: werner.kuehlbrandt@mpibp-frankfurt.mpg.de [Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main (Germany)

    2011-12-15

    We report the implementation of an electrostatic Einzel lens (Boersch) phase plate in a prototype transmission electron microscope dedicated to aberration-corrected cryo-EM. The combination of phase plate, C{sub s} corrector and Diffraction Magnification Unit (DMU) as a new electron-optical element ensures minimal information loss due to obstruction by the phase plate and enables in-focus phase contrast imaging of large macromolecular assemblies. As no defocussing is necessary and the spherical aberration is corrected, maximal, non-oscillating phase contrast transfer can be achieved up to the information limit of the instrument. A microchip produced by a scalable micro-fabrication process has 10 phase plates, which are positioned in a conjugate, magnified diffraction plane generated by the DMU. Phase plates remained fully functional for weeks or months. The large distance between phase plate and the cryo sample permits the use of an effective anti-contaminator, resulting in ice contamination rates of <0.6 nm/h at the specimen. Maximal in-focus phase contrast was obtained by applying voltages between 80 and 700 mV to the phase plate electrode. The phase plate allows for in-focus imaging of biological objects with a signal-to-noise of 5-10 at a resolution of 2-3 nm, as demonstrated for frozen-hydrated virus particles and purple membrane at liquid-nitrogen temperature. -- Highlights: Black-Right-Pointing-Pointer We implement an electrostatic Boersch phase plate into a dedicated prototypical TEM. Black-Right-Pointing-Pointer Phase contrast aberration-corrected electron microscope (PACEM) includes a diffraction magnification unit (DMU). Black-Right-Pointing-Pointer DMU minimizes obstruction of low spatial frequencies by the phase plate. Black-Right-Pointing-Pointer In-focus phase contrast generation is demonstrated for frozen-hydrated biological specimens.

  19. Characteristics of recycled and electron beam irradiated high density polyethylene samples

    International Nuclear Information System (INIS)

    Cardoso, Jessica R.; Gabriel, Leandro; Geraldo, Aurea B.C.; Moura, Eduardo

    2015-01-01

    Polymers modification by irradiation is a well-known process that allows degradation and cross-linking in concurrent events; this last is expected when an increase of mechanical properties is required. Actually, the interest of recycling and reuse of polymeric material is linked to the increase of plastics ending up in waste streams. Therefore, these both irradiation and recycling process may be conducted to allow a new use to this material that would be discarded by an improvement of its mechanical properties. In this work, the High Density Polyethylene (HDPE) matrix has been recycled five times from original substrate. The electron beam irradiation process was applied from 50 kGy to 200 kGy in both original and recycled samples; in this way, mechanical properties and thermal characteristics were evaluated. The results of applied process and material characterization are discussed. (author)

  20. Importance sampling techniques and treatment of electron transport in MCNP 4A

    International Nuclear Information System (INIS)

    Ueki, K.

    1994-01-01

    The continuous energy Monte Carlo code MCNP was developed by the Radiation Transport Group at Los Alamos National Laboratory and the MCNP 4A version is available, now. The MCNP 4A is able to do the coupled neutron-secondary gamma-ray-electron-bremsstrahlung calculation. The calculated results, such as energy spectra, tally fluctuation chart, and geometrical input data can be displayed by using a work station. The document of the MCNP 4A code has no description on the subroutines, except few ones of 'SOURCE', 'TALLYX'. However, when we want to improve the MCNP Monte Carlo sampling techniques to get more accuracy or efficiency results for some problems, some subroutines are required or needed to revised. Three subroutines have been revised and built in the MCNP 4A code. (author)

  1. Characteristics of recycled and electron beam irradiated high density polyethylene samples

    Energy Technology Data Exchange (ETDEWEB)

    Cardoso, Jessica R.; Gabriel, Leandro; Geraldo, Aurea B.C.; Moura, Eduardo, E-mail: jrcardoso@ipen.br, E-mail: lgabriell@gmail.com, E-mail: ageraldo@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    Polymers modification by irradiation is a well-known process that allows degradation and cross-linking in concurrent events; this last is expected when an increase of mechanical properties is required. Actually, the interest of recycling and reuse of polymeric material is linked to the increase of plastics ending up in waste streams. Therefore, these both irradiation and recycling process may be conducted to allow a new use to this material that would be discarded by an improvement of its mechanical properties. In this work, the High Density Polyethylene (HDPE) matrix has been recycled five times from original substrate. The electron beam irradiation process was applied from 50 kGy to 200 kGy in both original and recycled samples; in this way, mechanical properties and thermal characteristics were evaluated. The results of applied process and material characterization are discussed. (author)

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

    Science.gov (United States)

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

    2018-01-01

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

  3. Study of runaway electrons using the conditional average sampling method in the Damavand tokamak

    Energy Technology Data Exchange (ETDEWEB)

    Pourshahab, B., E-mail: bpourshahab@gmail.com [University of Isfahan, Department of Nuclear Engineering, Faculty of Advance Sciences and Technologies (Iran, Islamic Republic of); Sadighzadeh, A. [Nuclear Science and Technology Research Institute, Plasma Physics and Nuclear Fusion Research School (Iran, Islamic Republic of); Abdi, M. R., E-mail: r.abdi@phys.ui.ac.ir [University of Isfahan, Department of Physics, Faculty of Science (Iran, Islamic Republic of); Rasouli, C. [Nuclear Science and Technology Research Institute, Plasma Physics and Nuclear Fusion Research School (Iran, Islamic Republic of)

    2017-03-15

    Some experiments for studying the runaway electron (RE) effects have been performed using the poloidal magnetic probes system installed around the plasma column in the Damavand tokamak. In these experiments, the so-called runaway-dominated discharges were considered in which the main part of the plasma current is carried by REs. The induced magnetic effects on the poloidal pickup coils signals are observed simultaneously with the Parail–Pogutse instability moments for REs and hard X-ray bursts. The output signals of all diagnostic systems enter the data acquisition system with 2 Msample/(s channel) sampling rate. The temporal evolution of the diagnostic signals is analyzed by the conditional average sampling (CAS) technique. The CASed profiles indicate RE collisions with the high-field-side plasma facing components at the instability moments. The investigation has been carried out for two discharge modes—low-toroidal-field (LTF) and high-toroidal-field (HTF) ones—related to both up and down limits of the toroidal magnetic field in the Damavand tokamak and their comparison has shown that the RE confinement is better in HTF discharges.

  4. 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.

  5. Lights Will Guide You : Sample Preparation and Applications for Integrated Laser and Electron Microscopy

    Science.gov (United States)

    Karreman, M. A.

    2013-03-01

    Correlative microscopy is the combined use of two different forms of microscopy in the study of a specimen, allowing for the exploitation of the advantages of both imaging tools. The integrated Laser and Electron Microscope (iLEM), developed at Utrecht University, combines a fluorescence microscope (FM) and a transmission electron microscope (TEM) in a single set-up. The region of interest in the specimen is labeled or tagged with a fluorescent probe and can easily be identified within a large field of view with the FM. Next, this same area is retraced in the TEM and can be studied at high resolution. The iLEM demands samples that can be imaged with both FM and TEM. Biological specimen, typically composed of light elements, generate low image contrast in the TEM. Therefore, these samples are often ‘contrasted’ with heavy metal stains. FM, on the other hand, images fluorescent samples. Sample preparation for correlative microscopy, and iLEM in particular, is complicated by the fact that the heavy metals stains employed for TEM quench the fluorescent signal of the probe that is imaged with FM. The first part of this thesis outlines preparation procedures for biological material yielding specimen that can be imaged with the iLEM. Here, approaches for the contrasting of thin sections of cells and tissue are introduced that do not affect the fluorescence signal of the probe that marks the region of interest. Furthermore, two novel procedures, VIS2FIXH and VIS2FIX­FS are described that allow for the chemical fixation of thin sections of cryo-immobilized material. These procedures greatly expedite the sample preparation process, and open up novel possibilities for the immuno-labeling of difficult antigens, eg. proteins and lipids that are challenging to preserve. The second part of this thesis describes applications of iLEM in research in the field of life and material science. The iLEM was employed in the study of UVC induced apoptosis (programmed cell death) of

  6. Effect of the sample annealing temperature and sample crystallographic orientation on the charge kinetics of MgO single crystals subjected to keV electron irradiation.

    Science.gov (United States)

    Boughariou, A; Damamme, G; Kallel, A

    2015-04-01

    This paper focuses on the effect of sample annealing temperature and crystallographic orientation on the secondary electron yield of MgO during charging by a defocused electron beam irradiation. The experimental results show that there are two regimes during the charging process that are better identified by plotting the logarithm of the secondary electron emission yield, lnσ, as function of the total trapped charge in the material QT. The impact of the annealing temperature and crystallographic orientation on the evolution of lnσ is presented here. The slope of the asymptotic regime of the curve lnσ as function of QT, expressed in cm(2) per trapped charge, is probably linked to the elementary cross section of electron-hole recombination, σhole, which controls the trapping evolution in the reach of the stationary flow regime. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

  7. 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.

  8. Time evolution of the characteristic electron energy losses spectra of the electrons scattered on polycrystal samples of Al mechanically cleaned in vacuum

    International Nuclear Information System (INIS)

    Szczesny, R.; Baranowski, A.; Beliczynski, J.

    1982-01-01

    Measurements by the reflection technique of characteristic electron energy losses (CEEL) with a primary electron beam of energy E 0 =1 keV have been carried out on polycrystal samples of Al. The sample surfaces have been mechanically cleaned in a dinamical vacuum of the order 10 -6 Tr before each measurement. The CEEL spectra have been corrected for the resolving power of the apparatus by the deconvolution method. We have ascertained that the measuring technique and elaboration data method are useful for quickly obtaining the plasmon energy loss spectrum for an investigated material. (author)

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

    Musser, Jeffrey M B; Gonzalez, Rosa

    2011-01-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

  12. Sample preparation and study by electronic diffraction of oxidations and fluorinations of some metals and alloys

    International Nuclear Information System (INIS)

    Auguin, B.

    1963-06-01

    After having recalled that electron diffraction is particularly adapted to the study of thin films and surface layers, notably those forming during corrosions, and recalled some characteristics of this technique (wavelength, interactions with substances, parasite reactions, observation by transmission or reflection, obtained diagrams for polycrystalline and mono-crystalline substances), the author describes how samples are prepared in the case of examinations performed by transmission and by reflection. As fluorination agents are used for the separation of uranium 235 and 238, the second part discusses some works related to the fluorination of metals and alloys, some of them being used in these separation installations. Chlorine trifluoride is generally used and materials are generally oxidised. Thus, the author reports the study of the action of ClF 3 on different oxides. Oxidations of iron, nickel and Monel are addressed, as well as the behaviour of stainless steel. The study of fluorinations of metals (nickel, chromium, copper), alloys (stainless steel, Monel) and oxides is reported. The author finally addresses treatments performed after fluorinations: vacuum heating, action of humid air

  13. 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®

  14. 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.

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2016-08-01

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

  18. 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.

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

    OpenAIRE

    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

    2016-01-01

    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 through...

  20. Electron microprobe analyses of selected samples from deep rock disposal experiment No. 1

    International Nuclear Information System (INIS)

    Hlava, P.F.; Chambers, W.F.

    1976-04-01

    Deep Rock Disposal Experiment No. 1 was designed to provide information about the interaction between a molten, glass-based, nuclear waste simulant and rock material. Selected samples from this experiment were examined by optical microscopy and electron probe microanalysis. Analysis of the homogenized material in the convection cell that was created in the central portion of the melt region shows that an amount of rock equal to about one-half of the original amount of waste simulant was incorporated in the melt during the experiment. Stagnant melt at the sides of the cell formed a glass with large compositional gradients. A white band separated the convected and stagnant materials. The color of the band is attributed to light scattering by small crystallites formed during cooling. Four types of crystallites grew from the melt: two oxides, a Mg--Fe borate, and a silicate. Spinel (MgO, Cr 2 O 3 , FeO (Fe 2 O 3 ), and NiO) was the most common crystallite in the glass. The spinel crystallites found within the convection cell displayed skeletal morphology and oscillatory zoning which indicates growth at varying temperatures as they were carried along by convection. A single cluster of nonskeletal (Fe,Cr) 2 O 3 crystallites was found at the bottom of the melt zone where convection did not occur. Mg--Fe borate crystallites grew in clusters in the central portion of the convection cell after convection ceased. A silicate similar to Fe-rich diopside (CaMgSi 2 O 6 ) with unusual amounts of Ce 2 O 3 and other heavy metal oxides formed as larger crystallites in the stagnant melt at the side of the convection cell and as many very small crystallites in the white band

  1. Electronic module for control of sample feeding device of spectrometers of X-ray fluorescent analysis of CRV type

    International Nuclear Information System (INIS)

    Petrov, V.A.; Fursov, A.V.

    2002-01-01

    The scheme of electronic module for sample feeding device control for the CRV type X-ray fluorescence analysis spectrometers is considered. This module provides realization of next functions: sample change operations and installation in starting position; signaling and defense at emergency cases; indication of any sample amount in the spectrometer chamber; testing function at tuning and testing of modules. All these principal functions are entrusted with microcontroller. Programming of the microcontroller is putting into effect by algorithm of the whole sample feeding device. In the capacity of microcontroller the single crystalline processor PICI16C54 and stepping motor of NV-306-V2202 model have been used

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

    Directory of Open Access Journals (Sweden)

    Paulis G

    2015-11-01

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

  3. U-10Mo Sample Preparation and Examination using Optical and Scanning Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Prabhakaran, Ramprashad [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Joshi, Vineet V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rhodes, Mark A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Schemer-Kohrn, Alan L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Guzman, Anthony D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lavender, Curt A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-10-01

    The purpose of this document is to provide guidelines to prepare specimens of uranium alloyed with 10 weight percent molybdenum (U-10Mo) for optical metallography and scanning electron microscopy. This document also provides instructions to set up an optical microscope and a scanning electron microscope to analyze U-10Mo specimens and to obtain the required information.

  4. U-10Mo Sample Preparation and Examination using Optical and Scanning Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Prabhakaran, Ramprashad [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Joshi, Vineet V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rhodes, Mark A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Schemer-Kohrn, Alan L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Guzman, Anthony D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lavender, Curt A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-30

    The purpose of this document is to provide guidelines to prepare specimens of uranium alloyed with 10 weight percent molybdenum (U-10Mo) for optical metallography and scanning electron microscopy. This document also provides instructions to set up an optical microscope and a scanning electron microscope to analyze U-10Mo specimens and to obtain the required information.

  5. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy

    NARCIS (Netherlands)

    Faas, F.G.A.; Bárcena, M.A.; Agronskaia, A.V.; Gerritsen, H.C.; Moscicka, K.B.; Diebolder, C.A.; Driel, L.F.; Limpens, R.W.A.L.; Bos, E.; Ravelli, R.B.G.; Koning, R.I.; Koster, A.J.

    2013-01-01

    Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain

  6. U-10Mo Sample Preparation and Examination using Optical and Scanning Electron Microscopy. Rev. 1

    International Nuclear Information System (INIS)

    Prabhakaran, Ramprashad; Joshi, Vineet V.; Rhodes, Mark A.; Schemer-Kohrn, Alan L.; Guzman, Anthony D.; Lavender, Curt A.

    2016-01-01

    The purpose of this document is to provide guidelines to prepare specimens of uranium alloyed with 10 weight percent molybdenum (U-10Mo) for optical metallography and scanning electron microscopy. This document also provides instructions to set up an optical microscope and a scanning electron microscope to analyze U-10Mo specimens and to obtain the required information.

  7. Sample preparation methods for scanning electron microscopy of homogenized Al-Mg-Si billets: A comparative study

    International Nuclear Information System (INIS)

    Österreicher, Johannes Albert; Kumar, Manoj; Schiffl, Andreas; Schwarz, Sabine; Hillebrand, Daniel; Bourret, Gilles Remi

    2016-01-01

    Characterization of Mg-Si precipitates is crucial for optimizing the homogenization heat treatment of Al-Mg-Si alloys. Although sample preparation is key for high quality scanning electron microscopy imaging, most common methods lead to dealloying of Mg-Si precipitates. In this article we systematically evaluate different sample preparation methods: mechanical polishing, etching with various reagents, and electropolishing using different electrolytes. We demonstrate that the use of a nitric acid and methanol electrolyte for electropolishing a homogenized Al-Mg-Si alloy prevents the dissolution of Mg-Si precipitates, resulting in micrographs of higher quality. This preparation method is investigated in depth and the obtained scanning electron microscopy images are compared with transmission electron micrographs: the shape and size of Mg-Si precipitates appear very similar in either method. The scanning electron micrographs allow proper identification and measurement of the Mg-Si phases including needles with lengths of roughly 200 nm. These needles are β″ precipitates as confirmed by high resolution transmission electron microscopy. - Highlights: •Secondary precipitation in homogenized 6xxx Al alloys is crucial for extrudability. •Existing sample preparation methods for SEM are improvable. •Electropolishing with nitric acid/methanol yields superior quality in SEM. •The obtained micrographs are compared to TEM micrographs.

  8. Sample preparation methods for scanning electron microscopy of homogenized Al-Mg-Si billets: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Österreicher, Johannes Albert; Kumar, Manoj [LKR Light Metals Technologies Ranshofen, Austrian Institute of Technology, Postfach 26, 5282 Ranshofen (Austria); Schiffl, Andreas [Hammerer Aluminium Industries Extrusion GmbH, Lamprechtshausener Straße 69, 5282 Ranshofen (Austria); Schwarz, Sabine [University Service Centre for Transmission Electron Microscopy, Vienna University of Technology, Wiedner Hauptstr. 8-10, 1040 Wien (Austria); Hillebrand, Daniel [Hammerer Aluminium Industries Extrusion GmbH, Lamprechtshausener Straße 69, 5282 Ranshofen (Austria); Bourret, Gilles Remi, E-mail: gilles.bourret@sbg.ac.at [Department of Materials Science and Physics, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg (Austria)

    2016-12-15

    Characterization of Mg-Si precipitates is crucial for optimizing the homogenization heat treatment of Al-Mg-Si alloys. Although sample preparation is key for high quality scanning electron microscopy imaging, most common methods lead to dealloying of Mg-Si precipitates. In this article we systematically evaluate different sample preparation methods: mechanical polishing, etching with various reagents, and electropolishing using different electrolytes. We demonstrate that the use of a nitric acid and methanol electrolyte for electropolishing a homogenized Al-Mg-Si alloy prevents the dissolution of Mg-Si precipitates, resulting in micrographs of higher quality. This preparation method is investigated in depth and the obtained scanning electron microscopy images are compared with transmission electron micrographs: the shape and size of Mg-Si precipitates appear very similar in either method. The scanning electron micrographs allow proper identification and measurement of the Mg-Si phases including needles with lengths of roughly 200 nm. These needles are β″ precipitates as confirmed by high resolution transmission electron microscopy. - Highlights: •Secondary precipitation in homogenized 6xxx Al alloys is crucial for extrudability. •Existing sample preparation methods for SEM are improvable. •Electropolishing with nitric acid/methanol yields superior quality in SEM. •The obtained micrographs are compared to TEM micrographs.

  9. A Miniaturized Variable Pressure Scanning Electron Microscope (MVP-SEM) for In-Situ Mars Surface Sample Analysis

    Science.gov (United States)

    Edmunson, J.; Gaskin, J. A.; Jerman, G. A.; Harvey, R. P.; Doloboff, I. J.; Neidholdt, E. L.

    2016-01-01

    The Miniaturized Variable Pressure Scanning Electron Microscope (MVP-SEM) project, funded by the NASA Planetary Instrument Concepts for the Advancement of Solar System Observations (PICASSO) Research Opportunities in Space and Earth Sciences (ROSES), will build upon previous miniaturized SEM designs and recent advancements in variable pressure SEM's to design and build a SEM to complete analyses of samples on the surface of Mars using the atmosphere as an imaging medium. This project is a collaboration between NASA Marshall Space Flight Center (MSFC), the Jet Propulsion Laboratory (JPL), electron gun and optics manufacturer Applied Physics Technologies, and small vacuum system manufacturer Creare. Dr. Ralph Harvery and environmental SEM (ESEM) inventor Dr. Gerry Danilatos serve as advisors to the team. Variable pressure SEMs allow for fine (nm-scale) resolution imaging and micron-scale chemical study of materials without sample preparation (e.g., carbon or gold coating). Charging of a sample is reduced or eliminated by the gas surrounding the sample. It is this property of ESEMs that make them ideal for locations where sample preparation is not yet feasible, such as the surface of Mars. In addition, the lack of sample preparation needed here will simplify the sample acquisition process and allow caching of the samples for future complementary payload use.

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

    Science.gov (United States)

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

    2013-09-01

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

  11. Multiple double cross-section transmission electron microscope sample preparation of specific sub-10 nm diameter Si nanowire devices.

    Science.gov (United States)

    Gignac, Lynne M; Mittal, Surbhi; Bangsaruntip, Sarunya; Cohen, Guy M; Sleight, Jeffrey W

    2011-12-01

    The ability to prepare multiple cross-section transmission electron microscope (XTEM) samples from one XTEM sample of specific sub-10 nm features was demonstrated. Sub-10 nm diameter Si nanowire (NW) devices were initially cross-sectioned using a dual-beam focused ion beam system in a direction running parallel to the device channel. From this XTEM sample, both low- and high-resolution transmission electron microscope (TEM) images were obtained from six separate, specific site Si NW devices. The XTEM sample was then re-sectioned in four separate locations in a direction perpendicular to the device channel: 90° from the original XTEM sample direction. Three of the four XTEM samples were successfully sectioned in the gate region of the device. From these three samples, low- and high-resolution TEM images of the Si NW were taken and measurements of the NW diameters were obtained. This technique demonstrated the ability to obtain high-resolution TEM images in directions 90° from one another of multiple, specific sub-10 nm features that were spaced 1.1 μm apart.

  12. 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.

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

    Science.gov (United States)

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

    2012-12-01

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

  14. Breakdown of the independent electron picture in mesoscopic samples at low temperatures: The hunt for the Unicorn

    Science.gov (United States)

    Webb, R. A.

    1998-03-01

    A variety of experiments are discussed where, at low temperatures, it appears that the non-interacting picture of electrons in a Fermi liquid description of a mesoscopic sample is breaking down. Specifically, experiments on the temperature dependence of the phase-coherence time, energy relaxation rate, spin-flip scattering time, persistent currents in normal metals and transmission through a barrier in the fractional quantum Hall regime all display low-temperature properties which can not be accounted for in the independent electron picture.

  15. Documentary Realism, Sampling Theory and Peircean Semiotics: electronic audiovisual signs (analog or digital as indexes of reality

    Directory of Open Access Journals (Sweden)

    Hélio Godoy

    2007-07-01

    Full Text Available This paper addresses Documentary Realism, focusing on thephysical phenomena of transduction that take place in analog and digital audiovisual systems, herein analyzed in the light of the Sampling Theory, within the framework of Shannon and Weaver’s Information Theory. Transduction is a process by which one type of energy is transformed into another, or by which information is transcodified. Within the scope of Documentary Realism, it cannotbe claimed that electronic audiovisual signs, because of their technical digital features lead to a rupture with reality. Rather, the digital documentary, based on electronic digital cinematography, is still an index of reality.

  16. Proceedings of the FNCA 2002 workshop on application of electron accelerator. Radiation system for liquid samples

    International Nuclear Information System (INIS)

    Yoshii, Fumio; Kume, Tamikazu

    2003-10-01

    'Forum for Nuclear Cooperation in Asia (FNCA) Workshop on Application of Electron Accelerator' was sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and hosted by Japan Atomic Energy Research Institute (JAERI) and Japan Atomic Industry Forum (JAIF). It was held at the Takasaki Radiation Chemistry Research Establishment (TRCRE), JAERI, Takasaki, Japan from 16 to 20 December 2002. The attendants at the workshop were consisted of 13 experts on application of electron accelerator from each of the participating countries, i.e., China, Indonesia, Korea, Malaysia, the Philippines, Thailand and Vietnam, and 40 participants from Japan. A total of 18 papers including invited papers on liquid waste treatment by electron beam, reviews of the radiation systems, and designing and cost analysis of EB irradiation system were presented. The major areas of interest of FNCA countries for cooperation were identified for application of low energy electron accelerator as liquid, thin film and granules. The gas and wastewater treatments were added to the above major areas. Based on the proposal from the participating countries, discussions were carried out to re-formulate the work plan of the project for three years until FY 2004. All manuscripts submitted by every speaker were included in the proceedings. The 17 of the presented papers are indexed individually. (J.P.N.)

  17. 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.

  18. 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.

  19. New sampling electronics using CCD for DIOGENE: a high multiplicity, 4 π detector for relativistic heavy ions

    International Nuclear Information System (INIS)

    Babinet, R.P.

    1987-01-01

    DIOGENE is a small time projection chamber which has been developed to study central collisions of relativistic heavy ions. The maximum multiplicity (up to 40 charged particles) that can be accepted by this detector is limited by the present electronics. In view of the heavier mass ions that should become readily available at the Saturne national facility (France), a new sampling electronics has been tested. In the first part of this talk they will present a brief description of the actual detector, insisting on the performances that have been effectively obtained with α-particles and Neon beams. The motivation for and characteristics of a renewed electronic set-up should thus appear more clearly. The second part of the talk is devoted to results of the tests that have been performed using charged couple devices. They will finally conclude on the future perspectives that have been opened by these developments

  20. Readout electronics for fine dE/dx sampling with a longitudinal drift chamber

    International Nuclear Information System (INIS)

    Imanishi, A.; Shiino, K.; Ishii, T.; Ohshima, T.; Okuno, H.

    1982-04-01

    A fast, low noise preamplifier, a signal shaping filter and a fast sampling ADC circuit have been developed for fine sampling dE/dx measurement with a longitudinal drift chamber. dE/dx has been sampled with a time interval of 40 ns which corresponds to a gas thickness of 1.4 mm in Ar(90%)/CH 4 (10%). Parameters of each circuit have been adjusted to match with this sampling interval. It is found that the signal tail cancellation is crucial to obtain better dE/dx resolution when the wider drift space is used, and this can be realized with a pole-zero shortening filter and a semi-Gaussian shaping integrator. (author)

  1. 3D printing scanning electron microscopy sample holders: A quick and cost effective alternative for custom holder fabrication.

    Directory of Open Access Journals (Sweden)

    Gabriel N Meloni

    Full Text Available A simple and cost effective alternative for fabricating custom Scanning Electron Microscope (SEM sample holders using 3D printers and conductive polylactic acid filament is presented. The flexibility of the 3D printing process allowed for the fabrication of sample holders with specific features that enable the high-resolution imaging of nanoelectrodes and nanopipettes. The precise value of the inner semi cone angle of the nanopipettes taper was extracted from the acquired images and used for calculating their radius using electrochemical methods. Because of the low electrical resistivity presented by the 3D printed holder, the imaging of non-conductive nanomaterials, such as alumina powder, was found to be possible. The fabrication time for each sample holder was under 30 minutes and the average cost was less than $0.50 per piece. Despite being quick and economical to fabricate, the sample holders were found to be sufficiently resistant, allowing for multiple uses of the same holder.

  2. Examination of mycological samples by means of the scanning electron microscope

    Directory of Open Access Journals (Sweden)

    M. Thibaut

    1973-04-01

    Full Text Available Three species of Siphomycetes: Rhizopus arhizus, Rhizopus equinus and Rhizopus nigricans, as well as a Septomycete: Emericella nidulans, have been examined by means of a scanning electron microscope. Among the difjerent Rhizopus, this technique showed differences in the appearance of the sporangia. In Emericella nidulans, scanning microscopy enábled one to ascertain that the "Hull cells" were completely hollow and also demonstrated the ornemented aspect of the ascospores.

  3. Dynamical 'in situ' observation of biological samples using variable pressure scanning electron microscope

    International Nuclear Information System (INIS)

    Nedela, V

    2008-01-01

    Possibilities of 'in-situ' observation of non-conductive biological samples free of charging artefacts in dynamically changed surrounding conditions are the topic of this work. The observed biological sample, the tongue of a rat, was placed on a cooled Peltier stage. We studied the visibility of topographical structure depending on transition between liquid and gas state of water in the specimen chamber of VP SEM.

  4. Investigation of Deuterium Implantation into Beryllium Sample by Electron Energy Loss Spectroscopy

    Science.gov (United States)

    Afanas'ev, V. P.; Gryazev, A. S.; Kaplya, P. S.; Köppen, M.; Ridzel, O. Yu; Subbotin, N. Yu; Hansen, P.

    2017-11-01

    Quantitative analysis of hydrogen isotopes in first wall as well as in construction materials of future fusion devices plays a crucial role to understand the evolution of those materials under operation conditions. A quantitative understanding of hydrogen in materials is also an important issue for storing energy as well as for fuel cells. A combination of Electron Energy Loss Spectroscopy (EELS) and Elastic Peak Electron Spectroscopy (EPES) is presented in this study to tackle these problems of modern material research for energy production and storage. Accurate inelastic scattering background subtraction is a key part of the presented quantitative measurement of the Be/D ratio. The differential inelastic scattering cross-section is determined by the fitting procedure. The fitting procedure is based on the iterative solution of the direct problem and minimization of the residual between computed and measured spectra. This study also takes into account the difference in electron energy loss laws for surface and bulk. The inelastic scattering cross-sections for different doses of deuterium ions in beryllium substrate (5.5·1021 m-2 and 2.01·1022 m-2) were defined in a two-layered model. The analysis is carried out for the EELS spectra. Relative concentration of D atoms is defined.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    NARCIS (Netherlands)

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

    2005-01-01

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

  7. Polymerase chain reaction for detection of Mycobacterium leprae in nasal swab specimens

    NARCIS (Netherlands)

    de Wit, M. Y.; Douglas, J. T.; McFadden, J.; Klatser, P. R.

    1993-01-01

    The polymerase chain reaction based on the selective amplification of a 531-bp fragment of the gene encoding the proline-rich antigen of Mycobacterium leprae was applied to nasal swab specimens from leprosy patients, occupational contacts, and endemic and nonendemic controls. To prevent

  8. 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…

  9. Frequency and Antimicrobial Susceptibility Pattern of Acinetobacter Species Isolated from Pus and Pus Swab Specimens

    International Nuclear Information System (INIS)

    Fayyaz, M.; Akbar, N.; Khan, I. U.; Hussain, A.; Ali, S.; Mirza, I. A.

    2015-01-01

    Objective: To evaluate the frequency and antimicrobial susceptibility pattern of Acinetobacter species isolated from pus and pus swab specimens at a tertiary care setting. Study Design: Cross-sectional observational study. Place and Duration of Study: Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, from July 2008 to July 2012. Methodology: Data regarding positive culture and antimicrobial sensitivity pattern was retrieved from the pus and pus swab culture records of the Microbiology Department, AFIP, Rawalpindi. Only those pus and pus swab specimens which yielded the growth of Acinetobacter species were included in the study. Results:Out of 2781, 1848 were of pure pus while 933 were pus swab specimens. Out of 2538 culture positive isolates, 276 (10.9 percentage) were identified as Acinetobacterspecies. Among 276 Acinetobacter species, 245 (88.8 percentage) were Acinetobacter baumannii and 31 (11.2 percentage) were Acinetobacter johnsonii. Male/female ratio of the affected patients was 5.6:1. Doxycycline was the most sensitive antibiotic to which 45 percentage of the tested isolates were sensitive. Sensitivity to all other antimicrobials was 15 percentage or less. Conclusion: About 11 percentage of soft tissue and wound infections are caused by Acinetobacter species in our set up particularly in male. Doxycycline was the most sensitive antibiotic. Sensitivity to all other antimicrobials was 15 percentage or less. In vitro sensitivity to carbapenems is very low. (author)

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

    African Journals Online (AJOL)

    Infective vaginal discharge, when left untreated, is a possible risk of acquisition of HIV/AIDS as well as other complications. 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 ...

  11. 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 ...

  12. A new fractionator principle with varying sampling fractions: exemplified by estimation of synapse number using electron microscopy

    DEFF Research Database (Denmark)

    Witgen, Brent Marvin; Grady, M. Sean; Nyengaard, Jens Randel

    2006-01-01

    The quantification of ultrastructure has been permanently improved by the application of new stereological principles. Both precision and efficiency have been enhanced. Here we report for the first time a fractionator method that can be applied at the electron microscopy level. This new design...... the total object number using section sampling fractions based on the average thickness of sections of variable thicknesses. As an alternative, this approach estimates the correct particle section sampling probability based on an estimator of the Horvitz-Thompson type, resulting in a theoretically more...

  13. 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

  14. Electron spin resonance dating of bones samples from recently excavated in Karnataka, India

    International Nuclear Information System (INIS)

    Ramamurthy, Ramya; Godhandabani, Velraj

    2011-01-01

    The study of radiation defects created in biomaterials, such as bone and teeth, can be used in dating with importance to paleontology and archaeology. A preliminary attempt has been made to date the bone samples from the archaeological site Gudnapur in Karnataka state, India. Each sample was divided into five sets which were given an artificial dose (AD) by using γ rays of 50 Gy, 300 Gy, 800 Gy and 1500 Gy and 3200 Gy. All the samples show similar EPR spectra having g-values 2.0026, 2.0025 and 2.0013 corresponding to CO 2 - orthorhombic and axial CO 2 - respectively. These signals have been used for the age estimation of the archaeological bone samples assuming the dose rate to be 1.12 mGy/a. The calculated ages of the samples are 199 ± 54 ka, 28 ± 23 ka and 225 ± 74 ka. The first and third correspond to the III interglacial stage whereas the second one corresponds to I glacial stage of the Pleistocene epoch respectively and in good agreement with age predicted by archaeological Department. (author)

  15. Characterization of electron microscopes with binary pseudo-random multilayer test samples

    International Nuclear Information System (INIS)

    Yashchuk, Valeriy V.; Conley, Raymond; Anderson, Erik H.; Barber, Samuel K.; Bouet, Nathalie; McKinney, Wayne R.; Takacs, Peter Z.; Voronov, Dmitriy L.

    2010-01-01

    We discuss the results of SEM and TEM measurements with the BPRML test samples fabricated from a BPRML (WSi2/Si with fundamental layer thickness of 3 nm) with a Dual Beam FIB (focused ion beam)/SEM technique. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize x-ray microscopes. Corresponding work with x-ray microscopes is in progress.

  16. Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Leapman, R.D.; Kocsis, E.; Zhang, G.; Talbot, T.L.; Laquerriere, P

    2004-07-15

    By combining electron tomography with energy-filtered electron microscopy, we have shown the feasibility of determining the three-dimensional distributions of phosphorus in biological specimens. Thin sections of the nematode, Caenorhabditis elegans were prepared by high-pressure freezing, freeze-substitution and plastic embedding. Images were recorded at energy losses above and below the phosphorus L{sub 2,3} edge using a post-column imaging filter operating at a beam energy of 120 keV. The unstained specimens exhibited minimal contrast in bright-field images. After it was determined that the specimen was sufficiently thin to allow two-window ratio imaging of phosphorus, pairs of pre-edge and post-edge images were acquired in series over a tilt range of {+-}55 deg. at 5 deg. increments for two orthogonal tilt axes. The projected phosphorus distributions were aligned using the pre-edge images that contained inelastic contrast from colloidal gold particles deposited on the specimen surface. A reconstruction and surface rendering of the phosphorus distribution clearly revealed features 15-20 nm in diameter, which were identified as ribosomes distributed along the stacked membranes of endoplasmic reticulum and in the cytoplasm. The sensitivity of the technique was estimated at <35 phosphorus atoms per voxel based on the known total ribosomal phosphorus content of approximately 7000 atoms. Although a high electron dose of approximately 10{sup 7} e/nm{sup 2} was required to record two-axis tilt series, specimens were sufficiently stable to allow image alignment and tomographic reconstruction.

  17. Investigation of argon ion sputtering on the secondary electron emission from gold samples

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jing; Cui, Wanzhao, E-mail: cuiwanzhao@126.com; Li, Yun; Xie, Guibai; Zhang, Na; Wang, Rui; Hu, Tiancun; Zhang, Hongtai

    2016-09-30

    Highlights: • An “equivalent work function” is presented in this thesis to establish the relationship between SE yield and surface properties. • After sputtering, A decrease of δmax and an increase of E1 were observed with increasing Eion. • Further sputtering at higher energies broaden the SE spectra, and the equivalent work function, ϕ, increase considerably to 12.6 eV. - Abstract: Secondary electron (SE) yield, δ, is a very sensitive surface property. The values of δ often are not consistent for even identical materials. The influence of surface changes on the SE yield was investigated experimentally in this article. Argon ion sputtering was used to remove the contamination from the surface. Surface composition was monitored by X-ray photoelectron spectroscopy (XPS) and surface topography was scanned by scanning electron microscope (SEM) and atomic force microscope (AFM) before and after every sputtering. It was found that argon sputtering can remove contamination and roughen the surface. An “equivalent work function” is presented in this thesis to establish the relationship between SE yield and surface properties. Argon ion sputtering of 1.5keV leads to a significant increase of so called “work function” (from 3.7 eV to 6.0 eV), and a decrease of SE yield (from 2.01 to 1.54). These results provided a new insight into the influence of surface changes on the SE emission.

  18. Composition of plastics from waste electrical and electronic equipment (WEEE) by direct sampling

    International Nuclear Information System (INIS)

    Martinho, Graça; Pires, Ana; Saraiva, Luanha; Ribeiro, Rita

    2012-01-01

    Highlights: ► The article shows WEEE plastics characterization from a recycling unit in Portugal. ► The recycling unit has low machinery, with hand sorting of plastics elements. ► Most common polymers are PS, ABS, PC/ABS, HIPS and PP. ► Most plastics found have no identification of plastic type or flame retardants. ► Ecodesign is still not practiced for EEE, with repercussions in end of life stage. - Abstract: This paper describes a direct analysis study carried out in a recycling unit for waste electrical and electronic equipment (WEEE) in Portugal to characterize the plastic constituents of WEEE. Approximately 3400 items, including cooling appliances, small WEEE, printers, copying equipment, central processing units, cathode ray tube (CRT) monitors and CRT televisions were characterized, with the analysis finding around 6000 kg of plastics with several polymer types. The most common polymers are polystyrene, acrylonitrile–butadiene–styrene, polycarbonate blends, high-impact polystyrene and polypropylene. Additives to darken color are common contaminants in these plastics when used in CRT televisions and small WEEE. These additives can make plastic identification difficult, along with missing polymer identification and flame retardant identification marks. These drawbacks contribute to the inefficiency of manual dismantling of WEEE, which is the typical recycling process in Portugal. The information found here can be used to set a baseline for the plastics recycling industry and provide information for ecodesign in electrical and electronic equipment production.

  19. Composition of plastics from waste electrical and electronic equipment (WEEE) by direct sampling.

    Science.gov (United States)

    Martinho, Graça; Pires, Ana; Saraiva, Luanha; Ribeiro, Rita

    2012-06-01

    This paper describes a direct analysis study carried out in a recycling unit for waste electrical and electronic equipment (WEEE) in Portugal to characterize the plastic constituents of WEEE. Approximately 3400 items, including cooling appliances, small WEEE, printers, copying equipment, central processing units, cathode ray tube (CRT) monitors and CRT televisions were characterized, with the analysis finding around 6000 kg of plastics with several polymer types. The most common polymers are polystyrene, acrylonitrile-butadiene-styrene, polycarbonate blends, high-impact polystyrene and polypropylene. Additives to darken color are common contaminants in these plastics when used in CRT televisions and small WEEE. These additives can make plastic identification difficult, along with missing polymer identification and flame retardant identification marks. These drawbacks contribute to the inefficiency of manual dismantling of WEEE, which is the typical recycling process in Portugal. The information found here can be used to set a baseline for the plastics recycling industry and provide information for ecodesign in electrical and electronic equipment production. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Investigation of argon ion sputtering on the secondary electron emission from gold samples

    International Nuclear Information System (INIS)

    Yang, Jing; Cui, Wanzhao; Li, Yun; Xie, Guibai; Zhang, Na; Wang, Rui; Hu, Tiancun; Zhang, Hongtai

    2016-01-01

    Highlights: • An “equivalent work function” is presented in this thesis to establish the relationship between SE yield and surface properties. • After sputtering, A decrease of δmax and an increase of E1 were observed with increasing Eion. • Further sputtering at higher energies broaden the SE spectra, and the equivalent work function, ϕ, increase considerably to 12.6 eV. - Abstract: Secondary electron (SE) yield, δ, is a very sensitive surface property. The values of δ often are not consistent for even identical materials. The influence of surface changes on the SE yield was investigated experimentally in this article. Argon ion sputtering was used to remove the contamination from the surface. Surface composition was monitored by X-ray photoelectron spectroscopy (XPS) and surface topography was scanned by scanning electron microscope (SEM) and atomic force microscope (AFM) before and after every sputtering. It was found that argon sputtering can remove contamination and roughen the surface. An “equivalent work function” is presented in this thesis to establish the relationship between SE yield and surface properties. Argon ion sputtering of 1.5keV leads to a significant increase of so called “work function” (from 3.7 eV to 6.0 eV), and a decrease of SE yield (from 2.01 to 1.54). These results provided a new insight into the influence of surface changes on the SE emission.

  1. Investigation of argon ion sputtering on the secondary electron emission from gold samples

    Science.gov (United States)

    Yang, Jing; Cui, Wanzhao; Li, Yun; Xie, Guibai; Zhang, Na; Wang, Rui; Hu, Tiancun; Zhang, Hongtai

    2016-09-01

    Secondary electron (SE) yield, δ, is a very sensitive surface property. The values of δ often are not consistent for even identical materials. The influence of surface changes on the SE yield was investigated experimentally in this article. Argon ion sputtering was used to remove the contamination from the surface. Surface composition was monitored by X-ray photoelectron spectroscopy (XPS) and surface topography was scanned by scanning electron microscope (SEM) and atomic force microscope (AFM) before and after every sputtering. It was found that argon sputtering can remove contamination and roughen the surface. An ;equivalent work function; is presented in this thesis to establish the relationship between SE yield and surface properties. Argon ion sputtering of 1.5keV leads to a significant increase of so called ;work function; (from 3.7 eV to 6.0 eV), and a decrease of SE yield (from 2.01 to 1.54). These results provided a new insight into the influence of surface changes on the SE emission.

  2. Transmission Electron Microscopy (TEM) Sample Preparation of Si(1-x)Gex in c-Plane Sapphire Substrate

    Science.gov (United States)

    Kim, Hyun Jung; Choi, Sang H.; Bae, Hyung-Bin; Lee, Tae Woo

    2012-01-01

    The National Aeronautics and Space Administration-invented X-ray diffraction (XRD) methods, including the total defect density measurement method and the spatial wafer mapping method, have confirmed super hetero epitaxy growth for rhombohedral single crystalline silicon germanium (Si1-xGex) on a c-plane sapphire substrate. However, the XRD method cannot observe the surface morphology or roughness because of the method s limited resolution. Therefore the authors used transmission electron microscopy (TEM) with samples prepared in two ways, the focused ion beam (FIB) method and the tripod method to study the structure between Si1-xGex and sapphire substrate and Si1?xGex itself. The sample preparation for TEM should be as fast as possible so that the sample should contain few or no artifacts induced by the preparation. The standard sample preparation method of mechanical polishing often requires a relatively long ion milling time (several hours), which increases the probability of inducing defects into the sample. The TEM sampling of the Si1-xGex on sapphire is also difficult because of the sapphire s high hardness and mechanical instability. The FIB method and the tripod method eliminate both problems when performing a cross-section TEM sampling of Si1-xGex on c-plane sapphire, which shows the surface morphology, the interface between film and substrate, and the crystal structure of the film. This paper explains the FIB sampling method and the tripod sampling method, and why sampling Si1-xGex, on a sapphire substrate with TEM, is necessary.

  3. Detection and differentiation of Mycoplasma gallisepticum and Mycoplasma synoviaeby PCR from tracheal swabs from birds with respiratory symptoms

    International Nuclear Information System (INIS)

    Ventura, Cesar E; Ramirez, Gloria; Vera, Victor

    2012-01-01

    Mycoplasmas are worldwide pathogens that affect the poultry industry causing respiratory illness which cause a negative economic impact. Two mycoplasmas species are the most important in the commercial poultry: mycoplasma gallisepticum (MG) and mycoplasma synoviae (MS). By its importance and necessity to know and differentiate between mycoplasmas species in local's poultry houses this study used the PCR technique like a diagnosis tool, using tracheal swabs from bird with respiratory symptoms. A total of 91 samples from broilers, layers and breeders farms located in the departments of Cundinamarca and Boyaca was processed. The punctual prevalence founded in this study was 39.6 % for mg and 47.3 % for MS. statistical differences for type of production and positive samples for mg y MS (p < 0.05) were founded, a bigger number of positive samples from layers and breeder in comparison to broilers were found. In the same way, the positive samples for the layers and breeder from the age group between 20 and 60 weeks was greater, while for the broilers group most of the positive samples were from five weeks old birds for mg and two weeks old birds for MS.

  4. Examination of mycological samples by means of the scanning electron microscope

    Directory of Open Access Journals (Sweden)

    M. Thibaut

    1973-04-01

    Full Text Available Three species of Siphomycetes: Rhizopus arhizus, Rhizopus equinus and Rhizopus nigricans, as well as a Septomycete: Emericella nidulans, have been examined by means of a scanning electron microscope. Among the difjerent Rhizopus, this technique showed differences in the appearance of the sporangia. In Emericella nidulans, scanning microscopy enábled one to ascertain that the "Hull cells" were completely hollow and also demonstrated the ornemented aspect of the ascospores.Três espécies de Sifomicetas: Rhizopus arhizus, Rhizopus equinus, Rhizopus nigricans e um Septomiceta: Emericella nidulans foram examinados em microscopia de exploração. Esta técnica mostrou detalhes não evidenciáveis ao poder de resolução do microscópio óptico, demonstrando ser útil para o diagnóstico em micologia.

  5. Sample Preparation Methodologies for In Situ Liquid and Gaseous Cell Analytical Transmission Electron Microscopy of Electropolished Specimens.

    Science.gov (United States)

    Zhong, Xiang Li; Schilling, Sibylle; Zaluzec, Nestor J; Burke, M Grace

    2016-12-01

    In recent years, an increasing number of studies utilizing in situ liquid and/or gaseous cell scanning/transmission electron microscopy (S/TEM) have been reported. Because of the difficulty in the preparation of suitable specimens, these environmental S/TEM studies have been generally limited to studies of nanoscale structured materials such as nanoparticles, nanowires, or sputtered thin films. In this paper, we present two methodologies which have been developed to facilitate the preparation of electron-transparent samples from conventional bulk metals and alloys for in situ liquid/gaseous cell S/TEM experiments. These methods take advantage of combining sequential electrochemical jet polishing followed by focused ion beam extraction techniques to create large electron-transparent areas for site-specific observation. As an example, we illustrate the application of this methodology for the preparation of in situ specimens from a cold-rolled Type 304 austenitic stainless steel sample, which was subsequently examined in both 1 atm of air as well as fully immersed in a H2O environment in the S/TEM followed by hyperspectral imaging. These preparation techniques can be successfully applied as a general procedure for a wide range of metals and alloys, and are suitable for a variety of in situ analytical S/TEM studies in both aqueous and gaseous environments.

  6. Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation.

    Directory of Open Access Journals (Sweden)

    Ahmadreza Baghaie

    Full Text Available Scanning Electron Microscope (SEM as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D. In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.

  7. ``Low-cost Electronic nose evaluated on Thai-herb of Northern-Thailand samples using multivariate analysis methods''

    Science.gov (United States)

    na ayudhaya, Paisarn Daungjak; Klinbumrung, Arrak; Jaroensutasinee, Krisanadej; Pratontep, Sirapat; Kerdcharoen, Teerakiat

    2009-05-01

    In case of species of natural and aromatic plant originated from the northern Thailand, sensory characteristics, especially odours, have unique identifiers of herbs. The instruments sensory analysis have performed by several of differential of sensing, so call `electronic nose', to be a significantly and rapidly for chemometrics. The signal responses of the low cost electronic nose were evaluated by principal component analysis (PCA). The aims of this paper evaluated various of Thai-herbs grown in Northern of Thailand as data preprocessing tools of the Low-cost electronic nose (enNU-PYO1). The essential oil groups of Thai herbs such as Garlic, Lemongrass, Shallot (potato onion), Onion, Zanthoxylum limonella (Dennst.) Alston (Thai name is Makaen), and Kaffir lime leaf were compared volatilized from selected fresh herbs. Principal component analysis of the original sensor responses did clearly distinguish either all samples. In all cases more than 97% for cross-validated group were classified correctly. The results demonstrated that it was possible to develop in a model to construct a low-cost electronic nose to provide measurement of odoriferous herbs.

  8. 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.

  9. Forming mechanism and avoiding measures of blue-ring on electronic beam welding sample after water corrosion

    International Nuclear Information System (INIS)

    Ren Defang; Luo Xiandian; Tong Shenxiu; Guo Xulin; Peng Haiqing

    2001-01-01

    After water corrosion in compliance with ASTM G2, the blue ring appears on the nuclear fuel rod samples of AFA 2G welded by using a Big Chamber Electron Beam Welder made in Russia. The characteristics, appearance, chemical composition, microstructure of b lue ring a nd some condition test are described. The mechanism of forming blue ring may be depicted as following: welding metal vapor and the splash produced by secondary and scatter electrons on metal clamp and gun body deposit in the area between HAZ and substrate because of the water cooling down effects on the clamp; these deposits, after water corrosion, appears as blue ring on the fuel rod surface. Avoiding measure is that the side of the clamp closing to weld seal is chamfered, while making the welding chamber cleaner

  10. Grinding and polishing instead of sectioning for the tissue samples with a graft: Implications for light and electron microscopy.

    Science.gov (United States)

    Mukhamadiyarov, Rinat A; Sevostyanova, Victoria V; Shishkova, Daria K; Nokhrin, Andrey V; Sidorova, Olga D; Kutikhin, Anton G

    2016-06-01

    A broad use of the graft replacement requires a detailed investigation of the host-graft interaction, including both histological examination and electron microscopy. A high quality sectioning of the host tissue with a graft seems to be complicated; in addition, it is difficult to examine the same tissue area by both of the mentioned microscopy techniques. To solve these problems, we developed a new technique of epoxy resin embedding with the further grinding, polishing, and staining. Graft-containing tissues prepared by grinding and polishing preserved their structure; however, sectioning frequently required the explantation of the graft and led to tissue disintegration. Moreover, stained samples prepared by grinding and polishing may then be assessed by both light microscopy and backscattered scanning electron microscopy. Therefore, grinding and polishing outperform sectioning when applied to the tissues with a graft. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Barbara Bażanów

    2018-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

  13. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

    Science.gov (United States)

    Fuller, Franklin D; Gul, Sheraz; Chatterjee, Ruchira; Burgie, E Sethe; Young, Iris D; Lebrette, Hugo; Srinivas, Vivek; Brewster, Aaron S; Michels-Clark, Tara; Clinger, Jonathan A; Andi, Babak; Ibrahim, Mohamed; Pastor, Ernest; de Lichtenberg, Casper; Hussein, Rana; Pollock, Christopher J; Zhang, Miao; Stan, Claudiu A; Kroll, Thomas; Fransson, Thomas; Weninger, Clemens; Kubin, Markus; Aller, Pierre; Lassalle, Louise; Bräuer, Philipp; Miller, Mitchell D; Amin, Muhamed; Koroidov, Sergey; Roessler, Christian G; Allaire, Marc; Sierra, Raymond G; Docker, Peter T; Glownia, James M; Nelson, Silke; Koglin, Jason E; Zhu, Diling; Chollet, Matthieu; Song, Sanghoon; Lemke, Henrik; Liang, Mengning; Sokaras, Dimosthenis; Alonso-Mori, Roberto; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Boal, Amie K; Bollinger, J Martin; Krebs, Carsten; Högbom, Martin; Phillips, George N; Vierstra, Richard D; Sauter, Nicholas K; Orville, Allen M; Kern, Jan; Yachandra, Vittal K; Yano, Junko

    2017-04-01

    X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

  14. Effects of gamma radiation and electron beam on samples of the Brazil nuts artificially inoculated with Aspergillus flavus

    International Nuclear Information System (INIS)

    Coelho, Ednei Assuncao Antunes

    2012-01-01

    The high level of contamination by aflatoxin produced by fungi in lots of Brazil nuts and the strict control by importing countries in relation to the levels of toxins in food, European Union countries decided in 2003 by the return of these lots products from Brazil. Despite the economic loss represented by contamination by toxigenic fungi in Brazil nuts, a major product of extractive Northern of Brazil, studies are still preliminary as the control of contamination aflatoxigenic fungal using methods such as gamma radiation (G.R) and mainly, electron beam (E.B). These facts motivated this research, which aimed to evaluate the effects of gamma radiation and application of electron beam in samples of Brazil nut artificially inoculated with Aspergillus flavus. This goal, we were studied 50 samples of the Brazil nut previously inoculated with spores of A. flavus and subsequently incubated at 30 °C in relative humidity controlled at 93%. After incubation, period of 15 days, the average water activity of the samples was 0.80, the samples were divided into 5 groups that received the following doses of radiation: control (0 kGy), 5 and 10 kGy 5 E.B and G.R. The mycobiota was performed by serial dilution, plated on surface using potato dextrose agar. The results demonstrated that treatment with E.B using a dose of 5 kGy and 10 kGy resulted in reduced growth of A. flavus in 74% (37/50) and 94% (47/50) of samples. The samples treated with G.R at the dose of 5 kGy and 10 kGy no fungal growth occurred in 92% (46/50) 100% (50/50) of. The study of aflatoxins showed that doses of E.B of 5 kGy and 10 kGy reduced levels of AFB1 at 53.32% and 65.66% respectively. The application of gamma rays at doses of 5 and 10 kGy reduced levels of toxins in 70.61% and 84.15% respectively. This result may be attributed to higher penetrability of gamma radiation. Sensory analysis showed greater acceptance of the judges for the samples irradiated with E.B and G.R at the dose of 10 kGy. We concluded

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  16. Localization and chemical forms of cadmium in plant samples by combining analytical electron microscopy and X-ray spectromicroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Isaure, Marie-Pierre [Section d' Application des Traceurs, LITEN, CEA-Grenoble, 17, rue des Martyrs, 38054 Grenoble cedex 9 (France) and Environmental Geochemistry Group, LGIT, UMR 5559, Universite J. Fourier and CNRS, BP 53, 38041 Grenoble cedex 9 (France)]. E-mail: mpisaure@ujf-grenoble.fr; Fayard, Barbara [Laboratoire de Physique des Solides, UMR 8502 Universite Paris Sud, 91405 Orsay (France); European Synchrotron Radiation Facility, ID-21, BP220, 38043 Grenoble (France); Sarret, Geraldine [Environmental Geochemistry Group, LGIT, UMR 5559, Universite J. Fourier and CNRS, BP 53, 38041 Grenoble cedex 9 (France); Pairis, Sebastien [Laboratoire de Cristallographie, UPR 5031, 25 Avenue des Martyrs, BP 166, 38042 Grenoble cedex 9 (France); Bourguignon, Jacques [Laboratoire de Physiologie Cellulaire Vegetale, UMR 5168 CEA/CNRS/INRA/UJF, DRDC, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble cedex 9 (France)

    2006-12-15

    Cadmium (Cd) is a metal of high toxicity for plants. Resolving its distribution and speciation in plants is essential for understanding the mechanisms involved in Cd tolerance, trafficking and accumulation. The model plant Arabidopsis thaliana was exposed to cadmium under controlled conditions. Elemental distributions in the roots and in the leaves were determined using scanning electron microscopy coupled with energy dispersive X-ray microanalysis (SEM-EDX), and synchrotron-based micro X-ray fluorescence ({mu}-XRF), which offers a better sensitivity. The chemical form(s) of cadmium was investigated using Cd L{sub III}-edge (3538 eV) micro X-ray absorption near edge structure ({mu}-XANES) spectroscopy. Plant {mu}-XANES spectra were fitted by linear combination of Cd reference spectra. Biological sample preparation and conditioning is a critical point because of possible artifacts. In this work we compared freeze-dried samples analyzed at ambient temperature and frozen hydrated samples analyzed at -170 deg. C. Our results suggest that in the roots Cd is localized in vascular bundles, and coordinated to S ligands. In the leaves, trichomes (epidermal hairs) represent the main compartment of Cd accumulation. In these specialized cells, {mu}-XANES results show that the majority of Cd is bound to O/N ligands likely provided by the cell wall, and a minor fraction could be bound to S-containing ligands. No significant difference in Cd speciation was observed between freeze-dried and frozen hydrated samples. This work illustrates the interest and the sensitivity of Cd L{sub III}-edge XANES spectroscopy, which is applied here for the first time to plant samples. Combining {mu}-XRF and Cd L{sub III}-edge {mu}-XANES spectroscopy offers promising tools to study Cd storage and trafficking mechanisms in plants and other biological samples.

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

    Science.gov (United States)

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

    2017-03-01

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

  18. Relationship between resist outgassing and EUV witness sample contamination in NXE outgas qualification using electrons and EUV photons

    Science.gov (United States)

    Pollentier, I.; Tirumala Venkata, A.; Gronheid, R.

    2014-04-01

    EUV photoresists are considered as a potential source of optics contamination, since they introduce irradiation-induced outgassing in the EUV vacuum environment. Therefore, before these resists can be used on e.g. ASML NXE:3100 or NXE:3300, they need to be tested in dedicated equipment according to a well-defined procedure, which is based on exposing a witness sample (WS) in the vicinity of a simultaneously exposed resist as it outgasses. Different system infrastructures are used at multiple sites (e.g. NIST, CNSE, Sematech, EIDEC, and imec) and were calibrated to each other by a detailed test plan. Despite this detailed tool qualifications, a first round robin comparison of identical materials showed inconsistent outgas test results, and required further investigation by a second round robin. Since the resist exposure mode is different at the various locations (some sites are using EUV photons while others use E-gun electrons), this difference has always a point of concern for variability of test results. In this work we compare the outgas test results from EUV photon and electron exposure using the resist materials of the second round robin. Since the imec outgas tester allows both exposure methods on the resist, a within-system comparison is possible and showed limited variation between photon and electron exposure mode. Therefore the system-to-system variability amongst the different outgas test sites is expected to be related to other parameters than the electron/photon exposure mode. Initial work showed that the variability might be related to temperature, E-gun emission excursion, and/or residual outgassing scaled by different wafer areas at the different sites.

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

    Science.gov (United States)

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

    2008-05-25

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

  20. Immunoassay of C-reactive protein by hot electron induced electrochemiluminescence using integrated electrodes with hydrophobic sample confinement

    Energy Technology Data Exchange (ETDEWEB)

    Ylinen-Hinkka, T., E-mail: tiina.ylinen-hinkka@aalto.fi [Laboratory of Analytical Chemistry, Aalto University School of Chemical Technology, P.O. Box 16100, FI-00076 Aalto (Finland); Niskanen, A.J.; Franssila, S. [Department of Materials Science and Engineering, Aalto University School of Chemical Technology, P.O. Box 16200, FI-00076 Aalto (Finland); Kulmala, S. [Laboratory of Analytical Chemistry, Aalto University School of Chemical Technology, P.O. Box 16100, FI-00076 Aalto (Finland)

    2011-09-19

    Highlights: {center_dot} C-reactive protein has been determined in the concentration range 0.01-10 mg L{sup -1} using an electrochemiluminescence microchip which employs integrated electrodes with hydrophobic sample confinement. {center_dot} This arrangement enables very simple and fast CRP analysis amenable to point-of-care applications. - Abstract: C-reactive protein (CRP) was determined in the concentration range 0.01-10 mg L{sup -1} using hot electron induced electrochemiluminescence (HECL) with devices combining both working and counter electrodes and sample confinement on a single chip. The sample area on the electrodes was defined by a hydrophobic ring, which enabled dispensing the reagents and the analyte directly on the electrode. Immunoassay of CRP by HECL using integrated electrodes is a good candidate for a high-sensitivity point-of-care CRP-test, because the concentration range is suitable, miniaturisation of the measurement system has been demonstrated and the assay method with integrated electrodes is easy to use. High-sensitivity CRP tests can be used to monitor the current state of cardiovascular disease and also to predict future cardiovascular problems in apparently healthy people.

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

    NARCIS (Netherlands)

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

    2006-01-01

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

  2. Low-cost monitoring of campylobacter in poultry houses by air sampling and quantitative PCR

    DEFF Research Database (Denmark)

    Søndergaard, Mette Sofie Rousing; Josefsen, Mathilde Hasseldam; Löfström, Charlotta

    2014-01-01

    approximately 10(4) and 10(5) CCE per sample for boot swabs and air, respectively. In conclusion, using air samples combined with quantitative real-time PCR, Campylobacter contamination could be detected earlier than by boot swabs and was found to be a more convenient technique for monitoring and/or to obtain......The present study describes the evaluation of a method for the quantification of Campylobacter by air sampling in poultry houses. Sampling was carried out in conventional chicken houses in Poland, in addition to a preliminary sampling in Denmark. Each measurement consisted of three air samples, two...... standard boot swab fecal samples, and one airborne particle count. Sampling was conducted over an 8-week period in three flocks, assessing the presence and levels of Campylobacter in boot swabs and air samples using quantitative real-time PCR. The detection limit for air sampling was approximately 100...

  3. Comparison of four sampling methods for the detection of Salmonella in broiler litter.

    Science.gov (United States)

    Buhr, R J; Richardson, L J; Cason, J A; Cox, N A; Fairchild, B D

    2007-01-01

    Experiments were conducted to compare litter sampling methods for the detection of Salmonella. In experiment 1, chicks were challenged orally with a suspension of naladixic acid-resistant Salmonella and wing banded, and additional nonchallenged chicks were placed into each of 2 challenge pens. Nonchallenged chicks were placed into each nonchallenge pen located adjacent to the challenge pens. At 7, 8, 10, and 11 wk of age the litter was sampled using 4 methods: fecal droppings, litter grab, drag swab, and sock. For the challenge pens, Salmonella-positive samples were detected in 3 of 16 fecal samples, 6 of 16 litter grab samples, 7 of 16 drag swabs samples, and 7 of 16 sock samples. Samples from the nonchallenge pens were Salmonella positive in 2 of 16 litter grab samples, 9 of 16 drag swab samples, and 9 of 16 sock samples. In experiment 2, chicks were challenged with Salmonella, and the litter in the challenge and adjacent nonchallenge pens were sampled at 4, 6, and 8 wk of age with broilers remaining in all pens. For the challenge pens, Salmonella was detected in 10 of 36 fecal samples, 20 of 36 litter grab samples, 14 of 36 drag swab samples, and 26 of 36 sock samples. Samples from the adjacent nonchallenge pens were positive for Salmonella in 6 of 36 fecal droppings samples, 4 of 36 litter grab samples, 7 of 36 drag swab samples, and 19 of 36 sock samples. Sock samples had the highest rates of Salmonella detection. In experiment 3, the litter from a Salmonella-challenged flock was sampled at 7, 8, and 9 wk by socks and drag swabs. In addition, comparisons with drag swabs that were stepped on during sampling were made. Both socks (24 of 36, 67%) and drag swabs that were stepped on (25 of 36, 69%) showed significantly more Salmonella-positive samples than the traditional drag swab method (16 of 36, 44%). Drag swabs that were stepped on had comparable Salmonella detection level to that for socks. Litter sampling methods that incorporate stepping on the sample

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

    Science.gov (United States)

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

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  7. 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.

  8. Supplementing electronic health records through sample collection and patient diaries: A study set within a primary care research database.

    Science.gov (United States)

    Joseph, Rebecca M; Soames, Jamie; Wright, Mark; Sultana, Kirin; van Staa, Tjeerd P; Dixon, William G

    2018-02-01

    To describe a novel observational study that supplemented primary care electronic health record (EHR) data with sample collection and patient diaries. The study was set in primary care in England. A list of 3974 potentially eligible patients was compiled using data from the Clinical Practice Research Datalink. Interested general practices opted into the study then confirmed patient suitability and sent out postal invitations. Participants completed a drug-use diary and provided saliva samples to the research team to combine with EHR data. Of 252 practices contacted to participate, 66 (26%) mailed invitations to patients. Of the 3974 potentially eligible patients, 859 (22%) were at participating practices, and 526 (13%) were sent invitations. Of those invited, 117 (22%) consented to participate of whom 86 (74%) completed the study. We have confirmed the feasibility of supplementing EHR with data collected directly from patients. Although the present study successfully collected essential data from patients, it also underlined the requirement for improved engagement with both patients and general practitioners to support similar studies. © 2017 The Authors. Pharmacoepidemiology & Drug Safety published by John Wiley & Sons Ltd.

  9. Evaluation of a nested PCR test and bacterial culture of swabs from the nasal passages and from abscesses in relation to diagnosis of Streptococcus equi infection (strangles)

    DEFF Research Database (Denmark)

    Grønbæk, L.M.; Angen, Øystein; Vigre, Håkan

    2006-01-01

    . Methods: Two herds with natural outbreaks of strangles were visited over a period of 15 weeks and 323 samples originating from 35 horses investigated. The diagnostic use of a nested PCR test was evaluated using a collection of 165 isolates of Lancefield group C streptococci (species specificity) and swabs...... from nasal passages or from abscesses from horses infected with S. equi (diagnostic sensitivity). Results: All 45 S. equi isolates tested positive in the nested PCR, whereas no amplicon was formed when testing the other 120 Lancefield group C isolates. A total of 43 samples were collected from 11...... horses with and without clinical signs. Conclusions and potential relevance: The nested PCR test represents a species-specific and -sensitive method for diagnosis of S. equi from clinical samples. It may, however, be desirable in future to develop detection methods with high diagnostic sensitivity...

  10. Electronics

    Science.gov (United States)

    2001-01-01

    International Acer Incorporated, Hsin Chu, Taiwan Aerospace Industrial Development Corporation, Taichung, Taiwan American Institute of Taiwan, Taipei, Taiwan...Singapore and Malaysia .5 - 4 - The largest market for semiconductor products is the high technology consumer electronics industry that consumes up...Singapore, and Malaysia . A new semiconductor facility costs around $3 billion to build and takes about two years to become operational

  11. 9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

    Science.gov (United States)

    2010-01-01

    ... laboratory within one day. If delivery is delayed, samples should be refrigerated. (a) For egg- and meat-type chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

  12. Critical assessment of the performance of electronic moisture analyzers for small amounts of environmental samples and biological reference materials.

    Science.gov (United States)

    Krachler, M

    2001-12-01

    Two electronic moisture analyzers were critically evaluated with regard to their suitability for determining moisture in small amounts (environmental matrices such as leaves, needles, soil, peat, sediments, and sewage sludge, as well as various biological reference materials. To this end, several homogeneous bulk materials were prepared which were subsequently employed for the development and optimization of all analytical procedures. The key features of the moisture analyzers included a halogen or ceramic heater and an integrated balance with a resolution of 0.1 mg, which is an essential prerequisite for obtaining precise results. Oven drying of the bulk materials in a conventional oven at 105 degrees C until constant mass served as reference method. A heating temperature of 65degrees C was found to provide accurate and precise results for almost all matrices investigated. To further improve the accuracy and precision, other critical parameters such as handling of sample pans, standby temperature, and measurement delay were optimized. Because of its ponderous heating behavior, the performance of the ceramic radiator was inferior to that of the halogen heater, which produced moisture results comparable to those obtained by oven drying. The developed drying procedures were successfully applied to the fast moisture analysis (1.4-6.3 min) of certified biological reference materials of similar provenance to the investigated the bulk materials. Moisture results for 200 mg aliquots ranged from 1.4 to 7.8% and good agreement was obtained between the recommended drying procedure for the reference materials and the electronic moisture analyzers with absolute uncertainties amounting to 0.1% and 0.2-0.3%, respectively.

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Carlo Mengoli

    2009-06-01

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

  15. Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. 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.

  17. 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 (Pquantitative swabs and the quantitative biopsies. The semi-quantitative swabs showed a significant, moderate correlation with the quantitative biopsies (Pquantitative 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.

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

    Science.gov (United States)

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

    1995-06-01

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

  19. 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)

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

    Science.gov (United States)

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

    1996-11-01

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

  1. Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.

    Science.gov (United States)

    Strauss, Mike; Schotte, Lise; Karunatilaka, Krishanthi S; Filman, David J; Hogle, James M

    2017-02-01

    By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events. Copyright © 2017 American Society for Microbiology.

  2. Waterpipe tobacco and electronic cigarette use in a southeast London adult sample: a cross-sectional analysis.

    Science.gov (United States)

    Jawad, Mohammed; Power, Gerald

    2016-06-01

    Waterpipe tobacco and electronic cigarettes (e-cigarettes) share several features: rising popularity, use of product flavourings and concerns about marketing to youth. We sought to compare prevalence and predictors of waterpipe tobacco and e-cigarette use, and explore knowledge of waterpipe tobacco and support for interventions. We used convenience sampling methods to conduct a cross-sectional survey among adults in the ethnically diverse southeast London area. Multivariate logistic regression identified predictors of waterpipe and e-cigarette use. Predictor variables were age, gender, ethnicity and current (past 30-day) cigarette use. Of 1176 respondents (23.0% aged 25-34 years, 56.0% male, 57.4% white ethnicity and 30.4% current cigarette smokers), 31.0% had tried waterpipe tobacco and 7.4% had tried e-cigarettes. Both products were significantly associated with younger age groups, non-white ethnicities and use of each other. Waterpipe tobacco was independently associated with consumption of cigarettes while e-cigarettes were not. Among those aware of waterpipe, a third answered incorrectly to knowledge questions. Among those self-identified as coming from a traditional waterpipe-using community, two-thirds supported further legislative and health promotion waterpipe interventions. Waterpipe tobacco was common and more prevalent than e-cigarettes in this population. Interventions to prevent and control waterpipe are unlikely to marginalize traditional waterpipe-using communities. © The Author 2015. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. A new method to detect and correct sample tilt in scanning transmission electron microscopy bright-field imaging

    Energy Technology Data Exchange (ETDEWEB)

    Brown, H.G. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Ishikawa, R.; Sánchez-Santolino, G. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Lugg, N.R., E-mail: shibata@sigma.t.u-tokyo.ac.jp [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Ikuhara, Y. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Allen, L.J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Shibata, N. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan)

    2017-02-15

    Important properties of functional materials, such as ferroelectric shifts and octahedral distortions, are associated with displacements of the positions of lighter atoms in the unit cell. Annular bright-field scanning transmission electron microscopy is a good experimental method for investigating such phenomena due to its ability to image light and heavy atoms simultaneously. To map atomic positions at the required accuracy precise angular alignment of the sample with the microscope optical axis is necessary, since misalignment (tilt) of the specimen contributes to errors in position measurements of lighter elements in annular bright-field imaging. In this paper it is shown that it is possible to detect tilt with the aid of images recorded using a central bright-field detector placed within the inner radius of the annular bright-field detector. For a probe focus near the middle of the specimen the central bright-field image becomes especially sensitive to tilt and we demonstrate experimentally that misalignment can be detected with a precision of less than a milliradian, as we also confirm in simulation. Coma in the probe, an aberration that can be misidentified as tilt of the specimen, is also investigated and it is shown how the effects of coma and tilt can be differentiated. The effects of tilt may be offset to a large extent by shifting the diffraction plane detector an amount equivalent to the specimen tilt and we provide an experimental proof of principle of this using a segmented detector system. - Highlights: • Octahedral distortions are associated with displacements of lighter atoms. • Annular bright-field imaging is sensitive to light and heavy atoms simultaneously. • Mistilt of the specimen leads to errors in position measurements of lighter elements. • It is possible to detect tilt using images taken by a central bright-field detector. • Tilt may be offset by shifting the diffraction plane detector by an equivalent amount.

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

    Science.gov (United States)

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

    1994-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Daniela Maneg

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  7. ESR response of powder samples of clear fused quartz material to high doses of 10 MeV electrons: possible applications for industrial radiation processing

    International Nuclear Information System (INIS)

    Aliabadi, R.; Amraei, R.; Ranjbar, A.H.; Rafieian, Sh.; Nasirimoghadam, S.

    2010-01-01

    Powder samples of clear fused quartz were irradiated by 10 MeV electrons at doses between 6-15 kGy and 25-37 kGy and analyzed with electron spin resonance. The reproducibility of the material dose response curve was studied, in which the irradiated samples were annealed and reused for further investigations. Results indicate a good linearity between the absorbed dose and the ESR intensity of the signals. They also showed that in the reuse processes, the electron spin resonance signal intensity, in both dose ranges was decreased. The thermal fading represented a relative sharp decay at room temperature through 15 days, after which the decay-rate was negligible for a measurement period of 60 days.

  8. Technique for preparation of transmission electron microscope specimens from wire samples of Al and Al-Al2O3 alloys

    DEFF Research Database (Denmark)

    Lindbo, Jørgen

    1966-01-01

    A technique for thinning 1 mm wire samples of aluminium and aluminium-alumina alloys for transmission electron microscopy is described. The essential feature of the technique, which involves spark machining and electropolishing in a polytetrafluoroethylene holder followed by chemical polishing...

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

    Science.gov (United States)

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

    2010-01-01

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

  10. [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.

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

    NARCIS (Netherlands)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2010-07-01

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

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

    OpenAIRE

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

    2010-01-01

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

  14. 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...

  15. [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

  16. Two sampling techniques for game meat

    OpenAIRE

    van der Merwe, Maretha; Jooste, Piet J.; Hoffman, Louw C.; Calitz, Frikkie J.

    2013-01-01

    A study was conducted to compare the excision sampling technique used by the export market and the sampling technique preferred by European countries, namely the biotrace cattle and swine test. The measuring unit for the excision sampling was grams (g) and square centimetres (cm2) for the swabbing technique. The two techniques were compared after a pilot test was conducted on spiked approved beef carcasses (n = 12) that statistically proved the two measuring units correlated. The two sampling...

  17. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

    Science.gov (United States)

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

    2012-01-01

    Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

  18. 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

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

    Science.gov (United States)

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

    2014-09-01

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

  20. Evaluation of the effects of storage in two different swab fabrics and under three different transport conditions on recovery of aerobic and anaerobic bacteria

    NARCIS (Netherlands)

    Roelofsen, E.; Leeuwen, M. van; Meijer-Severs, G.J.; Wilkinson, M.H.F.; Degener, J.E.

    Recovery of six anaerobic and five aerobic pathogens from viscose swabs and polyurethane swabs (Culturette EZ) was evaluated quantitatively, and transport in aerobic dry tubes, aerobic Amies transport medium (Transwab), and anaerobic universal transport medium (Port-a-Cul) was compared. The

  1. Metal-poor dwarf galaxies in the SIGRID galaxy sample. II. The electron temperature-abundance calibration and the parameters that affect it

    Energy Technology Data Exchange (ETDEWEB)

    Nicholls, David C.; Dopita, Michael A.; Sutherland, Ralph S.; Jerjen, Helmut; Kewley, Lisa J., E-mail: David.Nicholls@anu.edu.au [Research School of Astronomy and Astrophysics, Australian National University, Cotter Rd., Weston ACT 2611 (Australia)

    2014-07-20

    In this paper, we use the Mappings photoionization code to explore the physical parameters that impact on the measurement of electron temperature and abundance in H II regions. In our previous paper, we presented observations and measurements of physical properties from the spectra of 17 H II regions in 14 isolated dwarf irregular galaxies from the SIGRID sample. Here, we analyze these observations further, together with three additional published data sets. We explore the effects of optical thickness, electron density, ionization parameter, ionization source, and non-equilibrium effects on the relation between electron temperature and metallicity. We present a standard model that fits the observed data remarkably well at metallicities between one-tenth and 1 solar. We investigate the effects of optically thin H II regions, and show that they can have a considerable effect on the measured electron temperature, and that there is evidence that some of the observed objects are optically thin. We look at the role of the ionization parameter and find that lower ionization parameter values give better fits at higher oxygen abundance. We show that higher pressures combined with low optical depth, and also κ electron energy distributions at low κ values, can generate the apparent high electron temperatures in low-metallicity H II regions, and that the former provides the better fit to observations. We examine the effects of these parameters on the strong line diagnostic methods. We extend this to three-dimensional diagnostic grids to confirm how well the observations are described by the grids.

  2. In-situ transmission electron microscopy of the solid-phase epitaxial growth of GaAs: sample preparation and artifact characterization

    International Nuclear Information System (INIS)

    Llewellyn, D.J.; Llewellyn, D.J.; Belay, K.B.; Ridgway, M.C.

    1998-01-01

    In-situ transmission electron microscopy (TEM) has been used to characterize the solid phase epitaxial growth of amorphized GaAs at a temperature of 260 deg C. To maximize heat transfer from the heated holder to the sample and minimize electron-irradiation induced artifacts, non-conventional methodologies were utilized for the preparation of cross-sectional samples. GaAs 3x1 mm rectangular wafers were cleaved then glued face-to-face to form a wafer stack size of 3x3 mm while maintaining the TEM region at the center. This stack was subsequently polished on the cross-section to a thickness of ∼ 200 μm. A 3 mm disc was then cut perpendicular to the cross-section using a Gatan ultrasonic cutter. The disc was polished then dimpled on both sides to a thickness of ∼ 15 μm. This was ion-beam milled at liquid nitrogen temperature to an electron-transparent layer. From a comparison of in-situ and ex-situ measurements of the recrystallization rate, the actual sample temperature during in-situ characterization was estimated to deviate by ≤ 20 deg C from that of the heated holder. The influence of electron-irradiation was found to be negligible by comparing the recrystallization rate and microstructure of irradiated and unirradiated regions of comparable thickness. Similarly, the influence of the 'thin-foil effect' was found to be negligible by comparing the recrystallization rate and microstructure of thick and thin regions, the former determined after the removal of the sample from the microscope and further ion-beam milling of tens of microns of material. In conclusion, the potential influence of artifacts during in-situ TEM can be minimized by the appropriate choice of sample preparation procedures. (authors)

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

    Science.gov (United States)

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

    2017-08-01

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

  4. Sampling procedures using optical-data and partial wave cross sections in a Monte Carlo code for simulating kilovolt electron and positron transport in solids

    International Nuclear Information System (INIS)

    Fernandez-Varea, J.M.; Salvat, F.; Liljequist, D.

    1994-09-01

    The details of a Monte Carlo code for computing the penetration and energy loss of electrons and positrons in solids are described. The code, intended for electrons and positrons with energies from ∼ 100 eV to ∼ 100 keV, is based on the simulation of individual elastic and inelastic collisions. Elastic collisions are simulated using differential cross sections computed by the relativistic partial wave method applied to a muffin-tin Dirac-Hartree-Fock-Slater potential. Inelastic collisions are simulated by means of a model based on optical and photoelectric data, which are extended to the non-zero momentum transfer region by means of somewhat different algorithms for valence electron excitations and inner-shell excitations. This report focuses on the description of detailed formulae and sampling methods. 10 refs, 3 figs, 8 tabs

  5. Estimation of the sensitivity of various environmental sampling methods for detection of Salmonella in duck flocks.

    Science.gov (United States)

    Arnold, Mark E; Mueller-Doblies, Doris; Gosling, Rebecca J; Martelli, Francesca; Davies, Robert H

    2015-01-01

    Reports of Salmonella in ducks in the UK currently rely upon voluntary submissions from the industry, and as there is no harmonized statutory monitoring and control programme, it is difficult to compare data from different years in order to evaluate any trends in Salmonella prevalence in relation to sampling methodology. Therefore, the aim of this project was to assess the sensitivity of a selection of environmental sampling methods, including the sampling of faeces, dust and water troughs or bowls for the detection of Salmonella in duck flocks, and a range of sampling methods were applied to 67 duck flocks. Bayesian methods in the absence of a gold standard were used to provide estimates of the sensitivity of each of the sampling methods relative to the within-flock prevalence. There was a large influence of the within-flock prevalence on the sensitivity of all sample types, with sensitivity reducing as the within-flock prevalence reduced. Boot swabs (individual and pool of four), swabs of faecally contaminated areas and whole house hand-held fabric swabs showed the overall highest sensitivity for low-prevalence flocks and are recommended for use to detect Salmonella in duck flocks. The sample type with the highest proportion positive was a pool of four hair nets used as boot swabs, but this was not the most sensitive sample for low-prevalence flocks. All the environmental sampling types (faeces swabs, litter pinches, drag swabs, water trough samples and dust) had higher sensitivity than individual faeces sampling. None of the methods consistently identified all the positive flocks, and at least 10 samples would be required for even the most sensitive method (pool of four boot swabs) to detect a 5% prevalence. The sampling of dust had a low sensitivity and is not recommended for ducks.

  6. Electronic states of model hydrocarbon chromophores investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy on aligned samples

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Hoffmann, Søren Vrønning; Jones, Nykola

    2010-01-01

    Conventional UV-VIS absorption spectroscopy provides information on transition energies and intensities. Linear dichroism (LD) spectroscopy on aligned molecular samples yields additional information on transition moment directions, thereby frequently leading to resolution of otherwise overlapping...

  7. Construction of electron beam machine 350 keV/10 mA for multipurpose application of thin sample at P3TM-BATAN

    International Nuclear Information System (INIS)

    Darsono

    2004-01-01

    Research and development starting in 1984 of electron beam technology in Indonesia is first briefly presented. BATAN assigned to the Yogyakarta Nuclear Center the project of constructing an electron beam machine of 350 keV/10 mA for multipurpose applications especially for thin samples for duration of five years. The main objective of the project was the young scientists training and demonstration purposes in operation and maintenance of the machine. The engineers have learned through experience of the low energy ion accelerator (150 kV) many techniques to construct the system component such as E-gun, high voltage, vacuum, beam optics, scanning horn and window, beam stopper, and conveyer as well as the embedded control system. Because of the window cooling system, the uses of the machine are limited for irradiating a thin sample of plastics, hydrogel, powder, or liquid. Future plans for modification of the machine are stated. (S. Ohno)

  8. Preparation and Loading Process of Single Crystalline Samples into a Gas Environmental Cell Holder for In Situ Atomic Resolution Scanning Transmission Electron Microscopic Observation.

    Science.gov (United States)

    Straubinger, Rainer; Beyer, Andreas; Volz, Kerstin

    2016-06-01

    A reproducible way to transfer a single crystalline sample into a gas environmental cell holder for in situ transmission electron microscopic (TEM) analysis is shown in this study. As in situ holders have only single-tilt capability, it is necessary to prepare the sample precisely along a specific zone axis. This can be achieved by a very accurate focused ion beam lift-out preparation. We show a step-by-step procedure to prepare the sample and transfer it into the gas environmental cell. The sample material is a GaP/Ga(NAsP)/GaP multi-quantum well structure on Si. Scanning TEM observations prove that it is possible to achieve atomic resolution at very high temperatures in a nitrogen environment of 100,000 Pa.

  9. Electronic properties of polyamide-PPy/metal junction and electrical conductivity of a typical sample at low temperatures

    International Nuclear Information System (INIS)

    Suenel, N.; Sedef, A.G.; Parlak, M.; Toppare, L.

    2005-01-01

    Electronic properties of junctions fabricated by polyamide-polypyrrole composite films polymerized with adjusted doping concentration and various metal contacts (In, Al, Au and Ag) were investigated. For the junctions giving good rectification I 0 , n and φ b were specified. Conductivity of polyamide-polypyrrole composite polymer was obtained as a function of temperature in the 70-320 K range and was found to obey the VRH model. In addition the Mott parameters were evaluated

  10. Electronic properties of polyamide-PPy/metal junction and electrical conductivity of a typical sample at low temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Suenel, N. [Gaziosmanpasa University, Physics Department, Tasliciftlik Kampasu, Tokat (Turkey)]. E-mail: nsunel@gop.edu.tr; Sedef, A.G. [Gaziosmanpasa University, Physics Department, Tasliciftlik Kampasu, Tokat (Turkey); Parlak, M. [Middle East Technical University, Physics Department, Ankara (Turkey); Toppare, L. [Middle East Technical University, Chemistry Department, Ankara (Turkey)

    2005-05-15

    Electronic properties of junctions fabricated by polyamide-polypyrrole composite films polymerized with adjusted doping concentration and various metal contacts (In, Al, Au and Ag) were investigated. For the junctions giving good rectification I{sub 0}, n and {phi}{sub b} were specified. Conductivity of polyamide-polypyrrole composite polymer was obtained as a function of temperature in the 70-320 K range and was found to obey the VRH model. In addition the Mott parameters were evaluated.

  11. A comparison of temporal and location-based sampling strategies for global positioning system-triggered electronic diaries.

    Science.gov (United States)

    Törnros, Tobias; Dorn, Helen; Reichert, Markus; Ebner-Priemer, Ulrich; Salize, Hans-Joachim; Tost, Heike; Meyer-Lindenberg, Andreas; Zipf, Alexander

    2016-11-21

    Self-reporting is a well-established approach within the medical and psychological sciences. In order to avoid recall bias, i.e. past events being remembered inaccurately, the reports can be filled out on a smartphone in real-time and in the natural environment. This is often referred to as ambulatory assessment and the reports are usually triggered at regular time intervals. With this sampling scheme, however, rare events (e.g. a visit to a park or recreation area) are likely to be missed. When addressing the correlation between mood and the environment, it may therefore be beneficial to include participant locations within the ambulatory assessment sampling scheme. Based on the geographical coordinates, the database query system then decides if a self-report should be triggered or not. We simulated four different ambulatory assessment sampling schemes based on movement data (coordinates by minute) from 143 voluntary participants tracked for seven consecutive days. Two location-based sampling schemes incorporating the environmental characteristics (land use and population density) at each participant's location were introduced and compared to a time-based sampling scheme triggering a report on the hour as well as to a sampling scheme incorporating physical activity. We show that location-based sampling schemes trigger a report less often, but we obtain more unique trigger positions and a greater spatial spread in comparison to sampling strategies based on time and distance. Additionally, the location-based methods trigger significantly more often at rarely visited types of land use and less often outside the study region where no underlying environmental data are available.

  12. Electro-optic sampling at 90 degree interaction geometry for time-of-arrival stamping of ultrafast relativistic electron diffraction

    OpenAIRE

    C. M. Scoby; P. Musumeci; J. T. Moody; M. S. Gutierrez

    2010-01-01

    In this paper we study a new geometry setup for electro-optic sampling (EOS) where the electron beam runs parallel to the ⟨110⟩ face of a ZnTe crystal and the probe laser is perpendicular to it and to the beam path. The simple setup is used to encode the time-of-arrival information of a 3.5  MeV

  13. A flexible method for the preparation of thin film samples for in situ TEM characterization combining shadow-FIB milling and electron-beam-assisted etching

    Energy Technology Data Exchange (ETDEWEB)

    Liebig, J.P., E-mail: jan.p.liebig@fau.de [Department of Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstr. 5, 91058 Erlangen (Germany); Göken, M. [Department of Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstr. 5, 91058 Erlangen (Germany); Richter, G. [Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart (Germany); Mačković, M.; Przybilla, T.; Spiecker, E. [Institute of Micro, and Nanostructure Research & Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 6, 91058 Erlangen (Germany); Pierron, O.N. [G. W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0405 (United States); Merle, B. [Department of Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstr. 5, 91058 Erlangen (Germany)

    2016-12-15

    A new method for the preparation of freestanding thin film samples for mechanical testing in transmission electron microscopes is presented. It is based on a combination of focused ion beam (FIB) milling and electron-beam-assisted etching with xenon difluoride (XeF{sub 2}) precursor gas. The use of the FIB allows for the target preparation of microstructural defects and enables well-defined sample geometries which can be easily adapted in order to meet the requirements of various testing setups. In contrast to existing FIB-based preparation approaches, the area of interest is never exposed to ion beam irradiation which preserves a pristine microstructure. The method can be applied to a wide range of thin film material systems compatible with XeF{sub 2} etching. Its feasibility is demonstrated for gold and alloyed copper thin films and its practical application is discussed. - Highlights: • A new method for the preparation of sub-micron tensile specimens from thin films is presented. • The method is based on the combination of focused ion beam milling and electron-beam-assisted xenon difluoride etching. • It enables the target preparation of individual microstructural defects. • The sample section is protected from ion beam damage by the use of a shadow milling geometry.

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

    Science.gov (United States)

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

    2018-01-01

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

  15. Multiwalled carbon nanotubes coated fibers for solid-phase microextraction of polybrominated diphenyl ethers in water and milk samples before gas chromatography with electron-capture detection.

    Science.gov (United States)

    Wang, Jun-Xia; Jiang, Dong-Qing; Gu, Zhi-Yuan; Yan, Xiu-Ping

    2006-12-22

    Determination of polybrominated diphenyl ethers (PBDEs) in environmental samples has raised great concerns due to the widespread use of PBDEs and their potential risk to humans. Solid-phase microextraction (SPME) is a fast, simple, cost-effective, and green sample preparation technique and is widely used for environmental analysis, but reports on the application of SPME for determination of PBDEs are very limited, and only a few publications dealing with commercial SPME fibers are available for extraction of PBDEs. Herein, we report a novel SPME method using multiwalled carbon nanotubes (MWCNTs) as the SPME fiber coating for gas chromatography with electron-capture detection (GC-ECD) of PBDEs in environmental samples. The MWCNTs coating gave much higher enhancement factors (616-1756) than poly (5% dibenzene-95% dimethylsiloxane) coating (139-384) and activated carbon coating (193-423). Thirty-minute extraction of 10 mL of sample solution using the MWCNTs coated fiber for GC-ECD determination yielded the limits of detection of 3.6-8.6 ng L(-1) and exhibited good linearity of the calibration functions (r(2)>0.995). The precision (RSD%, n=4) for peak area and retention time at the 500 ng L(-1) level was 6.9-8.8% and 0.6-0.9%, respectively. The developed method was successfully applied for the analysis of real samples including local river water, wastewater, and milk samples. The recovery of the PBDEs at 500 ng L(-1) spiked in these samples ranged from 90 to 119%. No PBDEs were detected in the river water and skimmed milk samples, whereas in the wastewater sample, 134-215 ng L(-1) of PBDEs were found. The PBDEs were detected in all whole fat milk samples, ranging from 13 to 484 ng L(-1). In a semiskimmed milk sample, only BDE-47 was found at 21 ng L(-1).

  16. Different methods for volatile sampling in mammals.

    Directory of Open Access Journals (Sweden)

    Marlen Kücklich

    Full Text Available Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS. However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus using cotton swabs, thermal desorption (TD tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113, with half of those compounds being volatile (N = 52. The mobile GC-MS captured the fewest compounds (N = 35, of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55, but very few volatiles (N = 10. Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%. Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor.

  17. Size-segregated urban aerosol characterization by electron microscopy and dynamic light scattering and influence of sample preparation

    Science.gov (United States)

    Marvanová, Soňa; Kulich, Pavel; Skoupý, Radim; Hubatka, František; Ciganek, Miroslav; Bendl, Jan; Hovorka, Jan; Machala, Miroslav

    2018-04-01

    Size-segregated particulate matter (PM) is frequently used in chemical and toxicological studies. Nevertheless, toxicological in vitro studies working with the whole particles often lack a proper evaluation of PM real size distribution and characterization of agglomeration under the experimental conditions. In this study, changes in particle size distributions during the PM sample manipulation and also semiquantitative elemental composition of single particles were evaluated. Coarse (1-10 μm), upper accumulation (0.5-1 μm), lower accumulation (0.17-0.5 μm), and ultrafine (culture media. PM suspension of lower accumulation fraction in water agglomerated after freezing/thawing the sample, and the agglomerates were disrupted by subsequent sonication. Ultrafine fraction did not agglomerate after freezing/thawing the sample. Both lower accumulation and ultrafine fractions were stable in cell culture media with fetal bovine serum, while high agglomeration occurred in media without fetal bovine serum as measured during 24 h.

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

    Science.gov (United States)

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

    2016-01-01

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

  19. X-ray photoelectron spectroscopy and secondary electron yield analysis of Al and Cu samples exposed to an accelerator environment

    Science.gov (United States)

    Rosenberg, R. A.; McDowell, M. W.; Ma, Q.; Harkay, K. C.

    2003-09-01

    It is well known that exposure to an accelerator environment can cause ``conditioning'' of the vacuum chamber surfaces. In order to understand the manner in which the surface structure might influence the production of gases and electrons in the accelerator, such surfaces should be studied both before and after exposure to accelerator conditions. Numerous studies have been performed on representative materials prior to being inserted into an accelerator, but very little has been done on materials that have ``lived'' in the accelerator for extended periods. In the present work, we mounted Al and Cu coupons at different positions in a section of the Advanced Photon Source storage ring and removed them following exposures ranging from 6 to 18 months. X-ray photoelectron spectroscopy (XPS) of the surface was performed before and after exposure. Changes were observed that depended on the location and whether the coupon was facing the chamber interior or chamber wall. These results will be presented and compared to XPS and secondary electron yield data obtained from laboratory measurements meant to simulate the accelerator conditions.

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

    OpenAIRE

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

    1994-01-01

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

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

    DEFF Research Database (Denmark)

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

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

  2. Quantitative determination of iron, copper, lead, chromium and nickel in electronic waste samples using total reflection x-ray fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Elaseer, A. S.; Musbah, A. S; Ammar, M. M. G.; Salah, M. A.; Aisha, E. A.

    2015-01-01

    Total reflection x-ray fluorescence spectroscopy in conjunction with microwave assisted extraction technique was used for the analysis of twenty electronic waste samples. The analysis was limited to the printed circuit boards of electronic devices. Iron, copper, lead, chromium and nickel were quantitatively determined in the samples. The samples were carefully milled to fine powder and 50mg was digested by acid using microwave digestion procedure. The digested samples solution was spread together with gallium as internal standard on the reflection disk and analyzed. The results showed that the cassette recorder boards contain the highest concentration of iron, lead and nickel. The average concentrations of these metals were 78, 73 and 71g/Kg respectively. Computer boards contained the highest copper average concentration 39g/Kg. the highest chromium average concentration 3.6 g/Kg was in mobile phone boards. Measurements were made using PicoTAX portable x-ray device. the instrument was used for quantitative multi-element analysis. An air cooled x-ray tube (40KV, 1 mA) with Mo target and Be window was used as x-ray source. The optics of the device was a multilayer Ni/C, 17.5 keV, 80% reflectivity provides analysis of elements from Si to Zr (K series) and Rh to U (L series). A Si PIN-diode detector (7mm"2, 195eV) was used for the elements detection. In this study heavy metals average concentration in electronic circuit boards in the in the order of iron (35.25g/kg), copper (21.14g/Kg), lead (16.59g/Kg), nickel (16.01g/Kg) and chromium (1.07g/Kg).(author)

  3. Sample pretreatment optimization for the analysis of short chain chlorinated paraffins in soil with gas chromatography-electron capture negative ion-mass spectrometry.

    Science.gov (United States)

    Chen, Laiguo; Huang, Yumei; Han, Shuang; Feng, Yongbin; Jiang, Guo; Tang, Caiming; Ye, Zhixiang; Zhan, Wei; Liu, Ming; Zhang, Sukun

    2013-01-25

    Accurately quantifying short chain chlorinated paraffins (SCCPs) in soil samples with gas chromatograph coupled with electron capture negative ionization mass spectrometry (GC-ECNI-MS) is difficult because many other polychlorinated pollutants are present in the sample matrices. These pollutants (e.g., polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and toxaphene) can cause serious interferences during SCCPs analysis with GC-MS. Four main columns packed with different adsorbents, including silica gel, Florisil and alumina, were investigated in this study to determine their performance for separating interfering pollutants from SCCPs. These experimental results suggest that the optimum cleanup procedure uses a silica gel column and a multilayer silica gel-Florisil composite column. This procedure completely separated 22 PCB congeners, 23 OCPs and three toxaphene congeners from SCCPs. However, p,p'-DDD, cis-nonachlor and o,p'-DDD were not completely removed and only 53% of the total toxaphene was removed. This optimized method was successfully and effectively applied for removing interfering pollutants from real soil samples. SCCPs in 17 soil samples from different land use areas within a suburban region were analyzed with the established method. The concentrations of SCCPs in these samples were between 7 and 541 ng g(-1) (mean: 84 ng g(-1)). Similar homologue SCCPs patterns were observed between the soil samples collected from different land use areas. In addition, lower chlorinated (Cl(6/7)) C(10)- and C(11)- SCCPs were the dominant congeners. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Ultrasound-assisted extraction and solid-phase extraction for the simultaneous determination of five amide herbicides in fish samples by gas chromatography with electron capture detection.

    Science.gov (United States)

    Qu, Zhipeng; Bai, Xiuzhi; Zhang, Ting; Yang, Zhaoguang

    2017-03-01

    An efficient sample extraction and clean-up method was developed for simultaneous determination of five amide herbicides (alachlor, acetochlor, propisochlor, metazachlor, and butachlor) in fish samples. The protocol consisted of ultrasound-assisted solvent extraction and solid-phase extraction clean-up. In detail, aliquots of homogenized fish flesh were thoroughly mixed with 20 mL of n-hexane and then extracted with ultrasonication for 40 min. Each sample was centrifuged and the supernatant was collected for the subsequent clean-up. For the sample preparation, the above supernatant was processed with a C 18 column with 3 mL of dichloromethane/n-hexane (1:1, v/v) as the eluant. Then the samples were analyzed by gas chromatography with electron capture detection. The correlation coefficients of the five calibration curves were 0.9976-0.9998 (n = 3). The limits of detection (S/N = 3, n = 11) and limits of quantification (S/N = 10, n = 11) were 0.19-0.42 and 0.63-1.39 μg/kg, respectively. The recoveries of this method were 71.2-92.6% with good precision (<4.7% relative standard deviations, n = 6). The developed method was successfully applied to monitor the five amide herbicides in fish samples collected from different cities. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Biological Agent Sample Preparation for the Detection and Identification of Multiple Agents by Nucleic Acid-Based Analysis

    National Research Council Canada - National Science Library

    Fields, Robert

    2002-01-01

    .... The AutoLyser instrument which we have developed, provides fully automated purification of viral, bacterial and human genomic DNA and RNA from clinical samples, cell culture and swabs in as little...

  6. A comparative study of sampling techniques for monitoring carcass contamination

    NARCIS (Netherlands)

    Snijders, J.M.A.; Janssen, M.H.W.; Gerats, G.E.; Corstiaensen, G.P.

    1984-01-01

    Four bacteriological sampling techniques i.e. the excision, double swab, agar contract and modified agar contact techniques were compared by sampling pig carcasses before and after chilling. As well as assessing the advantages and disadvantages of the techniques particular attention was paid to

  7. Imaging of fullerene-like structures in CNx thin films by electron microscopy; sample preparation artefacts due to ion-beam milling

    International Nuclear Information System (INIS)

    Czigany, Zs.; Neidhardt, J.; Brunell, I.F.; Hultman, L.

    2003-01-01

    The microstructure of CN x thin films, deposited by reactive magnetron sputtering, was investigated by transmission electron microscopy (TEM) at 200 kV in plan-view and cross-sectional samples. Imaging artefacts arise in high-resolution TEM due to overlap of nm-sized fullerene-like features for specimen thickness above 5 nm. The thinnest and apparently artefact-free areas were obtained at the fracture edges of plan-view specimens floated-off from NaCl substrates. Cross-sectional samples were prepared by ion-beam milling at low energy to minimize sample preparation artefacts. The depth of the ion-bombardment-induced surface amorphization was determined by TEM cross sections of ion-milled fullerene-like CN x surfaces. The thickness of the damaged surface layer at 5 deg. grazing incidence was 13 and 10 nm at 3 and 0.8 keV, respectively, which is approximately three times larger than that observed on Si prepared under the same conditions. The shallowest damage depth, observed for 0.25 keV, was less than 1 nm. Chemical changes due to N loss and graphitization were also observed by X-ray photoelectron spectroscopy. As a consequence of chemical effects, sputtering rates of CN x films were similar to that of Si, which enables relatively fast ion-milling procedure compared to carbon compounds. No electron beam damage of fullerene-like CN x was observed at 200 kV

  8. Comparison of Lateral Flow Assay, Kidney Inhibition Swab, and Liquid Chromatography-Tandem Mass Spectrometry for the Detection of Penicillin G Residues in Sow Urine.

    Science.gov (United States)

    Shelver, Weilin L; Chakrabarty, Shubhashis; Smith, David J

    2017-03-01

    Sows (n = 126) were administered penicillin G; urine, collected at slaughter, was screened by kidney inhibition swab (KIS; 4 h testing time) and then stored at -80 °C (∼1200 days) until analysis by lateral flow assay (LF, ∼5 min testing time) and tandem quadrupole LC-MS/MS (TQ) analysis. The stability of penicillin in urine during storage was verified using TQ analyses. Quantitative results were well-correlated (R 2 = 0.98) with only a ∼10% decrease in penicillin concentration during the 3-year storage period. KIS retesting of stored samples returned results consistent with the original analyses. Lateral flow assay results were highly correlated with the KIS and TQ results. A KIS positive sample, which was not confirmed by TQ or LF, was assayed by Triple-TOF LC-MS to determine the cause of the apparent false positive. This study suggests LF can be used to quickly and efficiently screen for penicillin G residues before slaughter.

  9. 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.

  10. A new approach to the investigation of sexual offenses-cytoskeleton analysis reveals the origin of cells found on forensic swabs.

    Science.gov (United States)

    Schulz, Martin M; Buschner, Maximilian G D; Leidig, Richard; Wehner, Heinz-D; Fritz, Peter; Häbig, Karina; Bonin, Michael; Schütz, Monika; Shiozawa, Thomas; Wehner, Frank

    2010-03-01

    There are forensic inquiries in which an identification of epithelial cell types would provide important probative evidence. In cancer diagnosis, this information is yielded by histological examination of cytokeratin (Ck). Therefore, we tested 19 antibodies against different Cks (Ck1, Ck2e, Ck4, Ck5-6, Ck7, Ck8, Ck9, CK10, Ck13, Ck14, Ck15, Ck16, Ck17, Ck18, Ck19, Ck20, Ck903, PanCkAE1_3, and CAM5-2) on histological sections of epidermis, buccal mucosa, vaginal mucosa, penis, urogenital tract, and rectum and could identify two antigens unique to buccal-cell and vaginal-cell (Ck4) and skin epithelial-cell (Ck10) cytokeratin. Subsequently, we developed an immunocytological technique for distinguishing swabbed skin and mucosal cells up to at least 1 year after sampling. By the detection of the Ck4 and Ck10 mRNAs in biopsy and laser capture microdissection collected samples via quantitative real-time polymerase chain reaction, we were able to confirm our immunological findings. Hence, this study offers techniques to discriminate between skin and mucosal cells (buccal and vaginal) in forensic casework.

  11. 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

  12. Quality of determinations obtained from laboratory reference samples used in the calibration of X-ray electron probe microanalysis of silicate minerals

    International Nuclear Information System (INIS)

    Pavlova, Ludmila A.; Suvorova, Ludmila F.; Belozerova, Olga Yu.; Pavlov, Sergey M.

    2003-01-01

    Nine simple minerals and oxides, traditionally used as laboratory reference samples in the electron probe microanalysis (EPMA) of silicate minerals, have been quantitatively evaluated. Three separate series of data, comprising the average concentration, standard deviation, relative standard deviation, confidence interval and the z-score of data quality, were calculated for 21 control samples derived from calibrations obtained from three sets of reference samples: (1) simple minerals; (2) oxides; and (3) certified glass reference materials. No systematic difference was observed between the concentrations obtained from these three calibration sets when analyzed results were compared to certified compositions. The relative standard deviations obtained for each element were smaller than target values for all determinations. The z-score values for all elements determined fell within acceptable limits (-2< z<2) for concentrations ranging from 0.1 to 100%. These experiments show that the quality of data obtained from laboratory reference calibration samples is not inferior to that from certified reference glasses. The quality of results obtained corresponds to the 'applied geochemistry' type of analysis (category 2) as defined in the GeoPT proficiency testing program. Therefore, the laboratory reference samples can be used for calibrating EPMA techniques in the analysis of silicate minerals and for controlling the quality of results

  13. Dedicated Tool for Irradiation and Electrical Measurement of Large Surface Samples on the Beamline of a 2.5 Mev Pelletron Electron Accelerator: Application to Solar Cells

    OpenAIRE

    Lefèvre Jérémie; Le Houedec Patrice; Losco Jérôme; Cavani Olivier; Boizot Bruno

    2017-01-01

    We designed a tool allowing irradiation of large samples over a surface of A5 size dimension by means of a 2.5 MeV Pelletron electron accelerator. in situ electrical measurements (I-V, conductivity, etc.) can also be performed, in the dark or under illumination, to study radiation effects in materials. Irradiations and electrical measurements are achievable over a temperature range from 100 K to 300 K. The setup was initially developed to test real-size triple junction solar cells at low t...

  14. 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.

  15. Two sampling techniques for game meat

    Directory of Open Access Journals (Sweden)

    Maretha van der Merwe

    2013-03-01

    Full Text Available A study was conducted to compare the excision sampling technique used by the export market and the sampling technique preferred by European countries, namely the biotrace cattle and swine test. The measuring unit for the excision sampling was grams (g and square centimetres (cm2 for the swabbing technique. The two techniques were compared after a pilot test was conducted on spiked approved beef carcasses (n = 12 that statistically proved the two measuring units correlated. The two sampling techniques were conducted on the same game carcasses (n = 13 and analyses performed for aerobic plate count (APC, Escherichia coli and Staphylococcus aureus, for both techniques. A more representative result was obtained by swabbing and no damage was caused to the carcass. Conversely, the excision technique yielded fewer organisms and caused minor damage to the carcass. The recovery ratio from the sampling technique improved 5.4 times for APC, 108.0 times for E. coli and 3.4 times for S. aureus over the results obtained from the excision technique. It was concluded that the sampling methods of excision and swabbing can be used to obtain bacterial profiles from both export and local carcasses and could be used to indicate whether game carcasses intended for the local market are possibly on par with game carcasses intended for the export market and therefore safe for human consumption.

  16. Two sampling techniques for game meat.

    Science.gov (United States)

    van der Merwe, Maretha; Jooste, Piet J; Hoffman, Louw C; Calitz, Frikkie J

    2013-03-20

    A study was conducted to compare the excision sampling technique used by the export market and the sampling technique preferred by European countries, namely the biotrace cattle and swine test. The measuring unit for the excision sampling was grams (g) and square centimetres (cm2) for the swabbing technique. The two techniques were compared after a pilot test was conducted on spiked approved beef carcasses (n = 12) that statistically proved the two measuring units correlated. The two sampling techniques were conducted on the same game carcasses (n = 13) and analyses performed for aerobic plate count (APC), Escherichia coli and Staphylococcus aureus, for both techniques. A more representative result was obtained by swabbing and no damage was caused to the carcass. Conversely, the excision technique yielded fewer organisms and caused minor damage to the carcass. The recovery ratio from the sampling technique improved 5.4 times for APC, 108.0 times for E. coli and 3.4 times for S. aureus over the results obtained from the excision technique. It was concluded that the sampling methods of excision and swabbing can be used to obtain bacterial profiles from both export and local carcasses and could be used to indicate whether game carcasses intended for the local market are possibly on par with game carcasses intended for the export market and therefore safe for human consumption.

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

    Science.gov (United States)

    Moore, Catherine; Jones, Rachel

    2015-02-01

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

  18. Comparison of SVM, RF and ELM on an Electronic Nose for the Intelligent Evaluation of Paraffin Samples

    Directory of Open Access Journals (Sweden)

    Hong Men

    2018-01-01

    Full Text Available Paraffin odor intensity is an important quality indicator when a paraffin inspection is performed. Currently, paraffin odor level assessment is mainly dependent on an artificial sensory evaluation. In this paper, we developed a paraffin odor analysis system to classify and grade four kinds of paraffin samples. The original feature set was optimized using Principal Component Analysis (PCA and Partial Least Squares (PLS. Support Vector Machine (SVM, Random Forest (RF, and Extreme Learning Machine (ELM were applied to three different feature data sets for classification and level assessment of paraffin. For classification, the model based on SVM, with an accuracy rate of 100%, was superior to that based on RF, with an accuracy rate of 98.33–100%, and ELM, with an accuracy rate of 98.01–100%. For level assessment, the R2 related to the training set was above 0.97 and the R2 related to the test set was above 0.87. Through comprehensive comparison, the generalization of the model based on ELM was superior to those based on SVM and RF. The scoring errors for the three models were 0.0016–0.3494, lower than the error of 0.5–1.0 measured by industry standard experts, meaning these methods have a higher prediction accuracy for scoring paraffin level.

  19. Electronic cigarette use in the European Union: analysis of a representative sample of 27 460 Europeans from 28 countries.

    Science.gov (United States)

    Farsalinos, Konstantinos E; Poulas, Konstantinos; Voudris, Vassilis; Le Houezec, Jacques

    2016-11-01

    To assess prevalence of electronic cigarette (e-cigarette) use, reported changes in smoking status due to e-cigarette use and correlates of e-cigarette use in the European Union (EU) member states in 2014. Cross-sectional survey of EU citizens representative of the population (Special Eurobarometer 429). All 28 Member States of the EU. A total of 27 460 EU citizens aged ≥ 15 years (after excluding those who responded 'Do not know' to the questions about smoking status and e-cigarette use). Descriptive analysis [%, 95% confidence interval (CI)] of e-cigarette use prevalence (current use, past use and past experimentation) according to smoking status, self-reported changes in smoking status according to patterns of e-cigarette use and logistic regression analysis to examine correlates of e-cigarette use, especially socio-demographic factors and smoking status. Ever e-cigarette use was reported by 31.1% (95% CI = 30.0-32.2%) of current smokers, 10.8% (95% CI = 10.0-11.7%) of former smokers and 2.3% (95% CI = 2.1-2.6%) of never smokers. Past experimentation [7.2% (95% CI = 6.9-7.5%)] was more common than current [1.8% (95% CI = 1.6-1.9%)] and past use [2.6% (95% CI = 2.4-2.8%)]. Extrapolated to the whole population, approximately 48.5 million EU citizens were ever e-cigarette users, with 76.8% using nicotine-containing e-cigarettes. An estimated 6.1 and 9.2 million EU citizens had quit and reduced smoking with the help of e-cigarettes, respectively. Initiation with e-cigarettes was reported by 0.8% (95% CI = 0.6-0.9%) of participants who reported ever use of any tobacco-related product. Only 1.3% (95% CI = 1.1-1.5%) of never smokers used nicotine-containing e-cigarettes, with 0.09% (95% CI = 0.04-0.14%) reporting daily nicotine use. Smoking cessation with the help of e-cigarettes was reported by 35.1% (95% CI = 30.7-39.5%) of current e-cigarette users, while a further 32.2% (95% CI = 29.9-36.5%) reported smoking reduction. Being current

  20. Measuring PM2.5, Ultrafine Particles, Nicotine Air and Wipe Samples Following the Use of Electronic Cigarettes.

    Science.gov (United States)

    Melstrom, Paul; Koszowski, Bartosz; Thanner, Meridith Hill; Hoh, Eunha; King, Brian; Bunnell, Rebecca; McAfee, Tim

    2017-09-01

    Few studies have examined the extent of inhalation or dermal contact among bystanders following short-term, secondhand e-cigarette exposure. Measure PM2.5 (particles e-cigarette exposure. E-cigarettes were used ad libitum by three experienced users for 2 hours during two separate sessions (disposable e-cigarettes, then tank-style e-cigarettes, or "tanks") in a 1858 ft3 room. We recorded: uncorrected PM2.5 (using SidePak); UF (using P-Trak); air nicotine concentrations (using air samplers; SKC XAD-4 canisters); ambient air exchange rate (using an air capture hood). Wipe samples were taken by wiping 100 cm2 room surfaces pre- and post- both sessions, and clean cloth wipes were worn during the exposure and collected at the end. Uncorrected PM2.5 and UF were higher (p e-cigarette use can produce: elevated PM2.5; elevated UF; nicotine in the air; and accumulation of nicotine on surfaces and clothing. Short-term indoor e-cigarette use produced accumulation of nicotine on surfaces and clothing, which could lead to dermal exposure to nicotine. Short-term e-cigarette use produced elevated PM2.5 and ultrafine particles, which could lead to secondhand inhalation of these particles and any chemicals associated with them by bystanders. We measured significant differences in PM2.5 and ultrafine particles between disposable e-cigarettes and tank-style e-cigarettes, suggesting a difference in the exposure profiles of e-cigarette products. Published by Oxford University Press on behalf of Society for Research on Nicotine and Tobacco 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  1. Electro-optic sampling at 90 degree interaction geometry for time-of-arrival stamping of ultrafast relativistic electron diffraction

    Directory of Open Access Journals (Sweden)

    C. M. Scoby

    2010-02-01

    Full Text Available In this paper we study a new geometry setup for electro-optic sampling (EOS where the electron beam runs parallel to the ⟨110⟩ face of a ZnTe crystal and the probe laser is perpendicular to it and to the beam path. The simple setup is used to encode the time-of-arrival information of a 3.5  MeV<10  pC electron bunch on the spatial profile of the laser pulse. The electric field lines inside the dielectric bend at an angle due to a relatively large (n∼3 index of refraction of the ZnTe crystal. We found theoretically and experimentally that the EOS signal can be maximized with a proper choice of incoming laser polarization angle. We achieved single-shot nondestructive measurement of the relative time of arrival between the pump and the probe beams thus improving the temporal resolution of ultrafast relativistic electron diffraction experiments.

  2. Application of solid-phase micro extraction for the determination of pesticides in vegetable samples by gas chromatography with an electron capture detector

    International Nuclear Information System (INIS)

    Chai, Mee Kin; Tan, Guan Huat; Kumari, Asha

    2008-01-01

    A solid-phase micro extraction (SPME) method has been developed for the determination of 9 pesticides in 2 vegetables -cucumber and tomato - samples, based on direct immersion mode and subsequent desorption into the injection port of a gas chromatograph with an electron capture detector (GC-ECD). The main factors affecting the SPME process such as extraction time and temperature, desorption time and temperature, the effect of salt addition and fiber depth into the liner were studied and optimized. The analytical procedure proposed consisted of a 30 minute ultrasonic extraction of the target compounds from 1.0 g vegetable samples with 5 mL of distilled water. Then, the samples were filtered and topped up with distilled water to 10 mL. The analytes in this aqueous extract were extracted for 15 minutes with a 100 μm thickness polydimethylsiloxane SPME fiber. Relative standard deviations for triplicate analyses of samples were less than 10 %. The recoveries of the pesticides studied in cucumber and tomato ranged from 52 % to 82 % and the RSD were below 10 %. Therefore, the proposed method is applicable in the analysis of pesticides in vegetable matrices. SPME has been shown to be a simple extraction technique, which has a number of advantages such as solvent free extraction, simplicity and compatibility with the chromatographic analytical system. (author)

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

    OpenAIRE

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

    2017-01-01

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

  4. Determination of Anthracycline Drug Residual in Cleaning Validation Swabs of Stainless-Steel Equipment after Production of Cytostatic Injections Using HPLC Analytical Method

    Directory of Open Access Journals (Sweden)

    Zuzana Slivová

    2015-01-01

    Full Text Available Standard cleaning procedures of production line equipment were verified after manufacture of cytostatic injections containing Anthracycline derivate substance. Residual content of Anthracycline drug substance on stainless-steel equipment surface was determined using swab sampling with a specific HPLC-DAD analysis. The acceptance limit was decided as 200.0 μg/100 cm2. Recovery from the stainless-steel surface was 90.1%. Linearity of the method was observed in the concentration range of 0.155–194 μg/mL when estimated using Zorbax TMS (5 μm, 0.25 m × 4.6 mm ID column at 1.3 mL/min flow rate and 254 nm (DAD 190–600 nm. The mobile phase consisted of lauryl hydrogen sulphate solution (3.7 g/L : methanol : acetonitrile (54 : 16 : 30, v/v/v with pH adjusted to 2.5 using phosphoric acid (85%. The LOD and LOQ for Anthracycline derivate were found to be 0.047 and 0.155 μg/mL, respectively. The method validation confirmed the method provides acceptable degree of selectivity, linearity, accuracy, and precision for the intended purposes.

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

    Directory of Open Access Journals (Sweden)

    Guido Finazzi

    2016-08-01

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

  6. ANALYSIS AND IDENTIFICATION SPIKING CHEMICAL COMPOUNDS RELATED TO CHEMICAL WEAPON CONVENTION IN UNKNOWN WATER SAMPLES USING GAS CHROMATOGRAPHY AND GAS CHROMATOGRAPHY ELECTRON IONIZATION MASS SPECTROMETRY

    Directory of Open Access Journals (Sweden)

    Harry Budiman

    2010-06-01

    Full Text Available The identification and analysis of chemical warfare agents and their degradation products is one of important component for the implementation of the convention. Nowadays, the analytical method for determination chemical warfare agent and their degradation products has been developing and improving. In order to get the sufficient analytical data as recommended by OPCW especially in Proficiency Testing, the spiking chemical compounds related to Chemical Weapon Convention in unknown water sample were determined using two different techniques such as gas chromatography and gas chromatography electron-impact ionization mass spectrometry. Neutral organic extraction, pH 11 organic extraction, cation exchanged-methylation, triethylamine/methanol-silylation were performed to extract the chemical warfare agents from the sample, before analyzing with gas chromatography. The identification of chemical warfare agents was carried out by comparing the mass spectrum of chemicals with mass spectrum reference from the OPCW Central Analytical Database (OCAD library while the retention indices calculation obtained from gas chromatography analysis was used to get the confirmation and supported data of  the chemical warfare agents. Diisopropyl methylphosphonate, 2,2-diphenyl-2-hydroacetic acid and 3-quinuclidinol were found in unknown water sample. Those chemicals were classified in schedule 2 as precursor or reactant of chemical weapons compound in schedule list of Chemical Weapon Convention.   Keywords: gas chromatography, mass spectrometry, retention indices, OCAD library, chemical warfare agents

  7. Characterization and Identification of Gamma-Irradiated Kimchi Cabbage and Broccoli by Electron Spin Resonance Spectroscopy using Different Sample Pre-treatments

    International Nuclear Information System (INIS)

    Kwak, J.Y.; Ahn, J.J.; Kashif Akram; Kim, G.R.; Kwon, J.H.

    2012-01-01

    Electron spin resonance (ESR) spectroscopy of gamma-irradiated fresh broccoli and kimchi cabbage was conducted to identify their irradiation history. Different pretreatments, such as freeze-drying (FD), oven-drying (OD), alcoholic-drying (ALD), and water-washing and alcoholic-drying (WAD) were used to lower the moisture contents of the samples prior to ESR analysis. The non-irradiated samples exhibited a single central signal (g 0 = 2.0007) with clear effect of Mn 2+ , especially in kimchi cabbage. Upon irradiation, there was an increase in the intensity of the central signal, and two side peaks, mutually spaced at 6 mT, were also observed. These side peaks with g 1 (left) = 2.023 and g 2 (right) = 1.985 were attributed to radiation-induced cellulose radicals. Leaf and stem in broccoli, and root and stem in kimchi cabbage provided good ESR signal responses upon irradiation. The signal noise was reduced in case of ALD and WAD pretreatments, particularly due to Mn 2+ signals. The ALD treatment was found most feasible to detect the improved ESR spectra in the irradiated samples. (author)

  8. Alpha spectrometry of environmental and food samples with photon/electron-rejecting alpha liquid-scintillation (P.E.R.A.L.S.)

    International Nuclear Information System (INIS)

    Zehringer, M.; Stockli, M.

    2006-01-01

    Full text: In environmental and food monitoring radio-nuclides are normally analysed with gamma spectrometry. Routine analysis of cesium nuclides can be realised fast and without much sample preparation. Also a few nuclides of the uranium- and thorium-series can be detected with gamma spectrometry at the low Bq/kg level. 226 Ra, 224 Ra and 228 Ra can be determined via their decay products when secular equilibrium of the sample is reached (e.g. 226 Ra via its daughters 214 Pb and 214 Bi). Alpha spectrometry is the method of choice for the determination of alpha nuclides in the mBq range. The analytes have to be separated from interfering nuclides and quenching parameters prior to the spectrometry. So, the main ask in alpha spectrometry consists in an efficient sample preparation and an alpha/beta discrimination for the spectrometric measurement. Based on the work of Jack McDowell sensitive methods for the analyses of naturally occurring nuclides such as uranium, thorium, polonium and other alpha-nuclides in water, honey and spices were developed and validated [1]. Such techniques enables the tolerance and limit values for radionuclides in food to be controlled in accordance with of the Swiss Ordinance on contaminants and Ingredients (FIV) [2] he method principle is based on a selective extraction of the alpha nuclides rom water samples rsp. from an aqueous extract of mineralized samples. The extractant has also the function of a cocktail in the alpha liquid spectrometry nd therefore the extract can be analysed directly without further clean -up Photon/Electron-Rejecting Alpha-Liquid-Scintillation, P.E.R.A.L..S. [1]). Normally, one liter of water sample is extracted with 5 ml of cocktail to achieve low detection limits. The cocktail phase is separated from the aqueous phase by use of a phase separator for liquid samples. Methods were developed for the analyses of 234 U and 238 U, the thorium nuclides 228 Th, 230 Th, 232 Th and other alpha nuclides. The achieved

  9. Development of a non-destructive micro-analytical method for stable carbon isotope analysis of transmission electron microscope (TEM) samples

    Energy Technology Data Exchange (ETDEWEB)

    Hode, Tomas [Department of Geology, Portland State University, Portland, P.O. Box 751, OR 97201 (United States)], E-mail: hode@pdx.edu; Kristiansson, Per; Elfman, Mikael [Division of Nuclear Physics, Department of Physics, Lund Institute of Technology, Lund University, P.O. Box 118, SE-221 00 Lund (Sweden); Hugo, Richard C.; Cady, Sherry L. [Department of Geology, Portland State University, Portland, P.O. Box 751, OR 97201 (United States)

    2009-10-01

    The biogenicity of ancient morphological microfossil-like objects can be established by linking morphological (e.g. cell remnants and extracellular polymeric matrix) and chemical (e.g. isotopes, biomarkers and biominerals) evidence indicative of microorganisms or microbial activity. We have developed a non-destructive micro-analytical ion beam system capable of measuring with high spatial resolution the stable carbon isotope ratios of thin samples used for transmission electron microscopy. The technique is based on elastic scattering of alpha particles with an energy of 2.751 MeV. At this energy the {sup 13}C cross section is enhanced relative to the pure Rutherford cross section for {sup 13}C, whereas the {sup 12}C cross section is reduced relative to its pure Rutherford cross section. Here we report the initial results of this experimental approach used to characterize ultramicrotomed sections of sulfur-embedded graphite and microbial cells.

  10. Effect of planar magnetic field on electron transport properties of n-AlGaAs/GaAs heterojunction and photoluminescence measures in GaAs samples

    International Nuclear Information System (INIS)

    Alves, A.R.

    1991-01-01

    The effects of magnetic fields applied parallel to the interface of an heterojunction n-Al Ga As is studied. A qualitative analysis has shown that this field modifies the Fermi surface of the two dimensional electron gas (2 DEG) confined on the heterojunction. it produces a strong asymmetry on the magnetoresistance of the 2 DEG relative to the two directions of the electric current. This interpretation is confirmed by a self-consistent numerical calculation involving a solution of the Schroedinger and Poisson equations. To verify this result, measurements with samples grown by Molecular Beam Epitaxy (MBE) under magnetic fields up to 13.0 T are performed and the results obtained confirm the asymmetry in the magnetoresistance. Also, a strong negative magnetoresistance attributed to the imperfections of the interface is seen. It can be used to evaluate the quality of the heterojunction interface. The details about the implantation of the photoluminescence measurement system are discussed. Spectra of an asymmetric quantum well and delta-doped Ga As : Si samples at 300 K and 55 K are shown. (author)

  11. Development, validation and testing of a skin sampling method for assessment of metal exposure.

    Science.gov (United States)

    Erfani, Behnaz; Midander, Klara; Lidén, Carola; Julander, Anneli

    2017-07-01

    Nickel, cobalt and chromium are frequent skin sensitizers. Skin exposure results in eczema in sensitized individuals, the risk being related to the skin dose. To develop a self-sampling method for quantification of skin exposure to metals, to validate the method, and to assess its feasibility. Defined metal doses (0.01-5 µg) were applied to the fingers of 5 participants. Skin areas (2 cm 2 ) were sampled with 1% HNO 3 , either as 0.1 ml on a swab, or as 0.5 ml on a wipe. Furthermore, 17 participants performed self-sampling by swab after 2 h of leisure activity. Samples were extracted in 1% HNO 3 and analysed by inductively coupled plasma mass spectrometry. The sampling efficiency by swab was 46%, as compared with 93% for acid wipe sampling, for all tested doses. Most metal from the skin dose was detected in the first swab (33-43%). Despite lower sampling efficiency by swab, skin doses of metals following 2 h of leisure activity without hand washing were quantified in all participants, and ranged from 0.0016 to 0.15 µg/cm 2 , from 0.00014 to -0.0020 µg/cm 2 and from 0.00048 to -0.027 µg/cm 2 for nickel, cobalt, and chromium, respectively. The results indicate a future potential of skin sampling by swab to detect and monitor metals on skin by self-sampling. This will contribute to better knowledge of metal skin exposure among dermatitis patients, workers, and the general population. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Separation and screening of short-chain chlorinated paraffins in environmental samples using comprehensive two-dimensional gas chromatography with micro electron capture detection.

    Science.gov (United States)

    Xia, Dan; Gao, Lirong; Zhu, Shuai; Zheng, Minghui

    2014-11-01

    Short-chain chlorinated paraffins (SCCPs) are highly complex technical mixtures with thousands of isomers and numerous homologs. They are classified as priority candidate persistent organic pollutants under the Stockholm Convention for their persistence, bioaccumulation, and toxicity. Analyzing SCCPs is challenging because of the complexity of the mixtures. Chromatograms of SCCPs acquired using one-dimensional (1D) gas chromatography (GC) contain a large characteristic "peak" with a broad and unresolved profile. Comprehensive two-dimensional GC (GC×GC) shows excellent potential for separating complex mixtures. In this study, GC×GC coupled with micro electron capture detection (μECD) was used to separate and screen SCCPs. The chromatographic parameters, including the GC column types, oven temperature program, and modulation period, were systematically optimized. The SCCP congeners were separated into groups using a DM-1 column connected to a BPX-50 column. The SCCP congeners in technical mixtures were separated according to the number of chlorine substituents for a given carbon chain length and according to the number of carbon atoms plus chlorine atoms for different carbon chain lengths. A fish tissue sample was analyzed to illustrate the feasibility of the GC×GC-μECD method in analyzing biological samples. Over 1,500 compounds were identified in the fish extract, significantly more than were identified using 1D GC. The detection limits for five selected SCCP congeners were between 1 and 5 pg/L using the GC×GC method, and these were significantly lower than those achieved using 1D GC. This method is a good choice for analysis of SCCPs in environmental samples, exhibiting good separation and good sensitivity.

  13. Detection of lumpy skin disease virus in skin lesions, blood, nasal swabs and milk following preventive vaccination.

    Science.gov (United States)

    Bedeković, T; Šimić, I; Krešić, N; Lojkić, I

    2018-04-01

    Lumpy skin disease caused by Capripoxvirus is at the moment the most important threat to European cattle industry. The only way for successful control of disease is fast and efficient diagnosis and vaccination. According to EU legislation, vaccination against LDS can be conducted only after confirmation of the disease. Croatia has a special position regarding LSD-in 2016, for the first-time vaccination of the entire cattle population was conducted without an index case. The presence of vaccine viral particles was detected in milk, skin nodules, blood and nasal swabs in seven from total of eight herds. The presence of virus genome was detected in five cows from 10 up to 21-day post-vaccination. The virus was successfully isolated on cell culture from 10 up to 21-day post-vaccination from three animals. The obtained results support the need for further efforts to develop safer vaccines against LSDV. © 2017 Blackwell Verlag GmbH.

  14. A longitudinal study of electronic cigarette use among a population-based sample of adult smokers: association with smoking cessation and motivation to quit.

    Science.gov (United States)

    Biener, Lois; Hargraves, J Lee

    2015-02-01

    Increasingly popular electronic cigarettes (e-cigarettes) may be the most promising development yet to end cigarette smoking. However, there is sparse evidence that their use promotes cessation. We investigated whether e-cigarette use increases smoking cessation and/or has a deleterious effect on quitting smoking and motivation to quit. Representative samples of adults in 2 US metropolitan areas were surveyed in 2011/2012 about their use of novel tobacco products. In 2014, follow-up interviews were conducted with 695 of the 1,374 baseline cigarette smokers who had agreed to be re-contacted (retention rate: 51%). The follow-up interview assessed their smoking status and history of electronic cigarette usage. Respondents were categorized as intensive users (used e-cigarettes daily for at least 1 month), intermittent users (used regularly, but not daily for more than 1 month), and non-users/triers (used e-cigarettes at most once or twice). At follow-up, 23% were intensive users, 29% intermittent users, 18% had used once or twice, and 30% had not tried e-cigarettes. Logistic regression controlling for demographics and tobacco dependence indicated that intensive users of e-cigarettes were 6 times more likely than non-users/triers to report that they quit smoking (OR: 6.07, 95% CI = 1.11, 33.2). No such relationship was seen for intermittent users. There was a negative association between intermittent e-cigarette use and 1 of 2 indicators of motivation to quit at follow-up. Daily use of electronic cigarettes for at least 1 month is strongly associated with quitting smoking at follow-up. Further investigation of the underlying reasons for intensive versus intermittent use will help shed light on the mechanisms underlying the associations between e-cigarette use, motivation to quit, and smoking cessation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e

  15. Orthogonal identification of gunshot residue with complementary detection principles of voltammetry, scanning electron microscopy, and energy-dispersive X-ray spectroscopy: sample, screen, and confirm.

    Science.gov (United States)

    O'Mahony, Aoife M; Samek, Izabela A; Sattayasamitsathit, Sirilak; Wang, Joseph

    2014-08-19

    Field-deployable voltammetric screening coupled with complementary laboratory-based analysis to confirm the presence of gunshot residue (GSR) from the hands of a subject who has handled, loaded, or discharged a firearm is described. This protocol implements the orthogonal identification of the presence of GSR utilizing square-wave stripping voltammetry (SWSV) as a rapid screening tool along with scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX) to confirm the presence of the characteristic morphology and metal composition of GSR particles. This is achieved through the judicious modification of the working electrode of a carbon screen-printed electrode (CSPE) with carbon tape (used in SEM analysis) to fix and retain a sample. A comparison between a subject who has handled and loaded a firearm and a subject who has had no contact with GSR shows the significant variations in voltammetric signals and the presence or absence of GSR-consistent particles and constituent metals. This initial electrochemical screening has no effect on the integrity of the metallic particles, and SEM/EDX analysis conducted prior to and postvoltammetry show no differences in analytical output. The carbon tape is instrumental in retaining the GSR sample after electrochemical analysis, supported by comparison with orthogonal detection at a bare CSPE. This protocol shows great promise as a two-tier detection system for the presence of GSR from the hands of a subject, whereby initial screening can be conducted rapidly onsite by minimally trained operators; confirmation can follow at the same substrate to substantiate the voltammetric results.

  16. Examining assumptions regarding valid electronic monitoring of medication therapy: development of a validation framework and its application on a European sample of kidney transplant patients

    Directory of Open Access Journals (Sweden)

    Steiger Jürg

    2008-02-01

    Full Text Available Abstract Background Electronic monitoring (EM is used increasingly to measure medication non-adherence. Unbiased EM assessment requires fulfillment of assumptions. The purpose of this study was to determine assumptions needed for internal and external validity of EM measurement. To test internal validity, we examined if (1 EM equipment functioned correctly, (2 if all EM bottle openings corresponded to actual drug intake, and (3 if EM did not influence a patient's normal adherence behavior. To assess external validity, we examined if there were indications that using EM affected the sample representativeness. Methods We used data from the Supporting Medication Adherence in Renal Transplantation (SMART study, which included 250 adult renal transplant patients whose adherence to immunosuppressive drugs was measured during 3 months with the Medication Event Monitoring System (MEMS. Internal validity was determined by assessing the prevalence of nonfunctioning EM systems, the prevalence of patient-reported discrepancies between cap openings and actual intakes (using contemporaneous notes and interview at the end of the study, and by exploring whether adherence was initially uncharacteristically high and decreased over time (an indication of a possible EM intervention effect. Sample representativeness was examined by screening for differences between participants and non-participants or drop outs on non-adherence. Results Our analysis revealed that some assumptions were not fulfilled: 1 one cap malfunctioned (0.4%, 2 self-reported mismatches between bottle openings and actual drug intake occurred in 62% of the patients (n = 155, and 3 adherence decreased over the first 5 weeks of the monitoring, indicating that EM had a waning intervention effect. Conclusion The validity assumptions presented in this article should be checked in future studies using EM as a measure of medication non-adherence.

  17. Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.

    Science.gov (United States)

    Liao, Hstau Y; Hashem, Yaser; Frank, Joachim

    2015-06-02

    Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. Three-dimensional covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2016-10-01

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

  19. 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...

  20. Comparison of 2 electronic cowside tests to detect subclinical ketosis in dairy cows and the influence of the temperature and type of blood sample on the test results.

    Science.gov (United States)

    Iwersen, M; Klein-Jöbstl, D; Pichler, M; Roland, L; Fidlschuster, B; Schwendenwein, I; Drillich, M

    2013-01-01

    The objective of this study was to determine the suitability of 2 electronic hand-held devices [FreeStyle Precision (FSP), Abbott GmbH & Co. KG, Wiesbaden, Germany and GlucoMen LX Plus (GLX), A. Menarini GmbH, Vienna, Austria] for measuring β-hydroxybutyrate (BHBA) in dairy cows. Three experiments were conducted to evaluate (1) the diagnostic performance of the devices, (2) the effect of the type of blood sample, and (3) the influence of the ambient temperature on the determined results. A total of 415 blood samples from lactating Holstein and Simmental cows were collected and analyzed with both devices (whole blood) and in a laboratory (serum). Correlation coefficients between whole-blood and serum BHBA concentrations were highly significant, with 94% for the FSP and 80% for the GLX device. Based on thresholds for subclinical ketosis of 1.2 and 1.4 mmol of BHBA/L, results obtained with the hand-held devices were evaluated by receiver operating characteristics analyses. This resulted in adjusted thresholds of 1.2 and 1.4 mmol/L for the FSP and 1.1 and 1.3 mmol/L for the GLX device. Applying these thresholds, sensitivities were 98 and 100% for the FSP and 80 and 86% for the GLX device, respectively. Corresponding specificities were 90 and 97% for the FSP and 87 and 96% for the GLX device, respectively. Additionally, concentrations of BHBA were tested with both devices in whole blood, EDTA-added whole blood, and in their resulting serum and plasma, collected from 65 animals. Determined BHBA concentrations were similar within each device for whole and EDTA-added blood, and in serum and plasma, but differed between whole blood and serum and between EDTA-added blood and plasma. Blood samples with low (0.4 mmol/L), medium (1.1 mmol/L), and high (1.6 mmol/L) BHBA concentrations were stored between +5 to +32°C and analyzed repeatedly at temperature levels differing by 4°C. Additionally, devices and test strips were stored at equal conditions and used for measurement

  1. Sponge and skin excision sampling for recovery of Salmonella and Campylobacter from defeathered broiler carcasses

    Science.gov (United States)

    Introduction: Salmonella and Campylobacter contamination of broiler carcass skin increases during feather removal. There are several methods for sampling carcasses including sponging or swabbing of skin surface and skin excision. It is unclear whether sponge sampling is adequate to remove bacteria f...

  2. 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)

  3. Comparison of culture versus quantitative real-time polymerase chain reaction for the detection of Taylorella equigenitalis in field samples from naturally infected horses in Canada and Germany.

    Science.gov (United States)

    Nadin-Davis, Susan; Knowles, Margaret K; Burke, Teresa; Böse, Reinhard; Devenish, John

    2015-07-01

    A quantitative real-time polymerase chain reaction method (qPCR) was developed and tested for the detection of Taylorella equigenitalis. It was shown to have an analytical sensitivity of 5 colony-forming units (CFU) of T. equigenitalis when applied to the testing of culture swabs that mimicked field samples, and a high analytical specificity in not reacting to 8 other commensal bacterial species associated with horses. As designed, it could also differentiate specifically between T. equigenitalis and T. asinigenitalis. The qPCR was compared to standard culture in a study that included 45 swab samples from 6 horses (1 stallion, 5 mares) naturally infected with T. equigenitalis in Canada, 39 swab samples from 5 naturally infected stallions in Germany, and 311 swab samples from 87 culture negative horses in Canada. When the comparison was conducted on an individual sample swab basis, the qPCR had a statistical sensitivity and specificity of 100% and 96.4%, respectively, and 100% and 99.1% when the comparison was conducted on a sample set basis. A comparison was also made on 203 sample swabs from the 5 German stallions taken over a span of 4 to 9 mo following antibiotic treatment. The qPCR was found to be highly sensitive and at least as good as culture in detecting the presence of T. equigenitalis in post-treatment samples. The work demonstrates that the qPCR assay described here can potentially be used to detect the presence of T. equigenitalis directly from submitted sample swabs taken from infected horses and also for determining T. equigenitalis freedom following treatment.

  4. Electronic Nicotine Delivery Systems (E-cigarette/Vape) use and Co-Occurring Health-Risk Behaviors Among an Ethnically Diverse Sample of Young Adults.

    Science.gov (United States)

    Lanza, H Isabella; Teeter, Heather

    2018-01-02

    Prevalence rates of electronic nicotine delivery systems (ENDS; i.e., e-cigarette/vape) use has grown exponentially in the past few years. College students present a particularly vulnerable group for ENDS use. The current study sought to expand the literature by examining the context in which college students use ENDS, co-occurring health risks beyond traditional tobacco use, and the role of ethnicity in ENDS use. Health-risk behavior survey data was collected from 452 undergraduates attending a large, public urban university during the 2015-2016 academic year. Ever ENDS users vs. non-ENDS users were compared across potential demographic, health-risk, and other health-related correlates. Almost 40% of participants reported lifetime use of ENDS. No ethnic or sex differences were found. The primary source for obtaining ENDS was friends and ENDS were most often used with friends vs. alone or with others not considered friends. Participants engaging in risky alcohol use and cigarette smoking had a higher likelihood of endorsing ENDS use. Conclusions/Importance: The current study indicated that a large proportion of college students have tried ENDS irrespective of ethnicity or sex. An increasingly normative social context may inform the popularity of ENDS use across ethnicity and sex, but additional research using ethnically diverse samples is warranted. Risky alcohol use appears to be a significant correlate of ENDS use, even after accounting for the robust relationship between ENDS use and cigarette smoking. The robust relationship between alcohol and tobacco use likely extends to ENDS use.

  5. 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.

  6. Vaginal Swab Test Compared With the Urethral Q-tip Test for Urethral Mobility Measurement: A Randomized Controlled Trial.

    Science.gov (United States)

    Meyer, Isuzu; Szychowski, Jeff M; Illston, Jana D; Parden, Alison M; Richter, Holly E

    2016-02-01

    To assess whether use of a vaginal cotton-tipped swab is equivalent to the standard Q-tip test regarding urethral mobility. Secondarily, to examine whether both tests agree in hypermobility diagnosis, discomfort level, and patients' preference. In this randomized crossover trial, women with stress urinary incontinence without prolapse beyond the hymen were randomized to undergo either a vaginal or urethral mobility test first followed by the alternate approach. The primary outcome was the difference in rotation angle, from resting to maximum strain, between tests. The equivalence margin was ±10°. The secondary outcome was agreement in hypermobility diagnosis using two definitions: 1) maximum straining angle of 30° or greater from the horizontal plane; and 2) rotation angle 30° or greater. Discomfort was assessed using a 0-10 visual analog scale. Using 90% power assuming a standard deviation of 20°, 36 and 139 patients were needed for 10° and 5° equivalence margins, respectively. From January 2014 to March 2015, 140 women were randomized. The mean difference between the two tests was 5.1° (95% confidence interval 3.2-6.9°), meeting the predefined equivalence criteria. In the hypermobility diagnosis, the urethral and vaginal tests had no disagreement using definition 1 (P=.23), whereas the two tests disagreed using definition 2 (P=.03). The urethral approach had a higher discomfort level (Pstandard Q-tip test in measuring urethral mobility with less discomfort and is preferred by patients.

  7. How is the high vaginal swab used to investigate vaginal discharge in primary care and how do GPs' expectations of the test match the tests performed by their microbiology services?

    Science.gov (United States)

    Noble, H; Estcourt, C; Ison, C; Goold, P; Tite, L; Carter, Y H

    2004-06-01

    To describe the management of vaginal discharge in general practice, with particular regard to the use of the high vaginal swab (HVS), and to compare GPs' expectations of this test with the processing and reporting undertaken by different laboratories. A postal questionnaire survey of 2146 GPs in the North Thames area and postal questionnaire study of the 22 laboratories serving the same GPs were carried out. GPs were asked how they would manage a young woman with vaginal discharge and what information they would like on an HVS report. Laboratories were asked how they would process and report on the HVS sample from the same patient. Response rate was 26%. 72% of GPs would take an HVS and 62% would refer on to a genitourinary medicine (GUM) clinic. 45% would offer empirical therapy and 47% of these would treat for candida initially. 75% of GPs routinely request "M,C&S" on HVS samples but 55% only want to be informed about specific pathogens. Routine processing of HVS samples varies widely between laboratories and 86% only report specific pathogens. 78% of GPs would like to be offered a suggested diagnosis on HVS reports, and 74% would like a suggested treatment. 43% of laboratories ever provide a diagnosis, and 14% provide a suggested treatment. GPs frequently manage vaginal discharge and most of them utilise the HVS. GPs' expectations of the test are not well matched to laboratory processing or reporting of the samples.

  8. Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds.

    Science.gov (United States)

    Keeler, Shamus P; Ferro, Pamela J; Brown, Justin D; Fang, Xingwang; El-Attrache, John; Poulson, Rebecca; Jackwood, Mark W; Stallknecht, David E

    2012-03-01

    Current avian influenza (AI) virus surveillance programs involving wild birds rely on sample collection methods that require refrigeration or low temperature freezing to maintain sample integrity for virus isolation and/or reverse-transcriptase (RT) PCR. Maintaining the cold chain is critical for the success of these diagnostic assays but is not always possible under field conditions. The aim of this study was to test the utility of Finders Technology Associates (FTA) cards for reliable detection of AI virus from cloacal and oropharyngeal swabs of wild birds. The minimum detectable titer was determined, and the effect of room temperature storage was evaluated experimentally using multiple egg-propagated stock viruses (n = 6). Using real time RT-PCR, we compared results from paired cloacal swab and samples collected on FTA cards from both experimentally infected mallards (Anasplatyrhynchos) and hunter-harvested waterfowl sampled along the Texas Gulf Coast. Based on the laboratory trials, the average minimal detectable viral titer was determined to be 1 x 10(4.7) median embryo infectious dose (EID50)/ml (range: 1 x 10(4.3) to 1 x 10(5.4) EID50/ml), and viral RNA was consistently detectable on the FTA cards for a minimum of 20 days and up to 30 days for most subtypes at room temperature (23 C) storage. Real-time RT-PCR of samples collected using the FTA cards showed fair to good agreement in live birds when compared with both real-time RT-PCR and virus isolation of swabs. AI virus detection rates in samples from several wild bird species were higher when samples were collected using the FTA cards compared with cloacal swabs. These results suggest that FTA cards can be used as an alternative sample collection method when traditional surveillance methods are not possible, especially in avian populations that have historically received limited testing or situations in which field conditions limit the ability to properly store or ship swab samples.

  9. 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.

  10. Feeding of waste milk to Holstein calves affects antimicrobial resistance of Escherichia coli and Pasteurella multocida isolated from fecal and nasal swabs.

    Science.gov (United States)

    Maynou, G; Bach, A; Terré, M

    2017-04-01

    The use of milk containing antimicrobial residues in calf feeding programs has been shown to select for resistant fecal Escherichia coli in dairy calves. However, information is scarce about the effects of feeding calves waste milk (WM) on the prevalence of multidrug-resistant bacteria. The objective of this study was to determine the antimicrobial resistance patterns of fecal E. coli and nasal Pasteurella multocida isolates from calves fed either milk replacer (MR) or WM in 8 commercial dairy farms (4 farms per feeding program). Fecal and nasal swabs were collected from 20 ± 5 dairy calves at 42 ± 3.2 d of age, and from 10 of these at approximately 1 yr of age in each study farm to isolate the targeted bacteria. Furthermore, resistance of E. coli isolates from calf-environment and from 5 calves at birth and their dams was also evaluated in each study farm. Resistances were tested against the following antimicrobial agents: amoxicillin-clavulanic acid, ceftiofur, colistin, doxycycline (DO), enrofloxacin (ENR), erythromycin, florfenicol, imipenem, and streptomycin. A greater number of fecal E. coli resistant to ENR, florfenicol, and streptomycin and more multidrug-resistant E. coli phenotypes were isolated in feces of calves fed WM than in those fed MR. However, the prevalence of fecal-resistant E. coli was also influenced by calf age, as it increased from birth to 6 wk of age for ENR and DO and decreased from 6 wk to 1 yr of age for DO regardless of the feeding program. From nasal samples, an increase in the prevalence of colistin-resistant P. multocida was observed in calves fed WM compared with those fed MR. The resistance patterns of E. coli isolates from calves and their dams tended to differ, whereas similar resistance profiles among E. coli isolates from farm environment and calves were observed. The findings of this study suggest that feeding calves WM fosters the presence of resistant bacteria in the lower gut and respiratory tracts of dairy calves

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

    OpenAIRE

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    CUNHA Regina Ayr Florio da

    1998-01-01

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

  13. 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

    or F52/70 inoculation were detected as virus positive at day I post inoculation (p.i.). The D78 viral load peaked at day 4 and day 8 p.i., while the DK01 and F52/70 viral load showed relatively high levels at day 2 p.i. In cloacal swabs, viruses detectable were at day 2 p.i. for DK01 and F52/70, day 8...

  14. 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

    ). 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...

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sara Marani

    2017-03-01

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

  17. Internal validation of the DNAscan/ANDE™ Rapid DNA Analysis™ platform and its associated PowerPlex® 16 high content DNA biochip cassette for use as an expert system with reference buccal swabs.

    Science.gov (United States)

    Moreno, Lilliana I; Brown, Alice L; Callaghan, Thomas F

    2017-07-01

    Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories. Furthermore, point of collection analysis would allow searching against profiles from unsolved crimes during the normal booking process once the infrastructure to immediately search the Combined DNA Index System (CODIS) database from the booking station is established. The DNAscan/ANDE™ Rapid DNA Analysis™ System developed by Network Biosystems was evaluated for robustness and reliability in the production of high quality reference STR profiles for database enrollment and searching applications. A total of 193 reference samples were assessed for concordance of the CODIS 13 loci. Studies to evaluate contamination, reproducibility, precision, stutter, peak height ratio, noise and sensitivity were also performed. The system proved to be robust, consistent and dependable. Results indicated an overall success rate of 75% for the 13 CODIS core loci and more importantly no incorrect calls were identified. The DNAscan/ANDE™ could be confidently used without human interaction in both laboratory and non-laboratory settings to generate reference profiles. Published by Elsevier B.V.

  18. Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study.

    Science.gov (United States)

    Stewart, Christopher J; Auchtung, Thomas A; Ajami, Nadim J; Velasquez, Kenia; Smith, Daniel P; De La Garza, Richard; Salas, Ramiro; Petrosino, Joseph F

    2018-01-01

    The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls. We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with an increased relative abundance of Prevotella ( P = 0.006) and decreased Bacteroides ( P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced ( P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.

  19. Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

    Directory of Open Access Journals (Sweden)

    Christopher J. Stewart

    2018-04-01

    Full Text Available Background The use of electronic cigarettes (ECs has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls. Methods We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Results Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with an increased relative abundance of Prevotella (P = 0.006 and decreased Bacteroides (P = 0.036 in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009 in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. Discussion From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.

  20. LESM: a laser-driven sub-MeV electron source delivering ultra-high dose rate on thin biological samples

    Czech Academy of Sciences Publication Activity Database

    Labate, L.; Andreassi, M.G.; Baffigi, F.; Bizzarri, B.M.; Borghini, A.; Bussolino, G.C.; Fulgentini, L.; Ghetti, F.; Giulietti, A.; Köster, P.; Lamia, D.; Levato, Tadzio; Oishi, Y.; Pulignani, S.; Russo, G.; Sgarbossa, A.; Gizzi, L.A.

    2016-01-01

    Roč. 49, č. 27 (2016), s. 1-9, č. článku 275401. ISSN 0022-3727 R&D Projects: GA MŠk EF15_008/0000162; GA MŠk LQ1606 Grant - others:ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : laser-driven electron accelerators * sub-MeV electron sources * ultrahigh dose rate * radiobiology * cell radiation damage Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics ) Impact factor: 2.588, year: 2016

  1. Detection and genetic characterization of foot‐and‐mouth disease viruses in samples from clinically healthy animals in endemic settings

    DEFF Research Database (Denmark)

    Jamal, Syed Muhammad; Ferrari, G.; Hussain, M.

    2012-01-01

    A total of 1501 oral swab samples from Pakistan, Afghanistan and Tajikistan were collected from clinically healthy animals between July 2008 and August 2009 and assayed for the presence of foot‐and‐mouth disease virus (FMDV) RNA. The oral swab samples from two (of four) live animal markets...... for FMDV. In the Landhi dairy colony, Pakistan, a cohort of 179 apparently healthy animals was studied. On their arrival within the colony, thirty‐nine (22%) of these animals were found positive for FMDV RNA (serotype A was identified), while 130 (72.6%) had antibodies to FMDV non‐structural proteins. Thus...

  2. Effect of sampling and short isolation methodologies on the recovery of human pathogenic Yersinia enterocolitica from pig tonsils.

    Science.gov (United States)

    Van Damme, Inge; Berkvens, Dirk; De Zutter, Lieven

    2012-07-01

    The objective of this study was to determine the effect of sampling (swab samples compared to destructive samples) on isolation rates of human pathogenic Yersinia enterocolitica from pig tonsils. Moreover, the relative efficiency of different rapid, routinely applicable isolation methods was evaluated. Therefore, swab and destructive samples from tonsils of 120 pigs at slaughter were analyzed in parallel using direct plating and different enrichment methods. Salmonella-Shigella-desoxycholate-calcium chloride (SSDC) agar, cefsulodin-irgasan-novobiocin (CIN) agar, and Yersinia enterocolitica chromogenic medium (YeCM) were used as selective agar media. For enrichment, irgasan-ticarcillin-potassium chlorate (ITC) broth and peptone-sorbitol-bile (PSB) broth were incubated at 25°C for 48 h. Overall, 55 tonsils (45.8%) were positive for Y. enterocolitica bioserotype 4/O:3. Recovery was significantly higher using the destructive method compared to the swabbing method. Direct plating resulted in 47 and 28 Y. enterocolitica-positive destructive and swab samples, respectively. Alkali treatment of PSB and ITC enrichment broths significantly increased recovery of pathogenic Y. enterocolitica from destructive tonsil samples. The performance of YeCM for qualitative and quantitative isolation of pathogenic Y. enterocolitica from pig tonsils was equal to SSDC and CIN. In conclusion, direct plating and ISO 10273: 2003 with minor modifications are suitable and rapid methods for isolation of pathogenic Y. enterocolitica from destructive tonsil samples.

  3. Comparison of sampling procedures and microbiological and non-microbiological parameters to evaluate cleaning and disinfection in broiler houses.

    Science.gov (United States)

    Luyckx, K; Dewulf, J; Van Weyenberg, S; Herman, L; Zoons, J; Vervaet, E; Heyndrickx, M; De Reu, K

    2015-04-01

    Cleaning and disinfection of the broiler stable environment is an essential part of farm hygiene management. Adequate cleaning and disinfection is essential for prevention and control of animal diseases and zoonoses. The goal of this study was to shed light on the dynamics of microbiological and non-microbiological parameters during the successive steps of cleaning and disinfection and to select the most suitable sampling methods and parameters to evaluate cleaning and disinfection in broiler houses. The effectiveness of cleaning and disinfection protocols was measured in six broiler houses on two farms through visual inspection, adenosine triphosphate hygiene monitoring and microbiological analyses. Samples were taken at three time points: 1) before cleaning, 2) after cleaning, and 3) after disinfection. Before cleaning and after disinfection, air samples were taken in addition to agar contact plates and swab samples taken from various sampling points for enumeration of total aerobic flora, Enterococcus spp., and Escherichia coli and the detection of E. coli and Salmonella. After cleaning, air samples, swab samples, and adenosine triphosphate swabs were taken and a visual score was also assigned for each sampling point. The mean total aerobic flora determined by swab samples decreased from 7.7±1.4 to 5.7±1.2 log CFU/625 cm2 after cleaning and to 4.2±1.6 log CFU/625 cm2 after disinfection. Agar contact plates were used as the standard for evaluating cleaning and disinfection, but in this study they were found to be less suitable than swabs for enumeration. In addition to measuring total aerobic flora, Enterococcus spp. seemed to be a better hygiene indicator to evaluate cleaning and disinfection protocols than E. coli. All stables were Salmonella negative, but the detection of its indicator organism E. coli provided additional information for evaluating cleaning and disinfection protocols. Adenosine triphosphate analyses gave additional information about the

  4. Comparison of noninvasive sample collection procedures for canine leishmaniasis diagnosis by PCR-hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Sidney de Almeida; Andrade, Antero Silva Ribeiro de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)]. E-mail: vidasnino@yahoo.com.br; antero@cdtn.br; Ituassu, Leonardo Trindade; Melo, Maria Norma de [Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil)]. E-mail: melo@mono.icb.ufmg.br; ltituassu@yahoo.com.br

    2007-07-01

    The dogs are the main reservoir of the visceral leishmaniasis etiological agent Leishmania chagasi and these animals have to be systematically monitored. The aim of present work was to standardize a method for canine leishmaniasis diagnosis using DNA samples obtained by a noninvasive ways. Two kind of samples were compared: conjunctival swab and blood. The samples were analyzed by the Polymerase Chain Reaction (PCR) associated with the hybridization of {sup 32}P labeled DNA probes. An in vitro test was carried out using cotton swabs seeded with L. chagasi parasites at different cell numbers. After that, the PCR and hybridization sensitivity was evaluated in two groups of 23 seropositive dogs. Conjunctival swabs and 1,0 mL of blood were collected from each animal. 90 {mu}L of these blood were spotted onto filter paper and the remaining used to prepare the buffy coat. The DNA purification from cotton swabs was carried out through the phenol-chloroform (group 1) or boiling (group 2). The Wizard kit was used to DNA extraction from buffy coat. The filters were treated according to Dialab protocol. The analysis of the seeded samples showed that the PCR was able to identify until ten parasites while the following hybridization of the PCR products allows the detection of until one parasite. The PCR positivity for the conjunctival swabs were 73.9% and 52.2% respectively to the groups 1 and 2. For buffy coat the positivities were 43.5% and 56.5% respectively. The filters presented the lowest positivity. The hybridization step was not accomplished yet for these samples. (author)

  5. Being an Informed Consumer of Health Information and Assessment of Electronic Health Literacy in a National Sample of Internet Users: Validity and Reliability of the e-HLS Instrument.

    Science.gov (United States)

    Seçkin, Gül; Yeatts, Dale; Hughes, Susan; Hudson, Cassie; Bell, Valarie

    2016-07-11

    The Internet, with its capacity to provide information that transcends time and space barriers, continues to transform how people find and apply information to their own lives. With the current explosion in electronic sources of health information, including thousands of websites and hundreds of mobile phone health apps, electronic health literacy is gaining an increasing prominence in health and medical research. An important dimension of electronic health literacy is the ability to appraise the quality of information that will facilitate everyday health care decisions. Health information seekers explore their care options by gathering information from health websites, blogs, Web-based forums, social networking websites, and advertisements, despite the fact that information quality on the Internet varies greatly. Nonetheless, research has lagged behind in establishing multidimensional instruments, in part due to the evolving construct of health literacy itself. The purpose of this study was to examine psychometric properties of a new electronic health literacy (ehealth literacy) measure in a national sample of Internet users with specific attention to older users. Our paper is motivated by the fact that ehealth literacy is an underinvestigated area of inquiry. Our sample was drawn from a panel of more than 55,000 participants maintained by Knowledge Networks, the largest national probability-based research panel for Web-based surveys. We examined the factor structure of a 19-item electronic Health Literacy Scale (e-HLS) through exploratory factor analysis (EFA) and confirmatory factor analysis, internal consistency reliability, and construct validity on sample of adults (n=710) and a subsample of older adults (n=194). The AMOS graphics program 21.0 was used to construct a measurement model, linking latent factors obtained from EFA with 19 indicators to determine whether this factor structure achieved a good fit with our entire sample and the subsample (age ≥ 60

  6. Comparison of sample types and diagnostic methods for in vivo detection of Mycoplasma hyopneumoniae during early stages of infection.

    Science.gov (United States)

    Pieters, Maria; Daniels, Jason; Rovira, Albert

    2017-05-01

    Detection of Mycoplasma hyopneumoniae in live pigs during the early stages of infection is critical for timely implementation of control measures, but is technically challenging. This study compared the sensitivity of various sample types and diagnostic methods for detection of M. hyopneumoniae during the first 28days after experimental exposure. Twenty-one 8-week old pigs were intra-tracheally inoculated on day 0 with M. hyopneumoniae strain 232. Two age matched pigs were mock inoculated and maintained as negative controls. On post-inoculation days 0, 2, 5, 9, 14, 21 and 28, nasal swabs, laryngeal swabs, tracheobronchial lavage fluid, and blood samples were obtained from each pig and oral fluid samples were obtained from each room in which pigs were housed. Serum samples were assayed by ELISA for IgM and IgG M. hyopneumoniae antibodies and C-reactive protein. All other samples were tested for M. hyopneumoniae DNA by species-specific real-time PCR. Serum antibodies (IgG) to M. hyopneumoniae were detected in challenge-inoculated pigs on days 21 and 28. M. hyopneumoniae DNA was detected in samples from experimentally inoculated pigs beginning at 5days post-inoculation. Laryngeal swabs at all samplings beginning on day 5 showed the highest sensitivity for M. hyopneumoniae DNA Detection, while oral fluids showed the lowest sensitivity. Although laryngeal swabs are not considered the typical M. hyopneumoniae diagnostic sample, under the conditions of this study laryngeal swabs tested by PCR proved to be a practical and reliable diagnostic sample for M. hyopneumoniae detection in vivo during early-stage infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 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

  8. Characterization of sintered samples of La/Sr/Cu/O by X-ray diffraction, scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS)

    International Nuclear Information System (INIS)

    Gonzalez, C.O. de; Polla, Griselda; Manghi, Estela

    1987-01-01

    Samples of La/Sr/Cu/O were sinterized by solid state reaction starting from a nominal composition of La 1 .8, Sr 0 .2, CuO 4 . They presented superconductive properties with T c = 40.9 K (onset) and δ T c = 17 K. Two phases were observed by X-ray diffraction and the more abundant was the tetragonal phase. The mean grain size was 1-5 μm. The X-ray photoelectron spectroscopy measurements were carried out using Mg kα (1486.6 eV) as incident radiation. Sample temperature was varied between -180 deg C and 420 deg C, approximately. The temperature variation produces a change in the atomic concentration of the surface components. Deconvolutions of the O 1s peaks show three components with binding energies (B.E.). The decomposition of Cu 2p 3 /2 peaks presents two components corresponding to Cu + and Cu 2+ . (Author) [es

  9. Development of a multi-institutional cohort to facilitate cardiovascular disease biomarker validation using existing biorepository samples linked to electronic health records.

    Science.gov (United States)

    Cross, Deanna S; McCarty, Catherine A; Steinhubl, Steven R; Carey, David J; Erlich, Porat M

    2013-08-01

    Emerging biomarkers for acute myocardial infarction (AMI) may enhance conventional risk-prediction algorithms if they are informative and associated with risk independently of established predictors. In this study, we constructed a cohort for testing emerging biomarkers for AMI in managed-care populations using existing biospecimen repositories linked to electronic health records (EHR). Electronic health record-based biorepositories collected by healthcare systems can be federated to provide large, methodologically sound testing sets for biomarker validation. Subjects ages 40 to 80 years were selected from 2 existing population-based biospecimen repositories. Incident AMI status and covariates were ascertained from the EHR. An ad hoc model for AMI risk was parameterized and validated. Simulation was used to test incremental gains in performance due to the inclusion of biomarkers in this model. Gains in performance were assessed in terms of area under the receiver operating characteristic curve (ROC-AUC) and case reclassification. A total of 18 329 individuals (57% female) contributed 108 400 person-years of EHR follow-up. The crude AMI incidence was 10.8 and 5.0 per 1000 person-years among males and females, respectively. Compared with the model with risk factors alone, inclusion of a simulated biomarker yielded substantial gains in sensitivity without loss of specificity. Furthermore, a net ROC-AUC gain of 13.3% was observed, as well as correct reclassification of 9.8% of incident cases (79 of 806) that were otherwise not considered statin-indicated at baseline under the National Cholesterol Education Program Adult Treatment Panel III criteria. More research is needed to assess incremental contribution of emerging biomarkers for AMI prediction in managed-care populations. © 2013 Wiley Periodicals, Inc.

  10. Microbiological criteria in public catering: sampling and auditing experiences in canteens and cafeterias in Piedmont

    Directory of Open Access Journals (Sweden)

    Amaranta Traversa

    2013-02-01

    Full Text Available In the period 2006-2011 six public catering establishments (3 canteens and 3 cafeterias were monitored, trough audit and sampling, in order to verify the application of good manufacturing and hygiene practices during food production, handling and serving. The compliance to microbiological food safety criteria (Listeria monocytogenes and Salmonella spp. and process hygiene criteria were investigated using ISO standards for microbiological analyses. A total of 612 samples were collected: 192 food samples and 288 environmental swab samples from canteens; 33 food samples and 99 swab samples from cafeterias. Regarding food safety, two samples were in disagreement with criteria fixed in EU Regulation as Listeria monocytogenes was isolated from a turkey breast in a canteen and from a sandwich in a cafeteria. Regarding process hygiene criteria, as no microbiological limits are legally defined for catering services, for this study limits were fixed according to the quality standards of tender, scientific literature and laboratory experience. 23.4% foodstuffs and 8.7% swabs resulted non-compliant in canteens; 48.5% foodstuffs and 6.1% swabs resulted non-compliant in cafeterias. The count of coagulase-positive staphylococci (CPS was higher of the fixed limits in raw turkey meat and in cooked spinach: the presence among CPS of S. aureus was confirmed, strains were not able to produce enterotoxins. The most common non-compliance in hygiene criteria was represented by aerobic colony count (60.7% of total non-compliance in canteens and 75.0% in cafeterias and coliform bacteria (20.3% in canteens and 25.0% in cafeterias. Nine raw foods or raw readyto- eat food samples were non-compliant for both coliform bacteria and aerobic count; one sample (raw turkey meat was non-compliant for CPS and aerobic count but resulted to be compliant after cooking. Auditing and sampling are the most effective tools to improve food quality standard and to enhance food business

  11. Validation of a new HPV self-sampling device for cervical cancer screening: The Cervical and Self-Sample In Screening (CASSIS) study.

    Science.gov (United States)

    El-Zein, Mariam; Bouten, Sheila; Louvanto, Karolina; Gilbert, Lucy; Gotlieb, Walter; Hemmings, Robert; Behr, Marcel A; Franco, Eduardo L; Liang, Victoria; Martins, Claudia; Duarte, Silvy; Sarban, Natalia; Geddes, Patricia; Massa, Ana; Samios, Kathrin; Aboufadl, Siham; Verdon, Sophie; Pereria, Cynthia; Lacroix, Isabelle

    2018-04-17

    We compared the self-sampling performance of the newly designed HerSwab™ device with a physician-collected cervical sample and another self-sample using the cobas® PCR Female swab for the detection of cervical intraepithelial neoplasia (CIN) and cancer. Women referred for colposcopy at McGill University affiliated hospital clinics collected two consecutive self-samples, one with HerSwab™ and one with cobas® swab, after receiving instructions. The order of sampling was randomized. The colposcopist then collected a cervical sample and conducted a colposcopic examination. Samples were tested for human papillomavirus (HPV) DNA. Sensitivity and specificity to detect CIN2+ and respective 95% confidence intervals (CI) were calculated to compare sampling approaches. The HPV testing agreement between samples was measured using the Kappa statistic. Of 1217 women enrolled, 1076 had complete results for HPV and cytology; 148 (13.8%) had CIN1, 147 (13.7%) had CIN2/3, and 5 (0.5%) had cancer. There was very good agreement between methods for HPV detection (HerSwab™ versus physician: kappa=0.84; cobas® swabs versus physician: kappa=0.81; HerSwab™ versus cobas® swabs: kappa=0.87). The sensitivity of HPV detection for CIN2+ was 87.6% (95%CI: 79.8-93.2) with self-sampling using HerSwab™, 88.6% (95%CI: 80.9-94.0) with self-sampling using the cobas® swab, and 92.4% (95%CI: 85.5-96.7) with physician sampling. Corresponding estimates of specificity were 58.1% (95%CI: 54.1-62.1), 55.0% (95%CI: 50.9-59.0) and 58.7% (95%CI: 54.6-62.6). Cytology (ASC-US or more severe) done on the physician-collected specimen was 80.2% (95%CI: 70.8-87.6) sensitive and 61.4% (95%CI: 57.2-65.5) specific for CIN2+. The HerSwab™ had good agreement with physician sampling in detecting HPV, and adequate performance in detecting high-grade lesions among women referred to colposcopy for abnormal cytology. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Measurement of electron-spin transports in GaAs quantum wells using a transmission-grating-sampled circular dichroism absorption spectroscopy

    International Nuclear Information System (INIS)

    Yu, Hua-Liang; Fang, Shaoyin; Wen, Jinhui; Lai, Tianshu

    2014-01-01

    A transmission-grating-sampled circular dichroism absorption spectroscopy (TGS-CDAS) and its theoretical model are developed sensitively to measure decay dynamics of a transient spin grating (TSG). A binary transmission grating with the same period as TSG is set behind TSG. It allows only a same small part of each period in TSG measured by circular dichroism absorption effect of a probe. In this way, the zero average of spin-dependent effects measured over a whole period in TSG is avoided so that TGS-CDAS has a high sensitivity to spin evolution in TSG. Spin transport experiments are performed on GaAs/AlGaAs quantum wells. Experimental results prove the feasibility and reliability of TGS-CDAS

  13. Effective absorption correction for energy dispersive X-ray mapping in a scanning transmission electron microscope: analysing the local indium distribution in rough samples of InGaN alloy layers.

    Science.gov (United States)

    Wang, X; Chauvat, M-P; Ruterana, P; Walther, T

    2017-12-01

    We have applied our previous method of self-consistent k*-factors for absorption correction in energy-dispersive X-ray spectroscopy to quantify the indium content in X-ray maps of thick compound InGaN layers. The method allows us to quantify the indium concentration without measuring the sample thickness, density or beam current, and works even if there is a drastic local thickness change due to sample roughness or preferential thinning. The method is shown to select, point-by-point in a two-dimensional spectrum image or map, the k*-factor from the local Ga K/L intensity ratio that is most appropriate for the corresponding sample geometry, demonstrating it is not the sample thickness measured along the electron beam direction but the optical path length the X-rays have to travel through the sample that is relevant for the absorption correction. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  14. Detailed characterisation of focused ion beam induced lateral damage on silicon carbide samples by electrical scanning probe microscopy and transmission electron microscopy

    Science.gov (United States)

    Stumpf, F.; Abu Quba, A. A.; Singer, P.; Rumler, M.; Cherkashin, N.; Schamm-Chardon, S.; Cours, R.; Rommel, M.

    2018-03-01

    The lateral damage induced by focused ion beam on silicon carbide was characterized using electrical scanning probe microscopy (SPM), namely, scanning spreading resistance microscopy and conductive atomic force microscopy (c-AFM). It is shown that the damage exceeds the purposely irradiated circles with a radius of 0.5 μm by several micrometres, up to 8 μm for the maximum applied ion dose of 1018 cm-2. Obtained SPM results are critically compared with earlier findings on silicon. For doses above the amorphization threshold, in both cases, three different areas can be distinguished. The purposely irradiated area exhibits resistances smaller than the non-affected substrate. A second region with strongly increasing resistance and a maximum saturation value surrounds it. The third region shows the transition from maximum resistance to the base resistance of the unaffected substrate. It correlates to the transition from amorphized to defect-rich to pristine crystalline substrate. Additionally, conventional transmission electron microscopy (TEM) and annular dark-field STEM were used to complement and explain the SPM results and get a further understanding of the defect spreading underneath the surface. Those measurements also show three different regions that correlate well with the regions observed from electrical SPM. TEM results further allow to explain observed differences in the electrical results for silicon and silicon carbide which are most prominent for ion doses above 3 × 1016 cm-2. Furthermore, the conventional approach to perform current-voltage measurements by c-AFM was critically reviewed and several improvements for measurement and analysis process were suggested that result in more reliable and impactful c-AFM data.

  15. Electronics and electronic systems

    CERN Document Server

    Olsen, George H

    1987-01-01

    Electronics and Electronic Systems explores the significant developments in the field of electronics and electronic devices. This book is organized into three parts encompassing 11 chapters that discuss the fundamental circuit theory and the principles of analog and digital electronics. This book deals first with the passive components of electronic systems, such as resistors, capacitors, and inductors. These topics are followed by a discussion on the analysis of electronic circuits, which involves three ways, namely, the actual circuit, graphical techniques, and rule of thumb. The remaining p

  16. Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

    Science.gov (United States)

    Albujja, Mohammed H; Bin Dukhyil, Abdul Aziz; Chaudhary, Abdul Rauf; Kassab, Ahmed Ch; Refaat, Ahmed M; Babu, Saranya Ramesh; Okla, Mohammad K; Kumar, Sachil

    2018-01-01

    An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable. © 2017 American Academy of Forensic Sciences.

  17. Impact of enzymatic digestion on bacterial community composition in CF airway samples.

    Science.gov (United States)

    Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

    2017-01-01

    Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

  18. Evaluation of Two Surface Sampling Methods for Microbiological and Chemical Analyses To Assess the Presence of Biofilms in Food Companies.

    Science.gov (United States)

    Maes, Sharon; Huu, Son Nguyen; Heyndrickx, Marc; Weyenberg, Stephanie van; Steenackers, Hans; Verplaetse, Alex; Vackier, Thijs; Sampers, Imca; Raes, Katleen; Reu, Koen De

    2017-12-01

    Biofilms are an important source of contamination in food companies, yet the composition of biofilms in practice is still mostly unknown. The chemical and microbiological characterization of surface samples taken after cleaning and disinfection is very important to distinguish free-living bacteria from the attached bacteria in biofilms. In this study, sampling methods that are potentially useful for both chemical and microbiological analyses of surface samples were evaluated. In the manufacturing facilities of eight Belgian food companies, surfaces were sampled after cleaning and disinfection using two sampling methods: the scraper-flocked swab method and the sponge stick method. Microbiological and chemical analyses were performed on these samples to evaluate the suitability of the sampling methods for the quantification of extracellular polymeric substance components and microorganisms originating from biofilms in these facilities. The scraper-flocked swab method was most suitable for chemical analyses of the samples because the material in these swabs did not interfere with determination of the chemical components. For microbiological enumerations, the sponge stick method was slightly but not significantly more effective than the scraper-flocked swab method. In all but one of the facilities, at least 20% of the sampled surfaces had more than 10 2 CFU/100 cm 2 . Proteins were found in 20% of the chemically analyzed surface samples, and carbohydrates and uronic acids were found in 15 and 8% of the samples, respectively. When chemical and microbiological results were combined, 17% of the sampled surfaces were contaminated with both microorganisms and at least one of the analyzed chemical components; thus, these surfaces were characterized as carrying biofilm. Overall, microbiological contamination in the food industry is highly variable by food sector and even within a facility at various sampling points and sampling times.

  19. Effects of gamma radiation and electron beam on samples of the Brazil nuts artificially inoculated with Aspergillus flavus; Efeitos da radiacao gama e feixe de eletrons sobre amostras de castanhas-do-Brasil inoculadas artificialmente com Aspergillus flavus

    Energy Technology Data Exchange (ETDEWEB)

    Coelho, Ednei Assuncao Antunes

    2012-07-01

    The high level of contamination by aflatoxin produced by fungi in lots of Brazil nuts and the strict control by importing countries in relation to the levels of toxins in food, European Union countries decided in 2003 by the return of these lots products from Brazil. Despite the economic loss represented by contamination by toxigenic fungi in Brazil nuts, a major product of extractive Northern of Brazil, studies are still preliminary as the control of contamination aflatoxigenic fungal using methods such as gamma radiation (G.R) and mainly, electron beam (E.B). These facts motivated this research, which aimed to evaluate the effects of gamma radiation and application of electron beam in samples of Brazil nut artificially inoculated with Aspergillus flavus. This goal, we were studied 50 samples of the Brazil nut previously inoculated with spores of A. flavus and subsequently incubated at 30 °C in relative humidity controlled at 93%. After incubation, period of 15 days, the average water activity of the samples was 0.80, the samples were divided into 5 groups that received the following doses of radiation: control (0 kGy), 5 and 10 kGy 5 E.B and G.R. The mycobiota was performed by serial dilution, plated on surface using potato dextrose agar. The results demonstrated that treatment with E.B using a dose of 5 kGy and 10 kGy resulted in reduced growth of A. flavus in 74% (37/50) and 94% (47/50) of samples. The samples treated with G.R at the dose of 5 kGy and 10 kGy no fungal growth occurred in 92% (46/50) 100% (50/50) of. The study of aflatoxins showed that doses of E.B of 5 kGy and 10 kGy reduced levels of AFB1 at 53.32% and 65.66% respectively. The application of gamma rays at doses of 5 and 10 kGy reduced levels of toxins in 70.61% and 84.15% respectively. This result may be attributed to higher penetrability of gamma radiation. Sensory analysis showed greater acceptance of the judges for the samples irradiated with E.B and G.R at the dose of 10 kGy. We concluded

  20. 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

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

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Schelin, Jenny; Norling, Börje

    2011-01-01

    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...

  2. Boat sampling

    International Nuclear Information System (INIS)

    Citanovic, M.; Bezlaj, H.

    1994-01-01

    This presentation describes essential boat sampling activities: on site boat sampling process optimization and qualification; boat sampling of base material (beltline region); boat sampling of weld material (weld No. 4); problems accompanied with weld crown varieties, RPV shell inner radius tolerance, local corrosion pitting and water clarity. The equipment used for boat sampling is described too. 7 pictures

  3. Graph sampling

    OpenAIRE

    Zhang, L.-C.; Patone, M.

    2017-01-01

    We synthesise the existing theory of graph sampling. We propose a formal definition of sampling in finite graphs, and provide a classification of potential graph parameters. We develop a general approach of Horvitz–Thompson estimation to T-stage snowball sampling, and present various reformulations of some common network sampling methods in the literature in terms of the outlined graph sampling theory.

  4. [Determination of short-chain chlorinated paraffins in ambient air using high-volume sampling combined with high resolutimi gas chromatography-electron capture negative ion-low resolution mass spectrometry].

    Science.gov (United States)

    Shi, Loimeng; Gao, Yuan; Hou, Xiaohong; Zhang, Haijun; Zhang, Yichi; Chen, Jiping

    2016-02-01

    An analytical method for quantifying short-chain chlorinated paraffins (SCCPs) in ambient air using high-volume sampling combined with high resolution gas chromatography-electron capture negative ion-low resolution mass spectrometry ( HRGC-ECNI-LRMS) was developed. An acidified silica gel column and a basic alumina column were used to optimize the cleanup procedures. The results showed a good linearity (R2>0. 99) between the total response factors and the degree of chlorination of SCCPs in the content range of 58. 1%-63. 3%. The limits of detection (S/N ≥3) and the limits of quantification (S/N ≥ 10) were 4. 2 and 12 µg, respectively. The method detection limit (MDL) for SCCPs was 0. 34 ng/m3 (n = 7). The recoveries of SCCPs in air samples were in the range of 81. 9% to 94. 2%. It is demonstrated that the method is suitable for the quantitative analysis of SCCPs in air samples.

  5. Detection of Mycoplasma hyopneumoniae in lungs and nasal swabs of pigs by nested PCR Detecção de Mycoplasma hyopneumoniae em pulmões e suabes nasais de suínos por nested PCR

    Directory of Open Access Journals (Sweden)

    F.M.F. Silva

    2009-02-01

    Full Text Available Fifty-four samples were collected from growing and finishing pigs for the molecular diagnosis of enzootic porcine pneumonia. Nineteen lung fragments were obtained from pigs that showed signs of respiratory disease and 35 nasal swabs were obtained from clinically healthy pigs. For the detection of the bacterial genome in the samples, the nested PCR technique was used to amplify a fragment of 706bp. This fragment was subsequently cloned and sequenced. The sequence of obtained nucleotides was compared with six other sequences of Mycoplasma hyopneumoniae and 11 sequences of other bacteria available in the Genbank. To measure the sensitivity of the nested PCR, serial dilutions (10-1 to 10-15 of cloned fragments were conducted based on the concentration of 300ng. Ten lung fragments and eight nasal swabs showed positive for M. hyopneumoniae and the limit of detection was estimated to be 0.3fg DNA cloned. The sequence of nucleotides obtained showed 99.1% homology with the other sequences of M. hyopneumoniae, demonstrating that the nested PCR used in this study may provide an important diagnostic tool for the detection of this agent.Foram coletadas 54 amostras de animais em fase de crescimento e terminação para o diagnóstico molecular da pneumonia enzoótica suína. Dezenove fragmentos de pulmão foram obtidos de suínos que apresentavam sinais de doença respiratória e 35 suabes nasais foram obtidas de suínos clinicamente saudáveis. Para a detecção do genoma bacteriano nas amostras, foi utilizada a técnica de nested PCR que originou um fragmento de 706pb, o qual foi, posteriormente, clonado e sequenciado. A sequência de nucleotídeos obtida foi comparada com outras seis sequências de Mycoplasma hyopneumoniae e 11 sequências de outras bactérias disponíveis no Genbank. Para medir a sensibilidade da nested PCR, foram realizadas diluições seriadas (10-1 a 10-15 do fragmento clonado, partindo da concentração de 300ng. Dez fragmentos de pulm

  6. Direct impression on agar surface as a diagnostic sampling procedure for candida balanitis.

    Science.gov (United States)

    Lisboa, Carmen; Santos, António; Azevedo, Filomena; Pina-Vaz, Cidália; Rodrigues, Acácio Gonçalves

    2010-02-01

    The diagnosis of candida balanitis should be based upon both clinical and mycological data. The procedure of material collection is a critical issue to confirm or rule out the clinical diagnosis of candida balanitis. To compare direct impression of the glans on the agar surface of solid culture media with the collection of genital exudates with cotton swab for the diagnosis of candida balanitis. A prospective cross-sectional study was carried out during a 36-month period. Sexually transmitted disease clinic attendees with balanitis and asymptomatic men were included. Specimens for yeast culture were collected from the glans penis and inner preputial layer using the direct impression on CHROMagar candida medium and by swabbing with a sterile cotton swab. Among 478 men enrolled, 189 had balanitis. The prevalence of candida balanitis was 17.8% (85/478) confirmed after culture by direct impression; the swab method detected only 54/85 (63.5%) of these men. Of the 289 asymptomatic men, 36 (12.5%) yielded Candida spp; the swab method detected only 38.9% of these men. The risk of having candida balanitis is 8.9 (IC 95% 2.48 to 32.04) whenever the number of candida colonies recovered by direct impression was greater than 10. Direct impression on CHROMagar candida medium resulted in the highest Candida spp recovery rate. More than 10 colonies yielded by impression culture were statistically associated with candida balanitis. This method shows the ideal profile for sampling the male genital area for yeasts and should be included in the management of balanitis.

  7. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  8. Efficient recovery of fluoroquinolone-susceptible and fluoroquinolone-resistant Escherichia coli strains from frozen samples.

    Science.gov (United States)

    Lautenbach, Ebbing; Santana, Evelyn; Lee, Abby; Tolomeo, Pam; Black, Nicole; Babson, Andrew; Perencevich, Eli N; Harris, Anthony D; Smith, Catherine A; Maslow, Joel

    2008-04-01

    We assessed the rate of recovery of fluoroquinolone-resistant and fluoroquinolone-susceptible Escherichia coli isolates from culture of frozen perirectal swab samples compared with the results for culture of the same specimen before freezing. Recovery rates for these 2 classes of E. coli were 91% and 83%, respectively. The majority of distinct strains recovered from the initial sample were also recovered from the frozen sample. The strains that were not recovered were typically present only in low numbers in the initial sample. These findings emphasize the utility of frozen surveillance samples.

  9. Ensemble Sampling

    OpenAIRE

    Lu, Xiuyuan; Van Roy, Benjamin

    2017-01-01

    Thompson sampling has emerged as an effective heuristic for a broad range of online decision problems. In its basic form, the algorithm requires computing and sampling from a posterior distribution over models, which is tractable only for simple special cases. This paper develops ensemble sampling, which aims to approximate Thompson sampling while maintaining tractability even in the face of complex models such as neural networks. Ensemble sampling dramatically expands on the range of applica...

  10. Simultaneous analysis of non-steroidal anti-inflammatory drugs and estrogenic hormones in water and wastewater samples using gas chromatography-mass spectrometry and gas chromatography with electron capture detection

    Energy Technology Data Exchange (ETDEWEB)

    Migowska, Natalia; Caban, Magda; Stepnowski, Piotr; Kumirska, Jolanta, E-mail: kumirska@chem.univ.gda.pl

    2012-12-15

    Non-steroidal anti-inflammatory drugs are the group of pharmaceuticals that is most often found in the environment, whereas estrogenic hormones are considered to be potent endocrine disruptors. However, the fate and persistence of these compounds in the environment are still unclear. In this study we propose two approaches for determining these compounds in environmental water samples: GC-MS using time windows and operating in selected ion-monitoring mode (SIM) and, for the first time, gas chromatography with electron capture detection (GC-ECD). The identification criteria of both methods fulfilled the requirements of Directive 2002/657/EC. The use of time windows improved the sensitivity of GC-MS measurements. In GC-MS analysis the pharmaceuticals were determined as trimethylsilyl, in GC-ECD as pentafluoropropionyl derivatives. The influence of such parameters as the type of reagent, type of solvent, reaction time, reaction temperature and microwave irradiation in a household microwave oven on the efficacy of silylation was investigated. Derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and 1% trimethylchlorosilane (TMCS) in pyridine (1:1, v/v) for 30 min in 60 Degree-Sign C was found to be optimal. Optimization of the solid phase extraction procedure (SPE) confirmed that the application of Oasis HLB cartridges, the acidification of loading samples to pH 2 and the use of methanol as eluent gave the best absolute recoveries (ARs) of the target compounds. The following ARs of all the compounds were achieved: 58.2-106.8% in influent wastewater, 77.8-103.4% in effluent wastewater and 81.2-101.9% in surface water samples. Validation of the SPE-GC-MS method enables 13 pharmaceuticals to be determined with MDLs between 3.3 and 343.6 ng/L, depending on the analytes and matrices. GC-ECD analysis enables the determination of 6 pharmaceuticals in surface water samples with MDLs between 0.7 and 5.4 ng/L. The proposed methods were successfully used for

  11. Simultaneous analysis of non-steroidal anti-inflammatory drugs and estrogenic hormones in water and wastewater samples using gas chromatography–mass spectrometry and gas chromatography with electron capture detection

    International Nuclear Information System (INIS)

    Migowska, Natalia; Caban, Magda; Stepnowski, Piotr; Kumirska, Jolanta

    2012-01-01

    Non-steroidal anti-inflammatory drugs are the group of pharmaceuticals that is most often found in the environment, whereas estrogenic hormones are considered to be potent endocrine disruptors. However, the fate and persistence of these compounds in the environment are still unclear. In this study we propose two approaches for determining these compounds in environmental water samples: GC–MS using time windows and operating in selected ion-monitoring mode (SIM) and, for the first time, gas chromatography with electron capture detection (GC–ECD). The identification criteria of both methods fulfilled the requirements of Directive 2002/657/EC. The use of time windows improved the sensitivity of GC–MS measurements. In GC–MS analysis the pharmaceuticals were determined as trimethylsilyl, in GC–ECD as pentafluoropropionyl derivatives. The influence of such parameters as the type of reagent, type of solvent, reaction time, reaction temperature and microwave irradiation in a household microwave oven on the efficacy of silylation was investigated. Derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and 1% trimethylchlorosilane (TMCS) in pyridine (1:1, v/v) for 30 min in 60 °C was found to be optimal. Optimization of the solid phase extraction procedure (SPE) confirmed that the application of Oasis HLB cartridges, the acidification of loading samples to pH 2 and the use of methanol as eluent gave the best absolute recoveries (ARs) of the target compounds. The following ARs of all the compounds were achieved: 58.2–106.8% in influent wastewater, 77.8–103.4% in effluent wastewater and 81.2–101.9% in surface water samples. Validation of the SPE–GC–MS method enables 13 pharmaceuticals to be determined with MDLs between 3.3 and 343.6 ng/L, depending on the analytes and matrices. GC–ECD analysis enables the determination of 6 pharmaceuticals in surface water samples with MDLs between 0.7 and 5.4 ng/L. The proposed methods were successfully

  12. The influence of different skin types on GSR sampling by tape lifting for SEM analysis.

    Science.gov (United States)

    Kara, İlker

    2017-12-01

    In this study, the change in the amounts the gunshot residues (GSR) collected by the "swab" method from shooter's right hand was analyzed using Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS) to test dependency on various conditions (such as skin color of the shooter, various physical properties, hair density of hands, size of the hands, sweaty or creamy (oiliness) hands). As a result of the analysis, there was no significant difference in the amount of GSR according to skin color, however, there was a change in the amount of GSR depending on the physical characteristics of the shooter. These results thought to have practical benefits for the experts performing GSR analysis using the swab technique to assess the incidence. © 2017 Wiley Periodicals, Inc.

  13. Direct isolation of H1N2 recombinant virus from a throat swab of a patient simultaneously infected with H1N1 and H3N2 influenza A viruses.

    OpenAIRE

    Nishikawa, F; Sugiyama, T

    1983-01-01

    Two H1N2 recombinant viruses were isolated by a plaquing method from a throat swab of a patient who was simultaneously infected with H1N1 and H3N2 influenza viruses during the Tokyo epidemic of 1981. This is the first direct evidence that recombination of influenza viruses occurred in the human body.

  14. Correlated Raman micro-spectroscopy and scanning electron microscopy analyses of flame retardants in environmental samples: a micro-analytical tool for probing chemical composition, origin and spatial distribution.

    Science.gov (United States)

    Ghosal, Sutapa; Wagner, Jeff

    2013-07-07

    We present correlated application of two micro-analytical techniques: scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDS) and Raman micro-spectroscopy (RMS) for the non-invasive characterization and molecular identification of flame retardants (FRs) in environmental dusts and consumer products. The SEM/EDS-RMS technique offers correlated, morphological, molecular, spatial distribution and semi-quantitative elemental concentration information at the individual particle level with micrometer spatial resolution and minimal sample preparation. The presented methodology uses SEM/EDS analyses for rapid detection of particles containing FR specific elements as potential indicators of FR presence in a sample followed by correlated RMS analyses of the same particles for characterization of the FR sub-regions and surrounding matrices. The spatially resolved characterization enabled by this approach provides insights into the distributional heterogeneity as well as potential transfer and exposure mechanisms for FRs in the environment that is typically not available through traditional FR analysis. We have used this methodology to reveal a heterogeneous distribution of highly concentrated deca-BDE particles in environmental dust, sometimes in association with identifiable consumer materials. The observed coexistence of deca-BDE with consumer material in dust is strongly indicative of its release into the environment via weathering/abrasion of consumer products. Ingestion of such enriched FR particles in dust represents a potential for instantaneous exposure to high FR concentrations. Therefore, correlated SEM/RMS analysis offers a novel investigative tool for addressing an area of important environmental concern.

  15. Radioactive particles revealed by electron microscopy. Chemical and physical properties of radioactive particles in aerosol samples emitted during the early stage of Fukushima Dai-ichi Nuclear Power Plant accident

    International Nuclear Information System (INIS)

    Adachi, Kouji

    2015-01-01

    Water-insoluble radioactive materials emitted during an early stage of the Fukushima Dai-ichi Nuclear Power Plant accident in 2011 were identified, and their chemical and physical properties were characterized as particulate matters. In this report, studies on radioactive particles collected from filter samples in Tsukuba on March 14–15, 2011 are summarized. Their compositions, chemical states, sizes, shapes, crystallinity, and hygroscopicity were analyzed using microscopic analyses such as electron microscopy and synchrotron with a micro-beam. The results indicate that they include Cs, Fe, and Zn as well as elements from fission products and are water insoluble, spherical-glassy particles with ca. 2 micrometer in size. Understanding of their detailed properties is significant to improve the numerical models during the accident and to understand their occurrences in soil as well as the accident itself. In addition to the water-insoluble radioactive materials, water-soluble radioactive materials, which were likely emitted in different events during the accident, should be investigated to have comprehensive understanding of the accident and its environmental effects. More samples from various environments such as soil will be needed, and more detailed chemical and physical analyses will help to understand their formation process, influences on human health, and long term decrements in ambient conditions. (author)

  16. Techniques for the detection of pathogenic Cryptococcus species in wood decay substrata and the evaluation of viability in stored samples

    Directory of Open Access Journals (Sweden)

    Christian Alvarez

    2013-02-01

    Full Text Available In this study, we evaluated several techniques for the detection of the yeast form of Cryptococcus in decaying wood and measured the viability of these fungi in environmental samples stored in the laboratory. Samples were collected from a tree known to be positive for Cryptococcus and were each inoculated on 10 Niger seed agar (NSA plates. The conventional technique (CT yielded a greater number of positive samples and indicated a higher fungal density [in colony forming units per gram of wood (CFU.g-1] compared to the humid swab technique (ST. However, the difference in positive and false negative results between the CT-ST was not significant. The threshold of detection for the CT was 0.05.10³ CFU.g-1, while the threshold for the ST was greater than 0.1.10³ CFU-1. No colonies were recovered using the dry swab technique. We also determined the viability of Cryptococcus in wood samples stored for 45 days at 25ºC using the CT and ST and found that samples not only continued to yield a positive response, but also exhibited an increase in CFU.g-1, suggesting that Cryptococcus is able to grow in stored environmental samples. The ST.1, in which samples collected with swabs were immediately plated on NSA medium, was more efficient and less laborious than either the CT or ST and required approximately 10 min to perform; however, additional studies are needed to validate this technique.

  17. Primary secondary amine as a sorbent material in dispersive solid-phase extraction clean-up for the determination of indicator polychlorinated biphenyls in environmental water samples by gas chromatography with electron capture detection.

    Science.gov (United States)

    Guo, Yuanming; Hu, Hongmei; Li, Tiejun; Xue, Lijian; Zhang, Xiaoning; Zhong, Zhi; Zhang, Yurong; Jin, Yanjian

    2017-08-01

    A simple, rapid, and novel method has been developed and validated for determination of seven indicator polychlorinated biphenyls in water samples by gas chromatography with electron capture detection. 1 L of water samples containing 30 g of anhydrous sodium sulfate was first liquid-liquid extracted with an automated Jipad-6XB vertical oscillator using n-hexane/dichloromethane (1:1, v/v). The concentrated extract was cleaned up by dispersive solid-phase extraction with 100 mg of primary secondary amine as sorbent material. The linearity of this method ranged from 1.25 to 100 μg/L, with regression coefficients ranging between 0.9994 and 0.9999. The limits of detection were in the ng/L level, ranging between 0.2 and 0.3 ng/L. The recoveries of seven spiked polychlorinated biphenyls with external calibration method at different concentration levels in tap water, lake water, and sea water were in the ranges of 85-112, 76-116, and 72-108%, respectively, and with relative standard deviations of 3.3-4.5, 3.4-5.6, and 3.1-4.8% (n = 5), respectively. The performance of the proposed method was compared with traditional liquid-liquid extraction and solid-phase extraction clean-up methods, and comparable efficiencies were obtained. It is concluded that this method can be successfully applied for the determination of polychlorinated biphenyls in different water samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Identification of V-type nerve agents in vapor samples using a field-portable capillary gas chromatography/membrane-interfaced electron ionization quadrupole mass spectrometry instrument with Tri-Bed concentrator and fluoridating conversion tube.

    Science.gov (United States)

    Ohrui, Y; Nagoya, T; Kurimata, N; Sodeyama, M; Seto, Y

    2017-07-01

    A field-portable gas chromatography-mass spectrometry (GC-MS) system (Hapsite ER) was evaluated for the detection of nonvolatile V-type nerve agents (VX and Russian VX (RVX)) in the vapor phase. The Hapsite ER system consists of a Tri-Bed concentrator gas sampler, a nonpolar low thermal-mass capillary GC column and a hydrophobic membrane-interfaced electron ionization quadrupole mass spectrometer evacuated by a non-evaporative getter pump. The GC-MS system was attached to a VX-G fluoridating conversion tube containing silver nitrate and potassium fluoride. Sample vapors of VX and RVX were converted into O-ethyl methylphosphonofluoridate (EtGB) and O-isobutyl methylphosphonofluoridate (iBuGB), respectively. These fluoridated derivatives were detected within 10 min. No compounds were detected when the VX and RVX samples were analyzed without the conversion tube. A vapor sample of tabun (GA) was analyzed, in which GA and O-ethyl N,N-dimethylphosphoramidofluoridate were detected. The molar recovery percentages of EtGB and iBuGB from VX and RVX vapors varied from 0.3 to 17%, which was attributed to variations in the vaporization efficiency of the glass vapor container. The conversion efficiencies of the VX-G conversion tube for VX and RVX to their phosphonate derivatives were estimated to be 40%. VX and RVX vapors were detected at concentrations as low as 0.3 mg m -3 . Gasoline vapor was found to interfere with the analyses of VX and RVX. In the presence of 160 mg m -3 gasoline, the detection limits of VX and RVX vapor were increased to 20 mg m -3 . Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Laser sampling

    International Nuclear Information System (INIS)

    Gorbatenko, A A; Revina, E I

    2015-01-01

    The review is devoted to the major advances in laser sampling. The advantages and drawbacks of the technique are considered. Specific features of combinations of laser sampling with various instrumental analytical methods, primarily inductively coupled plasma mass spectrometry, are discussed. Examples of practical implementation of hybrid methods involving laser sampling as well as corresponding analytical characteristics are presented. The bibliography includes 78 references

  20. 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.

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

    Science.gov (United States)

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

    2017-12-06

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

  2. Comparison of Interfacial Electron Transfer Efficiency in [Fe(ctpy)2]2+-TiO2 and [Fe(cCNC)2]2+-TiO2 Assemblies: Importance of Conformational Sampling.

    Science.gov (United States)

    Mukherjee, Sriparna; Liu, Chang; Jakubikova, Elena

    2018-02-22

    Fe(II)-polypyridines have limited applications as chromophores in dye-sensitized solar cells due to the short lifetimes (∼100 fs) of their photoactive metal-to-ligand charge transfer (MLCT) states formed upon photoexcitation. Recently, a 100-fold increase in the MLCT lifetime was observed in a [Fe(CNC) 2 ] 2+ complex (CNC = 2,6-bis(3-methylimidazole-1-ylidine)pyridine) which has strong σ-donating N-heterocyclic carbene ligand in comparison to the weaker field parent [Fe(tpy) 2 ] 2+ complex (tpy = 2,2':6',2″-terpyridine). This study utilizes density functional theory (DFT), time-dependent DFT, and quantum dynamics simulations to investigate the interfacial electron transfer (IET) in [Fe(cCNC) 2 ] 2+ (cCNC = 4'-carboxy-2,6-bis(3-methylimidazole-1-ylidine)pyridine) and [Fe(ctpy) 2 ] 2+ (ctpy = 4'-carboxy-2,2':6',2″-terpyridine) sensitized TiO 2 . Our results suggest that the replacement of tpy by CNC ligand does not significantly speed up the IET kinetics in the [Fe(cCNC) 2 ] 2+ -TiO 2 assembly in comparison to the [Fe(ctpy) 2 ] 2+ -TiO 2 analogue. The high IET efficiency in the [Fe(cCNC) 2 ] 2+ -TiO 2 assemblies is therefore due to longer lifetime of [Fe(cCNC) 2 ] 2+ photoactive 3 MLCT states rather than faster electron injection kinetics. It was also found that the inclusion of conformational sampling in the computational model is important for proper description of the IET processes in these systems, as the models relying on the use of only fully optimized structures may yield misleading results. The simulations presented in this work also illustrate various pitfalls of utilizing properties such as electronic coupling, number of available acceptor states, and driving force, as well as calculations based on Fermi's golden rule framework, to reach conclusions on the IET efficiency in dye-semiconductor systems.

  3. Electron-electron interactions in artificial graphene

    Science.gov (United States)

    Rasanen, Esa

    2013-03-01

    Recent advances in the creation and modulation of graphenelike systems are introducing a science of ``designer Dirac materials.'' In its original definition, artificial graphene is a man-made nanostructure that consists of identical potential wells (quantum dots) arranged in an adjustable honeycomb lattice in the two-dimensional electron gas. As our ability to control the quality of artificial graphene samples improves, so grows the need for an accurate theory of its electronic properties, including the effects of electron-electron interactions. Here we determine those effects on the band structure and on the emergence of Dirac points, and discuss future investigations and challenges in this field.

  4. Hand Hygiene Practices and Microbial Investigation of Hand Contact Swab among Physiotherapists in an Ebola Endemic Region: Implications for Public Health.

    Science.gov (United States)

    Ibeneme, S; Maduako, V; Ibeneme, G C; Ezuma, A; Ettu, T U; Onyemelukwe, N F; Limaye, D; Fortwengel, G

    2017-01-01

    Hand hygiene practices (HHP), as a critical component of infection prevention/control, were investigated among physiotherapists in an Ebola endemic region. A standardized instrument was administered to 44 randomly selected physiotherapists (23 males and 21 females), from three tertiary hospitals in Enugu, Nigeria. Fifteen participants (aged 22-59 years) participated in focus group discussions (FGDs) and comprised 19 participants in a subsequent laboratory study. After treatment, the palms/fingers of physiotherapists were swabbed and cultured, then incubated aerobically overnight at 37°C, and examined for microbial growths. An antibiogram of the bacterial isolates was obtained. The majority (34/77.3%) of physiotherapists were aware of the HHP protocol, yet only 15/44.1% rated self-compliance at 71-100%. FGDs identified forgetfulness/inadequate HHP materials/infrastructure as the major barriers to HHP. Staphylococcus aureus were the most prevalent organisms, prior to (8/53.33%) and after (4/26.67%) HPP, while Pseudomonas spp. were acquired thereafter. E. coli were the most antibiotic resistant microbes but were completely removed after HHP. Ciprofloxacin and streptomycin were the most effective antibiotics. Poor implementation of HPP was observed due to inadequate materials/infrastructure/poor behavioral orientation. Possibly, some HPP materials were contaminated; hence, new microbes were acquired. Since HPP removed the most antibiotic resistant microbes, it might be more effective in infection control than antibiotic medication.

  5. Hand Hygiene Practices and Microbial Investigation of Hand Contact Swab among Physiotherapists in an Ebola Endemic Region: Implications for Public Health

    Directory of Open Access Journals (Sweden)

    S. Ibeneme

    2017-01-01

    Full Text Available Background. Hand hygiene practices (HHP, as a critical component of infection prevention/control, were investigated among physiotherapists in an Ebola endemic region. Method. A standardized instrument was administered to 44 randomly selected physiotherapists (23 males and 21 females, from three tertiary hospitals in Enugu, Nigeria. Fifteen participants (aged 22–59 years participated in focus group discussions (FGDs and comprised 19 participants in a subsequent laboratory study. After treatment, the palms/fingers of physiotherapists were swabbed and cultured, then incubated aerobically overnight at 37°C, and examined for microbial growths. An antibiogram of the bacterial isolates was obtained. Results. The majority (34/77.3% of physiotherapists were aware of the HHP protocol, yet only 15/44.1% rated self-compliance at 71–100%. FGDs identified forgetfulness/inadequate HHP materials/infrastructure as the major barriers to HHP. Staphylococcus aureus were the most prevalent organisms, prior to (8/53.33% and after (4/26.67% HPP, while Pseudomonas spp. were acquired thereafter. E. coli were the most antibiotic resistant microbes but were completely removed after HHP. Ciprofloxacin and streptomycin were the most effective antibiotics. Conclusion. Poor implementation of HPP was observed due to inadequate materials/infrastructure/poor behavioral orientation. Possibly, some HPP materials were contaminated; hence, new microbes were acquired. Since HPP removed the most antibiotic resistant microbes, it might be more effective in infection control than antibiotic medication.

  6. Hand Hygiene Practices and Microbial Investigation of Hand Contact Swab among Physiotherapists in an Ebola Endemic Region: Implications for Public Health

    Science.gov (United States)

    Maduako, V.; Ibeneme, G. C.; Ezuma, A.; Ettu, T. U.; Onyemelukwe, N. F.; Fortwengel, G.

    2017-01-01

    Background Hand hygiene practices (HHP), as a critical component of infection prevention/control, were investigated among physiotherapists in an Ebola endemic region. Method A standardized instrument was administered to 44 randomly selected physiotherapists (23 males and 21 females), from three tertiary hospitals in Enugu, Nigeria. Fifteen participants (aged 22–59 years) participated in focus group discussions (FGDs) and comprised 19 participants in a subsequent laboratory study. After treatment, the palms/fingers of physiotherapists were swabbed and cultured, then incubated aerobically overnight at 37°C, and examined for microbial growths. An antibiogram of the bacterial isolates was obtained. Results The majority (34/77.3%) of physiotherapists were aware of the HHP protocol, yet only 15/44.1% rated self-compliance at 71–100%. FGDs identified forgetfulness/inadequate HHP materials/infrastructure as the major barriers to HHP. Staphylococcus aureus were the most prevalent organisms, prior to (8/53.33%) and after (4/26.67%) HPP, while Pseudomonas spp. were acquired thereafter. E. coli were the most antibiotic resistant microbes but were completely removed after HHP. Ciprofloxacin and streptomycin were the most effective antibiotics. Conclusion Poor implementation of HPP was observed due to inadequate materials/infrastructure/poor behavioral orientation. Possibly, some HPP materials were contaminated; hence, new microbes were acquired. Since HPP removed the most antibiotic resistant microbes, it might be more effective in infection control than antibiotic medication. PMID:28691027

  7. SWAB/NVALT (Dutch Working Party on Antibiotic Policy and Dutch Association of Chest Physicians) guidelines on the management of community-acquired pneumonia in adults.

    Science.gov (United States)

    Wiersinga, W J; Bonten, M J; Boersma, W G; Jonkers, R E; Aleva, R M; Kullberg, B J; Schouten, J A; Degener, J E; Janknegt, R; Verheij, T J; Sachs, A P E; Prins, J M

    2012-03-01

    The Dutch Working Party on Antibiotic Policy (SWAB) and the Dutch Association of Chest Physicians (NVALT) convened a joint committee to develop evidence-based guidelines on the diagnosis and treatment of community acquired pneumonia (CAP). The guidelines are intended for adult patients with CAP who present at the hospital and are treated as outpatients as well as for hospitalised patients up to 72 hours after admission. Areas covered include current patterns of epidemiology and antibiotic resistance of causative agents of CAP in the Netherlands, the possibility to predict the causative agent of CAP on the basis of clinical data at first presentation, risk factors associated with specific pathogens, the importance of the severity of disease upon presentation for choice of initial treatment, the role of rapid diagnostic tests in treatment decisions, the optimal initial empiric treatment and treatment when a specific pathogen has been identified, the timeframe in which the first dose of antibiotics should be given, optimal duration of antibiotic treatment and antibiotic switch from the intravenous to the oral route. Additional recommendations are made on the role of radiological investigations in the diagnostic work-up of patients with a clinical suspicion of CAP, on the potential benefit of adjunctive immunotherapy, and on the policy for patients with parapneumonic effusions.

  8. Automatic sample changers maintenance manual

    International Nuclear Information System (INIS)

    Myers, T.A.

    1978-10-01

    This manual describes and provides trouble-shooting aids for the Automatic Sample Changer electronics on the automatic beta counting system, developed by the Los Alamos Scientific Laboratory Group CNC-11. The output of a gas detector is shaped by a preamplifier, then is coupled to an amplifier. Amplifier output is discriminated and is the input to a scaler. An identification number is associated with each sample. At a predetermined count length, the identification number, scaler data plus other information is punched out on a data card. The next sample to be counted is automatically selected. The beta counter uses the same electronics as the prior count did, the only difference being the sample identification number and sample itself. This manual is intended as a step-by-step aid in trouble-shooting the electronics associated with positioning the sample, counting the sample, and getting the needed data punched on an 80-column data card

  9. Soil sampling

    International Nuclear Information System (INIS)

    Fortunati, G.U.; Banfi, C.; Pasturenzi, M.

    1994-01-01

    This study attempts to survey the problems associated with techniques and strategies of soil sampling. Keeping in mind the well defined objectives of a sampling campaign, the aim was to highlight the most important aspect of representativeness of samples as a function of the available resources. Particular emphasis was given to the techniques and particularly to a description of the many types of samplers which are in use. The procedures and techniques employed during the investigations following the Seveso accident are described. (orig.)

  10. Language sampling

    DEFF Research Database (Denmark)

    Rijkhoff, Jan; Bakker, Dik

    1998-01-01

    This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our...... sampling method is used with different genetic classifications (Voegelin & Voegelin 1977, Ruhlen 1987, Grimes ed. 1997) and argue that —on the whole— our sampling technique compares favourably with other methods, especially in the case of exploratory research....

  11. Electron microscopy of boron carbide before and after electron irradiation

    International Nuclear Information System (INIS)

    Stoto, T.; Zuppiroli, L.; Beauvy, M.; Athanassiadis, T.

    1984-06-01

    The microstructure of boron carbide has been studied by electron microscopy and related to the composition of the material. After electron irradiations in an usual transmission electron microscope and in a high voltage electron microscope at different temperatures and fluxes no change of these microstructures have been observed but a sputtering of the surface of the samples, which has been studied quantitatively [fr

  12. Split-illumination electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Tanigaki, Toshiaki; Aizawa, Shinji; Suzuki, Takahiro; Park, Hyun Soon [Advanced Science Institute, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198 (Japan); Inada, Yoshikatsu [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Sendai 980-8577 (Japan); Matsuda, Tsuyoshi [Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 (Japan); Taniyama, Akira [Corporate Research and Development Laboratories, Sumitomo Metal Industries, Ltd., Amagasaki, Hyogo 660-0891 (Japan); Shindo, Daisuke [Advanced Science Institute, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198 (Japan); Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Sendai 980-8577 (Japan); Tonomura, Akira [Advanced Science Institute, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198 (Japan); Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa 904-0495 (Japan); Central Research Laboratory, Hitachi, Ltd., Hatoyama, Saitama 350-0395 (Japan)

    2012-07-23

    We developed a split-illumination electron holography that uses an electron biprism in the illuminating system and two biprisms (applicable to one biprism) in the imaging system, enabling holographic interference micrographs of regions far from the sample edge to be obtained. Using a condenser biprism, we split an electron wave into two coherent electron waves: one wave is to illuminate an observation area far from the sample edge in the sample plane and the other wave to pass through a vacuum space outside the sample. The split-illumination holography has the potential to greatly expand the breadth of applications of electron holography.

  13. Split-illumination electron holography

    International Nuclear Information System (INIS)

    Tanigaki, Toshiaki; Aizawa, Shinji; Suzuki, Takahiro; Park, Hyun Soon; Inada, Yoshikatsu; Matsuda, Tsuyoshi; Taniyama, Akira; Shindo, Daisuke; Tonomura, Akira

    2012-01-01

    We developed a split-illumination electron holography that uses an electron biprism in the illuminating system and two biprisms (applicable to one biprism) in the imaging system, enabling holographic interference micrographs of regions far from the sample edge to be obtained. Using a condenser biprism, we split an electron wave into two coherent electron waves: one wave is to illuminate an observation area far from the sample edge in the sample plane and the other wave to pass through a vacuum space outside the sample. The split-illumination holography has the potential to greatly expand the breadth of applications of electron holography.

  14. Electronic technology

    International Nuclear Information System (INIS)

    Kim, Jin Su

    2010-07-01

    This book is composed of five chapters, which introduces electronic technology about understanding of electronic, electronic component, radio, electronic application, communication technology, semiconductor on its basic, free electron and hole, intrinsic semiconductor and semiconductor element, Diode such as PN junction diode, characteristic of junction diode, rectifier circuit and smoothing circuit, transistor on structure of transistor, characteristic of transistor and common emitter circuit, electronic application about electronic equipment, communication technology and education, robot technology and high electronic technology.

  15. Simultaneous analysis of organochlorine pesticides and polychlorinated biphenyls in air samples by using accelerated solvent extraction (ASE) and solid-phase micro-extraction (SPME) coupled to gas chromatography dual electron capture detection.

    Science.gov (United States)

    Mokbel, Haifaa; Al Dine, Enaam Jamal; Elmoll, Ahmad; Liaud, Céline; Millet, Maurice

    2016-04-01

    An analytical method associating accelerated solvent extraction (ASE) and solid-phase micro-extraction (SPME) in immersion mode combined with gas chromatography dual electrons capture detectors (SPME-GC-2ECD) has been developed and studied for the simultaneous determination of 19 organochlorine pesticides (OCPs) and 22 polychlorinated biphenyls (PCBs) in air samples (active and XAD-2 passive samplers). Samples were extracted with ASE with acetonitrile using the following conditions: temperature, 150 °C; pressure, 1500 psi; static, 15 min; cycles, 3; purge, 300 s; flush, 100 %. Extracts were reduced to 1 mL, and 500 μL of this extract, filled with deionised water, was subject to SPME extraction. Experimental results indicated that the proposed method attained the best extraction efficiency under the optimised conditions: extraction of PCB-OCP mixture using 100-μm PDMS fibre at 80 °C for 40 min with no addition of salt. The performance of the proposed ASE-SPME-GC-2ECD methodology with respect to linearity, limit of quantification and detection was evaluated by spiking of XAD-2 resin with target compounds. The regression coefficient (R (2)) of most compounds was found to be high of 0.99. limits of detection (LODs) are between 0.02 and 4.90 ng m(-3), and limits of quantification (LOQs) are between 0.05 and 9.12 ng m(-3) and between 0.2 and 49 ng/sampler and 0.52 and 91 ng/sampler, respectively, for XAD-2 passive samplers. Finally, a developed procedure was applied to determine selected PCBs and OCPs in the atmosphere.

  16. The Electron

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, George

    1972-01-01

    Electrons are elementary particles of atoms that revolve around and outside the nucleus and have a negative charge. This booklet discusses how electrons relate to electricity, some applications of electrons, electrons as waves, electrons in atoms and solids, the electron microscope, among other things.

  17. Sample preparation

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    Sample preparation prior to HPLC analysis is certainly one of the most important steps to consider in trace or ultratrace analysis. For many years scientists have tried to simplify the sample preparation process. It is rarely possible to inject a neat liquid sample or a sample where preparation may not be any more complex than dissolution of the sample in a given solvent. The last process alone can remove insoluble materials, which is especially helpful with the samples in complex matrices if other interactions do not affect extraction. Here, it is very likely a large number of components will not dissolve and are, therefore, eliminated by a simple filtration process. In most cases, the process of sample preparation is not as simple as dissolution of the component interest. At times, enrichment is necessary, that is, the component of interest is present in very large volume or mass of material. It needs to be concentrated in some manner so a small volume of the concentrated or enriched sample can be injected into HPLC. 88 refs

  18. Sampling Development

    Science.gov (United States)

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  19. Environmental sampling

    International Nuclear Information System (INIS)

    Puckett, J.M.

    1998-01-01

    Environmental Sampling (ES) is a technology option that can have application in transparency in nuclear nonproliferation. The basic process is to take a sample from the environment, e.g., soil, water, vegetation, or dust and debris from a surface, and through very careful sample preparation and analysis, determine the types, elemental concentration, and isotopic composition of actinides in the sample. The sample is prepared and the analysis performed in a clean chemistry laboratory (CCL). This ES capability is part of the IAEA Strengthened Safeguards System. Such a Laboratory is planned to be built by JAERI at Tokai and will give Japan an intrinsic ES capability. This paper presents options for the use of ES as a transparency measure for nuclear nonproliferation

  20. Hard electronics; Hard electronics

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Hard material technologies were surveyed to establish the hard electronic technology which offers superior characteristics under hard operational or environmental conditions as compared with conventional Si devices. The following technologies were separately surveyed: (1) The device and integration technologies of wide gap hard semiconductors such as SiC, diamond and nitride, (2) The technology of hard semiconductor devices for vacuum micro- electronics technology, and (3) The technology of hard new material devices for oxides. The formation technology of oxide thin films made remarkable progress after discovery of oxide superconductor materials, resulting in development of an atomic layer growth method and mist deposition method. This leading research is expected to solve such issues difficult to be easily realized by current Si technology as high-power, high-frequency and low-loss devices in power electronics, high temperature-proof and radiation-proof devices in ultimate electronics, and high-speed and dense- integrated devices in information electronics. 432 refs., 136 figs., 15 tabs.

  1. Comparison of Gas Chromatography-Mass Spectrometry and Gas Chromatography-Tandem Mass Spectrometry with Electron Ionization and Negative-Ion Chemical Ionization for Analyses of Pesticides at Trace Levels in Atmospheric Samples

    Directory of Open Access Journals (Sweden)

    Renata Raina

    2008-01-01

    Full Text Available A comparison of detection limits of gas chromatography-mass spectrometry (GC-MS in selected ion monitoring (SIM with gas chromatography-tandem mass spectrometry (GC-MS/MS in selected reaction monitoring (SRM mode with both electron ionization (EI and negative-ion chemical ionization (NCI are presented for over 50 pesticides ranging from organochlorines (OCs, organophosphorus pesticides (OPs and pre-emergent herbicides used in the Canadian prairies (triallate, trifluralin, ethalfluralin. The developed GC-EI/SIM, GC-NCI/SIM, and GC-NCI/SRM are suitable for the determination of pesticides in air sample extracts at concentrations <100 pg µL -1 (< 100 pg m -3 in air. No one method could be used to analyze the range of pre-emergent herbicides, OPs, and OCs investigated. In general GC-NCI/SIM provided the lowest method detection limits (MDLs commonly 2.5-10 pg µL -1 along with best confirmation (<25% RSD of ion ratio, while GC-NCI/SRM is recommended for use where added selectivity or confirmation is required (such as parathion-ethyl, tokuthion, carbofenothion. GC-EI/SRM at concentration < 100 pg µL -1 was not suitable for most pesticides. GC-EI/SIM was more prone to interference issues than NCI methods, but gave good sensitivity (MDLs 1-10 pg µL -1 for pesticides with poor NCI response (OPs: sulfotep, phorate, aspon, ethion, and OCs: alachlor, aldrin, perthane, and DDE, DDD, DDT.

  2. Quantitative secondary electron detection

    Science.gov (United States)

    Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

    2018-05-08

    Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  4. Spherical sampling

    CERN Document Server

    Freeden, Willi; Schreiner, Michael

    2018-01-01

    This book presents, in a consistent and unified overview, results and developments in the field of today´s spherical sampling, particularly arising in mathematical geosciences. Although the book often refers to original contributions, the authors made them accessible to (graduate) students and scientists not only from mathematics but also from geosciences and geoengineering. Building a library of topics in spherical sampling theory it shows how advances in this theory lead to new discoveries in mathematical, geodetic, geophysical as well as other scientific branches like neuro-medicine. A must-to-read for everybody working in the area of spherical sampling.

  5. Electron radiography

    Science.gov (United States)

    Merrill, Frank E.; Morris, Christopher

    2005-05-17

    A system capable of performing radiography using a beam of electrons. Diffuser means receive a beam of electrons and diffuse the electrons before they enter first matching quadrupoles where the diffused electrons are focused prior to the diffused electrons entering an object. First imaging quadrupoles receive the focused diffused electrons after the focused diffused electrons have been scattered by the object for focusing the scattered electrons. Collimator means receive the scattered electrons and remove scattered electrons that have scattered to large angles. Second imaging quadrupoles receive the collimated scattered electrons and refocus the collimated scattered electrons and map the focused collimated scattered electrons to transverse locations on an image plane representative of the electrons' positions in the object.

  6. Fluidic sampling

    International Nuclear Information System (INIS)

    Houck, E.D.

    1992-01-01

    This paper covers the development of the fluidic sampler and its testing in a fluidic transfer system. The major findings of this paper are as follows. Fluidic jet samples can dependably produce unbiased samples of acceptable volume. The fluidic transfer system with a fluidic sampler in-line will transfer water to a net lift of 37.2--39.9 feet at an average ratio of 0.02--0.05 gpm (77--192 cc/min). The fluidic sample system circulation rate compares very favorably with the normal 0.016--0.026 gpm (60--100 cc/min) circulation rate that is commonly produced for this lift and solution with the jet-assisted airlift sample system that is normally used at ICPP. The volume of the sample taken with a fluidic sampler is dependant on the motive pressure to the fluidic sampler, the sample bottle size and on the fluidic sampler jet characteristics. The fluidic sampler should be supplied with fluid having the motive pressure of the 140--150 percent of the peak vacuum producing motive pressure for the jet in the sampler. Fluidic transfer systems should be operated by emptying a full pumping chamber to nearly empty or empty during the pumping cycle, this maximizes the solution transfer rate

  7. Throat swabs in children with respiratory tract infection: associations with clinical presentation and potential targets for point-of-care testing.

    Science.gov (United States)

    Thornton, Hannah V; Hay, Alastair D; Redmond, Niamh M; Turnbull, Sophie L; Christensen, Hannah; Peters, Tim J; Leeming, John P; Lovering, Andrew; Vipond, Barry; Muir, Peter; Blair, Peter S

    2017-08-01

    Diagnostic uncertainty over respiratory tract infections (RTIs) in primary care contributes to over-prescribing of antibiotics and drives antibiotic resistance. If symptoms and signs predict respiratory tract microbiology, they could help clinicians target antibiotics to bacterial infection. This study aimed to determine relationships between symptoms and signs in children presenting to primary care and microbes from throat swabs. Cross-sectional study of children ≥3 months to presenting with acute cough and RTI, with subset follow-up. Associations and area under receiver operating curve (AUROC) statistics sought between clinical presentation and baseline microbe detection. Microbe prevalence compared between baseline (symptomatic) and follow-up (asymptomatic) visits. At baseline, ≥1 bacteria was detected in 1257/2113 (59.5%) children and ≥1 virus in 894/2127 (42%) children. Clinical presentation was not associated with detection of ≥1 bacteria [AUROC 0.54 (95% CI 0.52-0.56)] or ≥1 virus [0.64 (95% CI 0.61-0.66)]. Individually, only respiratory syncytial virus (RSV) was associated with clinical presentation [AUROC 0.80 (0.77-0.84)]. Prevalence fell between baseline and follow-up; more so in viruses (68% versus 26%, P clinical presentation cannot distinguish the presence of bacteria or viruses in the upper respiratory tract. However, individual and overall microbe prevalence was greater when children were unwell than when well, providing some evidence that upper respiratory tract microbes may be the cause or consequence of the illness. If causal, selective microbial point-of-care testing could be beneficial. © The Author 2017. Published by Oxford University Press.

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

    Science.gov (United States)

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

    2017-05-04

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

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

    Directory of Open Access Journals (Sweden)

    Lenka A Vodstrcil

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

  10. Electron microscopy of surfaces

    International Nuclear Information System (INIS)

    Venables, J.A.

    1981-01-01

    Electron beam techniques used to study clean surfaces and surface processes on a microscopic scale are reviewed. Recent experimental examples and possible future developments are discussed. Special emphasis is given to (i) transmission diffraction and microscopy techniques, including atomic imaging; (ii) Auger microscopy on bulk and thin film samples; (iii) secondary electron microscopy, especially low energy secondaries for work-function imaging and photoelectron imaging; and (iv) reflection electron microscopy and diffraction. (orig.)

  11. Preanalytical Blood Sampling Errors in Clinical Settings

    International Nuclear Information System (INIS)

    Zehra, N.; Malik, A. H.; Arshad, Q.; Sarwar, S.; Aslam, S.

    2016-01-01

    Background: Blood sampling is one of the common procedures done in every ward for disease diagnosis and prognosis. Daily hundreds of samples are collected from different wards but lack of appropriate knowledge of blood sampling by paramedical staff and accidental errors make the samples inappropriate for testing. Thus the need to avoid these errors for better results still remains. We carried out this research with an aim to determine the common errors during blood sampling; find factors responsible and propose ways to reduce these errors. Methods: A cross sectional descriptive study was carried out at the Military and Combined Military Hospital Rawalpindi during February and March 2014. A Venous Blood Sampling questionnaire (VBSQ) was filled by the staff on voluntary basis in front of the researchers. The staff was briefed on the purpose of the survey before filling the questionnaire. Sample size was 228. Results were analysed using SPSS-21. Results: When asked in the questionnaire, around 61.6 percent of the paramedical staff stated that they cleaned the vein by moving the alcohol swab from inward to outwards while 20.8 percent of the staff reported that they felt the vein after disinfection. On contrary to WHO guidelines, 89.6 percent identified that they had a habit of placing blood in the test tube by holding it in the other hand, which should actually be done after inserting it into the stand. Although 86 percent thought that they had ample knowledge regarding the blood sampling process but they did not practice it properly. Conclusion: Pre analytical blood sampling errors are common in our setup. Eighty six percent participants though thought that they had adequate knowledge regarding blood sampling, but most of them were not adhering to standard protocols. There is a need of continued education and refresher courses. (author)

  12. Fast electron microscopy via compressive sensing

    Science.gov (United States)

    Larson, Kurt W; Anderson, Hyrum S; Wheeler, Jason W

    2014-12-09

    Various technologies described herein pertain to compressive sensing electron microscopy. A compressive sensing electron microscope includes a multi-beam generator and a detector. The multi-beam generator emits a sequence of electron patterns over time. Each of the electron patterns can include a plurality of electron beams, where the plurality of electron beams is configured to impart a spatially varying electron density on a sample. Further, the spatially varying electron density varies between each of the electron patterns in the sequence. Moreover, the detector collects signals respectively corresponding to interactions between the sample and each of the electron patterns in the sequence.

  13. Simultaneous differential detection of Chlamydophila abortus, Chlamydophila pecorum and Coxiella burnetii from aborted ruminant's clinical samples using multiplex PCR

    Directory of Open Access Journals (Sweden)

    Rodolakis Annie

    2009-07-01

    Full Text Available Abstract Background Chlamydiosis and Q fever, two zoonosis, are important causes of ruminants' abortion around the world. They are caused respectively by strictly intracellular and Gram negative bacterium Chlamydophila abortus (Cp. abortus and Coxiella burnetii (C. burnetii. Chlamydophila pecorum (Cp. pecorum is commonly isolated from the digestive tract of clinically inconspicuous ruminants but the abortive and zoonotic impact of this bacterium is still unknown because Cp. pecorum is rarely suspected in abortion cases of small ruminants. We have developed a multiplex PCR (m-PCR for rapid simultaneous differential detection of Cp. abortus, Cp. pecorum and C. burnetii in clinical samples taken from infected animals. Results Specific PCR primers were designed and a sensitive and specific m-PCR was developed to detect simultaneously, in one tube reaction, three specific fragments of 821, 526 and 687-bp long for Cp. abortus, Cp. pecorum and C. burnetii respectively. This m-PCR assay was performed on 253 clinical samples taken from infected ruminant's flocks that have showed problems of abortion diseases. Thus, 67 samples were infected by either one of the three pathogens: 16 (13 vaginal swabs and 3 placentas were positive for Cp. abortus, 2 were positive for Cp. pecorum (1 vaginal swab and 1 placenta and 49 samples (33 vaginal swabs, 11 raw milks, 4 faeces and 1 placenta were positive for C. burnetii. Two vaginal swabs were m-PCR positive of both Cp. abortus and C. burnetii and none of the tested samples was shown to be infected simultaneously with the three pathogens. Conclusion We have successfully developed a rapid multiplex PCR that can detect and differentiate Cp. abortus, Cp. pecorum and C. burnetii; with a good sensitivity and specificity. The diagnosis of chlamydiosis and Q fever may be greatly simplified and performed at low cost. In addition, the improvement in diagnostic techniques will enhance our knowledge regarding the prevalence and

  14. Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples.

    Science.gov (United States)

    Leach, L; Zhu, Y; Chaturvedi, S

    2018-02-01

    Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 ( ITS 2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. Copyright © 2018 Leach et al.

  15. First experience of electron microscopic and bacteriological examination of the prostate gland stones

    Directory of Open Access Journals (Sweden)

    I. V. Vinogradov

    2014-01-01

    Full Text Available The work is based on a study of prostate stones obtained by transurethral resection of the prostate in 5 patients with benign prostatic hyperplasia in combination with chronic calculous prostatitis. Stones have been investigated by scanning electron microscopy and X-ray microstructural analysis, as well as a comparative study of bacteriological swabs from the surface of the stones after ultrasonic treatment of stone and without it. Pretreatment ultrasound prostate stones before sowing on nutrient medium swabs improves bacteriological diagnosis, which may be due to the dispersion of biofilms and exit vegetative forms of bacteria from it. This feature can serve as ultrasound theoretical justification for its use to improve the efficiency of diagnosis of various forms of prostatitis.

  16. Detection of equine herpesvirus in horses with idiopathic keratoconjunctivitis and comparison of three sampling techniques.

    Science.gov (United States)

    Hollingsworth, Steven R; Pusterla, Nicola; Kass, Philip H; Good, Kathryn L; Brault, Stephanie A; Maggs, David J

    2015-09-01

    To determine the role of equine herpesvirus (EHV) in idiopathic keratoconjunctivitis in horses and to determine whether sample collection method affects detection of EHV DNA by quantitative polymerase chain reaction (qPCR). Twelve horses with idiopathic keratoconjunctivitis and six horses without signs of ophthalmic disease. Conjunctival swabs, corneal scrapings, and conjunctival biopsies were collected from 18 horses: 12 clinical cases with idiopathic keratoconjunctivitis and six euthanized controls. In horses with both eyes involved, the samples were taken from the eye judged to be more severely affected. Samples were tested with qPCR for EHV-1, EHV-2, EHV-4, and EHV-5 DNA. Quantity of EHV DNA and viral replicative activity were compared between the two populations and among the different sampling techniques; relative sensitivities of the sampling techniques were determined. Prevalence of EHV DNA as assessed by qPCR did not differ significantly between control horses and those with idiopathic keratoconjunctivitis. Sampling by conjunctival swab was more likely to yield viral DNA as assessed by qPCR than was conjunctival biopsy. EHV-1 and EHV-4 DNA were not detected in either normal or IKC-affected horses; EHV-2 DNA was detected in two of 12 affected horses but not in normal horses. EHV-5 DNA was commonly found in ophthalmically normal horses and horses with idiopathic keratoconjunctivitis. Because EHV-5 DNA was commonly found in control horses and in horses with idiopathic keratoconjunctivitis, qPCR was not useful for the etiological diagnosis of equine keratoconjunctivitis. Conjunctival swabs were significantly better at obtaining viral DNA samples than conjunctival biopsy in horses in which EHV-5 DNA was found. © 2015 American College of Veterinary Ophthalmologists.

  17. Salmonella spp. contamination in commercial layer hen farms using different types of samples and detection methods.

    Science.gov (United States)

    Soria, M C; Soria, M A; Bueno, D J; Godano, E I; Gómez, S C; ViaButron, I A; Padin, V M; Rogé, A D

    2017-08-01

    The performance of detection methods (culture methods and polymerase chain reaction assay) and plating media used in the same type of samples were determined as well as the specificity of PCR primers to detected Salmonella spp. contamination in layer hen farms. Also, the association of farm characteristics with Salmonella presence was evaluated. Environmental samples (feces, feed, drinking water, air, boot-swabs) and eggs were taken from 40 layer hen houses. Salmonella spp. was most detected in boot-swabs taken around the houses (30% and 35% by isolation and PCR, respectively) follow by fecal samples (15.2% and 13.6% by isolation and PCR, respectively). Eggs, drinking water, and air samples were negative for Salmonella detection. Salmonella Schwarzengrund and S. Enteritidis were the most isolated serotypes. For plating media, relative specificity was 1, and the relative sensitivity was greater for EF-18 agar than XLDT agar in feed and fecal samples. However, relative sensitivity was greater in XLDT agar than EF-18 agar for boot-swab samples. Agreement was between fair to good depending on the sample, and it was good between isolation and PCR (feces and boot-swabs), without agreement for feed samples. Salmonella spp. PCR was positive for all strains, while S. Typhimurium PCR was negative. Salmonella Enteritidis PCR used was not specific. Based in the multiple logistic regression analyses, categorization by counties was significant for Salmonella spp. presence (P-value = 0.010). This study shows the importance of considering different types of samples, plating media and detection methods during a Salmonella spp. monitoring study. In addition, it is important to incorporate the sampling of floors around the layer hen houses to learn if biosecurity measures should be strengthened to minimize the entry and spread of Salmonella in the houses. Also, the performance of some PCR methods and S. Enteritidis PCR should be improved, and biosecurity measures in hen farms must be

  18. Sampling methods

    International Nuclear Information System (INIS)

    Loughran, R.J.; Wallbrink, P.J.; Walling, D.E.; Appleby, P.G.

    2002-01-01

    Methods for the collection of soil samples to determine levels of 137 Cs and other fallout radionuclides, such as excess 210 Pb and 7 Be, will depend on the purposes (aims) of the project, site and soil characteristics, analytical capacity, the total number of samples that can be analysed and the sample mass required. The latter two will depend partly on detector type and capabilities. A variety of field methods have been developed for different field conditions and circumstances over the past twenty years, many of them inherited or adapted from soil science and sedimentology. The use of them inherited or adapted from soil science and sedimentology. The use of 137 Cs in erosion studies has been widely developed, while the application of fallout 210 Pb and 7 Be is still developing. Although it is possible to measure these nuclides simultaneously, it is common for experiments to designed around the use of 137 Cs along. Caesium studies typically involve comparison of the inventories found at eroded or sedimentation sites with that of a 'reference' site. An accurate characterization of the depth distribution of these fallout nuclides is often required in order to apply and/or calibrate the conversion models. However, depending on the tracer involved, the depth distribution, and thus the sampling resolution required to define it, differs. For example, a depth resolution of 1 cm is often adequate when using 137 Cs. However, fallout 210 Pb and 7 Be commonly has very strong surface maxima that decrease exponentially with depth, and fine depth increments are required at or close to the soil surface. Consequently, different depth incremental sampling methods are required when using different fallout radionuclides. Geomorphic investigations also frequently require determination of the depth-distribution of fallout nuclides on slopes and depositional sites as well as their total inventories

  19. Culture methods of allograft musculoskeletal tissue samples in Australian bacteriology laboratories.

    Science.gov (United States)

    Varettas, Kerry

    2013-12-01

    Samples of allograft musculoskeletal tissue are cultured by bacteriology laboratories to determine the presence of bacteria and fungi. In Australia, this testing is performed by 6 TGA-licensed clinical bacteriology laboratories with samples received from 10 tissue banks. Culture methods of swab and tissue samples employ a combination of solid agar and/or broth media to enhance micro-organism growth and maximise recovery. All six Australian laboratories receive Amies transport swabs and, except for one laboratory, a corresponding biopsy sample for testing. Three of the 6 laboratories culture at least one allograft sample directly onto solid agar. Only one laboratory did not use a broth culture for any sample received. An international literature review found that a similar combination of musculoskeletal tissue samples were cultured onto solid agar and/or broth media. Although variations of allograft musculoskeletal tissue samples, culture media and methods are used in Australian and international bacteriology laboratories, validation studies and method evaluations have challenged and supported their use in recovering fungi and aerobic and anaerobic bacteria.

  20. Electrons, Electronic Publishing, and Electronic Display.

    Science.gov (United States)

    Brownrigg, Edwin B.; Lynch, Clifford A.

    1985-01-01

    Provides a perspective on electronic publishing by distinguishing between "Newtonian" publishing and "quantum-mechanical" publishing. Highlights include media and publishing, works delivered through electronic media, electronic publishing and the printed word, management of intellectual property, and recent copyright-law issues…

  1. Impact of enzymatic digestion on bacterial community composition in CF airway samples

    Directory of Open Access Journals (Sweden)

    Kayla M. Williamson

    2017-05-01

    Full Text Available Background Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF. We sought to evaluate the effect of enzymatic digestion (EnzD prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP samples from patients with CF. Methods DNA from 81 samples (39 sputum and 42 OP collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA of individual genera for paired samples with and without EnzD. Results Shannon Diversity Index (alpha-diversity decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn, whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella (p < 0.01, Streptococcus (p < 0.01, and Rothia (p < 0.01. Staphylococcus (p < 0.01 was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella (p < 0.01, Granulicatella (p < 0.01, Prevotella (p < 0.01, and Gemella (p = 0.02. In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. Discussion We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP

  2. Self-sampling for human papillomavirus DNA detection: a preliminary study of compliance and feasibility in BOLIVIA.

    Science.gov (United States)

    Surriabre, Pedro; Allende, Gustavo; Prado, Marcela; Cáceres, Leyddy; Bellot, Diego; Torrico, Andrea; Ustariz, Karina; Rojas, Shirley; Barriga, Jaime; Calle, Pamela; Villarroel, Ligia; Yañez, Rosse Mary; Baay, Marc; Rodriguez, Patricia; Fontaine, Véronique

    2017-12-22

    Cervical cancer incidence and mortality rates in Bolivia are among the highest in Latin America. This investigation aims to evaluate the possibility of using simple devices, e.g. a cotton swab and a glass slide, for self-sampling in order to detect human papillomavirus (HPV) DNA by PCR in cervico-vaginal cells. In the first phase of our study we evaluated the use of a glass slide as a transport medium for cervical cells. A physician took paired-cervical samples from 235 women. One sample was transported in Easyfix® solution and the other sample was smeared over a glass slide. Both were further analyzed and compared for human DNA recovery and HPV detection. A kappa value was determined to evaluate the agreement between the HPV DNA detection rates. In the second phase of the study, 222 women from the urban, peri-urban and rural regions of Cochabamba were requested to perform self-sampling using the following devices: a cotton swab combined with a glass slide, and a vaginal tampon. Women gave their opinion about the self-sampling technique. Finally, the agreement for high risk-HPV detection between self- and physician-collected samples was performed in 201 samples in order to evaluate the self-sampling technique. Firstly, the comparison between Easyfix® solution and the glass slide to transport clinical samples gave a good agreement for HPV DNA detection (κ = 0.71, 95% CI 0.60-0.81). Secondly, self-sampling, especially with cotton swab combined with glass slide, would generally be preferred over clinician sampling for a screening program based on HPV detection. Finally, we showed a good agreement between self- and physician collected samples for high risk-HPV detection (κ = 0.71, 95% CI 0.55-0.88). Simple devices such as a cotton swab and a glass slide can be used to perform self-sampling and HPV DNA detection. Furthermore, most Bolivian women preferred self-sampling over clinician-sampling for cervical cancer screening.

  3. Identification of chemical warfare agents from vapor samples using a field-portable capillary gas chromatography/membrane-interfaced electron ionization quadrupole mass spectrometry instrument with Tri-Bed concentrator.

    Science.gov (United States)

    Nagashima, Hisayuki; Kondo, Tomohide; Nagoya, Tomoki; Ikeda, Toru; Kurimata, Naoko; Unoke, Shohei; Seto, Yasuo

    2015-08-07

    A field-portable gas chromatograph-mass spectrometer (Hapsite ER system) was evaluated for the detection of chemical warfare agents (CWAs) in the vapor phase. The system consisted of Tri-Bed concentrator gas sampler (trapping time: 3s(-1)min), a nonpolar low thermal-mass capillary gas chromatography column capable of raising temperatures up to 200°C, a hydrophobic membrane-interfaced electron ionization quadrupole mass spectrometer evacuated by a non-evaporative getter pump for data acquisition, and a personal computer for data analysis. Sample vapors containing as little as 22μg sarin (GB), 100μg soman (GD), 210μg tabun (GA), 55μg cyclohexylsarin (GF), 4.8μg sulfur mustard, 390μg nitrogen mustard 1, 140μg of nitrogen mustard 2, 130μg nitrogen mustard 3, 120μg of 2-chloroacetophenone and 990μg of chloropicrin per cubic meter could be confirmed after Tri-Bed micro-concentration (for 1min) and automated AMDIS search within 12min. Using manual deconvolution by background subtraction of neighboring regions on the extracted ion chromatograms, the above-mentioned CWAs could be confirmed at lower concentration levels. The memory effects were also examined and we found that blister agents showed significantly more carry-over than nerve agents. Gasoline vapor was found to interfere with the detection of GB and GD, raising the concentration limits for confirmation in the presence of gasoline by both AMDIS search and manual deconvolution; however, GA and GF were not subject to interference by gasoline. Lewisite 1, and o-chlorobenzylidene malononitrile could also be confirmed by gas chromatography, but it was hard to quantify them. Vapors of phosgene, chlorine, and cyanogen chloride could be confirmed by direct mass spectrometric detection at concentration levels higher than 2, 140, and 10mg/m(3) respectively, by bypassing the micro-concentration trap and gas chromatographic separation. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Electron detector

    International Nuclear Information System (INIS)

    Hashimoto, H.; Mogami, A.

    1975-01-01

    A device for measuring electron densities at a given energy level in an electron beam or the like having strong background noise, for example, in the detection of Auger electric energy spectrums is described. An electron analyzer passes electrons at the given energy level and at the same time electrons of at least one adjacent energy level. Detecting means associated therewith produce signals indicative of the densities of the electrons at each energy level and combine these signals to produce a signal indicative of the density of the electrons of the given energy level absent background noise

  5. Electron/electron acoustic instability

    International Nuclear Information System (INIS)

    Gary, S.P.

    1987-01-01

    The electron acoustic wave becomes a normal mode of an unmagnetized collisionless plasma in the presence of two electron components with similar densities, but strongly disparate temperatures. The characteristic frequency of this mode is the plasma frequency of the cooler electron component. If these two electron components have a relative drift speed several times the thermal speed of the cooler component, the electron/electron acoustic instability may arise. This paper describes the parametric dependences of the threshold drift speed and maximum growth rate of this instability, and compares these with the same properties of the electron/ion acoustic instability. Under the condition of zero current, the electron/ion acoustic instability typically has the lower threshold drift speed, so that observation of the electron/electron acoustic instability is a strong indication of the presence of an electrical current in the plasma

  6. Recovery rates, serotypes, and antimicrobial susceptibility patterns of Salmonellae isolated from cloacal swabs of wild Nile crocodiles (Crocodylus niloticus) in Zimbabwe

    DEFF Research Database (Denmark)

    Madsen, Mogens; Hangartner, P.; West, K.

    1998-01-01

    Samples from the cloaca and the ventral skin surface of 67 Nile crocodiles (Crocodylus niloticus) captured in four uninhabited areas at Lake Kariba, Zimbabwe, were cultured for Salmonella. All the skin samples tested negative for Salmonella, whereas 18 of 67 (26.9%) cloacal samples grew Salmonell...

  7. Electronic emission and electron guns

    International Nuclear Information System (INIS)

    Roy, Amitava

    2010-01-01

    This paper reviews the process of electron emission from metal surface. Although electrons move freely in conductors like metals, they normally do not leave the metal without some manipulation. In fact, heating and bombardment are the two primary ways in which electrons are emitted through the use of a heating element behind the cathode (termed thermionic emission) or as a result of bombardment with a beam of electrons, ions, or metastable atoms (termed secondary emission). Another important emission mechanism called Explosive Electron Emission (EEE) is also often used in various High Voltage Pulse Power Systems to generate very high current (few hundreds of kA) pulsed electron beams. The electron gun is the device in that it shoots off a continuous (or pulsed) stream of electrons. A brief idea about the evolution of the electron gun components and their basis of functioning are also discussed. (author)

  8. Sticker electronics

    KAUST Repository

    Hussain, Muhammad Mustafa; Torres Sevilla, Galo Andres; Diaz Cordero, Marlon Steven

    2017-01-01

    Electronic stickers may be manufactured on flexible substrates (110, 120, 130) as layers and packaged together. The package may then have an adhesive applied to one side to provide capability for sticking the electronic devices to surfaces

  9. ELECTRONIC SIGNATURES

    African Journals Online (AJOL)

    10332324

    "[to] promote the understanding and, acceptance of and growth in the number of electronic transactions .... Chapter III of the ECT Act is based on the UNCITRAL Model Law on Electronic. Commerce ... Communications Technology Law 146. 22.

  10. Electronic components

    CERN Document Server

    Colwell, Morris A

    1976-01-01

    Electronic Components provides a basic grounding in the practical aspects of using and selecting electronics components. The book describes the basic requirements needed to start practical work on electronic equipment, resistors and potentiometers, capacitance, and inductors and transformers. The text discusses semiconductor devices such as diodes, thyristors and triacs, transistors and heat sinks, logic and linear integrated circuits (I.C.s) and electromechanical devices. Common abbreviations applied to components are provided. Constructors and electronics engineers will find the book useful

  11. Understand electronics

    CERN Document Server

    Bishop, Owen

    2013-01-01

    Understand Electronics provides a readable introduction to the exciting world of electronics for the student or enthusiast with little previous knowledge. The subject is treated with the minimum of mathematics and the book is extensively illustrated.This is an essential guide for the newcomer to electronics, and replaces the author's best-selling Beginner's Guide to Electronics.The step-by-step approach makes this book ideal for introductory courses such as the Intermediate GNVQ.

  12. Electronic Commerce

    OpenAIRE

    Slavko Đerić

    2016-01-01

    Electronic commerce can be defined in different ways. Any definition helps to understand and explain that concept as better as possible.. Electronic commerce is a set of procedures and technologies that automate the tasks of financial transactions using electronic means. Also, according to some authors, electronic commerce is defined as a new concept, which is being developed and which includes process of buying and selling or exchanging products, services or information via computer networks...

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

    Directory of Open Access Journals (Sweden)

    Débora Costa Viegas de Lima

    2012-02-01

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

  14. Electronic Publishing.

    Science.gov (United States)

    Lancaster, F. W.

    1989-01-01

    Describes various stages involved in the applications of electronic media to the publishing industry. Highlights include computer typesetting, or photocomposition; machine-readable databases; the distribution of publications in electronic form; computer conferencing and electronic mail; collaborative authorship; hypertext; hypermedia publications;…

  15. Electronic states of myricetin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Karlsen, Eva; Spanget-Larsen, Jens

    2017-01-01

    Myricetin (3,3',4',5,5',7'-hexahydroxyflavone) was investigated by linear dichroism spectroscopy on molecular samples partially aligned in stretched poly(vinyl alcohol) (PVA). At least five electronic transitions in the range 40000 – 20000 cm–1 were characterized with respect to their wavenumbers......, relative intensities, and transition moment directions. The observed bands were assigned to electronic transitions predicted with TD-B3LYP/6-31+G(d,p)....

  16. Sticker electronics

    KAUST Repository

    Hussain, Muhammad Mustafa

    2017-09-08

    Electronic stickers may be manufactured on flexible substrates (110, 120, 130) as layers and packaged together. The package may then have an adhesive applied to one side to provide capability for sticking the electronic devices to surfaces. The stickers can be wrappable, placed on surfaces, glued on walls or mirrors or wood or stone, and have electronics (112, 122, 132) which may or may not be ultrathin. Packaging for the electronic sticker can use polymer on cellulose manufacturing and/or three dimensional (3-D) printing. The electronic stickers may provide lighting capability, sensing capability, and/or recharging capabilities.

  17. Basic electronics

    CERN Document Server

    Holbrook, Harold D

    1971-01-01

    Basic Electronics is an elementary text designed for basic instruction in electricity and electronics. It gives emphasis on electronic emission and the vacuum tube and shows transistor circuits in parallel with electron tube circuits. This book also demonstrates how the transistor merely replaces the tube, with proper change of circuit constants as required. Many problems are presented at the end of each chapter. This book is comprised of 17 chapters and opens with an overview of electron theory, followed by a discussion on resistance, inductance, and capacitance, along with their effects on t

  18. Inner-shell electron spectroscopy for microanalysis

    International Nuclear Information System (INIS)

    Joy, D.C.; Maher, D.M.

    1979-01-01

    The transmission electron energy-loss spectrum shows characteristic edges corresponding to the excitation of inner-shell electrons of atoms in a thin sample. Analysis of these edges provides detailed chemical, structural, and electronic data from the radiated volume. By combining electron spectroscopy and electron microscopy, this microanalytical technique can be performed in conjunction with high-resolution imaging of the sample. It is shown that this approach has advantages of sensitivity, spatial resolution, and convenience over other comparable techniques. 7 figures

  19. Electronic Commerce and Electronic Business

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    This special issue is motivated by the recent upsurge of research activity in the areas of electronic commerce and electronic business both in India and all over the world. The current ... Monte Carlo methods for pricing financial options are then.

  20. Electronic Government and Electronic Participation

    NARCIS (Netherlands)

    Tambouris, E; Scholl, H.J.; Janssen, M.F.W.H.A.; Wimmer, M.A.; Tarabanis, K; Gascó, M; Klievink, A.J.; Lindgren, I; Milano, M; Panagiotopoulos, P; Pardo, T.A.; Parycek, P; Sæbø, Ø

    2016-01-01

    Electronic government and electronic participation continue to transform the public sector and society worldwide and are constantly being transformed themselves by emerging information and communication technologies.This book presents papers from the 14th International Federation for Information

  1. Electronic Government and Electronic Participation

    NARCIS (Netherlands)

    Tambouris, E.; Scholl, H.J.; Janssen, M.F.W.H.A.; Wimmer, M.A.; Tarabanis, K.; Gascó, M.; Klievink, A.J.; Lindgren, I.; Milano, M.; Panagiotopoulos, P.; Pardo, T.A.; Parycek, P.; Sæbø, O.

    2015-01-01

    Electronic government and electronic participation continue to transform the public sector and society worldwide and are constantly being transformed themselves by emerging information and communication technologies. This book presents papers from the 14th International Federation for Information

  2. Nonadiabatic transition path sampling

    International Nuclear Information System (INIS)

    Sherman, M. C.; Corcelli, S. A.

    2016-01-01

    Fewest-switches surface hopping (FSSH) is combined with transition path sampling (TPS) to produce a new method called nonadiabatic path sampling (NAPS). The NAPS method is validated on a model electron transfer system coupled to a Langevin bath. Numerically exact rate constants are computed using the reactive flux (RF) method over a broad range of solvent frictions that span from the energy diffusion (low friction) regime to the spatial diffusion (high friction) regime. The NAPS method is shown to quantitatively reproduce the RF benchmark rate constants over the full range of solvent friction. Integrating FSSH within the TPS framework expands the applicability of both approaches and creates a new method that will be helpful in determining detailed mechanisms for nonadiabatic reactions in the condensed-phase.

  3. Cerenkov fiber sampling calorimeters

    International Nuclear Information System (INIS)

    Arrington, K.; Kefford, D.; Kennedy, J.; Pisani, R.; Sanzeni, C.; Segall, K.; Wall, D.; Winn, D.R.; Carey, R.; Dye, S.; Miller, J.; Sulak, L.; Worstell, W.; Efremenko, Y.; Kamyshkov, Y.; Savin, A.; Shmakov, K.; Tarkovsky, E.

    1994-01-01

    Clear optical fibers were used as a Cerenkov sampling media in Pb (electromagnetic) and Cu (hadron) absorbers in spaghetti calorimeters, for high rate and high radiation dose experiments, such as the forward region of high energy colliders. The fiber axes were aligned close to the direction of the incident particles (1 degree--7 degree). The 7 λ deep hadron tower contained 2.8% by volume 1.5 mm diameter core clear plastic fibers. The 27 radiation length deep electromagnetic towers had packing fractions of 6.8% and 7.2% of 1 mm diameter core quartz fibers as the active Cerenkov sampling medium. The energy resolution on electrons and pions, energy response, pulse shapes and angular studies are presented

  4. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

    The photo shows a close-up o